Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[J Man]

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

Abstract

Previous genomic studies understanding the dispersal of Homo sapiens have suggested that present-day East Eurasians and Native Americans can trace their ancestry to migrations from Southeast Asia. However, ineluctable adaptations during the Last Glacial Maximum (LGM) remain unclear. By analyzing 42 genomes of up to 30-fold coverage from prehistoric hunter-gatherers, Jomon, we reveal their descent from Upper Paleolithic (UP) foragers who migrated to and isolated in the Japanese archipelago during Late Pleistocene. We provide compelling evidence suggesting that these UP people underwent positive selection for cold environments, aiding their survival through the LGM facilitated by non-shivering thermogenesis and detecting it polygenically across multiple loci in the Jomon lineage. Our study pioneers the close estimation of the physiological adaptation of ancient humans by the paleogenomic approach.

https://www.biorxiv.org/content/10.1101/...91810v1?ct=

Could not find the data but it should be available at some point.

All raw genomic data (fastq files) are available for download in the DNA DataBank of
Japan (DDBJ) Sequence Read Archive (DRA. https://www.ddbj.nig.ac.jp/index-e.html)
under the accession numbers PRJDB14637, PRJDB18003 and PRJDB18005.

Have you been able to look at the samples from these two upcoming papers at all?


Scandinavian Late Neolithic  https://www.ebi.ac.uk/ena/browser/view/PRJEB76142




https://www.ebi.ac.uk/ena/browser/view/PRJEB70242 - "Paleogenomic data of Prehistoric Alps individuals"

"New insights into the genetic history of prehistoric populations in Eastern Italian Alps from Mesolithic to Middle Bronze Age and highlights of the importance of this region as a crossroads of human movements in prehistory." 98 files

[ilabv]

Integrative modern and ancient genomic resources reveal the evolutionary trajectory of complex disease traits

https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA023355

[teepean]

Isolation and female migration between Neolithic farmers and foragers on the Island of Gotland

Two genetically distinct archaeological groups, Neolithic farmers (4000 - 2600 BCE) and foragers (3300 – 2300 BCE) coexisted on the Island of Gotland for >500 years. Their interaction has long been debated, with some scholars suggesting that it was the same population practicing different ways of life. We generated and analyzed genome-sequence data of six individuals from the megalithic Ansarve burial (3500-2600 BCE) and investigated ancestry, admixture, and disease among both farmers and foragers on Gotland. The Ansarve individuals were genetically related to other European Neolithic farmer groups, demonstrating a different demographic history from the foragers on the island. They were also more closely related to each other, showing isolation on the island. The Ansarve genomes show some admixture with foragers, but this admixture happened mainly prior to their coexistence on Gotland. Interestingly, some of the forager’s genomes display recent gene-flow from female farmers, suggesting exogamy of farmer females into the forager communities on the island.

https://www.ebi.ac.uk/ena/browser/view/PRJEB67196

[Radko]

Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry

Abstract
The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.

https://www.nature.com/articles/s42003-024-06343-x

[Radko]

Ancient genomes reveal insights into ritual life at Chichén Itzá

Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600–1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1,2,3,4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population’s genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500–900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

https://www.nature.com/articles/s41586-024-07509-7

[teepean]

Ancient Plasmodium genomes shed light on the history of human malaria

Abstract

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.

https://www.nature.com/articles/s41586-024-07546-2

Raw sequencing data from 36 malaria-positive individuals, as well as newly reported data from 41 ancient individuals enriched at human ancestry-informative SNP positions, have been deposited at the European Nucleotide Archive.

https://www.ebi.ac.uk/ena/browser/view/PRJEB73276

[Radko]

Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe

Abstract
The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into Central Europe from Anatolia, along the Continental route of dispersal. We employed spatially explicit simulations of palaeogenomic diversity and high-quality palaeogenomic data from 67 prehistoric individuals to assess how population dynamics between indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the Continental route. We estimate that the effective population size of farmers was about five times that of the hunter-gatherers. Additionally, we infer that sporadic long distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited.

https://www.biorxiv.org/content/10.1101/...0.598301v1

[Rozenfeld]

https://www.biorxiv.org/content/10.1101/...1.597880v1

The Genetic History of the South Caucasus from the Bronze to the Early Middle Ages: 5000 years of genetic continuity despite high mobility

Eirini Skourtanioti, Xiaowen Jia, Nino Tavartkiladze, Liana Bitadze, Ramaz Shengelia, Nikoloz Tushabramishvili, Gunnar U. Neumann, Raffaela Angelina Bianco, Angela Mötsch, Kay Prüfer, Thiseas C. Lamnidis, Luca Traverso, Claudia Sagona, Luka Papac, Wolfgang Haak, David Reich, Sturla Ellingvåg, Philipp W. Stockhammer, Johannes Krause, Harald Ringbauer

doi: https://doi.org/10.1101/2024.06.11.597880

Abstract

Archaeological and archaeogenetic studies have highlighted the pivotal role of the Caucasus region throughout prehistory, serving as a central hub for cultural, technological, and linguistic innovations. However, despite its dynamic history, the critical area between the Greater and Lesser Caucasus mountain ranges, mainly corresponding to modern-day Georgia, has received limited attention. Here, we generated an ancient DNA time transect consisting of 219 individuals with genome-wide data from 47 sites in this region, supplemented by 97 new radiocarbon dates. Spanning from the Early Bronze Age 5000 years ago to the so-called "Migration Period" that followed the fall of the Western Roman Empire, we document a largely persisting local gene pool that continuously assimilated migrants from Anatolia/Levant and the populations of the adjacent Eurasian steppe. More specifically, we observe these admixture events as early as the Middle Bronze Age. Starting with Late Antiquity (late first century AD), we also detect an increasing number of individuals with more southern ancestry, more frequently associated with urban centers - landmarks of the early Christianization in eastern Georgia. Finally, in the Early Medieval Period starting 400 AD, we observe genetic outlier individuals with ancestry from the Central Eurasian steppe, with artificial cranial deformations (ACD) in several cases. At the same time, we reveal that many individuals with ACD descended from native South Caucasus groups, indicating that the local population likely adopted this cultural practice.

[VladMC]

Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland

Abstract
Cornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.

https://www.nature.com/articles/s41598-024-62524-y

[Mythbuster General]

Bronze age Northern Eurasian genetics in the context of development of metallurgy and Siberian ancestry

The Eurasian Bronze Age (BA) has been described as a period of substantial human migrations, the emergence of pastoralism, horse domestication, and development of metallurgy. This study focuses on two north Eurasian sites sharing Siberian genetic ancestry. One of the sites, Rostovka, is associated with the Seima-Turbino (ST) phenomenon (~2200-1900 BCE) that is characterized by elaborate metallurgical objects found throughout Northern Eurasia. The genetic profiles of Rostovka individuals vary widely along the forest-tundra Siberian genetic cline represented by many modern Uralic-speaking populations, and the genetic heterogeneity observed is consistent with the current understanding of the ST being a transcultural phenomenon. Individuals from the second site, Bolshoy Oleni Ostrov in Kola, in comparison form a tighter cluster on the Siberian ancestry cline. We further explore this Siberian ancestry profile and assess the role of the ST phenomenon and other contemporaneous BA cultures in the spread of Uralic languages and Siberian ancestry.

https://www.nature.com/articles/s42003-0...MTZieXRlcw

[HurrianFam]

No data yet

The rise and transformation of Bronze Age pastoralists in the Caucasus
Center Name:Max Planck Institute for Evolutionary Anthropology
Study Name:Bronze Age pastoralists in the Caucasus
ENA-FIRST-PUBLIC: 2024-06-17
ENA-LAST-UPDATE: 2024-06-17

“we present new genome-wide data of 131 individuals from 38 archaeological sites in the Caucasus, spanning 6,000 years.”

https://www.ebi.ac.uk/ena/browser/view/PRJEB73987

[VladMC]

Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome

Abstract
The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives’ genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.

https://www.science.org/doi/10.1126/sciadv.adl2468

[Riverman]

Late Neolithic collective burial reveals admixture dynamics during the third millennium BCE and the shaping of the European genome

Abstract
The third millennium BCE was a pivotal period of profound cultural and genomic transformations in Europe associated with migrations from the Pontic-Caspian steppe, which shaped the ancestry patterns in the present-day European genome. We performed a high-resolution whole-genome analysis including haplotype phasing of seven individuals of a collective burial from ~2500 cal BCE and of a Bell Beaker individual from ~2300 cal BCE in the Paris Basin in France. The collective burial revealed the arrival in real time of steppe ancestry in France. We reconstructed the genome of an unsampled individual through its relatives’ genomes, enabling us to shed light on the early-stage admixture patterns, dynamics, and propagation of steppe ancestry in Late Neolithic Europe. We identified two major Neolithic/steppe-related ancestry admixture pulses around 3000/2900 BCE and 2600 BCE. These pulses suggest different population expansion dynamics with striking links to the Corded Ware and Bell Beaker cultural complexes.

https://www.science.org/doi/10.1126/sciadv.adl2468

Article on the paper:
https://www.science.org/content/article/...ped-europe

[teepean]

Female lineages and changing kinship patterns in Neolithic Çatalhöyük

Abstract

Arguments have long suggested that the advent of early farming in the Near East and Anatolia was linked to a "Goddess" cult. However, evidence for a dominant female role in these societies has been scarce. We studied social organisation, mobility patterns and gendered practices in Neolithic Southwest Asia using 131 paleogenomes from Çatalhöyük East Mound (7100-5950 BCE), a major settlement in Central Anatolia with an uninterrupted occupation and an apparent egalitarian structure. In contrast to widespread genetic evidence for patrilocality in Neolithic Europe, the Çatalhöyük individuals revealed no indication of patrilocal mobility. Analysing genetic kin ties among individuals buried in the same house (co-burials) across 35 Çatalhöyük buildings, we identified close ties concentrated within buildings and among neighbours in Çatalhöyük's Early period, akin to those in the preceding Pre-Pottery Neolithic in Southwest Asia. This pattern weakened over time: by the late 7th millennium BCE, subadults buried in the same building were rarely closely genetically related, despite sharing similar diets. Still, throughout the site′s occupation, genetic connections within Çatalhöyük buildings were much more frequently connected via the maternal than the paternal line. We also identified differential funerary treatment of female subadults compared to those of males, with a higher frequency of grave goods associated with females. Our results reveal how kinship practices changed while key female roles persisted over one thousand years in a large Neolithic community in western Eurasia.

https://www.biorxiv.org/content/10.1101/...00259v1?ct=

[teepean]

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

In this study we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675-750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries in Koksijde, one shared with Early Medieval genomes from England and the Netherlands while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to -elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. The isotopic and genetic evidence combined support a model by which the burials, representing an established coastal non-elite community, had incorporated migrants from inland populations. The main group of burials shows abundance of >5cM long shared allelic intervals with the High Medieval site near Koksijde, implying continuity and suggesting that, similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.

https://www.ebi.ac.uk/ena/browser/view/PRJEB70768