Tuesday, June 30, 2015

Ancient DNA from the Carpathian Basin (5700 BCE to 3900 BCE)

A new study reviews ancient DNA results from six successive archaeological cultures from the terminal culture of pre-Neolithic hunter-gatherers to the middle Neolithic era in Western Hungary.

Bernard's blog provides the source data on mtDNA haplogroups, Y-DNA, the geographic context of the cultures, and PCA analysis based upon haplogroup frequencies.

While the results aren't paradigm busting, a few observations about the data are in order:

* There are a remarkable 336 ancient DNA samples in the study from which at least mtDNA results are obtained.

* All 19 of the hunter-gatherer samples have one of five different mtDNA U haplogroups (counting 2 mtDNA U not further specified due to degradation of the sample as a separate category).

* A quite significant share of the Vinca samples are also mtDNA U (about 22.5%), but it is quite rare in the Neolithic samples from the cultures that preceded and follow it.  This is a resurgence from the previous Starcezo culture.

* All of the Neolithic samples have substantial mtDNA diversity (at least six or more mtDNA top level haplogroups represented).  At least some Neolithic sample has examples of mtDNA not found in the hunter-gather sample including H, HV, V, J, K, N1a, T1, T2,  U3, U8, W and X.

* There is a significant mtDNA mix shift between Vinca and subsequent Neolithic cultures (starting with LBK), including a significant increase in the frequency of mtDNA H and a significant decrease in the frequency of mtDNA U.  The Starcezo culture has only 6.9% mtDNA H, which falls in Vinca, before rising in the LBK and subsequent cultures.

* Y-DNA R1b does not appear until the Bronze Age, where there are 2 Y-DNA R1b samples and there is one Y-DNA I1 sample.

* There is no hunter-gatherer ancient Y-DNA in the sample.

* The Neolithic samples (pre-Bronze Age) include Y-DNA G2a, F*, I2, E-M78, J2 and surprisingly C.  There is also one sample of Y-DNA I1 from the LBK culture.

Monday, June 29, 2015

Y-DNA E Better Understood

A new study of the phylogeny of Y-DNA E (via Bernard's blog) shows more regionally defined structure of different subclades of the Y-DNA haplogroup than had previously been discerned, particularly in Eastern and Southern Africa.

It also provides a wealth of data on the time depth of various Y-DNA E subclades, although given the wide disparities that exist in establishing mutation rate dates, this is more useful in terms of establishing relative ages than absolute one.

The study puts the split of Y-DNA D and Y-DNA E at 69,000 to 69,800 years ago.

Y-DNA E-M81, which is the predominant Berber clade (also found in moderate frequencies in Iberia, in Turkey and in Bedouins, and at low frequencies in Italy), breaks off from the clade that includes my own Y-DNA E-V13 (which is found in high frequencies in the Balkans and moderate frequencies in much of the rest of Europe and Turkey and among the Druze) between 24,100 and 25,000 years ago, around the time of the Last Glacial Maximum.

E-M81 probably arrives in Europe via the Strait of Gibraltar, in the Mesolithic or early Neolithic era, with an additional significant influx to Moorish Spain in the last 1,300 years.

E-V13 probably arrives in Europe via the Levant and disperses from there to the rest of Europe at roughly the same time or perhaps a bit later, around the Mesolithic or Neolithic era (mutation rate dating puts the origin of this clade at about 8,100 years ago).  Ancient DNA from clade E-M78 (which is a parent of E-V13) is found in Iberia ca. 7,000 years ago and Y-DNA clades that are part of the E-M78 clade are present in Iberia in similar frequencies to E-M81.  The spread of E-V13 to the Balkans and its expansion there must have happened sometime in pre-history, because no known historical migrations prior to first wave Neolithic migrations could account for its strong presence in the Balkans.

While a number of individuals have argued for an Eurasian origin for Y-DNA E, based on the fact that its sister clade Y-DNA D is predominantly found in Asia, an examination of the phylogeny of Y-DNA E together with the geographic distribution of its currently known branches argues strongly for an African origin for Y-DNA E, rather than a Eurasian one, as do other factors such as the presence of individuals with Y-DNA DE not further distinguished between D or E in both Tibet and Africa.

Many relatively basal branches of Y-DNA E are found almost entirely in Africa and the African diaspora (e.g. African-Americans and Afro-Caribbean populations), while only a couple of relatively young branches of Y-DNA E are found (mostly at moderate frequencies) in parts of Europe and the Near East adjacent to Africa. See, e.g., page 4 of the supplementary materials for the new study. Those branches of Y-DNA E found outside Africa, moreover, are related to each other only via branches of Y-DNA E found only in Africa.

As Wikipedia notes:
E1a and E-M75 are found almost exclusively in Africa. By looking at the major subclade frequencies, five broad regions of Africa can be defined: East, Central, North, Southern and West. The division can be distinguished by the prevalence of E-V38 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-V38 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions except the northernmost and easternmost portions of the continent. E-M243 (especially its subclades M78 and M81) is found at high frequencies in North East Africa and North Africa and is the only subclade that is found in Europe and Asia at significant frequencies. E-M243 is common among Afro-Asiatic speakers in the Near East and North Africa as well as among some Nilo-Saharan and Niger–Congo speakers in North East Africa and Sudan. E-M243 is far less common in West, Central, and Southern Africa[.]
It is also unlikely that Y-DNA had origins in Northwest, West, Central or Southern Africa. E-V38, which is most common in these regions, according to the new study, mostly expanded and diversified in the last 15,300 years, making it the youngest major branch of Y-DNA E. Y-DNA E diversity also tends to decline from East to West across North Africa. Instead, East Africa is the likely place of origin of Y-DNA E.

Ethio Helix has some solid analysis of the new data, although his page is hard to read in some browsers.  In particularly, he notes that the study localizes the older part of one of the main branches of Y-DNA E in Northern Ethiopia and Sudan.