Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)

[teepean47]

Neolithic genomes from Southern France showcase intensified interactions with hunter-gatherer communities

The onset of agriculture in Western Europe was accompanied by major demographic changes that shaped the genetic structure of human populations. The expansion of early farmers from Anatolia and the Near East is now well documented, but the complexity of interactions with local hunter-gatherers is less clear. Studies on the local scale can elucidate the regional variability during this transition phase and add nuance to the broader pan-European picture. Furthermore, some regions are still understudied, in particular those associated with the Neolithic expansion along the Mediterranean coastline. To address this, we report new data from Occitanie, a key geographical region in southern France, located between culturally-distinct Neolithic groups of the Iberian Peninsula, southeastern France, and northern Italy. We sequenced 28 ancient human genomes from six sites in Southern France covering a wide range of archaeological contexts and funerary practices, and report new 14C dates for 23 individuals. Spanning from c. 5,500 to c. 2,500 BCE, this dataset allowed us to characterize regional patterns of ancestries in farmer groups throughout the Neolithic in southern France. We find differences between the Mediterranean and Continental waves of the Neolithic expansion regarding the processes and modes of migration and interaction. We detect high proportions of hunter-gatherer ancestry in early Neolithic groups in the South of France, as opposed to other French and West European regions. Our results also highlight the persistence of a high level of hunter-gatherer ancestry in some late Neolithic individuals. The presence of this pattern of ancestry in multiple Western European regions in Late Neolithic communities suggests multiple pulses of inter-group gene flow throughout time and space pointing to complex demographic phenomena.

https://www.sciencedirect.com/scienc...89004222016595

https://www.ebi.ac.uk/ena/browser/view/PRJEB50995

[rozenfeld]

https://www.cell.com/heliyon/fulltex...440(22)03019-5

The genetic legacy of the Hunyadi descendants

Endre Neparáczki
Luca Kis
Zoltán Maróti
Bence Kovács
Gergely I.B. Varga
Miklós Makoldi
Pamjav Horolma
Éva Teiszler
Balázs Tihanyi
Péter L. Nagy
Kitti Maár
Attila Gyenesei
Oszkár Schütz
Eszter Dudás
Tibor Török
Vesna Pascuttini-Juraga
Ivančica Peharda
László Tamás Vizi
Gábor Horváth-Lugossy
Miklós Kásler

Open Access
Published:November 16, 2022
DOI:https://doi.org/10.1016/j.heliyon.2022.e11731

Abstract

The Hunyadi family is one of the most influential families in the history of Central Europe in the 14th–16th centuries. The family’s prestige was established by Johannes Hunyadi, a Turk-beater who rose to the position of governor of the Kingdom of Hungary. His second son, Matthias Hunyadi, became the elected ruler of the Kingdom of Hungary in 1458. The Hunyadi family had unknown origin. Moreover, Matthias failed to found a dynasty because of lacking a legitimate heir and his illegitimate son Johannes Corvinus was unable to obtain the crown. His grandson, Christophorus Corvinus, died in childhood, thus the direct male line of the family ended.

In the framework of on interdisciplinary research, we have determined the whole genome sequences of Johannes Corvinus and Christophorus Corvinus by next-generation sequencing technology. Both of them carried the Y-chromosome haplogroup is E1b1b1a1b1a6a1c ∼, which is widespread in Eurasia. The father-son relationship was verified using the classical STR method and whole genome data. Christophorus Corvinus belongs to the rare, sporadically occurring T2c1+146 mitochondrial haplogroup, most frequent around the Mediterranean, while his father belongs to the T2b mitochondrial haplogroup, widespread in Eurasia, both are consistent with the known origin of the mothers. Archaeogenomic analysis indicated that the Corvinus had an ancient European genome composition.
Based on the reported genetic data, it will be possible to identify all the other Hunyadi family member, whose only known grave site is known, but who are resting assorted with several other skeletons.

Keywords

Ancient genomes
Hunyadi
Corvinus
Hungarian Nobel family

[rozenfeld]

https://www.nature.com/articles/s42003-022-04190-2

Article
Open Access
Published: 18 November 2022

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave

Gabriele Scorrano, Sofie Holtsmark Nielsen, Domenico Lo Vetro, Rikai Sawafuji, Meaghan Mackie, Ashot Margaryan, Anna K. Fotakis, Cristina Martínez-Labarga, Pier Francesco Fabbri, Morten E. Allentoft, Marialetizia Carra, Fabio Martini, Olga Rickards, Jesper V. Olsen, Mikkel Winther Pedersen, Enrico Cappellini & Martin Sikora

Communications Biology volume 5, Article number: 1262 (2022)

Abstract

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.

[Shuzam87]

Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau

https://doi.org/10.1016/j.isci.2022.105636

Highlights

● The cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau
● Potential population movement into the Tubo-controlled regions from Central Asia


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.

[Waldemar]

Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard

Abstract
Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumours consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.

Cases of Mendelian genetic disease have been uncovered in the archaeological record, but diagnosis is restricted to osteologically visible conditions, with more commonly encountered conditions including achondroplasia, multiple epiphyseal dysplasia and Léri-Weill dyschondrosteosis [1].



https://www.nature.com/articles/s41431-022-01219-2

[Waldemar]

The mitochondrial genomes of two Pre-historic Hunter Gatherers in Sri Lanka

Abstract
Sri Lanka is an island in the Indian Ocean connected by the sea routes of the Western and Eastern worlds. Although settlements of anatomically modern humans date back to 48,000 years, to date there is no genetic information on pre-historic individuals in Sri Lanka. We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese. Both haplogroups are Indian derived and observed in the South Asian region and rarely outside the region.

https://www.nature.com/articles/s10038-022-01099-w

[VladimirTaraskin]

Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019–2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.

https://www.nature.com/articles/s41598-022-25200-7

[Waldemar]

The Mogou Multidisciplinary Investigation Project: insights into the kinship and social organisation of a Bronze Age population in north-west China

Abstract
Excavation at Mogou, a Bronze Age cemetery containing over 1700 burials and 6000 individuals, has revealed a diverse range of multiple burials. Building on this dataset, the Mogou Multidisciplinary Investigation Project aims to explore connections between kinship, burial space and social organisation in Bronze Age north-west China.

https://www.cambridge.org/core/journ...73D6ABE04F9B20

[Webb]

Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019–2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.

https://www.nature.com/articles/s41598-022-25200-7

Sorry, I didn’t see this post this morning. I started a dedicated thread to this paper in the DF27 subsection as it posted many samples from modern samples in Spain.

[Waldemar]

4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists

Abstract
Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.

https://www.nature.com/articles/s41598-022-25384-y