Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[Pribislav]

This is the already discussed paper, now available in english.

The Rurikids: The First Experience of Reconstructing the Genetic Portrait of the Ruling Family of Medieval Rus’ Based on Paleogenomic Data

https://actanaturae.ru/2075-8251/article/view/23425/pdf_1

[Radko]

Biological and substitute parents in Beaker period adult–child graves

Abstract
Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult–child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as ‘substitute parents’ in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult–child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.

https://www.nature.com/articles/s41598-023-45612-3

[Norfern-Ostrobothnian]

Chronological and genetic analysis of an Upper Palaeolithic female infant burial from
Borsuka Cave, Poland

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 to an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made towards minimally destructive methods and the benefits of integrating methods to maximise data retrieval from precious but highly degraded and contaminated prehistoric material.

https://www.cell.com/iscience/pdf/S2589-...2360-X.pdf

https://www.ebi.ac.uk/ena/browser/view/PRJEB66365

https://www.mediafire.com/file/9stwwy68d...5.zip/file

[J Man]

Medieval DNA from Kyiv.

https://www.ebi.ac.uk/ena/browser/view/PRJEB63275

Project: PRJEB63275
The town of Kyiv held a key position in Medieval Eastern Europe as it acted as the gateway to the Byzantine Empire. During the 10th to 12th centuries, Kyiv flourished economically, socially, politically and culturally. With the Mongolian siege in 1240 this development came to a halt. Here, we investigated DNA from eleven individuals, nine female and two male, from different gravesites in Kyiv, dated from the 10th to the 17th century.

[FR9CZ6]

[Shuzam87]

“The genetic diversity in the ancient human population of Upper Xiajiadian culture”
https://doi.org/10.1111/jse.13029

Abstract

The West Liao River (WLR) and Yellow River (YR) basins are two major centers of millet farming in northern China. The result from flotation analyses and the spatial distribution of archeological sites indicate that two distinct survival strategies—agriculture and pastoralism were adopted in the southern and western regions of the WLR. Previous studies of ancient populations from the western area of the WLR suggested a correlation between a pastoral economy in the Bronze Age Upper Xiajiadian culture with a decreased genetic affinity with YR farmers. However, the population history of the southern WLR is unknown mainly due to the lack of ancient genetic data. Here we report the genomic data of an ancient individual from the Majiazishan site from the Late Bronze Age southern WLR region associated with Upper Xiajiadian culture. Unlike individuals from western WLR, this individual derived ancestry entirely from Late Neolithic YR farmers. We found a genetic substructure of the ancient human population of Upper Xiajiadian culture, which is consistent with the differences in the subsistence strategies of western and southern WLR. Climate deterioration led to different populations occupying the west and the south, respectively, in the WLR: the nomadic population from the Amur River (AR) in the west and the agricultural population from the YR in the south.

[Mythbuster General]

More preliminary results regarding Sarmatians:

[FR9CZ6]

Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics

Borneo was a crossroad of ancient dispersals, with some of the earliest Southeast Asian human remains and rock art. The island is home to traditionally hunter-gatherer Punan communities, whose origins, whether of subsistence reversion or long-term foraging, are unclear. The connection between its past and present-day agriculturalist inhabitants, who currently speak Austronesian languages and have composite and complex genetic ancestry, is equally opaque. Here, we analyze the genetic ancestry of the northeastern Bornean Punan Batu (who still practice some mobile hunting and gathering), Tubu, and Aput. We find deep ancestry connections, with a shared Asian signal outgrouping modern and ancient Austronesian-ancestry proxies, suggesting a time depth of more than 7,500 years. They also largely lack the mainland Southeast Asian signals of agricultural Borneans, who are themselves genetically heterogeneous. Our results support long-term inhabitation of Borneo by some Punan ancestors and reveal unexpected complexity in the origins and dispersal of Austronesian-expansion-related ancestry.

https://www.cell.com/cell-reports/fullte...all%3Dtrue

[FR9CZ6]

Modelling the demographic history of human North African genomes points to soft split divergence between populations.

https://www.biorxiv.org/content/10.1101/...1.full.pdf

We conducted a comprehensive analysis of 364 genomes to construct detailed  demographic models for the North African region, encompassing its two primary ethnic33 groups, the Arab and Amazigh populations. This was achieved through the utilization of 34 the Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This  innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole-genomes at >30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both methods point to a back-to-Africa origin of North African individuals and a close relationship of North African with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, as early as 22.3 Kya. GP4PG model supports Arabization as the main source of Middle Eastern ancestry in North Africa. The GP4PG model better explaining the observed data includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous gene flow after the split between populations (migration decay). In contrast to what we observed in the ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa.

[R.Rocca]

Previously in pre-print, the paper is now published:

Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps
https://www.sciencedirect.com/science/ar...27#appsec2

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.

[Qrts]

Pre-print:

Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies
https://www.biorxiv.org/content/10.1101/...13.566841v

Abstract
Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P-values of qpAdm models, and f3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f2-statistics, demonstrating the improved demographic inference that could be achieved with advancements in f-statistic estimations.

[Song]

Human genetic adaptation related to cellular zinc homeostasis
Ana Roca-Umbert et al. PLoS Genet. 2023.
Authors
Ana Roca-Umbert 1, Jorge Garcia-Calleja 1, Marina Vogel-González 2, Alejandro Fierro-Villegas 2, Gerard Ill-Raga 2, Víctor Herrera-Fernández 2, Anja Bosnjak 2, Gerard Muntané 1 3 4, Esteban Gutiérrez 2, Felix Campelo 5, Rubén Vicente 2, Elena Bosch 1 4
https://pubmed.ncbi.nlm.nih.gov/37747921

SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans.

https://www.phys.org/news/2023-10-geneti...ental.html

Denisovan SLC30A9 gene in humans and its influence on adaption to cold, high altitudes, mental health.

"Apparently, the change was beneficial and proved a selective advantage for humans. As a consequence, this variation in the SLC30A9 gene was selected and has reached current populations," adds Jorge Garcia-Calleja, co-first author of the study."

"Although the variant was established in Asia as a result of interbreeding between Denisovans and Homo sapiens, it also spread to European and native American populations. In fact, it is found in populations all over the planet, although, in the case of African populations, it is much less frequent."

"The team points out that it is probably the Denisovan genetic adaptation to have the greatest geographical scope discovered to date. "For example, a variant in the EPAS1 gene inherited from the Denisovans allows adapting to life at altitude, but is found only in Tibetans. However, in our case, the impact extends to all populations outside Africa," Bosch concludes.

[Anthrofennica]

Phylogenetic study of the Hungarian-speaking Baranja (Croatia) and Zobor region (Slovakia) populations.

"In this study, we delved into the uniparental genetic lineage of Hungarian-speaking minorities residing in rural villages of Baranja and the Zobor region, located in contemporary Croatia and Slovakia, respectively. Our focus was on identifying ancestral patterns by examining genetic markers distributed across the entire mitogenome and on the Y-chromosomes. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations.

Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of Short Tandem Repeat (STR) data and mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities of East-Central Europe."

https://www.researchsquare.com/article/rs-3604738/v1

[Anthrofennica]

Vikings and Migrants: Unravelling Scandinavia's Genetic Mosaic in the Viking Era.

"We analysed ancient Scandinavian genomes over 2,000 years, revealing Viking-era influx from southern Europe, British-Irish Isles, and the east Baltic. Genetic diversity increased during that time, but later Scandinavians have less non-local ancestry. Uralic ancestry found 1,000 years ago still impacts northern Scandinavians."

https://www.thesciencebreaker.org/breaks...viking-era

[teepean]

Five ancient genomes from Britain (dating from the Iron Age to the Late and Post-Medieval Period) of individuals with aneuploidies.

Ancient DNA is a valuable tool for investigating genetic and evolutionary history but can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes (~0.0001X-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first prehistoric case of mosaic Turner syndrome (45,X0/46,XX) in an Iron Age individual sequenced to average 9-fold coverage, as well as new cases of Down syndrome (47,XY,+21) and Klinefelter syndrome (47,XXY). Overall, our approach provides the first accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can provide new interpretations of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

Data is already available:

https://www.ebi.ac.uk/ena/browser/view/PRJEB65239