Genetic Genealogy & Ancient DNA (TITLES/ABSTRACTS)

[teepean]

Detecting population continuity and ghost admixture among ancient genomes

Abstract

Ancient DNA (aDNA) can prove a valuable resource when investigating the evolutionary relationships between ancient and modern populations. Performing demographic inference using datasets that include aDNA samples however, requires statistical methods that explicitly account for the differences in drift expected among a temporally distributed sample. Such drift due to temporal structure can be challenging to discriminate from admixture from an unsampled, or "ghost", population, which can give rise to very similar summary statistics and confound methods commonly used in population genetics. Sequence data from ancient individuals also have unique characteristics, including short fragments, increased sequencing-error rates, and often limited genome-coverage that poses further challenges. Here we present a novel and conceptually simple approach for assessing questions of population continuity among a temporally distributed sample. We note that conditional on heterozygote sites in an individual genome at a particular point in time, the mean proportion of derived variants at those sites in other individuals has different expectations forwards in time and backwards in time. The difference in these processes enables us to construct a statistic that can detect population continuity in a temporal sample of genomes. We can show that the statistic is sensitive to historical admixture events from unsampled populations. Simulations are used to evaluate the power of this approach. We investigate a set of ancient genomes from Early Neolithic Scandinavia to assess levels of population continuity to an earlier Mesolithic individual. Individuals from hunter-gathering Neolithic Pitted Ware culture show marked continuity with the Mesolithic individual, whereas the contemporary Neolithic individuals from the and farming Funnel Beaker culture display much less continuity.

https://www.biorxiv.org/content/10.1101/...18676v2?ct=

No new data but interesting nevertheless.

[Riverman]

The paper is out in Nature:

Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin

Abstract

This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.

https://www.nature.com/articles/s41598-024-61978-4

Unfortunately, the yDNA results are extremely basal, like just E-M78 for E-V13.

[JMcB]

Posted May 16, 2024.

Simulating pedigrees ascertained on the basis of observed IBD sharing

Ethan M. Jewett, the 23andMe Research Team


Abstract

In large genotyping datasets, individuals often have thousands of distant cousins with whom they share detectable segments of DNA identically by descent (IBD). The ability to simulate these distant relationships is important for developing and testing methods, carrying out power analyses, and performing population genetic analyses. Because distant relatives are unlikely to share detectable IBD segments by chance, many simulation replicates are needed to sample IBD between any given pair of distant relatives. Exponentially more samples are needed to simulate observable segments of IBD simultaneously among multiple pairs of distant relatives in a single pedigree. Using existing pedigree simulation methods that do not condition on the event that IBD is observed among certain pairs of relatives, the chances of sampling shared IBD patterns that reflect those observed in real data ascertained from large genotyping datasets are vanishingly small, even for pedigrees of modest size. Here, we show how to sample recombination breakpoints on a fixed pedigree while conditioning on the event that specified pairs of individuals share at least one observed segment of IBD. The resulting simulator makes it possible to sample genotypes and IBD segments on pedigrees that reflect those ascertained from biobank scale data.

Competing Interest Statement

The author is an employee and shareholder of 23andMe, Inc.


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


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Posted May 16, 2024.

Correcting model misspecification in relationship estimates

View ORCID ProfileEthan M. Jewett, the 23andMe Research Team


ABSTRACT

The datasets of large genotyping biobanks and direct-to-consumer genetic testing companies contain many related individuals. Until now, it has been widely accepted that the most distant relationships that can be detected are around fifteen degrees (approximately 8th cousins) and that practical relationship estimates have a ceiling around ten degrees (approximately 5th cousins). However, we show that these assumptions are incorrect and that they are due to a misapplication of relationship estimators. In particular, relationship estimators are applied almost exclusively to putative relatives who have been identified because they share detectable tracts of DNA identically by descent (IBD). However, no existing relationship estimator conditions on the event that two individuals share at least one detectable segment of IBD anywhere in the genome. As a result, the relationship estimates obtained using existing estimators are dramatically biased for distant relationships, inferring all sufficiently distant relationships to be around ten degrees regardless of the depth of the true relationship. Moreover, existing relationship estimators are derived under a model that assumes that each pair of related individuals shares a single common ancestor (or mating pair of ancestors). This model breaks down for relationships beyond 10 generations in the past because individuals share many thousands of cryptic common ancestors due to pedigree collapse. We first derive a corrected likelihood that conditions on the event that at least one segment is observed between a pair of putative relatives and we demonstrate that the corrected likelihood largely eliminates the bias in estimates of pairwise relationships and provides a more accurate characterization of the uncertainty in these estimates. We then reformulate the relationship inference problem to account for the fact that individuals share many common ancestors, not just one. We demonstrate that the most distant relationship that can be inferred may be forty degrees or more, rather than ten, extending the time-to-common ancestor from approximately 200 years in the past to approximately 600 years in the past or more. This dramatic increase in the range of relationship estimators makes it possible to infer relationships whose common ancestors lived before historical events such as European settlement of the Americas and the Transatlantic Slave Trade, and possibly much earlier.

Competing Interest Statement

The author is an employee and shareholder of 23andMe.


https://www.biorxiv.org/content/10.1101/...pzdtt-pX-Q

[Capsian20]

This project presents the results of a large-scale, multi-proxy study of Medieval Sicily, a pivotal time period and location for the demographic formation of Europe. In this study, we compare the genetic affinities and diet of two communities of different faiths (Muslim and Christian) buried in adjacent cemeteries on the Sicilian site of Segesta at the end of the Norman period until the end of the Swabian period (late 12th/mid 13th century). This work has been part of the ERC Advanced grant "SICTRANSIT" which aimed to understand the impact of the regime changes in Sicily during the Middle Ages.


https://www.ebi.ac.uk/ena/browser/view/PRJNA1082095

[ilabv]

Ancient genomes revealed the complex human interactions of the ancient western Tibetans

The western Tibetan Plateau is the crossroad among the Tibetan Plateau, Central Asia, and South Asia and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture.

https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA019728

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Sending to Davidski for conversion soon

[VladMC]

Ancient genomes revealed the complex human interactions of the ancient western Tibetans

Summary
The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500–300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.

https://www.cell.com/current-biology/ful...24)00581-5

[AimSmall]

Eigenstrat data for the Ancient Western Tibetan samples...

https://ngdc.cncb.ac.cn/omix/release/OMIX004904

[J Man]

Another upcoming paper...No data uploaded yet unfortunately though.

ENA: https://www.ebi.ac.uk/ena/browser/view/PRJEB75495

"Repeated Plague Infections Across Six Generations of Neolithic Farmers" -

"In the period between 5,300 and 4,900 years before present (cal. BP), populations across large parts of Europe underwent a period of demographic decline. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline, others for the spread of an early form of plague. 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 reveals that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. Additionally, we reconstruct four multi-generation pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organisation. 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.nature.com/articles/s41598-024-61052-z

    Article
    Open access
    Published: 28 May 2024

Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth–seventh century BC, central Italy)

    G. Bagnasco, M. Marzullo, C. Cattaneo, L. Biehler-Gomez, D. Mazzarelli, V. Ricciardi, W. Müller, A. Coppa, R. McLaughlin, L. Motta, O. Prato, F. Schmidt, F. Gaveriaux, G. B. Marras, M. A. Millet, R. Madgwick, R. Ballantyne, C.A. Makarewicz, A. Trentacoste, P. Reimer, V. Mattiangeli, D. G. Bradley, C. Malone, C. Esposito, E. M. Breslin & S. Stoddart

Scientific Reports volume 14, Article number: 11895 (2024)

Abstract

Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.

[RCO]

North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period
Lehti Saag et al

Abstract
The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period, such as Scythian, Chernyakhiv, Saltiv and Nogai associated peoples. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to present-day Western European, Eastern European, Western Steppe and East Asian groups. We also infer high heterogeneity in ancestry within geographically, culturally and socially defined groups. Despite this, we find that ancestry components which are widespread in Eastern and Central Europe have been present in the Ukraine region since the Bronze Age.

https://www.biorxiv.org/content/10.1101/...4.595769v1
https://www.biorxiv.org/content/10.1101/...1.full.pdf

[alexfritz]

the paper (PHD) is now accessable

Palaeogenetic analyses on human ancient remains. The Etruscans from Felsina and surroundings: genomic evidence from the Po Valley during the Etruscan period

https://www.repository.unipr.it/handle/1889/5272
https://www.repository.unipr.it/bitstrea...entina.pdf