@article {pmid33857143,
year = {2021},
author = {Lanman, RB and Hylkema, L and Boone, CM and Allée, B and Castillo, RO and Moreno, SA and Flores, MF and DeSilva, U and Bingham, B and Kemp, BM},
title = {Ancient DNA analysis of archaeological specimens extends Chinook salmon's known historic range to San Francisco Bay's tributaries and southernmost watershed.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0244470},
doi = {10.1371/journal.pone.0244470},
pmid = {33857143},
issn = {1932-6203},
abstract = {Understanding a species' historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781-1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay's southernmost tributary watershed.},
}

@article {pmid33855818,
year = {2021},
author = {Zhang, M and Cao, P and Dai, Q and Wang, Y and Feng, X and Wang, H and Wu, H and Ko, AM and Mao, X and Liu, Y and Yu, L and Roos, C and Nadler, T and Xiao, W and Bennett, EA and Fu, Q},
title = {Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples.},
journal = {Zoological research},
volume = {42},
number = {3},
pages = {280-286},
doi = {10.24272/j.issn.2095-8137.2020.377},
pmid = {33855818},
issn = {2095-8137},
abstract = {DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.},
}

@article {pmid33844838,
year = {2021},
author = {Cascardo, P and Pucu, E and Leles, D},
title = {REVIEW OF PARASITES FOUND IN EXTINCT ANIMALS: WHAT CAN BE REVEALED.},
journal = {The Journal of parasitology},
volume = {107},
number = {2},
pages = {275-283},
doi = {10.1645/20-30},
pmid = {33844838},
issn = {1937-2345},
abstract = {Parasitism is inherent to life and observed in all species. Extinct animals have been studied to understand what they looked like, where and how they lived, what they fed on, and the reasons they became extinct. Paleoparasitology helps to clarify these questions based on the study of the parasites and microorganisms that infected those animals, using as a source material coprolites, fossils in rock, tissue, bone, mummy, and amber, analyses of ancient DNA, immunodiagnosis, and microscopy.},
}

@article {pmid33834210,
year = {2021},
author = {Oliva, A and Tobler, R and Cooper, A and Llamas, B and Souilmi, Y},
title = {Systematic benchmark of ancient DNA read mapping.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbab076},
pmid = {33834210},
issn = {1477-4054},
abstract = {The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA 'reads') against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30-80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software-BWA-aln, BWA-mem, NovoAlign and Bowtie2-and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.},
}

@article {pmid33833423,
year = {2021},
author = {Taylor, WTT and Pruvost, M and Posth, C and Rendu, W and Krajcarz, MT and Abdykanova, A and Brancaleoni, G and Spengler, R and Hermes, T and Schiavinato, S and Hodgins, G and Stahl, R and Min, J and Alisher Kyzy, S and Fedorowicz, S and Orlando, L and Douka, K and Krivoshapkin, A and Jeong, C and Warinner, C and Shnaider, S},
title = {Evidence for early dispersal of domestic sheep into Central Asia.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {33833423},
issn = {2397-3374},
support = {#19-78-10053//Russian Science Foundation (RSF)/ ; },
abstract = {The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.},
}

@article {pmid33831350,
year = {2021},
author = {Psonis, N and Vassou, D and Kafetzopoulos, D},
title = {Testing a series of modifications on genomic library preparation methods for ancient or degraded DNA.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {114193},
doi = {10.1016/j.ab.2021.114193},
pmid = {33831350},
issn = {1096-0309},
abstract = {Technological advancements have revolutionized ancient and degraded DNA analysis, moving the field to the Next Generation Sequencing era. One of the advancements, the ancient DNA-oriented high-throughput library preparation methods, enabled the sequencing of more endogenous molecules. Although fairly optimized, both single- and double-stranded library preparation methods hold the potential for further improvement. Here, we test a series of modifications made at different steps of both single- and double-stranded library preparation methods. Given all the modifications tested, we found that two of them provide further benefits, including the use of Endonuclease VIII as a pre-treatment step before preparing single-stranded libraries and the use of a modified second adapter of the single stranded-libraries as an alternative option to enable sequencing of single stranded-libraries with the standard Illumina sequencing primer instead of the custom designed as described in the single stranded library preparation method. Furthermore, we propose uracil-DNA-glycosylase (UDG) could also be considered for both single- and double-stranded library preparation methods, although additional parameters should be taken into account depending on the sequencing strategy and the sample characteristics. Further modifications were also tested and although they were not advantageous, they could be considered as equivalent to the published options.},
}

@article {pmid33821116,
year = {2021},
author = {Bendrey, R and Martin, D},
title = {Zoonotic diseases: New directions in human-animal pathology.},
journal = {International journal of osteoarchaeology},
volume = {},
number = {},
pages = {},
pmid = {33821116},
issn = {1047-482X},
abstract = {Zoonotic diseases-human diseases of animal origin-represent one of the world's greatest health challenges, both today and in the past. Since the Neolithic, zoonotic diseases have been one of the major factors shaping and influencing human adaptation. Archaeology is ideally situated to provide the long view on human-animal-pathogen relationships through combining cultural, environmental and biological datasets, yet long-term studies of linked human and animal records have often been overlooked and undertheorized. The seven papers in this special issue "Zoonotic diseases: New directions in human-animal pathology" cover a range of diseases caused by bacterial, viral, and parasitic pathogens, from case studies drawn from across Europe, Asia, Africa and the Americas. They speak to the diversity of human-animal-environment interactions that shaped disease emergence and transmission. They also review methodological advancements relating to disease identification and interpretation and discuss interdisciplinary approaches to effectively investigate these complex processes in the past. This introduction highlights their key themes and outcomes and identifies research priorities moving forward.},
}

@article {pmid33814550,
year = {2021},
author = {Geigl, EM},
title = {[Discussion about the presentation: "PCR and paleogenetics: for best and for worst"].},
journal = {Bulletin de l'Academie nationale de medecine},
volume = {205},
number = {4},
pages = {420-421},
doi = {10.1016/j.banm.2021.02.009},
pmid = {33814550},
issn = {0001-4079},
}

@article {pmid33811235,
year = {2021},
author = {Farrer, AG and Wright, SL and Skelly, E and Eisenhofer, R and Dobney, K and Weyrich, LS},
title = {Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7456},
pmid = {33811235},
issn = {2045-2322},
support = {DE150101574//Australian Research Council Discovery/ ; },
abstract = {Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.},
}

@article {pmid33809280,
year = {2021},
author = {Kusliy, MA and Vorobieva, NV and Tishkin, AA and Makunin, AI and Druzhkova, AS and Trifonov, VA and Iderkhangai, TO and Graphodatsky, AS},
title = {Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33809280},
issn = {2073-4425},
support = {19-59-15001//Russian Foundation for Basic Research/ ; 20-04-00213//Russian Foundation for Basic Research/ ; },
abstract = {The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.},
}

@article {pmid33807307,
year = {2021},
author = {Talas, L and Stivrins, N and Veski, S and Tedersoo, L and Kisand, V},
title = {Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia).},
journal = {Microorganisms},
volume = {9},
number = {4},
pages = {},
doi = {10.3390/microorganisms9040719},
pmid = {33807307},
issn = {2076-2607},
support = {PUT1389//Eesti Teadusagentuur/ ; },
abstract = {Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2-4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change.},
}

@article {pmid33801556,
year = {2021},
author = {Lindo, J and DeGiorgio, M},
title = {Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33801556},
issn = {2073-4425},
abstract = {The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.},
}

@article {pmid33790303,
year = {2021},
author = {Aznar-Cormano, L and Bonnald, J and Krief, S and Guma, N and Debruyne, R},
title = {Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7227},
pmid = {33790303},
issn = {2045-2322},
abstract = {It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.},
}

@article {pmid33787889,
year = {2021},
author = {Yair, S and Lee, KM and Coop, G},
title = {The timing of human adaptation from Neanderthal introgression.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyab052},
pmid = {33787889},
issn = {1943-2631},
abstract = {Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of Neanderthal adaptive introgression. From these, we identify cases in which Neanderthal introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.},
}

@article {pmid33781248,
year = {2021},
author = {Tagore, D and Aghakhanian, F and Naidu, R and Phipps, ME and Basu, A},
title = {Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {61},
pmid = {33781248},
issn = {1741-7007},
abstract = {BACKGROUND: The demographic history of South and Southeast Asia (S&SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&SEA at different time periods, to infer about the demographic history of this region.

RESULTS: We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between "language and genetics" or "geography and genetics" can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period.

CONCLUSION: Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&SEA. We postulate that pre-Neolithic ancestors of today's AAs were widespread in S&SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups.},
}

@article {pmid33777521,
year = {2021},
author = {Fellows Yates, JA and Lamnidis, TC and Borry, M and Andrades Valtueña, A and Fagernäs, Z and Clayton, S and Garcia, MU and Neukamm, J and Peltzer, A},
title = {Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10947},
pmid = {33777521},
issn = {2167-8359},
abstract = {The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.},
}

@article {pmid33772284,
year = {2021},
author = {Harney, É and Patterson, N and Reich, D and Wakeley, J},
title = {Assessing the performance of qpAdm: a statistical tool for studying population admixture.},
journal = {Genetics},
volume = {217},
number = {4},
pages = {},
doi = {10.1093/genetics/iyaa045},
pmid = {33772284},
issn = {1943-2631},
abstract = {qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.},
}

@article {pmid33768239,
year = {2021},
author = {Kapp, JD and Green, RE and Shapiro, B},
title = {A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esab012},
pmid = {33768239},
issn = {1465-7333},
abstract = {We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina's P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare five ancient DNA extracts into sequencing libraries using the SCR and two of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and temporally broader sample of preserved remains for genomic analysis.},
}

@article {pmid33767248,
year = {2021},
author = {Modi, A and Vergata, C and Zilli, C and Vischioni, C and Vai, S and Tagliazucchi, GM and Lari, M and Caramelli, D and Taccioli, C},
title = {Successful extraction of insect DNA from recent copal inclusions: limits and perspectives.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6851},
pmid = {33767248},
issn = {2045-2322},
abstract = {Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.},
}

@article {pmid33753899,
year = {2021},
author = {Teixeira, JC and Jacobs, GS and Stringer, C and Tuke, J and Hudjashov, G and Purnomo, GA and Sudoyo, H and Cox, MP and Tobler, R and Turney, CSM and Cooper, A and Helgen, KM},
title = {Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {33753899},
issn = {2397-334X},
abstract = {The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.},
}

@article {pmid33734062,
year = {2021},
author = {Waglechner, N and Culp, EJ and Wright, GD},
title = {Ancient Antibiotics, Ancient Resistance.},
journal = {EcoSal Plus},
volume = {9},
number = {2},
pages = {},
doi = {10.1128/ecosalplus.ESP-0027-2020},
pmid = {33734062},
issn = {2324-6200},
abstract = {As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.},
}

@article {pmid33726563,
year = {2021},
author = {Oswald, JA and Terrill, RS and Stucky, BJ and LeFebvre, MJ and Steadman, DW and Guralnick, RP and Allen, JM},
title = {Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World.},
journal = {Biology letters},
volume = {17},
number = {3},
pages = {20200760},
doi = {10.1098/rsbl.2020.0760},
pmid = {33726563},
issn = {1744-957X},
abstract = {Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.},
}

@article {pmid33724183,
year = {2021},
author = {Diaz-Maroto, P and Rey-Iglesia, A and Cartajena, I and Núñez, L and Westbury, MV and Varas, V and Moraga, M and Campos, PF and Orozco-terWengel, P and Marin, JC and Hansen, AJ},
title = {Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33724183},
issn = {2050-084X},
support = {1070040//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; 1020316//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; 1130917//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1140785//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
abstract = {The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.},
}

@article {pmid33723011,
year = {2021},
author = {Crump, SE and Fréchette, B and Power, M and Cutler, S and de Wet, G and Raynolds, MK and Raberg, JH and Briner, JP and Thomas, EK and Sepúlveda, J and Shapiro, B and Bunce, M and Miller, GH},
title = {Ancient plant DNA reveals High Arctic greening during the Last Interglacial.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {13},
pages = {},
pmid = {33723011},
issn = {1091-6490},
abstract = {Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.},
}

@article {pmid33721099,
year = {2021},
author = {Oliver-Guimerá, A and Hejtmánková, A and Jackson, K and Pesavento, PA},
title = {A polyomavirus detected in American black bear (Ursus americanus).},
journal = {Archives of virology},
volume = {166},
number = {5},
pages = {1521-1524},
pmid = {33721099},
issn = {1432-8798},
abstract = {Polyomaviruses are ancient DNA viruses that infect several species of animals. While recognition of the family Polyomaviridae has grown rapidly, there are few studies that consider their potential association with disease. Carnivora are a diverse and widespread order affected by polyomaviruses (PyVs) that have co-evolved with their hosts for millions of years. PyVs have been identified in sea lions, raccoons, badgers, Weddell seals, and dogs. We have discovered a polyomavirus, tentatively named "Ursus americanus polyomavirus 1" (UaPyV1) in black bears (Ursus americanus). UaPyV1 was detectable in various tissues of six out of seven bears submitted for necropsy. Based on viral phylogenetic clustering and detection of the virus in multiple individuals, we suggest that black bears are the natural hosts for UaPyV1. In this albeit small group, there is no clear relationship between UaPyV1 infection and any specific disease.},
}

@article {pmid33717447,
year = {2021},
author = {Meucci, S and Schulte, L and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, L and Bronken Eidesen, P and Herzschuh, U},
title = {Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.},
journal = {Ecology and evolution},
volume = {11},
number = {5},
pages = {2173-2193},
pmid = {33717447},
issn = {2045-7758},
abstract = {Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.},
}

@article {pmid33717442,
year = {2021},
author = {Seersholm, FV and Hansen, KL and Heydenrych, M and Hansen, AJ and Bunce, M and Allentoft, ME},
title = {Ancient DNA preserved in small bone fragments from the P.W. Lund collection.},
journal = {Ecology and evolution},
volume = {11},
number = {5},
pages = {2064-2071},
pmid = {33717442},
issn = {2045-7758},
abstract = {The Lund collection is one of the oldest subfossil collections in the world. The vast assemblage of subfossils was collected in the 1830s and 1840s by Peter Wilhelm Lund in Lagoa Santa, Brazil, and was shipped to Copenhagen in 1848, where it was stored in various locations around the city with little attention for the future preservation of the collection. So far, successful genetic research on the material collected by Lund has been limited to two samples of human petrous bone. However, less is known about the preservation conditions of the vast amounts of small and fragmentary bones stored in the collection. To address this, we studied ancient DNA from bulk bone samples of approximately 100 bone fragments from the P.W. Lund collection from boxes with varying degrees of physical preservation conditions. Using bulk bone metabarcoding, we found a high species diversity in all samples. In total, we identified 17 species, representing 11 mammals, two birds, one fish, and three frogs. Of these, two species are new to the collection. Collectively, these results exhibit the potential of future genetic studies on the famous P.W. Lund collection and suggest that the effects of poor storage conditions are probably negligible compared with the long-term in situ degradation that specimens undergo before excavation.},
}

@article {pmid33705715,
year = {2021},
author = {Kirch, M and Romundset, A and Gilbert, MTP and Jones, FC and Foote, AD},
title = {Ancient and modern stickleback genomes reveal the demographic constraints on adaptation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.02.027},
pmid = {33705715},
issn = {1879-0445},
abstract = {Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.},
}

@article {pmid33690651,
year = {2021},
author = {Novak, M and Olalde, I and Ringbauer, H and Rohland, N and Ahern, J and Balen, J and Janković, I and Potrebica, H and Pinhasi, R and Reich, D},
title = {Genome-wide analysis of nearly all the victims of a 6200 year old massacre.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247332},
pmid = {33690651},
issn = {1932-6203},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; },
abstract = {Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.},
}

@article {pmid33679884,
year = {2021},
author = {Diroma, MA and Modi, A and Lari, M and Sineo, L and Caramelli, D and Vai, S},
title = {New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {619950},
pmid = {33679884},
issn = {1664-8021},
abstract = {Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.},
}

@article {pmid33671794,
year = {2021},
author = {Kazarina, A and Petersone-Gordina, E and Kimsis, J and Kuzmicka, J and Zayakin, P and Griškjans, Ž and Gerhards, G and Ranka, R},
title = {The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33671794},
issn = {2073-4425},
support = {Nr.1.1.1.1/16/A/101//European Regional Development Fund/ ; },
abstract = {Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.},
}

@article {pmid33668883,
year = {2021},
author = {Lanubile, A and Borrelli, VMG and Soccio, M and Giorni, P and Stagnati, L and Busconi, M and Marocco, A},
title = {Loss of ZmLIPOXYGENASE4 Decreases Fusarium verticillioides Resistance in Maize Seedlings.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33668883},
issn = {2073-4425},
abstract = {Fusarium verticillioides is one of the most relevant fungal species in maize responsible for ear, stalk and seedling rot, as well as the fumonisin contamination of kernels. Plant lipoxygenases (LOX) synthesize oxylipins that play a crucial role in the regulation of defense mechanisms against pathogens and influence the outcome of pathogenesis. To better uncover the role of these signaling molecules in maize resistance against F. verticillioides, the functional characterization of the 9-LOX gene, ZmLOX4, was carried out in this study by employing mutants carrying Mu insertions in this gene (named as UFMulox4). In this regard, the genotyping of five UFMulox4 identified the mutant UFMu10924 as the only one having an insertion in the coding region of the gene. The impact of ZmLOX4 mutagenesis on kernel defense against F. verticillioides and fumonisin accumulation were investigated, resulting in an increased fungal susceptibility compared to the inbred lines W22 and Tzi18. Moreover, the expression of most of the genes involved in the LOX, jasmonic acid (JA) and green leaf volatiles (GLV) pathways, as well as LOX enzymatic activity, decreased or were unaffected by fungal inoculation in the mutant UFMu10924. These results confirm the strategic role of ZmLOX4 in controlling defense against F. verticillioides and its influence on the expression of several LOX, JA and GLV genes.},
}

@article {pmid33667394,
year = {2021},
author = {Kerner, G and Laval, G and Patin, E and Boisson-Dupuis, S and Abel, L and Casanova, JL and Quintana-Murci, L},
title = {Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years.},
journal = {American journal of human genetics},
volume = {108},
number = {3},
pages = {517-524},
pmid = {33667394},
issn = {1537-6605},
support = {R01 AI088364/AI/NIAID NIH HHS/United States ; },
mesh = {Body Remains ; DNA, Ancient/*analysis ; Europe ; Female ; Genome, Human/genetics ; History, Ancient ; Humans ; Male ; Polymorphism, Genetic/*genetics ; TYK2 Kinase/*genetics ; Tuberculosis/*genetics/history/microbiology ; },
abstract = {Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.},
}

Body Remains
DNA, Ancient/*analysis
Europe
Female
Genome, Human/genetics
History, Ancient
Humans
Male
Polymorphism, Genetic/*genetics
TYK2 Kinase/*genetics
Tuberculosis/*genetics/history/microbiology

@article {pmid33655354,
year = {2021},
author = {Rahmat, RA and Humphries, MA and Austin, JJ and Linacre, AMT and Self, P},
title = {The development of a tool to predict temperature-exposure of incinerated teeth using colourimetric and hydroxyapatite crystal size data.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {33655354},
issn = {1437-1596},
abstract = {This study presents a novel tool to predict temperature-exposure of incinerated pig teeth as a proxy for understanding impacts of fire on human teeth. Previous studies on the estimation of temperature-exposure of skeletal elements have been limited to that of heat-exposed bone. This predictive tool was developed using a multinomial regression model of colourimetric and hydroxyapatite crystal size variables using data obtained from unheated pig teeth and teeth incinerated at 300 °C, 600 °C, 800 °C and 1000 °C. An additional variable based on the observed appearance of the tooth was included in the tool. This enables the tooth to be classified as definitely burnt (600 °C-1000 °C) or uncertain (27 °C/300 °C). As a result, the model predicting the temperature-exposure of the incinerated teeth had an accuracy of 95%. This tool is a holistic, robust and reliable approach to estimate temperature of heat-exposed pig teeth, with high accuracy, and may act as a valuable proxy to estimate heat exposure for human teeth in forensic casework.},
}

@article {pmid33650010,
year = {2021},
author = {Yao, H and Wang, M and Zou, X and Li, Y and Yang, X and Li, A and Yeh, HY and Wang, P and Wang, Z and Bai, J and Guo, J and Chen, J and Ding, X and Zhang, Y and Lin, B and Wang, CC and He, G},
title = {New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy.},
journal = {Molecular genetics and genomics : MGG},
volume = {},
number = {},
pages = {},
pmid = {33650010},
issn = {1617-4623},
support = {X2123302//Nanqiang Outstanding Young Talents Program of Xiamen University/ ; 31801040//National Natural Science Foundation of China/ ; },
abstract = {Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.},
}

@article {pmid33643377,
year = {2021},
author = {Liu, Y and Wang, M and Chen, P and Wang, Z and Liu, J and Yao, L and Wang, F and Tang, R and Zou, X and He, G},
title = {Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians.},
journal = {Frontiers in genetics},
volume = {12},
number = {},
pages = {582357},
pmid = {33643377},
issn = {1664-8021},
abstract = {The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.},
}

@article {pmid33639719,
year = {2021},
author = {Matsumura, S and Terai, Y and Hongo, H and Ishiguro, N},
title = {Analysis of the Mitochondrial Genomes of Japanese Wolf Specimens in the Siebold Collection, Leiden.},
journal = {Zoological science},
volume = {38},
number = {1},
pages = {60-66},
doi = {10.2108/zs200019},
pmid = {33639719},
issn = {0289-0003},
mesh = {Animals ; Dogs/genetics ; *Genome, Mitochondrial ; Japan ; Phylogeny ; Sequence Analysis, DNA ; Wolves/*classification/*genetics ; },
abstract = {The taxonomic status of extinct Japanese or Honshu wolves (Canis lupus hodophilax) has been disputed since the name hodophilax was first proposed by Temminck in 1839 on the basis of specimens stored in Leiden, the Netherlands. Points of controversy include whether the type specimen of hodophilax (Jentink c: RMNH.MAM.39181) and the other two specimens from Leiden (Jentink a: RMNH.MAM.39182 and Jentink b: RMNH.MAM.39183) represent different varieties or subspecies of Japanese wolves or not. Two Japanese names, ookami and jamainu, used to describe wild Canis species, further complicate the issue. In this study, the taxonomic status of Japanese wolves was clarified using mitochondrial DNA of the three specimens stored at the Naturalis Biodiversity Center in Leiden, in addition to three Japanese wolf specimens stored at the Museum für Naturkunde in Berlin and five new samples from Japan. The mitochondrial genomes of the type specimen of hodophilax (Jentink c) and another sample from Leiden (Jentink b) as well as Berlin specimens were included in the cluster of Japanese wolves distinct from other grey wolves. However, the other sample from Leiden (Jentink a) was identified as a domestic dog. A mitochondrial genome analysis suggested that Japanese wolves could be categorized into two distinct clusters. Studies of nuclear genomes are needed to further clarify the taxonomic status, divergence time, and population genetic structure of Japanese wolves.},
}

Animals
Dogs/genetics
*Genome, Mitochondrial
Japan
Phylogeny
Sequence Analysis, DNA
Wolves/*classification/*genetics

@article {pmid33638983,
year = {2021},
author = {Yelmen, B and Marnetto, D and Molinaro, L and Flores, R and Mondal, M and Pagani, L},
title = {Improving Selection Detection with Population Branch Statistic on Admixed Populations.},
journal = {Genome biology and evolution},
volume = {13},
number = {4},
pages = {},
doi = {10.1093/gbe/evab039},
pmid = {33638983},
issn = {1759-6653},
abstract = {Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.},
}

@article {pmid33618348,
year = {2021},
author = {Wang, CC and Yeh, HY and Popov, AN and Zhang, HQ and Matsumura, H and Sirak, K and Cheronet, O and Kovalev, A and Rohland, N and Kim, AM and Mallick, S and Bernardos, R and Tumen, D and Zhao, J and Liu, YC and Liu, JY and Mah, M and Wang, K and Zhang, Z and Adamski, N and Broomandkhoshbacht, N and Callan, K and Candilio, F and Carlson, KSD and Culleton, BJ and Eccles, L and Freilich, S and Keating, D and Lawson, AM and Mandl, K and Michel, M and Oppenheimer, J and Özdoğan, KT and Stewardson, K and Wen, S and Yan, S and Zalzala, F and Chuang, R and Huang, CJ and Looh, H and Shiung, CC and Nikitin, YG and Tabarev, AV and Tishkin, AA and Lin, S and Sun, ZY and Wu, XM and Yang, TL and Hu, X and Chen, L and Du, H and Bayarsaikhan, J and Mijiddorj, E and Erdenebaatar, D and Iderkhangai, TO and Myagmar, E and Kanzawa-Kiriyama, H and Nishino, M and Shinoda, KI and Shubina, OA and Guo, J and Cai, W and Deng, Q and Kang, L and Li, D and Li, D and Lin, R and Nini, and Shrestha, R and Wang, LX and Wei, L and Xie, G and Yao, H and Zhang, M and He, G and Yang, X and Hu, R and Robbeets, M and Schiffels, S and Kennett, DJ and Jin, L and Li, H and Krause, J and Pinhasi, R and Reich, D},
title = {Genomic insights into the formation of human populations in East Asia.},
journal = {Nature},
volume = {591},
number = {7850},
pages = {413-419},
pmid = {33618348},
issn = {1476-4687},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; },
abstract = {The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.},
}

@article {pmid33602851,
year = {2021},
author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Bronk Ramsey, C and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R},
title = {A global environmental crisis 42,000 years ago.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6531},
pages = {811-818},
doi = {10.1126/science.abb8677},
pmid = {33602851},
issn = {1095-9203},
abstract = {Geological archives record multiple reversals of Earth's magnetic poles, but the global impacts of these events, if any, remain unclear. Uncertain radiocarbon calibration has limited investigation of the potential effects of the last major magnetic inversion, known as the Laschamps Excursion [41 to 42 thousand years ago (ka)]. We use ancient New Zealand kauri trees (Agathis australis) to develop a detailed record of atmospheric radiocarbon levels across the Laschamps Excursion. We precisely characterize the geomagnetic reversal and perform global chemistry-climate modeling and detailed radiocarbon dating of paleoenvironmental records to investigate impacts. We find that geomagnetic field minima ~42 ka, in combination with Grand Solar Minima, caused substantial changes in atmospheric ozone concentration and circulation, driving synchronous global climate shifts that caused major environmental changes, extinction events, and transformations in the archaeological record.},
}

@article {pmid33597786,
year = {2021},
author = {Callaway, E},
title = {Million-year-old mammoth genomes shatter record for oldest ancient DNA.},
journal = {Nature},
volume = {590},
number = {7847},
pages = {537-538},
pmid = {33597786},
issn = {1476-4687},
}

@article {pmid33597750,
year = {2021},
author = {van der Valk, T and Pečnerová, P and Díez-Del-Molino, D and Bergström, A and Oppenheimer, J and Hartmann, S and Xenikoudakis, G and Thomas, JA and Dehasque, M and Sağlıcan, E and Fidan, FR and Barnes, I and Liu, S and Somel, M and Heintzman, PD and Nikolskiy, P and Shapiro, B and Skoglund, P and Hofreiter, M and Lister, AM and Götherström, A and Dalén, L},
title = {Million-year-old DNA sheds light on the genomic history of mammoths.},
journal = {Nature},
volume = {591},
number = {7849},
pages = {265-269},
pmid = {33597750},
issn = {1476-4687},
support = {FC001595/MRC_/Medical Research Council/United Kingdom ; 852558/ERC_/European Research Council/International ; FC001595/WT_/Wellcome Trust/United Kingdom ; 310763/ERC_/European Research Council/International ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Acclimatization/genetics ; Alleles ; Animals ; Bayes Theorem ; DNA, Ancient/*analysis/isolation & purification ; Elephants/genetics ; Europe ; *Evolution, Molecular ; Female ; Fossils ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Mammoths/*genetics ; Markov Chains ; Molar ; North America ; *Phylogeny ; Radiometric Dating ; Siberia ; Time Factors ; },
abstract = {Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.},
}

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

@article {pmid33595921,
year = {2021},
author = {Sullivan, AP and Marciniak, S and O'Dea, A and Wake, TA and Perry, GH},
title = {Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13361},
pmid = {33595921},
issn = {1755-0998},
support = {//Smithsonian Tropical Research Institute/ ; //Secretaría Nacional de Ciencia y Tecnología e Innovación/ ; BCS-1554834//National Science Foundation/ ; DGE-1255832//National Science Foundation/ ; },
abstract = {Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984-1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.},
}

@article {pmid33594237,
year = {2021},
author = {Lammers, Y and Heintzman, PD and Alsos, IG},
title = {Environmental palaeogenomic reconstruction of an Ice Age algal population.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {220},
pmid = {33594237},
issn = {2399-3642},
abstract = {Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.},
}

@article {pmid33592193,
year = {2021},
author = {Barlow, A and Paijmans, JLA and Alberti, F and Gasparyan, B and Bar-Oz, G and Pinhasi, R and Foronova, I and Puzachenko, AY and Pacher, M and Dalén, L and Baryshnikov, G and Hofreiter, M},
title = {Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.01.073},
pmid = {33592193},
issn = {1879-0445},
abstract = {Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.},
}

@article {pmid33585897,
year = {2021},
author = {Lan, D and Tobler, R and Souilmi, Y and Llamas, B},
title = {Genozip - A Universal Extensible Genomic Data Compressor.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btab102},
pmid = {33585897},
issn = {1367-4811},
abstract = {We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities - universality (support for all common genomic file formats), high compression ratios, speed, feature-richness, and extensibility. Genozip delivers high-performance compression for widely-used genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP, and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Availability: Genozip is written in C. The code is open-source and available on GitHub (https://github.com/divonlan/genozip). The package is free for non-commercial use. It is distributed as a Docker container on DockerHub and through the conda package manager. Genozip is tested on Linux, Mac, and Windows. Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid33579752,
year = {2021},
author = {Harney, É and Cheronet, O and Fernandes, DM and Sirak, K and Mah, M and Bernardos, R and Adamski, N and Broomandkhoshbacht, N and Callan, K and Lawson, AM and Oppenheimer, J and Stewardson, K and Zalzala, F and Anders, A and Candilio, F and Constantinescu, M and Coppa, A and Ciobanu, I and Dani, J and Gallina, Z and Genchi, F and Nagy, EG and Hajdu, T and Hellebrandt, M and Horváth, A and Király, Á and Kiss, K and Kolozsi, B and Kovács, P and Köhler, K and Lucci, M and Pap, I and Popovici, S and Raczky, P and Simalcsik, A and Szeniczey, T and Vasilyev, S and Virag, C and Rohland, N and Reich, D and Pinhasi, R},
title = {A minimally destructive protocol for DNA extraction from ancient teeth.},
journal = {Genome research},
volume = {31},
number = {3},
pages = {472-483},
pmid = {33579752},
issn = {1549-5469},
abstract = {Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.},
}

@article {pmid33565584,
year = {2021},
author = {Ontano, AZ and Gainett, G and Aharon, S and Ballesteros, JA and Benavides, LR and Corbett, KF and Gavish-Regev, E and Harvey, MS and Monsma, S and Santibáñez-López, CE and Setton, EVW and Zehms, JT and Zeh, JA and Zeh, DW and Sharma, PP},
title = {Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msab038},
pmid = {33565584},
issn = {1537-1719},
abstract = {Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.},
}

@article {pmid33559126,
year = {2021},
author = {Yüncü, E and Açan, SC and Onar, V and Karakulak, FS and Gökoğlu, M and Alıçlı, TZ and Chiriboga, F and Togan, İ and Özer, F},
title = {Demography of swordfish (Xiphias gladius Linneus) populations from the coasts of Turkey, based on mitochondrial DNA and microsatellites.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.14696},
pmid = {33559126},
issn = {1095-8649},
support = {BAP-07-02-2012-101-9//Orta Doğu Teknik Üniversitesi/ ; 113Z405//Türkiye Bilimsel ve Teknolojik Araştirma Kurumu/ ; },
abstract = {The genetic diversity of the Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin, north of the Aegean Sea (Aegean-2013, n = 26) and the Mediterranean coast of Turkey (N.Levantine-2013, n = 42) were studied genetically, along with ancient samples from Yenikapı excavation (n = 6). Partial mitochondrial DNA control region sequences (entire sequences, clade I and clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., Molecular Phylogenetics and Evolution, 2005, 36, 169-187; Viñas et al., ICES Journal of Marine Science, 2010, 67, 1222-1229; Righi et al., Diversity, 2020, 12, 170) from the rest of the Mediterranean Sea. Pair-wise FST and pair-wise AMOVA tests showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the past 20 years. Therefore, the results direct reconsideration of previous descriptions of population sub-structure within the Mediterranean and support high gene flow throughout the region. On the contrary, the results of this study confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that θ, which is directly proportional to long-term female effective population size (Ne), decreased significantly (P < 0.05) in both regions over the past two decades. On the Turkish coasts, θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. Nonetheless, θ of the ancient sample was consistently and significantly (P < 0.001) higher than those of the eastern and western Mediterranean populations in clade I and clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples, suggesting that the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite-based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% c.i. and possibly even lower than 100 according to the mean of posterior distribution of the present Ne estimate calculated by the software package MSVAR. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here show that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need an immediate stringent action and management plan.},
}

@article {pmid33558418,
year = {2021},
author = {Sun, XF and Wen, SQ and Lu, CQ and Zhou, BY and Curnoe, D and Lu, HY and Li, HC and Wang, W and Cheng, H and Yi, SW and Jia, X and Du, PX and Xu, XH and Lu, YM and Lu, Y and Zheng, HX and Zhang, H and Sun, C and Wei, LH and Han, F and Huang, J and Edwards, RL and Jin, L and Li, H},
title = {Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {8},
pages = {},
pmid = {33558418},
issn = {1091-6490},
abstract = {The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.},
}

@article {pmid33556115,
year = {2021},
author = {Plomp, KA and Gestsdóttir, H and Dobney, K and Price, N and Collard, M},
title = {The composition of the founding population of Iceland: A new perspective from 3D analyses of basicranial shape.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0246059},
pmid = {33556115},
issn = {1932-6203},
abstract = {The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore this issue further, we used three-dimensional techniques to compare the basicrania of skeletons from archaeological sites in Iceland, Scandinavia, and the British Isles. Our analyses yielded two main results. One was that the founding population likely consisted of roughly equal numbers of Scandinavians and people from the British Isles. The other was that the immigrants who originated from the British Isles included individuals of southern British ancestry as well as individuals of Scottish and Irish ancestry. The first of these findings is consistent with the results of recent analyses of modern and ancient DNA, while the second is novel. Our study, therefore, strengthens the idea that the founding population was a mix of Scandinavians and people from the British Isles, but also raises a new possibility regarding the regions from which the settlers originated.},
}

@article {pmid33547403,
year = {2021},
author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M},
title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {169},
pmid = {33547403},
issn = {2399-3642},
support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; },
abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.},
}

@article {pmid33547359,
year = {2021},
author = {Armbrecht, L and Hallegraeff, G and Bolch, CJS and Woodward, C and Cooper, A},
title = {Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3220},
pmid = {33547359},
issn = {2045-2322},
support = {DP170102261//Australian Research Council/ ; DP170102261//Australian Research Council/ ; DP170102261//Australian Research Council/ ; DP170102261//Australian Research Council/ ; FL140100260//Australian Research Council/ ; H0025318//2018 MNF Grant/ ; H0025318//2018 MNF Grant/ ; H0025318//2018 MNF Grant/ ; },
abstract = {Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.},
}

@article {pmid33540755,
year = {2021},
author = {Davidson, R and Fehren-Schmitz, L and Llamas, B},
title = {A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33540755},
issn = {2073-4425},
abstract = {The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.},
}

@article {pmid33518701,
year = {2021},
author = {Ma, X and Zhang, L and Pei, Z and Zhang, L and Liu, Z and Liu, D and Hao, X and Jin, Z and Pei, Y},
title = {Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs.},
journal = {Horticulture research},
volume = {8},
number = {1},
pages = {19},
pmid = {33518701},
issn = {2662-6810},
abstract = {Heading Chinese cabbage (Brassica rapa L. syn. B. campestris L. ssp. chinensis Makino var. pekinensis (Rupr.) J. Cao et Sh. Cao) is a cruciferous Brassica vegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering in Arabidopsis and heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and four BraFLC, BraSOC I, and BraFT homologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of the BraSOC I and BraFT homologs, producing different binding patterns. Thus, there may be functionally diverse BraFLC homologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L-1 significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind most BraSOC I or BraFT promoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of the BraFT and BraSOC I homologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.},
}

@article {pmid33514802,
year = {2021},
author = {De Angelis, F and Pellegrini, M and Martínez-Labarga, C and Anzivino, L and Scorrano, G and Brilli, M and Giustini, F and Angle, M and Calattini, M and Carboni, G and Catalano, P and Ceccaroni, E and Cosentino, S and Di Giannantonio, S and Isola, I and Martini, F and Pacciani, E and Radina, F and Rolfo, MF and Silvestrini, M and Volante, N and Zanchetta, G and Sarti, L and Rickards, O},
title = {Exploring mobility in Italian Neolithic and Copper Age communities.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2697},
pmid = {33514802},
issn = {2045-2322},
support = {2010EL8TXP//Ministero dell&Istruzione, dell&Universit; e della Ricerca (Ministry of Education, University and Research)/ ; },
abstract = {As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.},
}

@article {pmid33514313,
year = {2021},
author = {García-Rodríguez, O and Hardouin, EA and Hambleton, E and Monteith, J and Randall, C and Richards, MB and Edwards, CJ and Stewart, JR},
title = {Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia.},
journal = {BMC ecology and evolution},
volume = {21},
number = {1},
pages = {9},
pmid = {33514313},
issn = {2730-7182},
abstract = {BACKGROUND: The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.

RESULTS: From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.

CONCLUSIONS: The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.},
}

@article {pmid33510007,
year = {2021},
author = {Grimm, D},
title = {Siberia may be long-sought site of dog domestication.},
journal = {Science (New York, N.Y.)},
volume = {371},
number = {6528},
pages = {451-452},
doi = {10.1126/science.371.6528.451},
pmid = {33510007},
issn = {1095-9203},
mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; *Domestication ; Humans ; Phenotype ; Siberia ; Wolves/genetics ; },
}

Animals
DNA, Ancient
DNA, Mitochondrial/genetics
Dogs/*genetics
*Domestication
Humans
Phenotype
Siberia
Wolves/genetics

@article {pmid33504886,
year = {2021},
author = {Hayer, S and Brandis, D and Immel, A and Susat, J and Torres-Oliva, M and Ewers-Saucedo, C and Krause-Kyora, B},
title = {Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2307},
pmid = {33504886},
issn = {2045-2322},
support = {01UQ1711//Bundesministerium für Bildung und Forschung/ ; 01UQ1711//Bundesministerium für Bildung und Forschung/ ; },
abstract = {The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.},
}

@article {pmid33500403,
year = {2021},
author = {Fellows Yates, JA and Andrades Valtueña, A and Vågene, ÅJ and Cribdon, B and Velsko, IM and Borry, M and Bravo-Lopez, MJ and Fernandez-Guerra, A and Green, EJ and Ramachandran, SL and Heintzman, PD and Spyrou, MA and Hübner, A and Gancz, AS and Hider, J and Allshouse, AF and Zaro, V and Warinner, C},
title = {Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.},
journal = {Scientific data},
volume = {8},
number = {1},
pages = {31},
pmid = {33500403},
issn = {2052-4463},
support = {ERC-2014-ADG 670518//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/International ; 208934/Z/17/Z//Wellcome Trust (Wellcome)/International ; IA201219 PAPIIT-DGAPA- UNAM//Universidad Nacional Autónoma de México (National Autonomous University of Mexico)/International ; AH/N005015/1//RCUK | Arts and Humanities Research Council (AHRC)/International ; EXC 2051-Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; DGE1255832//National Science Foundation (NSF)/International ; T32 GM007197/GM/NIGMS NIH HHS/United States ; },
mesh = {*Databases, Genetic ; Humans ; Metadata ; *Metagenome ; *Metagenomics ; Publications ; },
abstract = {Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.},
}

*Databases, Genetic
Humans
Metadata
*Metagenome
*Metagenomics
Publications

@article {pmid33499784,
year = {2021},
author = {Hu, J and Westbury, MV and Yuan, J and Zhang, Z and Chen, S and Xiao, B and Hou, X and Ji, H and Lai, X and Hofreiter, M and Sheng, G},
title = {Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1943},
pages = {20202934},
pmid = {33499784},
issn = {1471-2954},
abstract = {Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.},
}

@article {pmid33499220,
year = {2021},
author = {Xavier, C and Eduardoff, M and Bertoglio, B and Amory, C and Berger, C and Casas-Vargas, A and Pallua, J and Parson, W},
title = {Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33499220},
issn = {2073-4425},
abstract = {The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille's overall increased gain of DNA when enough tissue is available and Dabney's improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.},
}

@article {pmid33499169,
year = {2021},
author = {Taron, UH and Paijmans, JLA and Barlow, A and Preick, M and Iyengar, A and Drăgușin, V and Vasile, Ș and Marciszak, A and Roblíčková, M and Hofreiter, M},
title = {Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe.},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33499169},
issn = {2073-4425},
support = {310763/ERC_/European Research Council/International ; Project 126/2019 (KARSTHIVES 2)//EEA Grants 2014-2021/ ; },
abstract = {The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.},
}

@article {pmid33495362,
year = {2021},
author = {Perri, AR and Feuerborn, TR and Frantz, LAF and Larson, G and Malhi, RS and Meltzer, DJ and Witt, KE},
title = {Dog domestication and the dual dispersal of people and dogs into the Americas.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {6},
pages = {},
pmid = {33495362},
issn = {1091-6490},
support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM128946/GM/NIGMS NIH HHS/United States ; },
abstract = {Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a much deeper antiquity, and that the tandem movement of people and dogs may have begun soon after the domestication of the dog from a gray wolf ancestor in the late Pleistocene. Here, by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ∼23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ∼15,000 y ago.},
}

@article {pmid33494619,
year = {2021},
author = {Singh, G and Yellapu, S and Sandhu, HS and Sharma, I and Sharma, V and Bhanwer, A},
title = {Genetic Characterization of the North-West Indian Population: Analysis of Mitochondrial DNA Control Region Variation.},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/03014460.2021.1879933},
pmid = {33494619},
issn = {1464-5033},
abstract = {BACKGROUND: Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history and forensic science.

AIM: The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient.

SUBJECTS AND METHODS: The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution and pairwise FST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA.

RESULTS: The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30 and U7 were observed to be the most prevalent and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations.

CONCLUSION: The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.},
}

@article {pmid33486547,
year = {2021},
author = {Selberg, AGA and Gaucher, EA and Liberles, DA},
title = {Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.},
journal = {Journal of molecular evolution},
volume = {89},
number = {3},
pages = {157-164},
pmid = {33486547},
issn = {1432-1432},
support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; 2037635//Division of Molecular and Cellular Biosciences/ ; },
abstract = {As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches to conduct ancestral sequence reconstruction for proteins are built upon a conceptual framework from journal founder Emile Zuckerkandl. On top of this, work on maximum likelihood phylogenetics published in Journal of Molecular Evolution in 1996 was one of the first approaches for generating maximum likelihood ancestral sequences of proteins. From its computational history, future model development needs as well as potential applications in areas as diverse as computational systems biology, molecular community ecology, infectious disease therapeutics and other biomedical applications, and biotechnology are discussed. From its past in this journal, there is a bright future for ancestral sequence reconstruction in the field of evolutionary biology.},
}

@article {pmid33482498,
year = {2021},
author = {Melo, L and Matos, VMJ and Santos, AL and Ferreira, C and Silva, AM},
title = {The first probable evidence of leprosy in a male individual (17th-19th century AD) unearthed in Northern Portugal (Travanca, Santa Maria da Feira).},
journal = {International journal of paleopathology},
volume = {32},
number = {},
pages = {80-86},
doi = {10.1016/j.ijpp.2020.12.001},
pmid = {33482498},
issn = {1879-9825},
abstract = {OBJECTIVE: This study describes the first evidence of a probable paleopathological case of leprosy from northern Portugal.

MATERIALS: An adult male, skeleton 403, exhumed from the Christian cemetery associated with the church dedicated to Saint Mamede (Travanca, Santa Maria da Feira), dated from the 17th-19th century AD.

METHODS: Standard bioarchaeological methods were used for sex and age-at-death determinations, and leprosy-related bone lesions were identified through macroscopic analysis guided by paleopathological diagnostic criteria.

RESULTS: The macroscopic observation revealed probable leprosy-related skeletal lesions, namely tenuous rhinomaxillary changes, bilateral proliferative periosteal reactions on the tibiae and fibulae, as well as concentric atrophy, acro-osteolysis and ankyloses of foot bones.

CONCLUSIONS: Skeleton 403 represents a probable case of leprosy according to the nature and distribution pattern of bony lesions observed.

SIGNIFICANCE: This finding fills an important gap in the history of leprosy in Portugal. Although historical sources show that the majority of leprosaria were located in the northern part of the country, suggesting that leprosy was more prevalent in this area of Portugal in the past, no paleopathological evidence of this disease was reported for this region to date. Furthermore, the inhumation of a leprosy sufferer in a 17th-19th century AD Christian parish cemetery is deeply imbued with social meaning.

The future detailed study of the remaining skeletons unearthed from the cemetery of the Church of São Mamede will hopefully reveal further osteological evidence of leprosy in addition to the application of ancient DNA analysis to confirm the presence of the pathogen of this disease. Also, further documentary research is needed in order to expand appreciation of the epidemiological and social impact of leprosy in the 17th-19th century AD Portugal.},
}

@article {pmid33482383,
year = {2021},
author = {Phillips, MJ and Shazwani Zakaria, S},
title = {Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals.},
journal = {Molecular phylogenetics and evolution},
volume = {158},
number = {},
pages = {107082},
doi = {10.1016/j.ympev.2021.107082},
pmid = {33482383},
issn = {1095-9513},
abstract = {Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.},
}

@article {pmid33475153,
year = {2021},
author = {Gowland, R and Stewart, NA and Crowder, KD and Hodson, C and Shaw, H and Gron, KJ and Montgomery, J},
title = {Sex estimation of teeth at different developmental stages using dimorphic enamel peptide analysis.},
journal = {American journal of physical anthropology},
volume = {174},
number = {4},
pages = {859-869},
doi = {10.1002/ajpa.24231},
pmid = {33475153},
issn = {1096-8644},
abstract = {OBJECTIVES: This study tests, for the first time, the applicability of a new method of sex estimation utilizing enamel peptides on a sample of deciduous and permanent teeth at different stages of mineralization, from nonadults of unknown sex, including perinates.

MATERIALS AND METHODS: A total of 43 teeth from 29 nonadult individuals aged from 40 gestational weeks to 19 years old were analyzed. The sample included pairs of fully mineralized and just developing teeth from the same individual. The individuals were from four archaeological sites in England: Piddington (1st-2nd centuries AD), Coach Lane, Victoria Gate, and Fewston (all 18th-19th centuries). A method that identifies sex chromosome-linked isoforms of the peptide amelogenin from human tooth enamel was applied. The method utilizes a minimally destructive acid etching procedure and subsequent nano liquid chromatography tandem mass spectrometry.

RESULTS: It was possible to determine the sex of 28 of the nonadult individuals sampled (males = 20, females = 8, undetermined = 1). Only one sample failed (CL9), due to insufficient mineralization of the sampled tooth enamel. Data are available via ProteomeXchange with identifier PXD021683.

DISCUSSION: Sufficient peptide material to determine sex can be recovered even from the crowns of developing perinatal teeth that are not fully mineralized. The minimally destructive and inexpensive (compared to ancient DNA) nature of this procedure has significant implications for bioarchaeological studies of infancy and childhood.},
}

@article {pmid33463014,
year = {2021},
author = {Keighley, X and Bro-Jørgensen, MH and Ahlgren, H and Szpak, P and Ciucani, MM and Sánchez Barreiro, F and Howse, L and Gotfredsen, AB and Glykou, A and Jordan, P and Lidén, K and Olsen, MT},
title = {Predicting sample success for large-scale ancient DNA studies on marine mammals.},
journal = {Molecular ecology resources},
volume = {21},
number = {4},
pages = {1149-1166},
doi = {10.1111/1755-0998.13331},
pmid = {33463014},
issn = {1755-0998},
support = {//Joint Proxies Research Group, financed by Research Council of Norway (RCN) Grant Number 246899 and Faculty for Humanities, Social Sciences and Education, UiT The Arctic University of Norway/ ; 2015-02151//Swedish Research Council, Sweden/ ; #676154//European Union's Framework Programme for Research and Innovation Horizon 2020/ ; },
abstract = {In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.},
}

@article {pmid33455740,
year = {2021},
author = {Mitchell, KJ and Rawlence, NJ},
title = {Examining Natural History through the Lens of Palaeogenomics.},
journal = {Trends in ecology & evolution},
volume = {36},
number = {3},
pages = {258-267},
doi = {10.1016/j.tree.2020.10.005},
pmid = {33455740},
issn = {1872-8383},
mesh = {*Fossils ; *Genomics ; Humans ; Paleontology ; },
abstract = {The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.},
}

*Fossils
*Genomics
Humans
Paleontology

@article {pmid33453495,
year = {2021},
author = {Ramirez, DA and Saka, HA and Nores, R},
title = {Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD).},
journal = {International journal of paleopathology},
volume = {32},
number = {},
pages = {74-79},
doi = {10.1016/j.ijpp.2020.12.004},
pmid = {33453495},
issn = {1879-9825},
abstract = {OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic.

MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina.

METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed.

RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed.

CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic.

SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past.

LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number.

Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.},
}

@article {pmid33443182,
year = {2021},
author = {Ju, D and Mathieson, I},
title = {The evolution of skin pigmentation-associated variation in West Eurasia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {1},
pages = {},
pmid = {33443182},
issn = {1091-6490},
support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 GM008216/GM/NIGMS NIH HHS/United States ; },
abstract = {Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.},
}

@article {pmid33443177,
year = {2021},
author = {Pugach, I and Hübner, A and Hung, HC and Meyer, M and Carson, MT and Stoneking, M},
title = {Ancient DNA from Guam and the peopling of the Pacific.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {1},
pages = {},
pmid = {33443177},
issn = {1091-6490},
abstract = {Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.},
}

@article {pmid33442059,
year = {2021},
author = {Perri, AR and Mitchell, KJ and Mouton, A and Álvarez-Carretero, S and Hulme-Beaman, A and Haile, J and Jamieson, A and Meachen, J and Lin, AT and Schubert, BW and Ameen, C and Antipina, EE and Bover, P and Brace, S and Carmagnini, A and Carøe, C and Samaniego Castruita, JA and Chatters, JC and Dobney, K and Dos Reis, M and Evin, A and Gaubert, P and Gopalakrishnan, S and Gower, G and Heiniger, H and Helgen, KM and Kapp, J and Kosintsev, PA and Linderholm, A and Ozga, AT and Presslee, S and Salis, AT and Saremi, NF and Shew, C and Skerry, K and Taranenko, DE and Thompson, M and Sablin, MV and Kuzmin, YV and Collins, MJ and Sinding, MS and Gilbert, MTP and Stone, AC and Shapiro, B and Van Valkenburgh, B and Wayne, RK and Larson, G and Cooper, A and Frantz, LAF},
title = {Dire wolves were the last of an ancient New World canid lineage.},
journal = {Nature},
volume = {591},
number = {7848},
pages = {87-91},
pmid = {33442059},
issn = {1476-4687},
support = {S10 OD018174/OD/NIH HHS/United States ; /ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Extinction, Biological ; Fossils ; Gene Flow ; Genome/genetics ; Genomics ; Geographic Mapping ; North America ; Paleontology ; Phenotype ; *Phylogeny ; Wolves/*classification/genetics ; },
abstract = {Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.},
}

Animals
*Extinction, Biological
Fossils
Gene Flow
Genome/genetics
Genomics
Geographic Mapping
North America
Paleontology
Phenotype
*Phylogeny
Wolves/*classification/genetics

@article {pmid33437437,
year = {2021},
author = {Xu, W and Lin, Y and Zhao, K and Li, H and Tian, Y and Ngatia, JN and Ma, Y and Sahu, SK and Guo, H and Guo, X and Xu, YC and Liu, H and Kristiansen, K and Lan, T and Zhou, X},
title = {An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.},
journal = {Ecology and evolution},
volume = {11},
number = {1},
pages = {390-401},
pmid = {33437437},
issn = {2045-7758},
abstract = {Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.},
}

@article {pmid33434506,
year = {2021},
author = {Seguin-Orlando, A and Donat, R and Der Sarkissian, C and Southon, J and Thèves, C and Manen, C and Tchérémissinoff, Y and Crubézy, E and Shapiro, B and Deleuze, JF and Dalén, L and Guilaine, J and Orlando, L},
title = {Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.},
journal = {Current biology : CB},
volume = {31},
number = {5},
pages = {1072-1083.e10},
doi = {10.1016/j.cub.2020.12.015},
pmid = {33434506},
issn = {1879-0445},
abstract = {The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.},
}

@article {pmid33429070,
year = {2021},
author = {Kévin, R and Nicolas, C and Elsa, P and Paolo, L and Pasquino, P and Raffaella, B and Matthieu, LB},
title = {Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {90},
number = {},
pages = {104713},
doi = {10.1016/j.meegid.2021.104713},
pmid = {33429070},
issn = {1567-7257},
abstract = {The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.},
}

@article {pmid33418451,
year = {2021},
author = {Nowaczewska, W and Binkowski, M and Benazzi, S and Vazzana, A and Nadachowski, A and Stefaniak, K and Żarski, M and Talamo, S and Compton, T and Stringer, CB and Hajdinjak, M and Hublin, JJ},
title = {New hominin teeth from Stajnia Cave, Poland.},
journal = {Journal of human evolution},
volume = {151},
number = {},
pages = {102929},
doi = {10.1016/j.jhevol.2020.102929},
pmid = {33418451},
issn = {1095-8606},
}

@article {pmid33417716,
year = {2021},
author = {Greer, C and Bhakta, H and Ghanem, L and Refai, F and Linn, E and Avella, M},
title = {Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.},
journal = {Human reproduction (Oxford, England)},
volume = {36},
number = {3},
pages = {734-755},
doi = {10.1093/humrep/deaa347},
pmid = {33417716},
issn = {1460-2350},
abstract = {STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?

SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.

WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average ∼2%) present in non-African extant humans.

STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.

Ancient DNA from six Neanderthals and two Denisovans dated between ∼82 000 and 43 000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.

Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage ≥20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.

While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.

This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.

This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.

TRIAL REGISTRATION NUMBER: N/A.},
}

@article {pmid33373911,
year = {2021},
author = {Mckinnon, M and Higgins, D},
title = {Comparison of bone demineralisation procedures for DNA recovery from burned remains.},
journal = {Forensic science international. Genetics},
volume = {51},
number = {},
pages = {102448},
doi = {10.1016/j.fsigen.2020.102448},
pmid = {33373911},
issn = {1878-0326},
abstract = {Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.},
}

@article {pmid33366505,
year = {2019},
author = {Nedoluzhko, AV and Sharko, FS and Boulygina, ES and Tsygankova, SV and Slobodova, NV and Gruzdeva, NM and Rastorguev, SM and Spasskaya, NN and Maschenko, EN},
title = {The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {5},
number = {1},
pages = {243-245},
pmid = {33366505},
issn = {2380-2359},
abstract = {The complete mitochondrial genome from the Pleistocene stallion horse (Equus cf. lenensis) which complete skull was found in 1901 on Kotelny Island (New Siberian Archipelago, Sakha Republic, Russia) is published in this paper. The mitochondrial DNA (mtDNA) is 16,584 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. The overall base composition of the genome in descending order was 32.3% - A, 28.5% - C, 13.4% - G, 25.8% - T without a significant AT bias of 58.2%.},
}

@article {pmid33366359,
year = {2019},
author = {Grond, J and Płecha, M and Hahn, C and Wiig, Ø and Bachmann, L},
title = {Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {4},
number = {2},
pages = {4152-4154},
pmid = {33366359},
issn = {2380-2359},
abstract = {The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard (14C age estimate range: 215-8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.},
}

@article {pmid33352129,
year = {2020},
author = {Friedlaender, JS and Tucci, S},
title = {Human Migrations: Tales of the Pacific.},
journal = {Current biology : CB},
volume = {30},
number = {24},
pages = {R1478-R1481},
doi = {10.1016/j.cub.2020.11.008},
pmid = {33352129},
issn = {1879-0445},
abstract = {The mode and tempo of human dispersal to the far-flung Pacific Islands has been a source of fascination for centuries. New ancient DNA data from the archipelago of Vanuatu shed light on the ancient migrations that shaped the history of human settlement in the Pacific.},
}

@article {pmid33351947,
year = {2020},
author = {Hong, JH and Seo, M and Oh, CS and Chai, JY and Shin, DH},
title = {Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty.},
journal = {The Journal of parasitology},
volume = {106},
number = {6},
pages = {802-808},
doi = {10.1645/20-42},
pmid = {33351947},
issn = {1937-2345},
mesh = {Animals ; DNA, Helminth/history/*isolation & purification ; Feces/parasitology ; Female ; Heterophyidae/*genetics/isolation & purification ; History, 16th Century ; History, 17th Century ; Humans ; Korea ; Male ; Mummies/*history/*parasitology ; Trematode Infections/*history/parasitology ; },
abstract = {Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.},
}

Animals
DNA, Helminth/history/*isolation & purification
Feces/parasitology
Female
Heterophyidae/*genetics/isolation & purification
History, 16th Century
History, 17th Century
Humans
Korea
Male
Mummies/*history/*parasitology
Trematode Infections/*history/parasitology

@article {pmid33340848,
year = {2021},
author = {Senovska, A and Drozdova, E and Vaculik, O and Pardy, F and Brzobohata, K and Fialova, D and Smerda, J and Kos, P},
title = {Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA.},
journal = {Forensic science international},
volume = {319},
number = {},
pages = {110638},
doi = {10.1016/j.forsciint.2020.110638},
pmid = {33340848},
issn = {1872-6283},
abstract = {Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.},
}

@article {pmid33340012,
year = {2019},
author = {Lewis, D},
title = {Head of ancient-DNA lab sacked for 'serious misconduct'.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-019-03932-3},
pmid = {33340012},
issn = {1476-4687},
}

@article {pmid33319428,
year = {2021},
author = {Schulte, L and Bernhardt, N and Stoof-Leichsenring, K and Zimmermann, HH and Pestryakova, LA and Epp, LS and Herzschuh, U},
title = {Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest.},
journal = {Molecular ecology resources},
volume = {21},
number = {3},
pages = {801-815},
doi = {10.1111/1755-0998.13311},
pmid = {33319428},
issn = {1755-0998},
support = {EP98/2-1//German Research Foundation/ ; 772852//European Research Council/International ; },
abstract = {Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.},
}

@article {pmid33318213,
year = {2020},
author = {Kistler, L and Thakar, HB and VanDerwarker, AM and Domic, A and Bergström, A and George, RJ and Harper, TK and Allaby, RG and Hirth, K and Kennett, DJ},
title = {Archaeological Central American maize genomes suggest ancient gene flow from South America.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {52},
pages = {33124-33129},
pmid = {33318213},
issn = {1091-6490},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Central America ; *Evolution, Molecular ; *Gene Flow ; Genome, Plant ; Hybridization, Genetic ; *Plant Breeding ; South America ; Zea mays/*genetics ; },
abstract = {Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.},
}

Central America
*Evolution, Molecular
*Gene Flow
Genome, Plant
Hybridization, Genetic
*Plant Breeding
South America
Zea mays/*genetics

@article {pmid33304512,
year = {2020},
author = {Padró, J and Lambertucci, SA and Perrig, PL and Pauli, JN},
title = {Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories.},
journal = {Ecology and evolution},
volume = {10},
number = {23},
pages = {13011-13021},
pmid = {33304512},
issn = {2045-7758},
abstract = {While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co-occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.},
}

@article {pmid33304488,
year = {2020},
author = {Garrett Vieira, F and Samaniego Castruita, JA and Gilbert, MTP},
title = {Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.},
journal = {Ecology and evolution},
volume = {10},
number = {23},
pages = {12700-12709},
pmid = {33304488},
issn = {2045-7758},
abstract = {Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.},
}

@article {pmid33299013,
year = {2020},
author = {Balzeau, A and Turq, A and Talamo, S and Daujeard, C and Guérin, G and Welker, F and Crevecoeur, I and Fewlass, H and Hublin, JJ and Lahaye, C and Maureille, B and Meyer, M and Schwab, C and Gómez-Olivencia, A},
title = {Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21230},
pmid = {33299013},
issn = {2045-2322},
abstract = {The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -14C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct 14C age of 41.7-40.8 ka cal BP (95%), younger than the 14C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices.},
}

@article {pmid33273524,
year = {2020},
author = {Verma, S and Sharma, I and Sharma, V and Bhat, A and Shah, R and Bhat, GR and Sharma, B and Bakshi, D and Nagpal, A and Wakhloo, A and Bhat, A and Kumar, R},
title = {MassArray analysis of genomic susceptibility variants in ovarian cancer.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21101},
pmid = {33273524},
issn = {2045-2322},
mesh = {Alleles ; Case-Control Studies ; Female ; Gene Frequency ; *Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; Humans ; Middle Aged ; Molecular Sequence Annotation ; *Oligonucleotide Array Sequence Analysis ; Ovarian Neoplasms/*genetics ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Ovarian cancer (OC), a multifaceted and genetically heterogeneous malignancy is one of the most common cancers among women. The aim of the study is to unravel the genetic factors associated with OC and the extent of genetic heterogeneity in the populations of Jammu and Kashmir (J&K).Using the high throughput Agena MassARRAY platform, present case control study was designed which comprises 200 histopathological confirmed OC patients and 400 age and ethnicity matched healthy controls to ascertain the association of previously reported eleven single nucleotide polymorphisms (SNPs) spread over ten genes (DNMT3A, PIK3CA, FGFR2, GSTP1, ERCC5, AKT1, CASC16, CYP19A1, BCL2 and ERCC1) within the OC population of Jammu and Kashmir, India. The association of each variant was estimated using logistic regression analyses. Out of the 11 SNPs the odds ratio observed for three SNPs; rs2699887 was (1.72 at 95% CI: 1.19-2.48, p = 0.004), rs1695 was (1.87 at 95% CI: 1.28-2.71, p = 0.001), and rs2298881 was (0.66 at 95% CI: 0.46-0.96, p = 0.03) were found significantly associated with the OC after correction with confounding factors i.e. age & BMI. Furthermore, the estimation of interactive analyses was performed and odds ratio observed was 2.44 (1.72-3.47), p value < 0. 001 suggests that there was a strong existence of interplay between the selected genetic variants in OC, which demonstrate that interactive analysis highlights the role of gene-gene interaction that provides an insight among multiple little effects of various polymorphisms in OC.},
}

Alleles
Case-Control Studies
Female
Gene Frequency
*Genetic Predisposition to Disease
*Genetic Variation
*Genome, Human
Humans
Middle Aged
Molecular Sequence Annotation
*Oligonucleotide Array Sequence Analysis
Ovarian Neoplasms/*genetics
Polymorphism, Single Nucleotide/genetics

@article {pmid33272282,
year = {2020},
author = {Duggan, AT and Holmes, EC and Poinar, HN},
title = {Response to Brinkmann et al. "Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States".},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {287},
pmid = {33272282},
issn = {1474-760X},
mesh = {American Civil War ; Genomics ; Humans ; *Orthopoxvirus/genetics ; *Smallpox/prevention & control ; *Smallpox Vaccine ; United States ; },
abstract = {We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.},
}

American Civil War
Genomics
Humans
*Orthopoxvirus/genetics
*Smallpox/prevention & control
*Smallpox Vaccine
United States

@article {pmid33267779,
year = {2020},
author = {Dussex, N and Alberti, F and Heino, MT and Olsen, RA and van der Valk, T and Ryman, N and Laikre, L and Ahlgren, H and Askeyev, IV and Askeyev, OV and Shaymuratova, DN and Askeyev, AO and Döppes, D and Friedrich, R and Lindauer, S and Rosendahl, W and Aspi, J and Hofreiter, M and Lidén, K and Dalén, L and Díez-Del-Molino, D},
title = {Moose genomes reveal past glacial demography and the origin of modern lineages.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {854},
pmid = {33267779},
issn = {1471-2164},
support = {grant 2018-01640//FORMAS/ ; grant 2017-04647//Vetenskapsrådet/ ; CTS 17:109//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; CTS 19:257//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; },
abstract = {BACKGROUND: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.

RESULTS: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.

CONCLUSIONS: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.},
}

@article {pmid33259759,
year = {2020},
author = {Wellman, HP and Austin, RM and Dagtas, ND and Moss, ML and Rick, TC and Hofman, CA},
title = {Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1940},
pages = {20202343},
pmid = {33259759},
issn = {1471-2954},
mesh = {Alaska ; Animals ; *Archaeology ; British Columbia ; *Genome, Mitochondrial ; *Otters ; Washington ; },
abstract = {Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.},
}

Alaska
Animals
*Archaeology
British Columbia
*Genome, Mitochondrial
*Otters
Washington

@article {pmid33256612,
year = {2020},
author = {Feuerborn, TR and Palkopoulou, E and van der Valk, T and von Seth, J and Munters, AR and Pečnerová, P and Dehasque, M and Ureña, I and Ersmark, E and Lagerholm, VK and Krzewińska, M and Rodríguez-Varela, R and Götherström, A and Dalén, L and Díez-Del-Molino, D},
title = {Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {844},
pmid = {33256612},
issn = {1471-2164},
support = {VR 2012-3869//Swedish Research Council/ ; 2015-676//Svenska Forskningsrådet Formas/ ; 676154//H2020 Marie Skłodowska-Curie Actions/ ; 210119/Z/18/Z//Velux Fonden/ ; CTS17:109//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; },
abstract = {BACKGROUND: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

RESULTS: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.

CONCLUSIONS: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.},
}

@article {pmid33256122,
year = {2020},
author = {Koupadi, K and Fontani, F and Ciucani, MM and Maini, E and De Fanti, S and Cattani, M and Curci, A and Nenzioni, G and Reggiani, P and Andrews, AJ and Sarno, S and Bini, C and Pelotti, S and Caniglia, R and Luiselli, D and Cilli, E},
title = {Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age.},
journal = {Genes},
volume = {11},
number = {12},
pages = {},
pmid = {33256122},
issn = {2073-4425},
support = {RFO 2017//Università di Bologna/ ; },
abstract = {Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.},
}

@article {pmid33254911,
year = {2021},
author = {García-Rodríguez, F and Piccini, C and Carrizo, D and Sánchez-García, L and Pérez, L and Crisci, C and Oaquim, ABJ and Evangelista, H and Soutullo, A and Azcune, G and Lüning, S},
title = {Centennial glacier retreat increases sedimentation and eutrophication in Subantarctic periglacial lakes: A study case of Lake Uruguay.},
journal = {The Science of the total environment},
volume = {754},
number = {},
pages = {142066},
doi = {10.1016/j.scitotenv.2020.142066},
pmid = {33254911},
issn = {1879-1026},
mesh = {Antarctic Regions ; Eutrophication ; *Ice Cover ; *Lakes ; Uruguay ; },
abstract = {High resolution XRF scanning documented inter-annual paleolimnological changes of a Subantarctic periglacial lake, during a process of centennial glacier retreat in King George Island, Antarctica. Two major paleoenvironmental stages were inferred from the combined analysis of elemental, molecular and isotopic biomarkers, with a boundary or transition set at about 3200 yr BP. The first stage was characterized by a relatively low allochthonous organic content, reduced productivity and nitrogen levels. Such paleoenvironmental conditions are interpreted as a terrestrial system under periglacial influence, where material influx was related to erosion process from the melt water discharge, because of the proximity to the Collins Glacier ice cap. After the major Holocene glacier advance dated at about 3500 yr BP, the ice cap retreat led to the formation of Lake Uruguay, which involved in filling processes leading to moraine deposits, proglacial meltwater channels, and lakes next to the land glacier. During the second stage, with the onset of the Current Warm Period, prior to 1900 CE the stabilization of the Zr/Rb ratio within the laminated sediments documented the origin of the lacustrine sedimentation system, with subsequent increases in the sedimentation rate and biomass content (total nitrogen and organic carbon). Time series analyses revealed that the lake displayed variability cycles related to El Niño Southern Oscillation (ENSO), as reflected by high resolution sedimentological proxies for grain size, weathering, allochthonous inputs from the watershed, increase of biomass and productivity, and changes in redox conditions, all of which displayed similar oscillation cycles from 2 to 6 yr. During this periglacial recession and associated eutrophication process, we detected a striking loss in both bacterial specific richness and diversity as inferred from preliminary selected ancient DNA analyses. Thus, the Antarctic warming scenario leading to glacier depletion appears to exert deterioration consequences on the Subantarctic microbial web.},
}

Antarctic Regions
Eutrophication
*Ice Cover
*Lakes
Uruguay

@article {pmid33250022,
year = {2021},
author = {Loog, L},
title = {Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1816},
pages = {20190719},
pmid = {33250022},
issn = {1471-2970},
abstract = {Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.},
}