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Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not. [ABSTRACT FROM AUTHOR]

Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups. [ABSTRACT FROM AUTHOR]

When studying the DNA polymorphism of ancient seeds from archaeological excavations, and comparing them with modern ones, it is possible, depending on the evolutionary significance/neutrality of the identified differences, to either find traces of adaptation of genotypes used in ancient times to unfavorable environmental conditions, or to clarify the origin of the samples, establishing additional evidence of trade and economic ties between different regions in different eras. The purpose of this work was to study the DNA polymorphism by comparing the 12th-century barley seeds from the Usvyaty settlement of the Pskov Region and VIR collection accessions of different geographical origin using the CHI and ELF3 gene fragments sequencing data. Of the 18 polymorphic SNP loci identified in the studied genes during the analysis of the barley samples under study, seven SNPs were from the regions amenable for resequencing in ancient DNA samples. The identified allelic changes in those seven SNP loci were neutral and did not lead to amino acid substitutions, therefore they can be used for a comparative analysis of the sample origin. The haplotype revealed in ancient barley based on the seven studied SNPs did not completely coincide with any of the studied accessions from the VIR collection. At the same time, rare alleles showed similarities with a Belarusian cultivar ‘Krinichny’, and the frequently occurring ones with several accessions of H. vulgare L. of different origin (Sweden, Denmark, Armenia), as well as with H. spontaneum (K. Koch) Thell.

Based on paleogenetic analysis of anthropological remains from Denisova Cave in Altai Mountains, a previously unknown population of fossil people, the Denisovans, was discovered, and a complex picture of their interaction with Neanderthals was established. Currently, 17 skeletal remains of Paleolithic hominins discovered in the cave have been identified, and fragments of ancient human DNA have been isolated from its Pleistocene deposits. This work is devoted to the characteristics of the Denisova Cave inhabitants based on a comprehensive analysis of currently known paleoanthropological and paleogenetic data. We show that the oldest human remains in Altai were found in the basal deposits of the Denisova Cave. They belong to the Denisovans, hominins that share a common ancestor with Neanderthals but a different population history. The lower culture-bearing layers with finds from the initial stage of the Middle Paleolithic contain fragments of genomes that differ from the Denisovan genomes from the overlying sediments, indicating the existence of two different populations of Denisovans. The earliest evidence of the appearance of Neanderthals in Altai was also found in Denisova Cave. A complete genome sequence was isolated from the phalanx of the foot, which received the conditional name Altai Neanderthal. Between the populations of Neanderthals and Denisovans in Altai, there was a regular exchange of genetic material.

Throughout history, it has been observed that human populations have buried the deceased members of their communities following different patterns. During the Copper Age and the Bronze Age—periods on which this study focuses—in the northern sub-plateau of the Iberian Peninsula, we identified different patterns of multiple or collective burial. This work analyzes a total of 58 individuals buried in different multiple or collective graves, to investigate whether the practice of these burials implies a family or biological link between individuals buried together. With this aim, STR markers of nuclear DNA were analyzed, as well as the hypervariable regions I and II of mitochondrial DNA, establishing both close kinship relationships and relationships through maternal lineage. We observed different burial patterns, detecting certain maternal lines preserved in some common burials maintained over time. Close family relationships were observed to a lesser extent, with some occasional exceptions. The results of the analysis formed the basis for a discussion on the concepts of family and community. [ABSTRACT FROM AUTHOR]

Summary: West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22’s West Asian origin, associated population movements, and possible linguistic impacts.

The article addresses the challenges posed by the interdisciplinary collaboration that led to the recent Nature article presenting results of the extraction of ancient human DNA from a perforated deer tooth found in Denisova Cave. We provide a critical analysis of the contextual data that directly impacts the interpretation of the genetic data and the evaluation of the potential of the new DNA extraction technique for future studies. We discuss in greater detail Denisova, the only site that has produced truly exploitable palaeogenetic results. We highlight major unresolved dating inconsistencies at Denisova that need inquiry and explanation. We also emphasize the lack of an appropriate theoretical framework in the analysis of the tooth, of information on the lateralization, sex, age, perforation technique, wear, on the ochre residues, and the release of erroneous information on the associated faunal assemblage. We conclude that quality archaeological data and their sound evaluation should complement paleogenetic data to create unified, reliable, and verifiable narratives about human history. [ABSTRACT FROM AUTHOR]

Summary: The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros’s evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.

Summary: Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using

The paper focuses on the Pleistocene deposits in Perspektywiczna Cave, southern Poland, related to cave hyena (Crocuta crocuta). We used direct radiocarbon dating of hyena fossils supported by genetic and stable isotope analyses to infer the paleobiology of this population. Radiocarbon dating of 19 hyena remains suggests long inhabitation of the region during early MIS 3, around 50–34 ky cal BP. The youngest among our dates, 34,355–33,725 cal BP (1σ, combined of two dates for the same specimen) points out the latest appearance of a cave hyena north to Carpathians. Beside this long period of occupation, the Perspektywiczna Cave hyenas stayed ecologically stable, but their genetic structure changed. Two mtDNA haplogroups were present, one typical for other Late Pleistocene European populations and the other one known so far only from recent African populations. [ABSTRACT FROM AUTHOR]

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

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.

Throughout history, it has been observed that human populations have buried the deceased members of their communities following different patterns. During the Copper Age and the Bronze Age—periods on which this study focuses—in the northern sub-plateau of the Iberian Peninsula, we identified different patterns of multiple or collective burial. This work analyzes a total of 58 individuals buried in different multiple or collective graves, to investigate whether the practice of these burials implies a family or biological link between individuals buried together. With this aim, STR markers of nuclear DNA were analyzed, as well as the hypervariable regions I and II of mitochondrial DNA, establishing both close kinship relationships and relationships through maternal lineage. We observed different burial patterns, detecting certain maternal lines preserved in some common burials maintained over time. Close family relationships were observed to a lesser extent, with some occasional exceptions. The results of the analysis formed the basis for a discussion on the concepts of family and community.

Summary: In South Tyrol (Eastern Italian Alps), during Late Antiquity-Early Middle Ages, archeological records indicate cultural hybridization among alpine groups and peoples of various origin. Using paleogenomics, we reconstructed the ancestry of 20 individuals (4th–7th cent. AD) from a cemetery to analyze whether they had heterogeneous or homogeneous ancestry and to study their social organization. The results revealed a primary genetic ancestry from southern Europe and additional ancestries from south-western, western, and northern Europe, suggesting that cultural hybridization was accompanied by complex genetic admixture. Kinship analyses found no genetic relatedness between the only two individuals buried with grave goods. Instead, a father-son pair was discovered in one multiple grave, together with unrelated individuals and one possible non-local female. These genetic findings indicate the presence of a high social status familia, which is supported by the cultural materials and the proximity of the grave to the most sacred area of the church.

Summary: Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.

Summary: Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.

Summary: The Báthory family was one of the most powerful noble families in the medieval Hungarian Kingdom. Their influence peaked during the Ottoman occupation of Hungary, when the only partially autonomous region of the country was Transylvania, under Turkish protectorate. Several members of the family became Princes of Transylvania, and one of them, István Báthory, was also the elected King of Poland. We hereby present the first genetic data about this extinct family. Archaeological excavations in Pericei, a settlement now part of Romania, revealed the former family chapel of the Báthory family. Through this work, two Báthory family members were successfully identified among the 13 skeletons found at the site. The presence of Y chromosome haplogroup R-S498 fits the historical account describing the family’s German (Swabian) origins. Their genomic composition also indicates a family of Germanic origin that intermixed with medieval Hungarians.

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice‐free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long‐term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre‐ and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short‐lived LGM peak. [ABSTRACT FROM AUTHOR]

Summary: The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

BAČA, Martin. Ancient DNA, paleogenetics, cultural history and why historians should be interested. Historický časopis, 2022, 70, 3, pp. 487– 513, Bratislava. This paper advances understanding of the ancient genomics revolution of the last decade drawing upon the recent archaeological debate concerning key epistemological and methodological issues. On many levels, ancient DNA becomes a concept of general interest. It is evident that historians are also becoming increasingly professionally involved and should therefore engage more in this discussion. As a model for demonstrating the most evident interdisciplinary obstacles which occurs when dealing with the ancient DNA, I chose a popular topic, concerning the 3rd millennium BC migration from the Pontic-Caspian steppes westward. It has currently been backed by archaeogenetics and is supposed to correlate with the spread of Indo-European languages.

A correlation of the results of the study of the paleoanthropological materials from the necropolis of Maitan by different scientific methods has been carried out in order to establish chronological and spatial differentiation of the burial ground and origins of the group. The complex approach allows the analysis of the problems of absolute and relative chronologies of the necropolis, demographic dynamics of the group in the context of the natural environment, and anthropological and genetic structure of the Bronze Age populations of the Eurasian steppes. The paleodemographic context reconstructed for the Maitan group is typical for the populations of the Bronze Age; some of its features may indicate an early period of adaptation, possibly related to migration of the group into the new territory. The intergroup statistical analysis of craniological materials suggests primarily western origins of the people. Particular craniological characteristics of some interred of the necropolis correspond with the recorded on the Maitan ware long-distance imports from the Urals-Tobol region of the Alakul Culture. For the first time on the materials of a numerically representative series of samples of humans and terrestrial herbivores of the Bronze Age Central Kazakhstan, Upper Tobol River region, and Trans-Urals steppes, the regional isotopic background has been established. Some individuals from the earliest burials of Maitan, according to the radiocarbon dating, are similar in isotopic ratios of carbon and nitrogen to the groups from further western regions of the Upper Tobol River steppes, whereas the other interred correspond in the isotopic values with local Central Kazakhstan samples. It is possible that at the later stages of the spatial organization of the necropolis, women featuring a genetic profile different from other individuals and buried within the fences of the western planigraphic group took part in the formation of its remaining collective. In general, according to the series of calibrated radiocarbon dates, Maitan burial ground dates to the 18th — early 17th century BC.

In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.

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Summary: A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618–842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308–1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%–100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.

The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group. [ABSTRACT FROM AUTHOR]

The emergence and development of massive parallel sequencing (new generation sequencing) methods have opened up new prospects in the study of ancient organisms, including extinct ones. Numerous skeletal remains from archaeological and museum collections are often the only source of information on ancient species and populations. In this review, we discuss the features of human bone tissue and the advantages and disadvantages of bone material as a source of DNA for genomic analysis of ancient people. Here we present new methodological approaches to DNA extraction from ancient human skeletal remains and its preparation for large-scale parallel sequencing are presented, as well as prospects and directions for further research in a new interdisciplinary field, paleogenomics. [ABSTRACT FROM AUTHOR]

Summary: Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.

The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.

Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in "high impact" journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against 'helicopter science', such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos. [ABSTRACT FROM AUTHOR]

On May 16, 2020, the Center for Academic Research and Training in Anthropogeny organized the symposium "Impact of Infectious Disease on Humans and Our Origins". The symposium aimed to gather experts on infectious diseases in one place and discuss the interrelationship between different pathogens and humans in an evolutionary context. The talks discussed topics including SARS-CoV-2, dengue and Zika, the notion of human-specific diseases, streptococci, microbiome in the human reproductive tract, Salmonella enterica, malaria, and human immunological memory. [ABSTRACT FROM AUTHOR]

Changes, that have occurred in the area of distribution of the cultural complex Cucuteni-Trypillia can be considered using traditional methods for studying of pottery assemblages, of course, taking into account data from the natural sciences, including paleogenetics. For the period of the spreading of the painted pottery and formation of Cucuteni-Trypillia, reconstructions were carried out before only taking into account the interpretation of the results of ceramic studies, which showed both the progress and the formation of some new cultural groups of various levels. In the second case, the events of the last quarter of 5th mil. BC were examined and then verified using both the study of pottery assemblages, including pottery of the «Cucuteni C» type, paleogenetics and anthropology. A comparison of the results showed the possibilities of mutual verification, as well as the unique source-study capabilities of various methods that give the greatest effect with an interdisciplinary approach. As a result, it was possible to successfully compare the results of genetic studies that showed the penetration into the communities of Trypillia farmers some amount of representatives of populations related to western and eastern hunter-gatherers, partially connected with other groups of the farming population, indicated in some cases by archaeological materials.

Summary: Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.

Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in “high impact” journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against ‘helicopter science’, such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos.

Summary: The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals’ mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.

Introduction. The article presents the results of the analysis of mitochondrial DNA and Y-chromosome samples obtained from the representatives of Sarmatian populations from the Lower Volga region belonging to all stages of the culture. Methods and materials. The authors have screened samples from 202 individuals representing three cultural and chronological Sarmatian groups (Early Sarmatian, Middle Sarmatian and Late Sarmatian cultures). As a result, the researchers have determined the structure and phylogenetic position of 62 mitochondrial DNA samples and 12 Y-chromosome samples, carried out a comprehensive analysis of the results. The authors have interpreted the obtained results in terms of the formation of the Sarmatian genetic composition and their genetic relationships. Results and discussion. The paper shows that the Sarmatian mitochondrial DNA pool is characterized by a high level of diversity, which is also typical for other Early Iron Age nomadic groups. The mitochondrial DNA lineages of Western Eurasian origin dominate in the Sarmatian gene pool, while lineages of Eastern Eurasian haplogroups cover less than 13% of the total sample. Data on both genetic markers suggests that the formation of the main features of the Sarmatian gene pool could be alternatively influenced by populations from more eastern regions, genetically more related to the Andronovo historical and cultural community, which is consistent with the data of physical paleoanthropology, or autochthonous populations of the Lower Volga and adjacent regions. The mitochondrial DNA data indicates a significant genetic influence of the populations from more southern regions of the Eurasian steppe belt on the Sarmatian gene pool. In addition, the authors show the presence of Eastern Eurasian components in the gene pools of all chronological Sarmatian groups, which may indicate the genetic influence of early nomads from eastern regions of the Eurasian steppe belt. The exact time of the appearance of these eastern genetic components in the Lower Volga region remains unclear. At the same time, the authors did not find the signs of an increase in the role of eastern components during the transition from the Early to Middle and to Late stages of the Sarmatian culture, which could be expected based on the data of archaeology and physical anthropology. Prospects. Prospects for a more detailed reconstruction of the Sarmatian genetic history in the Lower Volga region are associated with the further development of the diachronic model, including the accumulation of more mitochondrial DNA and Y-chromosome data for the population of each stage of the Sarmatian culture, the involvement of groups preceding the Sarmatians in the region in the study and the analysis of additional markers of nuclear DNA.

Summary: Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.

ABSTRACT Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.

The Y chromosome is a unique tool for studying the structure of gene pools and the evolutionary history of human populations. Patrilinearity ensures the sequential accumulation of mutations, as a result of which the Y chromosome is a fairly simple marker system for reconstructing evolutionary changes, migration, and other demographic processes in human populations. The analysis of Y-chromosome haplogroups can be effectively applied both for the analysis of the genetic and demographic history of various populations and for large-scale phylogenetic and phylogeographic studies of individual monophyletic lineages of different hierarchical levels. The discovery of novel population-specific DNA markers of this part of the human genome makes it possible to analyze in great detail the population, subethnic, and generic structure of various ethnic groups throughout all periods of its formation. Determination of the allelic profile of male samples in paleogenetic studies is especially important for the reconstruction of migrations, component composition, continuity of the genetic heritage of ancient populations, and clarification of the phylogeny of various sublineages. The accumulation of big data on the distribution of various haplogroups specific to different populations and the specificity of their profiles by SNP and STR markers, in addition to solving fundamental problems, allows us to succeed in solving practical problems on the genetic genealogy of each man, as well as the ethnic identification of an unknown individual based on his DNA sample and the development of test systems for DNA identification. [ABSTRACT FROM AUTHOR]

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Summary: Anthropology began in the late nineteenth century with an emphasis on kinship as a key factor in human evolution. From the 1960s, archaeologists attempted increasingly sophisticated ways of reconstructing prehistoric kinship but ancient DNA analysis has transformed the field, making it possible, to directly examine kin relations from human skeletal remains. Here, we retrieved genomic data from four Late Neolithic individuals in central China associated with the Late Neolithic Longshan culture. We provide direct evidence of consanguineous mating in ancient China, revealing inbreeding among the Longshan populations. By combining ancient genomic data with anthropological and archaeological evidence, we further show that Longshan society household was built based on the extended beyond the nuclear family, coinciding with intensified social complexity during the Longshan period, perhaps showing the transformation of large communities through a new role of genetic kinship-based extended family units.

Summary: Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.

Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.

Summary: The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes—7 of which are novel—from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations. [ABSTRACT FROM AUTHOR]