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Sunday, August 24, 2014

Genetic structure in the Western Balkans


PLoS ONE has a new paper on the genetic structure of Western Balkan populations. Here's the abstract:

Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.

Among the most eye catching figures from the study is this TreeMix graph with ten migration edges or admixture events. Note the 44% migration edge running from the base of the Eastern European branch to the French. Is this perhaps a legacy of the Proto-Celts and early Germanics? In any case, something similar can be seen on this TreeMix graph from the supplementary PDF to Skoglund et al. 2014, where a French genome is modeled as a clade closely related to Upper Paleolithic Siberian forager MA-1, but with considerable Sardinian admixture.


Also, the position of the Poles at the tip of the tree, and thus near the North Russians, is somewhat curious. However, I know that several of these individuals are ethnic Poles from Estonia, so that might be the problem.

Update 25/08/2014: Here's a typical Eurogenes Principal Component Analysis (PCA) of West Eurasia with the new samples from this paper (Bosnians, Kosovars, Macedonians, Montenegrins and Serbs).



Citation...

Kovacevic L, Tambets K, Ilumäe A-M, Kushniarevich A, Yunusbayev B, et al. (2014) Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers. PLoS ONE 9(8): e105090. doi:10.1371/journal.pone.0105090


Tuesday, August 19, 2014

Complex paternal origins of the Han Chinese


There's an intriguing new paper at the AJHB on the paternal ancestry of a population from Iron Age China. It argues that the Han Chinese are the result of fairly recent admixture events, with Y-chromosome haplogroup Q1a1 entering the ancestral territory of the Han, the Central Plain of China, only around 3,000 years ago from the northwest. It's probably a sign of things to come, not only for the Han but many populations generally thought to be genetically homogeneous.

Note also how the Y-chromosome haplogroups appear to be associated with different burial customs and inferred social status. Q1a1 was found in the remains of three aristocrats and eight commoners, most of them buried in the extended prostrate position typical of Bronze and Iron Age steppe nomads of what is now western China. Most of the other remains were buried in the extended supine position, characteristic of the populations of the Chinese Central Plain at the time. I've put the details into a spreadsheet here.

It'll be interesting to learn about the genome-wide genetic structure of the people who introduced haplogroup Q1a1 into the ancestral Han gene pool. Were they perhaps in large part of Ancient North Eurasian (ANE) origin? The reason I say this is because Q is the most common Y-chromosome haplogroup in the Americas, where ANE peaks today. It's also the sister clade of haplogroup R, which is the paternal marker of Mal'ta boy, or the MA-1 genome, the main reference sample for ANE.

Indeed, haplogroup R was expanding in a big way across Europe and West and Central Asia at about the same time as Q1a1 in China. It also probably came from the steppe and was in all likelihood associated with the spread of ANE deep into Europe.

Objectives: Y chromosome haplogroup Q1a1 is found almost only in Han Chinese populations. However, it has not been found in ancient Han Chinese samples until now. Thus, the origin of haplogroup Q1a1 in Han Chinese is still obscure. This study attempts to provide answer to this question, and to uncover the origin and paternal genetic structure of the ancestors of the Han Chinese.

Methods: Eighty-nine ancient human remains that were excavated from the presumed geographic source of the Han Chinese and dated to approximately 3,000 years ago were treated by the amelogenin gene polymerase chain reaction test, to determine their sex. Then, Y chromosome single nucleotide polymorphisms were subsequently analyzed from the samples detected as male.

Results: Samples from 27 individuals were successfully amplified. Their haplotypes could be attributed to haplogroups N, O*, O2a, O3a, and Q1a1. Analyses showed that the assigned haplogroup of each sample is correlated to the suspected social status and observed burial custom associated with the sample.

Conclusions: The origins of the observed haplotypes and their distribution in present day Han Chinese and in the samples suggest that haplogroup Q1a1 was probably introduced into the Han Chinese population approximately 3,000 years ago.

Citation...

Yong-Bin Zhao et al., Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago, American Journal of Human Biology, Article first published online: 18 AUG 2014, DOI: 10.1002/ajhb.22604

See also...

Lots of ancient Y-DNA from China

First genome of an Upper Paleolithic human (Mal'ta boy)

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

Friday, August 15, 2014

Near Eastern-like mtDNA from Chalcolithic Spain


Ancient DNA studies based solely on low resolution mtDNA sequences aren't exactly cutting edge science nowadays, but this one is still interesting and somewhat surprising in that it describes an unusually Near Eastern-like population from post-Neolithic Iberia. These people were probably either fresh off the boat colonists from the Near East, or, alternatively, the descendants of Neolithic farmers from the Near East who were yet to begin mixing with other distinct populations to produce the modern Iberian mtDNA gene pool. The authors of this paper favor the second scenario:

Abstract: Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

Of course, these results don't debunk in any way the generally accepted theory that the enigmatic Bell Beakers first expanded from what is now Portugal. Indeed, a Principal Component Analysis (PCA) from the paper shows Bell Beaker mtDNA from Germany (BBC) right next to mtDNA from late Neolithic Portugal (NPO). On the other hand, the El Mirador cave sample (MIR) appears most similar to mtDNA from Germany belonging to the middle Neolithic Salzmunde culture (SMC).


Citation...

Gómez-Sánchez D, Olalde I, Pierini F, Matas-Lalueza L, Gigli E, et al. (2014) Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations. PLoS ONE 9(8): e105105. doi:10.1371/journal.pone.0105105

Wednesday, August 6, 2014

Haplotype-based PCA of West Eurasia and Europe


The Principal Component Analyses (PCA) below are based on pairwise Identity-by-Descent (IBD) sharing inferred with fastIBD. My aim was to create PCA that took into account haplotype information to see how they might differ from similar plots based on unlinked loci (such as here).






Clearly, they're less reflective of geography and isolation-by-distance, and instead more profoundly influenced by relatively recent isolation, founder effects and/or rapid expansions, especially in Northern and Eastern Europe, and in particular among the Finns, Balts and East Slavs. Unfortunately, I don't have time to say much more about these results. But feel free to post any questions or observations in the comments below. I have done something very similar in the past, but with far fewer samples (see here).

Please note, to ensure that the PCA were as informative as possible I was forced to drop several populations that produced unusual results, probably because of extreme founder effects. This is why, for instance, there are no Ashkenazi Jews on any of the plots, and the only Finns you'll find come from western Finland.

I'll try this again on a much larger dataset when more samples come in, and also include populations from Central and South Asia.

Update 7/8/2014: Apparently some people are wondering what the plots with Finns and Jews look like. Here you go...