Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[Pylsteen]

In this thread, titles/abstracts from papers can be posted.

They can be discussed in the discussion thread:  Genetic Genealogy & Ancient DNA (DISCUSSION ONLY)

[R.Rocca]

I think this thread needs to pinned. Thanks!

[JonikW]

A coming aDNA paper and a preliminary finding: I attended a viewing of the Anglo-Saxon Marlow Warlord's grave goods today. The archaeologists involved said his genome is currently being analysed by the Francis Crick Institute and they already have preliminary results that suggest he was a second generation Germanic immigrant to the middle Thames region where he was found.

While isotopic analysis suggests he was local to the Berkshire chalk area, those preliminary aDNA results show an origin in Germanic mainland Europe with no British ancestry. Radiocarbon dating gives a wide range in the Migration Period but his grave goods are late fifth century (so he’s a good number of generations earlier than finds such as Sutton Hoo).

They told me they haven’t yet been notified of a Y haplogroup but should have full results by the end of the year. They said that the warlord will feature in a paper along with other samples currently being analysed by Francis Crick, which should be published soon. They also said that this paper will focus exclusively on Britain and will feature Anglo-Saxon samples over the entire period, shedding more light on genetic changes through time than 2022’s Gretzinger et al study was able to do.

Some background: The warlord’s grave goods show he belonged to the elite, and he was unusually tall for his time at 6ft to perhaps 6ft 3in, and very robust. He was buried on what must have been the edge of his territory on the south bank of the Thames. I was interested to hear how he was interred facing the north bank, which they said was a British enclave and, given the context, presumably a hostile one. He had his hands on the sword at his left side, which makes him unique, according to the archaeologists’ assessment, suggesting he continued his role as his people’s guardian after death.

[Piquerobi]

Ancient Israelite DNA results (from the First Temple period) are about to be published:


Archaeologists Extract DNA of Ancient Israelites

A rare First Temple-period family burial opens the door to genetic studies on the true origin of the ancient Israelites - and their links to modern Jewish populations

For the first time, ancient DNA has been recovered from the bodies of ancient Israelites living in the First Temple period, Haaretz has learned.

This achievement, a Holy Grail in the study of lost civilizations, was enabled following the discovery near Jerusalem of a rare family tomb dating to the Iron Age.

So far the collaboration of archaeologists and geneticists has been able to extract genetic material from two individuals, producing partial information, which is a tiny sample indeed. But it promises to pave the way for further research on longstanding questions about the origins of the ancient Israelites, their links to earlier populations living in the Levant, as well as to modern-day Jewish people.

Preliminary results from the excavation and the DNA study were expected to be presented at a conference about new archaeological discoveries in Jerusalem and its environs on Wednesday, and Haaretz has obtained an advance copy of the researchers’ paper. The conference has since been delayed due to the ongoing conflict between Israel and Gaza.

https://www.haaretz.com/archaeology/2023...9b21fd0000

[G-Man]

Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps
 
In South Tyrol (Eastern Italian Alps) during Late Antiquity-Early Middle Ages, archeological records indicate cultural hybridization among alpine groups and peoples of various origin. Using paleogenomics, we reconstructed the ancestry of 20 individuals (4th-7th cent. AD) from a cemetery to analyse whether they had heterogeneous or homogenous ancestry and to study their social organization. The results revealed a primary genetic ancestry from southern Europe and additional ancestries from south-western, western and northern Europe suggesting that cultural hybridization was accompanied by complex genetic admixture. Kinship analyses found no genetic relatedness between the only two individuals buried with grave goods. Instead, a father-son pair was discovered in one multiple grave, together with unrelated individuals and one possible non-local female. These genetic findings indicate the presence of a high social status familia which is supported by the cultural materials and the proximity of the grave to the most sacred area of the church.

https://www.cell.com/iscience/fulltext/S...23)02292-7

[JMcB]

Published: 11 October 2023


Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Andrey Ziyatdinov, Jason Torres, Jesús Alegre-Díaz, Joshua Backman, Joelle Mbatchou, Michael Turner, Sheila M. Gaynor, Tyler Joseph, Yuxin Zou, Daren Liu, Rachel Wade, Jeffrey Staples, Razvan Panea, Alex Popov, Xiaodong Bai, Suganthi Balasubramanian, Lukas Habegger, Rouel Lanche, Alex Lopez, Evan Maxwell, Marcus Jones, Humberto García-Ortiz, Raul Ramirez-Reyes, Rogelio Santacruz-Benítez, Regeneron Genetics Center, Mexico City Prospective Study, …Roberto Tapia-Conyer


Abstract:

The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent.


https://www.nature.com/articles/s41586-0...3FEeSHC6kI

[VladMC]

The Selection Landscape and Genetic Legacy of Ancient Eurasians

Abstract
The Holocene (beginning ~12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical, and mental health of present-day populations. Using a dataset of >1600 imputed ancient genomes 1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify major selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported, and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in >400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic, and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, while risk alleles for diabetes and Alzheimer's disease are enriched for Western Hunter-gatherer ancestry. Our results suggest that ancient selection and migration were major contributors to the distribution of phenotypic diversity in present-day Europeans.

https://www.biorxiv.org/content/10.1101/...2.509027v3

[VladMC]

Rurikovich: the first experience of reconstructing the genetic appearance of the ruling family of medieval Russia according to paleogenomics
ABSTRACT
Representatives of the Rurikovich family were rulers of Russia for seven centuries, from the IX to the end of the XVI century. "The Tale of Bygone Years", the main chronicle source about the first centuries of the history of Russia, traces the origin of this princely family from the Varangian Rurik, called to reign in 862, however, direct genetic evidence of the origin of the early Rurikovich has not yet been received. In this work, for the first time, a full-genome paleogenetic analysis of the bone remains of the founder of the Rurikovich family – the Grand Duke of Vladimir Dmitry Alexandrovich (?-1294), the son of the Grand Duke of Kiev and Vladimir Alexander Yaroslavich Nevsky (1221-1263) was carried out. It was found that his Y chromosome belongs to the N1a haplogroup. The majority of modern Rurikovites, who, according to their pedigrees, belong to haplogroup N1a, have the most similar variations of Y chromosomes among themselves, as well as with the Y chromosome of Prince Dmitry Alexandrovich. The totality of genome-wide data of medieval and modern Rurik can unequivocally say that their genus, starting at least from the XI century. (since the time of Grand Duke Yaroslav the Wise), is characterized by the carrier of the N1a-haplogroup of the Y chromosome. All other alleged Rurikovichi, both ancient and modern, are carriers of other haplogroups (R1a, I2a), have high heterogeneity of the Y chromosome sequence and do not confirm a single origin. The most likely distant ancestors of Prince Dmitry Alexandrovich in the male line were men who left the Big Deer Island burial ground on the coast of the Kola Peninsula about 3,600 years ago. Modeling of the genome of Prince Dmitry Alexandrovich indicates the contribution of three ancestral components to its origin: (1) populations of the early Medieval population of eastern Scandinavia from the island of Eland; (2) representatives of the steppe nomadic peoples of the Eurasian steppes of the Iron Age or the early Medieval population of Central Europe (steppe nomads from Hungary) and (3) the ancient Siberian component. Reliable statistical values were also obtained when replacing the inhabitants of Scandinavia with representatives of the Slavic Old Russian population of the XI century . Thus, for the first time on the example of ancient Rurikovich, the genetic component of the complex nature of interethnic interactions in the formation of the nobility of medieval Russia is shown.

https://drive.google.com/file/d/1yOyGjdQ...p=drivesdk

Sequencing data for the NEV2 sample.3 are available for download via the link
http:// russiangenome.ru/NEV2_3.bam

[DNA archi]

Video and screenshots from a video conference: “A European mark in the East European cultural generation in the second half of the 3rd millennium BC” (as a result of David Reich laboratories not yet published)

The results of the IBD analysis of European cultures are presented, the Eastern European and Central European cultures of the Middle Bronze Age are discussed in detail: Post-catacomb/Babino/multi-cordoned ware, Abashevo, Sinintashta, Fatyanovo, Catacomob, (Proto-)Unitece, Nitra, Fuzisaboni, etc. Post-catacomb, Abashevo, Sintashta have the closest relationship to (Proto-)Unitece, Nitra, Fuzisaboni, but have no closest kinship to Fatyanovo and Catacomb.


https://youtu.be/SOeiOLRLgDc?t=8560

Screenshots with IBD nets:

[J Man]

No paper yet just an abstract I believe.


Preliminary results of bioanthropological and archaeogenetic analyzes of human osteological material from the Čik necropolis (6th-7th century)

Ksenija Djukic; Leonid Vyazov

This paper will present the preliminary results of bioanthropological and archaeogenetic analyzes of human osteological material from the early medieval necropolis in Chik. The archaeological locality Čik is located in the north of Serbia, in the Juznobački district, near the town of Bečej. During the archaeological investigations, which were carried out on several occasions, it was established that it is a multi-layered site. In professional literature, this locality is best known for its necropolis, which dates back to the period from the 6th to the 7th century, and the archaeological material found in the graves is determined to belong to the Avar cultural circle. The bioanthropological analysis of the skeletons from this necropolis included a total of 103 individuals, of which 27% were male, 28% were female, while 31% of the skeletons belonged to children. It was not possible to determine gender for 13% of individuals. To understand the archaeogenetic pattern of the population buried in Čik, we sequenced 28 individuals and analyzed them using methods based on allele frequencies and autosomal haplotypes. The obtained results suggest that only a few individuals show the presence of an Asian ancestral component, which varies from a very high (grave 109) to a low proportion (graves 76, 73). However, most individuals share genetic proportions typical of the local population of Europe and actually belong to a group of distant relatives, which can be linked to the Slavic speakers of the Avar Khaganate. Interestingly, some samples (grave 64) reveal distant relatives among early medieval Germanic-speaking populations, which may reflect the integration of local Gepid or Langobard groups into Avar period populations.

[Pribislav]

Sequencing data for the NEV2 sample.3 are available for download via the link
http:// russiangenome.ru/NEV2_3.bam

Grand Duke Dmitry Alexandrovich is N-L550>Y4341>Y4338>Y4339>Y10932>Y10931>VL11

VL11+  A>G (3G)

VL14, Y59140 and Y59577 are not covered.

IIRC these three noble families with Rurikid pedigree belong to clade VL11 as well: House of Putyatin, House of Lobanov-Rostovsky and House of Gagarin.

[VladMC]

Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea

Abstract
Populations genetically related to present-day Europeans first appeared in Europe at some point after 38,000–40,000 years ago, following a cold period of severe climatic disruption. These new migrants would eventually replace the pre-existing modern human ancestries in Europe, but initial interactions between these groups are unclear due to the lack of genomic evidence from the earliest periods of the migration. Here we describe the genomes of two 36,000–37,000-year-old individuals from Buran-Kaya III in Crimea as belonging to this newer migration. Both genomes share the highest similarity to Gravettian-associated individuals found several thousand years later in southwestern Europe. These genomes also revealed that the population turnover in Europe after 40,000 years ago was accompanied by admixture with pre-existing modern human populations. European ancestry before 40,000 years ago persisted not only at Buran-Kaya III but is also found in later Gravettian-associated populations of western Europe and Mesolithic Caucasus populations.

https://www.nature.com/articles/s41559-023-02211-9

[dilettante layman]

Past human expansions shaped the spatial pattern of Neanderthal ancestry

Abstract
The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.

https://www.science.org/doi/10.1126/sciadv.adg9817

[R.Rocca]

Project: PRJEB65118

Biological and substitute parents in Beaker period adult-child graves

Joint inhumations of adults and children are one of the most intriguing aspects of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. We present evidence that close blood relations, including a biological mother and her son at Altwies, were buried together. Ancestry modelling and patterns of shared IBD segments between the individuals examined and contemporary genomes from Central and Northwest Europe further highlight the continental connections of Bronze Age Britain. The practice of paired burial indicates the key role played by biological relationships in structuring third millennium BC social systems and burial practices. We propose that extended family, such as a paternal aunt at Dunstable Downs, could act as substitute parents to the child in the grave. Hypotheses are explored to explain the simultaneous inhumation of adults and children. While violence cannot be excluded, interpretations such as enemy raids fail to account for the pervasiveness of the phenomenon, as evidenced by a representative sample of 117 adult-child graves from 78 sites across Eurasia, all dating to the third and second millennia BC.

https://www.ebi.ac.uk/ena/browser/view/PRJEB65118

Associated paper on the samples:

Investigating the prehistory of Luxembourg using ancient genomes
https://www.cambridge.org/core/services/...enomes.pdf

[Radko]

Ancient DNA and Paleoproteomic Analysis on Roman Imperial-Era Individuals from Histria, Romania

Abstract
Ancient biomolecules have become an increasingly important part of archaeological investigations interested in understanding population movements and health. Despite their ability to elucidate historically-attested contexts of human mobility and interaction between different cultural groups, biomolecular techniques are still underutilized in certain historical and archaeological contexts. One such context is the Roman Imperial limes, or border zone, along the lower reaches of the Danube, which saw more than five hundred years of migration, conflict, and accommodation among a wide range of populations, from Mediterranean settlers to steppe pastoralists. In this region, more than a century of archaeological investigation has unearthed the remains of tens of thousands of Roman-era individuals. However, only a limited number of contexts have undergone biomolecular analyses. While applying biomolecular methods to these previously excavated human remains may offer an untapped reservoir of information, many were collected during a period when the standard precautions and protocols for ancient biomolecular researcher were not yet established. Because contamination is a major barrier for successfully recovering the ancient DNA and proteins from human remains, conducting a pilot study on a small dataset of human remains may minimize unnecessary destructive sampling. This study applies ancient DNA and paleoproteomic techniques to human remains from a Roman-period cemetery at Histria, a site located just south of the Danube at the edge of the Roman province of Moesia Inferior. These individuals were excavated between the 1940s and 1980s and have been held in storage since. Our results suggest that there is endogenous microbial and human DNA in the dental calculus and dentin samples, respectively. We also successfully recovered sex-specific amelogenin peptides in tooth enamel of three individuals, including a subadult. In conclusion, the results from this study are encouraging, signifying the feasibility of future aDNA and paleoproteomic research for this skeletal collection. Our findings not only open doors to gaining deeper insights into the individuals within this skeletal collection but also hold the promise of addressing broader anthropological inquiries, such as the impact of Roman annexation in this region.

https://papers.ssrn.com/sol3/papers.cfm?...id=4610283