Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[R.Rocca]

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

@RCO ... can you provide a better link? These links are broken and don't even bring up the abstract.

[Shuzam87]

“Ancient genome analyses shed light on the origin and kinship among humans of a cliff tomb from southwestern China”

https://doi.org/10.1016/j.jasrep.2023.104333

Highlights

• The inhabitants of cliff tomb from the southern China were genetically homogeneity with ancient populations from the northern China, which is striking distinct from previously published ancient genomes from southern China.

• We provide concrete evidence, for the first time, that the inhabitants of cliff tombs were originated from the Central Plains of China, rejecting either the local origin hypothesis or the exotic origin hypothesis.

• By combing genomic data with anthropological evidence, we find that these individuals that buried together share a first-degree relationship with each other, suggesting that the cliff tombs were specifically designed for family burials and that genetic kinship played a significant role in burial customs during the Eastern Han Dynasty in the Sichuan Basin.

Abstract

The cliff tomb was a distinctive regional burial form that lasted for centuries in the southwestern region of China. However, the origin of cliff tombs and the genetic relatedness among the co-buried individuals remain elusive. Here, we successfully identified four individuals from the scatted bone fragments in a single cliff tomb in the Sichuan Basin by using ancient DNA and physical anthropology analyses, and retrieved genomic data for the four individuals, to our best knowledge, the first ancient genomic data from the region. Our findings provide direct evidence supporting the Central Plains of China hypothesis for the people who practiced cliff tombs and further suggest that cliff tombs burial practices may also originate from the Central Plains of China, as supported by ancient DNA, archaeological and historical attestations. We successfully reconstructed the family tree of the four individuals and provided concrete evidence that individuals buried in the same cliff tomb are from a nuclear family rather than the long-hypothesized extended family, suggesting that genetic kinship plays a significant role for burial customs in the Sichuan Basin.

[Radko]

A genetic history of the Balkans from Roman frontier to Slavic migrations

Highlights
• A frontier region of ancient Rome was as cosmopolitan as the imperial center
• Genetic proof that migrants identified as Goths were ethnically diverse confederations
• Slavic-speaking migrants account for 30%–60% of the ancestry of Balkan peoples today
• A model for integrating archaeology with genetics

Summary
The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that “barbarian” migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%–60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.

https://www.cell.com/cell/fulltext/S0092...23)01135-2

[FR9CZ6]

Mass Graves of Únětice Culture New Discoveries from Roudnice nad Labem (Litoměřice District) and Chleby (Nymburk District) in the Czech Republic

https://www.arup.cas.cz/wp-content/uploa...AR_web.pdf

The subject of the article is the processing and genetic analysis of two mass graves of the Únětice culture from Roudnice nad Labem and Chleby and their possible interpretation. Both graves date to the early period of the Únětice culture and they deviate from the typical framework of this period’s burial rite primarily in the large number of identified buried individuals (18 and 15–18). A combined total of 15 individuals from both graves were subjected to DNA analysis (14 successfully) and the results were evaluated in the context of these graves possibly representing family tombs. However, based on the results of DNA analyses and identified biological kinship relationships, it was shown that in neither tomb did the buried individuals belong to a single biological family.

A combined total of 15 individuals (seven from Roudnice nad Labem and eight from Chleby) underwent aDNA analysis. An adequate amount of authentic endogenous human DNA was preserved on 14 of the 15 skeletons, enabling a sufficiently robust and reliable reconstruction of their genetic profile. Mitochondrial (U5, U2, K1, I4, H11, HV6 and H24) and Y-chromosomal (I2a2(3x), R1a-Z645(2x), R1b-P312) haplogroup diversity was typical for post-Neolithic Europeans, with increased Y-lineage diversity compared to preceding males of the Bohemian Bell Beaker cultural complex. Analysis of biological relatedness revealed closely related pairs of individuals in both multiple burials. In Roudnice nad Labem, three pairs of first-degree relatives and one pair of second-degree relatives were found. Chleby revealed three pairs of second-degree relatives and a relationship of approximately fifth-degree. In both graves, the majority of pair-wise comparisons (> 80%) were found to be between genetically unrelated (within 5th degree) individuals, challenging the hypothesis that these two mass graves represent single family mortuary contexts.

[RCO]

Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe
Samantha L. Cox, Nicole Nicklisch, Michael Francken, Joachim Wahl, Harald Meller, Wolfgang Haak, Kurt W. Alt, Eva Rosenstock & Iain Mathieson
Nature Human Behaviour (2023)
Article
Published: 11 December 2023

Abstract
The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.

https://www.nature.com/articles/s41562-023-01756-w

[teepean]

Medieval social landscape through the genetic history of Cambridgeshire before and after the Black Death

Abstract

The extent of the devastation of the Black Death pandemic (1346-53) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at local scale in the context of the social stratification of medieval communities. Here we study 275 newly reported ancient genomes from later medieval and post-medieval Cambridgeshire, from individuals buried before, during, and after the Black Death. The majority of individuals examined had local genetic ancestries. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. Accounting for the genetic component for height accentuates the disparities between social groups in stature estimated from long bones, as a proxy for health and the quality of life. While we detect long-term shifts in local genetic ancestry in Cambridgeshire that either pre- or postdate the Black Death, we find no evidence of major changes in genetic ancestry nor, in contrast to recent claims, higher differentiation of immune loci between cohorts living before and after the Black Death.

This a preprint from March but the data is available at ENA.

https://www.biorxiv.org/content/10.1101/...3.531048v1

https://www.ebi.ac.uk/ena/browser/view/PRJEB59976

[teepean]

Population Genomics of Postglacial Western Eurasia

Looks like Allentoft's massive stone age paper has changed names.

https://www.biorxiv.org/content/10.1101/...90594v6?ct=

[Shuzam87]

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

The article is finally out: "An ancient genome perspective on the dynamic history of the prehistoric Jomon people in and around the Japanese archipelago" https://doi.org/10.47248/hpgg2303040008

[pelop]

An individual with Sarmatian-related ancestry in Roman Britain

Marina Silva et al

Highlights
• Ancestry outlier identified in rural Roman Britain dating to 126–228 cal. CE
• Genetically related to contemporary Sarmatian- and Caucasus-associated groups
• Stable isotope analysis reveals life history of mobility
• Deployment of Sarmatian cavalry to Britain in 175 CE is a plausible explanation

Summary
In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.1,2,3 In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.4,5 Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126–228 calibrated [cal.] CE)—an outlier without traceable ancestry related to local populations in Britain—recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual’s extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.

[VladMC]

Accurate detection of identity-by-descent segments in human ancient DNA

Harald Ringbauer, Yilei Huang, Ali Akbari, Swapan Mallick, Iñigo Olalde, Nick Patterson & David Reich

Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.

https://www.nature.com/articles/s41588-023-01582-w

[AimSmall]

Revealing close and distant relatives in ancient DNA with unprecedented precision (phys.org)

If two persons are biologically related, they share long stretches of DNA that they co-inherited from their recent common ancestor. These almost identically shared stretches of genomes are called IBD ("Identity by Descent") segments. Up to the sixth-degree relatives—such as second to third cousins would be, or a great great great great grandparent—the two relatives even share multiple IBD segments. Personal genomics companies such as 23andme or Ancestry detect those segments routinely in DNA of their customers, and use this signal to distinctively reveal biological relatives in their databases.

In a new study published in Nature Genetics, researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and Harvard University, U.S., has now developed a powerful new tool named "ancIBD" to extract these IBD segments also in genomes of humans who lived hundreds, thousands, or even tens of thousands of years in the past.

The critical challenge was that such ancient genomes are often very degraded and therefore of much worse quality than modern DNA, so the authors had to come up with an innovative trick to fill in gaps in ancient genomes using modern reference DNA panels.

[VladMC]

Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand

Abstract
The Iron Age of highland Pang Mapha, northwestern Thailand, is characterised by a mortuary practice known as Log Coffin culture. Dating between 2300 and 1000 years ago, large coffins carved from individual teak trees have been discovered in over 40 caves and rock shelters. While previous studies focussed on the cultural development of the Log Coffin-associated sites, the origins of the practice, connections with other wooden coffin-using groups in Southeast Asia, and social structure within the region remain understudied. Here, we present genome-wide data from 33 individuals from five Log Coffin culture sites to study genetic ancestry profiles and genetic interconnectedness. The Log Coffin-associated genomes can be modelled as an admixture between Hòabìnhian hunter-gatherer-, Yangtze River farmer-, and Yellow River farmer-related ancestry. This indicates different influence spheres from Bronze and Iron Age individuals from northeastern Thailand as reflected by cultural practices. Our analyses also identify close genetic relationships within the sites and more distant connections between sites in the same and different river valleys. In combination with high mitochondrial haplogroup diversity and genome-wide homogeneity, the Log Coffin-associated groups from northwestern Thailand seem to have been a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual.

https://www.nature.com/articles/s41467-023-44328-2

[Glitch]

High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis

Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.

https://www.nature.com/articles/s41598-023-39069-7#Abs1

[VladMC]

Population Genomics of Postglacial Western Eurasia

Looks like Allentoft's massive stone age paper has changed names.

https://www.biorxiv.org/content/10.1101/...90594v6?ct=

version from December 21
https://www.biorxiv.org/content/10.1101/...4.490594v7

[teepean]

An individual with Sarmatian-related ancestry in Roman Britain

In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian-speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the Empire. In 175 CE, following their defeat in the Marcomannic Wars, Emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio. Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 cal. CE) - an outlier without traceable ancestry related to local populations in Britain - recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centres.

https://www.ebi.ac.uk/ena/browser/view/PRJEB67353