Online Ancient Genome Repository (OAGR)

This should prove to be a very useful resource in the near future. Click on the image below to check it out.

Aboriginal Australian Y-chromosomes

Based on a survey of 657 self-declared Aboriginal individuals:

C-M130*(xM8,M38,M217,M347) 1%
C-M347 19%
K-M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) 12%
S-P308 12%
M-M186 0.9%
Non-indigenous 56%

Unlike an earlier paper using genome-wide DNA, this study found no signals of gene flow from India to Australia during the Holocene.

Source...

Nagle, N., Ballantyne, K. N., van Oven, M., Tyler-Smith, C., Xue, Y., Taylor, D., Wilcox, S., Wilcox, L., Turkalov, R., van Oorschot, R. A.H., McAllister, P., Williams, L., Kayser, M., Mitchell, R. J. and The Genographic Consortium (2015), Antiquity and diversity of aboriginal Australian Y-chromosomes. Am. J. Phys. Anthropol.. doi: 10.1002/ajpa.22886

European-specific mtDNA U5a2a in ancient remains from Xinjiang, northwest China

I'm skeptical that a 700-year-old mito genome can be used as evidence of prehistoric population movements. Obviously, for that sort of thing we'd need a sequence from before recorded history. Nevertheless, the discovery of mtDNA haplogroup U5a2a in the Eastern Pamirs is still very interesting. The full text is behind a pay wall, but the images and supp info freely available here and here.

The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga–Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.

Ning et al., Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists, Journal of Human Genetics advance online publication 29 October 2015; doi: 10.1038/jhg.2015.128

Mitochondrial DNA from Maykop + Wolfgang Haak on Near Eastern-related ancestry in Yamnaya

From page 166 of a report posted recently at Academia.edu:

Majkop verfügen sowohl über eine «paläolithische» Haplogruppe (U8) als auch über «neolithische» Haplogruppen: V (Недолужко u. a. 2014), T2, N1. Bei einem Objekt aus einem Grab bei der Staniza Novosvobodnaja fanden wir auch die Haplogruppe М52. Die gewonnenen Daten sprechen für eine (auf dem Niveau der mitochondrialen DNA) mögliche genetische Gemeinschaft der archäologischen Kulturen von Majkop und Novosvobodnaja.

The presence of Indian-specific mtDNA haplogroup M52 is surprising. Maykop territory was located just south of the steppe, but M52 isn't found in any of the Bronze and Iron Age samples from the steppe tested to date.

Here's the comment from Haak, from an abstract titled The role of the Caucasus in the formation of the Eurasia's genetic makeup: Insights and questions from ancient DNA research.

Recent genetic research on autosomal and uniparentally-inherited markers has shown a remarkable genetic uniformity of Caucasian populations despite the region’s notable linguistic and cultural diversity. When compared to neighbouring regions, the smooth genetic transition from the Near/Middle East to the Caucasus is in stark contrast to the marked differences to populations from the East European steppes. Flanked by the Black and the Caspian Seas, it remains unclear to what extent the Caucasus served as a corridor and whether and if so when ancient migrations had affected and shaped the region’s genetic profile. Ancient DNA research on Mesolithic, Neolithic and Bronze Age individuals from Western Eurasia have recently thrown fresh light on the Caucasus as region, which appears to have played a critical role in the formation of the genetic ancestry of the Yamnaya people, Bronze Age pastoralist of the east European steppes. The Yamnaya carry strong signals of eastern hunter-gatherer (EHG) ancestry and ancient Near Eastern ancestry that is different from the one that giving rise to early European farmers. While modern-day Armenians are the best proxy for the putative source population of the EHG dilution in the steppes, it is highly likely that prehistoric cultural groups from the Caucasus will provide a much better temporal and contextual fit.

Actually, I'd say western Georgians are the best proxy for the putative source population of the EHG dilution in the steppes. See here...

Yamnaya's exotic ancestry: The Kartvelian connection

Prehistoric African admixture in Iberia

Open access at PLoS ONE:

Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of “migratory routes” in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians—from Huelva and Granada provinces—and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.

Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, et al. (2015) Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PLoS ONE 10(10): e0139784. doi:10.1371/journal.pone.0139784

Sardinians: relatively short by design

Behind a pay wall at Nature Genetics:

We report sequencing-based whole-genome association analyses to evaluate the impact of rare and founder variants on stature in 6,307 individuals on the island of Sardinia. We identify two variants with large effects. One variant, which introduces a stop codon in the GHR gene, is relatively frequent in Sardinia (0.87% versus <0.01% elsewhere) and in the homozygous state causes Laron syndrome involving short stature. We find that this variant reduces height in heterozygotes by an average of 4.2 cm (−0.64 s.d.). The other variant, in the imprinted KCNQ1 gene (minor allele frequency (MAF) = 7.7% in Sardinia versus <1% elsewhere) reduces height by an average of 1.83 cm (−0.31 s.d.) when maternally inherited. Additionally, polygenic scores indicate that known height-decreasing alleles are at systematically higher frequencies in Sardinians than would be expected by genetic drift. The findings are consistent with selection for shorter stature in Sardinia and a suggestive human example of the proposed 'island effect' reducing the size of large mammals.

Zoledziewska et al., Height-reducing variants and selection for short stature in Sardinia, Nature Genetics 47, 1352–1356 (2015) doi:10.1038/ng.3403

Also at Nature Genetics...

We report ~17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from previous sequencing-based compilations and are enriched for predicted functional consequences. Furthermore, ~76,000 variants common in our sample (frequency >5%) are rare elsewhere (<0.5% in the 1000 Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. We observe 14 signals, including 2 major new loci, for lipid levels and 19 signals, including 2 new loci, for inflammatory markers. The new associations would have been missed in analyses based on 1000 Genomes Project data, underlining the advantages of large-scale sequencing in this founder population.

Sidore et al., Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers, Nature Genetics 47, 1272–1281 (2015) doi:10.1038/ng.3368

Two papers on Ainu genetic structure and origins

Open access at the Journal of Human Genetics:

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

Jinam et al., Unique characteristics of the Ainu population in Northern Japan, Journal of Human Genetics (2015) 60, 565–571; doi:10.1038/jhg.2015.79; published online 16 July 2015

Open access at Genetics:

Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter-gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians.

Jeong et al., Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu, Genetics, Early Online October 23, 2015, doi: 10.1534/genetics.115.178673