Genetic Genealogy and Ancient DNA in the News

[Saetro]

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750)

Abstract
The first historically documented pandemic caused by Yersinia pestis started as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 20 sites in Austria, Britain, Germany, France and Spain for Y. pestis DNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumented Y. pestis diversity during the 6th-7th centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as southern France and Spain, and that southern Germany seems to have been affected by at least two distinct Y. pestis strains. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45 kb genomic region in the most recent First Pandemic strain affecting two virulence factors, intriguingly overlapping with a deletion found in 17th-18th-century genomes of the Second Pandemic.

https://www.biorxiv.org/content/early/2018/11/29/481226

If this was the First Pandemic, and the 17th-18th century had the Second Pandemic, then what do we call the wiping out of around 1/3 of Western Europe in the 1300s?

[Megalophias]

If this was the First Pandemic, and the 17th-18th century had the Second Pandemic, then what do we call the wiping out of around 1/3 of Western Europe in the 1300s?

The Black Death was the Second Pandemic, 17th-18th c was still part of the same pandemic. The Third Pandemic began in 1855 in China.

[Waldemar]

Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period

Abstract
Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.

http://www.pnas.org/content/early/2018/11/21/1812865115

A phylogeography of the second plague pandemic revealed through the analysis of historical Y. pestis genomes

Abstract
The second plague pandemic (14th - 18th century AD), caused by the bacterium Yersinia pestis, is infamous for its initial wave, the Black Death (1346-1353 AD), and its repeated scourges in Europe and the vicinity until the Early Modern Era. Here, we report 32 ancient Y. pestis genomes spanning the 14th to 17th century AD through the analysis of human remains from nine European archaeological sites. Our data support an initial entry of the bacterium from Eastern Europe and the absence of genetic diversity during the Black Death as well as low diversity during local outbreaks thereafter. Moreover, analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. Finally, we show the loss of a genomic region that includes virulence-associated genes in strains associated with late stages of the second plague pandemic (17th - 18th century AD). This deletion could not be detected in extant strains within our modern dataset, though it was identified in a today-extinct lineage associated with the first plague pandemic (6th - 8th century AD), suggesting convergent evolution during both pandemic events.

https://www.biorxiv.org/content/early/2018/11/29/481242

[Principe]

Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia

Natalija Kashuba, Emrah Kirdök, Hege Damlien, Mikael A. Manninen, Bengt Nordqvist, Per Persson, Anders Götherström

Abstract

The discussion of an early postglacial dual-route colonization of the Scandinavian Peninsula is largely based on associating genomic data to an early dispersal of lithic technology from the East European Plain. However, a direct link between the two has been lacking. We tackle this problem by analysing human DNA from birch bark pitch mastics, chewing gums, from Huseby Klev, a site in western Sweden with eastern lithic technology. We generate genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers, or more precisely, to individuals from postglacial Sweden. Our samples date to 9880-9540 calBP, expanding the temporal range of this genetic group as well as its distribution. Human DNA from mastics provides a clear connection between material culture and genetic data. We also propose that DNA from different types of mastics can be used to study environment, ecology, and oral microbiome of prehistoric populations.

https://www.biorxiv.org/content/early/2018/12/03/485045

All three belong to Mtdna U5a2d

[Waldemar]

Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza

Abstract
Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361–178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island’s modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.

https://www.nature.com/articles/s415...gical-sciences

[Bernard]

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

The Canary Islands’ indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian indigenous mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.

[Megalophias]

Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

Abstract

Previous studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, O2a2b1a1a-F5, O2a2b1a2a1-F46, and O2a1b1a1a1a-F11, but their relationships with the archaeological and written records remain unexplored. We here report genome wide DNA data for 12 ancient samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP). They belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Banpo (BP) of middle Yangshao Culture in the Central West, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while F11, C, O1, and O2 samples were closer to the BP group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the O2a2b1a1a1a2a-F2137 haplotype, belonging to the most prolific branch O2a2b1a1a1-F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6, implicating radiations of F5 subtypes from the putative place of F5 origin in ZX. These results are remarkably consistent with archaeological and written records.

[Waldemar]

Die Biografie der Frau können die Forscherinnen dank neuer wissenschaftlicher Methoden dagegen gut nachvollziehen: Eine DNA-Analyse der Knochen zeige, dass die Heilige aus dem südöstlichen Mittelmeerraum stammte und 35 bis 50 Jahre alt wurde. Ihren Lebensabend habe sie aber in Zentraleuropa verbracht.

https://science.orf.at/stories/2951528/







https://www.oeaw.ac.at/index.php?id=11463

[rozenfeld]

https://www.eurekalert.org/pub_relea...-aas112918.php

An ancient strain of plague may have led to the decline of Neolithic Europeans


https://www.sciencedirect.com/scienc...648?via%3Dihub

Available online 6 December 2018

In Press, Corrected Proof

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

Karl-GöranSjögren28, KristianKristiansen28, RasmusNielsen34, EskeWillerslev356, ChristelleDesnues1, SimonRasmussen7910

https://doi.org/10.1016/j.cell.2018.11.005

Highlights

• Discovery of the most ancient case of plague in humans, 4,900 years ago in Sweden
• Basal lineages of Y. pestis emerged and spread during the Neolithic decline
• Plague infections in distinct Eurasian populations during Neolithic and Bronze Age
• A plague pandemic likely emerged in large settlements and spread over trade routes

Summary

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersiniapestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

[rozenfeld]

https://journals.plos.org/plosone/ar...l.pone.0207459

Open Access

Research Article

The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France

Claire-Elise Fischer , Anthony Lefort, Marie-Hélène Pemonge, Christine Couture-Veschambre, Stéphane Rottier, Marie-France Deguilloux

PLOS x
Published: December 6, 2018
https://doi.org/10.1371/journal.pone.0207459

Abstract

The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.

2018 and we're still getting HVS ...