Phylogeographic refinement of haplogroup E

Genome Biol Evol (2015) 7 (7): 1940-1950.

Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent

Beniamino Trombetta et al.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.

Link

More Y-chromosome super-fathers

The time estimates are based on a mutation rate of 1x10-9 mutations/bp/year which is ~1/3 higher than mutation rate of Karmin et al.  So the values on the table may be a little lower.

There may be additional founders with recent time depths than shown in the table, e.g., a very shallow clusters within E-M35 (probably E-V13?) and a couple of shallow clusters within I-P215

Also of interest is the fact that Greeks and Anatolian Turks do not show evidence of the recent Y-chromosomal bottleneck:

The plots are consistent with patterns seen in the relative numbers of singletons, described above, in that the Saami and Palestinians show markedly different demographic histories compared with the rest, featuring very recent reductions, while the Turks and Greeks show evidence of general expansion, with increased growth rate around 14 KYA. A different pattern is seen in the remaining majority (13/17) of populations, which share remarkably similar histories featuring a minimum effective population size ~2.1–4.2 KYA (considering the 95% confidence intervals (CIs) reported in Supplementary Table 4), followed by expansion to the present.

Related:

• Y chromosome super-fathers 
• Bottleneck in human Y-chromosomes in the last 10,000 years

Nature Communications 6, Article number: 7152 doi:10.1038/ncomms8152

Large-scale recent expansion of European patrilineages shown by population resequencing

Chiara Batini, Pille Hallast et al.

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Link

E-M81 in Morocco

Hum Biol. 2014 May;86(2):105-12.

Phylogeography of e1b1b1b-m81 haplogroup and analysis of its subclades in morocco.

Reguig A, Harich N, Barakat A, Rouba H.

Abstract

In this study we analyzed 295 unrelated Berber-speaking men from northern, central, and southern Morocco to characterize frequency of the E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183, and E1b1b1b2a-M165. For this purpose, we typed four biallelic polymorphisms: M81, M107, M183, and M165. A large majority of the Berber-speaking male lineages belonged to the Y-chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1% to 98.5% in all localities sampled. E1b1b1b2-M183 was the most dominant subclade in our samples, ranging from 65.1% to 83.1%. In contrast, the E1b1b1b1-M107 and E1b1b1b2a-M165 subclades were not found in our samples. Our results suggest a predominance of the E1b1b1b-M81 haplogroup among Moroccan Berber-speaking males with a decreasing gradient from south to north. The most prevalent subclade in this haplogroup was E1b1b1b2-M183, for which diffferences among these three groups were statistically significant between central and southern groups.

Link

Recent origin of North African populations

This makes sense since North Africans are so close (phenotypically) to West Eurasians that it makes sense that they cannot have been isolated from them for very long, i.e., since Out-of-Africa.

PLoS ONE 8(11): e80293. doi:10.1371/journal.pone.0080293

Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa

Karima Fadhlaoui-Zid, Marc Haber et al.

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ~15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

Link

Y-chromosome of Napoleon the Great

A previous article had determined that Napoleon I had belonged to Y-haplogroup E-M34*, and a new one designates his haplogroup as "M123+, M34+, and L791 and L792+," and determines a multi-STR haplotype for his lineage based on two patrilineal relatives.

Such a well-resolved haplotype may now make it possible to both (i) find descendants and relatives of Napoleon that may be unaware of this connection, and (ii) to more precisely determine the ultimate origins of the house of Buonaparte.

International Journal of Sciences 2(9)

Reconstruction of the Lineage Y Chromosome Haplotype of Napoléon the First

Gerard Lucotte, Jacques Macé, Peter Hrechdakian

As part of the Napoléon I Genome (NIG) project we have reconstructed, based on more than one hundred Y-STRs (Y-short tandem repeats), the complete Y-haplotype of the non-recombinant part of the Y-chromosome (NRY) of French Emperor Napoléon I (1769-1821). We already knew the allelic values at Y-markers of the Y-chromosome of Napoléon I, but only for the palindromic STR YCAIIa and b and for the non-palindromic Y-STR DYS19. The present reconstruction aims to compare the allelic values at Y-STRs of the DNA of Charles Napoléon (C.N.), the living 4th generation descendant of Jérôme Bonaparte (Napoléon I’s youngest brother), with those of Alexandre Colonna Walewski (A.C.W.), the living 4th generation descendant of Count Alexandre Walewski (the son born of the union between Napoléon I and Countess Maria Walewska). We have previously established that Napoléon I, C.N. and A.C.W. are of the same Y-haplogroup E1b1b1b2a1. The allelic values for C.N. and A.C.W. are the same for ninety-three other non-palindromic markers (belonging to ninety different STRs) and for thirty-eight other palindromic markers (belonging to fifteen different STRs); these values then constitute those deduced in the reconstruction of the allelic values of the STR markers of the Napoléon I’s Y-haplotype. Four non-palindromic STRs and two palindromic STRs have different allelic values in C.N. and A.C.W.; we have deduced the allelic value of Napoléon I for one (DYS454), and the probable allelic values for two (Y-GATA-C4 and DYS712) of these non-palindromic variable STRs. To sum up, we have established, by reconstruction of the lineage, the allelic values of the markers of Napoléon I’s Y-haplotype for a total of one-hundred and thirty-three different Y-STR markers.

Link (pdf)

Y chromosomes of Bulgarians (Karachanak et al. 2013)

Bulgaria had been something of a blank area in studies of uniparental markers, so it's nice to finally see a comprehensive Y-chromosome study of the country.

The dates in the paper are based on the "evolutionary mutation rate". I suspect that ancient DNA will be the final arbiter in this issue, because, for example, a Mesolithic TMRCA of E-V13 in Bulgaria implies that we'll find a lot of it in Neolithic contexts, whereas a Bronze Age one implies that we'll find a little if any of it, and a discontinuity across time.

Of interest is the occurrence of some E*(xM35, M2) in this sample in Burgas, Varna, and Plovdiv. It would be interesting to trace the ancestry of the bearers of these Y-chromosomes. I know that there still exists a minority-within-a-minority of Black Muslims in Greek Thrace, and it's not inconceivable that these Y-chromosomes may represent the legacy of a similar population; in any case, their haplotypes can be found in Table S5 for anyone wanting to investigate.

SNP Diversity within R seems substantial, and as always, it is difficult to say much, since this may be a consequence of either (i) a plausible role of the Balkans as a staging point of the likely invasion of Europe in late prehistory, or (ii) back-migration of derived R-bearers into the Balkans, be them Slavs or Goths or "eastern" folks of various stripes during history. Once again, I suspect that ancient DNA might solve this riddle, or, alternatively, routine high-coverage sequencing of the Y chromosome that might inform us, e.g., about the TMRCA of a Bulgarian and a German R-U152 or a Bulgarian and Polish R-M458.

PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779

Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

Sena Karachanak et al

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.

Link

Y chromosomes of pastoralists and farmers from the Sahel

Am J Phys Anthropol DOI: 10.1002/ajpa.22236

Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel

Jana Bučková et al.

The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past.

Link

Algerian Y chromosomes and mtDNA

From the paper:

For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean

It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

• The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
• I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
• The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
• The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
• The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Link

Y chromosome of Ramesses III

From the paper:

Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a.

Ethiohelix has more.
Added in my compendium of ancient Y chromosome studies.

BMJ 2012; 345 doi: http://dx.doi.org/10.1136/bmj.e8268

Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study

Abstract

Objective To investigate the true character of the harem conspiracy described in the Judicial Papyrus of Turin and determine whether Ramesses III was indeed killed.

Design Anthropological, forensic, radiological, and genetic study of the mummies of Ramesses III and unknown man E, found together and taken from the 20th dynasty of ancient Egypt (circa 1190-1070 BC).

Results Computed tomography scans revealed a deep cut in Ramesses III’s throat, probably made by a sharp knife. During the mummification process, a Horus eye amulet was inserted in the wound for healing purposes, and the neck was covered by a collar of thick linen layers. Forensic examination of unknown man E showed compressed skin folds around his neck and a thoracic inflation. Unknown man E also had an unusual mummification procedure. According to genetic analyses, both mummies had identical haplotypes of the Y chromosome and a common male lineage.

Conclusions This study suggests that Ramesses III was murdered during the harem conspiracy by the cutting of his throat. Unknown man E is a possible candidate as Ramesses III’s son Pentawere.

Link

East Eurasian-like ancestry in Northern Europe (part 3)

(This is the third part of the series. See part 1 and part 2.)

In the first two parts of the series, I showed that northern European populations show hints of East Eurasian ancestry when compared against Sardinians. I used Dai, Han, and Karitiana as reference populations for East Eurasia. In the current post, I extend this analysis by using HGDP Papuans and the Onge (Reich et al. 2009) from the Andaman Islands.

The f4 statistics using Karitiana, Papuan, and Onge populations can be found in this spreadsheet.

Below, you can see that they are all near perfectly correlated with each other.

The visual appraisal is confirmed when we calculate the correlation coefficients:

The fact that all three populations track the same signal is strong evidence for the direction of gene flow: from Asia into northern Europe. If the signal was present in only one of the three populations, then it could conceivably be an artefact of gene flow in the opposite direction (from northern Europeans to the affected population). But, the fact that all three populations show the same pattern would require northern European-like admixture in the Andaman Islands, Papuan New Guinea and South America, which does not appear very parsimonious.

While the signals from the three populations are correlated, their intensity varies. The Z-scores provide a measure of this intensity. The mean Z-scores using a Karitiana, Papuan, and Onge reference across all populations are respectively -17.7, -8.0, and -6.0.

While I did not include the Han reference of part 1 in this analysis, inspection of the f4 statistics (which can be obtained at the bottom of that part), suggests that the Z-scores become more significant when using an Onge, Papuan, Han, and Karitiana reference in that order. For example, for the Finnish_D population, they are: -10.037, -13.2949, -23.9305, and -27.764 respectively.

It thus appears that the element contributing East Eurasian-like ancestry in northern Europeans was derived from the northern spectrum of East Eurasians; the Karitiana may live in South America today, but they trace their ancestors to northern Eurasia, having entered the Americas c. 15ka.

In my opinion, the signal has been formed by a superposition of a few factors:

1. The fact that Y-haplogroup R, the main lineage in modern northern Europeans has a common origin (Y-haplogroup P) with haplogroup Q, the main lineage in modern Amerindians, and many Siberians. We can hypothesize that the population that brought R into Europe was intermediate genetically across the Caucasoid-Mongoloid spectrum. In West Eurasia, this population admixed with the Palaeo-West Eurasians (Y-haplogroups IJ, G, and possibly LT), and contributed their DNA primarily to the northern Europeoids.
2. Other population movements of more regional impact, such as Y-haplogroup N, which affected mainly Uralic, Baltic, and East Slavic populations, as well as elements from the mixed West/East Eurasian mtDNA contact zone that ancient DNA analysis has revealed in Eastern Europe and Siberia.

The raw dumps of fourpop output for Papuan and Onge reference can be found here.

East Eurasian-like admixture in Northern Europe (part 2)

This is a continuation of my earlier post. Please refer to it for the methodology. A new part 3 can be found here.

I have repeated the experiment with a much larger set of populations:

English_D, British_D, Ukranians_Y,  Karitiana, Spaniards, Sardinian,  Serb_D, Mordovians_Y, Irish_D,  French, Finnish_D, Chuvashs_16,  Romanian_D, N_Italian_D, French_Basque,  Austrian_D, Russian_D, Hungarians_19,  Kent_1KG, German_D, Belorussian,  Tuscan, Lithuanian_D, Orkney_1KG,  Dutch_D, TSI30, Ukrainian_D,  Bulgarians_Y, Bulgarian_D, Russian,  Swedish_D, Pais_Vasco_1KG, French_D,  Castilla_Y_Leon_1KG, Lithuanians, San,  Polish_D, Romanians_14, Orcadian,  Cornwall_1KG, Valencia_1KG, North_Italian,  FIN30, Norwegian_D, CEU30

I used Sardinians as the Caucasoid reference population, Karitiana for Mongoloids, and San for Africans. The latter two were chosen because they live at maximally opposite corners of the Earth (South America vs. South Africa).

A first plot of the f4 statistics used for f4 regression ancestry estimation is seen below:

Clearly, some evidence of a cline is present, but several populations appear to deviate from it. In order to get the cleanest possible cline, I carried out the following greedy procedure: I calculate the correlation coefficient of this set, and iteratively remove one population that leads to the maximum improvement of the correlation, until no further improvement takes place. The following populations were removed with this procedure:

Spaniards, Serb_D, Romanian_D, N_Italian_D, Tuscan, TSI30, Bulgarians_Y, Bulgarian_D, Castilla_Y_Leon_1KG, Romanians_14, Valencia_1KG

This seems to make sense, as all these are southern European populations. Note that their removal does not mean that they do not partake in the same phenomenon as northern Europeans: they also exhibit Karitiana-shift relative to the Sardinians, but there are probably other confounding factors that make them fall "off-cline". Including them would diminish the clarity of the cline for Northern European populations. The regression of the remaining populations can be seen on the right:

f4 regression ancestry estimation results are shown on the left. These appear to be much higher than was the case with the Han and Dai in the previous experiment.

I can't say that I've made any obvious mistakes, but these admixture proportions are substantial, and call for an explanation. Whatever their true levels, I am fairly confident on at least a few points:

First, it is evident that northern Europeans have higher levels of this element than southern Europeans; the latter are not altogether deficient in it, but they fall "off-cline", making estimation of their admixture proportions more difficult.

Second, within northern Europe, there is a fairly clear east-west cline of diminishing Amerasian-like admixture. The minimum occurs in Sardinians and secondarily in Southwest Europe. Romance, Celtic, and Germanic populations all have less of it than Balto-Slavic and Uralic ones. And, some populations of northeastern Europe seem to have a noticeable excess of it.

The groups with the most Amerasian-like admixture possess Y-haplogroup N, a clear trace of eastern ancestry that is not shared by most Europeans. The arrival of this haplogroup, either with Comb Ceramic of the Baltic Neolithic or later with Seima Turbino Bronze Age expansions is probably responsible for the local excess in Northeastern Europe. The Chuvash are, of course, a Turkic population but of Finno-Ugrian genetic origin.

But, the presence of this element even in Western Europe cannot be explained on the basis of typically Mongoloid elements which are almost completely lacking there. If Mesolithic Europeans were themselves Asian-shifted, then this would account for the presence of the element, but not necessarily for its clinal manifestation. The double (north-south and east-west) cline indicates every sign of an intrusive element. So, for the time being, I will propose that this is associated with late (e.g., Copper and Bronze Age) phenomena, such as the northern stream of the Bronze Age Indo-European invasion of Europe.

This may be due to the

• (i) northern Indo-European groups picking up some native east European or Siberian elements as they made their way into Europe, 
• or (ii), more likely, in my opinion, that the Y-haplogroup R1 group of people, whose closest relatives are in Central/South Asia (R2) , and whose more distant relatives (Q) are in Siberia and the Americas, were from the beginning an "intermediate population" between West and East Eurasia. The R1 group of people in its R1b and R1a varieties first appear in Europe during the Copper Age, and they are lacking in early Neolithic sites.

Eight years ago, and in a totally different context, I wrote:

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids)   

... 

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies. 

If these data pan out, it may be revealed that the European branch of the Caucasoids is actually a product of admixture too, with at least two of its constituent elements being the "Palaeo-West Eurasians" (Y-haplogroups G, IJ, possibly LT) and the "Neo-NW Eurasians" (Y-haplogroups N1 and R1), with the "Neo-Afrasians" (Y-haplogroup E1b1b) forming a third element.

(A raw dump of fourpop output can be found here).

African Y chromosome news (E1b1a and R-V88)

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.176

Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people

Naser Ansari Pour1, Christopher A Plaster1 and Neil Bradman1

Abstract

The expansion of the Bantu-speaking people (EBSP) during the past 3000–5000 years is an event of great importance in the history of humanity. Anthropology, archaeology, linguistics and, in recent decades, genetics have been used to elucidate some of the events and processes involved. Although it is generally accepted that the EBSP has its origin in the so-called Bantu Homeland situated in the area of the border between Nigeria and the Grassfields of Cameroon, and that it followed both western and eastern routes, much less is known about the number and dates of those expansions, if more than one. Mitochondrial, Y-chromosome and autosomal DNA analyses have been carried out in attempts to understand the demographic events that have taken place. There is an increasing evidence that the expansion was a more complex process than originally thought and that neither a single demographic event nor an early split between western and eastern groups occurred. In this study, we analysed unique event polymorphism and short tandem repeat variation in non-recombining Y-chromosome haplogroups contained within the E1b1a haplogroup, which is exclusive to individuals of recent African ancestry, in a large, geographically widely distributed, set of sub-Saharan Africans (groups=43, n=2757), all of whom, except one Nilo-Saharan-speaking group, spoke a Niger-Congo language and most a Bantu tongue. Analysis of diversity and rough estimates of times to the most recent common ancestors of haplogroups provide evidence of multiple expansions along eastern and western routes and a late, exclusively eastern route, expansion.

Link

European Journal of Human Genetics advance online publication 15 August 2012; doi: 10.1038/ejhg.2012.167

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

Miguel González1, Verónica Gomes1,2, Ana Maria López-Parra3, António Amorim1,4, Ángel Carracedo2, Paula Sánchez-Diz2, Eduardo Arroyo-Pardo3 and Leonor Gusmão1

Abstract

Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a ‘back-to-Africa’ migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene.

Link

A look at Y chromosomes of Romania via Count Dracula

In short: researchers tried to see whether they could identify a specific Y chromosome lineage associated with the House of Basarab in Romania, the most famous member of which is Vlad the Impaler, an inspiration for the mythical Count Dracula. To do this, they tested Basarab-surnamed individuals, as well as the general Romanian population.

The whole exercise was, in a sense, a failure, since it neither disclosed a Basarab-specific lineage, nor resolved the historical question about the origin of the House of Basarab (Vlach or Cuman). But, it gave us some wonderful new data on Romania that is, of course, quite welcome.

This seems like a good candidate for a future ancient DNA study, assuming of course, that Vlad and his family are still in their final resting place, and there are brave enough researchers to disturb them (j/k).

On a more serious note, the authors correctly state that even if the Basarab house was originally Turkic, they could still have carried West Eurasian chromosomes, since incoming Turkic groups in Europe were not purely Mongoloid like their more remote ancestors. On the other hand, I note that most of the Basarab-surnamed individuals belonged to E-V13, I-P37.2, J-M241 all of which are almost certainly native Romanian. If one of them carries the original chromosome, then the odds are in favor of a Romanian origin, although nothing short of ancient DNA work can resolve the issue, assuming that's possible.

Table S1 contains the new Romanian data, and Table S2 data from surrounding populations (Hungary, Bulgaria, Ukraine).

PLoS ONE 7(7): e41803. doi:10.1371/journal.pone.0041803

Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings

Begoña Martinez-Cruz et al.

Vlad III The Impaler, also known as Dracula, descended from the dynasty of Basarab, the first rulers of independent Wallachia, in present Romania. Whether this dynasty is of Cuman (an admixed Turkic people that reached Wallachia from the East in the 11th century) or of local Romanian (Vlach) origin is debated among historians. Earlier studies have demonstrated the value of investigating the Y chromosome of men bearing a historical name, in order to identify their genetic origin. We sampled 29 Romanian men carrying the surname Basarab, in addition to four Romanian populations (from counties Dolj, N = 38; Mehedinti, N = 11; Cluj, N = 50; and Brasov, N = 50), and compared the data with the surrounding populations. We typed 131 SNPs and 19 STRs in the non-recombinant part of the Y-chromosome in all the individuals. We computed a PCA to situate the Basarab individuals in the context of Romania and its neighboring populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name. All haplogroups are common in Romania and other Central and Eastern European populations. In a PCA, the Basarab group clusters within other Romanian populations. We found several clusters of Basarab individuals having a common ancestor within the period of the last 600 years. The diversity of haplogroups found shows that not all individuals carrying the surname Basarab can be direct biological descendants of the Basarab dynasty. The absence of Eastern Asian lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of the Basarab dynasty, although it cannot be positively ruled out. It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

Link

Y chromosomes and mtDNA from late antique Bavaria

One of the papers in the aforementioned volume includes Y-STR and mtDNA data on a burial cemetery from Bavaria dating to the Imperial Roman age. I reproduce the DNA results below; the haplogroup assignments in red are my own and have been estimated with Whit Athey's haplogroup predictor using both Northwest European and Equal priors.

The number of Y-STRs is not sufficient to make very strong haplogroup assignments in some cases. Still, we can probably say that R1b, E1b1b, and I1 were present in the population. I1 might seem more likely than G2a in a few cases, but remember that a couple of G2a men were found in 7th c. Bavaria. E1b1b, another non-typical German haplogroup has also been found in Usedom from the medieval period.

Christina Sofeso, Marina Vohberger, Annika Wisnowsky, Bernd Päffgen, Michaela Harbeck, *

Verifying archaeological hypotheses: Investigations on origin and genealogical lineages of a privileged society in Upper Bavaria from Imperial Roman times (Erding, Kletthamer Feld)



During the years 2005 and 2006 approximately 2000 archaeological

finds ranging from the Neolithic Period to Late Antiquity 

were found on the Kletthamer Feld (Erding, Upper Bavaria). 

Out of this context a burial site was examined comprising 

13 individuals, some of them rich in precious grave goods. The 

inhumations were dated to the second half of the 4th to the first 

half of the 5th century – a time of upheavals in relation to the 

demographic structure of the former Roman province Raetia (today southern Bavaria).

The high proportion of male individuals within the skeletal population as well as the finding of a Roman fibula, which is seen as part of Roman military clothing, led to distinct hypotheses which we have attempted to support in this study. The hypothesis that the skeletal remains reflect a founder population from a Germanic region north of the Danube River could be rejected on the basis of stable isotope analyses. The theory of a buried family clan had to be dismissed as well, or rather, be extended to the scenario of several families being buried there with their servants. The results obtained fit the third presumption best, namely that the buried individuals were the members of a military unit interred with their families.

Serbian Y-chromosomes

Gene. 2012 Jan 31. [Epub ahead of print]

High levels of Paleolithic Y-chromosome lineages characterize Serbia.

Regueiro M, Rivera L, Damnjanovic T, Lukovic L, Milasin J, Herrera RJ.

Abstract

Whether present-day European genetic variation and its distribution patterns can be attributed primarily to the initial peopling of Europe by anatomically modern humans during the Paleolithic, or to latter Near Eastern Neolithic input is still the subject of debate. Southeastern Europe has been a crossroads for several cultures since Paleolithic times and the Balkans, specifically, would have been part of the route used by Neolithic farmers to enter Europe. Given its geographic location in the heart of the Balkan Peninsula at the intersection of Central and Southeastern Europe, Serbia represents a key geographical location that may provide insight to elucidate the interactions between indigenous Paleolithic people and agricultural colonists from the Fertile Crescent. In this study, we examine, for the first time, the Y-chromosome constitution of the general Serbian population. A total of 103 individuals were sampled and their DNA analyzed for 104 Y-chromosome bi-allelic markers and 17 associated STR loci. Our results indicate that approximately 58% of Serbian Y-chromosomes (I1-M253, I2a-P37.2, R1a1a-M198) belong to lineages believed to be pre-Neolithic. On the other hand, the signature of putative Near Eastern Neolithic lineages, including E1b1b1a1-M78, G2a-P15, J1-M267 and J2-M172 and R1b1a2-M269 accounts for 39% of the Y-chromosome. Furthermore, an examination of the distribution of Y-chromosome filiations in Europe indicates extreme levels of Paleolithic lineages in a region encompassing Serbia, Bosnia-Herzegovina and Croatia, possibly the result of Neolithic migrations encroaching on Paleolithic populations against the Adriatic Sea.

Link

Genes and Languages in the Caucasus

If there was ever a paper that was the equivalent of a box of candy, this is probably it. I will update this post with my comments.

UPDATE I (Genealogical rate, Gene-language concordance, Ossetes): I seriously don't know where to begin with this paper. So, given the serendipitous appearance of an abstract on Y-chromosome mutation rates, here is a major new pro-genealogical rate quote from the new paper:

We found that “evolutionary” estimates of most clusters fall far outside the range of the respective linguistic dates, while “genealogical” estimates gave a good fit with the linguistic 23 dates. At least two population events in the Caucasus are documented archaeologically, which allows additional comparison with these “historical” dates. In both cases, the historical (archaeological) date is similar to a genetic estimate based on the “genealogical” mutation rate (Supplementary Note 2).

And, here's a comparison of the linguistic and genetic (based on Y-chromosomes) trees from the paper:

The correspondence seems remarkable; the only major discrepancy is for Iranic (Indo-European) Ossetes who group with NW Caucasians genetically, which makes sense as the Ossetes are probably to a large extent NW Caucasians that underwent a language shift at the influence of the Alans.

Speaking of the Ossetes, their negligible R1a1-M198 frequency (0.4-0.8%) should be a warning that Iranic steppe nomads _does not equal_ R1a1. While a limited contribution of Alans to the Ossetes is expected, it is not expected that Ossetes will have two of the lowest M198 frequencies in the Caucassus: in all probability R1a1 was not particularly important among Alans, and, by implication (?) Sarmatians.

UPDATE II (4 haplogroups for 4 language families):

The most interesting discovery in this paper is, of course, the correspondence between Y-chromosome haplogroups and language groups, thanks to the very large number of individuals tested and the deep phylogenetic resolution of the haplogroups:

Overall, the most frequent haplogroups in the Caucasus were G2a3b1-P303 (12%), G2a1a-P18 (8%), J1*-M267(xP58) (34%), and J2a4b*-M67(xM92) (21%), which together encompassed 73% of the Y chromosomes, while the other 24 haplogroups identified in our study comprise the remaining 27% (Table 2). ... haplogroup G2a3b1-P303 comprised at least 21% (and up to 86%) of the Y chromosomes in the Shapsug, Abkhaz and Circassians ... haplogroup G2a1a-P18 comprised at least 56% (and up to 73%) of the Digorians and Ironians (both from the Central Caucasus Iranic linguistic group), while not being found at more than 12% (average 3%) in other populations... haplogroup J2a4b*-M67(xM92) comprised 51-79% of the Y chromosomes in the Ingush and three Chechen populations (North-East Caucasus, Nakh linguistic group), while, in the rest of the Caucasus, its frequency was not higher than 9% (average 3%) ... haplogroup J1*-M267(xP58) comprised 44-99% of the Avar, Dargins, Kaitak, Kubachi, and Lezghins (South-East Caucasus, Dagestan linguistic group) but was less than 25% in Nakh populations and less than 5% in the rest of Caucasus.

Interestingly, G2a3 is one of the lineages of early Central European farmers, and 2 medieval German knights. G2 is also, curiously, one of the West Eurasian lineages that are found in very small quantities in India, especially among upper caste Hindus. We are beginning to make connections across space and time, even though the patterns are far from clear yet.

The prevalence of J1*-M267(xP58) in Dagestan is well known (or suspected) from previous studies. Notice that J-P58, if we use the genealogical rate has an age of ~5.4ky in Semitic groups, and this is in concordance with the 5,750 years ago origin of Semitic languages based on Bayesian phylogenetics. So, it is clear that part of haplogroup J1 was prevalent in ancient Semitic groups, another, disjoint part in ancient Dagestani groups.

To make things more interesting, the Nakh groups (Ingush and Chechens) have J2a4b*-M67(xM92) as their modal haplogroup. Nakh is also a Northeast Caucasian language subfamily, like Dagestani, and indeed NE Caucasian is also called Nakho-Daghestanian. What did the early speakers of this family look like?

It would be tempting to think that Proto-Nakho-Dagestanians were J1-dominated, as J1 exists in both Nakh (16-25%) and Dagestani (58-99%) groups, whereas J2a4b-M67 (the Nakh modal haplogroup) is nearly completely absent in Dagestanians.

UPDATE III (No European influence):

Another interesting discovery of this study is the lack of European influence in the populations of the North Caucasus.

It seems that both R1a1a-M198 and I2a-P37 have a major barrier eastward in the Don river. Please note that the former is not strictly a European haplogroup, but it nonetheless experiences a massive drop in frequency, and is negligible everywhere except in Abkhaz-Circassians (NW Caucasus; 10.3-19.7%), with an outlier in Dargins (22%).

This seems to put a limit on the origin of any hypothetical movements across the Eurasian steppe east of the Don river, as haplogroup I2a-P37 is largely absent in Central Asia, and occurs 3 times in 1,525 individuals in this sample. So, while there have been proposals of a Central European origin of some steppe pastoralist groups, these are hard to reconcile with this picture.

UPDATE IV (Haplogroup G):

Two of the modal haplogroups in this paper are G2a1a-P18 (Iranic, 56-73%) and G2a3b1-P303 (NW Caucasians, 21-86%). Battaglia et al. (2008) also found a high frequency of G2a* in Georgians and Balkars (~30%, also modal in both populations). It appears that G2a is a mainly West (both NW and SW) Caucasian phenomenon within the context of this region.

UPDATE V (Starostin and Language depth)

The authors applied the methodology of the late Sergei Starostin to the problem of language time depth:

The present work employs Starostin’s methodology, and we made special efforts to create the high-quality linguistic databases required for this analysis. Thus, based on significantly extended and revised linguistic databases, we have applied a glotto-chronological approach to the North Caucasian languages. As a result, our study provides a unique opportunity to make direct comparisons of linguistic and genetic data from the same populations. Lexico-statistical methods have also been applied to a number of language families using a Bayesian approach to increase the statistical robustness of language classification (Gray and Atkinson, 2003; Kitchen et al., 2009; Greenhill et al., 2010). Using these methods with the Caucasus languages under

study here will be the focus of future work.

It will certainly be interesting to see Bayesian phylogenetic methods applied to the Caucasus languages in the future, using the linguistic datasets developed here. The concordance of genetic-linguistic results in this paper, in addition to the many successes of the G&A approach, is making it increasingly difficult for those who doubt our ability to estimate the age of language families in a manner similar to that with which biologists estimate the age of genetic variation.

See also Tower of Babel project and the Evolution of Human Languages project at the Santa Fe Institute.

UPDATE VI (Haplogroup J2a)

I have recently speculated about a possible link between the Caucasus region and India based on the appearance of a "Dagestan" component in India, the clear West Asian origin of Ancestral North Indians, as well as a possible linguistic link between Northeast Caucasian, Hurrian, and Indo-European.

A problem with that theory is that the high J1*(xP58) frequency in Dagestan has no counterpart in South Asia. The current study, however, adds data on the Nakh part of the Nakho-Dagestanian (Northeast Caucasian) family, showing this to be J2a4b-M67 dominated. So, while I think that J1*(xP58) may have been present among Proto-Northeast Caucasians, these must have interacted with J2a folk.

J-M67 is clearly intrusive into the Central Caucasus, from the South where a much greater variety of J2a-related lineages is observed among Armenians, North Iranians, and Anatolian Turks.

We now have good coverage of J2a in the entirety of the West Asian region, with the exception of Azerbaijan, and a few patterns are beginning to emerge:

1. The center of the J2a world is somewhere between eastern Turkey, Armenia, Azerbaijan, Iran, and Syria
2. The Caucasus is a northern extension of this world, just as Greece and Italy are its main western extensions, with a strong extension into Central Asia as far as Xinjiang, and well into South Asia all the way to upper caste South Indian Hindus.
3. In the Caucasus itself J-M67 is dominating Nakh speakers, but with little other J2a related variation.
4. In comparison to Nakhs, J2a seems more varied in Georgians, among Ossetes, and among NW Caucasian speakers

It is hard to make any pronouncements on how J2a spread northwards from its Transcaucasian cradle, but I would think that the Kura-Araxes and Maikop cultures are fairly good candidates for that spread, with the former being J2a dominated, and the latter being more G2a dominated. I would not, however, dismiss a more recent spread of J2a into the region.

UPDATE VII (Absence of E1b1b1):

This haplogroup has a more Mediterranean distribution and is conspicuously absent in the North Caucasus. Unfortunately no downstream markers were typed, but (a) its presence in small amounts in NW Caucasians (1-1.7%) together with a similar low frequency (1.5%) in Georgians, (b) its absolute absence among Nakho-Dagestanians, except for one Lezghin, suggest to me that it arrived to the region from the west, and is probably a low-frequency trace of Ancient Greek colonies of the Black Sea, just as it is associated with Greek colonists in the West Mediterranean and Sicily.

UPDATE VIII (Haplogroups L and T):

There is a little haplogroup L in the North Caucasus. L-M27 and L-M317 seems concentrated in the Northwest, while L-M357 is found only in Nakh speakers. The detection of L-M357 in North but not South Iran may be related with this population, and also the L-rich population of Syria, especially from the eastern inland area.

Haplogroup T has been the subject of a major recent paper. In this region, it is found in 2 NW Caucasians, 1 Ossete and a couple of Lezgins, but unfortunately with no fine phylogenetic resolution.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr126

Parallel Evolution of Genes and Languages in the Caucasus Region

Oleg Balanovsky1,2,*, Khadizhat Dibirova1,*, Anna Dybo3, Oleg Mudrak4, Svetlana Frolova1, Elvira Pocheshkhova5, Marc Haber6, Daniel Platt7, Theodore Schurr8, Wolfgang Haak9, Marina Kuznetsova1, Magomed Radzhabov1, Olga Balaganskaya1,2, Alexey Romanov1, Tatiana Zakharova1, David F. Soria Hernanz10,11, Pierre Zalloua6, Sergey Koshel12, Merritt Ruhlen13, Colin Renfrew14, R. Spencer Wells10, Chris Tyler-Smith15, Elena Balanovska1 and The Genographic Consortium16

We analyzed 40 SNP and 19 STR Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees, and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language co-evolution occurred within geographically isolated populations, probably due to its mountainous terrain.

Link

Variation in four Central Anatolian settlements

I had linked to the conference versions of this work in ISABS 2007 and AAPA 2008. Now there is a new paper in American Anthropologist on the topic of variation in four Central Anatolian settlements with very different origins. As I've mentioned before, this is a great illustration of the problem of uncritically treating modern Anatolian Muslim samples as representatives of the Neolithic population, for at least two reasons:

1. Modern Anatolian Muslims are only a part of the recent population of Anatolia, with a great part of the Christian population exchanged, killed, or forced to leave.
2. Modern Anatolian Muslims are ethnically, linguistically and religiously heterogeneous, and many of them have historical memories of descent from elsewhere, e.g., the Balkans, the Caucasus, or Central Asia

So, I have always been skeptical of grand reconstructions of prehistory based on treating modern Anatolian Muslims as little modified descendants of the Neolithic population. I don't doubt that a great deal of their ancestry, averaged over broad scales, is Neolithic Anatolian, but extracting this ancestry from the mosaic of heterogeneous Muslim groups inhabiting the modern Republic of Turkey is no trivial task.

From the current paper, in support of point #1:

Even though the data from official Ottoman records and other sources such as local church accounts are contradictory (Charanis 1972; Vryonis 1986), it is clear that Greek and Armenian peoples comprised the majority, or at least a very sizeable minority, of the late-19th-century Anatolian population (Finkel 2005; Levy 2002; Shaw et al. 1976). Muslim Turkic and Kurdish groups from different ancestral clans and, more importantly, from different sects of Islam made up the largest remaining part of the population (Cahen 1968, 2001; Finkel 2005). Therefore, the population of the Ottoman Empire came from different ancestral backgrounds, lived together, and constructed communities based on their religious affiliations.

In support of point #2, the authors have studied the inhabitants of a Central Anatolian region:

We worked in four geographically proximate Central Anatolian settlements located southeast of Ankara (see Figure 1) to test the abovementioned hypotheses and elucidate the regional complexity of Anatolian population history. Because of the current political sensitivities concerning ethnic–religious identity in Turkey, especially those relating to the Alevis and Kurds, the names of the specific settlements we visited are not identified in this article. Instead, for the sake of clarity, pseudonyms are used. This region, which we refer to as “Yuksekyer,” was selected for the study because, based on oral traditions and available historical records, it is home to linguistically, ethnically, and religiously distinct groups that live in close geographic proximity to one another. To assess the possible regional, religious, and ethnic differentiation in Central Anatolia, we collected additional samples from a settlement from Kizilyer, another region located about 500 kilometers east of Yuksekyer, the inhabitants of which are predominantly Alevi Turks.

"Yuksekyer" is 2,500 sq. km in size, so it's quite small in the broader Anatolian context. Here are details on the studied settlements:

Merkez is the current political and bureaucratic center with about 6,500 inhabitants, making it the most populous settlement in the region (Devlet İstatistik Enstitüsü 2001). It was probably founded by Cerkez (Circassian) people who had migrated there from the Caucasus region in the 14th century.

...

The inhabitants of the oldest known settlement, Eskikoy, claim a pre-Ottoman Karaman ancestry that traces back to a Turkic population that occupied the Konya region during the 13th century (Finkel 2005). To date, no historical records that confirm the connection between Eskikoy and its putative Karaman origin have been found. However, Ottoman records mention the presence of the Eskikoy settlement in the Yuksekyer region and place its foundation at around 1500 C.E.

...

The residents of Gocmenkoy identify themselves with the Afsar clan of the Oguz tribe, to which the Kayi and Turkmen lineages also belong (Cahen 1968). Their oral history, supported by local historical records, indicates that these people came from Central Asia in the 16th century.

...

The Kurdish-speaking inhabitants of Dogukoy were the last immigrants to populate Yuksekyer. They purportedly came into the region around 200 years ago from southeastern Turkey.

...

For comparative purposes, we also collected 30 additional samples from another Central Anatolian region, Kizilyer, which lies about 500 kilometers east of Yuksekyer. This region is roughly comparable to Yuksekyer region in its size and population density.

There are a lot of interesting genetic data, but I will focus on the Y-haplogroup profiles of the different populations:

A few things stand out:

• Haplogroup L is limited to Gocmenkoy. L is divided into informative subclades and is one of the less studied and more mysterious Caucasoid haplogroups; the authors erroneously state that it is more frequent in East Eurasians. In the Gocmenkoy sample it could very well be the legacy of Turkicized Central Asian Iranian speakers in which it is found at a high frequency. Most of the haplogroup Q is also found in Gocmenkoy and this may represent a genuine Turkic element.
• Haplogroup J1 is largely limited to Merkez; this is not surprising as Merkez is said to have been founded by Circassians, and J1 occurs at a substantial frequency in parts of the Caucasus
• Haplogroup N is mostly found in Eskikoy, and this is also a likely marker of Central Asian Turkic groups
• I find the high frequency of J2a (64.5%) in Dogukoy, the Kurdish settlement to be noteworthy. This haplogroup is also probably found at a high frequency in Parsis (although technically only J was studied in the relevant study), and I've noted before that a high J2/J1 ratio contrasts West Asian Indo-Europeans from Semitic groups. J2a also occurs at a high frequency in Indian upper caste populations, whereas it is virtually absent in low castes and tribals.

The fact that the names of the settlements had to be obfuscated by the authors speaks volumes about the political sensitivity of the subject. Hopefully this line of research will be allowed to continue.

Related:

• How Turkish are Anatolians? revisiting the question

American Anthropologist
Volume 113, Issue 1, pages 116–131, DOI: 10.1111/j.1548-1433.2010.01310.x

Biological Ancestries, Kinship Connections, and Projected Identities in Four Central Anatolian Settlements: Insights from Culturally Contextualized Genetic Anthropology

Ömer Gokcumen et al.

ABSTRACT  Previous population genetics studies in Turkey failed to delineate recent historical and social factors that shaped Anatolian cultural and genetic diversity at the local level. To address this shortcoming, we conducted focused ethnohistorical fieldwork and screened biological samples collected from the Yuksekyer region for mitochondrial, Y chromosome, and autosomal markers and then analyzed the data within an ethnohistorical context. Our results revealed that, at the village level, paternal genetic diversity is structured among settlements, whereas maternal genetic diversity is distributed more homogenously, reflecting the strong patrilineal cultural traditions that transcend larger ethnic and religious structures. Local ancestries and origin myths, rather than ethnic or religious affiliations, delineate the social boundaries and projected identities among the villages. Therefore, we conclude that broad, ethnicity-based sampling is inadequate to capture the genetic signatures of recent social and historical dynamics, which have had a profound influence on contemporary genetic and cultural regional diversity.

Link

Medieval DNA from Usedom, Germany

With respect to the Slavic/Germanic origin of the studied samples, I would like to point to a 2005 study on the differentiation between Germans and Poles. R-M458 should probably be assigned to the Slavic side, while E1b1b on the German. The absence of R1b (in the albeit limited sample) is interesting, and should be interpreted as further evidence for the Slavic side of the argument, as R1b strongly differentiates Germans from Slavs in today's populations and less than a millennium ago is probably too short a timespan to expect dramatic changes in haplogroup frequencies.

Related:

• Y chromosomes from 7th c. Ergolding (Bavaria, Germany)
• Ancient Y chromosome studies

Main title Die mittelalterlichen Skelette von Usedom
Subtitle Anthropologische Bearbeitung unter besonderer Berücksichtigung des ethnischen Hintergrundes
Title variations The mediaeval skeletons of Usedom
Subtitle for translated title Anthropological investigation in due consideration of the ethnical background
Author(s) Freder, Janine
Place of birth: Berlin
1. Referee Prof. Dr. Carsten Niemitz
Further Referee(s) Prof. Dr. Joachim Burger
Keywords Anthropology; osteometry; palaeodemography; Slavs; Danes; DNA; mitochondrial; Y chromosome
Classification (DDC) 570 Life sciences
Summary This study investigates 200 skeletons from an early Christian graveyard of the 12th to early 13th century in Usedom (Mecklenburg-Vorpommern, Germany). The city of Usedom was a notable maritime place of trade in a time of major political and social transformations. The Christianisation of the Slavic elite in 1128, the following raids of the Danes and the influx of German settlers starting in the 13th century were formative events.
The reconstruction of the living conditions of the Usedom population was achieved by means of well established anthropological and palaeodemographical methods. Age and sex distribution comply with other ordinary populations of that time frame: high proportion of children (32 %), comparatively few adolescents but many adults (59 %) as well as a slight surplus in men. Remarkably, a deficit in women in the mature age class is attended by an increased mortality of girls of the age class infans I. However, this may be due to a methodical error.
In order to clarify a possible Slavic, Danish or German background of the inhabitants of Usedom, eight skull measures, four skull indices and five measures of the long bones of the extremities were investigated typologically as well as statistically on the basis of their arithmetic means and compared to the measures of two series of Slavic or multiethnic/place of trade background (Sanzkow and Haithabu, respectively). The comparison of arithmetic means did yield statistically significant differences between the three populations. The men and women of Usedom seem to be more closely related to the Sanzkow population. However, they appear to take a position between the two other populations. Unfortunately, a comparison with Slavic and Germanic populations of the Neolithic till Early Middle Ages did not provide distinct results. The archaeologically based assumption of a mainly Slavic population cannot be rejected with anthropological means.
The analysis of mitochondrial and Y-chromosomal DNA, however, generated auspicious results despite adverse storage conditions. Results could be obtained from all four samples. Two individuals were of mtDNA haplogroup H and two of haplogroup K. Y-chromosome analysis yielded haplogroups E1b1b and R1a1a7, respectively, in two males. Future molecular research will see improved methods for the even more detailed reconstruction of human migration.

Link

Y chromosomes of Libyan Tuareg

The gene pool of these samples seems quite simple composed entirely of E1b1a8-U175 (sub-Saharan), E1b1b1b-M81 (Northwest African), and R-V88. I find the absence of other clades of Middle Eastern or European origin as extremely interesting, pointing to the extreme value of this population as a key to North African prehistory.

Haplogroup U175 is most frequent in Sub-Saharan Africa and it belong to clade E-M2 which trace their descent to east Africa but became more frequent in Sub-Saharan Africa.

In the next Dodecad Project update, I will probably have a North African sample of more varied composition than the HGDP Mozabites and Behar et al. (2010) Moroccans. Note that North Africans are part of the current call for submissions in the project, so I would love to have more samples from that region of the world.

Am J Phys Anthropol DOI: 10.1002/ajpa.21473

Deep into the roots of the Libyan Tuareg: A genetic survey of their paternal heritage

Claudio Ottoni et al.

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.

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Major new paper on haplogroup E1b1 (E-P2)

They sequenced ~45kb in 13 E1b1 chromosomes, producing an updated phylogeny of the -haplogroup (left).

As you can see, increased phylogenetic inference comes at the cost of increasingly long-winded haplogroup designations; hopefully I'll manage to familiarize myself with the new terminology soon enough, and update this post with my comments.

UPDATE:

From the paper:

Haplogroup E1b1 now contains two basal branches, E-V38 (E1b1a) and E-M215 (E1b1b), with V38/V100 joining the two previously separated lineages E-M2 (former E1b1a) and E-M329 (former E1b1c). Each of these two lineages has a peculiar geographic distribution. E-M2 is the most common haplogroup in sub-Saharan Africa, with frequency peaks in western (about 80%) and central Africa (about 60%). The same haplogroup is also present in North Africa, although at a lower frequency (usually below 10%) [9]–[11]. Haplogroup E-M329, on the other hand, was observed almost exclusively in eastern Africa [10], [12 and R.S. unpublished data], where E-M2 is virtually absent. The second basal branch of E1b1, E-M215, has a broad geographic distribution from southern Europe to northern and eastern Africa where it has been proposed to have originated [8]. The new topology here reported has important implications as to the origins of the haplogroup E1b1. Using the principle of the phylogeographic parsimony, the resolution of the E1b1b trifurcation in favor of a common ancestor of E-M2 and E-M329 strongly supports the hypothesis that haplogroup E1b1 originated in eastern Africa, as previously suggested [10], and that chromosomes E-M2, so frequently observed in sub-Saharan Africa, trace their descent to a common ancestor present in eastern Africa.

and:

Within E-M35, there are striking parallels between two haplogroups, E-V68 and E-V257. Both contain a lineage which has been frequently observed in Africa (E-M78 and E-M81, respectively) [6], [8], [10], [13]–[16] and a group of undifferentiated chromosomes that are mostly found in southern Europe (Table S2). An expansion of E-M35 carriers, possibly from the Middle East as proposed by other Authors [14], and split into two branches separated by the geographic barrier of the Mediterranean Sea, would explain this geographic pattern. However, the absence of E-V68* and E-V257* in the Middle East (Table S2) makes a maritime spread between northern Africa and southern Europe a more plausible hypothesis.

PLoS ONE 6(1): e16073. doi:10.1371/journal.pone.0016073

A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms


Beniamino Trombetta et al.

Haplogroup E1b1, defined by the marker P2, is the most represented human Y chromosome haplogroup in Africa. A phylogenetic tree showing the internal structure of this haplogroup was published in 2008. A high degree of internal diversity characterizes this haplogroup, as well as the presence of a set of chromosomes undefined on the basis of a derived character. Here we make an effort to update the phylogeny of this highly diverse haplogroup by including seven mutations which have been newly discovered by direct resequencing. We also try to incorporate five previously-described markers which were not, however, reported in the 2008 tree. Additionally, during the process of mapping, we found that two previously reported SNPs required a new position on the tree. There are three key changes compared to the 2008 phylogeny. Firstly, haplogroup E-M2 (former E1b1a) and haplogroup E-M329 (former E1b1c) are now united by the mutations V38 and V100, reducing the number of E1b1 basal branches to two. The new topology of the tree has important implications concerning the origin of haplogroup E1b1. Secondly, within E1b1b1 (E-M35), two haplogroups (E-V68 and E-V257) show similar phylogenetic and geographic structure, pointing to a genetic bridge between southern European and northern African Y chromosomes. Thirdly, most of the E1b1b1* (E-M35*) paragroup chromosomes are now marked by defining mutations, thus increasing the discriminative power of the haplogroup for use in human evolution and forensics.

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