Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[Riverman]

See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/376558253

Inferring the demographic history of Hexi Corridor over the past two millennia from ancient genomes

The Hexi Corridor in northwest China has for millennia served as a crossroads for interactions
between East Asia, Central Asia and lands further west, while also connecting the Chinese
heartland and the northern Mongolian Steppe and Tibetan Plateau (TP) to the south (Fig. 1a).
Previous studies have revealed the details of this cross-continental material and cultural
transmission as early as the Bronze Age onwards. Materials and technologies exchanged along the
ancient Silk Road included East Asian millets and painted pottery, West Asian wheat and barley,
bronze metallurgy, domesticated sheep, horses, and cattle [1]. To date, paleogenomic studies have
examined the genetic structure of the eastern Hexi Corridor [2] and neighboring populations, such
as northern China [2], the Western Regions (present-day Xinjiang) [3], Tibetan Plateau [4] and
Mongolia [5] for these formative Neolithic and Bronze Age periods. Uniparental or limited
autosomal studies have shed some light on demographic interactions in the east[2], center[6] and
far west[7] of the historical Hexi Corridor, and genome-wide single nucleotide polymorphisms
(SNPs) studies revealed the genetic landscape of western-eastern admixture pattern of the present-
day Hexi Corridor [8–10]. However, population dynamics in Hexi Corridor across a longer
tranche of time has been gravely under-represented. To address the limitations above, we sampled
and sequenced 30 ancient individuals across the Hexi Corridor (Fig. 1a, b and Table S1A online).
We sampled 17 human individuals from the Heishuiguo site from the central Hexi Corridor, dating
from the Western Han Dynasty (202 BC–8 AD) through the Eastern Han Dynasty (25–220 AD).
From the western Hexi Corridor, we sampled 13 human individuals from the Foyemiaowan
cemetery, dating from the Cao-Wei (220–265 AD) to the Tang dynasties (618–907 AD). To
establish the chronology of our study, we relied on both archaeological and radiocarbon dating
evidence. We list the detailed information of each sample in Table S1A (online)

When we used the Foyemiaowan/Heishuiguo/Dacaozi and western Eurasian-
related ancestry as sources in the well-fitted qpAdm models, we estimated that 10 out of 11 and 40
out of 41 admixture events occurred approximately 10–20 and 5–10 generations before the death
of Foyemiaowan_Cao-Wei_o and Foyemiaowan_Tang_o. These dates aligned closely with the
Warring States period (475/403–221 BC) to the Western Han Dynasty (220 BC–8 AD) and the
Eastern Jin (317–420 AD) to the Tang Dynasty (618–907 AD), respectively (Fig. S8b and Table
S3E online). The admixture dates of Foyemiaowan_Cao-Wei_o and Foyemiaowan_Tang_o
coincided with the Historical era, particularly the period following the reclaiming of the Hexi
Corridor and the establishment of the ancient Silk Road by the Han Empire. These findings
emphasize the significant role played by the Silk Road in facilitating genetic exchanges between
East and West.

Surprisingly, results showed an increased proportion of western Eurasian-related ancestry on the X
chromosome compared to autosomes in both Foyemiaowan_Cao-Wei_o and
Foyemiaowan_Tang_o (Fig. S8c and Table S3C online). These outlier individuals exhibited a
prominent female bias for western Eurasian-related ancestry. Interestingly, a similar pattern was
observed in the Khitan and Mongol empires [5]. However, a lack of archaeological and ancient
DNA studies on the sociocultural patterns (e.g., patrilocality or matrilocality; polygamy or
polyandry) in the historical Hexi Corridor hindered our ability to explain the female-biased
admixture with western Eurasian-related ancestry. However, historical documents, excavated
epitaphs, and Tang poetry [20] indicate that marriages between Han males and non-Han females
were common.

(iii) Western Eurasians account for ~5%–20% of the gene pool of present-day Hexi Corridor
ethnic groups. To quantify the genetic contribution of historical period Hexi Corridor-related
lineages to present-day ethnic groups residing in the Hexi Corridor, we reanalyzed published
genome-wide SNP data of present-day Gansu Han Chinese [8], Altaic-speaking Yugur, Baoan and
Dongxiang [9,10], who are indigenous in Gansu Province. In 2-way qpAdm modeling, we found
that Gansu ethnic groups possessed ~80%–95% historical period Hexi Corridor-related ancestry
(represented by Heishuiguo/Foyemiaowan/Dacaozi) and ~5%–20% western Eurasian-related
ancestry (Fig. 2c), while no significant sex-biased admixture pattern was observed within our
limited resolution (Fig. S10a–c, and Tables S4A–C and S5A–C online). According to our analysis
8
using present-day Han Chinese/Korean and Europeans/Inner Asians as sources (Fig. S10d, and
Tables S4D and S5D online), the admixture events for present-day Gansu ethnic groups, estimated
through ALDER, were dated to approximately 600–1000 years before the present, corresponding
to the Song and Yuan dynasties (960–1368 AD).

https://www.researchgate.net/publication...nt_genomes

https://www.sciencedirect.com/science/ar...via%3Dihub

[Shuzam87]

Ancient genomes reveal the origin and kinship burial patterns of human remains during the 11th to 13th centuries in northern China

https://doi.org/10.1002/oa.3274

Abstract

The analysis of familial relationships among individuals co-buried in a shared tomb is crucial for understanding burial practices and the underlying social organization of ancient human society. However, archaeological interpretation of these relationships has traditionally relied on conjecture and circumstantial evidence. The development of next-generation sequencing technologies makes it possible to obtain genomic data from ancient individuals and thus can further estimate the genetic relatedness among these individuals in an accurate manner. In this study, we obtained the genomes of four individuals excavated from a single tomb in northern China. We found that three out of the four individuals were from a nuclear family, including the parents and their son, while the remaining female individual was genetically unrelated to the others. Our study not only shows that the burial custom was organized based on both biological relatedness and social kinship ties but also suggests the presence of likely female exogamy in ancient China. Finally, we find the genetic profile of these individuals carried a majority ancestry from the sedentary agriculturalists from the Central Plains of China and subtle ancestry that derived a gene pool associated with nomadic pastoralism, implying a long-standing genetic continuity among ancient populations in northern China, but with genetic and cultural connections with nomadic groups during the 11th to 13th centuries.

[AimSmall]

Archaeologists uncover remains of allegedly new human species | RBC-Ukraine

In an archaeological site between Tel Aviv and Jerusalem in Israel, an international group of researchers has discovered fragments of a peculiar skull that may belong to a previously unknown population of Homo that lived in the region between 140,000 and 120,000 years ago, writes IFL.Science.

It is noted that the discovery itself was made in 2021. Researchers Israel Hershkovitz, Yossi Zaidner, and their colleagues speculated that this new population of hominids, known as Nesher Ramla Homo, exchanged both genes and culture with neighboring Homo sapiens populations over thousands of years.

[JMcB]

Published: 02 January 2024

Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split

Keren Levinstein Hallak & Saharon Rosset


Abstract

Background

We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree with a known structure (typically from one of the species). The number of transitions at each site from the first sequence to the other is assumed to be Poisson distributed, and only the parity of the number of transitions is observed. The detailed phylogenetic tree contains information about the transition rates in each site. We use this formulation to develop and analyze multiple estimators of the species’ TMRCA. To test our methods, we use mtDNA substitution statistics from the well-established Phylotree as a baseline for data simulation such that the substitution rate per site mimics the real-world observed rates.


Results

We evaluate our methods using simulated data and compare them to the Bayesian optimizing software BEAST2, showing that our proposed estimators are accurate for a wide range of TMRCAs and significantly outperform BEAST2. We then apply the proposed estimators on Neanderthal, Denisovan, and Chimpanzee mtDNA genomes to better estimate their TMRCA with modern humans and find that their TMRCA is substantially later, compared to values cited recently in the literature.


Conclusions

Our methods utilize the transition statistics from the entire known human mtDNA phylogenetic tree (Phylotree), eliminating the requirement to reconstruct a tree encompassing the specific sequences of interest. Moreover, they demonstrate notable improvement in both running speed and accuracy compared to BEAST2, particularly for earlier TMRCAs like the human-Chimpanzee split. Our results date the human – Neanderthal TMRCA to be ~ 408,000 years ago, considerably later than values cited in other recent studies.


https://bmcgenomdata.biomedcentral.com/a...23-01185-8

[fj-blanco]

Published: 10 January 2024

Population genomics of post-glacial western Eurasia

Morten E. Allentoft, Martin Sikora, Alba Refoyo-Martínez, Evan K. Irving-Pease, Anders Fischer, William Barrie, Andrés Ingason, Jesper Stenderup, Karl-Göran Sjögren, Alice Pearson, Bárbara Sousa da Mota, Bettina Schulz Paulsson, Alma Halgren, Ruairidh Macleod, Marie Louise Schjellerup Jørkov, Fabrice Demeter, Lasse Sørensen, Poul Otto Nielsen, Rasmus A. Henriksen, Tharsika Vimala, Hugh McColl, Ashot Margaryan, Melissa Ilardo, Andrew Vaughn, …Eske Willerslev

Nature volume 625, pages 301–311 (2024)

Abstract

Western Eurasia witnessed several large-scale human migrations during the Holocene1,2,3,4,5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

https://www.nature.com/articles/s41586-023-06865-0

[VladMC]

and

100 ancient genomes show repeated population turnovers in Neolithic Denmark

https://www.nature.com/articles/s41586-023-06862-3

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

https://www.nature.com/articles/s41586-023-06618-z

The selection landscape and genetic legacy of ancient Eurasians

https://www.nature.com/articles/s41586-023-06705-1

[Shuzam87]

”Archaeogenetics: Tracing ancient migrations from the Yellow River“

https://doi.org/10.1016/j.cub.2023.11.024

Summary

Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans in East Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history.

[pelop]

https://www.nature.com/articles/s42003-023-05642-z

Detection of chromosomal aneuploidy in ancient genomes

Kyriaki Anastasiadou et Al

Abstract
Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

[G-Man]

Genetic analysis of multiple burials from the medieval churchyard from the St. Peters church of old Cölln/Berlin

This article presents the genetic research results of selected multiple burials from one of the oldest medieval cemeteries in Berlin. Extensive excavations since 2007 have uncovered 3,121 graves containing 3,778 individuals at the former St. Peters churchyard in the city centre of the German capital Berlin. The use of the area as a cemetery started around 1150 and ended in 1717. The parish belonged to the medieval city of Cölln one of the two founding cores of Berlin. Among the found graves was a noticeably high amount (12%) of multiple burials. Eight selected grave complexes, which contained in total 17 individuals, were chosen that indicated some kind of relationship based on the arrangement of the bodies. Our main focus was to investigate the role of biological kinship in these medieval burial customs. Additionally we provide data about the genetic ancestry of all individuals as well as phenotyping predictions.

https://doi.org/10.1016/j.jasrep.2023.104337

[Capsian20]

Genetic analysis of multiple burials from the medieval churchyard from the St. Peters church of old Cölln/Berlin

This article presents the genetic research results of selected multiple burials from one of the oldest medieval cemeteries in Berlin. Extensive excavations since 2007 have uncovered 3,121 graves containing 3,778 individuals at the former St. Peters churchyard in the city centre of the German capital Berlin. The use of the area as a cemetery started around 1150 and ended in 1717. The parish belonged to the medieval city of Cölln one of the two founding cores of Berlin. Among the found graves was a noticeably high amount (12%) of multiple burials. Eight selected grave complexes, which contained in total 17 individuals, were chosen that indicated some kind of relationship based on the arrangement of the bodies. Our main focus was to investigate the role of biological kinship in these medieval burial customs. Additionally we provide data about the genetic ancestry of all individuals as well as phenotyping predictions.

https://doi.org/10.1016/j.jasrep.2023.104337

I found here too 
https://papers.ssrn.com/sol3/papers.cfm?...id=4534760

[VladMC]

White plague among the “forgotten people” from the Barbaricum of the Carpathian Basin–Cases with tuberculosis from the Sarmatian-period (3rd–4th centuries CE) archaeological site of Hódmezővásárhely–Kenyere-ér, Bereczki-tanya (Hungary)

Abstract
Tuberculosis (TB) is a bacterial infection that is well-known in the palaeopathological record because it can affect the skeleton and consequently leaves readily identifiable macroscopic alterations. Palaeopathological case studies provide invaluable information about the spatio-temporal distribution of TB in the past. This is true for those archaeological periods and geographical regions from when and where no or very few TB cases have been published until now–as in the Sarmatian period (1st–5th centuries CE) in the Barbaricum of the Carpathian Basin. The aim of our paper is to discuss five newly discovered TB cases (HK199, HK201, HK225, HK253, and HK309) from the Sarmatian-period archaeological site of Hódmezővásárhely–Kenyere-ér, Bereczki-tanya (Csongrád-Csanád county, Hungary). Detailed macromorphological evaluation of the skeletons focused on the detection of bony changes likely associated with different forms of TB. In all five cases, the presence of endocranial alterations (especially TB-specific granular impressions) suggests that these individuals suffered from TB meningitis. Furthermore, the skeletal lesions observed in the spine and both hip joints of HK225 indicate that this juvenile also had multifocal osteoarticular TB. Thanks to the discovery of HK199, HK201, HK225, HK253, and HK309, the number of TB cases known from the Sarmatian-period Carpathian Basin doubled, implying that the disease was likely more frequent in the Barbaricum than previously thought. Without the application of granular impressions, the diagnosis of TB could not have been established in these five cases. Thus, the identification of TB in these individuals highlights the importance of diagnostics development, especially the refinement of diagnostic criteria. Based on the above, the systematic macromorphological (re-)evaluation of osteoarchaeological series from the Sarmatian-period Carpathian Basin would be advantageous to provide a more accurate picture of how TB may have impacted the ancestral human communities of the Barbaricum

https://journals.plos.org/plosone/articl...ne.0294762#

[aganmu]

White plague among the “forgotten people” from the Barbaricum of the Carpathian Basin–Cases with tuberculosis from the Sarmatian-period (3rd–4th centuries CE) archaeological site of Hódmezővásárhely–Kenyere-ér, Bereczki-tanya (Hungary)

Abstract
Tuberculosis (TB) is a bacterial infection that is well-known in the palaeopathological record because it can affect the skeleton and consequently leaves readily identifiable macroscopic alterations. Palaeopathological case studies provide invaluable information about the spatio-temporal distribution of TB in the past. This is true for those archaeological periods and geographical regions from when and where no or very few TB cases have been published until now–as in the Sarmatian period (1st–5th centuries CE) in the Barbaricum of the Carpathian Basin. The aim of our paper is to discuss five newly discovered TB cases (HK199, HK201, HK225, HK253, and HK309) from the Sarmatian-period archaeological site of Hódmezővásárhely–Kenyere-ér, Bereczki-tanya (Csongrád-Csanád county, Hungary). Detailed macromorphological evaluation of the skeletons focused on the detection of bony changes likely associated with different forms of TB. In all five cases, the presence of endocranial alterations (especially TB-specific granular impressions) suggests that these individuals suffered from TB meningitis. Furthermore, the skeletal lesions observed in the spine and both hip joints of HK225 indicate that this juvenile also had multifocal osteoarticular TB. Thanks to the discovery of HK199, HK201, HK225, HK253, and HK309, the number of TB cases known from the Sarmatian-period Carpathian Basin doubled, implying that the disease was likely more frequent in the Barbaricum than previously thought. Without the application of granular impressions, the diagnosis of TB could not have been established in these five cases. Thus, the identification of TB in these individuals highlights the importance of diagnostics development, especially the refinement of diagnostic criteria. Based on the above, the systematic macromorphological (re-)evaluation of osteoarchaeological series from the Sarmatian-period Carpathian Basin would be advantageous to provide a more accurate picture of how TB may have impacted the ancestral human communities of the Barbaricum

Sorry, I don't see any case about Genetic Genealogy & Ancient DNA from this abstract.

[teepean]

Something different this time.

Cases of Trisomy 21 and Trisomy 18 among Historic and Prehistoric Individuals discovered from Ancient DNA

Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or prenatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice.

The paper was released as well.

https://www.nature.com/articles/s42003-023-05642-z

https://www.ebi.ac.uk/ena/browser/view/PRJEB71003

[Capsian20]

Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

Abstract
Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
https://www.nature.com/articles/s41598-023-48762-6

[ulf]

Redefining the treponemal history through pre-Columbian genomes from Brazil

ABSTRACT

The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus’ expeditions1,2. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico3,4,5,6. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.

https://www.nature.com/articles/s41586-0...of%20bejel