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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Ancient genomes document multiple waves of migration in south-east Asian prehistory

Open access preprint at bioRxiv Ancient genomes document multiple waves of migration in Southeast Asian prehistory, by Lipson, Cheronet, Mallick, et al. (2018).

Abstract (emphasis mine):

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from thirteen Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100-1700 years ago). Early agriculturalists from Man Bac in Vietnam possessed a mixture of East Asian (southern Chinese farmer) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic

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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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Genomics reveals four prehistoric migration waves into South-East Asia

Open access preprint article at bioRxiv Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia, by McColl, Racimo, Vinner, et al. (2018).

Abstract (emphasis mine):

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian

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Consequences of O&M 2018 (II): The unsolved nature of Suvorovo-Novodanilovka chiefs, and the route of Proto-Anatolian expansion

This is part of a series of posts analyzing the findings of the recent Nature papers Olalde et al.(2018) and Mathieson et al.(2018) (abbreviated O&M 2018).

I already expressed my predictions for 2018. One of the most interesting questions among them is the identification of the early Anatolian offshoot, and this is – I believe – where Genomics has the most to say in Indo-European migrations.

Linguistics and Archaeology had already a mainstream account from Late PIE/Yamna onwards, and it has been proven right in Genomic investigation. There is, however, no consensus on Indo-Hittite.

Suvorovo-Novodanilovka

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Signal of recent positive selection for African ancestry in the admixed population of Madagascar

Open Access Strong selection during the last millennium for African ancestry in the admixed population of Madagascar, by Pierron, Heiske, Razafindrazaka, et al. Nature Communications (2018) 9: 932.

Abstract (emphasis mine):

While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection,

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Quantitative analysis of population-scale family trees with millions of relatives

The paper Quantitative analysis of population-scale family trees with millions of relatives, by Kaplanis, Gordon, Shor, et al. Science (2018) 359(6379), based on a study of genealogical information at Geni, is today news worldwide.

Abstract:

Family trees have vast applications in multiple fields from genetics to anthropology and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. Here, we collected 86 million profiles from publicly-available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including

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Population substructure in Iberia, highest in the north-west territory (to appear in Nature)

A manuscript co-authored by Angel Carracedo, from the University of Santiago de Compostela, and (always according to him) pre-accepted in Nature, will offer more insight into the population substructure of Spain, based on autosomal DNA.

Carracedo’s lecture about DNA (in Galician), including his summary of the paper (from december 2017):

Some of the points made in the video:

The study shows a situation parallelling – as expected – the expansion of Spanish Medieval kingdoms during the Reconquista (and subsequent repopulation).
In it, the biggest surprise seems to be the greater substructure found in Galicia, the north-western Spanish

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Population turnover in Remote Oceania shortly after initial settlement

Open Access article Population Turnover in Remote Oceania Shortly after Initial Settlement, by Lipson, Skoglund, Spriggs, et al. (2018), based on the recent preprint at bioRxiv.

Summary:

Ancient DNA from Vanuatu and Tonga dating to about 2,900–2,600 years ago (before present, BP) has revealed that the “First Remote Oceanians” associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New

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