@article {pmid32973032,
year = {2020},
author = {Petr, M and Hajdinjak, M and Fu, Q and Essel, E and Rougier, H and Crevecoeur, I and Semal, P and Golovanova, LV and Doronichev, VB and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Vernot, B and Meyer, M and Kelso, J},
title = {The evolutionary history of Neanderthal and Denisovan Y chromosomes.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6511},
pages = {1653-1656},
doi = {10.1126/science.abb6460},
pmid = {32973032},
issn = {1095-9203},
abstract = {Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.},
}

@article {pmid32963029,
year = {2020},
author = {Bokelmann, L and Glocke, I and Meyer, M},
title = {Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.263863.120},
pmid = {32963029},
issn = {1549-5469},
abstract = {Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.},
}

@article {pmid32960653,
year = {2020},
author = {Orlando, L},
title = {The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics.},
journal = {Annual review of genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genet-021920-011805},
pmid = {32960653},
issn = {1545-2948},
abstract = {The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans. Expected final online publication date for the Annual Review of Genetics, Volume 54 is November 23, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid32958830,
year = {2020},
author = {Ermakova, GV and Kucheryavyy, AV and Zaraisky, AG and Bayramov, AV},
title = {Publisher Correction: Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {532},
doi = {10.1038/s42003-020-01272-x},
pmid = {32958830},
issn = {2399-3642},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32953046,
year = {2020},
author = {Røed, KH and Kvie, KS and Losey, RJ and Kosintsev, PA and Hufthammer, AK and Dwyer, MJ and Goncharov, V and Klokov, KB and Arzyutov, DV and Plekhanov, A and Anderson, DG},
title = {Temporal and structural genetic variation in reindeer (Rangifer tarandus) associated with the pastoral transition in Northwestern Siberia.},
journal = {Ecology and evolution},
volume = {10},
number = {17},
pages = {9060-9072},
doi = {10.1002/ece3.6314},
pmid = {32953046},
issn = {2045-7758},
abstract = {Just as the domestication of livestock is often cited as a key element in the Neolithic transition to settled, the emergence of large-scaled reindeer husbandry was a fundamental social transformation for the indigenous peoples of Arctic Eurasia. To better understand the history of reindeer domestication, and the genetic processes associated with the pastoral transition in the Eurasian Arctic, we analyzed archaeological and contemporary reindeer samples from Northwestern Siberia. The material represents Rangifer genealogies spanning from 15,000 years ago to the 18th century, as well as modern samples from the wild Taĭmyr population and from domestic herds managed by Nenetses. The wild and the domestic population are the largest populations of their kind in Northern Eurasia, and some Nenetses hold their domestic reindeer beside their wild cousins. Our analyses of 197 modern and 223 ancient mitochondrial DNA sequences revealed two genetic clusters, which are interpreted as representing the gene pools of contemporary domestic and past wild reindeer. Among a total of 137 different mitochondrial haplotypes identified in both the modern and archaeological samples, only 21 were detected in the modern domestic gene pool, while 11 of these were absent from the wild gene pool. The significant temporal genetic shift that we associate with the pastoral transition suggests that the emergence and spread of reindeer pastoralism in Northwestern Siberia originated with the translocation and subsequent selective breeding of a special type of animal from outside the region. The distinct and persistent domestic characteristics of the haplotype structure since the 18th century suggests little genetic exchange since then. The absence of the typical domestic clade in modern nearby wild populations suggests that the contemporary Nenets domestic breed feature an ancestry from outside its present main distribution, possibly from further South.},
}

@article {pmid32555485,
year = {2020},
author = {Cassidy, LM and Maoldúin, RÓ and Kador, T and Lynch, A and Jones, C and Woodman, PC and Murphy, E and Ramsey, G and Dowd, M and Noonan, A and Campbell, C and Jones, ER and Mattiangeli, V and Bradley, DG},
title = {A dynastic elite in monumental Neolithic society.},
journal = {Nature},
volume = {582},
number = {7812},
pages = {384-388},
doi = {10.1038/s41586-020-2378-6},
pmid = {32555485},
issn = {1476-4687},
support = {205072/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adult ; Burial/history ; *Consanguinity ; DNA, Ancient/analysis ; Family/history ; Female ; Genome, Human/genetics ; Haplotypes/genetics ; Hierarchy, Social/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Male ; Societies/*history ; },
abstract = {The nature and distribution of political power in Europe during the Neolithic era remains poorly understood1. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive2. Although co-operative ideology has often been emphasised as a driver of megalith construction1, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy3-of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites4-specifically within polygynous and patrilineal royal families that are headed by god-kings5,6. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.},
}

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

@article {pmid32943505,
year = {2020},
author = {Curry, A},
title = {Ancient DNA tracks Vikings across Europe.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6510},
pages = {1416-1417},
doi = {10.1126/science.369.6510.1416},
pmid = {32943505},
issn = {1095-9203},
}

@article {pmid32943086,
year = {2020},
author = {Martiniano, R and Garrison, E and Jones, ER and Manica, A and Durbin, R},
title = {Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {250},
doi = {10.1186/s13059-020-02160-7},
pmid = {32943086},
issn = {1474-760X},
abstract = {BACKGROUND: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods.

RESULTS: We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels.

CONCLUSIONS: Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.},
}

@article {pmid32939074,
year = {2020},
author = {Gibbon, VE},
title = {African ancient DNA research requires robust ethics and permission protocols.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41576-020-00285-w},
pmid = {32939074},
issn = {1471-0064},
}

@article {pmid32939067,
year = {2020},
author = {Margaryan, A and Lawson, DJ and Sikora, M and Racimo, F and Rasmussen, S and Moltke, I and Cassidy, LM and Jørsboe, E and Ingason, A and Pedersen, MW and Korneliussen, T and Wilhelmson, H and Buś, MM and de Barros Damgaard, P and Martiniano, R and Renaud, G and Bhérer, C and Moreno-Mayar, JV and Fotakis, AK and Allen, M and Allmäe, R and Molak, M and Cappellini, E and Scorrano, G and McColl, H and Buzhilova, A and Fox, A and Albrechtsen, A and Schütz, B and Skar, B and Arcini, C and Falys, C and Jonson, CH and Błaszczyk, D and Pezhemsky, D and Turner-Walker, G and Gestsdóttir, H and Lundstrøm, I and Gustin, I and Mainland, I and Potekhina, I and Muntoni, IM and Cheng, J and Stenderup, J and Ma, J and Gibson, J and Peets, J and Gustafsson, J and Iversen, KH and Simpson, L and Strand, L and Loe, L and Sikora, M and Florek, M and Vretemark, M and Redknap, M and Bajka, M and Pushkina, T and Søvsø, M and Grigoreva, N and Christensen, T and Kastholm, O and Uldum, O and Favia, P and Holck, P and Sten, S and Arge, SV and Ellingvåg, S and Moiseyev, V and Bogdanowicz, W and Magnusson, Y and Orlando, L and Pentz, P and Jessen, MD and Pedersen, A and Collard, M and Bradley, DG and Jørkov, ML and Arneborg, J and Lynnerup, N and Price, N and Gilbert, MTP and Allentoft, ME and Bill, J and Sindbæk, SM and Hedeager, L and Kristiansen, K and Nielsen, R and Werge, T and Willerslev, E},
title = {Population genomics of the Viking world.},
journal = {Nature},
volume = {585},
number = {7825},
pages = {390-396},
doi = {10.1038/s41586-020-2688-8},
pmid = {32939067},
issn = {1476-4687},
abstract = {The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.},
}

@article {pmid32938925,
year = {2020},
author = {François, O and Jay, F},
title = {Factor analysis of ancient population genomic samples.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {4661},
doi = {10.1038/s41467-020-18335-6},
pmid = {32938925},
issn = {2041-1723},
abstract = {The recent years have seen a growing number of studies investigating evolutionary questions using ancient DNA. To address these questions, one of the most frequently-used method is principal component analysis (PCA). When PCA is applied to temporal samples, the sample dates are, however, ignored during analysis, leading to imperfect representations of samples in PC plots. Here, we present a factor analysis (FA) method in which individual scores are corrected for the effect of allele frequency drift over time. We obtained exact solutions for the estimates of corrected factors, and we provided a fast algorithm for their computation. Using computer simulations and ancient European samples, we compared geometric representations obtained from FA with PCA and with ancestry estimation programs. In admixture analyses, FA estimates agreed with tree-based statistics, and they were more accurate than those obtained from PCA projections and from ancestry estimation programs. A great advantage of FA over existing approaches is to improve descriptive analyses of ancient DNA samples without requiring inclusion of outgroup or present-day samples.},
}

@article {pmid32938680,
year = {2020},
author = {Guimaraes, S and Arbuckle, BS and Peters, J and Adcock, SE and Buitenhuis, H and Chazin, H and Manaseryan, N and Uerpmann, HP and Grange, T and Geigl, EM},
title = {Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age.},
journal = {Science advances},
volume = {6},
number = {38},
pages = {},
doi = {10.1126/sciadv.abb0030},
pmid = {32938680},
issn = {2375-2548},
abstract = {Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.},
}

@article {pmid32937422,
year = {2020},
author = {Rivollat, M and Jeong, C and Schiffels, S and Küçükkalıpçı, İ and Pemonge, MH and Rohrlach, AB and Alt, KW and Binder, D and Friederich, S and Ghesquière, E and Gronenborn, D and Laporte, L and Lefranc, P and Meller, H and Réveillas, H and Rosenstock, E and Rottier, S and Scarre, C and Soler, L and Wahl, J and Krause, J and Deguilloux, MF and Haak, W},
title = {Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.},
journal = {Science advances},
volume = {6},
number = {22},
pages = {},
doi = {10.1126/sciadv.aaz5344},
pmid = {32937422},
issn = {2375-2548},
abstract = {Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.},
}

@article {pmid32934321,
year = {2020},
author = {Pawłowska, J and Wollenburg, JE and Zajączkowski, M and Pawlowski, J},
title = {Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {15102},
doi = {10.1038/s41598-020-72146-9},
pmid = {32934321},
issn = {2045-2322},
support = {2015/19/D/ST10/00244//Narodowe Centrum Nauki/ ; 2015/19/D/ST10/00244//Narodowe Centrum Nauki/ ; AWI-PS92_00//Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research/ ; 31003A_179125/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.},
}

@article {pmid32933569,
year = {2020},
author = {Peyrégne, S and Peter, BM},
title = {AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {246},
doi = {10.1186/s13059-020-02123-y},
pmid = {32933569},
issn = {1474-760X},
support = {694707/ERC_/European Research Council/International ; },
abstract = {Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.},
}

@article {pmid32612278,
year = {2020},
author = {Gansauge, MT and Aximu-Petri, A and Nagel, S and Meyer, M},
title = {Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA.},
journal = {Nature protocols},
volume = {15},
number = {8},
pages = {2279-2300},
doi = {10.1038/s41596-020-0338-0},
pmid = {32612278},
issn = {1750-2799},
mesh = {Automation ; Base Sequence ; *DNA, Ancient ; DNA, Single-Stranded/*genetics ; *Gene Library ; Sequence Analysis, DNA/*methods ; },
abstract = {It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.},
}

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

@article {pmid32915387,
year = {2020},
author = {Nores, R and Rena, V and Angeletti, SC and Demarchi, DA and Modesti, N and Fabra, M},
title = {Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12024-020-00296-3},
pmid = {32915387},
issn = {1556-2891},
support = {FONCyT, PICT 2015-3155//Agencia Nacional de Promoción Científica y Tecnológica/ ; PID 2018-79//Ministerio de Ciencia y Tecnología de la Provincia de Córdoba/ ; },
abstract = {Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 14C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices.},
}

@article {pmid32913324,
year = {2020},
author = {Ermakova, GV and Kucheryavyy, AV and Zaraisky, AG and Bayramov, AV},
title = {Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {501},
doi = {10.1038/s42003-020-01234-3},
pmid = {32913324},
issn = {2399-3642},
support = {20-04-00675A//Russian Foundation for Basic Research (RFBR)/ ; 18-29-07014 MK//Russian Foundation for Basic Research (RFBR)/ ; 18-04-00015//Russian Foundation for Basic Research (RFBR)/ ; 19-14-00098//Russian Science Foundation (RSF)/ ; },
abstract = {The secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress BMP but specifically modulates Wnt signalling. In this work, we described and investigated phylogeny and expression patterns of four Noggin genes in lampreys, which represent the most basally divergent group of extant vertebrates, the cyclostomes, belonging to the superclass Agnatha. Assuming that lampreys have Noggin homologues in all representatives of another superclass of vertebrates, the Gnathostomata, we propose a model for Noggin family evolution in vertebrates. This model is in agreement with the hypotheses suggesting two rounds of genome duplication in the ancestor of vertebrates before the divergence of Agnatha and Gnathostomata.},
}

@article {pmid32901061,
year = {2020},
author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S},
title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14778},
doi = {10.1038/s41598-020-71504-x},
pmid = {32901061},
issn = {2045-2322},
abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.},
}

@article {pmid32898493,
year = {2020},
author = {Ringbauer, H and Steinrücken, M and Fehren-Schmitz, L and Reich, D},
title = {Increased rate of close-kin unions in the central Andes in the half millennium before European contact.},
journal = {Current biology : CB},
volume = {30},
number = {17},
pages = {R980-R981},
doi = {10.1016/j.cub.2020.07.072},
pmid = {32898493},
issn = {1879-0445},
abstract = {Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources.},
}

@article {pmid32895707,
year = {2020},
author = {Duchene, S and Lemey, P and Stadler, T and Ho, SYW and Duchene, DA and Dhanasekaran, V and Baele, G},
title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa163},
pmid = {32895707},
issn = {1537-1719},
abstract = {Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.},
}

@article {pmid32699412,
year = {2020},
author = {Ardelean, CF and Becerra-Valdivia, L and Pedersen, MW and Schwenninger, JL and Oviatt, CG and Macías-Quintero, JI and Arroyo-Cabrales, J and Sikora, M and Ocampo-Díaz, YZE and Rubio-Cisneros, II and Watling, JG and de Medeiros, VB and De Oliveira, PE and Barba-Pingarón, L and Ortiz-Butrón, A and Blancas-Vázquez, J and Rivera-González, I and Solís-Rosales, C and Rodríguez-Ceja, M and Gandy, DA and Navarro-Gutierrez, Z and De La Rosa-Díaz, JJ and Huerta-Arellano, V and Marroquín-Fernández, MB and Martínez-Riojas, LM and López-Jiménez, A and Higham, T and Willerslev, E},
title = {Evidence of human occupation in Mexico around the Last Glacial Maximum.},
journal = {Nature},
volume = {584},
number = {7819},
pages = {87-92},
doi = {10.1038/s41586-020-2509-0},
pmid = {32699412},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Altitude ; Archaeology ; Bayes Theorem ; Caves ; Cultural Diversity ; DNA, Ancient/analysis ; History, Ancient ; Human Migration/*history ; Humans ; *Ice Cover ; Mexico ; },
abstract = {The initial colonization of the Americas remains a highly debated topic1, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations2. However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico3,4, the Chiapas Highlands5, Central Mexico6 and the Caribbean coast7-9 during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas10-17of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)18, and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.},
}

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

@article {pmid32894086,
year = {2020},
author = {Bakshi, D and Nagpal, A and Sharma, V and Sharma, I and Shah, R and Sharma, B and Bhat, A and Verma, S and Bhat, GR and Abrol, D and Sharma, R and Vaishnavi, S and Kumar, R},
title = {MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population.},
journal = {BMC cancer},
volume = {20},
number = {1},
pages = {861},
doi = {10.1186/s12885-020-07361-8},
pmid = {32894086},
issn = {1471-2407},
abstract = {BACKGROUND: Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis.

METHODS: SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study.

RESULTS: The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123-0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings.

CONCLUSION: It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.},
}

@article {pmid32888333,
year = {2020},
author = {Eerkens, JW and Ryder, A and Evoy, A and Hull, B},
title = {Hydrogen isotopes in serial hair samples record season of death in a mummified child from 19th century San Francisco, CA.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24137},
pmid = {32888333},
issn = {1096-8644},
abstract = {BACKGROUND: The mummified body of a small child was found in a sealed Barstow cast iron casket during construction activity in San Francisco in 2016. Using historical records and ancient DNA the child was determined to be Edith H. Cook. She was born 28 November, 1873 in the city of San Francisco, and died of "marasmus" on 13 October, 1876 also in San Francisco.

AIMS: Currently, there are few techniques for estimating human season of death in archaeological cases. Hydrogen isotope ratios (δ2H) in hair keratin is known to strongly correlate with drinking water. We explore δ2H in serial hair samples as a potential technique to estimate season of death by comparing the δ2H record from hair to the known date of death.

MATERIALS & METHODS: Approximately 50 hairs were removed from the scalp, aligned from the root, and cut into 5cm serial sections, each representing approximately 2 weeks of growth, and the total sequence a total of 1 year of growth. δ2H was measured on each 5cm segment and compared to previously-reported δ13C, δ15N, and δ34S values.

RESULTS: δ2H in the serial hair samples ranged between -56‰ and -48‰, consistent with her water values recorded in surface waters from San Francisco, and follow a sinusoidal pattern. Decreasing δ2H in terminal samples before death suggest Fall as the season of death, consistent with the known date of death.

DISCUSSION: This test case shows that archaeological hair preserves a seasonal signature in the form of changing keratin δ2H values that correlate to changing δ2H in surface drinking water. Terminal values in root record water ingested during the final week(s) before death.

CONCLUSIONS: We argue that this technique can be used to estimate season of death in future archaeological or forensic cases where hair has been preserved but date of death is unknown.},
}

@article {pmid32704107,
year = {2020},
author = {Spinney, L},
title = {Smallpox and other viruses plagued humans much earlier than suspected.},
journal = {Nature},
volume = {584},
number = {7819},
pages = {30-32},
doi = {10.1038/d41586-020-02083-0},
pmid = {32704107},
issn = {1476-4687},
mesh = {Bone and Bones/microbiology/virology ; DNA, Ancient/*analysis ; Disease Eradication/history ; Hepatitis B/epidemiology/history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Mummies/microbiology/virology ; Plague/enzymology/history ; Smallpox/*epidemiology/*history/virology ; Time Factors ; Variola virus/classification/genetics/*isolation & purification ; },
}

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

@article {pmid32879432,
year = {2020},
author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E},
title = {Author Correction: Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14783},
doi = {10.1038/s41598-020-71841-x},
pmid = {32879432},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32873779,
year = {2020},
author = {Karpinski, E and Hackenberger, D and Zazula, G and Widga, C and Duggan, AT and Golding, GB and Kuch, M and Klunk, J and Jass, CN and Groves, P and Druckenmiller, P and Schubert, BW and Arroyo-Cabrales, J and Simpson, WF and Hoganson, JW and Fisher, DC and Ho, SYW and MacPhee, RDE and Poinar, HN},
title = {American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {4048},
doi = {10.1038/s41467-020-17893-z},
pmid = {32873779},
issn = {2041-1723},
abstract = {Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.},
}

@article {pmid32859198,
year = {2020},
author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ},
title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {108},
doi = {10.1186/s12915-020-00839-8},
pmid = {32859198},
issn = {1741-7007},
support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/ ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/ ; },
abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.},
}

@article {pmid32457149,
year = {2020},
author = {Brunel, S and Bennett, EA and Cardin, L and Garraud, D and Barrand Emam, H and Beylier, A and Boulestin, B and Chenal, F and Ciesielski, E and Convertini, F and Dedet, B and Desbrosse-Degobertiere, S and Desenne, S and Dubouloz, J and Duday, H and Escalon, G and Fabre, V and Gailledrat, E and Gandelin, M and Gleize, Y and Goepfert, S and Guilaine, J and Hachem, L and Ilett, M and Lambach, F and Maziere, F and Perrin, B and Plouin, S and Pinard, E and Praud, I and Richard, I and Riquier, V and Roure, R and Sendra, B and Thevenet, C and Thiol, S and Vauquelin, E and Vergnaud, L and Grange, T and Geigl, EM and Pruvost, M},
title = {Ancient genomes from present-day France unveil 7,000 years of its demographic history.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {23},
pages = {12791-12798},
pmid = {32457149},
issn = {1091-6490},
mesh = {Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; France ; Gene Flow ; *Genome, Human ; *Human Migration ; Humans ; Male ; Polymorphism, Genetic ; Population/*genetics ; },
abstract = {Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.},
}

Chromosomes, Human, Y/genetics
*DNA, Ancient
DNA, Mitochondrial/genetics
*Evolution, Molecular
Female
France
Gene Flow
*Genome, Human
*Human Migration
Humans
Male
Polymorphism, Genetic
Population/*genetics

@article {pmid32828254,
year = {2020},
author = {Hofreiter, M and Hartmann, S},
title = {Reconstructing protein-coding sequences from ancient DNA.},
journal = {Methods in enzymology},
volume = {642},
number = {},
pages = {21-33},
doi = {10.1016/bs.mie.2020.05.008},
pmid = {32828254},
issn = {1557-7988},
abstract = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including miscoding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.},
}

@article {pmid32826299,
year = {2020},
author = {He, Z and Dai, X and Beaumont, M and Yu, F},
title = {Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.120.303463},
pmid = {32826299},
issn = {1943-2631},
abstract = {Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modelling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.},
}

@article {pmid32815536,
year = {2020},
author = {Pratas, D and Toppinen, M and Pyöriä, L and Hedman, K and Sajantila, A and Perdomo, MF},
title = {A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.},
journal = {GigaScience},
volume = {9},
number = {8},
pages = {},
doi = {10.1093/gigascience/giaa086},
pmid = {32815536},
issn = {2047-217X},
abstract = {BACKGROUND: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data.

FINDINGS: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs.

CONCLUSIONS: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.},
}

@article {pmid32811443,
year = {2020},
author = {Woods, R and Turvey, ST and Brace, S and McCabe, CV and Dalén, L and Rayfield, EJ and Brown, MJF and Barnes, I},
title = {Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {106},
doi = {10.1186/s12862-020-01668-7},
pmid = {32811443},
issn = {1471-2148},
support = {NE/L501803/1//Natural Environment Research Council/ ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.

RESULTS: Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.

CONCLUSIONS: Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.},
}

@article {pmid32483115,
year = {2020},
author = {Ning, C and Li, T and Wang, K and Zhang, F and Li, T and Wu, X and Gao, S and Zhang, Q and Zhang, H and Hudson, MJ and Dong, G and Wu, S and Fang, Y and Liu, C and Feng, C and Li, W and Han, T and Li, R and Wei, J and Zhu, Y and Zhou, Y and Wang, CC and Fan, S and Xiong, Z and Sun, Z and Ye, M and Sun, L and Wu, X and Liang, F and Cao, Y and Wei, X and Zhu, H and Zhou, H and Krause, J and Robbeets, M and Jeong, C and Cui, Y},
title = {Ancient genomes from northern China suggest links between subsistence changes and human migration.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2700},
doi = {10.1038/s41467-020-16557-2},
pmid = {32483115},
issn = {2041-1723},
mesh = {Agriculture/*methods ; Archaeology/methods ; Asian Continental Ancestry Group/genetics/statistics & numerical data ; China ; Crops, Agricultural/*growth & development ; DNA, Ancient/analysis ; Edible Grain/*growth & development ; Genetics, Population/methods ; *Genome, Human ; Geography ; *Human Migration ; Humans ; Population Dynamics ; Rivers ; Sequence Analysis, DNA/methods ; Time Factors ; },
abstract = {Northern China harbored the world's earliest complex societies based on millet farming, in two major centers in the Yellow (YR) and West Liao (WLR) River basins. Until now, their genetic histories have remained largely unknown. Here we present 55 ancient genomes dating to 7500-1700 BP from the YR, WLR, and Amur River (AR) regions. Contrary to the genetic stability in the AR, the YR and WLR genetic profiles substantially changed over time. The YR populations show a monotonic increase over time in their genetic affinity with present-day southern Chinese and Southeast Asians. In the WLR, intensification of farming in the Late Neolithic is correlated with increased YR affinity while the inclusion of a pastoral economy in the Bronze Age was correlated with increased AR affinity. Our results suggest a link between changes in subsistence strategy and human migration, and fuel the debate about archaeolinguistic signatures of past human migration.},
}

Agriculture/*methods
Archaeology/methods
Asian Continental Ancestry Group/genetics/statistics & numerical data
China
Crops, Agricultural/*growth & development
DNA, Ancient/analysis
Edible Grain/*growth & development
Genetics, Population/methods
*Genome, Human
Geography
*Human Migration
Humans
Population Dynamics
Rivers
Sequence Analysis, DNA/methods
Time Factors

@article {pmid32795443,
year = {2020},
author = {Majander, K and Pfrengle, S and Kocher, A and Neukamm, J and du Plessis, L and Pla-Díaz, M and Arora, N and Akgül, G and Salo, K and Schats, R and Inskip, S and Oinonen, M and Valk, H and Malve, M and Kriiska, A and Onkamo, P and González-Candelas, F and Kühnert, D and Krause, J and Schuenemann, VJ},
title = {Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.07.058},
pmid = {32795443},
issn = {1879-0445},
abstract = {Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.},
}

@article {pmid32795436,
year = {2020},
author = {Lord, E and Dussex, N and Kierczak, M and Díez-Del-Molino, D and Ryder, OA and Stanton, DWG and Gilbert, MTP and Sánchez-Barreiro, F and Zhang, G and Sinding, MS and Lorenzen, ED and Willerslev, E and Protopopov, A and Shidlovskiy, F and Fedorov, S and Bocherens, H and Nathan, SKSS and Goossens, B and van der Plicht, J and Chan, YL and Prost, S and Potapova, O and Kirillova, I and Lister, AM and Heintzman, PD and Kapp, JD and Shapiro, B and Vartanyan, S and Götherström, A and Dalén, L},
title = {Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.07.046},
pmid = {32795436},
issn = {1879-0445},
abstract = {Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.},
}

@article {pmid32788984,
year = {2020},
author = {Ford, BM and Cornellas, A and Leonard, JA and Weir, RD and Russello, MA},
title = {Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation.},
journal = {Ecology and evolution},
volume = {10},
number = {15},
pages = {8345-8357},
doi = {10.1002/ece3.6541},
pmid = {32788984},
issn = {2045-7758},
abstract = {Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.},
}

@article {pmid32778142,
year = {2020},
author = {Nakatsuka, N and Harney, É and Mallick, S and Mah, M and Patterson, N and Reich, D},
title = {ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {199},
doi = {10.1186/s13059-020-02111-2},
pmid = {32778142},
issn = {1474-760X},
support = {GM007753/GM/NIGMS NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; GM100233/NH/NIH HHS/United States ; 61220//John Templeton Foundation/ ; Allen Discovery Center grant//Allen Foundation/ ; },
abstract = {We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .},
}

@article {pmid32778135,
year = {2020},
author = {Sabin, S and Herbig, A and Vågene, ÅJ and Ahlström, T and Bozovic, G and Arcini, C and Kühnert, D and Bos, KI},
title = {A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {201},
doi = {10.1186/s13059-020-02112-1},
pmid = {32778135},
issn = {1474-760X},
support = {na//Max-Planck-Gesellschaft/ ; na//Erik Philip-Sörensen Foundation/ ; na//Crafoord Foundation/ ; },
abstract = {BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679).

RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.

CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.},
}

@article {pmid32769100,
year = {2020},
author = {He, Z and Dai, X and Beaumont, M and Yu, F},
title = {Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.120.303400},
pmid = {32769100},
issn = {1943-2631},
abstract = {Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backwards in time while re-weighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface for both the selection coefficient and the allele age to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and non-constant demographic histories. We apply our approach to re-analyse ancient DNA data associated with horse base coat colours. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.},
}

@article {pmid32767894,
year = {2020},
author = {Parolin, ML and Cortés, LI and Basso, N and Scattolin, MC},
title = {New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600-1,900 Years before Present).},
journal = {Human biology},
volume = {91},
number = {4},
pages = {225-247},
doi = {10.13110/humanbiology.91.4.02},
pmid = {32767894},
issn = {1534-6617},
abstract = {Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. To expand current information on genetic characterization of the first agricultural communities of the southern Calchaquí Valleys, we present and discuss the first mitochondrial ancient DNA information obtained on samples dated to ca. 3,600-1,900 years before present from the Cajón Valley, Catamarca Province. Reproducible mtDNA hypervariable region 1 (HVR-1) sequences were obtained in seven individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2. Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomic analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco, and the Amazon.},
}

@article {pmid32763189,
year = {2020},
author = {Wagner, JK and Colwell, C and Claw, KG and Stone, AC and Bolnick, DA and Hawks, J and Brothers, KB and Garrison, NA},
title = {Fostering Responsible Research on Ancient DNA.},
journal = {American journal of human genetics},
volume = {107},
number = {2},
pages = {183-195},
doi = {10.1016/j.ajhg.2020.06.017},
pmid = {32763189},
issn = {1537-6605},
abstract = {Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.},
}

@article {pmid32760427,
year = {2020},
author = {Barrera-Redondo, J and Piñero, D and Eguiarte, LE},
title = {Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {742},
doi = {10.3389/fgene.2020.00742},
pmid = {32760427},
issn = {1664-8021},
abstract = {In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.},
}

@article {pmid32747648,
year = {2020},
author = {Nakatsuka, N and Luisi, P and Motti, JMB and Salemme, M and Santiago, F and D'Angelo Del Campo, MD and Vecchi, RJ and Espinosa-Parrilla, Y and Prieto, A and Adamski, N and Lawson, AM and Harper, TK and Culleton, BJ and Kennett, DJ and Lalueza-Fox, C and Mallick, S and Rohland, N and Guichón, RA and Cabana, GS and Nores, R and Reich, D},
title = {Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3868},
doi = {10.1038/s41467-020-17656-w},
pmid = {32747648},
issn = {2041-1723},
support = {GM007753//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.},
}

@article {pmid32433609,
year = {2020},
author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T},
title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.},
journal = {Nature},
volume = {581},
number = {7808},
pages = {299-302},
doi = {10.1038/s41586-020-2259-z},
pmid = {32433609},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation & purification ; DNA, Mitochondrial/genetics/isolation & purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy & histology/metabolism ; },
abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.},
}

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

@article {pmid32745952,
year = {2020},
author = {Mathieson, I},
title = {Human adaptation over the past 40,000 years.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {97-104},
doi = {10.1016/j.gde.2020.06.003},
pmid = {32745952},
issn = {1879-0380},
abstract = {Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.},
}

@article {pmid32743069,
year = {2020},
author = {Shillito, LM and Whelton, HL and Blong, JC and Jenkins, DL and Connolly, TJ and Bull, ID},
title = {Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon.},
journal = {Science advances},
volume = {6},
number = {29},
pages = {eaba6404},
doi = {10.1126/sciadv.aba6404},
pmid = {32743069},
issn = {2375-2548},
abstract = {When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.},
}

@article {pmid32722461,
year = {2020},
author = {Del Corvo, M and Bongiorni, S and Stefanon, B and Sgorlon, S and Valentini, A and Ajmone Marsan, P and Chillemi, G},
title = {Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk.},
journal = {Genes},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/genes11080850},
pmid = {32722461},
issn = {2073-4425},
abstract = {Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.},
}

@article {pmid32693300,
year = {2020},
author = {Cao, X and Xu, X and Bian, R and Wang, Y and Yu, H and Xu, Y and Duan, G and Bi, L and Chen, P and Gao, S and Wang, J and Peng, J and Qu, J},
title = {Sedimentary ancient DNA metabarcoding delineates the contrastingly temporal change of lake cyanobacterial communities.},
journal = {Water research},
volume = {183},
number = {},
pages = {116077},
doi = {10.1016/j.watres.2020.116077},
pmid = {32693300},
issn = {1879-2448},
abstract = {Harmful cyanobacterial blooms consisting of toxic taxa can produce a wide variety of toxins to threaten water quality, ecosystem functions and services. Of greater concern was the changing patterns of cyanobacterial assemblage were not well understood due to the lack of long-term monitoring data over the temporal scale. Biodiversity change in cyanobacterial community and paleoenvironmental variables over the past 170 years in Lake Chenghai were investigated based on sedimentary ancient DNA metabarcoding and traditional paleolimnological analysis. The results showed species richness and homogenization of cyanobacterial assemblage increased in the most recent decades, which were synchronized with the growth of artificial fertilization and decline in precipitation. Cyanobacterial co-occurrence network analysis revealed more complex interactions and weak community stability after the change point of ∼1987, while the rare cyanobacterial genera such as Anabaena, Planktothrix, Oscillatoria and Microcystis were identified to be keystone taxa affecting cyanobacterial assemblage. Furthermore, an increase of toxin-producing cyanobacterial taxa was significantly and positively associated with TN and TP, as well as TN/IP and TN/TP, which was verified by quantitative real-time PCR of mcyA and rpoC1 genes. Threshold in total nitrogen (TN) concentration should be targeted no more than 0.60 mg/L to alleviate nuisance cyanobacterial blooms in Lake Chenghai. These findings reinforce the comprehensive understanding for the long-term dynamics of cyanobacterial assemblage responding to environmental change, which could contribute to proactively regulate environmental conditions for avoiding undesirable ecological consequences.},
}

@article {pmid32688244,
year = {2020},
author = {Zhang, M and Fu, Q},
title = {Human evolutionary history in Eastern Eurasia using insights from ancient DNA.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {78-84},
doi = {10.1016/j.gde.2020.06.009},
pmid = {32688244},
issn = {1879-0380},
abstract = {Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.},
}

@article {pmid32684155,
year = {2020},
author = {Duggan, AT and Klunk, J and Porter, AF and Dhody, AN and Hicks, R and Smith, GL and Humphreys, M and McCollum, AM and Davidson, WB and Wilkins, K and Li, Y and Burke, A and Polasky, H and Flanders, L and Poinar, D and Raphenya, AR and Lau, TTY and Alcock, B and McArthur, AG and Golding, GB and Holmes, EC and Poinar, HN},
title = {The origins and genomic diversity of American Civil War Era smallpox vaccine strains.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {175},
doi = {10.1186/s13059-020-02079-z},
pmid = {32684155},
issn = {1474-760X},
support = {430-2018-00662//Social Sciences and Humanities Research Council of Canada/ ; Unknown//Social Sciences and Humanities Research Council of Canada/ ; OGI-170//Ontario Genomics Institute/ ; RGPIN-2015-04477//Natural Sciences and Engineering Research Council of Canada/ ; Unknown//Australian Research Council/ ; Unknown/WT_/Wellcome Trust/United Kingdom ; PJT-156214/CAPMC/CIHR/Canada ; Unknown//Canadian Foundation for Innovation/ ; Unknown//Genome Canada/ ; Unknown//Red Wilson/ ; },
abstract = {Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.},
}

@article {pmid32682389,
year = {2020},
author = {Sheng, G and Hu, J and Tong, H and Llamas, B and Yuan, J and Hou, X and Chen, S and Xiao, B and Lai, X},
title = {Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {88},
doi = {10.1186/s12862-020-01656-x},
pmid = {32682389},
issn = {1471-2148},
support = {41672017//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history.

RESULTS: In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura.

CONCLUSION: Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.},
}

@article {pmid32678112,
year = {2020},
author = {Li, J and Zarzar, TG and White, JD and Indencleef, K and Hoskens, H and Matthews, H and Nauwelaers, N and Zaidi, A and Eller, RJ and Herrick, N and Günther, T and Svensson, EM and Jakobsson, M and Walsh, S and Van Steen, K and Shriver, MD and Claes, P},
title = {Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11850},
doi = {10.1038/s41598-020-68259-w},
pmid = {32678112},
issn = {2045-2322},
abstract = {Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.},
}

@article {pmid32674620,
year = {2020},
author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S},
title = {A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing.},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/03014460.2020.1797164},
pmid = {32674620},
issn = {1464-5033},
abstract = {Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.},
}

@article {pmid32667997,
year = {2020},
author = {Curry, CJ and Davis, BW and Bertola, LD and White, PA and Murphy, WJ and Derr, JN},
title = {Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation Across Africa.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa174},
pmid = {32667997},
issn = {1537-1719},
abstract = {Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE=0.833) to the modern (HE=0.796) populations, while mitochondrial genetic diversity was maintained (Hd = 0.98 for both). While the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified 4 clusters: Southern, Mixed, Eastern, and Western; and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, while mitochondrial structure and diversity were maintained over time.},
}

@article {pmid32666166,
year = {2020},
author = {Hallast, P and Agdzhoyan, A and Balanovsky, O and Xue, Y and Tyler-Smith, C},
title = {A Southeast Asian origin for present-day non-African human Y chromosomes.},
journal = {Human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00439-020-02204-9},
pmid = {32666166},
issn = {1432-1203},
support = {PUT1036//Eesti Teadusagentuur/ ; 098051/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.},
}

@article {pmid32664326,
year = {2020},
author = {Iwasaki, RL and Ishiya, K and Kanzawa-Kiriyama, H and Kawai, Y and Gojobori, J and Satta, Y},
title = {Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population.},
journal = {Genes},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/genes11070775},
pmid = {32664326},
issn = {2073-4425},
abstract = {A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.},
}

@article {pmid32661160,
year = {2020},
author = {Bongers, JL and Nakatsuka, N and O'Shea, C and Harper, TK and Tantaleán, H and Stanish, C and Fehren-Schmitz, L},
title = {Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.2005965117},
pmid = {32661160},
issn = {1091-6490},
abstract = {Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies.},
}

@article {pmid32659643,
year = {2020},
author = {Mendes, M and Alvim, I and Borda, V and Tarazona-Santos, E},
title = {The history behind the mosaic of the Americas.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {72-77},
doi = {10.1016/j.gde.2020.06.007},
pmid = {32659643},
issn = {1879-0380},
abstract = {Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.},
}

@article {pmid32653893,
year = {2020},
author = {Bai, F and Zhang, X and Ji, X and Cao, P and Feng, X and Yang, R and Peng, M and Pei, S and Fu, Q},
title = {Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes.},
journal = {Journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s10038-020-0796-9},
pmid = {32653893},
issn = {1435-232X},
support = {91731303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41925009//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630102//National Natural Science Foundation of China (National Science Foundation of China)/ ; XDB26000000//Chinese Academy of Sciences (CAS)/ ; },
abstract = {The genetic history of Southern East Asians is not well-known, especially prior to the Neolithic period. To address this, we successfully sequenced two complete mitochondrial genomes of 11,000-year-old human individuals from Southern China, thus generating the oldest ancient DNA sequences from this area. Integrating published mitochondrial genomes, we characterized M71d, a new subhaplogroup of haplogroup M71. Our results suggest a possible early migration between Southern China and mainland Southeast Asia by at least 22,000 BP.},
}

@article {pmid32650941,
year = {2020},
author = {Morrison, J and McColl, S and Louhelainen, J and Sheppard, K and May, A and Girdland-Flink, L and Watts, G and Dawnay, N},
title = {Assessing the performance of quantity and quality metrics using the QIAGEN Investigator® Quantiplex® pro RGQ kit.},
journal = {Science & justice : journal of the Forensic Science Society},
volume = {60},
number = {4},
pages = {388-397},
doi = {10.1016/j.scijus.2020.03.002},
pmid = {32650941},
issn = {1876-4452},
abstract = {The Quantiplex® Pro RGQ kit quantifies DNA in a sample, supports the detection of mixtures and assesses the extent of DNA degradation based on relative ratios of amplified autosomal and male markers. Data show no significant difference in the accuracy and sensitivity of quantification between this and the Promega PowerQuant® System, both detecting the lowest amount of DNA tested, 4 pg. Laboratory controlled mixed male:female DNA samples together with mock sexual assault samples were quantified across a range of mixture ratios. Analysis software detected mixed DNA samples across all ratios for both quantification kits. Subsequent STR analysis using the Investigator® 24Plex QS Kit was able to corroborate mixture detection down to 1:25 male:female DNA ratios, past which point mixtures appeared identical to single-source female samples. Analysis software also detected laboratory degraded DNA samples, with data showing a positive trend between the Degradation Index (DI) and length of time of sonication. When used on ancient remains the assay was able to triage samples for further analysis, and STR profiles were concordant with DNA quantification results in all instances. STR analyses of laboratory-controlled sensitivity, mixture, and degradation studies supports the quality metric obtained from quantification. These data support the use of the Quantiplex® Pro RGQ kit for sample screening and quantification in forensic casework and ancient DNA studies.},
}

@article {pmid32648350,
year = {2020},
author = {Peyrégne, S and Prüfer, K},
title = {Present-Day DNA Contamination in Ancient DNA Datasets.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2000081},
doi = {10.1002/bies.202000081},
pmid = {32648350},
issn = {1521-1878},
support = {//Max-Planck-Gesellschaft/ ; 694707/ERC_/European Research Council/International ; },
abstract = {Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.},
}

@article {pmid32647890,
year = {2020},
author = {Giuliani, C and Franceschi, C and Luiselli, D and Garagnani, P and Ulijaszek, S},
title = {Ecological Sensing Through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmaa078},
pmid = {32647890},
issn = {2156-5376},
abstract = {Ecological sensing and inflammation have evolved to ensure optima between organism survival and reproductive success in different and changing environments. At the molecular level, ecological sensing consists of many types of receptors located in different tissues that orchestrate integrated responses (immune, neuroendocrine systems) to external and internal stimuli. This review describes emerging data on taste and chemosensory receptors, proposing them as broad ecological sensors and providing evidence that taste perception is shaped not only according to sense epitopes from nutrients but also in response to highly diverse external and internal stimuli. We apply a biological anthropological approach to examine how ecological sensing has been shaped by these stimuli through human evolution for complex interkingdom communication between a host and pathological and symbiotic bacteria, focusing on population-specific genetic diversity. We then focus on how these sensory receptors play a major role in inflammatory processes that form the basis of many modern common metabolic diseases such as obesity, type 2 diabetes, and aging. The impacts of human niche construction and cultural evolution in shaping environments are described with emphasis on consequent biological responsiveness.},
}

@article {pmid32642779,
year = {2020},
author = {Santiago, E and Novo, I and Pardiñas, AF and Saura, M and Wang, J and Caballero, A},
title = {Recent demographic history inferred by high-resolution analysis of linkage disequilibrium.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa169},
pmid = {32642779},
issn = {1537-1719},
abstract = {Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than 10 individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudo-haploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.},
}

@article {pmid32554575,
year = {2020},
author = {Curry, A},
title = {Incest in ancient Ireland suggests an elite ruled early farmers.},
journal = {Science (New York, N.Y.)},
volume = {368},
number = {6497},
pages = {1299},
doi = {10.1126/science.368.6497.1299},
pmid = {32554575},
issn = {1095-9203},
mesh = {Archaeology ; DNA, Ancient ; Farmers/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Middle Aged ; },
}

Archaeology
DNA, Ancient
Farmers/*history
History, Ancient
Humans
Incest/*history
Ireland
Middle Aged

@article {pmid32632332,
year = {2020},
author = {Betti, L and Beyer, RM and Jones, ER and Eriksson, A and Tassi, F and Siska, V and Leonardi, M and Maisano Delser, P and Bentley, LK and Nigst, PR and Stock, JT and Pinhasi, R and Manica, A},
title = {Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41562-020-0897-7},
pmid = {32632332},
issn = {2397-3374},
support = {649307//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups.},
}

@article {pmid32621020,
year = {2020},
author = {Navarro-Romero, MT and Muñoz, ML and Alcala-Castañeda, E and Terreros-Espinosa, E and Domínguez-de-la-Cruz, E and García-Hernández, N and Moreno-Galeana, MÁ},
title = {A novel method of male sex identification of human ancient skeletal remains.},
journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10577-020-09634-1},
pmid = {32621020},
issn = {1573-6849},
support = {Scholarship-380118//Consejo Nacional de Ciencia y Tecnología/ ; Scholarship-2016-290936//Consejo Nacional de Ciencia y Tecnología/ ; Scholarship-177559//Consejo Nacional de Ciencia y Tecnología/ ; FIS/IMSS/PROT/PRIO/17/063, 2017-785-071//Instituto Mexicano del Seguro Social/ ; },
abstract = {Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.},
}

@article {pmid32619963,
year = {2020},
author = {Traversari, M and Da Via, S and Petrella, E and Feeney, RNM and Benazzi, S},
title = {A case of dwarfism in 6th century Italy: Bioarchaeological assessment of a hereditary disorder.},
journal = {International journal of paleopathology},
volume = {30},
number = {},
pages = {110-117},
doi = {10.1016/j.ijpp.2020.03.003},
pmid = {32619963},
issn = {1879-9825},
abstract = {OBJECTIVE: The skeletal remains of a short-statured individual (T17) are described and a differential diagnosis performed to determine the etiology of the condition.

MATERIALS: An individual considered pathologically short in stature was discovered in the burial site of Piazza XX Settembre, Modena (northern Italy).

METHODS: Morphological and morphometric analyses were performed, and T17 was compared to dwarfs from other localities and periods and to the adult female population from the same site. A paleopathological survey was undertaken to assess the degree of the skeletal elements of T17 were affected.

RESULTS: T17 was a female, 20-30 years of age at death, with a stature of 128 cm and disproportionate dwarfism associated with congenital skeletal dysplasia.

CONCLUSIONS: T17 likely affected by a form of hypochondroplasia.

SIGNIFICANCE: Anatomical consequences of hypochondroplasia are presented, and the timeframe and associated burial goods suggest a 6th-century Lombard short stature belonging to one of the earliest Lombard settlements in Italy.

Future genetic analysis would resolve if the mutation in the type 3 fibroblast growth factor receptor (FGFR3) is present in the remains of T17; however, it is not exclusivly linked to hypochondroplasia.},
}

@article {pmid32610222,
year = {2020},
author = {Olalde, I and Posth, C},
title = {Latest trends in archaeogenetic research of west Eurasians.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {36-43},
doi = {10.1016/j.gde.2020.05.021},
pmid = {32610222},
issn = {1879-0380},
abstract = {During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.},
}

@article {pmid32603999,
year = {2020},
author = {Barquera, R and Krause, J},
title = {An ancient view on host pathogen interaction across time and space.},
journal = {Current opinion in immunology},
volume = {65},
number = {},
pages = {65-69},
doi = {10.1016/j.coi.2020.05.004},
pmid = {32603999},
issn = {1879-0372},
abstract = {The ancient DNA revolution provided diverse fields with an unprecedented opportunity to look back into the past and shed light on research aspects that were until now subject to speculation and inference from modern data. In particular enrichment methods that allow the targeted retrieval of millions of SNP positions from ancient human genomes, or even complete bacterial and viral genomes have the potential to revolutionize our understanding of host pathogen interactions. Ancient DNA combined with new bioinformatic tools now even allows actual allele calling for immunogenetic systems such as Human Leukocyte Antigen (HLA) across time and space. The coming years will provide us with frequency data of human immunity genes, such as HLA, as well as genome wide data of ancient pathogens from many time periods of human history, and will therefore provide us with a dynamic view on historical human adaptation to pathogen exposure on a population wide scale.},
}

@article {pmid32598277,
year = {2020},
author = {Arning, N and Wilson, DJ},
title = {The past, present and future of ancient bacterial DNA.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000384},
pmid = {32598277},
issn = {2057-5858},
abstract = {Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.},
}

@article {pmid32582847,
year = {2020},
author = {Wang, K and Goldstein, S and Bleasdale, M and Clist, B and Bostoen, K and Bakwa-Lufu, P and Buck, LT and Crowther, A and Dème, A and McIntosh, RJ and Mercader, J and Ogola, C and Power, RC and Sawchuk, E and Robertshaw, P and Wilmsen, EN and Petraglia, M and Ndiema, E and Manthi, FK and Krause, J and Roberts, P and Boivin, N and Schiffels, S},
title = {Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa.},
journal = {Science advances},
volume = {6},
number = {24},
pages = {eaaz0183},
pmid = {32582847},
issn = {2375-2548},
abstract = {Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.},
}

@article {pmid32586278,
year = {2020},
author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA},
title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {432},
doi = {10.1186/s12864-020-06820-7},
pmid = {32586278},
issn = {1471-2164},
support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; },
abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.

RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.

CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.},
}

@article {pmid32584871,
year = {2020},
author = {Kontopoulos, I and Penkman, K and Mullin, VE and Winkelbach, L and Unterländer, M and Scheu, A and Kreutzer, S and Hansen, HB and Margaryan, A and Teasdale, MD and Gehlen, B and Street, M and Lynnerup, N and Liritzis, I and Sampson, A and Papageorgopoulou, C and Allentoft, ME and Burger, J and Bradley, DG and Collins, MJ},
title = {Screening archaeological bone for palaeogenetic and palaeoproteomic studies.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0235146},
doi = {10.1371/journal.pone.0235146},
pmid = {32584871},
issn = {1932-6203},
abstract = {The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.},
}

@article {pmid32574964,
year = {2020},
author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L},
title = {Harnessing epigenetics to study human evolution.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {23-29},
doi = {10.1016/j.gde.2020.05.023},
pmid = {32574964},
issn = {1879-0380},
abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.},
}

@article {pmid32573438,
year = {2020},
author = {Adrion, JR and Cole, CB and Dukler, N and Galloway, JG and Gladstein, AL and Gower, G and Kyriazis, CC and Ragsdale, AP and Tsambos, G and Baumdicker, F and Carlson, J and Cartwright, RA and Durvasula, A and Gronau, I and Kim, BY and McKenzie, P and Messer, PW and Noskova, E and Ortega Del Vecchyo, D and Racimo, F and Struck, TJ and Gravel, S and Gutenkunst, RN and Lohmueller, KE and Ralph, PL and Schrider, DR and Siepel, A and Kelleher, J and Kern, AD},
title = {A community-maintained standard library of population genetic models.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.54967},
pmid = {32573438},
issn = {2050-084X},
support = {R35GM119856/GM/NIGMS NIH HHS/United States ; R01GM117241/GM/NIGMS NIH HHS/United States ; R01GM127348/GM/NIGMS NIH HHS/United States ; R00HG008696/GM/NIGMS NIH HHS/United States ; R35GM127070/GM/NIGMS NIH HHS/United States ; R01HG010346/HG/NHGRI NIH HHS/United States ; 00025300//Villum Fonden/ ; },
abstract = {The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Re-cent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.},
}

@article {pmid32572090,
year = {2020},
author = {Debortoli, G and Abbatangelo, C and Ceballos, F and Fortes-Lima, C and Norton, HL and Ozarkar, S and Parra, EJ and Jonnalagadda, M},
title = {Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {10075},
doi = {10.1038/s41598-020-66953-3},
pmid = {32572090},
issn = {2045-2322},
abstract = {The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.},
}

@article {pmid32563853,
year = {2020},
author = {Vicente, M and Schlebusch, CM},
title = {African population history: an ancient DNA perspective.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {8-15},
doi = {10.1016/j.gde.2020.05.008},
pmid = {32563853},
issn = {1879-0380},
abstract = {The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.},
}

@article {pmid32557548,
year = {2020},
author = {Goude, G and Salazar-García, DC and Power, RC and Rivollat, M and Gourichon, L and Deguilloux, MF and Pemonge, MH and Bouby, L and Binder, D},
title = {New insights on Neolithic food and mobility patterns in Mediterranean coastal populations.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24089},
pmid = {32557548},
issn = {1096-8644},
support = {//ETICALP programme/ ; //Institut Danone France/Fondation pour la Recherche Médicale/ ; ANR-17-FRAL-0010//project INTERACT/ ; },
abstract = {OBJECTIVES: The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE.

MATERIALS AND METHODS: The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30).

RESULTS: Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel 87 Sr/86 Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization.

DISCUSSION: Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.},
}

@article {pmid32545993,
year = {2020},
author = {Vera-Villalobos, H and Pérez, V and Contreras, F and Alcayaga, V and Avalos, V and Riquelme, C and Silva-Aciares, F},
title = {Characterization and removal of biofouling from reverse osmosis membranes (ROMs) from a desalination plant in Northern Chile, using Alteromonas sp. Ni1-LEM supernatant.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/08927014.2020.1776268},
pmid = {32545993},
issn = {1029-2454},
abstract = {Biofouling control in reverse osmosis membranes (ROMs) is challenging due to the high cost of treatments, and reduction in the life of ROMs. This study characterizes the biofouling in the ROMs from a desalination plant and reports its effective removal using the supernatant obtained from Alteromonas sp. strain Ni1-LEM. The characterization of the bacterial community revealed that the most abundant taxa in ROMs were the genera Fulvivirga and Pseudoalteromonas, and unclassified species of the families Flavobacteriaceae and Sphingomonadaceae. This bacterial community significantly decreased upon treatment with the supernatant from Alteromonas sp. Ni1-LEM, resulting in the prevalence of the genus Pseudoalteromonas. Furthermore, this bacterial supernatant significantly inhibited cell adhesion of seven benthic microalgae isolated from ROMs as well as promoting cell detachment of the existing microbial biofilms. The study showed that the extracellular supernatant modified the conformation of extracellular polymeric substances (EPS) in the biofouling of ROMs without any biocidal effects.},
}

@article {pmid32539695,
year = {2020},
author = {Philips, A and Stolarek, I and Handschuh, L and Nowis, K and Juras, A and Trzciński, D and Nowaczewska, W and Wrzesińska, A and Potempa, J and Figlerowicz, M},
title = {Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {402},
pmid = {32539695},
issn = {1471-2164},
support = {2014/12/W/NZ2/00466//Narodowe Centrum Nauki/ ; 2016/21/B/NZ1/00292//Narodowe Centrum Nauki/ ; R21DE026280/DE/NIDCR NIH HHS/United States ; },
abstract = {BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death.

RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria.

CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.},
}

@article {pmid32523989,
year = {2020},
author = {Rivollat, M and Jeong, C and Schiffels, S and Küçükkalıpçı, İ and Pemonge, MH and Rohrlach, AB and Alt, KW and Binder, D and Friederich, S and Ghesquière, E and Gronenborn, D and Laporte, L and Lefranc, P and Meller, H and Réveillas, H and Rosenstock, E and Rottier, S and Scarre, C and Soler, L and Wahl, J and Krause, J and Deguilloux, MF and Haak, W},
title = {Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.},
journal = {Science advances},
volume = {6},
number = {22},
pages = {eaaz5344},
pmid = {32523989},
issn = {2375-2548},
abstract = {Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.},
}

@article {pmid32511234,
year = {2020},
author = {Segurel, L and Guarino-Vignon, P and Marchi, N and Lafosse, S and Laurent, R and Bon, C and Fabre, A and Hegay, T and Heyer, E},
title = {Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA.},
journal = {PLoS biology},
volume = {18},
number = {6},
pages = {e3000742},
pmid = {32511234},
issn = {1545-7885},
abstract = {The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?},
}

@article {pmid32497501,
year = {2020},
author = {Díez-Del-Molino, D and Dalén, L},
title = {Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials.},
journal = {Cell},
volume = {181},
number = {6},
pages = {1200-1201},
doi = {10.1016/j.cell.2020.05.031},
pmid = {32497501},
issn = {1097-4172},
abstract = {The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments.},
}

@article {pmid32497286,
year = {2020},
author = {Coutinho, A and Günther, T and Munters, AR and Svensson, EM and Götherström, A and Storå, J and Malmström, H and Jakobsson, M},
title = {The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24079},
pmid = {32497286},
issn = {1096-8644},
support = {//Knut och Alice Wallenbergs Stiftelse/ ; M13-0904:1//Riksbankens Jubileumsfond/ ; 2013-1905//Vetenskapsrådet/ ; 2017-02503//Vetenskapsrådet/ ; 2017-05267//Vetenskapsrådet/ ; },
abstract = {OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.

METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.

RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.

CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.},
}

@article {pmid32497204,
year = {2020},
author = {Buckley, M and Harvey, VL and Orihuela, J and Mychajliw, AM and Keating, J and Milan, JNA and Lawless, C and Chamberlain, AT and Egerton, VM and Manning, PL},
title = {Collagen sequence analysis reveals evolutionary history of extinct West Indies Nesophontes ('island-shrews').},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa137},
pmid = {32497204},
issn = {1537-1719},
abstract = {Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to provide species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba towards Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to the Cuban species, N. major rather than N. micrus as previously speculated. Our proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.},
}

@article {pmid32492404,
year = {2020},
author = {Anava, S and Neuhof, M and Gingold, H and Sagy, O and Munters, A and Svensson, EM and Afshinnekoo, E and Danko, D and Foox, J and Shor, P and Riestra, B and Huchon, D and Mason, CE and Mizrahi, N and Jakobsson, M and Rechavi, O},
title = {Illuminating Genetic Mysteries of the Dead Sea Scrolls.},
journal = {Cell},
volume = {181},
number = {6},
pages = {1218-1231.e27},
doi = {10.1016/j.cell.2020.04.046},
pmid = {32492404},
issn = {1097-4172},
abstract = {The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.},
}

@article {pmid32488006,
year = {2020},
author = {Seersholm, FV and Werndly, DJ and Grealy, A and Johnson, T and Keenan Early, EM and Lundelius, EL and Winsborough, B and Farr, GE and Toomey, R and Hansen, AJ and Shapiro, B and Waters, MR and McDonald, G and Linderholm, A and Stafford, TW and Bunce, M},
title = {Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2770},
pmid = {32488006},
issn = {2041-1723},
abstract = {Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.},
}

@article {pmid32483316,
year = {2020},
author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E},
title = {Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8901},
pmid = {32483316},
issn = {2045-2322},
abstract = {Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.},
}

@article {pmid32475052,
year = {2020},
author = {Barquera, R and Collen, E and Di, D and Buhler, S and Teixeira, J and Llamas, B and Nunes, JM and Sanchez-Mazas, A},
title = {Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide.},
journal = {HLA},
volume = {},
number = {},
pages = {},
pmid = {32475052},
issn = {2059-2310},
support = {//Australian Government Research Training Program Stipend (RTPS)/ ; IN180100017//Australian Research Council Discovery Indigenous Project/ ; FT170100448//Australian Research Council Future Fellowship/ ; BM0803//European Cooperation in Science and Technology/ ; //Max-Planck-Gesellschaft/ ; 310030_188820//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 31003A_144180//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {We report detailed peptide-binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide-binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.},
}

@article {pmid32470401,
year = {2020},
author = {Skourtanioti, E and Erdal, YS and Frangipane, M and Balossi Restelli, F and Yener, KA and Pinnock, F and Matthiae, P and Özbal, R and Schoop, UD and Guliyev, F and Akhundov, T and Lyonnet, B and Hammer, EL and Nugent, SE and Burri, M and Neumann, GU and Penske, S and Ingman, T and Akar, M and Shafiq, R and Palumbi, G and Eisenmann, S and D'Andrea, M and Rohrlach, AB and Warinner, C and Jeong, C and Stockhammer, PW and Haak, W and Krause, J},
title = {Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.},
journal = {Cell},
volume = {181},
number = {5},
pages = {1158-1175.e28},
doi = {10.1016/j.cell.2020.04.044},
pmid = {32470401},
issn = {1097-4172},
abstract = {Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.},
}

@article {pmid32470400,
year = {2020},
author = {Agranat-Tamir, L and Waldman, S and Martin, MAS and Gokhman, D and Mishol, N and Eshel, T and Cheronet, O and Rohland, N and Mallick, S and Adamski, N and Lawson, AM and Mah, M and Michel, M and Oppenheimer, J and Stewardson, K and Candilio, F and Keating, D and Gamarra, B and Tzur, S and Novak, M and Kalisher, R and Bechar, S and Eshed, V and Kennett, DJ and Faerman, M and Yahalom-Mack, N and Monge, JM and Govrin, Y and Erel, Y and Yakir, B and Pinhasi, R and Carmi, S and Finkelstein, I and Carmel, L and Reich, D},
title = {The Genomic History of the Bronze Age Southern Levant.},
journal = {Cell},
volume = {181},
number = {5},
pages = {1146-1157.e11},
doi = {10.1016/j.cell.2020.04.024},
pmid = {32470400},
issn = {1097-4172},
abstract = {We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.},
}

@article {pmid32446165,
year = {2020},
author = {Gonzalez, A and Cannet, C and Zvénigorosky, V and Geraut, A and Koch, G and Delabarde, T and Ludes, B and Raul, JS and Keyser, C},
title = {The petrous bone: Ideal substrate in legal medicine?.},
journal = {Forensic science international. Genetics},
volume = {47},
number = {},
pages = {102305},
doi = {10.1016/j.fsigen.2020.102305},
pmid = {32446165},
issn = {1878-0326},
abstract = {Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.},
}

@article {pmid32430331,
year = {2020},
author = {Gryseels, S and Watts, TD and Kabongo Mpolesha, JM and Larsen, BB and Lemey, P and Muyembe-Tamfum, JJ and Teuwen, DE and Worobey, M},
title = {A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {22},
pages = {12222-12229},
pmid = {32430331},
issn = {1091-6490},
abstract = {With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 ("DRC66")-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.},
}

@article {pmid32428013,
year = {2020},
author = {Aoki, K},
title = {A three-population wave-of-advance model for the European early Neolithic.},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0233184},
pmid = {32428013},
issn = {1932-6203},
abstract = {Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates.},
}

@article {pmid32421727,
year = {2020},
author = {Peña-Ahumada, B and Saldarriaga-Córdoba, M and Kardailsky, O and Moncada, X and Moraga, M and Matisoo-Smith, E and Seelenfreund, D and Seelenfreund, A},
title = {A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania.},
journal = {PloS one},
volume = {15},
number = {5},
pages = {e0233113},
pmid = {32421727},
issn = {1932-6203},
abstract = {Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.},
}

@article {pmid32411968,
year = {2019},
author = {Amankwaa, AO and Nsiah Amoako, E and Mensah Bonsu, DO and Banyeh, M},
title = {Forensic science in Ghana: A review.},
journal = {Forensic Science International (Online)},
volume = {1},
number = {},
pages = {151-160},
pmid = {32411968},
issn = {2589-871X},
abstract = {The use of forensic science continues to grow across the world. In Ghana, major advancements took off in 2011, including the introduction of modern DNA profiling and the establishment of an automated fingerprint identification system. These developments have led to some positive impacts on the delivery of justice, including the exoneration of a wrongly incarcerated individual. However, a review of the policy-related aspects of forensic science shows gaps in legislation, governance, service provision, quality assurance and accreditation, education and research. An important recommendation to improve forensic science in Ghana is the creation of a "national policy strategy", a blueprint informed by relevant stakeholders, best practice from other countries and the status of the field. Resolutions to the policy issues identified in this review will ensure a more robust application of forensic science in delivering safe justice and enhancing public security.},
}

@article {pmid32409524,
year = {2020},
author = {Yang, MA and Fan, X and Sun, B and Chen, C and Lang, J and Ko, YC and Tsang, CH and Chiu, H and Wang, T and Bao, Q and Wu, X and Hajdinjak, M and Ko, AM and Ding, M and Cao, P and Yang, R and Liu, F and Nickel, B and Dai, Q and Feng, X and Zhang, L and Sun, C and Ning, C and Zeng, W and Zhao, Y and Zhang, M and Gao, X and Cui, Y and Reich, D and Stoneking, M and Fu, Q},
title = {Ancient DNA indicates human population shifts and admixture in northern and southern China.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1126/science.aba0909},
pmid = {32409524},
issn = {1095-9203},
abstract = {Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome wide data from 26 ancient individuals from northern and southern East Asia spanning 9,500-300 years ago. Genetic differentiation was higher in the past than the present, reflecting a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient samples with Austronesian-related ancestry, supporting a southern China origin for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.},
}

@article {pmid32406954,
year = {2020},
author = {Li, J and Cai, D and Zhang, Y and Zhu, H and Zhou, H},
title = {Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24076},
pmid = {32406954},
issn = {1096-8644},
support = {2019M661226//China Postdoctoral Science Foundation/ ; 17ZDA221//The Major Projects of the National Social Science Foundation of China/ ; },
abstract = {OBJECTIVES: Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations.

MATERIALS AND METHODS: Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP).

RESULTS: After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut.

DISCUSSION: Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau.},
}

@article {pmid32405770,
year = {2020},
author = {Samida, S},
title = {[About Media Presence and Prominence of DNA-Supported Research of the Past].},
journal = {NTM},
volume = {28},
number = {2},
pages = {181-192},
doi = {10.1007/s00048-020-00249-5},
pmid = {32405770},
issn = {1420-9144},
abstract = {In recent years molecular genetics has provided a completely new approach/access to the human past. The still new and quite dynamic research field of archaeogenetics (also known as palaeogenetics or genetic history) claims to be able to write history using ancient DNA. Through numerous remarkable publications it has generated and received much interest not only in scientific discourse but also in the media. So far, however, scientists have not paid much attention to this coverage-a research desideratum this paper cannot resolve. But by looking at selected press clippings it seeks to capture first trends according to the following three theses: telling success stories, drawing boundaries, and writing in a conformist manner.},
}