Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[J1_DYS388=13]

Has anyone seen these 36 ancient Irish genomes published?
People of Ranelagh: Repopulating a forgotten settlement-cemetery in Co. Roscommon
https://the-past.com/feature/people-of-r...roscommon/

[teepean]

Has anyone seen these 36 ancient Irish genomes published?
People of Ranelagh: Repopulating a forgotten settlement-cemetery in Co. Roscommon
https://the-past.com/feature/people-of-r...roscommon/

This is the only one I found where Lara Cassidy is one of the authors.

Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard

https://pubmed.ncbi.nlm.nih.gov/36443465/

[JMcB]

Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations

Javier Rodriguez Luis, Leire Palencia-Madrid, Göran Runfeldt, Ralph Garcia-Bertrand & Rene J. Herrera


Abstract
This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.


https://www.nature.com/articles/s41598-024-52293-z


As noted by Göran Runström on the Family Tree DNA Big Y Group: “This is also the first time that the Discover Time Tree has been described (although briefly) in the scientific literature”.

https://www.nature.com/articles/s41598-0.../figures/6

[AimSmall]

Has anyone seen these 36 ancient Irish genomes published?
People of Ranelagh: Repopulating a forgotten settlement-cemetery in Co. Roscommon
https://the-past.com/feature/people-of-r...roscommon/

This is the only one I found where Lara Cassidy is one of the authors.

Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard

https://pubmed.ncbi.nlm.nih.gov/36443465/

Supplement teepean's post...   https://www.ebi.ac.uk/ena/browser/view/PRJEB50653

[Shuzam87]

Genome-wide data from 24 individuals dating to 3600 BCE~317 CE in Shandong, China

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA002160

[Shuzam87]

Ancient genomes illuminate the spatial genetic continuity between the Middle and Lower Yellow River

Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilisation. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we presented 21 ancient genomes from Shandong dating from the Han Dynasty to the Northern and Southern Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples were most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover during the Neolithic to the Historical Era. We detected a genetic similarity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese since the Han dynasty.

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006574

[Alain]

Evidence from personal ornaments suggest nine distinct cultural groups between 34,000 and 24,000 years ago in Europe

Abstract
Mechanisms governing the relationship between genetic and cultural evolution are the subject of debate, data analysis and modelling efforts. Here we present a new georeferenced dataset of personal ornaments worn by European hunter-gatherers during the so-called Gravettian technocomplex (34,000–24,000 years ago), analyse it with multivariate and geospatial statistics, model the impact of distance on cultural diversity and contrast the outcome of our analyses with up-to-date palaeogenetic data. We demonstrate that Gravettian ornament variability cannot be explained solely by isolation-by-distance. Analysis of Gravettian ornaments identified nine geographically discrete cultural entities across Europe. While broadly in agreement with palaeogenetic data, our results highlight a more complex pattern, with cultural entities located in areas not yet sampled by palaeogenetics and distinctive entities in regions inhabited by populations of similar genetic ancestry. Integrating personal ornament and biological data from other Palaeolithic cultures will elucidate the complex narrative of population dynamics of Upper Palaeolithic Europe.


https://www.nature.com/articles/s41562-023-01803-6

[Shuzam87]

Ancient genomes reveal the temporal change of Yellow River millet farmers-related ancestry in Xinjiang

Recent paleogenomic studies of Xinjiang revealed the dynamic demographic history in this region since the Bronze Age. However, the spatiotemporal ancestry change related to Yellow River (YR) millet farmers has been unsolved. Here, we presented genomic data from 4 individuals from the Jirentaigoukou (JRTGK) site dating to 4,400 B.P to 2,300 B.P and 44 individuals from the Lafuqueke (LFQK) cemetery dating to the Historical Era ranging from the Tang Dynasty and Gaochang-Uyghur period. We found a genetic transformation that occurred in Late Bronze Aage with the disappearance of indigenous ancestry and the gene inflow of YR ancestry. The presence of YR ancestry in JRTGK indicated the first identification of YR ancestry in Bronze Age Xinjiang. We also observed the increase of YR ancestry over time. Hence, the genetic contribution of YR ancestry was more extensive and frequent from the Iron Age to the Historical Era, showing the widespread presence of YR ancestry in populations of the Historical Era, and the proportion reached up to 100% in LFQK. These findings suggested that the enhancement of the Central Plains government's control of Xinjiang and the opening of the ancient Silk Road promoted the demographic contacts between Xinjiang and the Central Plains.

https://ngdc.cncb.ac.cn/gsa-human/browse/HRA006610

[ulf]

The preprint is now officially published.

Stable population structure in Europe since the Iron Age, despite high mobility

Abstract

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000–3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire’s mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.

https://elifesciences.org/articles/79714

[teepean]

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

Abstract

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe5,6,7,8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

https://www.nature.com/articles/s41586-023-06923-7

mtDNA:

https://www.ebi.ac.uk/ena/browser/view/PRJEB67776

[JMcB]

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

Dorothea Mylopotamitaki, Marcel Weiss, Helen Fewlass, Elena Irene Zavala, Hélène Rougier, et al.


Abstract

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe5,6,7,8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.


https://www.nature.com/articles/s41586-023-06923-7

&

Here are the original papers:

https://www.nature.com/articles/s41559-023-02303-6

https://www.nature.com/articles/d41586-024-00072-1

https://www.nature.com/articles/s41559-023-02318-z

[NebuchadnezzarII]

Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

---

Kendra Sirak, Julian Jansen Van Rensburg, Esther Brielle, Bowen Chen, Iosif Lazaridis, Harald Ringbauer, Matthew Mah, 

Swapan Mallick, Adam Micco, Nadin Rohland, Kimberly Callan, Elizabeth Curtis, Aisling Kearns, Ann Marie Lawson, J. Noah Workman, Fatma Zalzala, Ahmed Saeed Ahmed Al-Orqbi, Esmail Mohammed Ahmed Salem, Ali Mohammed Salem Hasan, Daniel Charles Britton & David Reich 

---

Abstract

Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. 

Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. 

The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter–gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.

---

https://www.nature.com/articles/s41559-0...ailability

[teepean]

Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the Neolithic in the Danube Gorges

Summary

While early Neolithic populations in Europe were largely descended from early Aegean farmers, there is also evidence of episodic gene flow from local Mesolithic hunter-gatherers into early Neolithic communities. Exactly how and where this occurred is still unknown. Here we report direct evidence for admixture between the two groups at the Danube Gorges in Serbia. Analysis of palaeogenomes recovered from skeletons revealed that second-generation mixed individuals were buried amidst individuals whose ancestry was either exclusively Aegean Neolithic or exclusively local Mesolithic. The mixed ancestry is also reflected in a corresponding mosaic of grave goods. With its deep sequence of occupation and its unique dwellings that suggest at least semi-sedentary occupation since the late Mesolithic, the area of the Danube Gorges has been at the center of the debate about the contribution of Mesolithic societies to the Neolithisation of Europe. As suggested by our data, which were processed exclusively with uncertainty-aware bioinformatic tools, it may have been precisely in such contexts that close interactions between these societies were established, and Mesolithic ancestry and cultural elements were assimilated.

Still a preprint but the data is now available.

https://www.biorxiv.org/content/10.1101/...512v1.full

https://www.ebi.ac.uk/ena/browser/view/PRJEB47916

[VladMC]

Vittrup Man–The life-history of a genetic foreigner in Neolithic Denmark

Abstract
The lethally maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features, he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a variable life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his teenage years.

https://journals.plos.org/plosone/articl...032#sec018

[TanTin]

Bronze Age Northern Eurasian Genetics in the Context of Development of Metallurgy and Siberian Ancestry

https://www.biorxiv.org/content/10.1101/...195v1.full

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 individuals associated with BA metallurgical production, specifically the Seima-Turbino (ST) phenomenon (∼2,200-1,900 BCE) associated with elaborate metal objects found across Northern Eurasia. The genetic profiles of nine ST-associated individuals vary widely ranging between ancestries maximized in individuals from the Eastern Siberian Late Neolithic/BA, and those of the Western Steppe Middle Late BA. The genetic heterogeneity observed is consistent with the current understanding of the ST metallurgical network as a transcultural phenomenon. The new data also shed light on the temporal and spatial range of an ancient Siberian genetic ancestry component, which is shared across many Uralic-speaking populations, and which we explore further via demographic modeling using additional genome-wide (2 individuals) and whole genome data (5 individuals, including a ∼30x genome) from northwestern Russia.

We present new genome-wide data from two additional BOO individuals and shotgun data for five published individuals (including one high coverage genome of ∼31x). Direct or indirect contacts between BOO and southern and western Scandinavia have been proposed based on genetic data and the archaeological record14–16, but BOO has not been associated with any known early Metal Age cultures.
(Someone started a discussion for this preprint, but it is not going on..
https://genarchivist.com/showthread.php?...Metallurgy)