@article {pmid37752842,
year = {2023},
author = {Ruiz-Puerta, EJ and Keighley, X and Desjardins, SPA and Gotfredsen, AB and Pan, SE and Star, B and Boessenkool, S and Barrett, JH and McCarthy, ML and Andersen, LW and Born, EW and Howse, LR and Szpak, P and Pálsson, S and Malmquist, HJ and Rufolo, S and Jordan, PD and Olsen, MT},
title = {Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2007},
pages = {20231349},
doi = {10.1098/rspb.2023.1349},
pmid = {37752842},
issn = {1471-2954},
abstract = {Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.},
}

@article {pmid37752477,
year = {2023},
author = {Kroes, R and Winkel, Y and Breeuwer, JAJ and van Loon, EE and Loader, SP and Maclaine, JS and Verdonschot, PFM and van der Geest, HG},
title = {Phylogenetic analysis of museum specimens of houting Coregonus oxyrinchus shows the need for a revision of its extinct status.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {57},
pmid = {37752477},
issn = {2730-7182},
abstract = {According to the IUCN Red List the anadromous houting Coregonus oxyrinchus is categorized as 'extinct'. However, this extinct status might be incorrect because taxonomic difference between C. oxyrinchus and the closely related C. lavaretus is based on a disputable morphological comparison. Also, phylogenetic studies on mtDNA only focused on recent obtained coregonids. We are the first to perform a mtDNA analysis on both historic and recent specimens, including the syntype specimen which was used for species description by Linnaeus originally. Two primer pairs for mitochondrial CytB and ND3 were used to extract sequences for phylogenetic analysis. Sequences from 14 out of 21 C. oxyrinchus museum specimens were successfully obtained and compared with sequences from recent obtained C. lavaretus. The sequences were combined with GenBank data from a previous phylogenetic study on houting to create a phylogenetic tree and two minimum spanning haplotype networks. Results show that C. oxyrinchus and C. lavaretus form a clade with limited genetic variation. Low bootstrap values also show weak support for geographical patterns in distribution of mitochondrial haplotypes. Statistical analysis of the haplotype networks also shows that historic and recent specimens are similar species. Our results suggest that C. oxyrinchus is a junior synonym of C. lavaretus. A definitive taxonomic revision could not be made because only CytB sequencing was successful for the syntype specimen. We discuss taxonomic consequences and the species-specific focus in nature conservation. We propose a shift in nature conservation to a more functional approach based on traits rather than species.},
}

@article {pmid37744037,
year = {2023},
author = {Singh, PP and Kumar, S and Pasupuleti, N and Weerasooriya, PR and van Driem, G and Tennekoon, KH and Rai, N and Chaubey, G and Ranasinghe, R},
title = {Reconstructing the population history of the Sinhalese, the major ethnic group in Śrī Laṅkā.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107797},
pmid = {37744037},
issn = {2589-0042},
abstract = {The Sinhalese are the major ethnic group in Śrī Laṅkā, inhabiting nearly the whole length and breadth of the island. They speak an Indo-European language of the Indo-Iranian branch, which is held to originate in northwestern India, going back to at least the fifth century BC. Previous genetic studies on low-resolution markers failed to infer the genomic history of the Sinhalese population. Therefore, we have performed a high-resolution fine-grained genetic study of the Sinhalese population and, in the broader context, we attempted to reconstruct the genetic history of Śrī Laṅkā. Our allele-frequency-based analysis showed a tight cluster of Sinhalese and Tamil populations, suggesting strong gene flow beyond the boundary of ethnicity and language. Interestingly, the haplotype-based analysis preserved a trace of the North Indian affiliation to the Sinhalese population. Overall, in the South Asian context, Śrī Laṅkān ethnic groups are genetically more homogeneous than others.},
}

@article {pmid37738339,
year = {2023},
author = {Oliveira, S and Fehn, AM and Amorim, B and Stoneking, M and Rocha, J},
title = {Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.},
journal = {Science advances},
volume = {9},
number = {38},
pages = {eadh3822},
doi = {10.1126/sciadv.adh3822},
pmid = {37738339},
issn = {2375-2548},
abstract = {Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.},
}

@article {pmid37719142,
year = {2023},
author = {Wang, K and Prüfer, K and Krause-Kyora, B and Childebayeva, A and Schuenemann, VJ and Coia, V and Maixner, F and Zink, A and Schiffels, S and Krause, J},
title = {High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry.},
journal = {Cell genomics},
volume = {3},
number = {9},
pages = {100377},
doi = {10.1016/j.xgen.2023.100377},
pmid = {37719142},
issn = {2666-979X},
abstract = {The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.},
}

@article {pmid37718006,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Austin, JJ},
title = {From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates.},
journal = {Science & justice : journal of the Forensic Science Society},
volume = {63},
number = {5},
pages = {588-597},
doi = {10.1016/j.scijus.2023.07.003},
pmid = {37718006},
issn = {1876-4452},
abstract = {Titanium dioxide (titania, TiO2) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO2 causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO2-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated. DNA in saliva and touch samples deposited on self-cleaning glass slides exposed to indoor fluorescent light for up to seven days was more degraded than control samples indicating some degree of fluorescent light-induced photocatalytic activity of the self-cleaning surfaces. When exposed to sunlight, DNA yields from saliva and touch samples deposited on the titania-coated substrates decreased rapidly, with a corresponding increase in DNA degradation. After three days no DNA samples applied to self-cleaning glass and exposed to natural sunlight yielded STR profiles. These results suggest that the photocatalytic activation of TiO2 is the likely mechanism of action underlying the extreme DNA degradation on the Bioclean® and SaniTise™ glasses. Consequently, rapid sample collection and use may be warranted in casework scenarios involving TiO2-coated materials.},
}

@article {pmid37717498,
year = {2023},
author = {Díaz-Navarro, S and Haber Uriarte, M and García-González, R},
title = {Holes in the Head. Double cranial surgery on an individual from the Chalcolithic burial site of Camino del Molino (SE Spain).},
journal = {International journal of paleopathology},
volume = {43},
number = {},
pages = {22-30},
doi = {10.1016/j.ijpp.2023.09.003},
pmid = {37717498},
issn = {1879-9825},
abstract = {OBJECTIVE: This article analyses new prehistoric evidence of trepanation from a collective burial site in the south-eastern Iberian Peninsula.

MATERIALS: The trepanned individual was documented in the Chalcolithic burial site of Camino del Molino, where 1348 individuals (30.7 % non-adults and 69.3 % adults) were deposited in two contiguous funerary phases, making it a reference site for the knowledge of Recent Prehistoric populations.

METHODS: The individual has been sexed using traditional anthropological methods and ancient DNA. C14 dating has also been obtained. The lesion has been analysed macroscopically and microscopically using SEM.

RESULTS: The skull under study belonged to an adult female deposited in the second burial phase (2566-2239 years cal BCE). It exhibits in the anterior region of the right temporal fossa two contiguous and partially overlapping holes that correspond to two trepanations performed using the scraping technique.

CONCLUSIONS: It is a double cranial trepanation with signs of bone remodelling suggesting survival from surgery. No pathological signs were identified potentially associated with the intervention.

SIGNIFICANCE: This is the second case of surgical interventions in the geographical area of study and one of the few evidences of this practice in women during prehistoric times.

LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed.

Further intensive review of skull collection is advised to learn more about these surgical interventions in Copper Age and to go deeper into the causes that motivated their execution.},
}

@article {pmid37712846,
year = {2023},
author = {Davidson, R and Williams, MP and Roca-Rada, X and Kassadjikova, K and Tobler, R and Fehren-Schmitz, L and Llamas, B},
title = {Allelic bias when performing in-solution enrichment of ancient human DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13869},
pmid = {37712846},
issn = {1755-0998},
support = {DE190101069//Australian Research Council/ ; FT170100448//Australian Research Council/ ; 1515138//National Science Foundation/ ; },
abstract = {In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.},
}

@article {pmid37230884,
year = {2023},
author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , },
title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.},
journal = {Trends in ecology & evolution},
volume = {38},
number = {10},
pages = {946-960},
doi = {10.1016/j.tree.2023.04.016},
pmid = {37230884},
issn = {1872-8383},
mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; },
abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.},
}

*Biodiversity
*DNA, Ancient
Computational Biology
DNA Barcoding, Taxonomic

@article {pmid37561011,
year = {2023},
author = {Sánchez-Barreiro, F and De Cahsan, B and Westbury, MV and Sun, X and Margaryan, A and Fontsere, C and Bruford, MW and Russo, IM and Kalthoff, DC and Sicheritz-Pontén, T and Petersen, B and Dalén, L and Zhang, G and Marquès-Bonet, T and Gilbert, MTP and Moodley, Y},
title = {Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.},
journal = {Molecular biology and evolution},
volume = {40},
number = {9},
pages = {},
doi = {10.1093/molbev/msad180},
pmid = {37561011},
issn = {1537-1719},
support = {681396//ERC Consolidator/ ; 7578//EMBO Short-Term Fellowship/ ; //National Research Foundation/ ; },
abstract = {The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.},
}

@article {pmid37704050,
year = {2023},
author = {Bruno, F and Abondio, P and Bruno, R and Ceraudo, L and Pararazzo, E and Citrigno, L and Luiselli, D and Bruni, AC and Passarino, G and Colao, R and Maletta, R and Montesanto, A},
title = {Alzheimer's Disease as A Viral Infectious Disease: Revisiting the Infectious Hypothesis.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102068},
doi = {10.1016/j.arr.2023.102068},
pmid = {37704050},
issn = {1872-9649},
abstract = {Alzheimer's disease (AD) represents the most frequent type of dementia in elderly people. Two major forms of the disease exist: sporadic - the causes of which have not yet been fully understood - and familial - inherited within families from generation to generation, with a clear autosomal dominant transmission of mutations in Presenilin 1 (PSEN1), 2 (PSEN2) or Amyloid Precursors Protein (APP) genes. The main hallmark of AD consists of extracellular deposits of amyloid-beta (Aβ) peptide and intracellular deposits of the hyperphosphorylated form of the tau protein (p-tau). An ever-growing body of research supports the viral infectious hypothesis of sporadic forms of AD. In particular, it has been shown that several herpes viruses (i.e., HHV-1, HHV-2, HHV-3 or varicella zoster virus, HHV-4 or Epstein Barr virus, HHV-5 or cytomegalovirus, HHV-6A and B, HHV-7), flaviviruses (i.e., Zika virus, Dengue fever virus, Japanese encephalitis virus) as well as Human Immunodeficiency Virus (HIV), the hepatitis viruses (HAV, HBV, HCV, HDV, HEV), SARS-CoV2, Ljungan virus (LV), Influenza A virus and Borna disease virus, could increase the risk of AD. Here, we summarized and discussed these results. Based on these findings, significant issues for future studies are also put forward.},
}

@article {pmid37701515,
year = {2022},
author = {Jaramillo-Valverde, L and Vásquez-Domínguez, A and Levano, KS and Castrejon-Cabanillas, R and Novoa-Bellota, P and Machacuay-Romero, M and Garcia-de-la-Guarda, R and Cano, RJ and Shady Solis, R and Guio, H},
title = {A mobile lab for ancient DNA extraction in Perug.},
journal = {Bioinformation},
volume = {18},
number = {12},
pages = {1114-1118},
doi = {10.6026/973206300181114},
pmid = {37701515},
issn = {0973-2063},
abstract = {We report the use of a mobile laboratory set up to extract ancient DNA (aDNA) from 34 human coprolites (fossilized faeces) samples. Our approach enabled the rapid genetic characterization of 5,000 years old archeological samples. It is useful for the on-site screening of museums and freshly excavated samples for DNA. This approach is accessible to other investigators as the mobile laboratory was set up using commercially available instruments.},
}

@article {pmid37699853,
year = {2023},
author = {Chocholova, E and Roudnicky, P and Potesil, D and Fialova, D and Krystofova, K and Drozdova, E and Zdrahal, Z},
title = {Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.3c00370},
pmid = {37699853},
issn = {1535-3907},
abstract = {Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.},
}

@article {pmid37683613,
year = {2023},
author = {Sandoval-Velasco, M and Jagadeesan, A and Ramos-Madrigal, J and Ávila-Arcos, MC and Fortes-Lima, CA and Watson, J and Johannesdóttir, E and Cruz-Dávalos, DI and Gopalakrishnan, S and Moreno-Mayar, JV and Niemann, J and Renaud, G and Robson Brown, KA and Bennett, H and Pearson, A and Helgason, A and Gilbert, MTP and Schroeder, H},
title = {The ancestry and geographical origins of St Helena's liberated Africans.},
journal = {American journal of human genetics},
volume = {110},
number = {9},
pages = {1590-1599},
doi = {10.1016/j.ajhg.2023.08.001},
pmid = {37683613},
issn = {1537-6605},
abstract = {The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.},
}

@article {pmid37592021,
year = {2023},
author = {Moots, HM and Antonio, M and Sawyer, S and Spence, JP and Oberreiter, V and Weiß, CL and Lucci, M and Cherifi, YMS and La Pastina, F and Genchi, F and Praxmeier, E and Zagorc, B and Cheronet, O and Özdoğan, KT and Demetz, L and Amrani, S and Candilio, F and De Angelis, D and Gasperetti, G and Fernandes, D and Gao, Z and Fantar, M and Coppa, A and Pritchard, JK and Pinhasi, R},
title = {A genetic history of continuity and mobility in the Iron Age central Mediterranean.},
journal = {Nature ecology & evolution},
volume = {7},
number = {9},
pages = {1515-1524},
pmid = {37592021},
issn = {2397-334X},
mesh = {Mediterranean Region ; Archaeology ; *Human Migration/history ; Humans ; Principal Component Analysis ; Human Genetics ; *DNA, Ancient/analysis ; Sequence Analysis, DNA ; Burial ; Anthropology ; History, Ancient ; },
abstract = {The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. Here, to investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbours together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.},
}

Mediterranean Region
Archaeology
*Human Migration/history
Humans
Principal Component Analysis
Human Genetics
*DNA, Ancient/analysis
Sequence Analysis, DNA
Burial
Anthropology
History, Ancient

@article {pmid37673908,
year = {2023},
author = {Hodgins, HP and Chen, P and Lobb, B and Wei, X and Tremblay, BJM and Mansfield, MJ and Lee, VCY and Lee, PG and Coffin, J and Duggan, AT and Dolphin, AE and Renaud, G and Dong, M and Doxey, AC},
title = {Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {5475},
pmid = {37673908},
issn = {2041-1723},
support = {RGPIN-2019-04266//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
abstract = {The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.},
}

@article {pmid37666338,
year = {2023},
author = {Han, W and Zhang, E and Sun, W and Lin, Q and Meng, X and Ni, Z and Ning, D and Shen, J},
title = {Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {166715},
doi = {10.1016/j.scitotenv.2023.166715},
pmid = {37666338},
issn = {1879-1026},
abstract = {Lakes on the Qinghai-Tibet Plateau (QTP) have been subject to multiple environmental pressures from rapid climate change and intensified human activity in recent decades. However, their ecological effects on the lake ecosystem remain largely unclear due to the lack of long-term monitoring data. This study presented the environmental and ecological changes of the lake Yamzhog Yumco (Southern QTP) over the past three decades based on multi-proxy analysis (geochemistry and sedaDNA) on a high-time resolution sediment core. The result showed that the lake exhibited a continuous eutrophication process from 2004 CE, which has accelerated since 2014 CE. The nutrient enrichment was mainly attributed to anthropogenic emissions from the catchment. The sedimentary ancient DNA (sedaDNA) metabarcoding data registered a sensitive response of aquatic communities to the additional nutrient supply. Eukaryotic algae and aquatic invertebrate communities exhibited similar temporal dynamics, characterized by the increase in eutrophic taxa and the decrease in oligotrophic taxa. Change points analysis suggested that lake ecosystems underwent a slight ecological shift in 2003 CE and an abrupt shift in 2012 CE driven by nutrient enrichment. Quantitative analysis revealed that nutrients and human activity accounted for 27.9 % and 21.7 % of the temporal variation in aquatic communities, whereas climate change only explained 6.9 % of the total variation. From a paleolimnological view, our study supported that regional human activity could distinctly alter the nutrient level and aquatic community structure of lake ecosystems in the QTP. Considering that anthropogenic disturbance will continuously increase, it is crucial to strengthen the field monitoring of the lakes on the plateau and make effective management measures to avoid irreversible ecological consequences.},
}

@article {pmid37652999,
year = {2023},
author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ},
title = {Ancient DNA reveals genetic admixture in China during tiger evolution.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {37652999},
issn = {2397-334X},
support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; },
abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.},
}

@article {pmid37652634,
year = {2023},
author = {Beltrame, MO and Moviglia, GS and De Tommaso, D and Quintana, S},
title = {Gastrointestinal parasites of domestic sheep from Patagonia throughout historical times: A paleoparasitological approach.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {44},
number = {},
pages = {100915},
doi = {10.1016/j.vprsr.2023.100915},
pmid = {37652634},
issn = {2405-9390},
abstract = {Sheep husbandry in Patagonia, Argentina, started at the beginning of the 20th century from European settlers. Sanitary management is minimal, which has serious implications for the sheep health. Sheep can be infested by diverse parasites, with well over 150 species of internal and external parasites reported worldwide. Gastrointestinal parasitism is one of the most common and important infections in sheep concerning the health status, and is the cause of significant morbidity and mortality, which generates considerable production losses. The present work is the first paleoparasitological study of sheep coprolites from Patagonia throughout historical times. Fifty-seven coprolites from the 'Cueva Peligro' archaeological site (Patagonia, Argentina) were analyzed using the Lutz spontaneous sedimentation technique and the modified Faust flotation technique. Ancient DNA (aDNA) study was carried out in order to identify the zoological origin of coprolites. The results obtained from Cytb analysis confirmed the identity of the host as Ovis aries (domestic sheep). A total of 39 coprolites examined were positive for parasites by at least one of the studied methods. Thirty eight samples were positive by spontaneous sedimentation and 10 samples were positive by the modified Faust technique. The parasitic fauna found was Trichuris sp. (Trichinellida: Trichuridae), Nematodirus sp., Nematodirus spathiger (Strongylida, Trichostrongyloidea), two unidentified Strongylida-type egg morphotypes, Fasciola hepatica (Trematoda: Digenea) and coccidia oocysts of Eimeria spp. (Apicomplexa: Eimeriidae). The modified Faust technique provided satisfactory results in terms of sensitivity for the detection of Eimeria spp. The use of this methodology as a routine procedure enables the processing of ancient samples, in order to increase recoveries. These results show the importance of integrating different diagnostic approaches in order to optimize parasitic findings. The recorded parasite diversity appears to have not changed over the last 120 years. The study displayed the presence of different parasitic species which suggests potential exposure to parasitic diseases through the historical times, both for sheep and for other domestic and wild mammals from Patagonia. Also, suggests the presence of fasciolosis, a zoonotic disease that implies a potential risk for Patagonian populations in the past.},
}

@article {pmid37644833,
year = {2023},
author = {Aoki, K and Takahata, N and Oota, H and Wakano, JY and Feldman, MW},
title = {Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2005},
pages = {20231262},
doi = {10.1098/rspb.2023.1262},
pmid = {37644833},
issn = {1471-2954},
abstract = {An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.},
}

@article {pmid37638716,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Simon, C and Henry, JM and Austin, JJ},
title = {Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis.},
journal = {Electrophoresis},
volume = {},
number = {},
pages = {},
doi = {10.1002/elps.202300070},
pmid = {37638716},
issn = {1522-2683},
abstract = {Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.},
}

@article {pmid37631973,
year = {2023},
author = {Burk, RD and Mirabello, L and DeSalle, R},
title = {Distinguishing Genetic Drift from Selection in Papillomavirus Evolution.},
journal = {Viruses},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/v15081631},
pmid = {37631973},
issn = {1999-4915},
support = {CA238592/NH/NIH HHS/United States ; P30CA013330/NH/NIH HHS/United States ; },
abstract = {Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.},
}

@article {pmid37628575,
year = {2023},
author = {Kusliy, MA and Yurlova, AA and Neumestova, AI and Vorobieva, NV and Gutorova, NV and Molodtseva, AS and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Semibratov, VP and Iderkhangai, TO and Kovalev, AA and Erdenebaatar, D and Graphodatsky, AS and Tishkin, AA},
title = {Genetic History of the Altai Breed Horses: From Ancient Times to Modernity.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/genes14081523},
pmid = {37628575},
issn = {2073-4425},
support = {22-18-00470//Russian Science Foundation/ ; },
abstract = {This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.},
}

@article {pmid37611212,
year = {2023},
author = {van Waaij, J and Li, S and Garcia-Erill, G and Albrechtsen, A and Wiuf, C},
title = {Evaluation of population structure inferred by principal component analysis or the admixture model.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyad157},
pmid = {37611212},
issn = {1943-2631},
abstract = {Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome wide human data we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.},
}

@article {pmid37608001,
year = {2023},
author = {Arbøll, TP and Rasmussen, SL and de Jonge, N and Hansen, AH and Pertoldi, C and Nielsen, JL},
title = {Revealing the secrets of a 2900-year-old clay brick, discovering a time capsule of ancient DNA.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13092},
pmid = {37608001},
issn = {2045-2322},
support = {CF19_0669//Carlsbergfondet/ ; 2020-3//Aalborg Zoos Naturbevaringsfond/ ; },
abstract = {The recent development of techniques to sequence ancient DNA has provided valuable insights into the civilisations that came before us. However, the full potential of these methods has yet to be realised. We extracted ancient DNA from a recently exposed fracture surface of a clay brick deriving from the palace of king Ashurnasirpal II (883-859 BCE) in Nimrud, Iraq. We detected 34 unique taxonomic groups of plants. With this research we have made the pioneering discovery that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2900-year-old clay brick. We encourage future research into this subject, as the scientific prospects for this approach are substantial, potentially leading to a deeper understanding of ancient and lost civilisations.},
}

@article {pmid37604894,
year = {2023},
author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L},
title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13635},
pmid = {37604894},
issn = {2045-2322},
support = {RFO//University of Bologna/ ; RFO//University of Bologna/ ; RFO//University of Bologna/ ; COST Action RGB-Net//European Union/ ; },
abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.},
}

@article {pmid37589132,
year = {2023},
author = {Essel, E},
title = {Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel.},
journal = {BioTechniques},
volume = {75},
number = {2},
pages = {42-46},
doi = {10.2144/btn-2023-0067},
pmid = {37589132},
issn = {1940-9818},
abstract = {Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow.},
}

@article {pmid37588356,
year = {2020},
author = {Cui, Y and Zhang, F and Ma, P and Fan, L and Ning, C and Zhang, Q and Zhang, W and Wang, L and Robbeets, M},
title = {Bioarchaeological perspective on the expansion of Transeurasian languages in Neolithic Amur River basin.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e15},
pmid = {37588356},
issn = {2513-843X},
abstract = {Owing to the development of sequencing technology, paleogenomics has become an important source of information on human migration and admixture, complementing findings from archaeology and linguistics. In this study, we retrieved the whole genome and Y chromosome lineage from late Neolithic Honghe individuals in the Middle Amur region in order to provide a bioarchaeological perspective on the origin and expansion of Transeurasian languages in the Amur River basin. Our genetic analysis reveals that the population of the Amur River basin has a stable and continuous genetic structure from the Mesolithic Age up to date. Integrating linguistic and archaeological evidence, we support the hypothesis that the expansion of the Transeurasian language system in the Amur River basin is related to the agricultural development and expansion of the southern Hongshan culture. The spread of agricultural technology resulted in the addition of millet cultivation to the original subsistence mode of fishing and hunting. It played a vital role in the expansion of the population of the region, which in its turn has contributed to the spread of language.},
}

@article {pmid37588383,
year = {2020},
author = {Wang, CC and Robbeets, M},
title = {The homeland of Proto-Tungusic inferred from contemporary words and ancient genomes.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e8},
pmid = {37588383},
issn = {2513-843X},
abstract = {The Tungusic languages form a language family spoken in Xinjiang, Siberia, Manchuria and the Russian Far East. There is a general consensus that these languages are genealogically related and descend from a common ancestral language, conventionally called 'Proto-Tungusic'. However, the exact geographical location where the ancestral speakers of Proto-Tungusic originated from is subject to debate. Here we take an unprecedented approach to this problem, by integrating linguistic, archaeological and genetic evidence in a single study. Our analysis of ancient DNA suggests genetic continuity between an ancient Amur genetic lineage and the contemporary speakers of the Tungusic languages. Adding an archaeolinguistic perspective, we infer that the most plausible homeland for the speakers of Proto-Tungusic is the region around Lake Khanka in the Russian Far East. Our study pushes the field forward in answering the tantalizing question about the location of the Tungusic homeland and in illustrating how these three disciplines can converge into a holistic approach to the human past.},
}

@article {pmid37588379,
year = {2020},
author = {Hudson, MJ and Nakagome, S and Whitman, JB},
title = {The evolving Japanese: the dual structure hypothesis at 30.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e6},
pmid = {37588379},
issn = {2513-843X},
abstract = {The population history of Japan has been one of the most intensively studied anthropological questions anywhere in the world, with a huge literature dating back to the nineteenth century and before. A growing consensus over the 1980s that the modern Japanese comprise an admixture of a Neolithic population with Bronze Age migrants from the Korean peninsula was crystallised in Kazurō Hanihara's influential 'dual structure hypothesis' published in 1991. Here, we use recent research in biological anthropology, historical linguistics and archaeology to evaluate this hypothesis after three decades. Although the major assumptions of Hanihara's model have been supported by recent work, we discuss areas where new findings have led to a re-evaluation of aspects of the hypothesis and emphasise the need for further research in key areas including ancient DNA and archaeology.},
}

@article {pmid37580949,
year = {2023},
author = {Bretschneider, A and Mazanec, J and Wittmeier, P and Flux, AL and Schmidt, D and Hummel, S},
title = {X-chromosomal STRs in aDNA kinship analysis.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {},
number = {},
pages = {},
doi = {10.1127/anthranz/2023/1714},
pmid = {37580949},
issn = {0003-5548},
abstract = {The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.},
}

@article {pmid37567955,
year = {2023},
author = {Kim, J and Rosenberg, NA},
title = {Record-matching of STR profiles with fragmentary genomic SNP data.},
journal = {European journal of human genetics : EJHG},
volume = {},
number = {},
pages = {},
pmid = {37567955},
issn = {1476-5438},
support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; },
abstract = {In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.},
}

@article {pmid37562011,
year = {2023},
author = {Gerber, D and Szeifert, B and Székely, O and Egyed, B and Gyuris, B and Giblin, JI and Horváth, A and Köhler, K and Kulcsár, G and Kustár, Á and Major, I and Molnár, M and Palcsu, L and Szeverényi, V and Fábián, S and Mende, BG and Bondár, M and Ari, E and Kiss, V and Szécsényi-Nagy, A},
title = {AInterdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad182},
pmid = {37562011},
issn = {1537-1719},
abstract = {In this study we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures (3530-1620 cal BCE). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture related population and one from a previously unrecognised source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe, but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analysing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.},
}

@article {pmid37559969,
year = {2023},
author = {Ozga, AT and Ottoni, C},
title = {Dental calculus as a proxy for animal microbiomes.},
journal = {Quaternary international : the journal of the International Union for Quaternary Research},
volume = {653-654},
number = {},
pages = {47-52},
pmid = {37559969},
issn = {1040-6182},
abstract = {The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.},
}

@article {pmid37559898,
year = {2023},
author = {Ciucani, MM and Ramos-Madrigal, J and Hernández-Alonso, G and Carmagnini, A and Aninta, SG and Sun, X and Scharff-Olsen, CH and Lanigan, LT and Fracasso, I and Clausen, CG and Aspi, J and Kojola, I and Baltrūnaitė, L and Balčiauskas, L and Moore, J and Åkesson, M and Saarma, U and Hindrikson, M and Hulva, P and Bolfíková, BČ and Nowak, C and Godinho, R and Smith, S and Paule, L and Nowak, S and Mysłajek, RW and Lo Brutto, S and Ciucci, P and Boitani, L and Vernesi, C and Stenøien, HK and Smith, O and Frantz, L and Rossi, L and Angelici, FM and Cilli, E and Sinding, MS and Gilbert, MTP and Gopalakrishnan, S},
title = {The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs.},
journal = {iScience},
volume = {26},
number = {8},
pages = {107307},
pmid = {37559898},
issn = {2589-0042},
abstract = {The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.},
}

@article {pmid37548135,
year = {2023},
author = {Arencibia, V and Muñoz, M and Crespo, CM and Russo, MG and Vera, P and Lia, VV and García Guraieb, S and Goñi, RA and Avena, S and Puebla, A and Dejean, CB},
title = {Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24822},
pmid = {37548135},
issn = {2692-7691},
support = {PICT 2014-3012//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Fundación Científica Felipe Fiorellino/ ; //Fundación de Historia Natural Félix Azara/ ; UBACyT 20020150200233BA//Universidad de Buenos Aires/ ; UBACyT 20020170200363BA//Universidad de Buenos Aires/ ; //CONICET/ ; },
abstract = {OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia.

MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network.

RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (≥1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established.

DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.},
}

@article {pmid37541241,
year = {2023},
author = {Harney, É and Sirak, K and Sedig, J and Micheletti, S and Curry, R and Ancona Esselmann, S and Reich, D},
title = {Ethical considerations when co-analyzing ancient DNA and data from private genetic databases.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2023.06.011},
pmid = {37541241},
issn = {1537-6605},
abstract = {Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.},
}

@article {pmid37537290,
year = {2023},
author = {Callaway, E},
title = {Ancient DNA reveals the living descendants of enslaved people through 23andMe.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37537290},
issn = {1476-4687},
}

@article {pmid37535713,
year = {2023},
author = {Jackson, FLC},
title = {Community-initiated genomics.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6657},
pages = {482-483},
doi = {10.1126/science.adj2380},
pmid = {37535713},
issn = {1095-9203},
mesh = {Humans ; *Black or African American/genetics ; *Metagenomics ; DNA, Ancient ; },
abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.},
}

Humans
*Black or African American/genetics
*Metagenomics
DNA, Ancient

@article {pmid37529780,
year = {2023},
author = {Zhao, C and Han, B and Yi, G and Jin, S and Zhang, Z and Li, S},
title = {Editorial: Epigenomics implication for economic traits in domestic animals.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1252640},
doi = {10.3389/fgene.2023.1252640},
pmid = {37529780},
issn = {1664-8021},
}

@article {pmid37528780,
year = {2023},
author = {Fesenko, DO and Aramova, OY and Vdovchenkov, EV and Ivanovsky, ID and Fesenko, OE and Polyakov, SA and Faleeva, TG and Filippova, MA and Florinskaya, VS and Kornienko, IV},
title = {[DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia].},
journal = {Molekuliarnaia biologiia},
volume = {57},
number = {4},
pages = {597-608},
pmid = {37528780},
issn = {0026-8984},
abstract = {Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate.},
}

@article {pmid37528222,
year = {2023},
author = {Delsol, N and Stucky, BJ and Oswald, JA and Cobb, CR and Emery, KF and Guralnick, R},
title = {Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12444},
pmid = {37528222},
issn = {2045-2322},
mesh = {Humans ; Animals ; Cattle/genetics ; *DNA, Ancient ; Phylogeny ; Americas ; Europe ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Haplotypes ; },
abstract = {Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.},
}

Humans
Animals
Cattle/genetics
*DNA, Ancient
Phylogeny
Americas
Europe
Caribbean Region
*DNA, Mitochondrial/genetics
Haplotypes

@article {pmid37525572,
year = {2023},
author = {Tamburrini, C and Dahinten, SL and Saihueque, RRR and Ávila-Arcos, MC and Parolin, ML},
title = {Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24821},
pmid = {37525572},
issn = {2692-7691},
abstract = {Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.},
}

@article {pmid37523413,
year = {2023},
author = {Long, GS and Hider, J and Duggan, AT and Klunk, J and Eaton, K and Karpinski, E and Giuffra, V and Ventura, L and Prowse, TL and Fornaciari, A and Fornaciari, G and Holmes, EC and Golding, GB and Poinar, HN},
title = {A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade.},
journal = {PLoS pathogens},
volume = {19},
number = {7},
pages = {e1011538},
doi = {10.1371/journal.ppat.1011538},
pmid = {37523413},
issn = {1553-7374},
abstract = {Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.},
}

@article {pmid37510218,
year = {2023},
author = {Zhang, N and Shao, X and Guo, Y and Zhang, X and Zhou, Y and Yuan, J and Tang, Z and Hu, S and Minyaev, SS and Cai, D},
title = {Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China.},
journal = {Genes},
volume = {14},
number = {7},
pages = {},
pmid = {37510218},
issn = {2073-4425},
mesh = {Animals ; Cattle/genetics ; *Genome, Mitochondrial ; Phylogeny ; Genetic Variation ; DNA, Ancient ; DNA, Mitochondrial/genetics ; China ; },
abstract = {Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle.},
}

Animals
Cattle/genetics
*Genome, Mitochondrial
Phylogeny
Genetic Variation
DNA, Ancient
DNA, Mitochondrial/genetics
China

@article {pmid37503227,
year = {2023},
author = {Simon, A and Coop, G},
title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37503227},
support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; },
abstract = {Genomic time-series from experimental evolution studies and ancient DNA datasets offer us a chance to more directly observe the interplay of various evolutionary forces. Here we show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide allele frequency change is due to gene flow. In both cases, after correcting for known major gene flow events in those populations, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.},
}

@article {pmid37499002,
year = {2023},
author = {Heggarty, P and Anderson, C and Scarborough, M and King, B and Bouckaert, R and Jocz, L and Kümmel, MJ and Jügel, T and Irslinger, B and Pooth, R and Liljegren, H and Strand, RF and Haig, G and Macák, M and Kim, RI and Anonby, E and Pronk, T and Belyaev, O and Dewey-Findell, TK and Boutilier, M and Freiberg, C and Tegethoff, R and Serangeli, M and Liosis, N and Stroński, K and Schulte, K and Gupta, GK and Haak, W and Krause, J and Atkinson, QD and Greenhill, SJ and Kühnert, D and Gray, RD},
title = {Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6656},
pages = {eabg0818},
doi = {10.1126/science.abg0818},
pmid = {37499002},
issn = {1095-9203},
mesh = {Horses ; Animals ; Phylogeny ; Bayes Theorem ; *Language ; *Agriculture ; Farms ; Europe ; },
abstract = {The origins of the Indo-European language family are hotly disputed. Bayesian phylogenetic analyses of core vocabulary have produced conflicting results, with some supporting a farming expansion out of Anatolia ~9000 years before present (yr B.P.), while others support a spread with horse-based pastoralism out of the Pontic-Caspian Steppe ~6000 yr B.P. Here we present an extensive database of Indo-European core vocabulary that eliminates past inconsistencies in cognate coding. Ancestry-enabled phylogenetic analysis of this dataset indicates that few ancient languages are direct ancestors of modern clades and produces a root age of ~8120 yr B.P. for the family. Although this date is not consistent with the Steppe hypothesis, it does not rule out an initial homeland south of the Caucasus, with a subsequent branch northward onto the steppe and then across Europe. We reconcile this hybrid hypothesis with recently published ancient DNA evidence from the steppe and the northern Fertile Crescent.},
}

Horses
Animals
Phylogeny
Bayes Theorem
*Language
*Agriculture
Farms
Europe

@article {pmid37495791,
year = {2023},
author = {Callaway, E},
title = {Seven generations of a prehistoric family mapped with ancient DNA.},
journal = {Nature},
volume = {620},
number = {7972},
pages = {19},
pmid = {37495791},
issn = {1476-4687},
mesh = {History, Ancient ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Human Migration ; },
}

History, Ancient
*DNA, Ancient
*DNA, Mitochondrial/genetics
Human Migration

@article {pmid37495780,
year = {2023},
author = {},
title = {Family trees of a Neolithic community uncovered by ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37495780},
issn = {1476-4687},
}

@article {pmid37495691,
year = {2023},
author = {Rivollat, M and Rohrlach, AB and Ringbauer, H and Childebayeva, A and Mendisco, F and Barquera, R and Szolek, A and Le Roy, M and Colleran, H and Tuke, J and Aron, F and Pemonge, MH and Späth, E and Télouk, P and Rey, L and Goude, G and Balter, V and Krause, J and Rottier, S and Deguilloux, MF and Haak, W},
title = {Extensive pedigrees reveal the social organization of a Neolithic community.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37495691},
issn = {1476-4687},
abstract = {Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations[1-4]. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality[5]. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.},
}

@article {pmid37494435,
year = {2023},
author = {Salazar, L and Burger, R and Forst, J and Barquera, R and Nesbitt, J and Calero, J and Washburn, E and Verano, J and Zhu, K and Sop, K and Kassadjikova, K and Ibarra Asencios, B and Davidson, R and Bradley, B and Krause, J and Fehren-Schmitz, L},
title = {Insights into the genetic histories and lifeways of Machu Picchu's occupants.},
journal = {Science advances},
volume = {9},
number = {30},
pages = {eadg3377},
doi = {10.1126/sciadv.adg3377},
pmid = {37494435},
issn = {2375-2548},
abstract = {Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.},
}

@article {pmid37494366,
year = {2023},
author = {Romboni, M and Arienzo, I and Di Vito, MA and Lubritto, C and Piochi, M and Di Cicco, MR and Rickards, O and Rolfo, MF and Sevink, J and De Angelis, F and Alessandri, L},
title = {La Sassa cave: Isotopic evidence for Copper Age and Bronze Age population dynamics in Central Italy.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288637},
pmid = {37494366},
issn = {1932-6203},
mesh = {Humans ; Spectroscopy, Fourier Transform Infrared ; Italy ; *Strontium Isotopes/analysis ; *Diet ; Nitrogen Isotopes/analysis ; Population Dynamics ; Archaeology ; },
abstract = {This study focuses on the changes in diet and mobility of people buried in the La Sassa cave (Latium, Central Italy) during the Copper and Bronze Ages to contribute to the understanding of the complex contemporary population dynamics in Central Italy. To that purpose, carbon and nitrogen stable isotope analyses, strontium isotope analyses, and FT-IR evaluations were performed on human and faunal remains from this cave. The stable isotope analyses evidence a slight shift in diet between Copper and Bronze Age individuals, which becomes prominent in an individual, dating from a late phase, when the cave was mainly used as a cultic shelter. This diachronic study documents an increased dietary variability due to the introduction of novel resources in these protohistoric societies, possibly related to the southward spread of northern human groups into Central Italy. This contact between different cultures is also testified by the pottery typology found in the cave. The latter shows an increase in cultural intermingling starting during the beginning of the middle Bronze Age. The local mobility during this phase likely involved multiple communities scattered throughout an area of a few kilometers around the cave, which used the latter as a burial site both in the Copper and Bronze ages.},
}

Humans
Spectroscopy, Fourier Transform Infrared
Italy
*Strontium Isotopes/analysis
*Diet
Nitrogen Isotopes/analysis
Population Dynamics
Archaeology

@article {pmid37491505,
year = {2023},
author = {Barsch, E and Kowarik, K and Rodler, K and Hörweg, C and Reschreiter, H and Sattmann, H and Walochnik, J},
title = {First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12055},
pmid = {37491505},
issn = {2045-2322},
mesh = {Animals ; Humans ; Ascaris lumbricoides/genetics ; Austria ; Ascaris/genetics ; *Ascariasis ; *Nematode Infections ; Trichuris/genetics ; Feces/parasitology ; Soil ; },
abstract = {Palaeoparasitological studies can provide valuable information on the emergence, distribution, and elimination of parasites during a particular time in the past. In the prehistoric salt mines of Hallstatt, located in the Austrian Alps, human faeces have been conserved in salt. The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. Altogether, 35 coprolites from the Hallstatt salt mines, dating back to the Bronze Age mining phase (1158-1063 BCE) and the Iron Age mining phase (750-662 BCE), respectively, were analysed by microscopy and molecular methods. In 91% of the coprolite samples, eggs of soil-transmitted helminths (STH), namely of Trichuris and/or Ascaris were detected by light microscopy. The Ascaris eggs were exceptionally well preserved. For further analysis, DNA was extracted from the palaeofaecal samples and species-specific primers targeting different genes were designed. While amplification of Trichuris DNA remained unsuccessful, sequence data of A. lumbricoides species complex were successfully obtained from 16 coprolites from three different genes, the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), the mitochondrial cytochrome B gene (cytB) and the mitochondrial NADH dehydrogenase subunit 1 gene (nadh1). Importantly, these included two Ascaris sequences from a coprolite from the Bronze Age, which to the best of our knowledge are the first molecular data of this genus from this period.},
}

Animals
Humans
Ascaris lumbricoides/genetics
Austria
Ascaris/genetics
*Ascariasis
*Nematode Infections
Trichuris/genetics
Feces/parasitology
Soil

@article {pmid37485357,
year = {2023},
author = {Ginja, C and Guimarães, S and da Fonseca, RR and Rasteiro, R and Rodríguez-Varela, R and Simões, LG and Sarmento, C and Belarte, MC and Kallala, N and Torres, JR and Sanmartí, J and Arruda, AM and Detry, C and Davis, S and Matos, J and Götherström, A and Pires, AE and Valenzuela-Lamas, S},
title = {Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.},
journal = {iScience},
volume = {26},
number = {7},
pages = {107196},
pmid = {37485357},
issn = {2589-0042},
abstract = {The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.},
}

@article {pmid37474518,
year = {2023},
author = {Campos, PE and Pruvost, O and Boyer, K and Chiroleu, F and Cao, TT and Gaudeul, M and Baider, C and Utteridge, TMA and Becker, N and Rieux, A and Gagnevin, L},
title = {Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4306},
pmid = {37474518},
issn = {2041-1723},
mesh = {Humans ; Phylogeny ; *Xanthomonas/genetics ; Genomics ; *Citrus/microbiology ; Plant Diseases/microbiology ; },
abstract = {Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).},
}

Humans
Phylogeny
*Xanthomonas/genetics
Genomics
*Citrus/microbiology
Plant Diseases/microbiology

@article {pmid37463654,
year = {2023},
author = {Lin, H and Hu, J and Baleka, S and Yuan, J and Chen, X and Xiao, B and Song, S and Du, Z and Lai, X and Hofreiter, M and Sheng, G},
title = {A genetic glimpse of the Chinese straight-tusked elephants.},
journal = {Biology letters},
volume = {19},
number = {7},
pages = {20230078},
pmid = {37463654},
issn = {1744-957X},
mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Elephants/genetics ; Fossils ; Phylogeny ; Phylogeography ; },
abstract = {Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.},
}

Animals
Biological Evolution
DNA, Mitochondrial/genetics
*Elephants/genetics
Fossils
Phylogeny
Phylogeography

@article {pmid37450551,
year = {2023},
author = {Pryor, Y and Lindo, J},
title = {Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21993},
pmid = {37450551},
issn = {1520-6505},
support = {1926075//Division of Behavioral and Cognitive Sciences/ ; 1945046//Division of Behavioral and Cognitive Sciences/ ; //Ford Foundation Predoctoral Fellowship/ ; 21602//National Science Foundation Graduate Research Fellowship/ ; },
abstract = {The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.},
}

@article {pmid37438988,
year = {2023},
author = {Lewis, DA and Simpson, R and Hermes, A and Brown, A and Llamas, B},
title = {More than dirt: Sedimentary ancient DNA and Indigenous Australia.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13835},
pmid = {37438988},
issn = {1755-0998},
support = {2011277//National Health and Medical Research Council/ ; 1137563//National Health and Medical Research Council/ ; },
abstract = {The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.},
}

@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 {pmid37438447,
year = {2023},
author = {Tran, HL and Mai, HP and Le Thi, D and Thi, ND and Le Tung, L and Thanh, TP and Manh, HT and Mau, HN and Chu, HH and Hoang, H},
title = {The first maternal genetic study of hunter-gatherers from Vietnam.},
journal = {Molecular genetics and genomics : MGG},
volume = {298},
number = {5},
pages = {1225-1235},
pmid = {37438447},
issn = {1617-4623},
support = {DL0000.08/20-23//Vietnam Academy of Science and Technology/ ; },
mesh = {Humans ; Vietnam ; *Archaeology ; *DNA, Ancient/analysis ; Genome, Human ; },
abstract = {The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.},
}

Humans
Vietnam
*Archaeology
*DNA, Ancient/analysis
Genome, Human

@article {pmid37433640,
year = {2023},
author = {Weissensteiner, MH and Cremona, MA and Guiblet, WM and Stoler, N and Harris, RS and Cechova, M and Eckert, KA and Chiaromonte, F and Huang, YF and Makova, KD},
title = {Accurate sequencing of DNA motifs able to form alternative (non-B) structures.},
journal = {Genome research},
volume = {33},
number = {6},
pages = {907-922},
doi = {10.1101/gr.277490.122},
pmid = {37433640},
issn = {1549-5469},
abstract = {Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.},
}

@article {pmid37431939,
year = {2023},
author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S},
title = {Diversity in matrilineages among the Jomon individuals of Japan.},
journal = {Annals of human biology},
volume = {50},
number = {1},
pages = {324-331},
doi = {10.1080/03014460.2023.2224060},
pmid = {37431939},
issn = {1464-5033},
mesh = {Humans ; Japan ; *Body Remains ; *Archaeology ; High-Throughput Nucleotide Sequencing ; Knowledge ; },
abstract = {BACKGROUND: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited.

AIM: We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.

SUBJECTS AND METHODS: For human remains dated to 8200-8600 cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing.

RESULTS: We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period.

CONCLUSION: The genetic diversity within the population was not found to be low even in the Initial Jomon period.},
}

Humans
Japan
*Body Remains
*Archaeology
High-Throughput Nucleotide Sequencing
Knowledge

@article {pmid37423869,
year = {2023},
author = {Bailey, E},
title = {Ancient DNA reveals an early adoption of horse culture by Native Americans.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.06.010},
pmid = {37423869},
issn = {0168-9525},
abstract = {Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.},
}

@article {pmid37422275,
year = {2023},
author = {Ibrahim, J and Rechav, K and Boaretto, E and Weiner, S},
title = {Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation.},
journal = {Journal of structural biology},
volume = {215},
number = {3},
pages = {107998},
doi = {10.1016/j.jsb.2023.107998},
pmid = {37422275},
issn = {1095-8657},
abstract = {We report on the 3D ultrastructure of the mineralized petrous bone of mature pig using focused ion beam - scanning electron microscopy (FIB-SEM). We divide the petrous bone into two zones based on the degree of mineralization; one zone close to the otic chamber has higher mineral density than the second zone further away from the otic chamber. The hypermineralization of the petrous bone results in the collagen D-banding being poorly revealed in the lower mineral density zone (LMD), and absent in the high mineral density zone (HMD). We therefore could not use D-banding to decipher the 3D structure of the collagen assembly. Instead we exploited the anisotropy option in the Dragonfly image processing software to visualize the less mineralized collagen fibrils and/or nanopores that surround the more mineralized zones known as tesselles. This approach therefore indirectly tracks the orientations of the collagen fibrils in the matrix itself. We show that the HMD bone has a structure similar to that of woven bone, and the LMD is composed of lamellar bone with a plywood-like structural motif. This agrees with the fact that the bone close to the otic chamber is fetal bone and is not remodeled. The lamellar structure of the bone further away from the otic chamber is consistent with modeling/remodeling. The absence of the less mineralized collagen fibrils and nanopores resulting from the confluence of the mineral tesselles may contribute to shielding DNA during diagenesis. We show that anisotropy evaluation of the less mineralized collagen fibrils could be a useful tool to analyze bone ultrastructures and in particular the directionality of collagen fibril bundles that make up the bone matrix.},
}

@article {pmid37380840,
year = {2023},
author = {Lewis, D},
title = {Ancient-DNA researcher fired for 'serious misconduct' lands new role.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-023-02147-x},
pmid = {37380840},
issn = {1476-4687},
}

@article {pmid37374141,
year = {2023},
author = {Abondio, P and Cilli, E and Luiselli, D},
title = {Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
pmid = {37374141},
issn = {2075-1729},
abstract = {A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.},
}

@article {pmid37372418,
year = {2023},
author = {Bonfigli, A and Cesare, P and Volpe, AR and Colafarina, S and Forgione, A and Aloisi, M and Zarivi, O and Poma, AMG},
title = {Estimation of DNA Degradation in Archaeological Human Remains.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372418},
issn = {2073-4425},
mesh = {Humans ; *DNA, Ancient ; Italy ; *Body Remains ; Bone and Bones ; DNA, Mitochondrial/genetics ; },
abstract = {The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.},
}

Humans
*DNA, Ancient
Italy
*Body Remains
Bone and Bones
DNA, Mitochondrial/genetics

@article {pmid37372367,
year = {2023},
author = {Song, S and Xiao, B and Hu, J and Lin, H and Du, Z and Xiang, K and Pan, D and Hou, X and Yuan, J and Lai, X and Sheng, G},
title = {Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372367},
issn = {2073-4425},
mesh = {Humans ; Animals ; Phylogeny ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Ruminants ; Asia ; },
abstract = {As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.},
}

Humans
Animals
Phylogeny
Bayes Theorem
*Genome, Mitochondrial/genetics
Ruminants
Asia

@article {pmid37341062,
year = {2023},
author = {Silva, V and Pérez, V and Gillanders, BM},
title = {Short-term plastisphere colonization dynamics across six plastic types.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16445},
pmid = {37341062},
issn = {1462-2920},
support = {//Australian Government Research Training Program Scholarship/ ; },
abstract = {Marine plastic pollution is a major concern worldwide, but the understanding of plastisphere dynamics remains limited in the southern hemisphere. To address this knowledge gap, we conducted a study in South Australia to investigate the prokaryotic community of the plastisphere and its temporal changes over 4 weeks. We submerged six plastic types (i.e., High-Density Polyethylene [HDPE], Polyvinyl chloride [PVC], Low-Density Polyethylene [LDPE], Polypropylene [PP], Polystyrene [PS] and the understudied textile, polyester [PET]) and wood in seawater and sampled them weekly to characterize the prokaryotic community using 16S rRNA gene metabarcoding. Our results showed that the plastisphere composition shifted significantly over short time scales (i.e., 4 weeks), and each plastic type had distinct groups of unique genera. In particular, the PVC plastisphere was dominated by Cellvibrionaceae taxa, distinguishing it from other plastics. Additionally, the textile polyester, which is rarely studied in plastisphere research, supported the growth of a unique group of 25 prokaryotic genera (which included the potential pathogenic Legionella genus). Overall, this study provides valuable insights into the colonization dynamics of the plastisphere over short time scales and contributes to narrowing the research gap on the southern hemisphere plastisphere.},
}

@article {pmid37339987,
year = {2023},
author = {Sousa da Mota, B and Rubinacci, S and Cruz Dávalos, DI and G Amorim, CE and Sikora, M and Johannsen, NN and Szmyt, MH and Włodarczak, P and Szczepanek, A and Przybyła, MM and Schroeder, H and Allentoft, ME and Willerslev, E and Malaspinas, AS and Delaneau, O},
title = {Imputation of ancient human genomes.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3660},
pmid = {37339987},
issn = {2041-1723},
support = {R35 GM142939/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Genotyping Techniques/methods ; *Genome, Human/genetics ; DNA, Ancient ; Genotype ; Genome-Wide Association Study/methods ; Polymorphism, Single Nucleotide ; },
abstract = {Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.},
}

Humans
*Genotyping Techniques/methods
*Genome, Human/genetics
DNA, Ancient
Genotype
Genome-Wide Association Study/methods
Polymorphism, Single Nucleotide

@article {pmid37337956,
year = {2023},
author = {Doan, K and Schnitzler, A and Preston, F and Griggo, C and Lang, G and Belhaoues, F and Blaise, E and Crégut-Bonnoure, E and Frère, S and Foucras, S and Gardeisen, A and Laurent, A and Müller, W and Picavet, R and Puissant, S and Yvinec, JH and Pilot, M},
title = {Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.},
journal = {Molecular ecology},
volume = {32},
number = {16},
pages = {4627-4647},
doi = {10.1111/mec.17054},
pmid = {37337956},
issn = {1365-294X},
support = {PPN/PPO/2018/1/00037//Narodowa Agencja Wymiany Akademickiej/ ; //National Fédération of Hunters/ ; },
mesh = {Dogs ; Animals ; *Wolves/genetics ; Phylogeny ; Biological Evolution ; Phylogeography ; France ; Haplotypes/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.},
}

Dogs
Animals
*Wolves/genetics
Phylogeny
Biological Evolution
Phylogeography
France
Haplotypes/genetics
DNA, Mitochondrial/genetics

@article {pmid37330109,
year = {2023},
author = {Yang, L and Zhang, X and Hu, Y and Zhu, P and Li, H and Peng, Z and Xiang, H and Zhou, X and Zhao, X},
title = {Ancient mitochondrial genome depicts sheep maternal dispersal and migration in eastern Asia.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2023.06.002},
pmid = {37330109},
issn = {1673-8527},
abstract = {Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 years old) found in Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region might have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in eastern Asia.},
}

@article {pmid37326229,
year = {2023},
author = {Bonsu, DNO and Higgins, D and Simon, C and Goodwin, CS and Henry, JM and Austin, JJ},
title = {Quantitative PCR overestimation of DNA in samples contaminated with tin.},
journal = {Journal of forensic sciences},
volume = {68},
number = {4},
pages = {1302-1309},
doi = {10.1111/1556-4029.15312},
pmid = {37326229},
issn = {1556-4029},
mesh = {Humans ; *Tin ; *DNA Fingerprinting/methods ; Microsatellite Repeats ; Real-Time Polymerase Chain Reaction ; DNA/analysis ; Metals ; },
abstract = {Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an "inhibition study" and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.},
}

Humans
*Tin
*DNA Fingerprinting/methods
Microsatellite Repeats
Real-Time Polymerase Chain Reaction
DNA/analysis
Metals

@article {pmid37323114,
year = {2023},
author = {Russo, MG and Arencibia, V and Emery, M and Bettera Marcat, G and Seldes, V and Mercolli, P and Soria, S and Maldonado, L and Kamenetzky, L and Avena, S and Dejean, C and Stone, AC},
title = {Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina.},
journal = {American journal of biological anthropology},
volume = {181},
number = {4},
pages = {597-610},
doi = {10.1002/ajpa.24795},
pmid = {37323114},
issn = {2692-7691},
mesh = {Humans ; Argentina ; *Genome, Mitochondrial/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; South America ; },
abstract = {OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina).

MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset.

RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya.

DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.},
}

Humans
Argentina
*Genome, Mitochondrial/genetics
Phylogeny
Bayes Theorem
DNA, Mitochondrial/genetics
South America

@article {pmid37311857,
year = {2023},
author = {de Sousa, AA and Beaudet, A and Calvey, T and Bardo, A and Benoit, J and Charvet, CJ and Dehay, C and Gómez-Robles, A and Gunz, P and Heuer, K and van den Heuvel, MP and Hurst, S and Lauters, P and Reed, D and Salagnon, M and Sherwood, CC and Ströckens, F and Tawane, M and Todorov, OS and Toro, R and Wei, Y},
title = {From fossils to mind.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {636},
pmid = {37311857},
issn = {2399-3642},
support = {P20 GM103653/GM/NIGMS NIH HHS/United States ; },
mesh = {*Fossils ; Phylogeny ; *Brain ; Archaeology ; Artifacts ; },
abstract = {Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.},
}

*Fossils
Phylogeny
*Brain
Archaeology
Artifacts

@article {pmid37291482,
year = {2023},
author = {Chen, N and Nedoluzhko, A},
title = {Ancient DNA: the past for the future.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {309},
pmid = {37291482},
issn = {1471-2164},
mesh = {Animals ; *DNA, Ancient ; Sequence Analysis, DNA/methods ; *Plants/genetics ; Laboratories ; },
abstract = {The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.},
}

Animals
*DNA, Ancient
Sequence Analysis, DNA/methods
*Plants/genetics
Laboratories

@article {pmid37286670,
year = {2023},
author = {Humphrey, L and Bouzouggar, A},
title = {Ancient DNA reveals how farming spread into northwest Africa.},
journal = {Nature},
volume = {618},
number = {7965},
pages = {460-461},
pmid = {37286670},
issn = {1476-4687},
mesh = {History, Ancient ; *DNA, Ancient ; Africa ; *Anthropology ; Agriculture ; Archaeology ; },
}

History, Ancient
*DNA, Ancient
Africa
*Anthropology
Agriculture
Archaeology

@article {pmid37284851,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M},
title = {Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {37284851},
issn = {1437-1596},
support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; },
abstract = {Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.},
}

@article {pmid37265549,
year = {2022},
author = {Elalouf, JM and Palacio, P and Bon, C and Berthonaud, V and Maksud, F and Stafford, TW and Hitte, C},
title = {The genome and diet of a 35,000-year-old Canis lupus specimen from the Paleolithic painted cave, Chauvet-Pont d'Arc, France.},
journal = {Ecology and evolution},
volume = {12},
number = {8},
pages = {e9238},
pmid = {37265549},
issn = {2045-7758},
abstract = {The Chauvet-Pont-d'Arc Cave (Ardèche, France) contains some of the oldest Paleolithic paintings recorded to date, as well as thousands of bones of the extinct cave bear, and some remains and footprints of other animals. As part of the interdisciplinary research project devoted to this reference cave site, we analyzed a coprolite collected within the deep cave. AMS radiocarbon dating of bone fragments from the coprolite yielded an age of 30,450 ± 550 RC yr. BP (AAR-19656; 36,150-34,000 cal BP), similar to ages assigned to Paleolithic artwork and cave bear remains from the same cave sector. Using high-throughput shotgun DNA sequencing, we demonstrated a high abundance of canid DNA and lesser amounts of DNA from the extinct cave bear. We interpret the sample as feces from a canid that had consumed cave bear tissue. The high amount of canid DNA allowed us to reconstruct a complete canid mitochondrial genome sequence (average coverage: 83×) belonging to a deeply divergent clade of extinct mitochondrial wolf lineages that are most closely related to coeval (~35 ka) Belgian wolves. Analysis of the nuclear genome yielded a similar coverage for the X chromosome (2.4×) and the autosomes (range: 2.3-3.2×), indicating that the Chauvet canid was a female. Comparing the relationship of the nuclear genome of this specimen with that of a variety of canids, we found it more closely related to gray wolves' genomes than to other wild canid or dog genomes, especially wolf genomes from Europe and the Middle East. We conclude that the coprolite is feces from an animal within an extinct wolf lineage. The consumption of cave bear by this wolf likely explains its intrusion into the dark cave sectors and sheds new light on the paleoecology of a major cave site.},
}

@article {pmid37259901,
year = {2023},
author = {Signore, AV and Morrison, PR and Brauner, CJ and Fago, A and Weber, RE and Campbell, KL},
title = {Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller's sea cows.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37259901},
issn = {2050-084X},
mesh = {Animals ; *Dugong ; Mammals ; Hemoglobins/genetics ; Climate ; Oxygen ; },
abstract = {The extinct Steller's sea cow (Hydrodamalis gigas; †1768) was a whale-sized marine mammal that manifested profound morphological specializations to exploit the harsh coastal climate of the North Pacific. Yet despite first-hand accounts of their biology, little is known regarding the physiological adjustments underlying their evolution to this environment. Here, the adult-expressed hemoglobin (Hb; α2β/δ2) of this sirenian is shown to harbor a fixed amino acid replacement at an otherwise invariant position (β/δ82Lys→Asn) that alters multiple aspects of Hb function. First, our functional characterization of recombinant sirenian Hb proteins demonstrates that the Hb-O2 affinity of this sub-Arctic species was less affected by temperature than those of living (sub)tropical sea cows. This phenotype presumably safeguarded O2 delivery to cool peripheral tissues and largely arises from a reduced intrinsic temperature sensitivity of the H. gigas protein. Additional experiments on H. gigas β/δ82Asn→Lys mutant Hb further reveal this exchange renders Steller's sea cow Hb unresponsive to the potent intraerythrocytic allosteric effector 2,3-diphosphoglycerate, a radical modification that is the first documented example of this phenotype among mammals. Notably, β/δ82Lys→Asn moreover underlies the secondary evolution of a reduced blood-O2 affinity phenotype that would have promoted heightened tissue and maternal/fetal O2 delivery. This conclusion is bolstered by analyses of two Steller's sea cow prenatal Hb proteins (Hb Gower I; ζ2ε2 and HbF; α2γ2) that suggest an exclusive embryonic stage expression pattern, and reveal uncommon replacements in H. gigas HbF (γ38Thr→Ile and γ101Glu→Asp) that increased Hb-O2 affinity relative to dugong HbF. Finally, the β/δ82Lys→Asn replacement of the adult/fetal protein is shown to increase protein solubility, which may have elevated red blood cell Hb content within both the adult and fetal circulations and contributed to meeting the elevated metabolic (thermoregulatory) requirements and fetal growth rates associated with this species cold adaptation.},
}

Animals
*Dugong
Mammals
Hemoglobins/genetics
Climate
Oxygen

@article {pmid37252429,
year = {2023},
author = {Furtwängler, A and Baumann, C and Majander, K and Wilkin, S and Tomoum, N and Rühli, F and Jaeggi, AV and Eppenberger, P and Bender, N and Schuenemann, VJ},
title = {The Mummy Explorer-a self-regulated open-access online teaching tool.},
journal = {Evolution, medicine, and public health},
volume = {11},
number = {1},
pages = {129-138},
pmid = {37252429},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Virtual teaching tools have gained increasing importance in recent years. In particular, the COVID-19 pandemic has reinforced the need for media-based and self-regulated tools. What is missing are tools that allow us to interlink highly interdisciplinary fields such as evolutionary medicine and, at the same time, allow us to adapt content to different lectures.

METHODOLOGY: We designed an interactive online teaching tool, namely, the Mummy Explorer, using open-access software (Google Web Designer), and we provided a freely downloadable template. We tested the tool on students and lecturers of evolutionary medicine using questionnaires and improved the tool according to their feedback.

RESULTS: The tool has a modular design and provides an overview of a virtual mummy excavation, including the subfields of palaeopathology, paleoradiology, cultural and ethnographic context, provenance studies, paleogenetics, and physiological analyses. The template allows lecturers to generate their own versions of the tool for any topic of interest by simply changing the text and pictures. Tests undertaken with students of evolutionary medicine showed that the tool was helpful during their studies. Lecturers commented that they appreciated having a similar tool in other fields.

CONCLUSIONS AND IMPLICATIONS: Mummy Explorer fills a gap in the virtual teaching landscape of highly interdisciplinary fields such as evolutionary medicine. It will be offered for free download and can be adapted to any educational topic. Translations into German and possibly other languages are in progress.},
}

@article {pmid37250315,
year = {2023},
author = {Clavel, P and Louis, L and Sarkissian, C and Thèves, C and Gillet, C and Chauvey, L and Tressières, G and Schiavinato, S and Calvière-Tonasso, L and Telmon, N and Clavel, B and Jonvel, R and Tzortzis, S and Bouniol, L and Fémolant, JM and Klunk, J and Poinar, H and Signoli, M and Costedoat, C and Spyrou, MA and Seguin-Orlando, A and Orlando, L},
title = {Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.},
journal = {iScience},
volume = {26},
number = {5},
pages = {106787},
pmid = {37250315},
issn = {2589-0042},
abstract = {Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17[th] and 18[th] centuries Common Era.},
}

@article {pmid37239398,
year = {2023},
author = {Buss, DL and Atmore, LM and Zicos, MH and Goodall-Copestake, WP and Brace, S and Archer, FI and Baker, CS and Barnes, I and Carroll, EL and Hart, T and Kitchener, AC and Sabin, R and Sremba, AL and Weir, CR and Jackson, JA},
title = {Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239398},
issn = {2073-4425},
mesh = {Animals ; *Fin Whale/genetics ; Whales/genetics ; Population Density ; Antarctic Regions ; },
abstract = {Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.},
}

Animals
*Fin Whale/genetics
Whales/genetics
Population Density
Antarctic Regions

@article {pmid37239354,
year = {2023},
author = {Thomas, JT and Cavagnino, C and Kjelland, K and Anderson, E and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Amory, C and Spatola, B and Moran, K and Parson, W and Marshall, C},
title = {Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239354},
issn = {2073-4425},
mesh = {Humans ; *DNA Fingerprinting/methods ; *Microsatellite Repeats/genetics ; Bone and Bones ; DNA, Mitochondrial/genetics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.},
}

Humans
*DNA Fingerprinting/methods
*Microsatellite Repeats/genetics
Bone and Bones
DNA, Mitochondrial/genetics
Polymorphism, Single Nucleotide/genetics

@article {pmid37224187,
year = {2023},
author = {Gibbon, VE and Feris, L and Gretzinger, J and Smith, K and Hall, S and Penn, N and Mutsvangwa, TEM and Heale, M and Finaughty, DA and Karanja, YW and Esterhuyse, J and Kotze, D and Barnes, N and Gunston, G and May, J and Krause, J and Wilkinson, CM and Schiffels, S and Februarie, D and Alves, S and Sealy, JC},
title = {Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0284785},
pmid = {37224187},
issn = {1932-6203},
mesh = {Humans ; South Africa ; *Anthropology ; *Archaeology ; Cemeteries ; DNA, Ancient ; },
abstract = {We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.},
}

Humans
South Africa
*Anthropology
*Archaeology
Cemeteries
DNA, Ancient

@article {pmid37220274,
year = {2023},
author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A},
title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {22},
pages = {e2213061120},
pmid = {37220274},
issn = {1091-6490},
mesh = {Humans ; Animals ; Africa ; *Neanderthals ; Acclimatization ; Arabia ; Selection, Genetic ; },
abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.},
}

Humans
Animals
Africa
*Neanderthals
Acclimatization
Arabia
Selection, Genetic

@article {pmid37216609,
year = {2023},
author = {Ciecierski, L and Stolarek, I and Figlerowicz, M},
title = {Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.},
journal = {Nucleic acids research},
volume = {51},
number = {W1},
pages = {W269-W273},
pmid = {37216609},
issn = {1362-4962},
mesh = {Humans ; *Genomics/methods ; Software ; Human Genetics ; DNA, Ancient ; Databases, Genetic ; },
abstract = {Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.},
}

Humans
*Genomics/methods
Software
Human Genetics
DNA, Ancient
Databases, Genetic

@article {pmid37215481,
year = {2023},
author = {Mármol-Sánchez, E and Heidemann, PL and Gredal, H and Cirera, S},
title = {MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1144084},
pmid = {37215481},
issn = {2297-1769},
abstract = {INTRODUCTION: Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment.

METHODS: By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group.

RESULTS: Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO.

DISCUSSION: Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.},
}

@article {pmid37212188,
year = {2023},
author = {Bunce, M},
title = {It is time for ancient DNA to sweat the small stuff.},
journal = {Molecular ecology},
volume = {32},
number = {11},
pages = {2689-2691},
doi = {10.1111/mec.16970},
pmid = {37212188},
issn = {1365-294X},
mesh = {Animals ; *DNA, Ancient ; Sweat ; DNA/genetics ; Biological Evolution ; Birds/genetics ; *Mammoths/genetics ; Fossils ; Phylogeny ; },
abstract = {When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs - despite the pervasive idea of 'dino DNA' from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected 'small stuff' - lizards, frogs, and other herpetofauna. But here's the rub - extracting DNA from the bones of this 'small stuff' is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.},
}

Animals
*DNA, Ancient
Sweat
DNA/genetics
Biological Evolution
Birds/genetics
*Mammoths/genetics
Fossils
Phylogeny

@article {pmid37207647,
year = {2023},
author = {Fleskes, RE and Owsley, DW and Bruwelheide, KS and Barca, KG and Griffith, DR and Cabana, GS and Schurr, TG},
title = {Historical genomes elucidate European settlement and the African diaspora in Delaware.},
journal = {Current biology : CB},
volume = {33},
number = {11},
pages = {2350-2358.e7},
doi = {10.1016/j.cub.2023.04.069},
pmid = {37207647},
issn = {1879-0445},
mesh = {Adult ; Child ; Humans ; *Black People/genetics ; Delaware ; DNA, Mitochondrial/genetics ; Genetics, Population ; Haplotypes ; *Human Migration ; White ; },
abstract = {The 17[th]-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.[1] The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.[2] European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.[3][,][4] To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.[5] Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17[th] and early 18[th] century North America.},
}

Adult
Child
Humans
*Black People/genetics
Delaware
DNA, Mitochondrial/genetics
Genetics, Population
Haplotypes
*Human Migration
White

@article {pmid37187366,
year = {2023},
author = {Wilke, T and Kehlmaier, C and Stelbrink, B and Albrecht, C and Bouchet, P},
title = {Historical DNA solves century-old mystery on sessility in freshwater gastropods.},
journal = {Molecular phylogenetics and evolution},
volume = {185},
number = {},
pages = {107813},
doi = {10.1016/j.ympev.2023.107813},
pmid = {37187366},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Fresh Water ; *Rivers ; DNA/genetics ; Snails/genetics ; },
abstract = {Extinction rates are increasing unabatedly but resources available for conservation action are limited. Therefore, some conservationists are pushing for ecology- and evolution-based conservation choices, prioritizing taxa with phylogenetic and trait-based originality. Extinction of original taxa may result in a disproportionate loss of evolutionary innovations and potentially prevent transformative changes in living systems. Here, we generated historical DNA data from an almost 120-year-old syntype of the enigmatic sessile snail Helicostoa sinensis from the Three Gorges region of the Yangtze River (PR China), using a next-generation sequencing protocol developed for ancient DNA. In a broader phylogenetic context, we assessed the phylogenetic and trait-based originality of this enigmatic taxon to solve the century-old puzzle of sessility in freshwater gastropods. Our multi-locus data confirm the phylogenetic and trait-based originality of H. sinensis. It is an ultra-rare, subfamily-level taxon (Helicostoinae stat. nov.) within the family Bithyniidae, which exhibits the evolutionary innovation of sessility. While we conservatively classify H. sinensis as "Critically Endangered", there is mounting evidence of the biological annihilation of this endemic species. Although rapidly rising extinction rates in invertebrates are increasingly recognized, the potential loss of originality in these "little things that run the world" has received little attention. We therefore call for comprehensive surveys of originality in invertebrates, particularly from extreme environments such as rapids of large rivers, as a basis for urgently needed ecology- and evolution-based conservation decisions.},
}

Animals
Phylogeny
*Fresh Water
*Rivers
DNA/genetics
Snails/genetics

@article {pmid37185708,
year = {2023},
author = {Abondio, P and Bruno, F and Luiselli, D},
title = {Apolipoprotein E (APOE) Haplotypes in Healthy Subjects from Worldwide Macroareas: A Population Genetics Perspective for Cardiovascular Disease, Neurodegeneration, and Dementia.},
journal = {Current issues in molecular biology},
volume = {45},
number = {4},
pages = {2817-2831},
pmid = {37185708},
issn = {1467-3045},
abstract = {Human APOE is a 299-amino acid long protein expressed and secreted in several tissues and body districts, where it exerts different functions mainly related to lipid metabolism, with specific activities around cholesterol transport and absorption/elimination. It has three main isoforms, determined by the pair of mutations rs7412-C/T and rs429358-C/T, which gives rise to the functionally different APOE variants ε2, ε3, and ε4. These have a distinct impact on lipid metabolism and are differentially implicated in Alzheimer's disease and neurodegeneration, cardiovascular disease, and dyslipidemia. A plethora of other single nucleotide variants along the sequence of the APOE gene have been studied in cohorts of affected individuals, where they also modulate the influence of the three main isoforms to determine the risk of developing the disease. However, no contextual analysis of gene-long haplotypes has been carried out so far, and never extensively in cohorts of healthy individuals from different worldwide populations. Leveraging a rich population genomics dataset, this study elucidates the distribution of APOE variants and haplotypes that are shared across populations and to specific macroareas, revealing a variety of risk-allele associations that distinguish specific ancestral backgrounds and can be leveraged for specific ancestry-informed screenings in medicine and public health.},
}

@article {pmid37167404,
year = {2023},
author = {Llamas, B and Roca-Rada, X},
title = {Paleogenomic study of the Mexican past.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6645},
pages = {578-579},
doi = {10.1126/science.adh7902},
pmid = {37167404},
issn = {1095-9203},
mesh = {Humans ; *DNA, Ancient ; Mexico ; *North American People/genetics/history ; Anthropology ; Genomics ; Demography ; },
abstract = {Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.},
}

Humans
*DNA, Ancient
Mexico
*North American People/genetics/history
Anthropology
Genomics
Demography

@article {pmid37163039,
year = {2023},
author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM},
title = {Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37163039},
abstract = {Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G12 ancient , on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.},
}

@article {pmid37157914,
year = {2023},
author = {Whitehouse, LS and Schrider, DR},
title = {Timesweeper: accurately identifying selective sweeps using population genomic time series.},
journal = {Genetics},
volume = {224},
number = {3},
pages = {},
pmid = {37157914},
issn = {1943-2631},
support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R35GM138286/GF/NIH HHS/United States ; },
mesh = {*Metagenomics ; Time Factors ; *Genetics, Population ; Polymorphism, Genetic ; Selection, Genetic ; },
abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations, only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper analyzes population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional convolutional neural network on said simulations, and inferring which polymorphisms in this serialized data set were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.},
}

*Metagenomics
Time Factors
*Genetics, Population
Polymorphism, Genetic
Selection, Genetic

@article {pmid37153511,
year = {2023},
author = {Sharko, FS and Zhur, KV and Trifonov, VA and Prokhortchouk, EB},
title = {Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.},
journal = {Acta naturae},
volume = {15},
number = {1},
pages = {87-96},
pmid = {37153511},
issn = {2075-8251},
abstract = {Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.},
}

@article {pmid37141673,
year = {2023},
author = {Zupanič Pajnič, I and Leskovar, T and Zupanc, T and Podovšovnik, E},
title = {A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples.},
journal = {Forensic science international. Genetics},
volume = {65},
number = {},
pages = {102882},
doi = {10.1016/j.fsigen.2023.102882},
pmid = {37141673},
issn = {1878-0326},
mesh = {Humans ; Aged ; Powders ; Edetic Acid ; *DNA Fingerprinting/methods ; *Microsatellite Repeats ; DNA ; },
abstract = {An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.},
}

Humans
Aged
Powders
Edetic Acid
*DNA Fingerprinting/methods
*Microsatellite Repeats
DNA

@article {pmid37141357,
year = {2023},
author = {Gibbons, A},
title = {The woman with the deer pendant.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6644},
pages = {446},
doi = {10.1126/science.adi5371},
pmid = {37141357},
issn = {1095-9203},
mesh = {Animals ; Female ; Humans ; Deer ; *DNA, Ancient/isolation & purification ; },
abstract = {Pioneering technique gleans DNA from a Stone Age ornament, revealing its last wearer.},
}

Animals
Female
Humans
Deer
*DNA, Ancient/isolation & purification

@article {pmid37141315,
year = {2023},
author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P},
title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6645},
pages = {619-624},
doi = {10.1126/science.adf5300},
pmid = {37141315},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Biological Products/metabolism ; *Genome, Bacterial ; *Hominidae/genetics ; Metagenome ; *Neanderthals/genetics ; *Furans/metabolism ; DNA, Ancient ; },
abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.},
}

Animals
Humans
*Biological Products/metabolism
*Genome, Bacterial
*Hominidae/genetics
Metagenome
*Neanderthals/genetics
*Furans/metabolism
DNA, 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},
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