Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[Shuzam87]

Genetic continuity and change among the Indigenous peoples of California

https://doi.org/10.1038/s41586-023-06771-5

Abstract

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400–200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.

[FR9CZ6]

Ancient DNA sheds light on the origin and migration patterns of the Xianbei confederation

https://link.springer.com/article/10.100...23-01899-x

Xianbei was one of the most powerful nomadic groups in Eastern Eurasia since the collapse of the Xiongnu empire. However, owing to a lack of first-hand written records, the origins of Xianbei and their relationships with surrounding populations remain enigmatic. Here, we produce genomic data of nine Xianbei individuals (ca. 200 CE to 300 CE) from northern China. By combining the available genomes in the literature, we assemble a database that covers almost the entire period of Xianbei as well as samples pre- and post-dating them, allowing us to set the Xianbei in a temporal context. Our study decisively addresses a longstanding hypothesis and supports that the Xianbei was originated from the Amur River region, more specifically from far northeastern China around the Great Khingan Mountain ranges. We also provide direct genetic evidence that during their initial process of moving southward toward the Central Plains of China, Xianbei only received limited exogenous genetic contribution from the local population they encountered, but after settling in northern China, Xianbei not only transformed from nomadic tribes to sedentary agriculturalists but also genetically admixed into the local residents there. In sum, our study represents the inaugural genomic exploration into the origins of the Xianbei, affirms the profound historical connection between the Xianbei and ancient Han Chinese communities, and elucidates the dynamic population history of northern China.

[R.Rocca]

Ancient Wheat Genomes Illuminate Domestication, Dispersal, and Diversity.

"Ancient DNA (aDNA) promises to revolutionise our understanding of crop evolution. Wheat has been a major crop for millennia and has a particularly interesting history of domestication, dispersal, and hybridisation, summarised briefly here. We review how the fledgling field of wheat archaeogenomics has already contributed to our understanding of this complex history, revealing the diversity of wheat in ancient sites, both in terms of species and genetic composition. Congruently, ancient genomics has identified introgression events from wild relatives during wheat domestication and dispersal. We discuss the analysis of degraded aDNA in the context of large, polyploid wheat genomes and how environmental effects on preservation may limit aDNA availability in wheat. Despite these challenges, wheat archaeogenomics holds great potential for answering open questions regarding the evolution of this crop, namely its domestication, the different dispersal routes of the early domestic forms and the diversity of ancient agricultural practices. Not only will this research enhance our understanding of human history, but it will also contribute valuable knowledge about ancient selective pressures and agriculture, thus aiding in addressing present and future agricultural challenges."

https://link.springer.com/chapter/10.100...-38294-9_7

Moderators, please move this as it is not ancient human DNA. Thanks!

[Shuzam87]

"Ancient DNA supports that the evolution of Skin Tone in East Asians intensified after their split with Native Americans"

https://doi.org/10.21203/rs.3.rs-3398597/v1

Abstract

Skin tone has been deeply studied in European populations both using modern and ancient DNA. However, other populations are underrepresented in such studies. One such population is East Asians, for which, interestingly, it has been claimed to evolve light skin tones in parallel to Europeans. Moreover, it is not clear whether this happened before or after their split from Native Americans. Over the last few years, several studies have sequenced hundreds of ancient genomes belonging to East Asians ancient populations. Additionally, some variants have been associated with light skin in East Asians. To shed some light, I applied a Polygenic Risk Score for some of the variants associated with light skin, in 237 modern Native Americans and East Asian individuals and in more than 700 East Asians ancient samples. The results suggest that this phenotype may have started to evolve in the ancestors of East Asians and Native Americans but intensified after their split.

[Shuzam87]

“Migration and social organization of human groups between the Neolithic and the Bronze Age in Southern France: a view from palaeogenomics”

https://theses.hal.science/tel-04300426

New 184 analyzed human remains and providing genomic data for 78 individuals from France

Through a multiscale paleogenomic approach, this study aims to document the genetic diversity of human groups in Southern France from the Neolithic to the Bronze Age in relation to the cultural transformations highlighted in the archaeological record. With a regional and diachronic perspective, this study was built around a broad chronological range, spanning from the VIth to the IInd millennium BCE, and a spatial area restricted to the Occitanie region. We focused on a corpus of eleven archaeological sites, totaling 184 analyzed human remains and providing genomic data for 78 individuals. We conducted a population-based approach, documenting regional genetic variability between the Neolithic and the Bronze Age. This allowed us to discuss the transformations in genetic pools and population dynamics identified during both the Mesolithic-Neolithic transition and the IIIrd millennium BCE. Our results reinforce the dichotomy between Continental and Mediterranean Neolithization waves. Mediterranean Neolithic diffusion appears to be associated with smaller groups, characterized by recurrent admixture with Mesolithic groups. The observation of regional genetic variability between the second phase of Neolithization and the first half of the IIIrd millennium BCE also illustrates a relative genetic continuity within the groups of southern France, despite cultural transformations. From the second half of the IIIrd millennium BCE, a different genetic ancestry originating from the Pontic steppes spreads more widely in Western Europe. Our results complement and support previous observations made at the scale of Western Europe, pointing to a later and less pronounced diffusion of this genetic ancestry in Southern France. Additionally, we characterized the genetic diversity of the studied groups at the scale of funerary sites to enhance understanding of the social functioning of these communities and their funerary practices. We extensively documented the Late Neolithic burial cavity of the Aven de la Boucle (Corconne, Gard) using genomic data, archaeo-anthropological data, and Bayesian modeling based on radiocarbon dates. The analyses revealed the existence of a patrilineal system in which the association to a specific paternal lineage and the access to the burial appear to be correlated. Through multiple scales of resolution, our results initiate the filling of a temporal and spatial gap for the groups inhabiting southern France between the VIth and Ist millennium BCE, highlighting the potential of a multidisciplinary paleogenomic approach, thus enabling a better understanding of regional funerary contexts.

[Anthrofennica]

"The genetic legacy of the expansion of Bantu-speaking peoples in Africa"

https://www.nature.com/articles/s41586-023-06770-6

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000–4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

[RCO]

A multidisciplinary overview on the Tupi-speaking people expansion
Marcos Araújo Castro e Silva, Tábita Hünemeier
First published: 22 November 2023 https://doi.org/10.1002/ajpa.24876
Towards a biocultural synthesis of the peopling of the Americas

Abstract
ENTHIS LINK GOES TO A ENGLISH SECTIONPTTHIS LINK GOES TO A ENGLISH SECTION
The cultural and biological diversity of South American indigenous groups represent extremes of human variability, exhibiting one of the highest linguistic diversities alongside a remarkably low within-population genetic variation and an extremely high inter-population genetic differentiation. On top of that, this region has seen some of the most dramatic demographic events in human history unleashed by the European colonization of the Americas. As a result of this process, the distribution of indigenous populations has been radically changed. In this review we focus on the Tupi, the largest and most widespread linguistic family in eastern South America. Tupi are believed to have originated in southwestern Amazon, from where some of its subfamilies expanded into other parts of the Amazon and, in the case of the Tupi-Guarani, beyond its borders. Recent evidence from archaeology, linguistics, and genetics aligns with José Brochado's Tupi Expansion model. He proposed that the gradual development of agricultural systems within the Amazon resulted in population growth and, eventually, territorial expansion. This model also supports separate Tupi Expansion branches: Tupinambá (Atlantic coast) and Guarani (south, midwest Brazil). Although being the most populous group on Brazil's Atlantic coast, which was the most affected by European colonization, the Tupi still account for roughly 20% of the country's overall indigenous population. Finally, despite its importance and more than a century of research on the Tupi and their expansion history, many key questions remain unanswered, which we attempt to summarize and explore here.

The Tupi-Guarani were socially organized into regional chiefdoms comprised of confederations of villages (Noelli, 1998). This societal structure enabled them to organize war expeditions that traversed great distances via major waterways. These expeditions had multiple objectives, including attacking enemies, annexing territories, capturing women, and, in some instances, enslaving the defeated (Santos-Granero, 2009). Central to the Tupi-Guarani culture was a strong bellicose ethos and a predatory cosmology. This found expression in practices such as anthropophagic ritual feasting, which carried significant social implications, particularly as a means of acquiring status, a practice that endured until colonial times (Fausto, 2012). Therefore, this expansionist ethos, deeply rooted in their culture and societal structure, likely propelled the Tupi-Guarani to undertake territorial expansion, engage in conflict, and extend their influence across vast territories. This illustrates how the social and cultural characteristics of the Tupi likely played a role in driving the vast territorial expansion of the group.

https://onlinelibrary.wiley.com/doi/10.1002/ajpa.24876

[Radko]

Pathways to the medieval hospital: collective osteobiographies of poverty and charity

Abstract
Medieval hospitals were founded to provide charity, but poverty and infirmity were broad and socially determined categories and little is known about the residents of these institutions and the pathways that led them there. Combining skeletal, isotopic and genetic data, the authors weave a collective biography of individuals buried at the Hospital of St John the Evangelist, Cambridge. By starting with the physical remains, rather than historical expectations, they demonstrate the varied life courses of those who were ultimately buried in the hospital's cemetery, illustrating the diverse faces of medieval poverty and institutional notions of charity. The findings highlight the value of collective osteobiography when reconstructing the social landscapes of the past.

https://www.cambridge.org/core/journals/...1B2A6035AA

https://www.aftertheplague.org/

https://www.theguardian.com/science/2023...-cambridge

[VladMC]

Data for "An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago"

This collection includes the EIGENSTRAT format genotype data of 23 Jomon-related ancient individuals for the 1240K SNP panel. These individuals were in-depth re-analyzed in the study "An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago". These individuals were previously published elsewhere.

https://edmond.mpg.de/dataset.xhtml?pers...7/3.CXKGCX

[RCO]

100 ANCIENT GENOMES SHOW REPEATED POPULATION TURNOVERS IN NEOLITHIC DENMARK
Morten E. Allentof, Kristian Kristiansen, Eske Willerslev et al.

67 Summary
68 Major migration events in Holocene Eurasia have been characterised genetically at broad
regional scales1–4 69 . However, insights on the population dynamics in the contact zones are
hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7 70 . To
71 address this we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300
72 years of the Mesolithic, Neolithic and early Bronze Age in Denmark and integrated these
with proxies for diet (δ13C & δ15N isotopes), mobility (87Sr/86 73 Sr isotopes), and vegetation
74 cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose,
75 Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western
76 European Hunter-Gatherers (HGs). Despite shifts in material culture they displayed genetic
77 homogeneity from ~10,500 cal. BP until 5,900 cal. BP when Neolithic farmers with
78 Anatolian-derived ancestry arrived. Although this process was delayed by more than a
79 millennium relative to Central Europe it was very abrupt and resulted in a population
80 turnover with limited genetic contribution from local HGs. The succeeding Neolithic
81 population, associated with the Funnel Beaker Culture, persisted for just ~1000 years before
82 immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid
83 population replacement gave rise to the Single Grave Culture with an ancestry profile more
84 similar to present-day Danes. In our multiproxy dataset these major demographic events are
85 manifested as parallel shifts in genotype, phenotype, diet, and land use 

Willerslev, E. (2024). 100 ancient genomes show repeated population turnovers in neolithic Denmark. Nature. https://doi.org/10.17863/CAM.104336

Repository version
https://www.repository.cam.ac.uk/items/7...400425345f

Repository URI
https://www.repository.cam.ac.uk/handle/1810/361551

Repository DOI
https://doi.org/10.17863/CAM.104336

[AimSmall]

https://www.repository.cam.ac.uk/handle/1810/361551
https://www.repository.cam.ac.uk/handle/1810/361551


No item found for the identifier
handle: 1810/361551

[RCO]

Intramural child burials in Iron Age Navarra: How ancient DNA can contribute to household archaeology
October 2023
DOI:10.11588/propylaeum.1280.c18012
In book: Kinship, Sex, and Biological Relatedness : The contribution of archaeogenetics to the understanding of social and biological relations. (pp.263-295) Publisher: Propylaeum & Landesmuseums für Vorgeschichte Halle

Abstract
The transition from the Late Bronze to the Iron Age on the Iberian Peninsula saw a shift in mortuary customs from mainly inhumation to cremation of the deceased. The poor preservation characteristic of cremated skeletal remains has hindered molecular analyses (isotope analyses, ancient DNA) of the Iberian Final Bronze and Iron Age communities of Iberia. Incidentally, a limited number of young children, often newborns, were exempt from the predominant cremation ritual, in favour of intramural inhumations inside buildings at certain settlements. The discourse surrounding the meaning and interpretation of this particular burial rite has developed over a long time in Iberian archaeology but has always been hampered by the limited anthropological, archaeological, and molecular data from these intramural inhumations. Here, we study the genomes of 37 intramurally buried children found in three Early Iron Age settlements, dated between c. 800–450 BC. Population genetic analyses on the newly reported individuals extend our understanding of ancient Iberia by revealing previously unsampled genetic diversity as well as showing a lesser influence of Mediterranean ancestry than on previously published Iron Age individuals from northern Spain. We also provide insights into the sex and biological relatedness of the children, and in so doing, elucidate different aspects of the intramural burial ritual and building use in settlements. More broadly, the genetic data from these individuals fill an important gap in the archaeogenetic record of northern Spain and offer a unique opportunity to study the genetic makeup and population changes from the Bronze Age to Antiquity.

https://www.researchgate.net/publication...rchaeology

[corrigendum]

Intramural child burials in Iron Age Navarra: How ancient DNA can contribute to household archaeology
October 2023
DOI:10.11588/propylaeum.1280.c18012
In book: Kinship, Sex, and Biological Relatedness : The contribution of archaeogenetics to the understanding of social and biological relations. (pp.263-295) Publisher: Propylaeum & Landesmuseums für Vorgeschichte Halle

Abstract
The transition from the Late Bronze to the Iron Age on the Iberian Peninsula saw a shift in mortuary customs from mainly inhumation to cremation of the deceased. The poor preservation characteristic of cremated skeletal remains has hindered molecular analyses (isotope analyses, ancient DNA) of the Iberian Final Bronze and Iron Age communities of Iberia. Incidentally, a limited number of young children, often newborns, were exempt from the predominant cremation ritual, in favour of intramural inhumations inside buildings at certain settlements. The discourse surrounding the meaning and interpretation of this particular burial rite has developed over a long time in Iberian archaeology but has always been hampered by the limited anthropological, archaeological, and molecular data from these intramural inhumations. Here, we study the genomes of 37 intramurally buried children found in three Early Iron Age settlements, dated between c. 800–450 BC. Population genetic analyses on the newly reported individuals extend our understanding of ancient Iberia by revealing previously unsampled genetic diversity as well as showing a lesser influence of Mediterranean ancestry than on previously published Iron Age individuals from northern Spain. We also provide insights into the sex and biological relatedness of the children, and in so doing, elucidate different aspects of the intramural burial ritual and building use in settlements. More broadly, the genetic data from these individuals fill an important gap in the archaeogenetic record of northern Spain and offer a unique opportunity to study the genetic makeup and population changes from the Bronze Age to Antiquity.

https://www.researchgate.net/publication...rchaeology

The full volume can be downloaded here:
https://books.ub.uni-heidelberg.de//prop.../book/1280

[Song]

Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals
Daniel N. Harris, Alexander Platt, Matthew E.B. Hansen, Charles Fokunang, Alfred K. Njamnshi, Sarah A. Tishkoff
Published:October 13, 2023 
https://www.cell.com/current-biology/ful...23)01315-5

Highlights

• Anatomically modern human-to-Neanderthal introgression occurred ∼250,000 years ago

•∼6% of the Altai Neanderthal genome was inherited from anatomically modern humans

• Recent non-African admixture brought Neanderthal ancestry to some African groups

• Modern human alleles were deleterious to Neanderthals

Summary

Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations.In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups—a hallmark of incipient speciation.

Unknown Human Lineage Found Buried in The Neanderthal Genome
https://www.sciencealert.com/unknown-hum...hal-genome

"We found this reflection of ancient interbreeding where genes flowed from ancient modern humans into Neanderthals," says Alexander Platt, an evolutionary biologist at the University of Pennsylvania.

"This group of individuals left Africa between 250,000 and 270,000 years ago. They were sort of the cousins to all humans alive today, and they were much more like us than Neanderthals," Platt says.

The early modern humans who made it to Eurasia later died out, the researchers note, and Neanderthals continued to dominate the continent for another 200,000 years or so. Hidden in the Neanderthal genome, however, were remnants from this ancient encounter.

[Shuzam87]

“Population dynamics in Iron Age Xinjiang inferred from ancient genomes of the Zhagunluke site”

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006152

Zhagunluke culture, as one of the Iron Age cultures in southern Xinjiang, was the representative of the ancient Qiemo kingdom that showed diverse cultural elements and the coexistence of agriculture and livestock farming. However, the genetic structure and formation of ancient Qiemo people were unclear. Here, we reported the ancient genomes of two individuals from Zhagunluke No.1 cemetery. Combined with previously published data, we observed that most Zhagunluke samples showed genetic admixtures between East and West Eurasians with varying proportions of ancestry. However, we also found a genetic outlier with dominant millet farmers-related ancestry from the Yellow River or the West Liao River basins. The genetic substructure of the Zhagunluke population demonstrated multi-way demographic interactions in Iron Age southern Xinjiang with populations from the surrounding areas of Western Steppe, Central Asia and East Asia.