@article {pmid41231995,
year = {2025},
author = {Zhang, SJ and Scarsbrook, L and Li, H and Carmagnini, A and Charlton, S and Feuerborn, T and Boeskorov, G and Chen, G and Deom, JM and Dimopoulos, EA and Dobney, K and Dong, J and Du, L and Hansen, AJ and Harris, A and Hernández-Alonso, G and Jia, X and Kim, A and Li, GM and Li, R and Linderholm, A and Outram, A and Qiu, M and Ren, L and Ruan, Q and Sala, R and Stepanov, A and Sun, Y and Tabbada, K and Thalmann, O and Varfolomeev, V and Wang, L and Wang, Q and Wang, S and Wei, W and Yang, Y and Yin, J and Zaibert, V and Zhang, Z and Dong, G and Rosengren, E and Sinding, MS and Ostrander, EA and Larson, G and Ma, M and Frantz, LAF and Wang, GD},
title = {Genomic evidence for the Holocene codispersal of dogs and humans across Eastern Eurasia.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {735-740},
doi = {10.1126/science.adu2836},
pmid = {41231995},
issn = {1095-9203},
mesh = {Animals ; *Dogs/genetics ; Humans ; Asia, Eastern ; DNA, Ancient ; Europe, Eastern ; *Genome ; History, Ancient ; *Human Migration ; Siberia ; *Animal Distribution ; },
abstract = {As the first domestic species, dogs likely dispersed with different cultural groups during the Late Pleistocene and Holocene. To test this hypothesis, we analyzed 73 ancient dog genomes, including 17 newly sequenced individuals sampled from East Asia to the West Eurasian Steppe spanning nearly 10,000 years. Our results indicate correlations between the ancestry of dogs and specific ancient human populations from eastern Europe to Eastern Siberia, including Ancient Paleo-Siberians, Eastern hunter-gatherers, East Asians, and Steppe pastoralists. We also identify multiple shifts in the ancestry of dogs that coincide with specific dispersals of hunter-gatherers, farmers, and pastoralists. Combined, our results reveal the long-term and integral role that dogs played in a multitude of human societies.},
}

Animals
*Dogs/genetics
Humans
Asia, Eastern
DNA, Ancient
Europe, Eastern
*Genome
History, Ancient
*Human Migration
Siberia
*Animal Distribution

@article {pmid41124126,
year = {2025},
author = {Capone, D and Holcomb, D and Lai, A and Meade, T and Reinhard, K and Brown, J},
title = {Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725-920 CE.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0318140},
pmid = {41124126},
issn = {1932-6203},
mesh = {*Feces/microbiology/parasitology ; Humans ; Mexico ; History, Ancient ; *DNA, Ancient/analysis ; Gastrointestinal Microbiome/genetics ; Animals ; Blastocystis/genetics/isolation & purification ; Entamoeba/genetics/isolation & purification ; },
abstract = {DNA analysis of ancient, desiccated feces - termed paleofeces - can unlock insights into the lives of ancient peoples, including through examination of the gut microbiome and identification of specific pathogens and parasites. We collected desiccated feces from the Cave of the Dead Children (La Cueva de Los Muertos Chiquitos) in the Rio Zape Valley in Mexico dated to 725-920 CE, for targeted pathogen analysis. First, we extracted DNA with methods previously optimized for paleofeces. Then, we applied highly sensitive modern molecular tools (i.e., PCR pre-amplification followed by multi-parallel qPCR) to assess the presence of 30 enteric pathogens and gut microbes. We detected ≥1 pathogen or gut microbe associated gene in each of the ten samples and a mean of 3.9 targets per sample. The targets detected included Blastocystis spp. (n = 7), atypical enteropathogenic E. coli (n = 7), Enterobius vermicularis (n = 6), Entamoeba spp. (n = 5), enterotoxigenic E. coli (n = 5), Shigella spp./enteroinvasive E. coli (n = 3), Giardia spp. (n = 2), and E. coli O157:H7 (n = 1). The protozoan pathogens we detected (i.e., Giardia spp. and Entamoeba spp.) have been previously detected in paleofeces via enzyme-linked immunoassay (ELISA), but not via PCR. This work represents the first detection of Blastocystis spp. atypical enteropathogenic E. coli, enterotoxigenic E. coli, Shigella spp./enteroinvasive E. coli, and E. coli O157:H7 in paleofeces. These results suggest that enteric infection may have been common among the Loma San Gabriel people, who lived in the Rio Zape Valley in Mexico during this period.},
}

*Feces/microbiology/parasitology
Humans
Mexico
History, Ancient
*DNA, Ancient/analysis
Gastrointestinal Microbiome/genetics
Animals
Blastocystis/genetics/isolation & purification
Entamoeba/genetics/isolation & purification

@article {pmid40877851,
year = {2025},
author = {He, H and Kong, X and Tao, L and Zhu, L and Wang, X and Xu, M and Chen, Y and Zhu, K and Xu, Y and Chen, H and Ma, H and Wang, R and Yang, X and Bai, T and Guo, J and Yang, Y and Jia, X and Wang, CC},
title = {Genetic stability in the lower Yangtze River basin from Song to Qing Dynasty.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {270},
pmid = {40877851},
issn = {1741-7007},
mesh = {China ; Humans ; Rivers ; *Genome, Human ; DNA, Ancient/analysis ; *Genetics, Population ; *Asian People/genetics ; Genetic Variation ; History, Ancient ; *Genomic Instability ; },
abstract = {BACKGROUND: The lower Yangtze River basin holds a pivotal role in Chinese history. As previous genetic research in this region has primarily focused on modern population datasets, the limited availability of ancient human genomes has hindered our capacity to reconstruct detailed ancient population histories and evaluate the genetic impact of Yellow River-related groups. RESULTS: Here, we present the first set of ancient human genomes from the lower Yangtze River basin, comprising eight individuals from the Song to Qing Dynasties (960-1921 CE). We observed a high degree of genetic homogeneity in most samples, suggesting long-term regional genetic stability. Seven individuals were estimated to derive 69.3-100% of their ancestry from ancient Yellow River-related populations, while the remainder can be attributed to a southern East Asian substrate. Contemporary Han Chinese residing in the lower Yangtze basin can be modelled as direct genetic descendants of historical individuals from this area. Notably, one Qing Dynasty sample reveals a genetic link to the Eastern Mediterranean.

CONCLUSIONS: Our findings illustrate enduring genetic continuity in the lower Yangtze River basin throughout historical times. These findings underscore the region's role as a genetic bridge between northern and southern East Asia, retaining local rice-farming ancestry while being shaped by southward expansions of Yellow River-related ancestry.},
}

China
Humans
Rivers
*Genome, Human
DNA, Ancient/analysis
*Genetics, Population
*Asian People/genetics
Genetic Variation
History, Ancient
*Genomic Instability

@article {pmid40634616,
year = {2025},
author = {Sikora, M and Canteri, E and Fernandez-Guerra, A and Oskolkov, N and Ågren, R and Hansson, L and Irving-Pease, EK and Mühlemann, B and Holtsmark Nielsen, S and Scorrano, G and Allentoft, ME and Valeur Seersholm, F and Schroeder, H and Gaunitz, C and Stenderup, J and Vinner, L and Jones, TC and Nystedt, B and Sjögren, KG and Parkhill, J and Fugger, L and Racimo, F and Kristiansen, K and Iversen, AKN and Willerslev, E},
title = {The spatiotemporal distribution of human pathogens in ancient Eurasia.},
journal = {Nature},
volume = {643},
number = {8073},
pages = {1011-1019},
pmid = {40634616},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; Archaeology ; Asia/epidemiology ; *Bacteria/isolation & purification/genetics/classification ; *Communicable Diseases/history/microbiology/parasitology/transmission ; DNA, Ancient/analysis ; Europe/epidemiology ; History, Ancient ; Human Migration/history ; Parasites/isolation & purification/genetics/classification ; *Spatio-Temporal Analysis ; Viruses/isolation & purification/genetics ; Zoonoses/history/transmission/microbiology/parasitology/virology/epidemiology ; },
abstract = {Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain[1]. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens[2], many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock[3]. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe[4,5].},
}

Animals
Humans
Archaeology
Asia/epidemiology
*Bacteria/isolation & purification/genetics/classification
*Communicable Diseases/history/microbiology/parasitology/transmission
DNA, Ancient/analysis
Europe/epidemiology
History, Ancient
Human Migration/history
Parasites/isolation & purification/genetics/classification
*Spatio-Temporal Analysis
Viruses/isolation & purification/genetics
Zoonoses/history/transmission/microbiology/parasitology/virology/epidemiology

@article {pmid40604286,
year = {2025},
author = {Morez Jacobs, A and Irish, JD and Cooke, A and Anastasiadou, K and Barrington, C and Gilardet, A and Kelly, M and Silva, M and Speidel, L and Tait, F and Williams, M and Brucato, N and Ricaut, FX and Wilkinson, C and Madgwick, R and Holt, E and Nederbragt, AJ and Inglis, E and Hajdinjak, M and Skoglund, P and Girdland-Flink, L},
title = {Whole-genome ancestry of an Old Kingdom Egyptian.},
journal = {Nature},
volume = {644},
number = {8077},
pages = {714-721},
pmid = {40604286},
issn = {1476-4687},
mesh = {Adult ; Humans ; Male ; *DNA, Ancient/analysis ; Egypt ; Egypt, Ancient ; *Genome, Human ; History, Ancient ; Phylogeny ; *Whole Genome Sequencing ; },
abstract = {Ancient Egyptian society flourished for millennia, reaching its peak during the Dynastic Period (approximately 3150-30 BCE). However, owing to poor DNA preservation, questions about regional interconnectivity over time have not been addressed because whole-genome sequencing has not yet been possible. Here we sequenced a 2× coverage whole genome from an adult male Egyptian excavated at Nuwayrat (Nuerat, نويرات). Radiocarbon dated to 2855-2570 cal. BCE, he lived a few centuries after Egyptian unification, bridging the Early Dynastic and Old Kingdom periods. The body was interred in a ceramic pot within a rock-cut tomb[1], potentially contributing to the DNA preservation. Most of his genome is best represented by North African Neolithic ancestry, among available sources at present. Yet approximately 20% of his genetic ancestry can be traced to genomes representing the eastern Fertile Crescent, including Mesopotamia and surrounding regions. This genetic affinity is similar to the ancestry appearing in Anatolia and the Levant during the Neolithic and Bronze Age[2-5]. Although more genomes are needed to fully understand the genomic diversity of early Egyptians, our results indicate that contacts between Egypt and the eastern Fertile Crescent were not limited to objects and imagery (such as domesticated animals and plants, as well as writing systems)[6-9] but also encompassed human migration.},
}

Adult
Humans
Male
*DNA, Ancient/analysis
Egypt
Egypt, Ancient
*Genome, Human
History, Ancient
Phylogeny
*Whole Genome Sequencing

@article {pmid40597302,
year = {2025},
author = {Wan, W and Huang, H and Hu, C and Zhang, X and Zhou, Q and Yang, M and Guo, J and Xie, M and Zhu, K and Yang, X and Ma, H and Wang, R and Zhao, J and Tao, L and He, H and Zhang, Q and Jin, L and Zhou, B and Huang, J and Wang, CC},
title = {Ancient genomes in Southwest China revealed genetic interactions among diverse populations in the historical period.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {174},
pmid = {40597302},
issn = {1741-7007},
mesh = {China ; Humans ; *Genetic Variation ; *Genome, Human ; *DNA, Ancient/analysis ; *Genetics, Population ; History, Ancient ; },
abstract = {BACKGROUND: Southwest China has been pivotal for agricultural spread, ethnic formation, and cultural diffusion. However, the genetic diversity and population structure of this area remain insufficiently explored, especially during the historical period.

RESULTS: Here, we report genome-wide data of eight ancient individuals from the Songshan site in Guizhou dating back to the Song and Ming Dynasty. Our results reveal that most Songshan individuals are closely related to the Yellow River Basin farmers, while also showing significant genetic influences from southern East Asia, including affinities with ancients in Guangxi, coastal Fujian, and Southeast Asia. Additionally, some Songshan individuals displayed a high genetic affinity with local Hmong-Mien populations.

CONCLUSIONS: These findings underscore the complexity of genetic interactions and population movements during the historical period, providing new insights into the genetic landscape and ethnic formation processes in Southwest China.},
}

China
Humans
*Genetic Variation
*Genome, Human
*DNA, Ancient/analysis
*Genetics, Population
History, Ancient

@article {pmid40399313,
year = {2025},
author = {Jacobs, Z and Zavala, EI and Li, B and O'Gorman, K and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Uliyanov, VA and Goldberg, P and Agadjanian, AK and Vasiliev, SK and Brink, F and Peyrégne, S and Slon, V and Pääbo, S and Kelso, J and Meyer, M and Roberts, RG},
title = {Pleistocene chronology and history of hominins and fauna at Denisova Cave.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4738},
pmid = {40399313},
issn = {2041-1723},
support = {FT140100384//Department of Education and Training | Australian Research Council (ARC)/ ; FT150100138//Department of Education and Training | Australian Research Council (ARC)/ ; FL130100116//Department of Education and Training | Australian Research Council (ARC)/ ; 24-18-00069//Russian Science Foundation (RSF)/ ; 24-18-00069//Russian Science Foundation (RSF)/ ; 24-18-00069//Russian Science Foundation (RSF)/ ; 24-18-00069//Russian Science Foundation (RSF)/ ; 24-18-00069//Russian Science Foundation (RSF)/ ; },
mesh = {Animals ; *Caves ; Siberia ; *Hominidae/genetics ; DNA, Mitochondrial/genetics ; Fossils ; Humans ; Neanderthals/genetics ; Geologic Sediments ; Archaeology ; DNA, Ancient/analysis ; Mammals/genetics ; History, Ancient ; },
abstract = {Denisova Cave in southern Siberia is the only site known to have been occupied by Denisovans, Neanderthals and modern humans. The cave consists of three chambers (Main, East and South), with the archaeological assemblages and remains of hominins, fauna and flora recovered from Main and East Chambers being the most thoroughly investigated to date. Here we report the results of analyses of the Palaeolithic artefacts, faunal remains and hominin and mammalian mitochondrial (mt) DNA recovered from renewed excavations in South Chamber. We construct a calendar-year time scale for the stratified Pleistocene deposits from optical dating of the sediments. The timing of hominin occupation and major turnovers in the mtDNA of Denisovans and large mammals largely accords with the patterns detected in Main and East Chambers. Time gaps in those sequences are partly filled by the South Chamber data and the sediment DNA record of Denisovans after 80,000 years ago is more than doubled in size. We combine the sediment dating and DNA records for all three chambers to reveal the whole-of-cave history of this unique site and the climatic conditions experienced by hominins and fauna over the past 300,000 years, including potential changes in habitat suitability for Denisovans and Neanderthals.},
}

Animals
*Caves
Siberia
*Hominidae/genetics
DNA, Mitochondrial/genetics
Fossils
Humans
Neanderthals/genetics
Geologic Sediments
Archaeology
DNA, Ancient/analysis
Mammals/genetics
History, Ancient

@article {pmid40106766,
year = {2025},
author = {Henneberger, K and Barlow, A and Alberti, F and Preick, M and Constantin, S and Döppes, D and Rosendahl, W and Hofreiter, M and Paijmans, JLA},
title = {A method for PCR-free library preparation for sequencing palaeogenomes.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319573},
pmid = {40106766},
issn = {1932-6203},
mesh = {*Gene Library ; Animals ; *Sequence Analysis, DNA/methods ; Polymerase Chain Reaction ; *Ursidae/genetics ; Phylogeny ; *DNA, Ancient/analysis ; *Genomics/methods ; Fossils ; DNA, Single-Stranded/genetics ; },
abstract = {In recent years, methodological advances have substantially improved our ability to recover DNA molecules from ancient samples, raising the possibility to sequence palaeogenomes without PCR amplification. Here we present an amplification-free library preparation method based on a benchmark library preparation protocol in palaeogenomics based on single-stranded DNA, and demonstrate suitability of the new method for a range of sample types. Furthermore, we use the method to generate the first amplification-free nuclear genome of a Pleistocene cave bear, and analyse the resulting data in the context of cave bear population genetics and phylogenetics using standard genomic clustering analyses. We find that the PCR-free adaptation provides endogenous DNA contents, GC contents and fragment lengths consistent with the standard protocol, although with reduced conversion efficiency, and shows no biases in downstream population clustering analyses. Our amplification-free library preparation method could find application in experimental designs where the original template molecule needs to be characterised more directly.},
}

*Gene Library
Animals
*Sequence Analysis, DNA/methods
Polymerase Chain Reaction
*Ursidae/genetics
Phylogeny
*DNA, Ancient/analysis
*Genomics/methods
Fossils
DNA, Single-Stranded/genetics

@article {pmid39910299,
year = {2025},
author = {Nikitin, AG and Lazaridis, I and Patterson, N and Ivanova, S and Videiko, M and Dergachev, V and Kotova, N and Lillie, M and Potekhina, I and Krenz-Niedbała, M and Łukasik, S and Makhortykh, S and Renson, V and Shephard, H and Sirbu, G and Svyryd, S and Tkachuk, T and Włodarczak, P and Callan, K and Curtis, E and Harney, E and Iliev, L and Kearns, A and Lawson, AM and Michel, M and Mah, M and Micco, A and Oppenheimer, J and Qiu, L and Workman, JN and Zalzala, F and Mallick, S and Rohland, N and Reich, D},
title = {A genomic history of the North Pontic Region from the Neolithic to the Bronze Age.},
journal = {Nature},
volume = {639},
number = {8053},
pages = {124-131},
pmid = {39910299},
issn = {1476-4687},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; History, Ancient ; *Human Migration/history ; *Genome, Human/genetics ; *Genomics ; DNA, Ancient/analysis ; Male ; Farmers ; Female ; Europe/ethnology ; White People/genetics ; White ; },
abstract = {The North Pontic Region was the meeting point of the farmers of Old Europe and the foragers and pastoralists of the Eurasian steppe[1,2], and the source of migrations deep into Europe[3-5]. Here we report genome-wide data from 81 prehistoric North Pontic individuals to understand the genetic makeup of its people. North Pontic foragers had ancestry from Balkan and Eastern hunter-gatherers[6] as well as European farmers and, occasionally, Caucasus hunter-gatherers. During the Eneolithic period, a wave of migrants from the Caucasus-Lower Volga area[7] bypassed local foragers to mix in equal parts with Trypillian farmers, forming the people of the Usatove culture around 4500 BCE. A temporally overlapping wave of migrants from the Caucasus-Lower Volga blended with foragers instead of farmers to form Serednii Stih people[7]. The third wave was the Yamna-descendants of the Serednii Stih who formed by mixture around 4000 BCE and expanded during the Early Bronze Age (3300 BCE). The temporal gap between Serednii Stih and the Yamna is bridged by a genetically Yamna individual from Mykhailivka, Ukraine (3635-3383 BCE), a site of archaeological continuity across the Eneolithic-Bronze Age transition and a likely epicentre of Yamna formation. Each of these three waves of migration propagated distinctive ancestries while also incorporating outsiders, a flexible strategy that may explain the success of the peoples of the North Pontic in spreading their genes and culture across Eurasia[3-5,8-10].},
}

Humans
History, Ancient
*Human Migration/history
*Genome, Human/genetics
*Genomics
DNA, Ancient/analysis
Male
Farmers
Female
Europe/ethnology
White People/genetics
White

@article {pmid39814899,
year = {2025},
author = {Cassidy, LM and Russell, M and Smith, M and Delbarre, G and Cheetham, P and Manley, H and Mattiangeli, V and Breslin, EM and Jackson, I and McCann, M and Little, H and O'Connor, CG and Heaslip, B and Lawson, D and Endicott, P and Bradley, DG},
title = {Continental influx and pervasive matrilocality in Iron Age Britain.},
journal = {Nature},
volume = {637},
number = {8048},
pages = {1136-1142},
pmid = {39814899},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {United Kingdom ; Humans ; Female ; Male ; Haplotypes/genetics ; History, Ancient ; *Human Migration/history ; DNA, Mitochondrial/genetics ; Burial/history ; Archaeology ; DNA, Ancient/analysis ; Genome, Human/genetics ; },
abstract = {Roman writers found the relative empowerment of Celtic women remarkable[1]. In southern Britain, the Late Iron Age Durotriges tribe often buried women with substantial grave goods[2]. Here we analyse 57 ancient genomes from Durotrigian burial sites and find an extended kin group centred around a single maternal lineage, with unrelated (presumably inward migrating) burials being predominantly male. Such a matrilocal pattern is undescribed in European prehistory, but when we compare mitochondrial haplotype variation among European archaeological sites spanning six millennia, British Iron Age cemeteries stand out as having marked reductions in diversity driven by the presence of dominant matrilines. Patterns of haplotype sharing reveal that British Iron Age populations form fine-grained geographical clusters with southern links extending across the channel to the continent. Indeed, whereas most of Britain shows majority genomic continuity from the Early Bronze Age to the Iron Age, this is markedly reduced in a southern coastal core region with persistent cross-channel cultural exchange[3]. This southern core has evidence of population influx in the Middle Bronze Age but also during the Iron Age. This is asynchronous with the rest of the island and points towards a staged, geographically granular absorption of continental influence, possibly including the acquisition of Celtic languages.},
}

United Kingdom
Humans
Female
Male
Haplotypes/genetics
History, Ancient
*Human Migration/history
DNA, Mitochondrial/genetics
Burial/history
Archaeology
DNA, Ancient/analysis
Genome, Human/genetics

@article {pmid39743601,
year = {2025},
author = {Speidel, L and Silva, M and Booth, T and Raffield, B and Anastasiadou, K and Barrington, C and Götherström, A and Heather, P and Skoglund, P},
title = {High-resolution genomic history of early medieval Europe.},
journal = {Nature},
volume = {637},
number = {8044},
pages = {118-126},
pmid = {39743601},
issn = {1476-4687},
support = {FC001595/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Female ; Humans ; Male ; DNA, Ancient/analysis ; Europe/ethnology ; *Genetics, Population ; *Genome, Human ; *Genomics ; Haplotypes ; History, Medieval ; Human Migration ; Scandinavian and Nordic Countries ; },
abstract = {Many known and unknown historical events have remained below detection thresholds of genetic studies because subtle ancestry changes are challenging to reconstruct. Methods based on shared haplotypes[1,2] and rare variants[3,4] improve power but are not explicitly temporal and have not been possible to adopt in unbiased ancestry models. Here we develop Twigstats, an approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,556 available ancient whole genomes from Europe in the historical period. We are able to model individual-level ancestry using preceding genomes to provide high resolution. During the first half of the first millennium CE, we observe at least two different streams of Scandinavian-related ancestry expanding across western, central and eastern Europe. By contrast, during the second half of the first millennium CE, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries. In Scandinavia, we document a major ancestry influx by approximately 800 CE, when a large proportion of Viking Age individuals carried ancestry from groups related to central Europe not seen in individuals from the early Iron Age. Our findings suggest that time-stratified ancestry analysis can provide a higher-resolution lens for genetic history.},
}

Female
Humans
Male
DNA, Ancient/analysis
Europe/ethnology
*Genetics, Population
*Genome, Human
*Genomics
Haplotypes
History, Medieval
Human Migration
Scandinavian and Nordic Countries

@article {pmid39694065,
year = {2025},
author = {Barquera, R and Sitter, TL and Kirkpatrick, CL and Ramirez, DA and Kocher, A and Spyrou, MA and Couoh, LR and Talavera-González, JA and Castro, M and von Hunnius, T and Guevara, EK and Hamilton, WD and Roberts, P and Scott, E and Fabra, M and Da Peña, GV and Pacheco, A and Rodriguez, M and Aspillaga, E and Tiliakou, A and Nelson, EA and Giffin, KL and Bianco, RA and Rohrlach, AB and de Los Ángeles García Martínez, M and Ballesteros Solís, FA and Sajantila, A and Saunders, SR and Nores, R and Herbig, A and Krause, J and Bos, KI},
title = {Ancient genomes reveal a deep history of Treponema pallidum in the Americas.},
journal = {Nature},
volume = {640},
number = {8057},
pages = {186-193},
pmid = {39694065},
issn = {1476-4687},
mesh = {Humans ; Americas/epidemiology ; *DNA, Ancient/analysis ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; Phylogeny ; *Syphilis/microbiology/history ; *Treponema pallidum/genetics/classification/isolation & purification ; Yaws/microbiology/history ; },
abstract = {Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most notably, syphilis[1]. Debates on a common origin for these pathogens and the history of syphilis itself have weighed evidence for the 'Columbian hypothesis'[2], which argues for an American origin, against that for the 'pre-Columbian hypothesis'[3], which argues for the presence of the disease in Eurasia in the Medieval period and possibly earlier. Although molecular data has provided a genetic basis for distinction of the typed subspecies[4], deep evolution of the complex has remained unresolved owing to limitations in the conclusions that can be drawn from the sparse palaeogenomic data that are currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the T. pallidum subsp. pallidum (syphilis), T. pallidum subsp. pertenue (yaws) and T. pallidum subsp. endemicum (bejel) lineages. Our data indicate unexplored diversity and an emergence of T. pallidum that post-dates human occupation in the Americas. Together, these results support an American origin for all T. pallidum characterized at the genomic level, both modern and ancient.},
}

Humans
Americas/epidemiology
*DNA, Ancient/analysis
*Evolution, Molecular
*Genome, Bacterial/genetics
Phylogeny
*Syphilis/microbiology/history
*Treponema pallidum/genetics/classification/isolation & purification
Yaws/microbiology/history

@article {pmid39667410,
year = {2025},
author = {Sümer, AP and Rougier, H and Villalba-Mouco, V and Huang, Y and Iasi, LNM and Essel, E and Bossoms Mesa, A and Furtwaengler, A and Peyrégne, S and de Filippo, C and Rohrlach, AB and Pierini, F and Mafessoni, F and Fewlass, H and Zavala, EI and Mylopotamitaki, D and Bianco, RA and Schmidt, A and Zorn, J and Nickel, B and Patova, A and Posth, C and Smith, GM and Ruebens, K and Sinet-Mathiot, V and Stoessel, A and Dietl, H and Orschiedt, J and Kelso, J and Zeberg, H and Bos, KI and Welker, F and Weiss, M and McPherron, SP and Schüler, T and Hublin, JJ and Velemínský, P and Brůžek, J and Peter, BM and Meyer, M and Meller, H and Ringbauer, H and Hajdinjak, M and Prüfer, K and Krause, J},
title = {Earliest modern human genomes constrain timing of Neanderthal admixture.},
journal = {Nature},
volume = {638},
number = {8051},
pages = {711-717},
pmid = {39667410},
issn = {1476-4687},
mesh = {Animals ; Humans ; DNA, Ancient/analysis ; Europe ; Fossils ; *Genome, Human ; Germany ; *Neanderthals/genetics/classification ; Phylogeny ; Time Factors ; Human Genetics ; *Biological Evolution ; },
abstract = {Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals[1-4]. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia[3] and Bacho Kiro, Bulgaria[2]. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany[4], and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.},
}

Animals
Humans
DNA, Ancient/analysis
Europe
Fossils
*Genome, Human
Germany
*Neanderthals/genetics/classification
Phylogeny
Time Factors
Human Genetics
*Biological Evolution

@article {pmid39570888,
year = {2024},
author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C},
title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0311115},
pmid = {39570888},
issn = {1932-6203},
mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; },
abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.},
}

*DNA, Mitochondrial/genetics
Humans
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Software
Forensic Genetics/methods
DNA, Ancient/analysis

@article {pmid39261618,
year = {2024},
author = {Moreno-Mayar, JV and Sousa da Mota, B and Higham, T and Klemm, S and Gorman Edmunds, M and Stenderup, J and Iraeta-Orbegozo, M and Laborde, V and Heyer, E and Torres Hochstetter, F and Friess, M and Allentoft, ME and Schroeder, H and Delaneau, O and Malaspinas, AS},
title = {Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {389-397},
pmid = {39261618},
issn = {1476-4687},
mesh = {Female ; Humans ; Male ; *American Indian or Alaska Native/genetics/history ; Americas/ethnology ; Bayes Theorem ; *DNA, Ancient/analysis ; *Genetics, Population ; *Genome, Human/genetics ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; History, Medieval ; *Human Migration/history ; Phylogeny ; Polynesia/ethnology ; Population Density ; Radiometric Dating ; Whole Genome Sequencing ; *Pacific Island People/genetics/history ; },
abstract = {Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai[1]. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory[2-4]. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated[5-7]. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 CE) and whole-genome sequenced (0.4-25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 CE.},
}

Female
Humans
Male
*American Indian or Alaska Native/genetics/history
Americas/ethnology
Bayes Theorem
*DNA, Ancient/analysis
*Genetics, Population
*Genome, Human/genetics
History, 17th Century
History, 18th Century
History, 19th Century
History, 20th Century
History, Ancient
History, Medieval
*Human Migration/history
Phylogeny
Polynesia/ethnology
Population Density
Radiometric Dating
Whole Genome Sequencing
*Pacific Island People/genetics/history

@article {pmid39232174,
year = {2024},
author = {Bolognini, D and Halgren, A and Lou, RN and Raveane, A and Rocha, JL and Guarracino, A and Soranzo, N and Chin, CS and Garrison, E and Sudmant, PH},
title = {Recurrent evolution and selection shape structural diversity at the amylase locus.},
journal = {Nature},
volume = {634},
number = {8034},
pages = {617-625},
pmid = {39232174},
issn = {1476-4687},
support = {R01 HG013017/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; R01 GM123489/GM/NIGMS NIH HHS/United States ; U01 DA057530/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Agriculture/history/statistics & numerical data ; *Amylases/genetics/chemistry ; *Evolution, Molecular ; *Gene Dosage/genetics ; Gene Duplication/genetics ; Genetic Loci/genetics ; *Genome, Human/genetics ; *Haplotypes/genetics ; History, Ancient ; Mutation Rate ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Hunting/statistics & numerical data ; Gene Deletion ; DNA, Ancient/analysis ; },
abstract = {The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations[1]. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake[2], although evidence of recent selection is lacking[3,4]. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately 5,600 contemporary and ancient humans, we resolve the diversity and evolutionary history of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in agricultural populations than in fishing, hunting and pastoral populations. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events with mutation rates up to more than 10,000-fold the single-nucleotide polymorphism mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome-based approach, we infer structural haplotypes across thousands of humans identifying extensively duplicated haplotypes at higher frequency in modern agricultural populations. Leveraging 533 ancient human genomes, we find that duplication-containing haplotypes (with more gene copies than the ancestral haplotype) have rapidly increased in frequency over the past 12,000 years in West Eurasians, suggestive of positive selection. Together, our study highlights the potential effects of the agricultural revolution on human genomes and the importance of structural variation in human adaptation.},
}

Humans
*Agriculture/history/statistics & numerical data
*Amylases/genetics/chemistry
*Evolution, Molecular
*Gene Dosage/genetics
Gene Duplication/genetics
Genetic Loci/genetics
*Genome, Human/genetics
*Haplotypes/genetics
History, Ancient
Mutation Rate
Polymorphism, Single Nucleotide/genetics
*Selection, Genetic
Hunting/statistics & numerical data
Gene Deletion
DNA, Ancient/analysis

@article {pmid39112623,
year = {2024},
author = {Callaway, E},
title = {From Vikings to Beethoven: what your DNA says about your ancient relatives.},
journal = {Nature},
volume = {632},
number = {8024},
pages = {246-249},
pmid = {39112623},
issn = {1476-4687},
mesh = {Female ; Humans ; Male ; *Databases, Nucleic Acid ; *DNA, Ancient/analysis ; *Genealogy and Heraldry ; Genomics ; History, Ancient ; Human Genetics ; History, 18th Century ; History, 19th Century ; },
}

Female
Humans
Male
*Databases, Nucleic Acid
*DNA, Ancient/analysis
*Genealogy and Heraldry
Genomics
History, Ancient
Human Genetics
History, 18th Century
History, 19th Century

@article {pmid38867050,
year = {2024},
author = {Michel, M and Skourtanioti, E and Pierini, F and Guevara, EK and Mötsch, A and Kocher, A and Barquera, R and Bianco, RA and Carlhoff, S and Coppola Bove, L and Freilich, S and Giffin, K and Hermes, T and Hiß, A and Knolle, F and Nelson, EA and Neumann, GU and Papac, L and Penske, S and Rohrlach, AB and Salem, N and Semerau, L and Villalba-Mouco, V and Abadie, I and Aldenderfer, M and Beckett, JF and Brown, M and Campus, FGR and Chenghwa, T and Cruz Berrocal, M and Damašek, L and Duffett Carlson, KS and Durand, R and Ernée, M and Fântăneanu, C and Frenzel, H and García Atiénzar, G and Guillén, S and Hsieh, E and Karwowski, M and Kelvin, D and Kelvin, N and Khokhlov, A and Kinaston, RL and Korolev, A and Krettek, KL and Küßner, M and Lai, L and Look, C and Majander, K and Mandl, K and Mazzarello, V and McCormick, M and de Miguel Ibáñez, P and Murphy, R and Németh, RE and Nordqvist, K and Novotny, F and Obenaus, M and Olmo-Enciso, L and Onkamo, P and Orschiedt, J and Patrushev, V and Peltola, S and Romero, A and Rubino, S and Sajantila, A and Salazar-García, DC and Serrano, E and Shaydullaev, S and Sias, E and Šlaus, M and Stančo, L and Swanston, T and Teschler-Nicola, M and Valentin, F and Van de Vijver, K and Varney, TL and Vigil-Escalera Guirado, A and Waters, CK and Weiss-Krejci, E and Winter, E and Lamnidis, TC and Prüfer, K and Nägele, K and Spyrou, M and Schiffels, S and Stockhammer, PW and Haak, W and Posth, C and Warinner, C and Bos, KI and Herbig, A and Krause, J},
title = {Ancient Plasmodium genomes shed light on the history of human malaria.},
journal = {Nature},
volume = {631},
number = {8019},
pages = {125-133},
pmid = {38867050},
issn = {1476-4687},
mesh = {Female ; Humans ; Male ; Altitude ; Americas/epidemiology ; Asia/epidemiology ; Biological Evolution ; Disease Resistance/genetics ; *DNA, Ancient/analysis ; Europe/epidemiology ; *Genome, Mitochondrial/genetics ; *Genome, Protozoan/genetics ; History, Ancient ; *Malaria/parasitology/history/transmission/epidemiology ; Malaria, Falciparum/epidemiology/history/parasitology/transmission ; Malaria, Vivax/epidemiology/history/parasitology/transmission ; *Plasmodium/genetics/classification ; Plasmodium falciparum/genetics/isolation & purification ; Plasmodium malariae/genetics/isolation & purification ; Plasmodium vivax/genetics/isolation & purification ; },
abstract = {Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species[1]. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe[1,2]. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia[3]. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.},
}

Female
Humans
Male
Altitude
Americas/epidemiology
Asia/epidemiology
Biological Evolution
Disease Resistance/genetics
*DNA, Ancient/analysis
Europe/epidemiology
*Genome, Mitochondrial/genetics
*Genome, Protozoan/genetics
History, Ancient
*Malaria/parasitology/history/transmission/epidemiology
Malaria, Falciparum/epidemiology/history/parasitology/transmission
Malaria, Vivax/epidemiology/history/parasitology/transmission
*Plasmodium/genetics/classification
Plasmodium falciparum/genetics/isolation & purification
Plasmodium malariae/genetics/isolation & purification
Plasmodium vivax/genetics/isolation & purification

@article {pmid38867041,
year = {2024},
author = {Barquera, R and Del Castillo-Chávez, O and Nägele, K and Pérez-Ramallo, P and Hernández-Zaragoza, DI and Szolek, A and Rohrlach, AB and Librado, P and Childebayeva, A and Bianco, RA and Penman, BS and Acuña-Alonzo, V and Lucas, M and Lara-Riegos, JC and Moo-Mezeta, ME and Torres-Romero, JC and Roberts, P and Kohlbacher, O and Warinner, C and Krause, J},
title = {Ancient genomes reveal insights into ritual life at Chichén Itzá.},
journal = {Nature},
volume = {630},
number = {8018},
pages = {912-919},
pmid = {38867041},
issn = {1476-4687},
mesh = {Humans ; Mexico ; *Genome, Human/genetics ; Male ; *Ceremonial Behavior ; *DNA, Ancient/analysis ; History, Ancient ; Female ; Burial/history ; Archaeology ; Twins/genetics ; History, Medieval ; },
abstract = {The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica[1-4]. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered[2]. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes[5], but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.},
}

Humans
Mexico
*Genome, Human/genetics
Male
*Ceremonial Behavior
*DNA, Ancient/analysis
History, Ancient
Female
Burial/history
Archaeology
Twins/genetics
History, Medieval

@article {pmid38297117,
year = {2024},
author = {Mylopotamitaki, D and Weiss, M and Fewlass, H and Zavala, EI and Rougier, H and Sümer, AP and Hajdinjak, M and Smith, GM and Ruebens, K and Sinet-Mathiot, V and Pederzani, S and Essel, E and Harking, FS and Xia, H and Hansen, J and Kirchner, A and Lauer, T and Stahlschmidt, M and Hein, M and Talamo, S and Wacker, L and Meller, H and Dietl, H and Orschiedt, J and Olsen, JV and Zeberg, H and Prüfer, K and Krause, J and Meyer, M and Welker, F and McPherron, SP and Schüler, T and Hublin, JJ},
title = {Homo sapiens reached the higher latitudes of Europe by 45,000 years ago.},
journal = {Nature},
volume = {626},
number = {7998},
pages = {341-346},
pmid = {38297117},
issn = {1476-4687},
mesh = {Animals ; Humans ; Body Remains/metabolism ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis/genetics ; Europe ; Extinction, Biological ; Fossils ; Germany ; History, Ancient ; Neanderthals/classification/genetics/metabolism ; Proteomics ; Radiometric Dating ; *Human Migration/history ; Time Factors ; },
abstract = {The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe[1]. Local hybridization between the two groups occurred[2], but not on all occasions[3]. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups[4]. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe[5-8]. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.},
}

Animals
Humans
Body Remains/metabolism
DNA, Ancient/analysis
DNA, Mitochondrial/analysis/genetics
Europe
Extinction, Biological
Fossils
Germany
History, Ancient
Neanderthals/classification/genetics/metabolism
Proteomics
Radiometric Dating
*Human Migration/history
Time Factors

@article {pmid37438588,
year = {2023},
author = {Dance, A},
title = {Germs, genes and soil: tales of pathogens past.},
journal = {Nature},
volume = {619},
number = {7969},
pages = {424-426},
pmid = {37438588},
issn = {1476-4687},
mesh = {*Soil ; *Soil Microbiology ; *Bacteria/genetics/isolation & purification ; *DNA, Ancient/analysis/isolation & purification ; History, Ancient ; },
}

*Soil
*Soil Microbiology
*Bacteria/genetics/isolation & purification
*DNA, Ancient/analysis/isolation & purification
History, Ancient

@article {pmid37138083,
year = {2023},
author = {Essel, E and Zavala, EI and Schulz-Kornas, E and Kozlikin, MB and Fewlass, H and Vernot, B and Shunkov, MV and Derevianko, AP and Douka, K and Barnes, I and Soulier, MC and Schmidt, A and Szymanski, M and Tsanova, T and Sirakov, N and Endarova, E and McPherron, SP and Hublin, JJ and Kelso, J and Pääbo, S and Hajdinjak, M and Soressi, M and Meyer, M},
title = {Ancient human DNA recovered from a Palaeolithic pendant.},
journal = {Nature},
volume = {618},
number = {7964},
pages = {328-332},
pmid = {37138083},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; Female ; Humans ; Archaeology/methods ; *Bone and Bones/chemistry ; Deer/genetics ; *DNA, Ancient/analysis/isolation & purification ; DNA, Mitochondrial/analysis/isolation & purification ; History, Ancient ; Siberia ; *Tooth/chemistry ; Caves ; Russia ; },
abstract = {Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals[1] who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited[2-5]. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.},
}

Animals
Female
Humans
Archaeology/methods
*Bone and Bones/chemistry
Deer/genetics
*DNA, Ancient/analysis/isolation & purification
DNA, Mitochondrial/analysis/isolation & purification
History, Ancient
Siberia
*Tooth/chemistry
Caves
Russia

@article {pmid37095409,
year = {2023},
author = {Callaway, E},
title = {'Truly gobsmacked': Ancient-human genome count surpasses 10,000.},
journal = {Nature},
volume = {617},
number = {7959},
pages = {20},
pmid = {37095409},
issn = {1476-4687},
mesh = {Humans ; *Anthropology/trends ; *Archaeology/trends ; *DNA, Ancient ; *Genome, Human/genetics ; },
}

Humans
*Anthropology/trends
*Archaeology/trends
*DNA, Ancient
*Genome, Human/genetics

@article {pmid36859677,
year = {2023},
author = {Callaway, E},
title = {Ancient genomes show how humans escaped Europe's deep freeze.},
journal = {Nature},
volume = {615},
number = {7951},
pages = {197-198},
pmid = {36859677},
issn = {1476-4687},
mesh = {Humans ; Europe ; *Genome, Human ; *DNA, Ancient/analysis ; *Human Migration/history ; Freezing ; *Cold Temperature ; History, Ancient ; },
}

Humans
Europe
*Genome, Human
*DNA, Ancient/analysis
*Human Migration/history
Freezing
*Cold Temperature
History, Ancient

@article {pmid36476770,
year = {2022},
author = {Callaway, E},
title = {Oldest-ever DNA shows mastodons roamed Greenland 2 million years ago.},
journal = {Nature},
volume = {612},
number = {7940},
pages = {384},
pmid = {36476770},
issn = {1476-4687},
mesh = {Animals ; Fossils ; Greenland ; *Mastodons/genetics ; *DNA, Ancient/analysis ; History, Ancient ; },
}

Animals
Fossils
Greenland
*Mastodons/genetics
*DNA, Ancient/analysis
History, Ancient

@article {pmid36192444,
year = {2022},
author = {Callaway, E and Ledford, H},
title = {Geneticist who unmasked lives of ancient humans wins medicine Nobel.},
journal = {Nature},
volume = {610},
number = {7930},
pages = {16-17},
pmid = {36192444},
issn = {1476-4687},
mesh = {*DNA, Ancient ; Humans ; *Medicine/standards ; *Nobel Prize ; },
}

*DNA, Ancient
Humans
*Medicine/standards
*Nobel Prize

@article {pmid35999365,
year = {2022},
author = {Kreier, F},
title = {Ancient tooth DNA reveals how 'cold sore' herpes virus has evolved.},
journal = {Nature},
volume = {609},
number = {7925},
pages = {21-22},
pmid = {35999365},
issn = {1476-4687},
mesh = {*DNA, Ancient/analysis ; DNA, Viral/analysis/genetics ; *Evolution, Molecular ; *Herpes Labialis/history/virology ; *Herpesvirus 1, Human/genetics/isolation & purification ; History, Ancient ; *Tooth/metabolism ; },
}

*DNA, Ancient/analysis
DNA, Viral/analysis/genetics
*Evolution, Molecular
*Herpes Labialis/history/virology
*Herpesvirus 1, Human/genetics/isolation & purification
History, Ancient
*Tooth/metabolism

@article {pmid35768506,
year = {2022},
author = {Bergström, A and Stanton, DWG and Taron, UH and Frantz, L and Sinding, MS and Ersmark, E and Pfrengle, S and Cassatt-Johnstone, M and Lebrasseur, O and Girdland-Flink, L and Fernandes, DM and Ollivier, M and Speidel, L and Gopalakrishnan, S and Westbury, MV and Ramos-Madrigal, J and Feuerborn, TR and Reiter, E and Gretzinger, J and Münzel, SC and Swali, P and Conard, NJ and Carøe, C and Haile, J and Linderholm, A and Androsov, S and Barnes, I and Baumann, C and Benecke, N and Bocherens, H and Brace, S and Carden, RF and Drucker, DG and Fedorov, S and Gasparik, M and Germonpré, M and Grigoriev, S and Groves, P and Hertwig, ST and Ivanova, VV and Janssens, L and Jennings, RP and Kasparov, AK and Kirillova, IV and Kurmaniyazov, I and Kuzmin, YV and Kosintsev, PA and Lázničková-Galetová, M and Leduc, C and Nikolskiy, P and Nussbaumer, M and O'Drisceoil, C and Orlando, L and Outram, A and Pavlova, EY and Perri, AR and Pilot, M and Pitulko, VV and Plotnikov, VV and Protopopov, AV and Rehazek, A and Sablin, M and Seguin-Orlando, A and Storå, J and Verjux, C and Zaibert, VF and Zazula, G and Crombé, P and Hansen, AJ and Willerslev, E and Leonard, JA and Götherström, A and Pinhasi, R and Schuenemann, VJ and Hofreiter, M and Gilbert, MTP and Shapiro, B and Larson, G and Krause, J and Dalén, L and Skoglund, P},
title = {Grey wolf genomic history reveals a dual ancestry of dogs.},
journal = {Nature},
volume = {607},
number = {7918},
pages = {313-320},
pmid = {35768506},
issn = {1476-4687},
support = {310763/ERC_/European Research Council/International ; 852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; FC001595/WT_/Wellcome Trust/United Kingdom ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; ERC-2013-STG-337574-UNDEAD/ERC_/European Research Council/International ; ERC-2019-STG-853272-PALAEOFARM/ERC_/European Research Council/International ; },
mesh = {Africa ; Animals ; DNA, Ancient/analysis ; *Dogs/genetics ; Domestication ; Europe ; *Genome/genetics ; *Genomics ; History, Ancient ; Middle East ; Mutation ; North America ; *Phylogeny ; Selection, Genetic ; Siberia ; Tumor Suppressor Proteins/genetics ; *Wolves/classification/genetics ; },
abstract = {The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived[1-8]. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.},
}

Africa
Animals
DNA, Ancient/analysis
*Dogs/genetics
Domestication
Europe
*Genome/genetics
*Genomics
History, Ancient
Middle East
Mutation
North America
*Phylogeny
Selection, Genetic
Siberia
Tumor Suppressor Proteins/genetics
*Wolves/classification/genetics

@article {pmid35165121,
year = {2022},
author = {Li, J and Zhao, B and Huang, T and Qin, Z and Wang, SM},
title = {Human BRCA pathogenic variants were originated during recent human history.},
journal = {Life science alliance},
volume = {5},
number = {5},
pages = {},
pmid = {35165121},
issn = {2575-1077},
mesh = {Animals ; BRCA1 Protein/*genetics ; BRCA2 Protein/*genetics ; Biological Evolution ; DNA, Ancient/analysis ; Databases, Genetic ; Evolution, Molecular ; Female ; Genetic Predisposition to Disease/genetics ; Germ-Line Mutation/genetics ; Haplotypes/genetics ; Humans ; Mutation ; },
abstract = {BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.},
}

Animals
BRCA1 Protein/*genetics
BRCA2 Protein/*genetics
Biological Evolution
DNA, Ancient/analysis
Databases, Genetic
Evolution, Molecular
Female
Genetic Predisposition to Disease/genetics
Germ-Line Mutation/genetics
Haplotypes/genetics
Humans
Mutation

@article {pmid34949860,
year = {2022},
author = {Carlin, N},
title = {A grave matter of ancient kinship in Neolithic Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {510-512},
pmid = {34949860},
issn = {1476-4687},
mesh = {*Archaeology ; *DNA, Ancient ; United Kingdom ; },
}

*Archaeology
*DNA, Ancient
United Kingdom

@article {pmid34937885,
year = {2022},
author = {Bradley, DG},
title = {Bronze Age genomes reveal migration to Britain.},
journal = {Nature},
volume = {601},
number = {7894},
pages = {512-513},
pmid = {34937885},
issn = {1476-4687},
mesh = {*DNA, Ancient ; *Human Migration ; United Kingdom ; },
}

*DNA, Ancient
*Human Migration
United Kingdom

@article {pmid34671162,
year = {2021},
author = {Librado, P and Khan, N and Fages, A and Kusliy, MA and Suchan, T and Tonasso-Calvière, L and Schiavinato, S and Alioglu, D and Fromentier, A and Perdereau, A and Aury, JM and Gaunitz, C and Chauvey, L and Seguin-Orlando, A and Der Sarkissian, C and Southon, J and Shapiro, B and Tishkin, AA and Kovalev, AA and Alquraishi, S and Alfarhan, AH and Al-Rasheid, KAS and Seregély, T and Klassen, L and Iversen, R and Bignon-Lau, O and Bodu, P and Olive, M and Castel, JC and Boudadi-Maligne, M and Alvarez, N and Germonpré, M and Moskal-Del Hoyo, M and Wilczyński, J and Pospuła, S and Lasota-Kuś, A and Tunia, K and Nowak, M and Rannamäe, E and Saarma, U and Boeskorov, G and Lōugas, L and Kyselý, R and Peške, L and Bălășescu, A and Dumitrașcu, V and Dobrescu, R and Gerber, D and Kiss, V and Szécsényi-Nagy, A and Mende, BG and Gallina, Z and Somogyi, K and Kulcsár, G and Gál, E and Bendrey, R and Allentoft, ME and Sirbu, G and Dergachev, V and Shephard, H and Tomadini, N and Grouard, S and Kasparov, A and Basilyan, AE and Anisimov, MA and Nikolskiy, PA and Pavlova, EY and Pitulko, V and Brem, G and Wallner, B and Schwall, C and Keller, M and Kitagawa, K and Bessudnov, AN and Bessudnov, A and Taylor, W and Magail, J and Gantulga, JO and Bayarsaikhan, J and Erdenebaatar, D and Tabaldiev, K and Mijiddorj, E and Boldgiv, B and Tsagaan, T and Pruvost, M and Olsen, S and Makarewicz, CA and Valenzuela Lamas, S and Albizuri Canadell, S and Nieto Espinet, A and Iborra, MP and Lira Garrido, J and Rodríguez González, E and Celestino, S and Olària, C and Arsuaga, JL and Kotova, N and Pryor, A and Crabtree, P and Zhumatayev, R and Toleubaev, A and Morgunova, NL and Kuznetsova, T and Lordkipanize, D and Marzullo, M and Prato, O and Bagnasco Gianni, G and Tecchiati, U and Clavel, B and Lepetz, S and Davoudi, H and Mashkour, M and Berezina, NY and Stockhammer, PW and Krause, J and Haak, W and Morales-Muñiz, A and Benecke, N and Hofreiter, M and Ludwig, A and Graphodatsky, AS and Peters, J and Kiryushin, KY and Iderkhangai, TO and Bokovenko, NA and Vasiliev, SK and Seregin, NN and Chugunov, KV and Plasteeva, NA and Baryshnikov, GF and Petrova, E and Sablin, M and Ananyevskaya, E and Logvin, A and Shevnina, I and Logvin, V and Kalieva, S and Loman, V and Kukushkin, I and Merz, I and Merz, V and Sakenov, S and Varfolomeyev, V and Usmanova, E and Zaibert, V and Arbuckle, B and Belinskiy, AB and Kalmykov, A and Reinhold, S and Hansen, S and Yudin, AI and Vybornov, AA and Epimakhov, A and Berezina, NS and Roslyakova, N and Kosintsev, PA and Kuznetsov, PF and Anthony, D and Kroonen, GJ and Kristiansen, K and Wincker, P and Outram, A and Orlando, L},
title = {The origins and spread of domestic horses from the Western Eurasian steppes.},
journal = {Nature},
volume = {598},
number = {7882},
pages = {634-640},
pmid = {34671162},
issn = {1476-4687},
mesh = {Animals ; Archaeology ; Asia ; DNA, Ancient ; *Domestication ; Europe ; *Genetics, Population ; Genome ; Grassland ; *Horses/genetics ; Phylogeny ; },
abstract = {Domestication of horses fundamentally transformed long-range mobility and warfare[1]. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling[2-4] at Botai, Central Asia around 3500 BC[3]. Other longstanding candidate regions for horse domestication, such as Iberia[5] and Anatolia[6], have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association[7] between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC[8,9] driving the spread of Indo-European languages[10]. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture[11,12].},
}

Animals
Archaeology
Asia
DNA, Ancient
*Domestication
Europe
*Genetics, Population
Genome
Grassland
*Horses/genetics
Phylogeny

@article {pmid34671161,
year = {2021},
author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E},
title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.},
journal = {Nature},
volume = {600},
number = {7887},
pages = {86-92},
pmid = {34671161},
issn = {1476-4687},
support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; },
abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood[1-8]. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.},
}

Animals
Arctic Regions
*Biota
Climate Change/history
DNA, Ancient/*analysis
DNA, Environmental/*analysis
Databases, Genetic
Datasets as Topic
Extinction, Biological
Geologic Sediments
Grassland
Greenland
Haplotypes/genetics
Herbivory/genetics
History, Ancient
Humans
Lakes
Mammoths
*Metagenomics
Mitochondria/genetics
Perissodactyla
Permafrost
Phylogeny
Plants/genetics
Population Dynamics
Rain
Siberia
Spatio-Temporal Analysis
Wetlands

@article {pmid34433944,
year = {2021},
author = {Carlhoff, S and Duli, A and Nägele, K and Nur, M and Skov, L and Sumantri, I and Oktaviana, AA and Hakim, B and Burhan, B and Syahdar, FA and McGahan, DP and Bulbeck, D and Perston, YL and Newman, K and Saiful, AM and Ririmasse, M and Chia, S and Hasanuddin, and Pulubuhu, DAT and Suryatman, and Supriadi, and Jeong, C and Peter, BM and Prüfer, K and Powell, A and Krause, J and Posth, C and Brumm, A},
title = {Genome of a middle Holocene hunter-gatherer from Wallacea.},
journal = {Nature},
volume = {596},
number = {7873},
pages = {543-547},
pmid = {34433944},
issn = {1476-4687},
mesh = {Asia, Southeastern ; Australia ; Bone and Bones/metabolism ; Caves ; DNA, Ancient/*analysis ; Female ; *Fossils ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; Indonesia/ethnology ; Islands/*ethnology ; New Guinea ; *Phylogeny ; },
abstract = {Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA[1]. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)[1]. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge[2] in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex[3,4], shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago[5]. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.},
}

Asia, Southeastern
Australia
Bone and Bones/metabolism
Caves
DNA, Ancient/*analysis
Female
*Fossils
Genome, Human/*genetics
*Genomics
History, Ancient
Human Migration/history
Humans
Indonesia/ethnology
Islands/*ethnology
New Guinea
*Phylogeny

@article {pmid34410492,
year = {2021},
author = {Aneli, S and Caldon, M and Saupe, T and Montinaro, F and Pagani, L},
title = {Through 40,000 years of human presence in Southern Europe: the Italian case study.},
journal = {Human genetics},
volume = {140},
number = {10},
pages = {1417-1431},
pmid = {34410492},
issn = {1432-1203},
mesh = {DNA, Ancient/*analysis ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Genomics/*history ; History, Ancient ; History, Medieval ; Humans ; Italy ; White People/*genetics/*history ; },
abstract = {The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.},
}

DNA, Ancient/*analysis
*Evolution, Molecular
*Genetic Variation
*Genome, Human
Genomics/*history
History, Ancient
History, Medieval
Humans
Italy
White People/*genetics/*history

@article {pmid34163072,
year = {2021},
author = {Zavala, EI and Jacobs, Z and Vernot, B and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Essel, E and de Fillipo, C and Nagel, S and Richter, J and Romagné, F and Schmidt, A and Li, B and O'Gorman, K and Slon, V and Kelso, J and Pääbo, S and Roberts, RG and Meyer, M},
title = {Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.},
journal = {Nature},
volume = {595},
number = {7867},
pages = {399-403},
pmid = {34163072},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; Archaeology ; *Caves ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis/genetics ; Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Hominidae/*genetics ; Neanderthals/genetics ; Siberia ; },
abstract = {Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals[1-4]. The dozen hominin remains recovered from the deposits also include Neanderthals[5,6] and the child of a Neanderthal and a Denisovan[7], which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages[5,8-11]. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.},
}

Animals
Archaeology
*Caves
DNA, Ancient/*analysis
DNA, Mitochondrial/analysis/genetics
Fossils
Geologic Sediments/*chemistry
History, Ancient
Hominidae/*genetics
Neanderthals/genetics
Siberia

@article {pmid33945536,
year = {2021},
author = {Nerlich, AG and Kirchhoff, SM and Panzer, S and Lehn, C and Bachmeier, BE and Bayer, B and Anslinger, K and Röcker, P and Peschel, OK},
title = {Chronic active non-lethal human-type tuberculosis in a high royal Bavarian officer of Napoleonic times-a mummy study.},
journal = {PloS one},
volume = {16},
number = {5},
pages = {e0249955},
pmid = {33945536},
issn = {1932-6203},
mesh = {DNA, Ancient/chemistry ; Humans ; Male ; Mummies/diagnostic imaging/microbiology/*pathology ; Spine/diagnostic imaging/pathology ; Tomography, X-Ray Computed ; Tuberculosis/diagnostic imaging/microbiology/*pathology ; },
abstract = {In paleopathology, morphological and molecular evidence for infection by mycobacteria of the M. tuberculosis complex (MTC) is frequently associated with early death. In the present report, we describe a multidisciplinary study of a well-preserved mummy from Napoleonic times with a long-standing tuberculous infection by M. tuberculosis senso stricto who died at the age of 88 years of focal and non-MTB related bronchopneumonia. The well-preserved natural mummy of the Royal Bavarian General, Count Heinrich LII Reuss-Köstritz (1763-1851 CE), was extensively investigated by macro- and histomorphology, whole body CT scans and organ radiography, various molecular tissue analyses, including stable isotope analysis and molecular genetic tests. We identified signs for a long-standing, but terminally inactive pulmonary tuberculosis, tuberculous destruction of the second lumbar vertebral body, and a large tuberculous abscess in the right (retroperitoneal) psoas region (a cold abscess). This cold abscess harboured an active tuberculous infection as evidenced by histological and molecular tests. Radiological and histological analysis further revealed extensive arteriosclerosis with (non-obliterating) coronary and significant carotid arteriosclerosis, healthy bone tissue without evidence of age-related osteopenia, evidence for diffuse idiopathic skeletal hyperostosis and mild osteoarthrosis of few joints. This suggests excellent living conditions correlating well with his diet indicated by stable isotope results and literary evidence. Despite the clear evidence of a tuberculous cold abscess with bacterioscopic and molecular proof for a persisting MTC infection of a human-type M. tuberculosis strain, we can exclude the chronic MTC infection as cause of death. The detection of MTC in historic individuals should therefore be interpreted with great caution and include further data, such as their nutritional status.},
}

DNA, Ancient/chemistry
Humans
Male
Mummies/diagnostic imaging/microbiology/*pathology
Spine/diagnostic imaging/pathology
Tomography, X-Ray Computed
Tuberculosis/diagnostic imaging/microbiology/*pathology

@article {pmid33828320,
year = {2021},
author = {Hajdinjak, M and Mafessoni, F and Skov, L and Vernot, B and Hübner, A and Fu, Q and Essel, E and Nagel, S and Nickel, B and Richter, J and Moldovan, OT and Constantin, S and Endarova, E and Zahariev, N and Spasov, R and Welker, F and Smith, GM and Sinet-Mathiot, V and Paskulin, L and Fewlass, H and Talamo, S and Rezek, Z and Sirakova, S and Sirakov, N and McPherron, SP and Tsanova, T and Hublin, JJ and Peter, BM and Meyer, M and Skoglund, P and Kelso, J and Pääbo, S},
title = {Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.},
journal = {Nature},
volume = {592},
number = {7853},
pages = {253-257},
pmid = {33828320},
issn = {1476-4687},
support = {694707/ERC_/European Research Council/International ; 852558/ERC_/European Research Council/International ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Alleles ; Americas/ethnology ; Animals ; Archaeology ; Bulgaria/ethnology ; Caves ; DNA, Ancient/*analysis ; Asia, Eastern/ethnology ; Female ; Genome, Human/*genetics ; History, Ancient ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; },
abstract = {Modern humans appeared in Europe by at least 45,000 years ago[1-5], but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago[6], and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria[1,2]. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania[7] and Siberia[8] who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.},
}

Alleles
Americas/ethnology
Animals
Archaeology
Bulgaria/ethnology
Caves
DNA, Ancient/*analysis
Asia, Eastern/ethnology
Female
Genome, Human/*genetics
History, Ancient
Humans
Male
Neanderthals/*genetics
Phylogeny

@article {pmid33597750,
year = {2021},
author = {van der Valk, T and Pečnerová, P and Díez-Del-Molino, D and Bergström, A and Oppenheimer, J and Hartmann, S and Xenikoudakis, G and Thomas, JA and Dehasque, M and Sağlıcan, E and Fidan, FR and Barnes, I and Liu, S and Somel, M and Heintzman, PD and Nikolskiy, P and Shapiro, B and Skoglund, P and Hofreiter, M and Lister, AM and Götherström, A and Dalén, L},
title = {Million-year-old DNA sheds light on the genomic history of mammoths.},
journal = {Nature},
volume = {591},
number = {7849},
pages = {265-269},
pmid = {33597750},
issn = {1476-4687},
support = {310763/ERC_/European Research Council/International ; 852558/ERC_/European Research Council/International ; FC001595/WT_/Wellcome Trust/United Kingdom ; T32 HG008345/HG/NHGRI NIH HHS/United States ; },
mesh = {Acclimatization/genetics ; Alleles ; Animals ; Bayes Theorem ; DNA, Ancient/*analysis/isolation & purification ; Elephants/genetics ; Europe ; *Evolution, Molecular ; Female ; Fossils ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Mammoths/*genetics ; Markov Chains ; Molar ; North America ; *Phylogeny ; Radiometric Dating ; Siberia ; Time Factors ; },
abstract = {Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale[1], the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago[2]. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.},
}

Acclimatization/genetics
Alleles
Animals
Bayes Theorem
DNA, Ancient/*analysis/isolation & purification
Elephants/genetics
Europe
*Evolution, Molecular
Female
Fossils
Genetic Variation/genetics
Genome, Mitochondrial/*genetics
*Genomics
Mammoths/*genetics
Markov Chains
Molar
North America
*Phylogeny
Radiometric Dating
Siberia
Time Factors

@article {pmid33444387,
year = {2021},
author = {Egfjord, AF and Margaryan, A and Fischer, A and Sjögren, KG and Price, TD and Johannsen, NN and Nielsen, PO and Sørensen, L and Willerslev, E and Iversen, R and Sikora, M and Kristiansen, K and Allentoft, ME},
title = {Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244872},
pmid = {33444387},
issn = {1932-6203},
mesh = {*Archaeology ; DNA, Ancient ; Denmark ; Female ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Male ; Sex Determination Analysis ; Skeleton/*metabolism ; },
abstract = {The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.},
}

*Archaeology
DNA, Ancient
Denmark
Female
*Genomics
Haplotypes
History, Ancient
Human Migration
Humans
Male
Sex Determination Analysis
Skeleton/*metabolism

@article {pmid33196640,
year = {2020},
author = {Sjögren, KG and Olalde, I and Carver, S and Allentoft, ME and Knowles, T and Kroonen, G and Pike, AWG and Schröter, P and Brown, KA and Brown, KR and Harrison, RJ and Bertemes, F and Reich, D and Kristiansen, K and Heyd, V},
title = {Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0241278},
pmid = {33196640},
issn = {1932-6203},
mesh = {*Anthropology ; *Archaeology ; *Cemeteries ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Female ; Geography ; Germany ; Haplotypes/genetics ; *Hierarchy, Social ; Humans ; *Isotope Labeling ; Male ; Models, Theoretical ; Principal Component Analysis ; Sex Determination Analysis ; Time Factors ; },
abstract = {We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.},
}

*Anthropology
*Archaeology
*Cemeteries
DNA, Ancient/*analysis
DNA, Mitochondrial/genetics
Female
Geography
Germany
Haplotypes/genetics
*Hierarchy, Social
Humans
*Isotope Labeling
Male
Models, Theoretical
Principal Component Analysis
Sex Determination Analysis
Time Factors

@article {pmid33122839,
year = {2020},
author = {Callaway, E},
title = {Ancient dog DNA reveals 11,000 years of canine evolution.},
journal = {Nature},
volume = {587},
number = {7832},
pages = {20},
pmid = {33122839},
issn = {1476-4687},
mesh = {Animals ; *DNA, Ancient ; Dogs ; Evolution, Molecular ; *Heredity ; Phylogeny ; },
}

Animals
*DNA, Ancient
Dogs
Evolution, Molecular
*Heredity
Phylogeny

@article {pmid33083459,
year = {2020},
author = {Bazarragchaa, M and Uuganbayar, U and Lee, KH and Kim, KY and Kim, K},
title = {Skin Pigmentation Differences between Mongolian, Korean, and Uzbekistan Ancient Human DNA Samples.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {2585324},
pmid = {33083459},
issn = {2314-6141},
mesh = {Asian People/*genetics ; DNA, Ancient/*analysis ; Genotype ; Humans ; Mongolia ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Republic of Korea ; Skin Pigmentation/*genetics ; Uzbekistan ; },
abstract = {BACKGROUND: This study reports the use of real-time PCR to identify the SNP rs1545397 in the intron region on the OCA2 gene from ancient and degraded DNA isolated from ancient human bones from Mongolia, Korea, and Uzbekistan. This SNP is a marker for skin pigmentation. LightCycler-based probes (HybProbes) were designed. A LightCycler (version 2.0) system was used for the real-time PCR.

RESULTS: The results of the real-time PCRs of three different genotypes of SNP rs1545397 were compared with those of the direct sequencing. Melting curve analysis was used for genotype determination. Three genotypes were distinguished: the homozygous T (T/T) SNP type formed a distinct melting peak at 53.3 ± 0.14°C, the homozygous A (A/A) SNP type formed a distinct melting peak at 57.8 ± 0.12°C, and the heterozygous A/T SNP type formed two distinct melting peaks at 53.3 ± 0.17°C and 57.8 ± 0.15°C. Mongolian aDNA samples tested in this study carried all three types of the SNP (A/T, A/A, and T/T) with no distinctly predominant type observed. In contrast, Korean aDNA samples carried the Asian genotype (T/T), while the Uzbekistan aDNA samples carried the European genotype (A/A) more often than the Asian genotype (T/T).

CONCLUSIONS: Human Mongolian aDNA samples had A/T, A/A, and T/T SNP rs1545397 with no distinct predominant genotype. When combined with the archeological and aDNA studies of other coupling morphologies with aDNA, our results infer that Mongolia's prehistoric population had considerable heterogeneity of skin color and morphological traits and that in the Neolithic period, a Eurasian or mixed population inhabited the western part of Mongolia.},
}

Asian People/*genetics
DNA, Ancient/*analysis
Genotype
Humans
Mongolia
Polymerase Chain Reaction
Polymorphism, Single Nucleotide/genetics
Republic of Korea
Skin Pigmentation/*genetics
Uzbekistan

@article {pmid32970680,
year = {2020},
author = {Toncheva, D and Serbezov, D and Karachanak-Yankova, S and Nesheva, D},
title = {Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease.},
journal = {PloS one},
volume = {15},
number = {9},
pages = {e0233666},
pmid = {32970680},
issn = {1932-6203},
mesh = {*DNA, Ancient ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Female ; *Genes, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mitochondrial Diseases/*genetics ; Mutation ; RNA, Transfer/genetics ; },
abstract = {Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.},
}

*DNA, Ancient
DNA, Mitochondrial/*genetics
Databases, Genetic
Female
*Genes, Mitochondrial
Humans
Male
Mitochondria/genetics
Mitochondrial Diseases/*genetics
Mutation
RNA, Transfer/genetics

@article {pmid32704107,
year = {2020},
author = {Spinney, L},
title = {Smallpox and other viruses plagued humans much earlier than suspected.},
journal = {Nature},
volume = {584},
number = {7819},
pages = {30-32},
pmid = {32704107},
issn = {1476-4687},
mesh = {Bone and Bones/microbiology/virology ; DNA, Ancient/*analysis ; Disease Eradication/history ; Hepatitis B/epidemiology/history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Mummies/microbiology/virology ; Plague/enzymology/history ; Smallpox/*epidemiology/*history/virology ; Time Factors ; Variola virus/classification/genetics/*isolation & purification ; },
}

Bone and Bones/microbiology/virology
DNA, Ancient/*analysis
Disease Eradication/history
Hepatitis B/epidemiology/history
History, 15th Century
History, 16th Century
History, 17th Century
History, 18th Century
History, 19th Century
History, 20th Century
History, 21st Century
History, Ancient
History, Medieval
Humans
Mummies/microbiology/virology
Plague/enzymology/history
Smallpox/*epidemiology/*history/virology
Time Factors
Variola virus/classification/genetics/*isolation & purification

@article {pmid32699412,
year = {2020},
author = {Ardelean, CF and Becerra-Valdivia, L and Pedersen, MW and Schwenninger, JL and Oviatt, CG and Macías-Quintero, JI and Arroyo-Cabrales, J and Sikora, M and Ocampo-Díaz, YZE and Rubio-Cisneros, II and Watling, JG and de Medeiros, VB and De Oliveira, PE and Barba-Pingarón, L and Ortiz-Butrón, A and Blancas-Vázquez, J and Rivera-González, I and Solís-Rosales, C and Rodríguez-Ceja, M and Gandy, DA and Navarro-Gutierrez, Z and De La Rosa-Díaz, JJ and Huerta-Arellano, V and Marroquín-Fernández, MB and Martínez-Riojas, LM and López-Jiménez, A and Higham, T and Willerslev, E},
title = {Evidence of human occupation in Mexico around the Last Glacial Maximum.},
journal = {Nature},
volume = {584},
number = {7819},
pages = {87-92},
pmid = {32699412},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Altitude ; Archaeology ; Bayes Theorem ; Caves ; Cultural Diversity ; DNA, Ancient/analysis ; History, Ancient ; Human Migration/*history ; Humans ; *Ice Cover ; Mexico ; },
abstract = {The initial colonization of the Americas remains a highly debated topic[1], and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations[2]. However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico[3,4], the Chiapas Highlands[5], Central Mexico[6] and the Caribbean coast[7-9] during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas[10-17]of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)[18], and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.},
}

Altitude
Archaeology
Bayes Theorem
Caves
Cultural Diversity
DNA, Ancient/analysis
History, Ancient
Human Migration/*history
Humans
*Ice Cover
Mexico

@article {pmid32612278,
year = {2020},
author = {Gansauge, MT and Aximu-Petri, A and Nagel, S and Meyer, M},
title = {Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA.},
journal = {Nature protocols},
volume = {15},
number = {8},
pages = {2279-2300},
pmid = {32612278},
issn = {1750-2799},
mesh = {Automation ; Base Sequence ; *DNA, Ancient ; DNA, Single-Stranded/*genetics ; *Gene Library ; Sequence Analysis, DNA/*methods ; },
abstract = {It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.},
}

Automation
Base Sequence
*DNA, Ancient
DNA, Single-Stranded/*genetics
*Gene Library
Sequence Analysis, DNA/*methods

@article {pmid32555485,
year = {2020},
author = {Cassidy, LM and Maoldúin, RÓ and Kador, T and Lynch, A and Jones, C and Woodman, PC and Murphy, E and Ramsey, G and Dowd, M and Noonan, A and Campbell, C and Jones, ER and Mattiangeli, V and Bradley, DG},
title = {A dynastic elite in monumental Neolithic society.},
journal = {Nature},
volume = {582},
number = {7812},
pages = {384-388},
pmid = {32555485},
issn = {1476-4687},
support = {205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adult ; Burial/history ; *Consanguinity ; DNA, Ancient/analysis ; Family/history ; Female ; Genome, Human/genetics ; Haplotypes/genetics ; Hierarchy, Social/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Male ; Societies/*history ; },
abstract = {The nature and distribution of political power in Europe during the Neolithic era remains poorly understood[1]. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive[2]. Although co-operative ideology has often been emphasised as a driver of megalith construction[1], the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy[3]-of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites[4]-specifically within polygynous and patrilineal royal families that are headed by god-kings[5,6]. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.},
}

Adult
Burial/history
*Consanguinity
DNA, Ancient/analysis
Family/history
Female
Genome, Human/genetics
Haplotypes/genetics
Hierarchy, Social/*history
History, Ancient
Humans
Incest/*history
Ireland
Male
Societies/*history

@article {pmid32438927,
year = {2020},
author = {Sazzini, M and Abondio, P and Sarno, S and Gnecchi-Ruscone, GA and Ragno, M and Giuliani, C and De Fanti, S and Ojeda-Granados, C and Boattini, A and Marquis, J and Valsesia, A and Carayol, J and Raymond, F and Pirazzini, C and Marasco, E and Ferrarini, A and Xumerle, L and Collino, S and Mari, D and Arosio, B and Monti, D and Passarino, G and D'Aquila, P and Pettener, D and Luiselli, D and Castellani, G and Delledonne, M and Descombes, P and Franceschi, C and Garagnani, P},
title = {Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {51},
pmid = {32438927},
issn = {1741-7007},
support = {602757//Seventh Framework Programme/International ; 634821//Horizon 2020 Framework Programme/International ; ADAGE//JPco-fuND/International ; 074-02-2018-330//Ministry of Education and Science of the Russian Federation/International ; FFABR2017//Italian Ministry of Education and Research/International ; },
mesh = {Archaeology ; DNA, Ancient/analysis ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Humans ; Italy ; White People ; },
abstract = {BACKGROUND: The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes.

RESULTS: We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition.

CONCLUSIONS: We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.},
}

Archaeology
DNA, Ancient/analysis
*Evolution, Molecular
*Genetic Variation
*Genome, Human
Humans
Italy
White People

@article {pmid32433609,
year = {2020},
author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T},
title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.},
journal = {Nature},
volume = {581},
number = {7808},
pages = {299-302},
pmid = {32433609},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation & purification ; DNA, Mitochondrial/genetics/isolation & purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy & histology/metabolism ; },
abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin[1]. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts[2], from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago[3]. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe[4-6]. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations[7,8].},
}

Animals
Asia
Bone and Bones/metabolism
Bulgaria
Caves
DNA, Ancient/isolation & purification
DNA, Mitochondrial/genetics/isolation & purification
Europe
*Fossils
History, Ancient
Human Migration/*history
Humans
Neanderthals/genetics
Phylogeny
Tool Use Behavior
Tooth/anatomy & histology/metabolism

@article {pmid32343728,
year = {2020},
author = {Guiry, E and Royle, TCA and Matson, RG and Ward, H and Weir, T and Waber, N and Brown, TJ and Hunt, BPV and Price, MHH and Finney, BP and Kaeriyama, M and Qin, Y and Yang, DY and Szpak, P},
title = {Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0232180},
pmid = {32343728},
issn = {1932-6203},
mesh = {Animal Migration ; Animal Scales/chemistry ; Animals ; Archaeology ; Biodiversity ; Bone and Bones/chemistry ; Carbon Isotopes/analysis ; Collagen/*chemistry ; Conservation of Natural Resources ; DNA, Ancient/analysis ; Ecotype ; Female ; Fish Proteins/*chemistry ; Lakes ; Male ; Pacific Ocean ; Salmon/classification/genetics/*physiology ; Salmonidae/classification/genetics/*physiology ; },
abstract = {The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.},
}

Animal Migration
Animal Scales/chemistry
Animals
Archaeology
Biodiversity
Bone and Bones/chemistry
Carbon Isotopes/analysis
Collagen/*chemistry
Conservation of Natural Resources
DNA, Ancient/analysis
Ecotype
Female
Fish Proteins/*chemistry
Lakes
Male
Pacific Ocean
Salmon/classification/genetics/*physiology
Salmonidae/classification/genetics/*physiology

@article {pmid31969706,
year = {2020},
author = {Lipson, M and Ribot, I and Mallick, S and Rohland, N and Olalde, I and Adamski, N and Broomandkhoshbacht, N and Lawson, AM and López, S and Oppenheimer, J and Stewardson, K and Asombang, RN and Bocherens, H and Bradman, N and Culleton, BJ and Cornelissen, E and Crevecoeur, I and de Maret, P and Fomine, FLM and Lavachery, P and Mindzie, CM and Orban, R and Sawchuk, E and Semal, P and Thomas, MG and Van Neer, W and Veeramah, KR and Kennett, DJ and Patterson, N and Hellenthal, G and Lalueza-Fox, C and MacEachern, S and Prendergast, ME and Reich, D},
title = {Ancient West African foragers in the context of African population history.},
journal = {Nature},
volume = {577},
number = {7792},
pages = {665-670},
pmid = {31969706},
issn = {1476-4687},
support = {100719/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM100233/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Alleles ; Animals ; Archaeology ; Black People/*genetics/*history ; Burial ; Cameroon ; Child ; Child, Preschool ; Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; Feeding Behavior/*ethnology ; Female ; Genetic Markers/genetics ; Genetics, Population ; Genome, Human/genetics ; Haplotypes/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Language/history ; Male ; Pan troglodytes/genetics ; *Phylogeny ; Principal Component Analysis ; },
abstract = {Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group[1-11]. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region[12,13]. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.},
}

Alleles
Animals
Archaeology
Black People/*genetics/*history
Burial
Cameroon
Child
Child, Preschool
Chromosomes, Human, Y/genetics
DNA, Ancient/analysis
Feeding Behavior/*ethnology
Female
Genetic Markers/genetics
Genetics, Population
Genome, Human/genetics
Haplotypes/genetics
History, Ancient
Human Migration/*history
Humans
Language/history
Male
Pan troglodytes/genetics
*Phylogeny
Principal Component Analysis

@article {pmid31721774,
year = {2019},
author = {Wasef, S and Subramanian, S and O'Rorke, R and Huynen, L and El-Marghani, S and Curtis, C and Popinga, A and Holland, B and Ikram, S and Millar, C and Willerslev, E and Lambert, D},
title = {Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0223964},
pmid = {31721774},
issn = {1932-6203},
mesh = {Africa ; Animal Husbandry/history ; Animals ; Birds/classification/*genetics ; DNA, Ancient ; DNA, Mitochondrial/blood/genetics/history ; Egypt, Ancient ; Genetic Variation ; *Genome, Mitochondrial ; History, Ancient ; *Mummies ; Phylogeny ; Religion/history ; },
abstract = {The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.},
}

Africa
Animal Husbandry/history
Animals
Birds/classification/*genetics
DNA, Ancient
DNA, Mitochondrial/blood/genetics/history
Egypt, Ancient
Genetic Variation
*Genome, Mitochondrial
History, Ancient
*Mummies
Phylogeny
Religion/history

@article {pmid31462783,
year = {2019},
author = {Fox, K and Hawks, J},
title = {Use ancient remains more wisely.},
journal = {Nature},
volume = {572},
number = {7771},
pages = {581-583},
pmid = {31462783},
issn = {1476-4687},
mesh = {Animals ; Archaeology/*ethics/*methods ; DNA, Ancient/*analysis/*isolation & purification ; Female ; Genomics/*ethics/*methods ; Hawaii/ethnology ; History, 18th Century ; History, Ancient ; Humans ; Male ; Neanderthals/genetics ; Stakeholder Participation ; },
}

Animals
Archaeology/*ethics/*methods
DNA, Ancient/*analysis/*isolation & purification
Female
Genomics/*ethics/*methods
Hawaii/ethnology
History, 18th Century
History, Ancient
Humans
Male
Neanderthals/genetics
Stakeholder Participation

@article {pmid31279340,
year = {2019},
author = {Velsko, IM and Fellows Yates, JA and Aron, F and Hagan, RW and Frantz, LAF and Loe, L and Martinez, JBR and Chaves, E and Gosden, C and Larson, G and Warinner, C},
title = {Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {102},
pmid = {31279340},
issn = {2049-2618},
mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biofilms/*growth & development ; Bone and Bones/microbiology ; DNA, Ancient/analysis ; DNA, Bacterial/genetics ; Dental Calculus/history/*microbiology ; Dental Plaque/*microbiology ; Female ; History, Ancient ; Humans ; Male ; Metagenomics ; Microbiota/*physiology ; Periodontal Diseases/microbiology ; Proteomics ; Tooth/*microbiology ; },
abstract = {BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.},
}

Bacteria/*classification
*Bacterial Physiological Phenomena
Bacterial Proteins/genetics
Biofilms/*growth & development
Bone and Bones/microbiology
DNA, Ancient/analysis
DNA, Bacterial/genetics
Dental Calculus/history/*microbiology
Dental Plaque/*microbiology
Female
History, Ancient
Humans
Male
Metagenomics
Microbiota/*physiology
Periodontal Diseases/microbiology
Proteomics
Tooth/*microbiology

@article {pmid31243383,
year = {2019},
author = {Warren, M},
title = {Move over, DNA: ancient proteins are starting to reveal humanity's history.},
journal = {Nature},
volume = {570},
number = {7762},
pages = {433-436},
doi = {10.1038/d41586-019-01986-x},
pmid = {31243383},
issn = {1476-4687},
mesh = {Animals ; Bone and Bones/chemistry ; Caves ; China ; DNA, Ancient/analysis/isolation & purification ; Egg Shell/chemistry ; Evolution, Molecular ; *Fossils ; Hominidae/*classification ; Humans ; Paleontology/*methods/*trends ; Protein Stability ; Proteins/*analysis/*isolation & purification ; Proteomics/trends ; Time Factors ; Tooth/chemistry ; },
}

Animals
Bone and Bones/chemistry
Caves
China
DNA, Ancient/analysis/isolation & purification
Egg Shell/chemistry
Evolution, Molecular
*Fossils
Hominidae/*classification
Humans
Paleontology/*methods/*trends
Protein Stability
Proteins/*analysis/*isolation & purification
Proteomics/trends
Time Factors
Tooth/chemistry

@article {pmid31168093,
year = {2019},
author = {Sikora, M and Pitulko, VV and Sousa, VC and Allentoft, ME and Vinner, L and Rasmussen, S and Margaryan, A and de Barros Damgaard, P and de la Fuente, C and Renaud, G and Yang, MA and Fu, Q and Dupanloup, I and Giampoudakis, K and Nogués-Bravo, D and Rahbek, C and Kroonen, G and Peyrot, M and McColl, H and Vasilyev, SV and Veselovskaya, E and Gerasimova, M and Pavlova, EY and Chasnyk, VG and Nikolskiy, PA and Gromov, AV and Khartanovich, VI and Moiseyev, V and Grebenyuk, PS and Fedorchenko, AY and Lebedintsev, AI and Slobodin, SB and Malyarchuk, BA and Martiniano, R and Meldgaard, M and Arppe, L and Palo, JU and Sundell, T and Mannermaa, K and Putkonen, M and Alexandersen, V and Primeau, C and Baimukhanov, N and Malhi, RS and Sjögren, KG and Kristiansen, K and Wessman, A and Sajantila, A and Lahr, MM and Durbin, R and Nielsen, R and Meltzer, DJ and Excoffier, L and Willerslev, E},
title = {The population history of northeastern Siberia since the Pleistocene.},
journal = {Nature},
volume = {570},
number = {7760},
pages = {182-188},
pmid = {31168093},
issn = {1476-4687},
support = {143393/SNSF_/Swiss National Science Foundation/Switzerland ; 166605/SNSF_/Swiss National Science Foundation/Switzerland ; 207492/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Asia/ethnology ; DNA, Ancient/analysis ; Europe/ethnology ; Gene Pool ; Genome, Human/*genetics ; Haplotypes ; History, 15th Century ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Indians, North American ; Male ; Siberia/ethnology ; },
abstract = {Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.},
}

Asia/ethnology
DNA, Ancient/analysis
Europe/ethnology
Gene Pool
Genome, Human/*genetics
Haplotypes
History, 15th Century
History, Ancient
History, Medieval
Human Migration/*history
Humans
Indians, North American
Male
Siberia/ethnology

@article {pmid31095634,
year = {2019},
author = {Yuan, JX and Hou, XD and Barlow, A and Preick, M and Taron, UH and Alberti, F and Basler, N and Deng, T and Lai, XL and Hofreiter, M and Sheng, GL},
title = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China.},
journal = {PloS one},
volume = {14},
number = {5},
pages = {e0216883},
pmid = {31095634},
issn = {1932-6203},
mesh = {Animals ; *Biological Evolution ; *DNA, Ancient ; *Equidae/classification/genetics ; *Genome, Mitochondrial ; *Haplotypes ; *Phylogeny ; },
abstract = {The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.},
}

Animals
*Biological Evolution
*DNA, Ancient
*Equidae/classification/genetics
*Genome, Mitochondrial
*Haplotypes
*Phylogeny

@article {pmid30992587,
year = {2019},
author = {Guglielmi, G},
title = {Facing up to injustice in genome science.},
journal = {Nature},
volume = {568},
number = {7752},
pages = {290-293},
pmid = {30992587},
issn = {1476-4687},
mesh = {DNA, Ancient/analysis ; Female ; Genomics/*ethics ; Humans ; Indians, North American/genetics ; Minority Groups/psychology ; Population Groups/*genetics/psychology ; Pregnancy ; *Research Design ; Research Personnel/*ethics/psychology ; *Social Marginalization/psychology ; },
}

DNA, Ancient/analysis
Female
Genomics/*ethics
Humans
Indians, North American/genetics
Minority Groups/psychology
Population Groups/*genetics/psychology
Pregnancy
*Research Design
Research Personnel/*ethics/psychology
*Social Marginalization/psychology

@article {pmid30664775,
year = {2019},
author = {Lin, M and Kussell, E},
title = {Inferring bacterial recombination rates from large-scale sequencing datasets.},
journal = {Nature methods},
volume = {16},
number = {2},
pages = {199-204},
doi = {10.1038/s41592-018-0293-7},
pmid = {30664775},
issn = {1548-7105},
mesh = {Computational Biology/*methods ; Computer Simulation ; *DNA, Ancient ; DNA, Bacterial ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Genetic Techniques ; Genetic Variation ; Helicobacter pylori/genetics ; History, Medieval ; Humans ; Metagenomics/*methods ; Models, Genetic ; Mutation ; Plague/history/microbiology ; *Recombination, Genetic ; *Sequence Analysis, DNA ; Yersinia pestis/genetics ; },
abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.},
}

Computational Biology/*methods
Computer Simulation
*DNA, Ancient
DNA, Bacterial
Databases, Genetic
Drug Resistance, Bacterial/*genetics
Escherichia coli/genetics
Gastrointestinal Microbiome
Genetic Techniques
Genetic Variation
Helicobacter pylori/genetics
History, Medieval
Humans
Metagenomics/*methods
Models, Genetic
Mutation
Plague/history/microbiology
*Recombination, Genetic
*Sequence Analysis, DNA
Yersinia pestis/genetics

@article {pmid30425363,
year = {2018},
author = {Callaway, E},
title = {Ancient genomics is recasting the story of the Americas' first residents.},
journal = {Nature},
volume = {563},
number = {7731},
pages = {303-304},
pmid = {30425363},
issn = {1476-4687},
mesh = {Archaeology ; Central America/ethnology ; DNA, Ancient/*analysis ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Indians, North American/genetics ; Infant ; Male ; Montana ; Native Hawaiian or Pacific Islander/genetics ; South America/ethnology ; },
}

Archaeology
Central America/ethnology
DNA, Ancient/*analysis
Genome, Human/*genetics
*Genomics
History, Ancient
Human Migration/*history
Humans
Indians, North American/genetics
Infant
Male
Montana
Native Hawaiian or Pacific Islander/genetics
South America/ethnology

@article {pmid30323185,
year = {2018},
author = {Rohland, N and Glocke, I and Aximu-Petri, A and Meyer, M},
title = {Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing.},
journal = {Nature protocols},
volume = {13},
number = {11},
pages = {2447-2461},
doi = {10.1038/s41596-018-0050-5},
pmid = {30323185},
issn = {1750-2799},
mesh = {Bone and Bones/*chemistry ; DNA, Ancient/*isolation & purification ; Fossils ; Gene Library ; Geologic Sediments/chemistry ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Magnets ; Silicon Dioxide/chemistry ; Solid Phase Extraction/instrumentation/*methods ; Tooth/*chemistry ; },
abstract = {DNA preserved in ancient bones, teeth and sediments is typically highly fragmented and present only in minute amounts. Here, we provide a highly versatile silica-based DNA extraction protocol that enables the retrieval of short (≥35 bp) or even ultrashort (≥25 bp) DNA fragments from such material with minimal carryover of substances that inhibit library preparation for high-throughput sequencing. DNA extraction can be performed with either silica spin columns, which offer the most convenient choice for manual DNA extraction, or silica-coated magnetic particles. The latter allow a substantial cost reduction as well as automation on liquid-handling systems. This protocol update replaces a now-outdated version that was published 11 years ago, before high-throughput sequencing technologies became widely available. It has been thoroughly optimized to provide the highest DNA yields from highly degraded samples, as well as fast and easy handling, requiring not more than ~15 min of hands-on time per sample.},
}

Bone and Bones/*chemistry
DNA, Ancient/*isolation & purification
Fossils
Gene Library
Geologic Sediments/chemistry
High-Throughput Nucleotide Sequencing/*methods
Humans
Magnets
Silicon Dioxide/chemistry
Solid Phase Extraction/instrumentation/*methods
Tooth/*chemistry

@article {pmid29933384,
year = {2018},
author = {Matsumura, H and Shinoda, KI and Shimanjuntak, T and Oktaviana, AA and Noerwidi, S and Octavianus Sofian, H and Prastiningtyas, D and Nguyen, LC and Kakuda, T and Kanzawa-Kiriyama, H and Adachi, N and Hung, HC and Fan, X and Wu, X and Willis, A and Oxenham, MF},
title = {Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198689},
pmid = {29933384},
issn = {1932-6203},
mesh = {Anthropometry ; Asia, Southeastern ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Datasets as Topic ; *Human Migration ; Humans ; Skull/*anatomy & histology ; },
abstract = {The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712-5591cal BP to 1864-1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin's standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.},
}

Anthropometry
Asia, Southeastern
DNA, Ancient/*analysis
DNA, Mitochondrial/*analysis
Datasets as Topic
*Human Migration
Humans
Skull/*anatomy & histology

@article {pmid29562232,
year = {2018},
author = {Hajdinjak, M and Fu, Q and Hübner, A and Petr, M and Mafessoni, F and Grote, S and Skoglund, P and Narasimham, V and Rougier, H and Crevecoeur, I and Semal, P and Soressi, M and Talamo, S and Hublin, JJ and Gušić, I and Kućan, Ž and Rudan, P and Golovanova, LV and Doronichev, VB and Posth, C and Krause, J and Korlević, P and Nagel, S and Nickel, B and Slatkin, M and Patterson, N and Reich, D and Prüfer, K and Meyer, M and Pääbo, S and Kelso, J},
title = {Reconstructing the genetic history of late Neanderthals.},
journal = {Nature},
volume = {555},
number = {7698},
pages = {652-656},
pmid = {29562232},
issn = {1476-4687},
support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Africa/ethnology ; Animals ; Bone and Bones ; DNA, Ancient/analysis ; Europe/ethnology ; Female ; Gene Flow ; Genetics, Population ; Genome/*genetics ; Genomics ; Humans ; Hypochlorous Acid ; Male ; Neanderthals/*classification/*genetics ; *Phylogeny ; Siberia/ethnology ; Tooth ; },
abstract = {Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.},
}

Africa/ethnology
Animals
Bone and Bones
DNA, Ancient/analysis
Europe/ethnology
Female
Gene Flow
Genetics, Population
Genome/*genetics
Genomics
Humans
Hypochlorous Acid
Male
Neanderthals/*classification/*genetics
*Phylogeny
Siberia/ethnology
Tooth

@article {pmid29522562,
year = {2018},
author = {Hamilton-Brehm, SD and Hristova, LT and Edwards, SR and Wedding, JR and Snow, M and Kruger, BR and Moser, DP},
title = {Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194223},
pmid = {29522562},
issn = {1932-6203},
mesh = {Archaeology ; *Carbon Radioisotopes ; *DNA, Ancient ; *DNA, Mitochondrial ; Evolution, Molecular ; Genetic Variation ; Humans ; Nevada ; Population Dynamics ; *Radiometric Dating ; Sequence Analysis, DNA ; },
abstract = {Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.},
}

Archaeology
*Carbon Radioisotopes
*DNA, Ancient
*DNA, Mitochondrial
Evolution, Molecular
Genetic Variation
Humans
Nevada
Population Dynamics
*Radiometric Dating
Sequence Analysis, DNA

@article {pmid29466337,
year = {2018},
author = {Olalde, I and Brace, S and Allentoft, ME and Armit, I and Kristiansen, K and Booth, T and Rohland, N and Mallick, S and Szécsényi-Nagy, A and Mittnik, A and Altena, E and Lipson, M and Lazaridis, I and Harper, TK and Patterson, N and Broomandkhoshbacht, N and Diekmann, Y and Faltyskova, Z and Fernandes, D and Ferry, M and Harney, E and de Knijff, P and Michel, M and Oppenheimer, J and Stewardson, K and Barclay, A and Alt, KW and Liesau, C and Ríos, P and Blasco, C and Miguel, JV and García, RM and Fernández, AA and Bánffy, E and Bernabò-Brea, M and Billoin, D and Bonsall, C and Bonsall, L and Allen, T and Büster, L and Carver, S and Navarro, LC and Craig, OE and Cook, GT and Cunliffe, B and Denaire, A and Dinwiddy, KE and Dodwell, N and Ernée, M and Evans, C and Kuchařík, M and Farré, JF and Fowler, C and Gazenbeek, M and Pena, RG and Haber-Uriarte, M and Haduch, E and Hey, G and Jowett, N and Knowles, T and Massy, K and Pfrengle, S and Lefranc, P and Lemercier, O and Lefebvre, A and Martínez, CH and Olmo, VG and Ramírez, AB and Maurandi, JL and Majó, T and McKinley, JI and McSweeney, K and Mende, BG and Modi, A and Kulcsár, G and Kiss, V and Czene, A and Patay, R and Endrődi, A and Köhler, K and Hajdu, T and Szeniczey, T and Dani, J and Bernert, Z and Hoole, M and Cheronet, O and Keating, D and Velemínský, P and Dobeš, M and Candilio, F and Brown, F and Fernández, RF and Herrero-Corral, AM and Tusa, S and Carnieri, E and Lentini, L and Valenti, A and Zanini, A and Waddington, C and Delibes, G and Guerra-Doce, E and Neil, B and Brittain, M and Luke, M and Mortimer, R and Desideri, J and Besse, M and Brücken, G and Furmanek, M and Hałuszko, A and Mackiewicz, M and Rapiński, A and Leach, S and Soriano, I and Lillios, KT and Cardoso, JL and Pearson, MP and Włodarczak, P and Price, TD and Prieto, P and Rey, PJ and Risch, R and Rojo Guerra, MA and Schmitt, A and Serralongue, J and Silva, AM and Smrčka, V and Vergnaud, L and Zilhão, J and Caramelli, D and Higham, T and Thomas, MG and Kennett, DJ and Fokkens, H and Heyd, V and Sheridan, A and Sjögren, KG and Stockhammer, PW and Krause, J and Pinhasi, R and Haak, W and Barnes, I and Lalueza-Fox, C and Reich, D},
title = {The Beaker phenomenon and the genomic transformation of northwest Europe.},
journal = {Nature},
volume = {555},
number = {7695},
pages = {190-196},
pmid = {29466337},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; },
mesh = {Chromosomes, Human, Y/genetics ; Cultural Evolution/*history ; DNA, Ancient ; Europe ; Gene Pool ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Spatio-Temporal Analysis ; },
abstract = {From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.},
}

Chromosomes, Human, Y/genetics
Cultural Evolution/*history
DNA, Ancient
Europe
Gene Pool
Genetics, Population
Genome, Human/*genetics
*Genomics
Haplotypes
History, Ancient
Human Migration/*history
Humans
Male
Spatio-Temporal Analysis

@article {pmid29300782,
year = {2018},
author = {Patterson Ross, Z and Klunk, J and Fornaciari, G and Giuffra, V and Duchêne, S and Duggan, AT and Poinar, D and Douglas, MW and Eden, JS and Holmes, EC and Poinar, HN},
title = {The paradox of HBV evolution as revealed from a 16th century mummy.},
journal = {PLoS pathogens},
volume = {14},
number = {1},
pages = {e1006750},
pmid = {29300782},
issn = {1553-7374},
mesh = {Base Sequence ; Bayes Theorem ; Child, Preschool ; Consensus Sequence ; DNA, Ancient/*chemistry/isolation & purification ; *Evolution, Molecular ; Gene Library ; *Genome, Viral ; Hepatitis B virus/*genetics/isolation & purification/metabolism/ultrastructure ; High-Throughput Nucleotide Sequencing ; Humans ; Italy ; Microscopy, Electron, Scanning ; *Models, Genetic ; Mummies/*virology ; Mutation ; Phylogeny ; Reproducibility of Results ; Sequence Alignment ; Virion/genetics/isolation & purification/metabolism/ultrastructure ; },
abstract = {Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.},
}

Base Sequence
Bayes Theorem
Child, Preschool
Consensus Sequence
DNA, Ancient/*chemistry/isolation & purification
*Evolution, Molecular
Gene Library
*Genome, Viral
Hepatitis B virus/*genetics/isolation & purification/metabolism/ultrastructure
High-Throughput Nucleotide Sequencing
Humans
Italy
Microscopy, Electron, Scanning
*Models, Genetic
Mummies/*virology
Mutation
Phylogeny
Reproducibility of Results
Sequence Alignment
Virion/genetics/isolation & purification/metabolism/ultrastructure

@article {pmid29300040,
year = {2018},
author = {Gibney, E},
title = {What to expect in 2018: science in the new year.},
journal = {Nature},
volume = {553},
number = {7686},
pages = {12-13},
doi = {10.1038/d41586-018-00009-5},
pmid = {29300040},
issn = {1476-4687},
mesh = {Astronauts ; Astronomy/trends ; Climate Change ; Clinical Trials as Topic ; DNA, Ancient ; Drug Resistance, Microbial ; European Union/organization & administration ; Gene Editing/trends ; Genomics/trends ; Human Migration ; Humans ; Indians, North American/genetics ; Induced Pluripotent Stem Cells/transplantation ; Moon ; Neoplasms/genetics ; Open Access Publishing/trends ; Parkinson Disease/pathology/therapy ; Phage Therapy/trends ; Physics ; Politics ; Science/*trends ; Space Flight/trends ; Synchrotrons ; },
}

Astronauts
Astronomy/trends
Climate Change
Clinical Trials as Topic
DNA, Ancient
Drug Resistance, Microbial
European Union/organization & administration
Gene Editing/trends
Genomics/trends
Human Migration
Humans
Indians, North American/genetics
Induced Pluripotent Stem Cells/transplantation
Moon
Neoplasms/genetics
Open Access Publishing/trends
Parkinson Disease/pathology/therapy
Phage Therapy/trends
Physics
Politics
Science/*trends
Space Flight/trends
Synchrotrons

@article {pmid28880302,
year = {2017},
author = {Callaway, E},
title = {Skeleton plundered from Mexican cave was one of the Americas' oldest.},
journal = {Nature},
volume = {549},
number = {7670},
pages = {14-15},
doi = {10.1038/nature.2017.22521},
pmid = {28880302},
issn = {1476-4687},
mesh = {Archaeology/methods ; Calcium Carbonate/*chemistry ; *Caves ; DNA, Ancient/analysis/isolation & purification ; Humans ; Indians, Central American ; Indians, North American ; Male ; Mexico ; Montana ; Radiometric Dating/*methods ; *Skeleton ; *Theft ; },
}

Archaeology/methods
Calcium Carbonate/*chemistry
*Caves
DNA, Ancient/analysis/isolation & purification
Humans
Indians, Central American
Indians, North American
Male
Mexico
Montana
Radiometric Dating/*methods
*Skeleton
*Theft

@article {pmid28746407,
year = {2017},
author = {Kemp, BM and Judd, K and Monroe, C and Eerkens, JW and Hilldorfer, L and Cordray, C and Schad, R and Reams, E and Ortman, SG and Kohler, TA},
title = {Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest.},
journal = {PloS one},
volume = {12},
number = {7},
pages = {e0178882},
pmid = {28746407},
issn = {1932-6203},
mesh = {Animals ; Animals, Domestic ; Archaeology ; Climate Change ; DNA, Ancient/chemistry ; DNA, Mitochondrial/chemistry/genetics/*history ; Dogs ; *Fossils ; Genetic Variation ; Haplotypes ; History, Medieval ; *Human Migration ; Humans ; Indians, North American/history ; Population Dynamics ; Sequence Analysis, DNA/methods ; Southwestern United States ; Turkeys ; },
abstract = {The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.},
}

Animals
Animals, Domestic
Archaeology
Climate Change
DNA, Ancient/chemistry
DNA, Mitochondrial/chemistry/genetics/*history
Dogs
*Fossils
Genetic Variation
Haplotypes
History, Medieval
*Human Migration
Humans
Indians, North American/history
Population Dynamics
Sequence Analysis, DNA/methods
Southwestern United States
Turkeys

@article {pmid27560131,
year = {2016},
author = {Lech, T},
title = {A Discovered Ducal Seal Does Not Belong to the Incorporation Charter for the City of Krakow Solving the Mystery Using Genetic Methods.},
journal = {PloS one},
volume = {11},
number = {8},
pages = {e0161591},
pmid = {27560131},
issn = {1932-6203},
mesh = {Animals ; Cattle ; Cultural Characteristics ; Cytochromes b/metabolism ; DNA Primers ; DNA, Ancient/*analysis ; Haplotypes ; *History, Medieval ; *Microsatellite Repeats ; Poland ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Spectrophotometry ; },
abstract = {The Incorporation Charter for the city of Krakow, the former capital of Poland, is one of the most valuable documents stored in the National Archives in Krakow. The document, which was written in 1257 on parchment, grants Krakow the Magdeburg rights and regulates its legal, statutory, economic and settlement-related aspects. The Charter was placed in the National Register of the Memory of the World UNESCO programme in 2014. A ducal seal, considered to be the lost seal detached from the Incorporation Charter, was found in the sphragistic collection after nearly 500 years. Unfortunately, it was uncertain whether the seal in question was indeed the missing part of the document. The aim of the study presented below was to solve this mystery. For this purpose, the parchment on which the Incorporation Charter was written was compared with the fragment of the parchment attached to the discovered seal. The study involved the analysis of selected mitochondrial DNA sequences and additional analysis at the level of nuclear DNA using microsatellite markers in the form of 11 STR (Short Tandem Repeat) loci, to identify the species and individual whose skin had been used to make the parchment. This analysis revealed that seal and parchment was from different individuals and thereby discovered that the seal was never a part of the Incorporation Charter. The study is further an example of informative DNA preservation in cultural heritage objects.},
}

Animals
Cattle
Cultural Characteristics
Cytochromes b/metabolism
DNA Primers
DNA, Ancient/*analysis
Haplotypes
*History, Medieval
*Microsatellite Repeats
Poland
Polymerase Chain Reaction
*Sequence Analysis, DNA
Spectrophotometry

@article {pmid40920634,
year = {2025},
author = {Fu, Q and Cao, P and Dai, Q and Bennett, EA and Feng, X and Yang, MA and Ping, W and Pääbo, S and Ji, Q},
title = {Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium.},
journal = {Cell},
volume = {188},
number = {15},
pages = {3919-3926.e9},
doi = {10.1016/j.cell.2025.05.040},
pmid = {40920634},
issn = {1097-4172},
mesh = {*DNA, Mitochondrial/genetics/isolation & purification ; *Dental Calculus/chemistry ; Animals ; *Fossils ; *Hominidae/genetics/classification/anatomy & histology ; *Skull/anatomy & histology ; China ; Phylogeny ; DNA, Ancient ; Humans ; },
abstract = {Denisovans have yet to be directly associated with a hominin cranium, limiting our understanding of their morphology and geographical distribution. We have attempted to retrieve DNA from a nearly complete Middle Pleistocene cranium from Harbin (>146 ka), northeastern China. Although no DNA could be retrieved from a tooth or the petrous bone, mitochondrial DNA (mtDNA) could be isolated from dental calculus. The mtDNA falls within Denisovan mtDNA variation and is related to an mtDNA branch carried by early Denisovan individuals in southern Siberia, previously observed in Denisova Cave. This suggests that Denisovans inhabited a large geographical range in Asia in the Middle Pleistocene. The association of Denisovan mtDNA with the Harbin cranium allows a better understanding of the morphological relationships between Denisovans and other East Asian Middle Pleistocene fossils. Furthermore, the retrieval of host DNA from dental calculus opens new possibilities for genetic research on Middle Pleistocene hominins.},
}

*DNA, Mitochondrial/genetics/isolation & purification
*Dental Calculus/chemistry
Animals
*Fossils
*Hominidae/genetics/classification/anatomy & histology
*Skull/anatomy & histology
China
Phylogeny
DNA, Ancient
Humans

@article {pmid41249624,
year = {2025},
author = {Kocher, A and Krause, J and Spyrou, MA},
title = {Insights into infectious diseases through ancient pathogen genomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41249624},
issn = {1740-1534},
abstract = {Major advances in metagenomic and biomolecular techniques have opened avenues for the recovery and sequencing of rare and highly fragmented DNA molecules from ancient biological samples, including those of pathogens that may persist in the remains of infected hosts long after their death. Initially consisting of relatively rare findings for a few disease-causing agents of historical importance, the field of ancient pathogen genomics is rapidly progressing towards genome-level analyses of larger sample sets encompassing a wider range of bacterial, viral and eukaryotic taxa. These advances have provided important insights into past pathogen distribution and genomic make-up, and the unprecedented opportunity to track their evolution 'in action' over large timescales. In this Review, we explore the major contributions of ancient DNA research to the understanding of pathogen evolution and its association with past epidemics, as well as human sociocultural and migration history, including numerous important studies that have been published in recent years. Moreover, we discuss existing limitations and future prospects of ancient pathogen genomics and the relevance of the field to current public health challenges.},
}

@article {pmid41240910,
year = {2025},
author = {Mármol-Sánchez, E and Fromm, B and Oskolkov, N and Pochon, Z and Dehasque, M and Aslanzadeh, M and Bozlak, E and Brown, K and van der Valk, T and Kalogeropoulos, P and Chacón-Duque, JC and Biryukova, I and Heintzman, PD and Furugård, C and Plotnikov, V and Protopopov, A and Andersson, B and Ersmark, E and Peterson, KJ and Friedländer, MR and Dalén, L},
title = {Ancient RNA expression profiles from the extinct woolly mammoth.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.10.025},
pmid = {41240910},
issn = {1097-4172},
abstract = {Ancient DNA has revolutionized the study of extinct and extant organisms that lived up to 2 million years ago, enabling the reconstruction of genomes from multiple extinct species, as well as the ecosystems where they once thrived. However, current DNA sequencing techniques alone cannot directly provide insights into tissue identity, gene expression dynamics, or transcriptional regulation, as these are encoded in the RNA fraction. Here, we report transcriptional profiles from 10 Late Pleistocene woolly mammoths. One of these, dated to be ∼39,000 years old, yielded sufficient detail to recover tissue-specific regulatory mechanisms and biological functions essential for skeletal muscle metabolism, representing the oldest ancient RNA sequences recorded to date. We showcase the potential to study ancient RNA molecules beyond preconceived limitations, providing an analytical framework for validating and decoding preserved transcriptomes through time. With our findings, we anticipate the emergence of integrative paleo-studies combining genomics, proteomics, and transcriptomics.},
}

@article {pmid41233739,
year = {2025},
author = {Nebet, ER and Aprea, C and Zoodsma, JD and Raab, WJ and Sirotkin, HI and Wollmuth, LP},
title = {Conservation of human NMDA receptor subunits and disease variants in zebrafish.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1042},
pmid = {41233739},
issn = {1471-2164},
support = {F31 NS145927/NS/NINDS NIH HHS/United States ; RO1 NS088479//National Institute of Health/ ; },
mesh = {Animals ; *Zebrafish/genetics ; *Receptors, N-Methyl-D-Aspartate/genetics/chemistry/metabolism ; Humans ; *Conserved Sequence ; Protein Subunits/genetics/chemistry ; Amino Acid Sequence ; Models, Molecular ; },
abstract = {BACKGROUND: NMDA receptors (NMDARs) are widely expressed, ligand-gated ion channels that play key roles in brain development and function. Variants have been identified in the GRIN genes encoding NMDAR subunits that are linked to neurodevelopmental disorders, among other manifestations. Zebrafish are a powerful model to study brain development and function given their rapid development and ease of genetic manipulation. As a result of an ancient genome duplication, zebrafish possess two paralogues for most human NMDAR subunits. To evaluate the degree of conservation between human NMDAR subunits and their respective zebrafish paralogues, we carried out detailed in silico analyses, with an emphasis on key functional elements. To further assess the suitability of zebrafish for modeling NMDAR-associated neurodevelopmental disorders, we analyzed the conservation of positions with identified missense variants.

RESULTS: We find that the human NMDAR subunits are generally well conserved across zebrafish paralogs. Moreover, variants classified as pathogenic and putatively pathogenic are highly conserved, reflecting the importance of key protein regions to neurotypical receptor function. Positions with putatively benign and benign variants are less conserved. Across NMDAR domains, the transmembrane domain is most highly conserved, followed by the ligand-binding domain, which maintains conservation of amino acids that participate in the binding of ligands. The N-terminal domain is less well conserved but aligned models show high degrees of structural similarity. The C-terminal domain is the most poorly conserved region across zebrafish paralogs, but certain key regions that undergo phosphorylation, palmitoylation, and ubiquitylation as well as protein-binding motifs are better conserved.

CONCLUSIONS: Our findings highlight a strong conservation of human NMDAR subunits in zebrafish, with some exceptions. The ligand-binding domain, the transmembrane domain forming the ion channel, and the short polypeptide linkers that connect them are highly conserved. The N- and C-terminal domains are less conserved but functional motifs in general are more highly conserved relative to the entire domain. Overall, our findings support the utility of zebrafish as a model for studying neurodevelopment and disease mechanisms and provide a template for rigorously considering the relationship between human and zebrafish paralogues.},
}

Animals
*Zebrafish/genetics
*Receptors, N-Methyl-D-Aspartate/genetics/chemistry/metabolism
Humans
*Conserved Sequence
Protein Subunits/genetics/chemistry
Amino Acid Sequence
Models, Molecular

@article {pmid41221507,
year = {2025},
author = {Clinton, CK and Jackson, FLC},
title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf181},
pmid = {41221507},
issn = {2730-6151},
abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.},
}

@article {pmid41210987,
year = {2025},
author = {Ran, J and Liu, Y and Wangdue, S and Yang, X and Wang, T and Gao, Y and Cao, P and Tong, Y and Dai, Q and Chen, S and Shi, H and Liu, F and Feng, X and Li, Y and Chen, F and Fu, Q},
title = {Ancient genomes reveal basal Asian ancestries and dynamic population interactions over time on the southern Tibetan Plateau.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113676},
pmid = {41210987},
issn = {2589-0042},
abstract = {The southern Tibetan Plateau is a key region for the settlement and flourishing of Tibetan populations, but the long-term population dynamics in this area remain poorly understood. By analyzing 16 newly sequenced genomes from the Mabu Co site (4400 masl), we reconstructed the population history on the southern Tibetan Plateau spanning 4,400-3,500 BP. While the local southern plateau ancestry was maintained over a millennium, genetic diversity within these populations was observed over time. We revealed multiple admixtures, including Basal Asian Xingyi-related ancestry linked to hunter-gatherer populations from southwestern China, and provided the first evidence of this ancestry influencing the ancient southern Tibetan Plateau populations again after 4,000 BP. Moreover, mtDNA and Y haplogroups reveal that individuals exhibit greater maternal genetic diversity alongside restricted paternal lineage conservation. This study provides a higher-resolution population history in the ultra-highlands, contributing to understanding human adaptation to extreme environments.},
}

@article {pmid41208726,
year = {2025},
author = {Erven, JAM and Etourneau, A and Mashkour, M and Neupane, M and Bardou, P and Stella, A and Talenti, A and Masiga, CW and Van Tassell, CP and Clark, E and Pompanon, F and Colli, L and Amills, M and Milanesi, M and Crepaldi, P and Servin, B and Rosen, BD and Tosser-Klopp, G and Daly, KG},
title = {Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf181},
pmid = {41208726},
issn = {1759-6653},
support = {21/PATH-S/9515(T)//Taighde Éireann-Research Ireland/ ; BBS/OS/GC/000012F//BBSRC Awards/ ; BBS/E/D/10002070//BBSRC Awards/ ; BBS/E/RL/230001A//BBSRC Awards/ ; ANR-10-INBS-09-08//France Génomique 'Call for high impact projects'"/ ; },
abstract = {Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.},
}

@article {pmid41208551,
year = {2025},
author = {Gwee, CY and Tassoni, L and Boev, Z and Tomek, T and Bochenski, ZM and Talamo, S and Wolf, JBW},
title = {Performance of Two Custom Probe Kits for In-Solution Enrichment of Ancient Avian DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70071},
doi = {10.1111/1755-0998.70071},
pmid = {41208551},
issn = {1755-0998},
support = {WO 1426/7-1//Deutsche Forschungsgemeinschaft/ ; //FARE (Framework per l'attrazione ed il rafforzamento delle eccellenze per la Ricerca in Italia - III edizione)/ ; Prot. R20L4N7MS5 CUP J53C2200374000//Evaluate the precision of time in Human Evolution adopting spectrometric methods for archaeological bones - EURHOPE/ ; },
abstract = {Ancient DNA (aDNA) analysis remains challenging due to low endogenous DNA content of degraded samples. Hybridisation-based in-solution enrichment has emerged as an effective tool for targeting genomic regions, enhancing endogenous DNA yield while minimising overall sequencing effort. Despite their widespread use, the performance of different probe kits in capture efficiency remains insufficiently understood, particularly in nonhuman model organisms. In this study, we examined the performance of two commercially available custom probe systems, the RNA-based myBaits and DNA-based Twist, in enriching endogenous aDNA (0.9%-90.1%) extracted from crow bones collected from the early to late Holocene (100-14,000 years ago). The target regions included a panel of 104 K genome-wide single nucleotide polymorphisms (SNPs) identified from modern populations of the Corvus corone species complex. Both custom probe kits substantially improved fold enrichment and target site detection rates compared with shotgun sequencing. Between the two kits, myBaits consistently achieved higher capture efficiency. In contrast, Twist retained a greater proportion of endogenous DNA, but most of this originated from off-target regions, resulting in lower target efficiency under our experimental conditions. Twist demonstrated higher coverage in regions with extreme GC content, highlighting its utility for applications targeting GC-rich genomic regions. These findings provide insights into the performance of commercially available DNA enrichment methods and help guide study design.},
}

@article {pmid41206445,
year = {2025},
author = {Gilardet, A and Oppenheimer, J and Sinding, MS and Lord, E and Chacón-Duque, JC and Oteo-García, G and Xenikoudakis, G and Kosintsev, P and Southon, J and Vasiliev, SK and Shunkov, MV and Kozlikin, MB and Douka, K and Shapiro, B and Heintzman, PD and Dalén, L},
title = {Palaeogenomics reveals a loss of bovine lineages in mid-latitude Asia over the last 200,000 years.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf206},
pmid = {41206445},
issn = {1759-6653},
abstract = {Bovines have a complex yet poorly understood evolutionary history that is characterised by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically-widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby palaeontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or palaeoproteomics. In this study, we screened these bovine bones for ancient DNA (aDNA) and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harboured diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.},
}

@article {pmid41206140,
year = {2025},
author = {},
title = {Correction to: Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf241},
pmid = {41206140},
issn = {1751-7370},
}

@article {pmid41205605,
year = {2025},
author = {Cox, SL and Kaymak-Loveless, K and Shin, C and Alihodžić, T and Alt, KW and Atanassova, N and Binder, D and Čaušević-Bully, M and Chohadzhiev, A and Chokhadzhiev, S and Duday, H and Gaydarska, B and Khudaverdyan, A and Perez, RM and Nicklisch, N and Novak, M and Caravatti, CO and Réveillas, H and Rivollat, M and Rottier, S and Tončinić, D and Zaüner, S and Mathieson, I},
title = {Effects of ancestry, agriculture, and lactase persistence on the stature of prehistoric Europeans.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.054},
pmid = {41205605},
issn = {1879-0445},
abstract = {Ancient DNA has revolutionized our understanding of human evolutionary history, but studies focusing solely on genetic variation tell an incomplete story by neglecting phenotypic outcomes. The relationships between genotype and phenotype can change over time, making it desirable to study them directly in ancient populations rather than in present-day data. Here, we present a large-scale integration of ancient genomic and phenotypic data, analyzing femur length as a proxy for stature in 659 individuals with published whole-genome ancient DNA data across western Eurasia. Polygenic scores derived from modern European and East Asian genome-wide association studies[1] retain predictive power in ancient populations, explaining up to 10% of phenotypic variance. Contrary to long-standing archaeological hypotheses,[2][,][3] we find that Neolithic populations were only modestly shorter than preceding Mesolithic groups, with differences at least partly attributable to genetic rather than environmental factors, challenging narratives of systematic stature decline following the transition to agriculture. Finally, we find that the lactase persistence allele had a large positive effect on stature in ancient individuals (0.20 standard deviations), even though it shows no association with height in present-day populations.[4] This gene-environment interaction highlights the limitation of using present-day genetic data to infer past phenotypic relationships. Our results underscore the value of integrating genetic and morphological data from ancient populations to reconstruct the dynamics of human adaptation.},
}

@article {pmid41199726,
year = {2025},
author = {Grillo, JF and Tirpitz, V and Reichert, J and Canesi, M and Reynaud, S and Douville, E and Ziegler, M},
title = {Coral Skeletal Cores as Windows Into Past Symbiodiniaceae Community Dynamics.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70575},
pmid = {41199726},
issn = {1365-2486},
support = {469364832//Deutsche Forschungsgemeinschaft/ ; ANR-22-CE02-0025//Agence Nationale de la Recherche/ ; //German Academic Exchange Service/ ; },
mesh = {*Anthozoa/physiology ; Animals ; *Symbiosis ; *Dinoflagellida/physiology/genetics ; Coral Reefs ; Palau ; },
abstract = {The symbiosis between the dinoflagellate Symbiodiniaceae family and reef-building corals underpins the productivity of coral reefs. This relationship facilitates the deposition of calcium-carbonate skeletons that build the reef structure thanks to the energy derived from photosynthesis. The loss of Symbiodiniaceae from coral tissues-resulting in coral bleaching-impedes coral growth and can lead to mass mortality if the symbiosis fails to recover. Given that Symbiodiniaceae communities are dynamic and can shift in response to environmental stressors in the decades to centuries-long lifespan of coral colonies, understanding these changes is crucial. Although the reconstruction of Symbiodiniaceae communities from coral skeleton records has recently been demonstrated as feasible, no studies have yet assessed reconstructions across different species and locations. Here, we present an approach to use coral skeletons for reconstructing the Symbiodiniaceae community on decadal and centennial scales and for resolving dynamics related to coral species and the environmental history of sampling locations. For this, we used dated coral skeleton cores from Porites lobata and Diploastrea heliopora, species commonly used as climate archives, sampled in Palau and Papua New Guinea. We also examined the effect of various DNA extraction protocols on community reconstruction. Here we show that the reconstructed Symbiodiniaceae communities significantly varied across all cores and DNA extraction methods, with decalcification-based protocols enhancing the retrieval of skeletal-bound DNA. Moreover, we observed distinct community dynamics related to the specific coral host and sampling location. Notably, associations of Symbiodiniaceae dynamics with past heat stress events were apparent in cores of both species from Palau. Our findings enable a deeper understanding of the temporal and spatial variability in Symbiodiniaceae communities, offering insights that may refine the use of paleobiological proxies in climate studies and reveal broader ecological trends and microbially aided adaptation pathways in corals.},
}

*Anthozoa/physiology
Animals
*Symbiosis
*Dinoflagellida/physiology/genetics
Coral Reefs
Palau

@article {pmid41197624,
year = {2025},
author = {Souilmi, Y and Oliva, A and Davidson, R and Williams, MP and Ravishankar, S and Roca-Rada, X and Peréz, V and Tobler, R and Llamas, B},
title = {Lessons learned: Recommendations for reproducible paleogenomic data analyses.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2025.10.011},
pmid = {41197624},
issn = {1537-6605},
abstract = {Paleogenomics is an increasingly data-rich research discipline that has become hugely influential in our understanding of the population history of humans and many other species. Given its reliance on destructive sampling to extract ancient DNA (aDNA) from skeletal remains and other organic sources, minimum reporting standards are crucial to inform the review process, improve transparency and reproducibility, increase the usability of research findings, and maximize the value gained from finite and unique samples. Additionally, paleogenomics researchers routinely face choices that can meaningfully impact results and influence conclusions, including decisions regarding sample usage and parameter options for data processing and analyses. From our collective experience as a paleogenomics research group extensively interacting with other researchers in the field, we identified critical information for key analytical areas required for reproducible research. Our recommendations are compatible with findable, accessible, interoperable, and reusable (FAIR) and collective benefit, authority to control, responsibility, and ethics (CARE) frameworks for data management and include the use of standardized data formats, amendments to standard metadata formats, and the provision of a reporting checklist detailing sample preparation and analytical workflows. Developing detailed documentation and clear reporting of analytical workflows will ensure that transparent, robust, and reproducible conclusions are routinely achieved to warrant confidence in paleogenomics research outcomes.},
}

@article {pmid41197516,
year = {2025},
author = {Hajdu, T and Borbély, N and Bernert, Z and Buzár, Á and Szeniczey, T and Major, I and Cavazzuti, C and Molnár, M and Horváth, A and Palcsu, L and Árpád Kelentey, B and Angyal, J and Mende, BG and Jakab, K and Lisztes-Szabó, Z and Takács, Á and Cheronet, O and Pinhasi, R and Reich, DE and Trautmann, M and Szécsényi-Nagy, A},
title = {Murder in cold blood? Forensic and bioarchaeological identification of the skeletal remains of Béla, Duke of Macsó (c. 1245-1272).},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103381},
doi = {10.1016/j.fsigen.2025.103381},
pmid = {41197516},
issn = {1878-0326},
abstract = {In 1915, the remains of a male were discovered in a 13th-century monastery on Margaret Island, Budapest. Historical context suggested that the remains might have belong to Duke Béla of Macsó (c. 1245-1272), grandson of King Béla IV of Hungary (House of Árpád) and son of Duke Rostislav (Rurik dynasty). We applied a complex approach to identify the individual and reconstruct the circumstances of his death. Radiocarbon dating, when adjusted for freshwater reservoir effects linked to a high-protein diet, placed the burial in the mid-13th century. Skeletal features corresponded to a young adult male. Stable isotope and dental calculus analyses indicated a high-status diet rich in animal proteins and C3 cereals. Ancient DNA confirmed descent from King Béla III (Árpád dynasty) and Y-chromosomal affiliation with the Rurikid lineage. Forensic evidence revealed 26 perimortem injuries, suggesting a coordinated, premeditated assassination involving at least three assailants. The pattern of injuries indicated both planning and intense emotional involvement. Our findings provide the first genetic identification of a medieval royal, and resolve a century-old archaeological question, and illustrate the power of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past with unprecedented detail. TEASER: With unprecedented details, this study shows the impact of integrating multidisciplinary methods to confirm historical hypotheses and reconstruct violent deaths from the past.},
}

@article {pmid41197464,
year = {2025},
author = {Muthu, S},
title = {Commentary on "Zupanic Pajnic and Leskovar. Nondestructive automated DNA extraction method from the tooth root surface".},
journal = {Forensic science international},
volume = {378},
number = {},
pages = {112704},
doi = {10.1016/j.forsciint.2025.112704},
pmid = {41197464},
issn = {1872-6283},
}

@article {pmid41193808,
year = {2025},
author = {Maravall-López, J and Motti, JMB and Pastor, N and Tavella, MP and Fabra, M and Babot, P and Bonomo, M and Cornero, SE and Lamenza, GN and Leon, DC and Miranda de Zela, PC and Politis, GG and Angeletti, SC and Cattáneo, GR and Dantas, M and Drube, H and Gonzalez Baroni, LG and Hocsman, S and Izeta, AD and Moralejo, RA and Aldazabal, V and Basso, DM and Bayón, C and Couso, MG and D'Andrea, U and Del Río, P and Figueroa, GG and Frontini, R and Gonzalez, ME and Laguens, AG and Martínez, JG and Messineo, PG and Nores, B and Olivera, DE and Sario, GM and Sbattella, A and Scabuzzo, C and Tavarone, AM and Vecchi, R and Callan, K and Caughran, E and Estrada, O and Frost, T and Iliev, L and Kearns, A and Kellogg, J and Krettek, KL and Lawson, AM and Mah, M and Manjila, N and Micco, A and Patterson, I and Qiu, L and Roca-Rada, X and Soos, G and Webb, PA and Workman, JN and Rohland, N and Patterson, N and Lazaridis, I and Fehren-Schmitz, L and Posth, C and Llamas, B and Mallick, S and Demarchi, DA and Cabana, GS and Reich, D and Nores, R},
title = {Eight millennia of continuity of a previously unknown lineage in Argentina.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41193808},
issn = {1476-4687},
abstract = {The central Southern Cone of South America was one of the last regions of the globe to become inhabited by people[1], and remains under-represented in studies of ancient DNA. Here we report genome-wide data from 238 ancient individuals spanning ten millennia. The oldest, from the Pampas region and dating to 10,000 years before present (BP), had distinct genetic affinity to Middle Holocene Southern Cone individuals, showing that differentiation from the central Andes and central east Brazil had begun by this time. Individuals dating to 4,600-150 BP primarily descended from a previously unsampled deep lineage of which the earliest representative is an individual dating to around 8,500 BP. This central Argentina lineage co-existed with two other lineages during the Mid-Holocene and, within central Argentina, this ancestry persisted for thousands of years with little evidence of inter-regional migration. Central Argentina ancestry was involved in three distinct gene flows: it mixed into the Pampas by 3,300 BP and seemingly became the main component there after 800 BP, with central Andes ancestry in northwest Argentina, and with tropical and subtropical forest ancestry in the Gran Chaco. In northwest Argentina, there was an increased rate of close-kin unions by 1,000 BP, paralleling the pattern in the central Andes. In the Paraná River region, a 400 BP individual with a Guaraní archaeological association clusters with Brazilian groups, consistent with Guaraní presence by this time.},
}

@article {pmid41172588,
year = {2025},
author = {Gaens, N and Souche, E and Kivisild, T and Geypen, J and Seneca, S and Calafell, F and Larmuseau, MHD},
title = {The first population scale compendium of complete mitochondrial genomes from Flanders, Belgium.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103382},
doi = {10.1016/j.fsigen.2025.103382},
pmid = {41172588},
issn = {1878-0326},
abstract = {Mitochondrial DNA (mtDNA) plays a crucial role in forensics and population genetics, especially for analysing highly degraded samples. Yet, most mitogenomic reference datasets are still limited to control region (CR) sequences, that have limited discriminatory power. This is particularly true for Belgium, where despite the introduction of new legislation in 2024 to increase the use of mitochondrial DNA in familial searching, comprehensive mitogenomic reference data remain scarce. To fill this gap, we present a new forensic-grade dataset comprising complete mitochondrial genomes from 264 individuals with maternal ancestry from Flanders, the northern part of Belgium. Maternal lineages were verified through validated genealogical records extending prior to 1750. Our Flemish dataset reveals 252 unique haplotypes, a mean pairwise difference of 27.3, and a random match probability of 0.0042, demonstrating forensic resolution comparable to other high-quality European datasets. Haplogroups H, U, and T predominate in Flanders, aligning with broadly observed European patterns, while clustering analyses show close genetic affinities with neighbouring Western European populations. Furthermore, comparison with ancient genomes from the Middle Ages reveals notable continuity in maternal ancestry in Flanders throughout the historical era. Our data substantially expand the mitochondrial reference for Flanders, providing a high-quality resource based on autochthonous maternal lineages, suitable for forensic applications, genetic genealogical analyses, and microgeographic population studies.},
}

@article {pmid41160688,
year = {2025},
author = {Bandyopadhyay, E and Witonsky, D and de la Fuente Castro, C and Pasupuleti, N and Urban Aragon, JA and Lee, J and Shastry, V and Sander, N and Ahlawat, B and Dwivedi, A and Angmo, T and Sharma, A and Kaushik, A and Moots, HM and Moreno-Mayar, JV and Kumar, S and Bhatt, RC and Mengwal, KB and Chauhan, H and Ganjoo, RK and Mushrif-Tripathy, V and Ota, SB and Warinner, C and Aldenderfer, M and Di Rienzo, A and Jeong, C and Rawat, NS and Norbu, T and Singh, E and Nautiyal, V and Raghavan, M and Rai, N},
title = {Dynamic human admixture histories over the past ~1300 years at the northern Himalayan frontier.},
journal = {Science advances},
volume = {11},
number = {44},
pages = {eadu9625},
pmid = {41160688},
issn = {2375-2548},
mesh = {Humans ; *Genetics, Population ; Nepal ; Altitude ; *Asian People/genetics ; Archaeology ; Genome, Human ; History, Ancient ; },
abstract = {Archaeological and paleogenomic evidence from the Tibetan Plateau and high-altitude Central Himalayas suggest biocultural connections with each other and with lowland East, Central, and South Asia. However, genetic histories at the northern frontier of the Indian Himalayas, which is geographically more proximal to Central and lowland South Asia, remain underexplored. We analyzed genome-wide data from 7 ancient (~2300 to 100 years old) and 10 present-day individuals from the northern Indian Himalayas and one ~3370-year-old individual from the Central Himalayas in Nepal. Ancient and present-day individuals from the northern Himalayas predominantly have Tibetan-related genetic ancestry, likely the source of high-altitude adaptive variants in these individuals, with substantial Steppe-related genetic ancestry that is observed in all individuals dating between ~1300 years and present day. In addition, some present-day individuals have lowland South Asian admixture. Our analyses reveal a dynamic interplay between genetic admixture and continuity in the northern Himalayas.},
}

Humans
*Genetics, Population
Nepal
Altitude
*Asian People/genetics
Archaeology
Genome, Human
History, Ancient

@article {pmid41157877,
year = {2025},
author = {Guyon, L and Heyer, E and Chaix, R},
title = {Was descent in Neolithic and Bronze Age Europe patrilineal or bilateral?.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2057},
pages = {20250815},
doi = {10.1098/rspb.2025.0815},
pmid = {41157877},
issn = {1471-2954},
support = {//Fondation Fyssen/ ; //Ecole normale supérieure/ ; },
mesh = {Humans ; Male ; Female ; Europe ; *DNA, Ancient/analysis ; History, Ancient ; Chromosomes, Human, Y/genetics ; *Genetic Variation ; *Genetics, Population ; *White People/genetics ; },
abstract = {Many studies have attempted to gain insights into the kinship systems of past human populations using ancient DNA data. Several studies focusing on Neolithic and Bronze Age European sites reported a high male relatedness and a low Y chromosome diversity, and concluded that descent in these past societies was patrilineal and residence was patrilocal. Here, we used simulations to assess male and female relatedness as well as the uniparental genetic diversity expected under different types of descent and residence systems. We confirm that ancient DNA data from most of these sites are compatible with patrilocal residence; however, the claim that many Neolithic and Bronze Age European populations had patrilineal descent is not supported.},
}

Humans
Male
Female
Europe
*DNA, Ancient/analysis
History, Ancient
Chromosomes, Human, Y/genetics
*Genetic Variation
*Genetics, Population
*White People/genetics

@article {pmid41153833,
year = {2025},
author = {Ciammaruconi, A and Di Spirito, M and Pascolini, C and Molinari, F and Rozov, O and Cavalli, M and Campoli, G and Totaro, N and Recchia, E and Chimienti, S and Monte, A and Spagnolo, F and Lista, F and D'Amelio, R and Fillo, S},
title = {Plagued by the Past, Pressed by the Present: A One Health Perspective on Yersinia pestis.},
journal = {Biomedicines},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/biomedicines13102555},
pmid = {41153833},
issn = {2227-9059},
abstract = {Yersinia pestis, the causative agent of plague, is arguably the most devastating pathogen in human history. Paleogenomic studies indicate its presence as early as the Neolithic era. It evolved from Yersinia pseudotuberculosis, with divergence estimates ranging from 1500 to 20,000 years ago, most often placed around 5000 years ago. Its natural reservoirs are wild mammals, particularly rodents, with fleas serving as vectors, while humans are incidental hosts. Over time, Y. pestis has acquired multiple virulence factors that disrupt immune responses and can lead to rapid, often fatal disease. Because the bacterium is maintained in wildlife cycles and can spill over to domestic animals, eradication is difficult, if not impossible. Nevertheless, mitigation is achievable using a One Health approach integrating human health, animal health, and the health of the environment. Neither vaccines nor monoclonal antibodies are currently licensed in most Western countries, thus, antibiotics remain the mainstay of therapy. Timely administration, ideally within 24 h of symptom onset, is critical, particularly in pneumonic forms. Phage therapy is under investigation as a potential treatment. Though often neglected in high-income settings, plague remains endemic in several regions, with the highest burden reported in Madagascar and the Democratic Republic of the Congo.},
}

@article {pmid41153366,
year = {2025},
author = {Adamov, D and Shlykov, A and Potanina, A and Voronina, M and Gorin, I and Ponomarev, G and Kabaev, D and Chernyaeva, L and Gavrilov, A and Rusakov, D and Pocheshkhova, E and Zhur, K and Prokhortchouk, E and Goncharova, N and Balanovska, E},
title = {Pre-Slavic and Slavic Interaction at Eastern Periphery of Slavic Expansion in Northeastern Europe (Y-Gene Pools of Volga-Oka Region).},
journal = {Genes},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/genes16101149},
pmid = {41153366},
issn = {2073-4425},
support = {25-28-01594//Russian Science Foundation/ ; 124060400040-3//State Assignment from Russia's Ministry of Science and Higher Education/ ; },
mesh = {*Chromosomes, Human, Y/genetics ; Humans ; Phylogeny ; *Gene Pool ; Haplotypes/genetics ; Polymorphism, Single Nucleotide ; Genetics, Population ; DNA, Ancient/analysis ; Europe ; Male ; Microsatellite Repeats ; *White People/genetics ; Russia ; },
abstract = {Background/Objectives: The eastern periphery of the Slavic expansion (the Volga-Oka region) is the most promising region for reconstructing interactions between Slavic and pre-Slavic populations of the East European Plain. Unlike most pre-Slavic tribes, its autochthonous population practiced inhumation instead of cremation, leaving us with some ancient DNA for analysis. Methods: The region's modern and ancient Y-chromosome gene pools are dominated by the haplogroup R1a: its frequency reaches 56% in Ryazan Russians (n = 302) and 44% in the Finnic peoples of Mordovia (n = 633). This encouraged us to analyze its Y-SNPs and Y-STRs. Results: Using 2 independent methods of phylogeny analysis, we identified 10 informative Y-STR clusters within R1a, dating back 1600-2900 YBP. The clusters included 48% of modern Ryazan Russians, 40% of Mordovia's Finnic populations, and ancient DNA samples from the Ryazan-Oka culture (6-7th centuries), Suzdal (12-13th centuries) and Vladimir (13th century). Such a unique combination and pre-Slavic TMRCA indicate that the informative clusters represent pre-Slavic Y lineages. The presence of ancient samples from Vladimir and Suzdal in the clusters suggests that the autochthonous tribes contributed to shaping the urban population of the Vladimir-Suzdal Rus. Some of the informative clusters are associated with the ancient population of the Baltics (2000-4000 YBP). Conclusions: About half of Russian R1a carriers in the Volga-Oka region are descended from a pre-Slavic population, suggesting that the Slavs did not fully replace the autochthonous population but rather mostly culturally assimilated the Meshchyora documented in the Russian chronicles and other local tribes.},
}

*Chromosomes, Human, Y/genetics
Humans
Phylogeny
*Gene Pool
Haplotypes/genetics
Polymorphism, Single Nucleotide
Genetics, Population
DNA, Ancient/analysis
Europe
Male
Microsatellite Repeats
*White People/genetics
Russia

@article {pmid41151757,
year = {2025},
author = {Kessler, C and Haddrath, O and Lim, BK and Shafer, A},
title = {Ancient DNA of the Toronto Subway Deer adds to the extinction list of ice age megafauna.},
journal = {Biology letters},
volume = {21},
number = {10},
pages = {20250497},
doi = {10.1098/rsbl.2025.0497},
pmid = {41151757},
issn = {1744-957X},
support = {//Trent University/ ; //NSERC/ ; //French American Charitable Trust/ ; //Government of Ontario/ ; //Canadian Foundation for Innovation/ ; //ComputeCanada/ ; },
mesh = {Animals ; *Deer/genetics/classification ; *Extinction, Biological ; *DNA, Ancient/analysis ; Fossils ; DNA, Mitochondrial/genetics ; Phylogeny ; Ontario ; Canada ; Climate Change ; },
abstract = {The Late Pleistocene was a time of global megafaunal extinctions that were particularly severe in North America. The continent lost many mammal taxa, but the validity of several remains ambiguous, including a high proportion of Cervidae taxa. Torontoceros hypogaeus is represented by a single specimen (ROMM75974) discovered in 1976 during excavation work for the Toronto subway in Canada. The species was described based on its unique antler morphology, but the variable nature of that trait and the species near absence in the fossil record leads to uncertainty concerning its systematic relationships. We used ancient DNA to clarify the taxonomic relationship and evolutionary history of T. hypogaeus. We performed mitochondrial and whole genome analyses with related cervids and showed that ROMM75974 has a close affinity, but relatively high divergence from Odocoileus sister species. While some ambiguity remains, ROMM75974 could represent a distinct Odocoileus species to be included in the list of extinct North American taxa. This unique population was likely adapted to open landscape, which was rapidly replaced with dense woodland in this region at the end of the Pleistocene, highlighting the role of climate change in the extinction of megafauna biodiversity at the end of the ice age.},
}

Animals
*Deer/genetics/classification
*Extinction, Biological
*DNA, Ancient/analysis
Fossils
DNA, Mitochondrial/genetics
Phylogeny
Ontario
Canada
Climate Change

@article {pmid41151755,
year = {2025},
author = {Przelomska, NAS and Campana, MG and James, HF and Kistler, L and Rotzel McInerney, N and Pérez-Escobar, OA and Hagemann, M and Groombridge, JJ and Fleischer, RC},
title = {Population structure and inter-species admixture within a likely extinct yet formerly widespread Hawaiian honeycreeper.},
journal = {Biology letters},
volume = {21},
number = {10},
pages = {20250265},
doi = {10.1098/rsbl.2025.0265},
pmid = {41151755},
issn = {1744-957X},
support = {//Research England/ ; //Smithsonian Institution/ ; //National Science Foundation/ ; //Beeson Fund/ ; },
mesh = {Animals ; Hawaii ; *Passeriformes/genetics/anatomy & histology ; Extinction, Biological ; *Hybridization, Genetic ; Genetic Variation ; Phenotype ; },
abstract = {The Hawaiian honeycreepers simultaneously represent one of the most spectacular avian adaptive radiations and are one of the most endangered avian groups. This clade's few geographically widespread species can serve as a model to understand population-level processes shaping differentiation and characterizing decline. One such species is the likely extinct 'ō'ū (Psittirostra psittacea), a parrot-like beaked honeycreeper with a frugivorous feeding ecology. We compiled morphological and hybridization-captured ancient DNA datasets for the 'ō'ū from museum specimens from across the Hawaiian archipelago. We find (i) genomic differentiation among 'ō'ū from Kaua'i, Lāna'i, and the remaining Hawaiian Islands and (ii) a larger phenotype on Kaua'i and smaller Maui Nui morphological phenotypes. While the differentiated population on Kaua'i is likely a result of Kaua'i's geographical isolation, the divergent population on Lāna'i is harder to explain by biogeography alone. Thus, we investigated whether the unexpected divergence of Lāna'i 'ō'ū could be attributed to inter-species admixture with the geographically overlapping, now extinct 'parrot-billed' Lāna'i hookbill (Dysmorodrepanis munroi) or a critically endangered Maui endemic, the kiwikiu (Pseudonestor xanthophrys). We detect significant admixture between the Lāna'i 'ō'ū population and the Lāna'i hookbill, possibly explaining the observed population structure and associating interspecific breeding with populations on the precipice of extinction.},
}

Animals
Hawaii
*Passeriformes/genetics/anatomy & histology
Extinction, Biological
*Hybridization, Genetic
Genetic Variation
Phenotype

@article {pmid41146290,
year = {2025},
author = {Kraft, L and Söding, J and Steinegger, M and Jochheim, A and Wad Sackett, P and Fernandez-Guerra, A and Renaud, G},
title = {CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {372},
pmid = {41146290},
issn = {1474-760X},
support = {NNF20OC0062491//Novo Nordisk Fonden/ ; NNF20OC0062491//Novo Nordisk Fonden/ ; 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B//German Network for Bioinformatics Infrastructure (de.NBI)/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Software ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Humans ; },
abstract = {De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam demonstrates improved recovery of longer continuous sequences and protein sequences in many simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities.},
}

*Metagenome
*Metagenomics/methods
*Software
*DNA, Ancient/analysis
Sequence Analysis, DNA/methods
Humans

@article {pmid41145628,
year = {2025},
author = {Sato, T and Kubo, D and Hirasawa, Y and Yoneda, M and Kimura, R and Tajima, A and Kato, H},
title = {Genome of an early Okhotsk individual reveals ancient admixture between Jomon and Kamchatka lineages.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37520},
pmid = {41145628},
issn = {2045-2322},
support = {19H01356//Japan Society for the Promotion of Science/ ; 16H01954//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Japan ; *Genome, Human ; Genetics, Population ; *Asian People/genetics ; Human Migration ; DNA, Ancient/analysis ; History, Ancient ; Whole Genome Sequencing ; },
abstract = {The prehistoric Okhotsk culture was distributed along the southern coastal regions of the Sea of Okhotsk during the late first millennium AD. A previous study that performed whole-genome sequencing of a late Okhotsk individual suggested two migration waves from the Russian Far East to northern Japan. The first wave is estimated to have originated from the Kamchatka Peninsula around 2000 years before present (BP), and the second from the Amur Basin around 1600 BP. These findings suggest the past existence of an admixed hypothetical population between the Kamchatka and indigenous Jomon lineages in northern Japan between 2000 and 1600 BP, although direct genetic evidence has not yet been obtained. Here, we present the genome data of an early Okhotsk individual (NAT004) excavated from northern Japan. Admixture modelling reveals that the genome can be explained as a mixture of Kamchatka and Jomon ancestries, providing direct support for the existence of the previously hypothesized hypothetical population. This result offers new insights into the prehistoric population dynamics of northern Japan and contributes to the broader understanding of its archaeological and anthropological history.},
}

Humans
Japan
*Genome, Human
Genetics, Population
*Asian People/genetics
Human Migration
DNA, Ancient/analysis
History, Ancient
Whole Genome Sequencing

@article {pmid41144685,
year = {2025},
author = {Pigott, EM and Cheshmedzhieva, K and Zeller, E and van der Sluis, LG and Pal Chowdhury, M and Gianni, M and Végh, E and Uthmeier, T and Chabai, V and Patou-Mathis, M and Šimková, PG and Voglmayr, JN and Weber, GW and Pinhasi, R and Timmermann, A and Kuhlwilm, M and Douka, K and Higham, T},
title = {A new late Neanderthal from Crimea reveals long-distance connections across Eurasia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {45},
pages = {e2518974122},
doi = {10.1073/pnas.2518974122},
pmid = {41144685},
issn = {1091-6490},
mesh = {Animals ; *Neanderthals/genetics ; Humans ; *Fossils ; Bone and Bones/chemistry ; Radiometric Dating ; Europe ; Archaeology ; Genome, Mitochondrial ; Collagen ; DNA, Mitochondrial/genetics ; },
abstract = {The Crimean Peninsula contains several important Middle and Upper Paleolithic sites, including Starosele, Kabazi II, and Siuren I. The region has been considered a potential refugium for Neanderthals before their replacement by Homo sapiens. However, no genetic data have been obtained from any of these late Neanderthals, some being inaccessible or badly preserved. Starosele is a notable site which has undergone excavations in recent years. We used collagen peptide mass fingerprinting (Zooarchaeology by Mass Spectrometry, ZooMS), to screen for potential human remains among thousands of fragmented bones from the site. Of the 150 bone fragments we analyzed, 97.3% had sufficient collagen preservation for taxonomic identification. Our results suggest Paleolithic humans primarily hunted horses. One ~5 cm bone fragment yielded peptide mass fingerprints matching Hominidae. Radiocarbon dating revealed an age range of 46 to 45,000 y old, close to the transition from the disappearance of Neanderthals to the dispersal of H. sapiens in western Europe. We sequenced a twofold coverage mitochondrial genome from this bone, indicating the individual belongs to the Neanderthal lineage. The mitogenome clusters with other Neanderthal mitogenomes previously generated from the Russian Altai region. Alongside this, an analysis of the lithic corpus from both regions suggests that a wider Neanderthal dispersal, linked to the Micoquian stone tool industry, occurred after ~60,000 y ago. We assessed the paleoclimate connection (temperature and precipitation) between these locations and identified a high habitat suitability corridor along 55°N, suggesting that the long-distance movement of Neanderthals would have been facilitated by periods of favorable climate.},
}

Animals
*Neanderthals/genetics
Humans
*Fossils
Bone and Bones/chemistry
Radiometric Dating
Europe
Archaeology
Genome, Mitochondrial
Collagen
DNA, Mitochondrial/genetics

@article {pmid41144656,
year = {2025},
author = {Myburgh, DA and da Silva, NA and Haller-Caskie, M and Colominas, L and Castanyer, P and Frigola, J and Tremoleda, J and Hölzel, C and Unterweger, D and Nebel, A and Krause-Kyora, B},
title = {Detection of Clostridium sporogenes in a Roman-era cattle mass grave at Vilauba.},
journal = {Virulence},
volume = {},
number = {},
pages = {2580731},
doi = {10.1080/21505594.2025.2580731},
pmid = {41144656},
issn = {2150-5608},
abstract = {In the ancient Roman world, cattle played an integral role in daily agricultural tasks, providing the means necessary to plow fields, mill grains, and transport goods. The research presented here deals with the remains of 14 cattle discovered in a mass grave at the Roman villa of Vilauba in Catalonia, Spain. According to the archeological record, it can be ruled out that the animals were slaughtered for consumption, banqueting, or sacrificial purposes. By investigating the metagenomic sequences generated from the bovine remains, we identified in three individuals a group I Clostridium strain, phylogenetically related to known producers of botulinum neurotoxins - suggesting that the Vilauba strain may have had toxigenic potential. Moreover, we discovered a Mycolicibacterium species phylogenetically related to known opportunistic pathogens. While no definitive conclusions can be drawn about disease, the phylogenetic placement of these taxa and the detection of Clostridium virulence-associated genes suggest a possible role beyond postmortem contamination. Collectively, these findings draw attention to atypical bacterial species, such as C. sporogenes, which are often overlooked in palaeogenomic studies due to their ambiguous status as environmental microbes, commensals, or potential pathogens. Their detection in animal remains highlights that they may represent a blind spot in our current understanding of livestock health. More broadly, this study underscores the current complexity of investigating such taxa and emphasizes the need for novel methods to disentangle the roles of these bacterial species.},
}

@article {pmid41140832,
year = {2025},
author = {Ramadan, NS and El-Sayed, MM and Ramadan, HS and Ismail, M and Abdelmegeed, H and Gaber, N and Sakr, MM},
title = {Comprehensive review of understanding ancient dietary habits using modern analytical techniques.},
journal = {Food chemistry. Molecular sciences},
volume = {11},
number = {},
pages = {100304},
pmid = {41140832},
issn = {2666-5662},
abstract = {Understanding ancient dietary habits is essential for reconstructing ancient lifestyles. Archaeobotanical and archaeological remains, such as seeds, plant fibers, and pottery, serve as vital indicators of agriculture and daily life. We proposed that contemporary biomolecular and analytical methods provide unique insights into dietary habits through these artifacts. To assess this, we examined recent analytical platforms utilized in isotope analysis, multi-omics techniques viz. genomics, proteomics, lipidomics, and metabolomics applied to food residues, dental calculus, coprolites, and ceramics. Isotope research has shed light on climate changes and human movement; lipid and protein examinations uncovered methods of food preparation and preservation; and multi-omics strategies have enhanced the detail of dietary reconstructions, increasingly aided by artificial intelligence. Ongoing challenges persist, such as sample preservation, contamination, and potential methodological bias. Nevertheless, our review affirms that biomolecular archaeology significantly enhances our understanding of ancient diets and sharpens archaeological interpretations regarding health, subsistence, and interactions between humans and their environment.},
}

@article {pmid41138723,
year = {2025},
author = {Barbieri, R and Fumey, J and Kabral, H and Scheib, CL and Signoli, M and Costedoat, C and Rascovan, N},
title = {Paratyphoid fever and relapsing fever in 1812 Napoleon's devastated army.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.09.047},
pmid = {41138723},
issn = {1879-0445},
abstract = {During Napoleon's retreat from Russia in 1812,[1] countless soldiers of the French army succumbed to infectious diseases, but the responsible pathogen or pathogens remain debated.[2][,][3][,][4][,][5] We recovered and sequenced ancient DNA from the teeth of 13 soldiers who, based on historical records, likely died from infectious diseases, aiming to identify the pathogens responsible for their deaths.[6] Our results confirmed the presence of Salmonella enterica subsp. enterica belonging to the lineage Paratyphi C, the causative agent of paratyphoid fever[7]; and Borrelia recurrentis, responsible for relapsing fever transmitted by body lice.[8] We were not able to detect Rickettsia prowazekii (the agent of typhus) and Bartonella quintana (the cause of trench fever), which had previously been associated with this deadly event, based on PCR results and historical symptom descriptions.[3] The presence of these previously unsuspected pathogens in these soldiers reveal that they could have contributed to the devastation of Napoleon's Grande Armée during its disastrous retreat in 1812.},
}