@article {pmid31626767,
year = {2019},
author = {Raghavan, M and Schroeder, H and Malaspinas, AS},
title = {An Ancient Genome from the Indus Valley Civilization.},
journal = {Cell},
volume = {179},
number = {3},
pages = {586-588},
doi = {10.1016/j.cell.2019.09.027},
pmid = {31626767},
issn = {1097-4172},
abstract = {Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool.},
}

@article {pmid31611588,
year = {2019},
author = {Shamoon-Pour, M and Li, M and Merriwether, DA},
title = {Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14751},
doi = {10.1038/s41598-019-48596-1},
pmid = {31611588},
issn = {2045-2322},
support = {BCS-1455744//National Science Foundation (NSF)/ ; 9005//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; },
abstract = {Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.},
}

@article {pmid31611361,
year = {2019},
author = {Guitor, AK and Raphenya, AR and Klunk, J and Kuch, M and Alcock, B and Surette, MG and McArthur, AG and Poinar, HN and Wright, GD},
title = {Capturing the Resistome: A targeted capture method to reveal antibiotic resistance determinants in metagenomes.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1128/AAC.01324-19},
pmid = {31611361},
issn = {1098-6596},
abstract = {The identification and association of the nucleotide sequences encoding antibiotic resistance elements is critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, which are both heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probeset on DNA libraries generated from multi-drug resistant bacteria to selectively capture resistance genes reproducibly produced higher reads on-target at greater length of coverage when compared to shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables sensitive gene detection in diverse environments where antibiotic resistance represents less than 0.1% of the metagenome.},
}

@article {pmid31607556,
year = {2019},
author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N},
title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2019.08.018},
pmid = {31607556},
issn = {1934-6069},
abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.},
}

@article {pmid31603617,
year = {2019},
author = {Crump, SE and Miller, GH and Power, M and Sepúlveda, J and Dildar, N and Coghlan, M and Bunce, M},
title = {Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.14836},
pmid = {31603617},
issn = {1365-2486},
support = {DGE1144083//NSF/ ; BCS1657743//NSF/ ; ARC1737712//NSF/ ; //National Geographic Society/ ; //Geological Society of America/ ; //CU Department of Geological Sciences/ ; //CU Center for the Study of Origins/ ; //INSTAAR/ ; },
abstract = {Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic 10 Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.},
}

@article {pmid29895902,
year = {2018},
author = {Kılınç, GM and Kashuba, N and Yaka, R and Sümer, AP and Yüncü, E and Shergin, D and Ivanov, GL and Kichigin, D and Pestereva, K and Volkov, D and Mandryka, P and Kharinskii, A and Tishkin, A and Ineshin, E and Kovychev, E and Stepanov, A and Alekseev, A and Fedoseeva, SA and Somel, M and Jakobsson, M and Krzewińska, M and Storå, J and Götherström, A},
title = {Investigating Holocene human population history in North Asia using ancient mitogenomes.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8969},
pmid = {29895902},
issn = {2045-2322},
mesh = {Asia, Northern ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; *Genome, Microbial ; History, Ancient ; Humans ; Male ; },
abstract = {Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.},
}

Asia, Northern
*DNA, Ancient
DNA, Mitochondrial/*genetics
Female
*Genetic Variation
*Genome, Microbial
History, Ancient
Humans
Male

@article {pmid31594846,
year = {2019},
author = {Cox, SL and Ruff, CB and Maier, RM and Mathieson, I},
title = {Genetic contributions to variation in human stature in prehistoric Europe.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1910606116},
pmid = {31594846},
issn = {1091-6490},
abstract = {The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height-consistent with genetic predictions-although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.},
}

@article {pmid31594508,
year = {2019},
author = {Malmström, H and Günther, T and Svensson, EM and Juras, A and Fraser, M and Munters, AR and Pospieszny, Ł and Tõrv, M and Lindström, J and Götherström, A and Storå, J and Jakobsson, M},
title = {The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1912},
pages = {20191528},
doi = {10.1098/rspb.2019.1528},
pmid = {31594508},
issn = {1471-2954},
abstract = {The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.},
}

@article {pmid31593209,
year = {2019},
author = {Fiumi Sermattei, I and Traversari, M and Serventi, P and Cilli, E and Gruppioni, G and Tomassini, L and Benazzi, S and Galassi, FM},
title = {Pope Leo XII's death: the twist to a longstanding dispute by novel historical documents and paleopathographic analysis.},
journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen},
volume = {},
number = {},
pages = {},
doi = {10.1127/homo/2019/1138},
pmid = {31593209},
issn = {1618-1301},
abstract = {Although the practice of autopsy on the Pope's corpse was performed from the 16th century, autopsy reports are only rarely analysed, and never with the aim of investigating the real causes of the death from a concomitant medical and historical point of view. Here, for the first time, we report on the discovery of new unpublished documents from the Vatican Secret Archives and their investigation by a scientific and inter-disciplinary approach. This analysis allows us to draw new conclusions on the true cause of Leo XII's mysterious death. His sudden death, that occurred on February 10th, 1829 after a short illness, particularly struck the public. Suspicions of poisoning or surgeon's guilt or inexperience and even the shadow of a venereal disease, contributed to create a "black legend" on his pontificate and death. On the contrary, the present paleopathographic analysis points toward a new conclusion. The regular use of catheterization with a silver syringe provided an easy access for bacterial superinfection, confirmed by the observed early emphysematous stage of the corpse. So, the most substantiated hypothesis concerning the cause of Leo XII's death indicates a severe form of sepsis, exacerbated by a weakened state due to chronic hemorrhoids.},
}

@article {pmid31589588,
year = {2019},
author = {Kowal, E and Llamas, B},
title = {Race in a genome: long read sequencing, ethnicity-specific reference genomes and the shifting horizon of race.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {97},
number = {},
pages = {},
doi = {10.4436/JASS.97004},
pmid = {31589588},
issn = {2037-0644},
abstract = {The sequencing of the human genome at the turn of the 21st century was hailed as revealing the overwhelming genetic similarity of human groups. Scholars of genomics have critiqued the subsequent persistence of race-based genetic science, but were reassured that the wide availability of gene sequencing would end the use of race as a proxy for genetic difference. Once an individual's whole gene sequence could be read, they hoped, their ethnoracial classification would become redundant. At the same time, genome science was recognising that the differences between human genomes went beyond the genome sequence to the structure of the genome itself. 'Structural variation' between genomes, including insertions, deletions, translocations, inversions, and copy number variations, mean that the 'universal' reference genome used for genome sequencing is not so universal. As conventional, 'short-read' sequencing wrongly assumes that all genomes have the same structure, significant genetic variation can be missed. This paper examines the twin phenomena that have been posed as a solution to the biases of short-read sequencing: 'long-read' sequencing and 'ethnicity-specific reference genomes'. Long-read sequencing is a method of generating a genome sequence that can be assembled de novo rather than relying on the reference genome. In recent years, a number of countries including China, Korea, and Denmark have used long-read sequencing and de novo assembly to develop 'national' reference genomes. Our analysis of one ethnicity-specific reference genome project, the Korean Reference Genome (KOREF), finds that it unduly emphasises the importance of population structural variation, framed in nationalist terms, and discounts the importance of individual structural variation. We argue that the intellectual labour required to make a Korean reference genome a coherent concept works to extend the horizon of race, prolonging the temporality of the 'meantime' in which race remains a seemingly valid concept in genomic science.},
}

@article {pmid30408262,
year = {2018},
author = {Karafet, TM and Osipova, LP and Savina, OV and Hallmark, B and Hammer, MF},
title = {Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {30},
number = {6},
pages = {e23194},
doi = {10.1002/ajhb.23194},
pmid = {30408262},
issn = {1520-6300},
support = {0324-2018-0016//State Research Project/International ; PLR-1203874//National Science Foundation/International ; },
mesh = {Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; *Genetic Variation ; Human Migration ; Humans ; *Linguistics ; *Polymorphism, Single Nucleotide ; Siberia ; },
abstract = {OBJECTIVES: We examined autosomal genome-wide SNPs and Y-chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples.

METHODS: Samples were genotyped for 567 096 autosomal SNPs and 147 Y-chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA, FST , TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied.

RESULTS: Analyses of autosomal and Y-chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations.

CONCLUSIONS: Autosomal SNP and Y-chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.},
}

Chromosomes, Human, Y/genetics
DNA, Ancient/analysis
*Genetic Variation
Human Migration
Humans
*Linguistics
*Polymorphism, Single Nucleotide
Siberia

@article {pmid30064915,
year = {2018},
author = {Laza, IM and Ventades, NG and Hervella, M and de-la-Rúa, C},
title = {Contribution of ancient human remains analysis to the understanding of the variability in HLA-B gene variants in relation to the diagnosis of spondyloarthropathies.},
journal = {Journal of autoimmunity},
volume = {94},
number = {},
pages = {70-82},
doi = {10.1016/j.jaut.2018.07.011},
pmid = {30064915},
issn = {1095-9157},
mesh = {Alleles ; Arthritis, Rheumatoid/*diagnosis/genetics/immunology/pathology ; Body Remains ; Bone and Bones/immunology/pathology ; Climate ; Cold Temperature ; DNA, Ancient/analysis ; Diagnosis, Differential ; Female ; Genetic Predisposition to Disease ; HLA-B27 Antigen/*genetics/immunology ; HLA-B35 Antigen/*genetics/immunology ; HLA-B40 Antigen/*genetics/immunology ; History, Medieval ; Humans ; Joints/immunology/pathology ; Male ; Osteoarthritis/*diagnosis/genetics/immunology/pathology ; Paleopathology/methods ; *Polymorphism, Genetic ; Spain ; Spondylarthropathies/*diagnosis/genetics/immunology/pathology ; },
abstract = {Genetic investigations on ancient human remains affected by rheumatological pathologies are a research field of particular interest for identifying the pathogenesis of diseases, especially those having an autoimmune background such as spondyloarthopaties (SpA). Reliable studies concerning this topic require collaboration between multiple disciplines, usually starting from paleopathologic observations up to molecular genetic screening. Here, we focused our investigation in a medieval necropolis in the Basque Country (13th-15th century, N = 163), which presents a high frequency of joint pathologies through two approaches: on the one hand, the analysis of joint manifestations for the differential diagnosis of the SpA and, on the other hand, the determination of the alleles of the HLA-B gene. The morphological analysis allowed determining that 30% of the individuals had rheumatic bone manifestations, with SpA being the most frequent (45%). The genetic analysis of individuals with and without pathologies, based on the study of the HLA-B gene, allowed finding 17 alleles for this gene, with HLA-B40, HLA-B27 and HLA-B35 being the most frequent. Although these alleles have been traditionally described as genetic markers associated to the development of SpA, in this study they were also found in individuals with other rheumatic diseases (osteoarthritis and rheumatoid arthritis) and even in individuals without pathologies. These data confirm the complexity of the relationship of the HLA-B gene variants with SpA, since it is not possible to establish a diagnosis of SpA with these variants alone. However, we suggest that allele HLA-B40, in combination with some specific rheumatic bone manifestations, facilitates the diagnosis of SpA.},
}

Alleles
Arthritis, Rheumatoid/*diagnosis/genetics/immunology/pathology
Body Remains
Bone and Bones/immunology/pathology
Climate
Cold Temperature
DNA, Ancient/analysis
Diagnosis, Differential
Female
Genetic Predisposition to Disease
HLA-B27 Antigen/*genetics/immunology
HLA-B35 Antigen/*genetics/immunology
HLA-B40 Antigen/*genetics/immunology
History, Medieval
Humans
Joints/immunology/pathology
Male
Osteoarthritis/*diagnosis/genetics/immunology/pathology
Paleopathology/methods
*Polymorphism, Genetic
Spain
Spondylarthropathies/*diagnosis/genetics/immunology/pathology

@article {pmid27726813,
year = {2016},
author = {Spigelman, M and Rubini, M},
title = {Paleomicrobiology of Leprosy.},
journal = {Microbiology spectrum},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/microbiolspec.PoH-0009-2015},
pmid = {27726813},
issn = {2165-0497},
mesh = {Bacteriological Techniques/methods ; Bone and Bones/microbiology ; Coinfection/microbiology ; Fossils/*microbiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Leprosy/*epidemiology/*history ; Mycobacterium leprae/*isolation & purification ; Mycobacterium tuberculosis/isolation & purification ; Paleopathology/methods ; },
abstract = {The use of paleomicrobiological techniques in leprosy has the potential to assist paleopathologists in many important aspects of their studies on the bones of victims, solving at times diagnostic problems. With Mycobacterium leprae, because of the unique nature of the organism, these techniques can help solve problems of differential diagnosis. In cases of co-infection with Mycobacterium tuberculosis, they can also suggest a cause of death and possibly even trace the migratory patterns of people in antiquity, as well as explain changes in the rates and level of infection within populations in antiquity.},
}

Bacteriological Techniques/methods
Bone and Bones/microbiology
Coinfection/microbiology
Fossils/*microbiology
History, 15th Century
History, 16th Century
History, 17th Century
History, 18th Century
History, 19th Century
History, 20th Century
History, 21st Century
History, Ancient
History, Medieval
Humans
Leprosy/*epidemiology/*history
Mycobacterium leprae/*isolation & purification
Mycobacterium tuberculosis/isolation & purification
Paleopathology/methods

@article {pmid31565086,
year = {2019},
author = {Robson, HK and Skipitytė, R and Piličiauskienė, G and Lucquin, A and Heron, C and Craig, OE and Piličiauskas, G},
title = {Diet, cuisine and consumption practices of the first farmers in the southeastern Baltic.},
journal = {Archaeological and anthropological sciences},
volume = {11},
number = {8},
pages = {4011-4024},
doi = {10.1007/s12520-019-00804-9},
pmid = {31565086},
issn = {1866-9557},
abstract = {With the arrival of the Early Neolithic Globular Amphora and Corded Ware cultures into the southeastern Baltic, ca. 2900/2800-2400 cal BC, a new type of economy was introduced, animal husbandry. However, the degree to which this transformed the subsistence economy is unknown. Here, we conducted organic residue analyses of 64 ceramic vessels to identify their contents. The vessels were sampled from 10 Lithuanian archaeological sites dating across the Subneolithic-Neolithic transition to the Early Bronze Age (ca. 2900/2800-1300 cal BC). Our results demonstrate that regardless of location or vessel type, many ceramics were used to process aquatic resources. Against our expectations, this association continued even after marked economic change concurrent with the migration of pastoralists from central and southeastern Europe, as evidenced by recent ancient DNA analysis of human remains. Moreover, we observed dairy fats in pottery from all cultures of the Early Neolithic (i.e. Rzucewo, Globular Amphora and Corded Ware) but unlike other regions of Europe, it seems that these were incorporated into indigenous culinary practices. Furthermore, some vessels were used to process plant foods, and others may have been used for the production and/or storage of birch bark tar. However, evidence for domesticated plant processing, for example millet, was absent. We show that organic residue analysis of pottery provides a different picture of past consumption patterns compared to the stable isotope analysis of human remains from isolated burials where a clear dietary shift is evident.},
}

@article {pmid31563810,
year = {2019},
author = {Jones, R and Velasco, MS and Harris, LG and Morgan, S and Temple, M and Ruddy, MC and Williams, R and Perry, MD and Hitchings, M and Wilkinson, TS and Humphrey, T and Gilbert, MTP and Davies, AP},
title = {Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {119},
number = {},
pages = {101865},
doi = {10.1016/j.tube.2019.101865},
pmid = {31563810},
issn = {1873-281X},
abstract = {This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods.},
}

@article {pmid31561553,
year = {2019},
author = {Yankova, I and Marinov, M and Neov, B and Petrova, M and Spassov, N and Hristov, P and Radoslavov, G},
title = {Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages.},
journal = {Genes},
volume = {10},
number = {10},
pages = {},
doi = {10.3390/genes10100757},
pmid = {31561553},
issn = {2073-4425},
support = {H21/32 2018//National Scientific Fund of the Bulgarian Ministry of Education and Science/ ; },
abstract = {The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs' populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.},
}

@article {pmid31558742,
year = {2019},
author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG},
title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13785},
doi = {10.1038/s41598-019-49930-3},
pmid = {31558742},
issn = {2045-2322},
abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.},
}

@article {pmid31552062,
year = {2019},
author = {Wang, C and Lu, H and Zhang, J and Mao, L and Ge, Y},
title = {Bulliform Phytolith Size of Rice and Its Correlation With Hydrothermal Environment: A Preliminary Morphological Study on Species in Southern China.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {1037},
doi = {10.3389/fpls.2019.01037},
pmid = {31552062},
issn = {1664-462X},
abstract = {In the last decade, our understanding of rice domestication has improved by new archaeological findings using advanced analytical techniques such as morphological and morphometric analyses on rice grains, spikelet bases and phytoliths, and ancient DNA analysis on rice remains. Previous studies have considered the size of rice bulliform phytoliths as a proxy for tracking the domestication process. These phytoliths are often abundant and well preserved in sediments, and their shape is under the control of numerous genes, which may shift toward larger sizes by genetic mutation in domestication. Therefore, it has been assumed that the bulliforms of domesticated rice are usually larger than those of wild ones; however, morphometric data supporting this assumption are lacking in the literature, thereby requiring additional evidence to test its veracity. In this study, the vertical and horizonal lengths of bulliform phytoliths were measured in four rice species (domesticated Oryza sativa and wild Oryza rufipogon, Oryza officinalis, and Oryza meyeriana) from different regions of southern China. We found that the bulliform morphometric data of wild and domesticated rice overlapped and that there was no statistically significant difference between them. Therefore, bulliform size could not be used as a diagnostic indicator to distinguish domesticated rice from wild species and is a supporting rather than conclusive proxy for determining the domesticated status of rice in archaeological research. We further found that larger rice bulliform sizes likely occurred at the locations with higher temperature, precipitation, and water levels, indicating hydrothermal environment is an alternative factor influencing the size of rice bulliform phytoliths. For further archaeological use of an increasing size trend of bulliform phytoliths to reveal the process of rice domestication, we present some suggestions for controlling the influence of hydrothermal factors. Even so, the combination of bulliform phytolith size with other established criteria is strongly suggested to provide precise identification of wild and domesticated rice in future research.},
}

@article {pmid31542986,
year = {2019},
author = {Chen, SG and Li, J and Zhang, F and Xiao, B and Hu, JM and Cui, YQ and Hofreiter, M and Hou, XD and Sheng, GL and Lai, XL and Yuan, JX},
title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2019.1659250},
pmid = {31542986},
issn = {2470-1408},
abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.},
}

@article {pmid31537848,
year = {2019},
author = {Tamm, E and Cristofaro, JD and Mazières, S and Pennarun, E and Kushniarevich, A and Raveane, A and Semino, O and Chiaroni, J and Pereira, L and Metspalu, M and Montinaro, F},
title = {Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {13581},
doi = {10.1038/s41598-019-49901-8},
pmid = {31537848},
issn = {2045-2322},
support = {IUT24-1//Eesti Teadusagentuur (Estonian Research Council)/ ; IUT24-1//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG243//Eesti Teadusagentuur (Estonian Research Council)/ ; PUT1339//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG243//Eesti Teadusagentuur (Estonian Research Council)/ ; 2014-2020.4.01.16-0030//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; 2014-2020.4.01.15-0012//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; 2014-2020.4.01.16-0030//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; 810645//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.},
}

@article {pmid31523131,
year = {2019},
author = {Ishiya, K and Mizuno, F and Wang, L and Ueda, S},
title = {MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.},
journal = {Bioinformatics and biology insights},
volume = {13},
number = {},
pages = {1177932219873884},
doi = {10.1177/1177932219873884},
pmid = {31523131},
issn = {1177-9322},
abstract = {The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.},
}

@article {pmid31517046,
year = {2019},
author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM},
title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.},
journal = {Science advances},
volume = {5},
number = {9},
pages = {eaaw3950},
doi = {10.1126/sciadv.aaw3950},
pmid = {31517046},
issn = {2375-2548},
abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.},
}

@article {pmid31513651,
year = {2019},
author = {Menardo, F and Duchêne, S and Brites, D and Gagneux, S},
title = {The molecular clock of Mycobacterium tuberculosis.},
journal = {PLoS pathogens},
volume = {15},
number = {9},
pages = {e1008067},
doi = {10.1371/journal.ppat.1008067},
pmid = {31513651},
issn = {1553-7374},
abstract = {The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.},
}

@article {pmid31511700,
year = {2019},
author = {Cappellini, E and Welker, F and Pandolfi, L and Ramos-Madrigal, J and Samodova, D and Rüther, PL and Fotakis, AK and Lyon, D and Moreno-Mayar, JV and Bukhsianidze, M and Rakownikow Jersie-Christensen, R and Mackie, M and Ginolhac, A and Ferring, R and Tappen, M and Palkopoulou, E and Dickinson, MR and Stafford, TW and Chan, YL and Götherström, A and Nathan, SKSS and Heintzman, PD and Kapp, JD and Kirillova, I and Moodley, Y and Agusti, J and Kahlke, RD and Kiladze, G and Martínez-Navarro, B and Liu, S and Sandoval Velasco, M and Sinding, MS and Kelstrup, CD and Allentoft, ME and Orlando, L and Penkman, K and Shapiro, B and Rook, L and Dalén, L and Gilbert, MTP and Olsen, JV and Lordkipanidze, D and Willerslev, E},
title = {Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-019-1555-y},
pmid = {31511700},
issn = {1476-4687},
abstract = {The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.},
}

@article {pmid31504166,
year = {2019},
author = {Moreno-Mayar, JV and Korneliussen, TS and Dalal, J and Renaud, G and Albrechtsen, A and Nielsen, R and Malaspinas, AS},
title = {A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz660},
pmid = {31504166},
issn = {1367-4811},
abstract = {MOTIVATION: The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.

RESULTS: We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e., when the contaminant and the target come from closely related populations or with increased error rates. With a running time below five minutes, our method is applicable to large scale aDNA genomic studies.

AVAILABILITY: The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.},
}

@article {pmid31283430,
year = {2019},
author = {Bos, KI and Kühnert, D and Herbig, A and Esquivel-Gomez, LR and Andrades Valtueña, A and Barquera, R and Giffin, K and Kumar Lankapalli, A and Nelson, EA and Sabin, S and Spyrou, MA and Krause, J},
title = {Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.},
journal = {Annual review of microbiology},
volume = {73},
number = {},
pages = {639-666},
doi = {10.1146/annurev-micro-090817-062436},
pmid = {31283430},
issn = {1545-3251},
abstract = {The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.},
}

@article {pmid31495572,
year = {2019},
author = {Shinde, V and Narasimhan, VM and Rohland, N and Mallick, S and Mah, M and Lipson, M and Nakatsuka, N and Adamski, N and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Jadhav, N and Kim, YJ and Chatterjee, M and Munshi, A and Panyam, A and Waghmare, P and Yadav, Y and Patel, H and Kaushik, A and Thangaraj, K and Meyer, M and Patterson, N and Rai, N and Reich, D},
title = {An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2019.08.048},
pmid = {31495572},
issn = {1097-4172},
abstract = {We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.},
}

@article {pmid31495003,
year = {2019},
author = {Littleford-Colquhoun, BL and Weyrich, LS and Kent, N and Frere, CH},
title = {City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15240},
pmid = {31495003},
issn = {1365-294X},
abstract = {Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes. This article is protected by copyright. All rights reserved.},
}

@article {pmid31486822,
year = {2019},
author = {Balázs, J and Rózsa, Z and Bereczki, Z and Marcsik, A and Tihanyi, B and Karlinger, K and Pölöskei, G and Molnár, E and Donoghue, HD and Pálfi, G},
title = {Osteoarcheological and biomolecular evidence of leprosy from an 11-13th century CE Muslim cemetery in Europe (Orosháza, Southeast Hungary).},
journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen},
volume = {},
number = {},
pages = {},
doi = {10.1127/homo/2019/1071},
pmid = {31486822},
issn = {1618-1301},
abstract = {Orosháza site no. 10 (Southeast Hungary) contains the partially excavated archaeological remains of an 11-13th century CE Muslim merchant village and its cemetery located in close proximity to Christian villages of the same era. The skeleton of a young woman (grave no. 16) from the last phase of the cemetery use was identified with rhinomaxillary lesions associated with lepromatous leprosy. The right parietal bone also exhibited signs of cranial trauma, possibly caused by symbolic trepanation, a well-known ritual practice in the 9-11th century CE Carpathian Basin. The retrospective diagnosis of the disease was supported by ancient DNA analysis, as the samples were positive for Mycobacterium leprae aDNA, shown to be of genotype 3. Contrary to the general practice of the era, the body of the young female with severe signs of leprosy was interred among the regular graves of the Muslim cemetery in Orosháza, which may reflect the unique cultural background of the community.},
}

@article {pmid31481615,
year = {2019},
author = {Gilbert, E and O'Reilly, S and Merrigan, M and McGettigan, D and Vitart, V and Joshi, PK and Clark, DW and Campbell, H and Hayward, C and Ring, SM and Golding, J and Goodfellow, S and Navarro, P and Kerr, SM and Amador, C and Campbell, A and Haley, CS and Porteous, DJ and Cavalleri, GL and Wilson, JF},
title = {The genetic landscape of Scotland and the Isles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1904761116},
pmid = {31481615},
issn = {1091-6490},
abstract = {Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and "Celtic" to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora.},
}

@article {pmid31481609,
year = {2019},
author = {Gower, G and Fenderson, LE and Salis, AT and Helgen, KM and van Loenen, AL and Heiniger, H and Hofman-Kamińska, E and Kowalczyk, R and Mitchell, KJ and Llamas, B and Cooper, A},
title = {Widespread male sex bias in mammal fossil and museum collections.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1903275116},
pmid = {31481609},
issn = {1091-6490},
abstract = {A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pečnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.},
}

@article {pmid31480978,
year = {2019},
author = {Hermes, TR and Frachetti, MD and Doumani Dupuy, PN and Mar'yashev, A and Nebel, A and Makarewicz, CA},
title = {Early integration of pastoralism and millet cultivation in Bronze Age Eurasia.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1910},
pages = {20191273},
doi = {10.1098/rspb.2019.1273},
pmid = {31480978},
issn = {1471-2954},
abstract = {Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ13C, δ15N and δ18O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China.},
}

@article {pmid31462911,
year = {2019},
author = {Oosting, T and Star, B and Barrett, JH and Wellenreuther, M and Ritchie, PA and Rawlence, NJ},
title = {Unlocking the potential of ancient fish DNA in the genomic era.},
journal = {Evolutionary applications},
volume = {12},
number = {8},
pages = {1513-1522},
doi = {10.1111/eva.12811},
pmid = {31462911},
issn = {1752-4571},
abstract = {Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.},
}

@article {pmid31455916,
year = {2019},
author = {Lewis, D},
title = {'Paralysed by anxiety': researchers speak about life in troubled ancient-DNA lab.},
journal = {Nature},
volume = {572},
number = {7771},
pages = {571-572},
doi = {10.1038/d41586-019-02540-5},
pmid = {31455916},
issn = {1476-4687},
}

@article {pmid31437436,
year = {2019},
author = {Leles, D and Frías, L and Araújo, A and Brener, B and Sudré, A and Chame, M and Laurentino, V},
title = {Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material?.},
journal = {Experimental parasitology},
volume = {205},
number = {},
pages = {107739},
doi = {10.1016/j.exppara.2019.107739},
pmid = {31437436},
issn = {1090-2449},
abstract = {Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context.},
}

@article {pmid31433816,
year = {2019},
author = {Fernandes, D and Sirak, K and Cheronet, O and Howcroft, R and Čavka, M and Los, D and Burmaz, J and Pinhasi, R and Novak, M},
title = {Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0216366},
doi = {10.1371/journal.pone.0216366},
pmid = {31433816},
issn = {1932-6203},
abstract = {Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period.},
}

@article {pmid31431750,
year = {2019},
author = {Lewis, D},
title = {Head of prestigious ancient-DNA lab suspended amid bullying allegations.},
journal = {Nature},
volume = {572},
number = {7770},
pages = {424-425},
doi = {10.1038/d41586-019-02490-y},
pmid = {31431750},
issn = {1476-4687},
}

@article {pmid31431628,
year = {2019},
author = {Harney, É and Nayak, A and Patterson, N and Joglekar, P and Mushrif-Tripathy, V and Mallick, S and Rohland, N and Sedig, J and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Culleton, BJ and Ferry, M and Harper, TK and Michel, M and Oppenheimer, J and Stewardson, K and Zhang, Z and Harashawaradhana, and Bartwal, MS and Kumar, S and Diyundi, SC and Roberts, P and Boivin, N and Kennett, DJ and Thangaraj, K and Reich, D and Rai, N},
title = {Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3670},
doi = {10.1038/s41467-019-11357-9},
pmid = {31431628},
issn = {2041-1723},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; },
abstract = {Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.},
}

@article {pmid31424543,
year = {2019},
author = {Aris-Brosou, S},
title = {Direct Evidence of an Increasing Mutational Load in Humans.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz192},
pmid = {31424543},
issn = {1537-1719},
abstract = {The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. While the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations, but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.},
}

@article {pmid31412470,
year = {2019},
author = {Legrand, B and Miras, Y and Beauger, A and Dussauze, M and Latour, D},
title = {Akinetes and ancient DNA reveal toxic cyanobacterial recurrences and their potential for resurrection in a 6700-year-old core from a eutrophic lake.},
journal = {The Science of the total environment},
volume = {687},
number = {},
pages = {1369-1380},
doi = {10.1016/j.scitotenv.2019.07.100},
pmid = {31412470},
issn = {1879-1026},
abstract = {In order to evaluate the recurrence of toxic cyanobacterial blooms and to determine the survival capabilities of the resistance cells through time, a sedimentary core spanning 6700 years was drilled in the eutrophic Lake Aydat. A multiproxy approach (density, magnetic susceptibility, XRF, pollen and non-pollen palynomorph analyses), was used initially to determine the sedimentation model and the land uses around the lake. Comparison with the akinete count revealed that Nostocales cyanobacteria have been present in Lake Aydat over a six thousand year period. This long-term cyanobacterial recurrence also highlights the past presence of both the anaC and mcyB genes, involved in anatoxin-a and microcystin biosynthesis, respectively, throughout the core. The first appearance of cyanobacteria seems to be linked to the natural damming of the river, while the large increase in akinete density around 1800 cal.yr BP can be correlated with the intensification of human activities (woodland clearance, crop planting, grazing, etc.) in the catchment area of the lake, and marks the beginning of a long period of eutrophication. This first investigation into the viability and germination potential of cyanobacteria over thousands of years reveals the ability of intact akinetes to undergo cell divisions even after 1800 years of sedimentation, which is 10 times longer than previously observed. This exceptional cellular resistance, coupled with the long-term eutrophic conditions of this lake, could partly explain the past and current recurrences of cyanobacterial proliferations.},
}

@article {pmid31397436,
year = {2019},
author = {Kornienko, IV and Faleeva, TG and Oreshkova, NV and Grigoriev, SE and Grigorieva, LV and Putintseva, YA and Krutovsky, KV},
title = {[Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius)].},
journal = {Molekuliarnaia biologiia},
volume = {53},
number = {4},
pages = {627-637},
doi = {10.1134/S0026898419040062},
pmid = {31397436},
issn = {0026-8984},
abstract = {The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.},
}

@article {pmid31389360,
year = {2019},
author = {DAS, R},
title = {OnPeopling of India: Ancient DNA perspectives By K Thangaraj and Niraj Rai.},
journal = {Journal of biosciences},
volume = {44},
number = {3},
pages = {},
pmid = {31389360},
issn = {0973-7138},
}

@article {pmid31389359,
year = {2019},
author = {Thangaraj, K and Rai, N},
title = {Peopling of India: Ancient DNA perspectives.},
journal = {Journal of biosciences},
volume = {44},
number = {3},
pages = {},
pmid = {31389359},
issn = {0973-7138},
abstract = {To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent.},
}

@article {pmid31386837,
year = {2019},
author = {Valente, L and Etienne, RS and Garcia-R, JC},
title = {Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna.},
journal = {Current biology : CB},
volume = {29},
number = {15},
pages = {2563-2569.e4},
doi = {10.1016/j.cub.2019.06.058},
pmid = {31386837},
issn = {1879-0445},
abstract = {Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.},
}

@article {pmid31381968,
year = {2019},
author = {Oswald, JA and Allen, JM and Witt, KE and Folk, RA and Albury, NA and Steadman, DW and Guralnick, RP},
title = {Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.},
journal = {Molecular phylogenetics and evolution},
volume = {140},
number = {},
pages = {106576},
doi = {10.1016/j.ympev.2019.106576},
pmid = {31381968},
issn = {1095-9513},
abstract = {Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts.},
}

@article {pmid31361744,
year = {2019},
author = {Smith, O and Dunshea, G and Sinding, MS and Fedorov, S and Germonpre, M and Bocherens, H and Gilbert, MTP},
title = {Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival.},
journal = {PLoS biology},
volume = {17},
number = {7},
pages = {e3000166},
doi = {10.1371/journal.pbio.3000166},
pmid = {31361744},
issn = {1545-7885},
abstract = {While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.},
}

@article {pmid31353181,
year = {2019},
author = {Ning, C and Wang, CC and Gao, S and Yang, Y and Zhang, X and Wu, X and Zhang, F and Nie, Z and Tang, Y and Robbeets, M and Ma, J and Krause, J and Cui, Y},
title = {Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.},
journal = {Current biology : CB},
volume = {29},
number = {15},
pages = {2526-2532.e4},
doi = {10.1016/j.cub.2019.06.044},
pmid = {31353181},
issn = {1879-0445},
abstract = {Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.},
}

@article {pmid31351222,
year = {2019},
author = {Molto, JE and Kirkpatrick, CL and Keron, J},
title = {The paleoepidemiology of Sacral Spina Bifida Occulta in population samples from the Dakhleh Oasis, Egypt.},
journal = {International journal of paleopathology},
volume = {26},
number = {},
pages = {93-103},
doi = {10.1016/j.ijpp.2019.06.006},
pmid = {31351222},
issn = {1879-9825},
abstract = {OBJECTIVE: To document sacral spina bifida occulta (SSB0) prevalence in a population sample from the Dakhleh Oasis, Egypt, and address methodological issues in recording and quantifying SSBO variations.

MATERIALS: 442 adult sacra from two temporally disjunct samples from the same deme traversing the 3rd intermediate (TIP) and the Roman Periods.

METHODS: Sacra were scored for SSBO, excluding the sacral hiatus. Risk of SSBO was calculated with the common odds ratio and statistical significance by X2. Data were compared to other archaeological SSBO data.

RESULTS: SSBO was present in 15.6% of the sample with a slight, but not significant, temporal increase (TIP to Roman Period) in males, and a significant age-correlated increase in both sexes. Most open sacra occurred in young adults.

CONCLUSIONS: Data support that SSBO can be considered as a morphogenetic variant. Dakhleh data fall within the prevalence range for most populations, however inter-population comparisons are complicated by methodological inconsistencies.

SIGNIFICANCE: SSBO can be used in paleogenetic research.

LIMITATIONS: Methodological differences in scoring SSBO prevent effective comparative study.

SUGGESTED FUTURE RESEARCH: Future studies require more rigorous and standardized scoring methods. aDNA may be used to corroborate the morphogenetic value of SSBO and determine its clinical significance.},
}

@article {pmid31348818,
year = {2019},
author = {Günther, T and Nettelblad, C},
title = {The presence and impact of reference bias on population genomic studies of prehistoric human populations.},
journal = {PLoS genetics},
volume = {15},
number = {7},
pages = {e1008302},
doi = {10.1371/journal.pgen.1008302},
pmid = {31348818},
issn = {1553-7404},
abstract = {Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.},
}

@article {pmid31328768,
year = {2019},
author = {Mas-Sandoval, A and Arauna, LR and Gouveia, MH and Barreto, ML and Horta, BL and Lima-Costa, MF and Pereira, AC and Salzano, FM and Hünemeier, T and Tarazona-Santos, E and Bortolini, MC and Comas, D},
title = {Reconstructed lost Native American populations from Eastern Brazil are shaped by differential Jê/Tupi ancestry.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evz161},
pmid = {31328768},
issn = {1759-6653},
abstract = {After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African and the Native American. The study of the Native American genetic history is challenged by the availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies and the low proportions of the Native American component in the admixed Brazilian populations (in average 7%). We analysed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North East), Bambui (South East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui and 197 in Pelotas). We compared the reconstructed populations with non-admixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê- speaking ancestry related groups. We also show evidence of a decrease of the diversity of non-admixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.},
}

@article {pmid31318917,
year = {2019},
author = {Prufer, KM and Alsgaard, AV and Robinson, M and Meredith, CR and Culleton, BJ and Dennehy, T and Magee, S and Huckell, BB and Stemp, WJ and Awe, JJ and Capriles, JM and Kennett, DJ},
title = {Linking late Paleoindian stone tool technologies and populations in North, Central and South America.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219812},
doi = {10.1371/journal.pone.0219812},
pmid = {31318917},
issn = {1932-6203},
abstract = {From the perspective of Central and South America, the peopling of the New World was a complex process lasting thousands of years and involving multiple waves of Pleistocene and early Holocene period immigrants entering into the neotropics. These Paleoindian colonists initially brought with them technologies developed for adaptation to environments and resources found in North America. As the ice age ended across the New World people adapted more generalized stone tools to exploit changing environments and resources. In the neotropics these changes would have been pronounced as patchy forests and grasslands gave way to broadleaf tropical forests. We document a late Pleistocene/early Holocene stone tool tradition from Belize, located in southern Mesoamerica. This represents the first endogenous Paleoindian stone tool technocomplex recovered from well dated stratigraphic contexts for Mesoamerica. Previously designated Lowe, these artifacts share multiple features with contemporary North and South American Paleoindian tool types. Once hafted, these bifaces appear to have served multiple functions for cutting, hooking, thrusting, or throwing. The tools were developed at a time of technological regionalization reflecting the diverse demands of a period of pronounced environmental change and population movement. Combined stratigraphic, technological, and population paleogenetic data suggests that there were strong ties between lowland neotropic regions at the onset of the Holocene.},
}

@article {pmid31310584,
year = {2019},
author = {Hong, JH and Seo, M and Oh, CS and Shin, DH},
title = {Genetic Analysis of Small-Subunit Ribosomal RNA, Internal Transcribed Spacer 2, and ATP Synthase Subunit 8 of Trichuris trichiura Ancient DNA Retrieved from the 15th to 18th Century Joseon Dynasty Mummies' Coprolites from Korea.},
journal = {The Journal of parasitology},
volume = {105},
number = {4},
pages = {539-545},
pmid = {31310584},
issn = {1937-2345},
abstract = {Although parasitic infection by Trichuris trichiura is a very common intestinal helminthic disease worldwide, there is still insufficient information on the genetic characteristics of ancient T. trichiura in different spatiotemporal perspectives. Utilizing coprolite specimens obtained from 15th-18th century mummies dating to the Joseon Dynasty, we analyzed small-subunit ribosomal RNA, internal transcribed spacer 2, and ATP synthase subunit 8 of T. trichiura ancient DNA (aDNA). In BLAST and phylogenetic analyses, the T. trichiura aDNA sequences of this study belong to a separate cluster that is evidently distinct from the other genus Trichuris spp. reported in GenBank. This report characterizes T. trichiura aDNA of pre-20th century East Asia, and in so doing, it also proves the potential of aDNA analysis for differential diagnosis of T. trichiura in cases where ancient parasite eggs are morphologically indeterminate for species identification.},
}

@article {pmid31308224,
year = {2019},
author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C},
title = {A genetic analysis of the Gibraltar Neanderthals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {31},
pages = {15610-15615},
doi = {10.1073/pnas.1903984116},
pmid = {31308224},
issn = {1091-6490},
support = {//Wellcome Trust/United Kingdom ; },
abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.},
}

@article {pmid31303491,
year = {2019},
author = {Järve, M and Saag, L and Scheib, CL and Pathak, AK and Montinaro, F and Pagani, L and Flores, R and Guellil, M and Saag, L and Tambets, K and Kushniarevich, A and Solnik, A and Varul, L and Zadnikov, S and Petrauskas, O and Avramenko, M and Magomedov, B and Didenko, S and Toshev, G and Bruyako, I and Grechko, D and Okatenko, V and Gorbenko, K and Smyrnov, O and Heiko, A and Reida, R and Sapiehin, S and Sirotin, S and Tairov, A and Beisenov, A and Starodubtsev, M and Vasilev, V and Nechvaloda, A and Atabiev, B and Litvinov, S and Ekomasova, N and Dzhaubermezov, M and Voroniatov, S and Utevska, O and Shramko, I and Khusnutdinova, E and Metspalu, M and Savelev, N and Kriiska, A and Kivisild, T and Villems, R},
title = {Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance.},
journal = {Current biology : CB},
volume = {29},
number = {14},
pages = {2430-2441.e10},
doi = {10.1016/j.cub.2019.06.019},
pmid = {31303491},
issn = {1879-0445},
abstract = {The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.},
}

@article {pmid31303107,
year = {2019},
author = {Houldcroft, CJ and Rifkin, RF and Underdown, SJ},
title = {Human biology and ancient DNA: exploring disease, domestication and movement.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {95-98},
doi = {10.1080/03014460.2019.1629536},
pmid = {31303107},
issn = {1464-5033},
}

@article {pmid31300536,
year = {2019},
author = {Teixeira, JC and Cooper, A},
title = {Using hominin introgression to trace modern human dispersals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {31},
pages = {15327-15332},
doi = {10.1073/pnas.1904824116},
pmid = {31300536},
issn = {1091-6490},
abstract = {The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.},
}

@article {pmid31297530,
year = {2019},
author = {Koch, E and Schweizer, RM and Schweizer, TM and Stahler, DR and Smith, DW and Wayne, RK and Novembre, J},
title = {De novo mutation rate estimation in wolves of known pedigree.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz159},
pmid = {31297530},
issn = {1537-1719},
abstract = {Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 x 10-9 per base pair per generation and provide conservative bounds from 2.6 x 10-9 and 7.1 x 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 x 10-9 and 3.0-4.5 x 10-9), it implies a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000 - 64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates, and is likely to be vital to future investigations of mutation rate evolution.},
}

@article {pmid31296442,
year = {2019},
author = {Cornille, A and Antolín, F and Garcia, E and Vernesi, C and Fietta, A and Brinkkemper, O and Kirleis, W and Schlumbaum, A and Roldán-Ruiz, I},
title = {A Multifaceted Overview of Apple Tree Domestication.},
journal = {Trends in plant science},
volume = {24},
number = {8},
pages = {770-782},
doi = {10.1016/j.tplants.2019.05.007},
pmid = {31296442},
issn = {1878-4372},
abstract = {The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.},
}

@article {pmid31291259,
year = {2019},
author = {Zimmermann, HH and Harms, L and Epp, LS and Mewes, N and Bernhardt, N and Kruse, S and Stoof-Leichsenring, KR and Pestryakova, LA and Wieczorek, M and Trense, D and Herzschuh, U},
title = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0216966},
doi = {10.1371/journal.pone.0216966},
pmid = {31291259},
issn = {1932-6203},
abstract = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.},
}

@article {pmid31284503,
year = {2019},
author = {Lan, TM and Lin, Y and Njaramba-Ngatia, J and Guo, XS and Li, RG and Li, HM and Kumar-Sahu, S and Wang, X and Yang, XJ and Guo, HB and Xu, WH and Kristiansen, K and Liu, H and Xu, YC},
title = {Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.},
journal = {Genes},
volume = {10},
number = {7},
pages = {},
doi = {10.3390/genes10070509},
pmid = {31284503},
issn = {2073-4425},
abstract = {The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.},
}

@article {pmid31281897,
year = {2019},
author = {Feldman, M and Master, DM and Bianco, RA and Burri, M and Stockhammer, PW and Mittnik, A and Aja, AJ and Jeong, C and Krause, J},
title = {Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.},
journal = {Science advances},
volume = {5},
number = {7},
pages = {eaax0061},
doi = {10.1126/sciadv.aax0061},
pmid = {31281897},
issn = {2375-2548},
abstract = {The ancient Mediterranean port city of Ashkelon, identified as "Philistine" during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called "Sea Peoples." Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.},
}

@article {pmid31270812,
year = {2019},
author = {Fleskes, RE and Bruwelheide, KS and West, FL and Owsley, DW and Griffith, DR and Barca, KG and Cabana, GS and Schurr, TG},
title = {Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23887},
pmid = {31270812},
issn = {1096-8644},
support = {//The University of Pennsylvania/ ; },
abstract = {OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America.

MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence.

RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa.

DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.},
}

@article {pmid31256878,
year = {2019},
author = {Joseph, TA and Pe'er, I},
title = {Inference of Population Structure from Time-Series Genotype Data.},
journal = {American journal of human genetics},
volume = {105},
number = {2},
pages = {317-333},
doi = {10.1016/j.ajhg.2019.06.002},
pmid = {31256878},
issn = {1537-6605},
support = {U54 CA209997/CA/NCI NIH HHS/United States ; },
abstract = {Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.},
}

@article {pmid31251487,
year = {2019},
author = {Angelici, FM and Ciucani, MM and Angelini, S and Annesi, F and Caniglia, R and Castiglia, R and Fabbri, E and Galaverni, M and Palumbo, D and Ravegnini, G and Rossi, L and Siracusa, AM and Cilli, E},
title = {The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population.},
journal = {Zoological science},
volume = {36},
number = {3},
pages = {189-197},
doi = {10.2108/zs180180},
pmid = {31251487},
issn = {0289-0003},
mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Genotype ; Haplotypes ; Phylogeny ; Sicily ; Wolves/*genetics ; },
abstract = {Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.},
}

Animal Distribution
Animals
DNA, Mitochondrial/genetics
Extinction, Biological
Genotype
Haplotypes
Phylogeny
Sicily
Wolves/*genetics

@article {pmid31249793,
year = {2019},
author = {Silva, PC and Malabarba, MC and Vari In Memoriam, R and Malabarba, LR},
title = {Comparison and optimization for DNA extraction of archived fish specimens.},
journal = {MethodsX},
volume = {6},
number = {},
pages = {1433-1442},
doi = {10.1016/j.mex.2019.06.001},
pmid = {31249793},
issn = {2215-0161},
abstract = {The DNA extracted from museum alcohol-fixed specimens can be a valuable source of information for solving taxonomic, phylogenetic, ecological and conservational questions. However, this type of DNA, also called ancient DNA, is routinely obtained in small portions and highly fragmented. We have tested two different extraction kits in museum type-specimens of the fish family Characidae. Aiming to increase the DNA yield, we made modifications on a Qiagen manufacturer protocol, in the elution step. Also, to overcome the issue of DNA fragmentation, we applied our efforts in Sanger sequencing, to find a highly variable and, in result, informative COI fragment. Based on our results, there is no correlation between amount of the DNA extracted and the age of the sample. The Sanger sequencing generated sequences which are useful in solving taxonomic puzzles. Here are presented the customization and guidelines that allowed us to recover DNA from the archived fish specimens. •DNA extraction from archived fish specimens is more effective when using silica columns.•Change of the elution times from minutes in room temperature to 24 h in freezer greatly improved the DNA yielded.•Short but highly variable sequences replace the need to sequence the entire gene to identify a species.},
}

@article {pmid31246567,
year = {2019},
author = {Botbayev, D and Ravegnini, G and Sammarini, G and Kazymbet, P and Cilli, E and Serventi, P and Khanseitova, A and Alzhanuly, B and Belkozhaev, A and Aitkhozhina, N and Bakhtin, M and Lodi, V and Hrelia, P and Angelini, S},
title = {Absence of mutations in the human interferon alpha-2b gene in workers chronically exposed to ionising radiation.},
journal = {Arhiv za higijenu rada i toksikologiju},
volume = {70},
number = {2},
pages = {104-108},
doi = {10.2478/aiht-2019-70-3202},
pmid = {31246567},
issn = {1848-6312},
abstract = {Individuals chronically exposed to low-level ionising radiation (IR) run the risk of harmful and long-term adverse health effects, including gene mutations and cancer development. The search for reliable biomarkers of IR exposure in human population is still of great interest, as they may have a great implementation potential for the surveillance of occupationally exposed individuals. In this context, and considering previous literature, this study aimed to identify mutations in the human interferon alpha-2b (hIFNα-2b) as a potential biomarker of occupational chronic low-dose IR exposure linking low-IR exposure to the effects on haematopoiesis and reduced immunity. The analysis was performed in the genomic DNA of 51 uranium miners and 38 controls from Kazakhstan, and in 21 medical radiology workers and 21 controls from Italy. hIFNα-2b gene mutations were analysed with the real-time polymerase chain reaction (PCR) or Sanger sequencing. However, none of the investigated workers had the hIFNα-2b mutation. This finding highlights the need for further research to identify biomarkers for early detection of health effects associated with chronic low-dose IR exposure.},
}

@article {pmid31235841,
year = {2019},
author = {De Schepper, S and Ray, JL and Skaar, KS and Sadatzki, H and Ijaz, UZ and Stein, R and Larsen, A},
title = {The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0457-1},
pmid = {31235841},
issn = {1751-7370},
support = {268062//Norges Forskningsråd (Research Council of Norway)/ ; 273455/E10//Norges Forskningsråd (Research Council of Norway)/ ; 610055//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; 610055//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; NE/L011958/1//RCUK | Natural Environment Research Council (NERC)/ ; Lord Kelvin Adam Smith Leadership Fellowship//University of Glasgow/ ; },
abstract = {Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.},
}

@article {pmid31223116,
year = {2019},
author = {Eisenhofer, R and Cooper, A},
title = {A new home for microbes.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.48493},
pmid = {31223116},
issn = {2050-084X},
abstract = {Modern microorganisms growing in fossils provide major challenges for researchers trying to detect ancient molecules in the same fossils.},
}

@article {pmid31220249,
year = {2019},
author = {Borówka, P and Pułaski, Ł and Marciniak, B and Borowska-Strugińska, B and Dziadek, J and Żądzińska, E and Lorkiewicz, W and Strapagiel, D},
title = {Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.},
journal = {GigaScience},
volume = {8},
number = {6},
pages = {},
doi = {10.1093/gigascience/giz065},
pmid = {31220249},
issn = {2047-217X},
abstract = {BACKGROUND: Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results.

RESULTS: Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases.

CONCLUSIONS: Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.},
}

@article {pmid31216503,
year = {2019},
author = {Xavier, C and Eduardoff, M and Strobl, C and Parson, W},
title = {SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference.},
journal = {Forensic science international. Genetics},
volume = {42},
number = {},
pages = {39-44},
doi = {10.1016/j.fsigen.2019.06.004},
pmid = {31216503},
issn = {1878-0326},
abstract = {Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).},
}

@article {pmid31216315,
year = {2019},
author = {Wren, CD and Burke, A},
title = {Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0217996},
doi = {10.1371/journal.pone.0217996},
pmid = {31216315},
issn = {1932-6203},
abstract = {Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated "genomes" (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.},
}

@article {pmid31216119,
year = {2019},
author = {Epp, LS},
title = {A global perspective for biodiversity history with ancient environmental DNA.},
journal = {Molecular ecology},
volume = {28},
number = {10},
pages = {2456-2458},
doi = {10.1111/mec.15118},
pmid = {31216119},
issn = {1365-294X},
support = {98/3-1//DFG/ ; //Belmont Forum/ ; //BiodivScen ERA-Net COFUND programme/ ; },
abstract = {The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long-term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA - historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) - but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries - the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.},
}

@article {pmid31209287,
year = {2019},
author = {Bradshaw, CJA and Ulm, S and Williams, AN and Bird, MI and Roberts, RG and Jacobs, Z and Laviano, F and Weyrich, LS and Friedrich, T and Norman, K and Saltré, F},
title = {Minimum founding populations for the first peopling of Sahul.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1057-1063},
doi = {10.1038/s41559-019-0902-6},
pmid = {31209287},
issn = {2397-334X},
abstract = {The timing, context and nature of the first people to enter Sahul is still poorly understood owing to a fragmented archaeological record. However, quantifying the plausible demographic context of this founding population is essential to determine how and why the initial peopling of Sahul occurred. We developed a stochastic, age-structured model using demographic rates from hunter-gatherer societies, and relative carrying capacity hindcasted with LOVECLIM's net primary productivity for northern Sahul. We projected these populations to determine the resilience and minimum sizes required to avoid extinction. A census founding population of between 1,300 and 1,550 individuals was necessary to maintain a quasi-extinction threshold of ≲0.1. This minimum founding population could have arrived at a single point in time, or through multiple voyages of ≥130 people over ~700-900 years. This result shows that substantial population amalgamation in Sunda and Wallacea in Marine Isotope Stages 3-4 provided the conditions for the successful, large-scale and probably planned peopling of Sahul.},
}

@article {pmid31196226,
year = {2019},
author = {Petrigh, RS and Martínez, JG and Mondini, M and Fugassa, MH},
title = {Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America.},
journal = {Parasitology},
volume = {146},
number = {10},
pages = {1284-1288},
doi = {10.1017/S0031182019000787},
pmid = {31196226},
issn = {1469-8161},
abstract = {Parasitological analysis of coprolites has allowed exploring ecological relationships in ancient times. Ancient DNA analysis contributes to the identification of coprolites and their parasites. Pleistocene mammalian carnivore coprolites were recovered from paleontological and archaeological site Peñas de las Trampas 1.1 in the southern Puna of Argentina. With the aim of exploring ancient ecological relationships, parasitological analysis was performed to one of them, dated to 16 573-17 002 calibrated years BP, with 95.4% probability. Parasite eggs attributed to Toxascaris sp. by morphological characters were isolated. DNA of coprolite and eggs was extracted to molecular identification. Ancient mitochondrial DNA analysis confirmed the zoological origin of the coprolite as Puma concolor and that of parasite eggs as Toxascaris leonina. This is the oldest molecular parasite record worldwide, and it supports the presence of this parasite since the Pleistocene in America. These findings have implications for the biogeographic history of parasites and for the natural history of the region.},
}

@article {pmid31184205,
year = {2019},
author = {Scheib, CL and Hui, R and D'Atanasio, E and Wohns, AW and Inskip, SA and Rose, A and Cessford, C and O'Connell, TC and Robb, JE and Evans, C and Patten, R and Kivisild, T},
title = {East Anglian early Neolithic monument burial linked to contemporary Megaliths.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {145-149},
doi = {10.1080/03014460.2019.1623912},
pmid = {31184205},
issn = {1464-5033},
abstract = {In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.},
}

@article {pmid31178321,
year = {2019},
author = {Delsuc, F and Kuch, M and Gibb, GC and Karpinski, E and Hackenberger, D and Szpak, P and Martínez, JG and Mead, JI and McDonald, HG and MacPhee, RDE and Billet, G and Hautier, L and Poinar, HN},
title = {Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths.},
journal = {Current biology : CB},
volume = {29},
number = {12},
pages = {2031-2042.e6},
doi = {10.1016/j.cub.2019.05.043},
pmid = {31178321},
issn = {1879-0445},
abstract = {Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.},
}

@article {pmid31171860,
year = {2019},
author = {Presslee, S and Slater, GJ and Pujos, F and Forasiepi, AM and Fischer, R and Molloy, K and Mackie, M and Olsen, JV and Kramarz, A and Taglioretti, M and Scaglia, F and Lezcano, M and Lanata, JL and Southon, J and Feranec, R and Bloch, J and Hajduk, A and Martin, FM and Salas Gismondi, R and Reguero, M and de Muizon, C and Greenwood, A and Chait, BT and Penkman, K and Collins, M and MacPhee, RDE},
title = {Palaeoproteomics resolves sloth relationships.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1121-1130},
doi = {10.1038/s41559-019-0909-z},
pmid = {31171860},
issn = {2397-334X},
abstract = {The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.},
}

@article {pmid31164419,
year = {2019},
author = {Keller, M and Spyrou, MA and Scheib, CL and Neumann, GU and Kröpelin, A and Haas-Gebhard, B and Päffgen, B and Haberstroh, J and Ribera I Lacomba, A and Raynaud, C and Cessford, C and Durand, R and Stadler, P and Nägele, K and Bates, JS and Trautmann, B and Inskip, SA and Peters, J and Robb, JE and Kivisild, T and Castex, D and McCormick, M and Bos, KI and Harbeck, M and Herbig, A and Krause, J},
title = {Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {25},
pages = {12363-12372},
doi = {10.1073/pnas.1820447116},
pmid = {31164419},
issn = {1091-6490},
support = {//Wellcome Trust/United Kingdom ; },
abstract = {The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.},
}

@article {pmid31163991,
year = {2019},
author = {Santander, C and Montinaro, F and Capelli, C},
title = {Searching for archaic contribution in Africa.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {129-139},
doi = {10.1080/03014460.2019.1624823},
pmid = {31163991},
issn = {1464-5033},
abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.},
}

@article {pmid31161006,
year = {2019},
author = {Ersmark, E and Baryshnikov, G and Higham, T and Argant, A and Castaños, P and Döppes, D and Gasparik, M and Germonpré, M and Lidén, K and Lipecki, G and Marciszak, A and Miller, R and Moreno-García, M and Pacher, M and Robu, M and Rodriguez-Varela, R and Rojo Guerra, M and Sabol, M and Spassov, N and Storå, J and Valdiosera, C and Villaluenga, A and Stewart, JR and Dalén, L},
title = {Genetic turnovers and northern survival during the last glacial maximum in European brown bears.},
journal = {Ecology and evolution},
volume = {9},
number = {10},
pages = {5891-5905},
doi = {10.1002/ece3.5172},
pmid = {31161006},
issn = {2045-7758},
abstract = {The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.},
}

@article {pmid31147405,
year = {2019},
author = {Prendergast, ME and Lipson, M and Sawchuk, EA and Olalde, I and Ogola, CA and Rohland, N and Sirak, KA and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Callan, K and Culleton, BJ and Eccles, L and Harper, TK and Lawson, AM and Mah, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Ambrose, SH and Ayodo, G and Gates, HL and Gidna, AO and Katongo, M and Kwekason, A and Mabulla, AZP and Mudenda, GS and Ndiema, EK and Nelson, C and Robertshaw, P and Kennett, DJ and Manthi, FK and Reich, D},
title = {Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6448},
pages = {},
doi = {10.1126/science.aaw6275},
pmid = {31147405},
issn = {1095-9203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.},
}

@article {pmid31137975,
year = {2019},
author = {Donoghue, HD},
title = {Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {120-128},
doi = {10.1080/03014460.2019.1624822},
pmid = {31137975},
issn = {1464-5033},
abstract = {Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.},
}

@article {pmid31134682,
year = {2019},
author = {Wu, X and Ding, B and Zhang, B and Feng, J and Wang, Y and Ning, C and Wu, H and Zhang, F and Zhang, Q and Li, N and Zhang, Z and Sun, X and Zhang, Q and Li, W and Liu, B and Cui, Y and Gong, L},
title = {Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces.},
journal = {The Plant journal : for cell and molecular biology},
volume = {99},
number = {2},
pages = {201-215},
doi = {10.1111/tpj.14421},
pmid = {31134682},
issn = {1365-313X},
support = {2016YFD0101004//National key research and development programme of China/ ; 41472024//National Natural Science Foundation of China/ ; 2412017BJ005//Fundamental Research Fund for the Central Universities/ ; //Recruitment Programme of Global Youth Experts/ ; //Programme of Changbai Mountain Scholars/ ; },
abstract = {Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.},
}

@article {pmid31124326,
year = {2019},
author = {Hong, JH and Oh, CS and Chai, JY and Seo, M and Shin, DH},
title = {Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens.},
journal = {Journal of Korean medical science},
volume = {34},
number = {20},
pages = {e149},
doi = {10.3346/jkms.2019.34.e149},
pmid = {31124326},
issn = {1598-6357},
support = {NRF-2016R1A2B4015669/NRF/National Research Foundation of Korea/Korea ; },
abstract = {We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.},
}

@article {pmid31123709,
year = {2019},
author = {Kashuba, N and Kırdök, E and Damlien, H and Manninen, MA and Nordqvist, B and Persson, P and Götherström, A},
title = {Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {185},
doi = {10.1038/s42003-019-0399-1},
pmid = {31123709},
issn = {2399-3642},
abstract = {Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.},
}

@article {pmid31116227,
year = {2019},
author = {Hong, JH and Oh, CS and Seo, M and Shin, DH},
title = {Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {114},
number = {},
pages = {e180595},
doi = {10.1590/0074-02760180595},
pmid = {31116227},
issn = {1678-8060},
mesh = {Animals ; Asia ; DNA, Helminth/*genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Feces/*parasitology ; Humans ; Mummies/*parasitology ; Paleodontology ; Paragonimus westermani/genetics/*isolation & purification ; Parasite Egg Count ; Phylogeny ; },
abstract = {The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.},
}

Animals
Asia
DNA, Helminth/*genetics
DNA, Ribosomal Spacer/*genetics
Electron Transport Complex IV/*genetics
Feces/*parasitology
Humans
Mummies/*parasitology
Paleodontology
Paragonimus westermani/genetics/*isolation & purification
Parasite Egg Count
Phylogeny

@article {pmid31113254,
year = {2019},
author = {Ham, E and Underdown, SJ and Houldcroft, CJ},
title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.},
journal = {Annals of human biology},
volume = {46},
number = {2},
pages = {99-108},
doi = {10.1080/03014460.2019.1622038},
pmid = {31113254},
issn = {1464-5033},
abstract = {Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.},
}

@article {pmid31109769,
year = {2019},
author = {Perry, GH and Makarewicz, CA},
title = {Horse Paleogenomes and Human-Animal Interactions in Prehistory.},
journal = {Trends in genetics : TIG},
volume = {35},
number = {7},
pages = {473-475},
doi = {10.1016/j.tig.2019.04.006},
pmid = {31109769},
issn = {0168-9525},
abstract = {A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities.},
}

@article {pmid31092597,
year = {2019},
author = {Bennett, RJ and Baker, KS},
title = {Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes.},
journal = {Journal of clinical microbiology},
volume = {57},
number = {8},
pages = {},
doi = {10.1128/JCM.00100-19},
pmid = {31092597},
issn = {1098-660X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.},
}

@article {pmid31088861,
year = {2019},
author = {Renaud, G and Hanghøj, K and Korneliussen, TS and Willerslev, E and Orlando, L},
title = {Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.},
journal = {Genetics},
volume = {212},
number = {3},
pages = {587-614},
doi = {10.1534/genetics.119.302057},
pmid = {31088861},
issn = {1943-2631},
abstract = {Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.},
}

@article {pmid31080507,
year = {2019},
author = {Upadhyay, M and Bortoluzzi, C and Barbato, M and Ajmone-Marsan, P and Colli, L and Ginja, C and Sonstegard, TS and Bosse, M and Lenstra, JA and Groenen, MAM and Crooijmans, RPMA},
title = {Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs.},
journal = {Evolutionary applications},
volume = {12},
number = {5},
pages = {951-963},
doi = {10.1111/eva.12770},
pmid = {31080507},
issn = {1752-4571},
abstract = {The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.},
}

@article {pmid31080083,
year = {2019},
author = {Saag, L and Laneman, M and Varul, L and Malve, M and Valk, H and Razzak, MA and Shirobokov, IG and Khartanovich, VI and Mikhaylova, ER and Kushniarevich, A and Scheib, CL and Solnik, A and Reisberg, T and Parik, J and Saag, L and Metspalu, E and Rootsi, S and Montinaro, F and Remm, M and Mägi, R and D'Atanasio, E and Crema, ER and Díez-Del-Molino, D and Thomas, MG and Kriiska, A and Kivisild, T and Villems, R and Lang, V and Metspalu, M and Tambets, K},
title = {The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.},
journal = {Current biology : CB},
volume = {29},
number = {10},
pages = {1701-1711.e16},
doi = {10.1016/j.cub.2019.04.026},
pmid = {31080083},
issn = {1879-0445},
support = {261213//European Research Council/International ; },
abstract = {In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.},
}

@article {pmid31075917,
year = {2019},
author = {Merheb, M and Matar, R and Hodeify, R and Siddiqui, SS and Vazhappilly, CG and Marton, J and Azharuddin, S and Al Zouabi, H},
title = {Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.},
journal = {Cells},
volume = {8},
number = {5},
pages = {},
doi = {10.3390/cells8050433},
pmid = {31075917},
issn = {2073-4409},
abstract = {Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.},
}

@article {pmid31074010,
year = {2019},
author = {Maurer-Alcalá, XX and Nowacki, M},
title = {Evolutionary origins and impacts of genome architecture in ciliates.},
journal = {Annals of the New York Academy of Sciences},
volume = {1447},
number = {1},
pages = {110-118},
doi = {10.1111/nyas.14108},
pmid = {31074010},
issn = {1749-6632},
support = {//NCCR RNA & Disease/ ; G-EDIT//H2020 European Research Council/ ; },
abstract = {Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon-rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ-line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ-line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ-line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.},
}

@article {pmid31061125,
year = {2019},
author = {Schroeder, H and Margaryan, A and Szmyt, M and Theulot, B and Włodarczak, P and Rasmussen, S and Gopalakrishnan, S and Szczepanek, A and Konopka, T and Jensen, TZT and Witkowska, B and Wilk, S and Przybyła, MM and Pospieszny, Ł and Sjögren, KG and Belka, Z and Olsen, J and Kristiansen, K and Willerslev, E and Frei, KM and Sikora, M and Johannsen, NN and Allentoft, ME},
title = {Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {22},
pages = {10705-10710},
doi = {10.1073/pnas.1820210116},
pmid = {31061125},
issn = {1091-6490},
abstract = {The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.},
}

@article {pmid31056281,
year = {2019},
author = {Fages, A and Hanghøj, K and Khan, N and Gaunitz, C and Seguin-Orlando, A and Leonardi, M and McCrory Constantz, C and Gamba, C and Al-Rasheid, KAS and Albizuri, S and Alfarhan, AH and Allentoft, M and Alquraishi, S and Anthony, D and Baimukhanov, N and Barrett, JH and Bayarsaikhan, J and Benecke, N and Bernáldez-Sánchez, E and Berrocal-Rangel, L and Biglari, F and Boessenkool, S and Boldgiv, B and Brem, G and Brown, D and Burger, J and Crubézy, E and Daugnora, L and Davoudi, H and de Barros Damgaard, P and de Los Ángeles de Chorro Y de Villa-Ceballos, M and Deschler-Erb, S and Detry, C and Dill, N and do Mar Oom, M and Dohr, A and Ellingvåg, S and Erdenebaatar, D and Fathi, H and Felkel, S and Fernández-Rodríguez, C and García-Viñas, E and Germonpré, M and Granado, JD and Hallsson, JH and Hemmer, H and Hofreiter, M and Kasparov, A and Khasanov, M and Khazaeli, R and Kosintsev, P and Kristiansen, K and Kubatbek, T and Kuderna, L and Kuznetsov, P and Laleh, H and Leonard, JA and Lhuillier, J and Liesau von Lettow-Vorbeck, C and Logvin, A and Lõugas, L and Ludwig, A and Luis, C and Arruda, AM and Marques-Bonet, T and Matoso Silva, R and Merz, V and Mijiddorj, E and Miller, BK and Monchalov, O and Mohaseb, FA and Morales, A and Nieto-Espinet, A and Nistelberger, H and Onar, V and Pálsdóttir, AH and Pitulko, V and Pitskhelauri, K and Pruvost, M and Rajic Sikanjic, P and Rapan Papeša, A and Roslyakova, N and Sardari, A and Sauer, E and Schafberg, R and Scheu, A and Schibler, J and Schlumbaum, A and Serrand, N and Serres-Armero, A and Shapiro, B and Sheikhi Seno, S and Shevnina, I and Shidrang, S and Southon, J and Star, B and Sykes, N and Taheri, K and Taylor, W and Teegen, WR and Trbojević Vukičević, T and Trixl, S and Tumen, D and Undrakhbold, S and Usmanova, E and Vahdati, A and Valenzuela-Lamas, S and Viegas, C and Wallner, B and Weinstock, J and Zaibert, V and Clavel, B and Lepetz, S and Mashkour, M and Helgason, A and Stefánsson, K and Barrey, E and Willerslev, E and Outram, AK and Librado, P and Orlando, L},
title = {Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.},
journal = {Cell},
volume = {177},
number = {6},
pages = {1419-1435.e31},
doi = {10.1016/j.cell.2019.03.049},
pmid = {31056281},
issn = {1097-4172},
support = {U01 MH106874/MH/NIMH NIH HHS/United States ; },
abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.},
}

@article {pmid31040238,
year = {2019},
author = {Aouizerat, T and Gutman, I and Paz, Y and Maeir, AM and Gadot, Y and Gelman, D and Szitenberg, A and Drori, E and Pinkus, A and Schoemann, M and Kaplan, R and Ben-Gedalya, T and Coppenhagen-Glazer, S and Reich, E and Saragovi, A and Lipschits, O and Klutstein, M and Hazan, R},
title = {Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.},
journal = {mBio},
volume = {10},
number = {2},
pages = {},
doi = {10.1128/mBio.00388-19},
pmid = {31040238},
issn = {2150-7511},
mesh = {Archaeology/*methods ; Fossils/*microbiology ; Genotype ; Geologic Sediments/*microbiology ; Microbiological Techniques/*methods ; Yeasts/*isolation & purification ; },
abstract = {Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.},
}

Archaeology/*methods
Fossils/*microbiology
Genotype
Geologic Sediments/*microbiology
Microbiological Techniques/*methods
Yeasts/*isolation & purification

@article {pmid31036834,
year = {2019},
author = {Stahlschmidt, MC and Collin, TC and Fernandes, DM and Bar-Oz, G and Belfer-Cohen, A and Gao, Z and Jakeli, N and Matskevich, Z and Meshveliani, T and Pritchard, JK and McDermott, F and Pinhasi, R},
title = {Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {6628},
doi = {10.1038/s41598-019-43147-0},
pmid = {31036834},
issn = {2045-2322},
support = {GOIPD/775//Irish Research Council (An Chomhairle um Thaighde in Éirinn)/ ; },
abstract = {Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.},
}

@article {pmid31036632,
year = {2019},
author = {Shaw, B and Burrell, CL and Green, D and Navarro-Martinez, A and Scott, D and Daroszewska, A and van 't Hof, R and Smith, L and Hargrave, F and Mistry, S and Bottrill, A and Kessler, BM and Fischer, R and Singh, A and Dalmay, T and Fraser, WD and Henneberger, K and King, T and Gonzalez, S and Layfield, R},
title = {Molecular insights into an ancient form of Paget's disease of bone.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {116},
number = {21},
pages = {10463-10472},
doi = {10.1073/pnas.1820556116},
pmid = {31036632},
issn = {1091-6490},
support = {//Wellcome Trust/United Kingdom ; },
abstract = {Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.},
}

@article {pmid31013797,
year = {2019},
author = {Santiago-Rodriguez, TM and Fornaciari, A and Fornaciari, G and Luciani, S and Marota, I and Vercellotti, G and Toranzos, GA and Giuffra, V and Cano, RJ},
title = {Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
doi = {10.3390/genes10040299},
pmid = {31013797},
issn = {2073-4425},
abstract = {The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.},
}