January 31, 2013

Lineages of West Asia compared to Africa and Europe

Just a quick mention of this new paper on the matri- and partilineages of West Asia:

Danielle A. Badro et al., Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0054616]


The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.

Maybe most interesting is this map:

Figure 1. Geographic distribution of mtDNA haplogroups.
Frequencies distribution from the current study and from the published data [30], [31], [35][48] as reported in Table 1.

A very important issue with this map is that "Malians" and "Burkinabe" are actually Tuaregs from those countries (samples taken from Pereira 2010), hence their large fractions of Eurasian lineage H (H1 in fact). Also I am a bit perplex at the large portions of "other", which in the region considered can only be: L4, L5, L6 (all them small lineages from Africa and Yemen), R0(xH,V), N1, W, X and M1 (important in West Asia and some parts of Africa - I wonder why they are not listed on their own right) and maybe some other very rare lineages.

Regarding Y-DNA (and also largely mtDNA) the study focuses on statistical comparisons, not providing any comprehensive table nor map of haplogroup distribution. However for those interested in data mining the whole list of haplotypes (with purported haplogroup) of this study is available in table S2.

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