A history of male migration in and out of the Green Sahara

Open access research highlight A history of male migration in and out of the Green Sahara, by Yali Xue, Genome Biology (2018) 19:30, on the recent paper by D’Atanasio et al.

Insights from the Green Saharan Y-chromosomal findings (emphasis mine):

It is widely accepted that sub-Saharan Y chromosomes are dominated by E-M2 lineages carried by Bantu-speaking farmers as they expanded from West Africa starting < 5 kya, reaching South Africa within recent centuries [4]. The E-M2-Bantu lineages lie phylogenetically within the E-M2-Green Sahara lineage and show at least three explosive lineage expansions beginning 4.9–5.3 kya [5] (Fig. 1a). These events of

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Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

Open access preprint (which I announced already) at bioRxiv Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula, by Bycroft et al. (2018).

Abstract (emphasis mine):

Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian

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Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data

Brief communication (behind paywall) Yleaf: software for human Y-chromosomal haplogroup inference from next generation sequencing data, by Arwin Ralf, Diego Montiel González, Kaiyin Zhong, and Manfred Kayser, Mol Biol Evol (2018), msy032.

Abstract

Next generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data it now contains many thousands. The complexity of both, Y tree and NGS data

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The Indus Valley Civilisation in genetics – the Harappan Rakhigarhi project

Razib Khan reports on his new website about an article by Tony Joseph, Who built the Indus Valley civilisation?, itself referring to the potential upcoming results of a genetic analysis project involving Rakhigarhi, the biggest Harappan site.

The possible scenarios based on potential sample results in terms of Y-DNA and mtDNA haplogroups seem to be generally well described, and I would bet – like Khan – for some kind of an East-West Eurasian connection. This is all pure speculation, though, and after all we only have to wait one month and see.

Out of the potential models … Read the rest “The Indus Valley Civilisation in genetics – the Harappan Rakhigarhi project”

Review article about Ancient Genomics, by Pontus Skoglund and Iain Mathieson

A preprint article by two of the most prolific researchers in Human Ancestry is out, and they request feedback: Ancient genomics: a new view into human prehistory and evolution, by Skoglund and Mathieson (2017). Right now, it is downloadable on Dropbox.

.@pontus_skoglund and I wrote a review article about ancient genomics. Comments on the preprint very welcome! https://t.co/YrZS45Q0xt

— Iain Mathieson (@mathiesoniain) November 27, 2017

Abstract:

The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on ancient genomic data, including greatly increased resolution of the timing and

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mtDNA haplogroup frequency analysis from Verteba Cave supports a strong cultural frontier between farmers and hunter-gatherers in the North Pontic steppe

New preprint paper at BioRxiv, led by a Japanese researcher, with analysis of mtDNA of Trypillians from Verteba Cave, Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture, by Wakabayashi et al. (2017).

Abstract:

Background: The Eneolithic (~5,500 yrBP) site of Verteba Cave in Western Ukraine contains the largest collection of human skeletal remains associated with the archaeological Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and had some of the largest and most dense settlement sites during the Middle Neolithic in

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Before steppe ancestry: Europe’s genetic diversity shaped mainly by local processes, with varied sources and proportions of hunter-gatherer ancestry

The definitive publication of a BioRxiv preprint article, in Nature: Parallel palaeogenomic transects reveal complex genetic history of early European farmers, by Lipson et al. (2017).

The dataset with all new samples is available at the Reich Lab’s website. You can try my drafts on how to do your own PCA and ADMIXTURE analysis with some of their new datasets.

Abstract:

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of

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Analysis of R1b-DF27 haplogroups in modern populations adds new information that contrasts with ‘steppe admixture’ results

New open access article published in Scientific Reports, Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ, by Solé-Morata et al. (2017).

Abstract

Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where

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How to do modern phylogeography: Relationships between clans and genetic kin explain cultural similarities over vast distances

A preprint paper has been published in BioRxiv, Relationships between clans and genetic kin explain cultural similarities over vast distances: the case of Yakutia, by Zvenigorosky et al (2017).

Abstract:

Archaeological studies sample ancient human populations one site at a time, often limited to a fraction of the regions and periods occupied by a given group. While this bias is known and discussed in the literature, few model populations span areas as large and unforgiving as the Yakuts of Eastern Siberia. We systematically surveyed 31,000 square kilometres in the Sakha Republic (Yakutia) and completed the archaeological study of 174

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