35,000 year old mtDNA haplogroup U6 from Romania

I wouldn't be very surprised if many of the markers supposedly signifying recent gene flow Africa and Eurasia were actually quite old in Eurasia. The trouble is that reports of such gene flow were often based on simply observing that marker "X" occurs at a higher frequency in Africa than in Eurasia, so a common sense explanation is that it reflects limited recent gene flow between the continents. But, it is now known that common sense is not always the best guide, as e.g., ancient Europeans had mtDNA haplogroup M (in the past considered evidence of Asian admixture), Y-chromosome haplogroup C (ditto), and now U6.

The same should also apply to the Middle East where there has been admixture with Africans since the Islamic period at least. The existence of such admixture does not mean that every single lineage that occurs at low frequency in the Middle East and high frequency in Africa is diagnostic of this later period of admixture. Some of them could well be relics of old Middle Eastern populations. Who knows what people inhabited the presently inhospitable landscape of the Saharan-Arabian desert zone? The living populations can certainly make no claim to being the first ones there, but the genetic heritage of those earlier occupants may still persist in them in traces.

Similarly for the New World; in that case, there is a better case that European-looking lineages are indeed due to the colonization of the Americas over the last five centuries. However, that does not mean that all of them are, and we should be mindful of the possibility of pre-Columbian contact between the Old and New worlds.

Scientific Reports 6, Article number: 25501 (2016)

The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa

M. Hervella et al.

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

Link

Oase1 had a Neandertal ancestor no earlier than ~200 years before his time

Several important conclusions of the discovery that Oase1 had a Neandertal ancestor 4-6 generations before his time (37-42 thousand years ago):

• This is a smoking gun that modern humans interbred with Neandertals, following up on the publication of the Ust'Ishim and Kostenki-14 genomes; these two had longer Neandertal chunks than modern humans, from which it was estimated that their Neandertal admixture happened more than 50,000 years ago, roughly what one gets when looking at Neandertal chunks in modern humans alone. The Oase1 has even longer Neandertal chunks, and Neandertal admixture happened in its very recent past. 
• So, it seems that Neandertal admixture was not a one-off event but is bracketed at least by the period 50-40 thousand years ago and happened in at least two places: Europe and the Near East.
• The fact that the earliest European sample (N=1) has a recent Neandertal ancestor indicates that Neandertal admixture in the earliest Europeans cannot have been extremely rare or non-existent; if it were, the chances of finding one with the first try would be extremely low.
• It is unlikely that Neandertals were killed off by modern humans immediately after the arrival of the latter in Europe, as the Oase1 is dated well after the arrival of modern humans to Europe.
• Modern Europeans don't seem to be particularly related to the population of Oase1. After one substracts contamination and Neandertal admixture, what is left over is actually closer to East Asians than modern Europeans. But, it's equally close to East Asians and European hunter-gatherers. This can be explained if modern Europeans have ancestry from the mysterious "Basal Eurasians" via the Neolithic farmers.

Why did the Neandertals (and the significantly-Neandertal admixed AMH like Oase1) disappear? My bet is on the Campanian Ignibrite eruption.

Nature (2015) doi:10.1038/nature14558

An early modern human from Romania with a recent Neanderthal ancestor

Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel, Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich & Svante Pääbo

Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

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

ESHG 2012 abstracts

I had posted some interesting titles in April, and it is finally time for us, mere mortals, to have access to the abstracts. A few of the abstracts:


Title: P10.39 - Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania

Keywords: mitochondrial DNA; haplotypes; Bronze and Age populations

Authors: A. Rodewald1, G. Cardos2, C. Tesio3;

Abstract: Our genetic study was focused on old human populations from the Bronze and Iron Ages from Romania in order to analysed their genetic variation and their genetic kinship al mitochondrial DNA(mtDNA)level with today´s Romanian populations and other modern European populations. The ancient DNA(aDNA)was extracted from skeletal remains of 50 individuals from the Bronze and Iron Age by a phenol-chloroform DNA extraction method.MtDNA HVR I and HVR II regions were amplified by PCR and sequenced by the dideoxy chain terminator method.The aDNA data were analysed in comparison with corresponding mtDNA data of modern Romanian people and other 11 European populations.The ancient mtDNA haplotypes were framed into 12 haplogroups. The most frequent mtDNA haplotype identified in the old individual sample from Romania was the CRS-like, and the most frequent haplogroup was H. Significant differences in haplogroup frequencies between the old people and modern Romanians were found. Low values of internal standard genetic diversity indices suggested reduced genetic variability within old human populations from the Bronze and Iron Age from Romania, in contrast to all modern European populations and also modern Romanians, which showed higher mitochondrial haplogroup diversity values. This fact might be the result of social and cultural local organization in small tribes, partially reproductively isolated. Concerning the genetic relationships at mitochondrial level, old human populations from Romania have shown closer genetic relationship to Turks of Thracian origin,while modern Romanians were closer to modern Bulgarian, Italian, Greek and Spanish populations.

The relationship between prehistoric Romanian mtDNA and modern Thracian Turkish one is not very surprising, given that the latter are basically descended from populations of indigenous origin that converted to Islam during the Ottoman era. It will be worthwhile to see exactly which locations/communities were used to sample from. It is awesome that we are beginning to get ancient DNA data from southeastern Europe.



Title: P10.40 - Complete mitochondrial DNA diversity in Iranians
Keywords: Mitochondrial DNA; population; Iran
Authors: A. Bahmanimehr1, M. Derenko2, B. Malyarchuk2, G. Denisova2, M. Perkova2, S. Farjadian3, L. Yepiskoposyan1;

Abstract: The complete sequencing of mitochondrial DNA has contributed a great deal to the understanding of the timing and direction of human dispersals around the world. To elucidate the early stages of human colonization process outside of Africa and to investigate the demographic history of human populations from the Middle East we have completely sequenced the mtDNAs of 275 Iranians represented by Persians (N=105), Mazandaranians (N=4), Azerbaijanians (N=22), Kurds (N=5), Lurs (N=5), Armenians (N=10), Bakhtiarians (N=2), Gilakis (N=2), Indians (N=1), Turkmens (N=10), and Qashqais (N=109). Overall diversity is very high, with 252 different sequences falling into 75 major haplogroups within macrohaplogroups L, N and M. The majority of Iranian mtDNAs (90.9%) belongs to Western Eurasian component composed of haplogroups N1, N2, X, R2’JT, U, and R0, though the impact of African (L2a, L3d, L3f), Southern Asian (R8, M4, M5, M18, M42), and Eastern Eurasian (A4, B4, C4, C5, D4, F1, G2a) lineages is also perceptible being found at frequencies of 1.5%, 2.5%, and 5.1%, respectively. Results of molecular dating of Iranian mtDNA lineages show that macrohaplogroup N and its haplogroups N1, R, U, R2’JT coalesce to the time of 45-60 kya, marking the first stages of modern humans movement out of Africa. The ancient ancestry of Iranian gene pool is also confirmed by revealing of the unique N23 lineage survived both in Persians and Qashqais, albeit at low frequencies. This study was supported by Russian Foundation for Basic Research (11-04-00620) and by Far-East Branch of the Russian Academy of Sciences (12-III-A-06-101).

Title: P10.58 - A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
Keywords: Y chromosome; Bulgarians; haplogroup
Authors: S. Karachanak1,2, V. Grugni2, D. Nesheva1, N. Al-Zahery2, V. Battaglia2, C. Nici2, V. Carossa2, Y. Yordanov3, A. Torroni2, A. S. Galabov4, O. Semino2,5, D. Toncheva1,5;

Abstract: To address the structure and evolution of the Bulgarian paternal gene pool, we have examined the Y chromosome variation in 809 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within certain haplogroups. The biallelic markers were analyzed by PCR/RFLP and PCR/DHPLC assay. Seventeen fast-evolving Y-STRs were amplified using the multiplex AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems) and were read on ABI 310 genetic analyzer with GeneMapper software.We found that the Bulgarian Y chromosome gene pool is primarily contained within haplogroups common in Europe and surrounding areas. Furthermore, when patrilineal relationships are visualized in a broader context by principal component analysis, Bulgarians are located among European populations. The analysis of molecular variance shows that the genetic variation within the country is structured among Western, Central and Eastern Bulgaria, rather than among the Black Sea coast, the Danubian Plane, Thrace and the Southwest mountainous region; which indicates that the Balkan Mountains have been permeable to human movements.
Y-STR variation ages and median joining networks of haplogroups E-V13, J-M241, R-M458, R-L23 and I-M423 were calculated together with data from other populations. For this purpose, the analyses of STR variation within haplogroups were based on 8 STR loci, with the exception of haplogroup R-M458, for which the STR profiles were further reduced to 7 loci. In general, the Y-STR data reveal that different prehistoric and historic events have left detectable traces in the Bulgarian Y chromosome gene pool.

This is quite welcome, as Bulgaria has been a bit of a "black hole" in population genetics. Finally having an authoritative sample on its Y-chromosome composition is extremely important.


Title: P10.45 - Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
Keywords: population isolate; genetic association; rare variants
Authors: I. Tachmazidou1, A. Farmaki2, L. Southam1, K. Palin1, N. W. Rayner1,3, E. Daoutidou2, I. Ntalla2, K. Panoutsopoulou1, G. Dedousis2, E. Zeggini1;

Abstract: The study of low-frequency and rare variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. Sequencing is efficient in isolates, because variants are shared in extended haplotype contexts, supporting accurate imputation. Here we assess sample sets collected from two Greek populations: the Pomak villages are a set of religiously-isolated mountainous villages in the North (population size 11,000); Anogia is a mountainous village on Crete, with high levels of longevity (population size 4,000). 747 and 1118 individuals respectively were typed on the Illumina OmniExpress platform. We calculated genome-wide IBS statistics to assess the degree of relatedness and compared it with the general Greek population (707 samples with OmniExpress data, TEENAGE study). We additionally calculated the proportion of individuals with at least one “surrogate parent” as a means for accurate long-range haplotype phasing and imputation, as proposed by Kong et al, Nature Genetics 2008. We find 1-1.4% of individual pairs with pi-hat>0.05, and ~0.4% with pi-hat>0.1 in the isolates compared to 0% in the general Greek population. We also find that ~80%-82% of subjects have at least one surrogate parent in the isolates, compared to ~1% in the outbred Greek population. We have established the HELIC-Pomak and MANOLIS cohorts as genetic isolates and are currently whole-genome sequencing 250 individuals to enable imputation and subsequent association testing. This approach has the potential to identify novel robust associations with disease-related complex traits.

It will be wonderful if some of these population samples become publicly available.

More detailed analysis of Eurasian populations (K=10)

I have removed some populations from the previous run (such as Moroccan Jews and Samaritans) that tended to generate mini-clusters due to the presence of close relatives and/or inbreeding in the sample. I have removed some redundant populations to even out the dataset, and I have also added North Kannadi and Gujarati, which helped reveal the gradient of ancestry in South Asia.

ADMIXTURE results:

Admixture proportions:

Some interesting observations:

• The occurrence of 3.8% South Asian in Romanians may signify its Roma population. Indeed, almost all of this comes from a 25% South Asian individual, almost certainly a Roma.
• The small African component in Spaniards which was revealed in a previous K=8 run turns out to be East African (0.5%) rather than West African (0.1%). If this holds up in larger sets then it might signify that its origin is from East African admixed populations from the east, rather than Sub-Saharan Africans.
• The multiplicity of ancestries of the Uygur is made evident, in agreement with the extensive craniometric and genetic data on prehistoric and extant populations from the area.
• The proportion of the two East Eurasian components in Turkic populations is interesting. It seems that the earliest departures from the Turkic homeland (such as the Chuvash and Yakut) have a predominance of the NE Asian component, the Anatolian Turks are intermediate, and the Uygurs, the only ones to have stayed close to the homeland, have experienced an increase in the E Asian component.
• The absence of the West African component in Ethiopians is striking. Here are the individual results for Ethiopians, illustrating the variability of the Southwest African vs. East African components. The Ethiopian sample consists of a number different ethnic groups of the country, some of which (like the Amharas) are of Western Eurasian linguistic origin.

I am currently running K=11 and K=12 on the exact same data to see how the LogLikelihood and Bayes Information Criterion will move and whether new mini-clusters will appear, or if the mega-components (such as the "West Asian", "South European", and "North European") will split informatively. I will update this post with information on what actually happened, and with additional plots -- if I get robust results.

R1b founder effect in Central and Western Europe

Post will be updated after I read the paper. (Last Update: Aug. 29)

UPDATE I:

From the paper:

The ages of various haplogroups in populations were estimated using the
methodology described by Zhivotovsky et al,30 modified according to Sengupta
et al,10 using the evolutionary effective mutation rate of 6.9 x 10^-4 per 25 years.
The accuracy and appropriateness of this mutation rate has been independently
confirmed in several deep-rooted pedigrees of the Hutterites.

Of course readers of the blog are aware that I disagree with the use of the evolutionary rate. My comments on the Hutterites paper will be posted separately after I read it. I will simply say that there are numerous cases where the use of the genealogical rate makes better sense of the evidence than use of the "evolutionary" rate. Off the top of my head, the genealogical rate harmonizes with the Genghis Khan cluster, the expansion of Na-Dene speakers into the Americas, the expansion of Balto-Slavic, the Bronze Age spread of Semitic speakers, in accordance with the linguistic evidence, the expansion of Bantu in Angola, more recent British surnames, the formation of Arabian kingdoms, Greek colonization of Sicily, and the Bronze Age origin of Indo-Aryans and Finno-Ugrians (and I skipped a few).

UPDATE II (Aug 26):

Here is the phylogeny of R-M207 from the paper. For reference, the R-M207 page from ISOGG.


UPDATE III (Aug 26):

Going through the material in this paper in a systematic manner is not easy, so I will probably do a potpourri of updates covering various topics of interest.



As noted in the other recent paper, and shown in the above Figure from the current one, R-U106 peaks in northern Europe. Its frequency (including the R-U198 sublineage) is 36.8% in the Netherlands, 20.9% in Germany and Austria, 18.2% in Denmark, 18.2% in England, 12.6% in Switzerland, 7.5% in France, 6.1% in Ireland, 5.9% in Poland, 5.6% in north Italy 4.4% in Czech Republic and Slovakia, 3.5% in Hungary, 4.8% in Estonia, 4.3% in south Sweden, 2.5% in Spain and Portugal, 1.3% in eastern Slavs, 0.8% in south Italy, 0.6% in Balkan Slavs, 0.5% in Greeks (i.e. 2 of 193 Cretans, and no mainland Greeks), 0.4% in Turks, 0% in Middle East.

The age of R-U106 is estimated by the authors as 8.7ky BP, which translates to about 2.5ky BP with the germline rate. The existence of R-U106 as a major lineage within the Germanic group is self-evident, as Germanic populations have a higher frequency against all their neighbors (Romance, Irish, Slavs, Finns). Indeed, highest frequencies are attained in the Germanic countries, followed by countries where Germanic speakers are known to have settled in large numbers but to have ultimately been absorbed or fled (such as Ireland, north Italy, and the lands of the Austro-Hungarian empire). South Italy, the Balkans, and West Asia are areas of the world where no Germanic settlement of any importance is attested, and correspondingly R-U106 shrinks to near-zero.

UPDATE IV (Aug 26):

Another informative lineage, as noted in the other recent paper as well is R-U152:


Of interest is the fact that while R-U152 has a clear French-Italian center of weight, the locations exhibiting highest STR variance are Germany and Slovakia, i.e., Central Europe. My guess is that R-U152 originated in Central Europe spreading to the west and south, perhaps with Italo-Celtic speakers or some subset thereof. In its home territory of Central Europe, its frequency decreased by the introduction of the Germanic and Slavic speaking elements which dominate the region.

Irrespective of what the ultimate origin of R-U152 is, it provides us with a good diagnostic marker for population movements out of the French-Italian area. In Italy for example it is noted at 26.6% for the north and 10.5% in the south. It would be extremely interesting to see its occurrence in Balkan Vlachs, as this would confirm/disprove the Italian component in their origin. However, R-U152 occurs in 7.3% of Cretans, suggesting introgression Y-chromosomes of North Italian (Venetian) origin, from the 4-century period of Venetian rule of the island. It also occurs in 4.1% of Greeks, where it might come from any period since the Roman annexation of the Hellenistic states to the Vlachs. However, its presence at only 1.8% of Romanians makes a large Italian contribution to the Romanian population unlikely. Balkan R-U152 chromosomes should be better resolved to determine when they arrived from the northwest.

The paucity of R-U152 in Turks (0.6%) make tales of wandering Galatians less likely to be true. There is no doubt that Galatians settled in Anatolia, but they were probably so few in numbers that they did not permanently alter the population. Knowledgeable readers should chime in about the Lebanese Christian R1b which was posited as a signature of the Crusades a couple of years ago, and its position in the phylogeny.

UPDATE V (Aug 26):

The most commong R1b subgroup in Europe is R-M269 and the most common subgroup is R-L23 which encompasses the vast majority of European R-M269 chromosomes. It is interesting to see where R-M269(xL23) is concentrated. In Europe I see cases in Germany, Switzerland, Slovenia, Poland, Hungary, Russia, the Ukraine. It is most prominent, however, in the Balkans, where every population except Croatia mainland (N=108) possesses it. In the Caucasus it does not exist except in the northeast. In Turkey and Iran there is some, albeit it is not clear in which regions.

UPDATE VI (Aug 27):

The authors write with respect to haplogroup R-V88:

With the exception of rareincidences of R1b-V88 in Corsica, Sardinia13 and Southern France(Supplementary Table S4), there is nearly mutually exclusive patterning of V88 across trans-Saharan Africa vs the prominence of P297-related varieties widespread across the Caucasus, Circum-Uralic regions, Anatolia and Europe. The detection of V88 in Iran, Palestine and especially the Dead Sea, Jordan (Supplementary Table S4) provides an insight into the back to Africa migration route.

Haplogroup R-V88 has been the subject of a recent study and was associated with the migration of Chadic speakers in Africa. It is difficult to say whether or not the authors' results really provide any insight into an alleged movement of this haplogroup from Asia to Africa, as it occurs in only a single Palestinian, and a single Iranian. Neither is the higher frequency (13.7%) observed in the Amman and Dead Sea area of Jordan really evidence of its antiquity there.

Neither the aforementioned paper nor the current one presents any evidence (e.g., Y-STR variance) for any great antiquity of the Asian R-V88 with respect to the African one. Indeed, with the exception of the aforementioned Jordanian sample, R-V88 is rare in Asia, while it is widespread in African Berbers. I see no clear reason at present to think that it migrated to Africa from Asia, and not to think of it as a relic of an older, widely dispersed R1b population leading to R-V88 in Africa itself.

UPDATE VII (Aug 28):

The paper repeats the standard claims about the origin of R1b and its main sublineage R-M269 in Asia, but presents no new information that would support this claim. With the state of the evidence, I see no real reason to prefer a West Asian to a Southeastern European origin for this haplogroup.

I don't give much credence to small differences in Y-STR variance, due to the large confidence intervals associated with such estimates, and it is interesting that the authors do not present an argument from Y-STR variation about the origin of R1b, preferring to make broad statements about Mesolithic-Neolithic movements into Europe.

A study of supplementary table S2 which gives coalescent times reveals that there is no clear pattern of greater Asian diversity within haplogroup R1b or its subclades. And, while Central-Western Europe does appear to be an outgrowth of R1b rather than a place of origin (with the dominance of derived R-M412 lineages) there is nothing in the paper that would make one prefer West Asia to Southeastern Europe as a place of origin.

Personally I think the issue cannot be settled yet, but there are reasons to prefer the latter option. An Asian origin of R1b has a major parsimony hurdle: it would require a seemingly directed drang nach westen for R1b, into Europe, and into North Africa, with a paucity of R1b in the opposite direction (among Arabians and to the south and in South Asia) and a scattering of very young R-M73 and R-M269 to the east of Europe.

UPDATE VIII (Aug 29):

R-S116 shows maximum Y-STR diversity in France and Germany but maximum frequency in Iberia and the British Isles. In the latter region it is represented mainly by R-M529 with the R-M222 subclade being particularly prominent in Ireland but also North England. It would be interesting to see data for Scotland, and I do not doubt that R-M222 would be prominent there as well. R-S116 also shows signs of being a Celtic, or Celtiberian-related lineage.

European Journal of Human Genetics doi: 10.1038/ejhg.2010.146

A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe

Natalie M Myres et al.

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

Link

Guess the origin of these four composites

ANSWER (15/1/2010):

Russian, Cypriot

Romanian, Spanish

END ANSWER

These were sent to me by an Italian reader of the blog.

You can guess their country of origin, language group (e.g., Slavic, Germanic, Romance, Finno-Ugrian, Greek, etc.), geographical origin (N/S/W/E Europe or W/S/C Asia), or whatever else you can intuit about them.

mtDNA from the Carpathian Highlands

Hum Biol. 2009 Feb;81(1):43-58.

Mitochondrial DNA sequence variation in the boyko, hutsul, and lemko populations of the carpathian highlands.

Nikitin AG et al.

Abstract Genetic studies of the distribution of mitochondrial DNA (mtDNA) haplogroups in human populations residing within the Carpathian Mountain range have been scarce. We present an analysis of mtDNA haplogroup composition of the Boykos, Hutsuls, and Lemkos, three population groups of the Carpathian highlands. In our study Hutsuls had the highest frequency of subhaplogroup H1 in central and eastern Europe. Lemkos shared the highest frequency of haplogroup I ever reported and the highest frequency of haplogroup M(*) in the region. MtDNA haplogroup frequencies in Boykos were different from most modern European populations. We interpreted these unique mtDNA frequencies to be evidence of diverse and dynamic population histories in the Carpathian highland region.

Link

German origin of Transylvanian Saxons

Using Athey's haplogroup predictor, with equal priors and a threshold of 50 and probability of 90%, the following haplogroups were predicted in the 59 males:

5 E1b1b
1 G1
2 G2a
2 H
4 I1
3 I2a(xI2a2)
1 I2a2
1 I2b1
1 J2b
1 N
2 R1a
22 R1b

Rom J Leg Med 12 (4) 247 – 255 (2004)

A study on Y-STR haplotypes in the Saxon population from Transylvania (Siebenbürger Sachsen): is there an evidence for a German origin?

Ligia Barbarii et al.

ABSTRACT: A study on Y-STR haplotypes in the Saxon population from Transylvania
(Siebenbürger Sachsen): is there an evidence for a German origin? Y chromosome markers are increasingly used to investigate human population histories, being considered to be sensitive systems for detecting the population movements. In this study we present Y-STR data for a male population of Transylvanian Saxons in
comparison with Y-haplotypes from Romanians and other European populations. The Transylvanian Saxons, called like that since medieval times, are representing a western population with unknown origin, settled in the Arch of Romanian Carpathian Mountains in the earliest of the 12th century. Historical and dialectal studies strongly suggest that they do not originate from Saxony, but more probably from the Mosel riversides (Rhine affluent) and also from the Eifel Mountains Valley (present territory of Luxembourg). Living protected by fortified cities in compact communities, they still represent a quite distinct population in Transylvania. For this study, 59 male samples were collected from the Siebenburgen area, subjects being selected by their Saxon surnames and paternal grandfather birthplace. A set of nine STR polymorphic systems mapping on the male-specific region of the human Y chromosome (DYS19, DYS385, DYS389 I/II, DYS390, DYS391, DYS392, DYS393) were typed by means of
one or two two multiplex PCR reactions and capillary electrophoresis. The typing results reflect high Saxon population haplotype diversity. Furthermore, we present data on the haplotype sharing of the Saxon population with other European populations, especially with Germans as well as with the Romanians and the Transylvanian Szekely.

Link (pdf)

Ancient Thracian mtDNA

The presentation of the results isn't very clear. From a cursory comparison of the results listed in the text with the Genographic project list of motifs, at least the following seem represented in the ancient Thracian individuals:

• 1 individual seems to be 16129A 16223T
• 1 individual seems to be 16145A
• 1 individual seems to be 16186T 16190C (however, this looks like 16189C in Fig. 4, 186T and 189C are found in haplogroup T1)
• 1 individual seems to be 16193T 16283C (16193T is found in J2, which also carries 16069T (beyond the region sequenced) 16126C (in the region sequenced but not found).
• 1 individual seems to be 16311C
• 2 individuals seems to be 16362C which in West Eurasia seems to be found in R0a and R6

Anyway, feel free to comment if you can make better sense of these results.

Rom J Leg Med 12 (4) 239 – 246 (2004)

Paleo-mtDNA analysis and population genetic aspects of old Thracian populations from South-East of Romania

Cardos G. et al.

ABSTRACT: Paleo-mtDNA analysis and population genetic aspects of old Thracian populations from South-East of Romania. We have performed a study of mtDNA polymorphisms (HVR I and HVR II sequences) on the skeletal remains of some old Thracian populations from SE of Romania, dating from the Bronze and Iron Age in order to show their contribution to the foundation of the modern Romanian genetic pool and the degree of their genetic kinships with other old and modern human European populations. For this purpose we have applied and adapted three DNA extraction methods: the phenol/chloroform, the guanidine isotiocianat and silica particles and thirdly the Invisorb Forensic Kit (Invitek)-based DNA extraction method. We amplified by PCR short fragments of HVR I and HVR II and sequenced them by the Sanger method. So far, we have obtained mtDNA from 13 Thracian individuals, which we have compared with several modern mtDNA sequences from 5 European present-day populations. Our results reflect an evident genetic similarity between the old Thracian individuals and the modern populations from SE of Europe.

Link (pdf)

ESHG 2007 abstracts

I had previously posted about a presentation in this year's ESHG conference about the Y chromosomes of Etruscans. At that time, there was no abstract online, but I noticed that the book of abstracts is available (pdf). The conference took place last June and there will be probably publications coming out of the presentations there.

Some interesting abstracts; you will probably find many more in the volume's 396 pages.

Related to the abstract below about ACTN in Finnish athletes.

P1206. ACTN and ACE genotypes in Greek elite athletes

I. D. Papadimitriou et al.

Only a few attempts have been made to shed light upon the influence of genes in making an Olympic champion. The aim of our study is to elucidate the genetic differences among a group of 101 elite Greek power-oriented track and field athletes and a random representative sample (181) of the Greek population by analyzing ACTN3 and ACE genotypes. Athletes were defined as elite and included to the sample if they had represented Greece at the international level. Standard molecular genetic methodologies were followed. Genotype and allele frequencies were compared between elite athletes and controls by the Chi-squared test using the statistical package GENEPOP V. 3.4. Preliminary results for ACE locus indicated that the gene frequencies in the Greek elite athletes are similar to other northern European populations. Furthermore, concerning the ACTN3 locus, it was showed that ACTN3 genotype and allele frequencies in the top power-oriented athletes were statistically significantly different from those in the random
sample of the Greek population: the frequency of the RR ACTN3 genotype in power-oriented athletes vs. the general population was 47.94% vs. 25.97%. The difference was even more prominent for comparison of the subgroup of sprinters to controls. The results suggest an overall
strong association between the presence of the RR genotype and elite power performance. Therefore, the ACTN3 gene might be used as a molecular genetic marker to at least partially predict an athlete’s ability to achieve peak power and sprinting performance.


C17. Origin of the Etruscans: novel clues from the Y chromosome lineages

A. Piazza et al.

Three hypotheses have been proposed on the origin of the distinctive Etruscan civilization and language that flourished ca. 3,000 years before present (BP) in Central Italy: 1) an external Anatolian source (Lydia and Lemnos) as claimed by Herodotus, 2) an autochthonous
process of formation from the preceding Villanovan society as firstly proposed by Dionysius of Halicarnassus and 3) an influence from Northern Europe. A synthetic geographical map summarizing 34 classical genetic markers in Italy differentiates a genetically homogeneous
Central Italian region between the Arno and Tiber rivers (ancient Etruria) from the rest of Italy. While this fact was tentatively interpreted as a genetic footprint of the Etruscans, its verification remained a challenge due to lack of data on differentiation of such markers and its calibration
with time. Here we show the genetic relationships of modern Etrurians, who mostly settled in Tuscany, with other Italian, Near Eastern and Aegean peoples by comparing the Y-chromosome DNA variation in 1,264 unrelated healthy males from: Tuscany-Italy (n=263), North Italy (n=306), South Balkans (n=359), Lemnos island (n=60), Sicily and Sardinia (n=276). The Tuscany samples were collected in Volterra (n=116), Murlo (n=86) and Casentino Valley (n=61).
We found traces of recent Near Eastern gene flow still present in Tuscany, especially in the archaeologically important village of Murlo. The samples from Tuscany show eastern haplogroups E3b1-M78, G2*-P15, J2a1b*-M67 and K2-M70 with frequencies very similar to those observed in Turkey and surrounding areas, but significantly different from those of neighbouring Italian regions. The microsatellite haplotypes associated to these haplogroups allow inference of ancestor lineages for Etruria and Near East whose time to the most recent common ancestors is relatively recent (about 3,500 years BP) and supports a possible non autochthonous post-Neolithic signal associated with the Etruscans.

P1135. Y chromosome analysis in subpopulations of Bashkirs from Russia

A. S. Lobov et al.

The Volga-Ural region which is located between Europe and Asia has been the arena of permanent genetic exchanges among Siberian, Central Asian, Eastern European populations. We have sampled seven Bashkir subpopulations from different parts of the Volga-Ural region and neighboring areas of Russia: Orenburg (N=79), Perm (N=72), Samara and Saratov (N=51), and from Bashkortostan Republic: Abzelilovskiy (N=152), Sterlibashevskiy (N=54), Baimakskiy (N=95), and Burzaynskiy area (N=82). These samples are currently being analyzed using 24 diallelic markers of Y-chromosome (M89, M9, M20, M48, M73, M130, M170, M172, M175, M201, M207, M214, M217, M231, M253, M269, M306(M173), P15, P37, P43, SRY1532, Tat, 92R7(M74), 12f2). According to our preliminary findings Turkic speaking Bashkirs are characterized by prevalence of R1b3 and R1a lineages. Among all subpopulations, Perm and Baimakskiy area represent with hight frequency (0.748 0.769,).It indicate there closeness with West European populations. Haplogroup R1a have frequency value 0.486 in Samara and Saratov’s Bashkirs and frequency value 0.370 Bashkirs from Sterlibashevskiy area. The N3 characterize for subpopulation Bashkirs from Sterlibashevskiy area (0.537), Orenburg (0.342). Bashkirs from Abzelilovskiy area have main frequency (0.474). These differences possibly indicate that different subpopulations of Bashkirs have different origin. We found that Bashkirs from Perm district were characterized by relatively low genetic diversity, which could be explained by founder effect. Bashkirs from Orenburg region which are anthropologically closer to Ugro-Finnic populations are characterized by high frequency of N3 haplogroup. We will try to compare our results with archeologycal, historycal and anthropological data in discussed about of origin of different groups Bashkir

P1191. Analysis of mitochondrial DNA polymorphism in four Siberian ethnic groups

M. V. Golubenko et al.

Mitochondrial DNA polymorphism was studied in 1130 individuals from 12 populations of the most numerous Siberian peoples - Altaians (4 populations), Tivinians (3 populations), Yakuts (2 populations) and Buryats (3 populations). 308 different HVS1 haplotypes were revealed
in total which belong to 34 different mtDNA haplogroups, mainly of East-Eurasian origin. Portion of “West-Eurasian” mtDNA haplogroups was the highest in Altaians (up to 46%) and Buryats (up to 20%). AMOVA analysis has shown that 95,78% of HVSI variation was within populations, 2.09% could be explained by inter-population differentiation and 2.09% was variability between ethnic groups. Test on differentiation of polymorphism in population pairs has shown that in all cases except the pair of Yakut samples the differentiation was significant. AMOVA analysis for separate ethnic groups revealed the highest degree of intraethnic differentiation for Altaians (3.78%), followed by Tuvinians (2.61%) and then Buryats (0.43%). Comparison of spectrum of
haplogroups and individual haplotypes in the populations under investigation also shows significant differentiation of native Siberian populations. Only two haplotypes from haplogroup C and one haplotype from D could be considered as common for all four ethnicities. One more
haplotype from C was abundant in Tuvinians, Yakuts and Buryats but rare in Altaians. Substantial number of haplotypes was population-specific. Analysis of migrations and interethnic marriages revealed various effects of these factors depending both on ethnicity and particular
population. The results suggest considerable ethnic differentiation in the studied Siberian peoples, as well as geographic differentiation.


P1192. Paleomolecular genetic analyses (mitochondrial and nuclear DNA polymorphisms) on some Thracian populations from Romania, dating from the Bronze and Iron Age

G. M. Cardos et al.

We have performed this study on the skeletal remains of some old Thracian populations from Romania, dating from the Bronze and Iron Age. Therefore, within our research we analysed mtDNA (HVR I and HVR II regions) and nuclear DNA (vWA31A Microsatellite) polymorphisms
in order to show the degree of their genetic kinship with other old and modern European populations, especially with nowadays Romanian population. We also amplified the Amelogenin gene to identify the genetic sex of old individuals. We have used three methods for DNA-extraction from human fossils and adapted them on the degradation
state of the biological material: the phenol-chloroform DNA extraction method, the DNA extraction method with guanidine-tiocianate and silica-particles, and the DNA-extraction method with Invisorb Forensic After amplifying by PCR, the mtDNA sequences were sequenced
by the Sanger method. The nuclear vWA31A Microsatellite polymorphisms and the Amelogenin gene sequences were demonstrated on PAA gel, Ag-stained.
We have compared the mtDNA sequences of 50 old Thracian individuals with mtDNA sequences of the present-day Romanian population and other European, Asian and African modern and old populations. The frequencies of vWA31A Microsatellite were compared with similar genetic data of other modern populations from all over the world. Our results suggest that the old Thracian populations might have made an important contribution to the foundation of the modern genetic Romanian pool and also reflect an evident genetic similarity between the old Thracian populations and other modern populations from South-East Europe.

P1193. Analyses of mitochondrial and Y-chromosomal lineages in modern Hungarian, Szekler and ancient Hungarian populations

B. Csányi et al.

Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic language family. High-resolution mtDNA analysis of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Szekler samples was performed. Only two of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups. Statistical analyses, including 57 European and Asian populations, revealed that some Asian affinities and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Though strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. mtDNA results demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations. The Y-chromosomal base substitution ”Tat”, proved to be a valuable marker in the Finno-Ugric context. The Tat C allele is widespread in many Uralic-speaking populations, while it is virtually absent in recent Hungarians. To further elucidate this finding we studied this polymorphism on 100 modern Hungarian, 97 Szekler and 4 ancient Hungarian samples. Our data revealed that only one Szekler men carries the C allele among the modern individuals, whereas out of the four skeletal remains two possess the mutation. Furthermore we examined 22 Y-chromosomal binary markers to analyze the paternal genetic diversity of the two recent populations.
Our results show that Hungarians and Szeklers share basically the same genetic components found in other European populations, genetically closely related and close to other populations from Central Europe and the Balkan.

P1219. Possible common origin for the Tibeto-Burman and Austro-Asiatic speaking populations of India: a Y-chromosome study

Ancient mtDNA from Iron Age Denmark

Am J Phys Anthropol. 2007 Nov 28 [Epub ahead of print]

Rare mtDNA haplogroups and genetic differences in rich and poor Danish Iron-Age villages.

Melchior L, Gilbert MT, Kivisild T, Lynnerup N, Dissing J.

The Roman Iron-Age (0-400 AD) in Southern Scandinavia was a formative period, where the society changed from archaic chiefdoms to a true state formation, and the population composition has likely changed in this period due to immigrants from Middle Scandinavia. We have analyzed mtDNA from 22 individuals from two different types of settlements, Bøgebjerggård and Skovgaarde, in Southern Denmark. Bøgebjerggård (ca. 0 AD) represents the lowest level of free, but poor farmers, whereas Skovgaarde 8 km to the east (ca. 200-270 AD) represents the highest level of the society. Reproducible results were obtained for 18 subjects harboring 17 different haplotypes all compatible (in their character states) with the phylogenetic tree drawn from present day populations of Europe. This indicates that the South Scandinavian Roman Iron-Age population was as diverse as Europeans are today. Several of the haplogroups (R0a, U2, I) observed in Bøgebjerggård are rare in present day Scandinavians. Most significantly, R0a, harbored by a male, is a haplogroup frequent in East Africa and Arabia but virtually absent among modern Northern Europeans. We suggest that this subject was a soldier or a slave, or a descendant of a female slave, from Roman Legions stationed a few hundred kilometers to the south. In contrast, the haplotype distribution in the rich Skovgaarde shows similarity to that observed for modern Scandinavians, and the Bøgebjerggård and Skovgaarde population samples differ significantly (P approximately 0.01). Skovgaarde may represent a new upper-class formed by migrants from Middle Scandinavia bringing with them Scandinavian haplogroups.

Link

Migration routes in Romania

Ann Hum Genet. 2007 May 28; [Epub ahead of print]

Migration Rates and Genetic Structure of two Hungarian Ethnic Groups in Transylvania, Romania.

Brandstatter A, Egyed B, Zimmermann B, Duftner N, Padar Z, Parson W.

Institute of Legal Medicine, Innsbruck Medical University, Austria.

Transylvania's ethnic mosaic is composed of Romanians, German Saxons and Hungarians. The ethnic groups of the Hungarian minority that settled in Romania show differences in dialects, customs and religious affiliations. In this study entire mtDNA control region sequences from 360 individuals of Hungarian ethnicity from two populations (the Csango and the Szekely), settled in the historical region of Transylvania in Romania, were generated and analyzed following high quality sequencing standards. Phylogenetic analyses were used for haplogroup determination, quasi-median network analyses were applied for the visualization of character conflicts, and median joining reconstructions were used for depicting haplotype structures. Affiliation of haplotypes to major west Eurasian haplogroups was confirmed using coding region SNPs. Gene flow between the two populations was low and biased towards a higher migration rate from the Csango to the Szekely than vice versa. Phylogeographic analyses revealed effects of genetic isolation within the Csango population, which is, in its genetic structure, clearly different from the Szekely population. The pronounced genetic divergence between the two populations is in sharp contrast to the expectation of high genetic similarity due to the close geographic proximity of their native homelands. The population data will be incorporated in the EMPOP database (http://www.empop.org).


Link