Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[HurrianFam]

Population genomics of Central Asian peoples unveil ancient Trans-Eurasian genetic admixture and cultural exchanges
https://www.sciencedirect.com/science/ar...via%3Dihub

Abstract
Central Asia, a crucible of prehistoric and historical Trans-Eurasian interactions, has been pivotal in shaping cultural exchanges, population dynamics, and genetic admixture. Recent insights from ancient DNA studies have shed light on the extensive population turnover within this region, encompassing a spectrum of groups from Paleolithic hunter-gatherers to Holocene herders and the nomadic pastoralist empires of historical times. The genomic analysis of ancient pathogens across the Eurasian steppe has further deepened our understanding of pathogen origins, clonal expansions, and the intricate processes of host-pathogen coevolution in relation to varying pathogen exposures and their spread. We consolidate the latest findings pertaining to the ancient human and pathogen genomes of Central Asia, elucidating their profound influence on the genomic tapestry of contemporary Central Asians. A notable gap in the current genomic databases for Central Asia is underscored, particularly within the scope of genomics-driven precision medicine. We stress the urgent need for the development of extensive, region-specific genomic resources that hold promise for revealing the genetic blueprints underlying human traits and diseases, refining polygenic scoring models for predictive medicine, and bolstering genomic research endeavors across Central Asia.

[Pribislav]

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

Dilek Koptekin et al.

Abstract

Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. Using 30 new palaeogenomes from Anatolia c.8000-6000 BCE we describe the early Holocene genetic landscape of Western Anatolia, suggesting population continuity since the late Upper Pleistocene. Our findings indicate that the Neolithisation of Western Anatolia in the 7th millennium BCE was a multifaceted process, characterised by the assimilation of Neolithic practices by indigenous groups and the influx of populations from the east, their admixed descendants eventually laying the foundations of Neolithic Southeast Europe. Intriguingly, the observed diversity in material culture among Aegean Early Neolithic communities correlates with their geographical distances but not their genetic differences, signifying a decoupling between cultural developments and genetic admixture processes.

https://www.biorxiv.org/content/10.1101/...3.599747v1

[ilabv]

Life history and ancestry of the Late Upper Palaeolithic infant from Grotta delle Mura (southern Italy, 17 ka)

University of Florence

Abstract

Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. Using 30 new palaeogenomes from Anatolia c.8000-6000 BCE we describe the early Holocene genetic landscape of Western Anatolia, suggesting population continuity since the late Upper Pleistocene. Our findings indicate that the Neolithisation of Western Anatolia in the 7th millennium BCE was a multifaceted process, characterised by the assimilation of Neolithic practices by indigenous groups and the influx of populations from the east, their admixed descendants eventually laying the foundations of Neolithic Southeast Europe. Intriguingly, the observed diversity in material culture among Aegean Early Neolithic communities correlates with their geographical distances but not their genetic differences, signifying a decoupling between cultural developments and genetic admixture processes.

https://www.ebi.ac.uk/ena/browser/view/PRJEB66279



Sending to David tomorrow

[old europe]

the correct abstract of the paper


Life history and ancestry of the Late Upper Palaeolithic infant from Grotta delle Mura (southern Italy, 17 ka)

University of Florence

Abstract



At the end of the Last Glacial Maximum (LGM), a general climate improvement determined a period of great transformation, with new human expansions and changes in material culture across Europe. Despite recent works on social and population dynamics, the role of southern refugia and the biological aspects related to early life history of late Upper Palaeolithic individuals are still not well understood. This study presents a multidisciplinary, high temporal resolution investigation of an Upper Palaeolithic infant from Grotta delle Mura (Apulia, Italy) combining palaeogenomics, dental palaeohistology, spatially-resolved geochemical analyses, and direct AMS radiocarbon dating. The skeletal remains of the infant – Le Mura 1 – were directly dated to 17,079-16,990 cal BP. The results portray a biological history of the development, early life, health and death of the infant. They reveal mobility patterns during gestation, identify several phenotypic traits and a potential congenital disease, and indicate a high level of endogamy. Furthermore, they remark an early spread of the Villabruna-like components along the Italian peninsula, confirming a population turnover around the time of the LGM, and highlight a general reduction in genetic variability from northern to southern Italy. Overall, Le Mura 1 contributes to our better understanding of the early stages of life and the genetic puzzle in the Italian peninsula at the end of the LGM.

[ilabv]

The demic diffusion of Han culture into the eastern Yunnan-Guizhou plateau inferred from ancient genomes

Guizhou Provincial Institute of Cultural Relics and Archaeology, Guiyang

Abstract

The expansion of Han culture into southern China via demic or cultural diffusion remains debated owing to the lack of ancient genomes from historical periods in southern China. Here, we reported 99 ancient human genomes from the Songshan site with Han cultural influence in the eastern Yunnan-Guizhou plateau dated from the Song to Qing dynasties (990 to 1649 AD). We also sequenced the genomes of 51 individuals from present-day Tai-Kadai and Hmong-Mien-speaking populations. We observed genetic stability in the Songshan site over 700 years, with the majority of samples deriving 64% of their ancestry from Han-related Yellow River farmers and the remaining from local hunter-gatherers-related and Tai-Kadai-Austronesian related groups. There were three outliers sharing an excess affinity with present-day Hmong-Mien speakers and one outlier showing a higher proportion of Tai-Kadai-Austronesian-related ancestry. Our result supports the demic-diffusion model of the expansion of Han culture to southern China.

https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA021487


Data may be available imminently, will send to Davidski when it is.

[TanTin]

Population History and Admixture of the Fulani People from the Sahel
Cesar A. Fortes-Lima, Mame Yoro Diallo, Václav Janoušek, Viktor Černý, Carina M. Schlebusch

doi: https://doi.org/10.1101/2024.06.22.600206
https://www.biorxiv.org/content/10.1101/...2.600206v1

[teepean]

DNA sequences from 3 17th century Scottish individuals infected with Yersinia pestis.

This paper has several aims: to determine if Yersinia pestis was the causative agent in the last Scottish plague outbreak in the mid-17th century; map the geographic spread of the epidemic and isolate potential contributing factors to its spread and severity; and examine funerary behaviours in the context of a serious plague epidemic in early modern Scotland. Results confirm the presence of Y. pestis in individuals associated with a mid-17th century plague pit in Aberdeen. This is the first time this pathogen has been identified in an archaeological sample from Scotland. The geographic spread of the plague from 1644 through to 1649 is generally, with some key exceptions, restricted to the central lowlands of Scotland. The role of administrative responses to the epidemic in managing its spread and distribution is unclear. Finally, normative funerary practices tended to co-exist with mass burial scenarios. In conclusion, the distribution of the epidemic is arguably a function of population density/distribution, transportation networks, and the chaos associated with the concurrent civil war. Administrative responses to the epidemic likely had a variable, albeit limited, effect in the central lowlands. More peripheral cities, such as Aberdeen, while also employing sophisticated plague prevention measures, were perhaps initially spared simply due to their distance from the central plague belt. It is unclear if a general fear of the dead and contracting the Pest from plague victims can be used to characterise mid-17th century Scottish public opinion. Mass burial appears to have been a practical approach to the logistical problems mass mortality presented, while many instances of normative burial treatment can also be seen.

https://www.ebi.ac.uk/ena/browser/view/PRJEB76262

Not data available.

[Rozenfeld]

https://www.nature.com/articles/s41598-024-66191-x

    Article
    Open access
    Published: 05 July 2024

Anatolian genetic ancestry in North Lebanese populations

    Daniel E. Platt, Andreas Henschel, Nassim Nicholas Taleb & Pierre Zalloua

Scientific Reports volume 14, Article number: 15518 (2024)

Abstract

Lebanon’s rich history as a cultural crossroad spanning millennia has significantly impacted the genetic composition of its population through successive waves of migration and conquests from surrounding regions. Within modern-day Lebanon, the Koura district stands out with its unique cultural foundations, primarily characterized by a notably high concentration of Greek Orthodox Christians compared to the rest of the country. This study investigates whether the prevalence of Greek Orthodoxy in Koura can be attributed to modern Greek heritage or continuous blending resulting from the ongoing influx of refugees and trade interactions with Greece and Anatolia. We analyzed both ancient and modern DNA data from various populations in the region which could have played a role in shaping the current population of Koura using our own and published data. Our findings indicate that the genetic influence stemming directly from modern Greek immigration into the area appears to be limited. While the historical presence of Greek colonies has left its mark on the region’s past, the distinctive character of Koura seems to have been primarily shaped by cultural and political factors, displaying a stronger genetic connection mostly with Anatolia, with affinity to ancient but not modern Greeks.

Note: this is re-analysis of previously published data.

[miquirumba]

https://www.nature.com/articles/s41598-024-66191-x

    Article
    Open access
    Published: 05 July 2024

Anatolian genetic ancestry in North Lebanese populations

    Daniel E. Platt, Andreas Henschel, Nassim Nicholas Taleb & Pierre Zalloua

Scientific Reports volume 14, Article number: 15518 (2024)

Abstract

Lebanon’s rich history as a cultural crossroad spanning millennia has significantly impacted the genetic composition of its population through successive waves of migration and conquests from surrounding regions. Within modern-day Lebanon, the Koura district stands out with its unique cultural foundations, primarily characterized by a notably high concentration of Greek Orthodox Christians compared to the rest of the country. This study investigates whether the prevalence of Greek Orthodoxy in Koura can be attributed to modern Greek heritage or continuous blending resulting from the ongoing influx of refugees and trade interactions with Greece and Anatolia. We analyzed both ancient and modern DNA data from various populations in the region which could have played a role in shaping the current population of Koura using our own and published data. Our findings indicate that the genetic influence stemming directly from modern Greek immigration into the area appears to be limited. While the historical presence of Greek colonies has left its mark on the region’s past, the distinctive character of Koura seems to have been primarily shaped by cultural and political factors, displaying a stronger genetic connection mostly with Anatolia, with affinity to ancient but not modern Greeks.

Note: this is re-analysis of previously published data.

Do you know how unzip submitted raw data?
https://www.ebi.ac.uk/biostudies/arrayex...MTAB-13882
solved
https://github.com/freeseek/gtc2vcf

[teepean]

https://www.nature.com/articles/s41598-024-66191-x

    Article
    Open access
    Published: 05 July 2024

Anatolian genetic ancestry in North Lebanese populations

    Daniel E. Platt, Andreas Henschel, Nassim Nicholas Taleb & Pierre Zalloua

Scientific Reports volume 14, Article number: 15518 (2024)

Abstract

Lebanon’s rich history as a cultural crossroad spanning millennia has significantly impacted the genetic composition of its population through successive waves of migration and conquests from surrounding regions. Within modern-day Lebanon, the Koura district stands out with its unique cultural foundations, primarily characterized by a notably high concentration of Greek Orthodox Christians compared to the rest of the country. This study investigates whether the prevalence of Greek Orthodoxy in Koura can be attributed to modern Greek heritage or continuous blending resulting from the ongoing influx of refugees and trade interactions with Greece and Anatolia. We analyzed both ancient and modern DNA data from various populations in the region which could have played a role in shaping the current population of Koura using our own and published data. Our findings indicate that the genetic influence stemming directly from modern Greek immigration into the area appears to be limited. While the historical presence of Greek colonies has left its mark on the region’s past, the distinctive character of Koura seems to have been primarily shaped by cultural and political factors, displaying a stronger genetic connection mostly with Anatolia, with affinity to ancient but not modern Greeks.

Note: this is re-analysis of previously published data.

Do you know how unzip submitted raw data?
https://www.ebi.ac.uk/biostudies/arrayex...MTAB-13882
solved
https://github.com/freeseek/gtc2vcf

It is possible and I already did that:

https://genarchivist.com/showthread.php?tid=687

[HurrianFam]

Metagenomic peek into a corn mummy

Abstract:
Numerous studies have shown that metagenomics has opened up a new dimension in reading the contents of archaeological remains as time capsules. Corn mummies are ritual objects made in ancient Egypt by forming human-shaped figures made of cereal grains grown in a mixture of water and earth. We performed metagenomic analyses on samples from a corn mummy dated to the second half of the 3rd century BC. Alongside a number of clearly modern contaminants, we identified organisms that cannot be excluded as being of historical origin. Besides considerable amounts of bacterial sequences belonging to the genera Bacillus, Coprococcus, Metabacillus, Niallia and Roseburia, we also found traces of plants, animals, and humans. Sequences assigned to the genus Triticum showed the highest similarity to ancient T. turgidum ssp. dicoccum specimens from Egypt and the southern Levant. Sequences classified in the genus Populus showed the highest identity with the genome of P. nigra. The fragments that were identified as being of Lepidopteran origin showed the greatest similarity to the genomes of the Sphingidae. Haplotype analysis of H. sapiens sequences suggests haplogroups L3 and E, based on the mitogenome and Y chromosome, respectively, which are the two common lineages in sub-Saharan Africa today.

https://www.biorxiv.org/content/10.1101/...2.601727v1

[ilabv]

Genetic affinity of cave burial and Hmong-Mien populations in Guangxi inferred from ancient genomes


Abstract

Cave burial has been prevalent in southern China for thousands of years. The population history and the genetic contribution of cave burial groups to the formation of present-day southern minorities are largely unknown due to the lack of ancient genomic data. Here, we present the genomic data from 4 ancient individuals from cave burial sites from the Late Yuan to Ming dynasties in Guangxi. We observed a close genetic affinity between the four individuals and published contemporaneous cave burial samples. However, our samples received gene flows from northern East Asians compared to the cave burial groups around 1600-1400 years ago. We identified a strong genetic link between these ancient cave burial groups and present-day Hmong-Mien-speaking populations, particularly the geographically adjacent Baiku Yao population, indicating population stability in the mountainous region of southern China over the past few centuries.

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA005681



Sending to David tonight or tomorrow

[JMcB]

Resolving the source of branch length variation in the Y chromosome phylogeny

Yaniv Swiel, Janet Kelso, Stéphane Peyrégne

2024.07.05.


Abstract

Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome lineages has been observed, notably amongst those that are highly diverged from the human reference Y chromosome. Understanding the origin of this variation, which has previously been attributed to changes in generation time, mutation rate, or efficacy of selection, is important for accurately reconstructing human evolutionary and demographic history. Here, we analyze Y chromosomes from present-day and ancient modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination of branch lengths in the Y chromosome phylogeny. Finally, we show that this approach allows us to estimate the age of ancient samples from Y chromosome sequence data and provide updated TMRCA estimates using the portion of the Y chromosome where the effect of reference bias is minimized.


https://www.biorxiv.org/content/10.1101/...XHI7aC82BA

[Rozenfeld]

https://www.nature.com/articles/s41586-024-07651-2

Repeated plague infections across six generations of Neolithic Farmers

    Frederik Valeur Seersholm, Karl-Göran Sjögren, Julia Koelman, Malou Blank, Emma M. Svensson, Jacqueline Staring, Magdalena Fraser, Thomaz Pinotti, Hugh McColl, Charleen Gaunitz, Tatiana Ruiz-Bedoya, Lena Granehäll, Berenice Villegas-Ramirez, Anders Fischer, T. Douglas Price, Morten E. Allentoft, Astrid K. N. Iversen, Tony Axelsson, Torbjörn Ahlström, Anders Götherström, Jan Storå, Kristian Kristiansen, Eske Willerslev, Mattias Jakobsson, Helena Malmström & Martin Sikora

Nature (2024)

Abstract

In the period between 5,300 and 4,900 calibrated years before present (cal. bp), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.

[Rozenfeld]

https://www.science.org/doi/10.1126/science.adi1768

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years

Liming Li, Troy J. Comi, Rob F. Bierman, and Joshua M. Akey

Science 12 Jul 2024
Vol 385, Issue 6705
DOI: 10.1126/science.adi1768

Editor’s summary

Our understanding of admixture between humans and Neanderthals has changed dramatically over the past decade and a half. Once thought not to have occurred at all, there is now ample evidence for gene flow from Neanderthals to humans and vice versa. Li et al. used a new framework to model the increasingly complex dynamics of introgression between humans and Neanderthals and the ramifications for both populations. They identified regions of human ancestry in Neanderthals, estimated population sizes for Neanderthals were about 20% lower than previously thought, and proposed the possibility of two pulses of gene flow from humans to Neanderthals. This study comprehensively synthesizes our current knowledge of hominin admixture. —Corinne N. Simonti

Structured Abstract

INTRODUCTION

For much of modern human history, we were only one of several different groups of hominins that existed. Studies of ancient and modern DNA have shown that admixture occurred multiple times among different hominin lineages, including between the ancestors of modern humans and Neanderthals. A number of methods have been developed to identify Neanderthal-introgressed sequences in the DNA of modern humans, which have provided insight into how admixture with Neanderthals shaped the biology and evolution of modern human genomes. Although gene flow from an early modern human population to Neanderthals has been described, the consequences of admixture on the Neanderthal genome have received comparatively less attention.

RATIONALE

A better understanding of how admixture with modern humans influenced patterns of Neanderthal genomic variation may provide insights into hominin evolutionary history. For example, DNA sequences inherited from modern human ancestors in Neanderthals can be used to test hypotheses on the frequency, magnitude, and timing of admixture and the population genetics characteristics of Neanderthals. Introgressed modern human sequences in Neanderthals can also be used to refine estimates of Neanderthal ancestry in contemporary individuals. We developed a simple framework to investigate introgressed human sequences in Neanderthals that is predicated on the expectation that sequences inherited from modern human ancestors would be, on average, more genetically diverse and would result in local increases in heterozygosity across the Neanderthal genome.

RESULTS

We first used a method referred to as IBDmix to identify introgressed Neanderthal sequences in 2000 modern humans sequenced by the 1000 Genomes Project. We found that sequences identified by IBDmix as Neanderthal in African individuals from the 1000 Genomes Project are significantly enriched in regions of high heterozygosity in the Neanderthal genome, whereas no such enrichment is observed with sequences detected as introgressed in non-African individuals. We show that these patterns are caused by gene flow from modern humans to Neanderthals and estimate that the Vindija and Altai Neanderthal genomes have 53.9 Mb (2.5%) and 80.0 Mb (3.7%) of human-introgressed sequences, respectively. We leverage human-introgressed sequences in Neanderthals to revise estimates of the amount of Neanderthal-introgressed sequences in modern humans. Additionally, we show that human-introgressed sequences cause Neanderthal population size to be overestimated and that accounting for their effects decrease estimates of Neanderthal population size by ~20%. Finally, we found evidence for two distinct epochs of human gene flow into Neanderthals.

CONCLUSION

Our results provide insights into the history of admixture between modern humans and Neanderthals, show that gene flow had substantial impacts on patterns of modern human and Neanderthal genomic variation, and show that accounting for human-introgressed sequences in Neanderthals enables more-accurate inferences of admixture and its consequences in both Neanderthals and modern humans. More generally, the smaller estimated population size and inferred admixture dynamics are consistent with a Neanderthal population that was decreasing in size over time and was ultimately being absorbed into the modern human gene pool.