October 30, 2013

Visualizing Y-haplogroup distributions in west Eurasia

From the paper:
The database contains distributions representing 90 populations (N = 16,751 males) by the frequencies of the published and unpublished Y-chromosome Hgs. These Hgs were combined into 18 different Hgs (C, E, ABDF*, G, H, I1, I2, J1, J2, K*, L, N, O, Q, R1a, R1b, R2, T), so that published sources could be used for comparisons. 
As shown in Fig. 1, Middle Eastern (Class 7) and Central European Classes (Class 8) form one non-separable cluster in the central part of the figure. All of the others of the 10 classes can be identified in different well separable areas around this central region. The Central Asian (Class 4) and Northwest Caucasian (Class 9) Classes are in neighbouring areas in the upper and upper-left parts, while the Arab-Dagestanian Class (Class 1) occupies the opposite, lower-left part of the map. The North-Central and Western European (Class 3 + Class 6) as well as the Atlantic (Class 10) Classes form a common branch in the lower-left part of the figure. The opposite, upper-right branch contains the East Baltic (Class 5) and North Eurasian (Class 2) Classes.
Forensic Science International: Genetics Supplement Series Available online 26 October 2013

Classification of the Y-haplogroup distributions of Western Eurasian populations using a self-learning algorithm

H. Pamjav et al.

The understanding of historical relationship between populations is a core aspect of human population history studies. We have compared the frequency of 18 different Y-SNP haplogroups in 90 Western Eurasian populations. Classification of haplogroup distribution vectors using a new self-learning classification algorithm so called “self-organizing cloud (SOC)” proved to be an effective tool to identify population groups, which share common paternal genetic features. By means of the algorithm, we have determined 10 different classes of populations based on the similarity of haplogroup composition. The analysis showed that paternal genetic markers tend to reflect geographical proximity of populations better than linguistic relationship, although certain Y-SNP haplogroups have relatively good correlation with specific language families. These observations are based on the comparative analysis of the Hg distributions of contemporary populations may reflect demographic history of them in the past.


October 29, 2013

Intra-African variation in Neandertal admixture is due to non-African admixture

I haven't read this, but the idea seems to be that variation between Africans in Neandertal admixture can be wholly explained by recent admixture with Eurasians (who already had this type of admixture). This is not very surprising, given that Neandertals were a Eurasian-distributed species, so that admixture with them cannot have taken place in Africa.

The finding that Africans don't vary in their Neandertal admixture suggests that the source cannot have been an unknown African hominin related of Neandertals (in which case we'd expect to see variation in Africans). I don't know of any anthropologically plausible African cousin of the Neandertals, but, of course, the lack of anthropological evidence does not mean non-existence (cf. Denisovans as an anthropologically invisible Neandertal relative in Eurasia).

Genome Biol Evol. 2013 Oct 25. [Epub ahead of print]

Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations.

Wang S, Lachance J, Tishkoff S, Hey J, Xing J.


Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and the modern humans descended from the Out-of-Africa (OOA) migration. Here we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression while others do not. To test this alternative model we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like SNP alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern human and Neanderthal-like hominid within Africa.


Interesting talks @ Penn: Zheng He and Mount Vesuvius

I had recently mentioned Zheng He on account of his Y chromosome.

Great Voyages: Zheng He

Pompeii Lecture Series: Mount Vesuvius in Human History

October 26, 2013

Afghan mega-paper (Di Cristofaro et al.)

The admixture results nicely presented on a map:

The authors note that none of the ancestral components peaks in Central Asia, concluding that this region has been a destination rather than a source of population movements. I certainly agree that Central Asia has a lot of recent history affecting it from virtually all directions. On the other hand, we should be cautious about interpreting geographical clines in terms of directionality of population movement; a good example is Sardinia which often emerges as a "focus" of Mediterranean ancestry, but this does not mean that it is the origin of such ancestry. It would certainly be interesting to remove the layers of more recent ancestry from Central Asia to see what was there before the last few thousand years.

The PCA based on autosomal data:

The Y-chromosome haplogroup data can be found in Figure S7. The authors comment:
94% of the chromosomes are distributed within the following 9 main haplogroups: R-M207 (34%), J-M304 (16%), C-M130 (15%), L-M20 (6%), G-M201 (6%), Q-M242 (6%), N-M231 (4%), O-M175 (4%) and E-M96 (3%). Within the core haplogroups observed in the Afghan populations, there are sub-haplogroups that provide more refined insights into the underlying structure of the Y-chromosome gene pool. One of the important sub-haplogroups includes the C3b2b1-M401 lineage that is amplified in Hazara, Kyrgyz and Mongol populations. Haplogroup G2c-M377 reaches 14.7% in Pashtun, consistent with previous results [31], whereas it is virtually absent from all other populations. J2a1-Page55 is found in 23% of Iranians, 13% of the Hazara from the Hindu Kush, 11% of the Tajik and Uzbek from the Hindu Kush, 10% of Pakistanis, 4% of the Turkmen from the Hindu Kush, 3% of the Pashtun and 2% of the Kyrgyz and Mongol populations. Concerning haplogroup L, L1c-M357 is significantly higher in Burusho and Kalash (15% and 25%) than in other populations. L1a-M76 is most frequent in Balochi (20%), and is found at lower levels in Kyrgyz, Pashtun, Tajik, Uzbek and Turkmen populations. Q1a2-M25 lineage is characteristic of Turkmen (31%), significantly higher than all other populations. Haplogroup R1a1a-M198/M17 is characterized by its absence or very low frequency in Iranian, Mongol and Hazara populations and its high frequency in Pashtun and Kyrgyz populations.

PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748

Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

Julie Di Cristofaro et al.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.


New aDNA capture method (plus some data on ancient individuals from Bulgaria, Denmark, and Peru)

This seems to present an alternative method for capture of ancient DNA libraries than the one used on the Tianyuan individual. It is mostly a methods paper, but also has some initial analysis of some ancient individuals. From the paper:
We were able to tentatively call mtDNA haplogroups for these samples (Table S1). The two Bulgarian Iron Age individuals (P192-1 and T2G5) fell into haplogroups U3b and HV(16311), respectively. Haplogroup U3 is especially common in the countries surrounding the Black Sea, including Bulgaria, and in the Near East, and HV is also found at low frequencies in Europe and peaks in the Near East.41 The three Peruvian mummies fell into haplogroups B2, M (an ancestor of D), and D1, all derived from founder Native American lineages and previously observed in both pre-Columbian and modern populations from Peru. 
P192-1 was an Iron Age Thracian; T2G5 was from an Iron Age Thracian tumulus burial.

For the Peruvian mummies, we also included 10 Native American individuals from Central and South America in the PCA (Figures 3E and 3F). Interestingly, all of the mummies fell between the Native American populations (KAR, MAY, AYM) and East Asian populations (JPT, CHS, CHB), as would be expected for a nonadmixed Native American individual (Figures 3E, 3F, and S2). These mummies belonged to the pre-Columbian Chachapoya culture, who, by some accounts, were unusually fair-skinned,39 suggesting a potential for pre- Columbian European admixture. However, based on our preliminary results, these individuals appear to have been ancestrally Native American. 
The Peruvian mummies were from 1000-1500AD, so it's not very surprising that they don't appear to have European admixture and to be "ancestrally Native American".

Hopefully a more complete analysis of this data and production of more data with this method will follow in the future.

The American Journal of Human Genetics (2013), http://dx.doi.org/10.1016/j.ajhg.2013.10.002

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Meredith L. Carpenter et al.

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain less than 1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

Link (pdf)

October 22, 2013

A Persian in China (Y chromosome of Sayyid Ajjal)

Quite remarkable that a Persian (Sayyid Ajjal) would leave many descendants in faraway China, and one of this descendants (Zheng He) would one day set out to explore the West (from the perspective of China). A nice reminder of how far a Y-chromosome lineage might travel, even in the span of a couple of centuries.

arXiv:1310.5466 [q-bio.PE]

Present Y chromosomes support the Persian ancestry of Sayyid Ajjal Shams al-Din Omar and Eminent Navigator Zheng He

Chuan-Chao Wang et al.

Sayyid Ajjal is the ancestor of many Muslims in areas all across China. And one of his descendants is the famous Navigator of Ming Dynasty, Zheng He, who led the largest armada in the world of 15th century. The origin of Sayyid Ajjal's family remains unclear although many studies have been done on this topic of Muslim history. In this paper, we studied the Y chromosomes of his present descendants, and found they all have haplogroup L1a-M76, proving a southern Persian origin.


October 18, 2013

#paleoamericanodyssey tweets on 24,000-year old Mal'ta Siberian

I had blogged about this conference a year ago, and a few people seem to be tweeting from it.

Here is one intriguing tweet:
Wllierslev: 24,000-yr-old Siberian Mal'ta  person geneticall similar to native amer and west eurasians. No east asian #paleoamericanodyssey
and another:
Willerslev: Native Americans formed by an admixture of east Asian ancestors and the ancestors of western Eurasians #paleoamericanodyssey
and another:
Willerslev: Based on genomes, "the Mal'ta is much darker if you want than the iceman (Otzi)" #paleoamericanodyssey
I'll be occasionally looking at the #paleoamericanodyssey tag, but feel free to point to any other interesting tweets from the conference in the comments.


From the Met:
The Mal'ta tradition is known from a vast area spanning west of Lake Baikal and the Yenisey River. The site of Mal'ta, for which the culture is named, is composed of a series of subterranean houses made of large animal bones and reindeer antler which had likely been covered with animal skins and sod to protect inhabitants from the severe, prevailing northerly winds. Among the artistic accomplishments evident at Mal'ta are remains of expertly carved bone, ivory, and antler objects. Figurines of birds and human females are the most commonly found items. 
 From a review article:
Debetz (1946) identified the remains of “nothern Asian Mongoloids” at the site of
Afontova Gora 2; they included a fragment of the frontal bone. Mongoloid features had
been originally acknowledged in the skeletal remains of a child found at the site of
Malta. Alexeev (1998, 323) in his later publication was more cautious, stating that this
area was “inhabited by a population of Mongoloid appearance.” 
UPDATE (Oct 26):

Michael Balter has an article on this topic in Science:
Yet the child's Y chromosome belongs to a genetic group called Y haplogroup R, and its mitochondrial DNA to a haplogroup U. Today, those haplogroups are found almost exclusively in people living in Europe and regions of Asia west of the Altai Mountains, which are near the borders of Russia, China, and Mongolia.
This suggests that the Mal'ta boy was not ancestral to Native Americans (since Native Americans don't possess Y-haplogroup R and mt-haplogroup U), although obviously is in some way related to them based on the autosomal evidence. It's hard to read between the lines, but I guess a paper in Nature will come out soon enough as it is currently "in press".

D4500 and the unity of early Homo

Science 18 October 2013:

Vol. 342 no. 6156 pp. 326-331

DOI: 10.1126/science.1238484

A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo

David Lordkipanidze et al.

The site of Dmanisi, Georgia, has yielded an impressive sample of hominid cranial and postcranial remains, documenting the presence of Homo outside Africa around 1.8 million years ago. Here we report on a new cranium from Dmanisi (D4500) that, together with its mandible (D2600), represents the world's first completely preserved adult hominid skull from the early Pleistocene. D4500/D2600 combines a small braincase (546 cubic centimeters) with a large prognathic face and exhibits close morphological affinities with the earliest known Homo fossils from Africa. The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.


October 16, 2013

Neolithic super-grandfathers of the Chinese

An interesting new paper on the arXiv. The title focuses on three star-like Neolithic expansions that account for ~40% of the modern Chinese. From ~3 men to ~270 million male descendants over ~6,000 years ain't too shabby.

Also of interest in the paper is the authors' work on the rest of the Y-chromosome tree (see Figure on the left). As always with age estimates, the details matter. From the paper:
It is worth to point out that
recently, Wei et al. published a similar study about Y chromosome sequencing of 36 individuals (mainly Haplogroup R1b and E1b), in which 3.15 or 8.83 Mbp range was sequenced 19, and they achieved a time of out-of-Africa at 57 – 74 kya using various methods, which is slightly older than our result  (54 kya), although the same mutation rate of 1×10-9 substitution/base/year were employed. The difference could be ascribed to the regions chosen for date estimation; we compared the regions that Wei et al. and we studied, and found that in their study, the SNP density in the region that was sequenced only in their study is significantly higher than that in the region that both studies have sequenced (P less than 0.005) (Table S3).

It thus seems that the time estimates may be lower than true. An interesting new finding from the paper is the near-simultaneous D/CF and C/F splits. The authors comment:
It remained mysterious that how many times the anatomically modern human migrated out of Africa, since that among the three superhaplogrous C, DE and F, Haplogroup F distributes in whole Eurasia, C in Asia and Austronesia, D exclusively in Asia, while D’s brother clade E distribute mainly in Africa 62, so there are two hypotheses, 1) haplogroups D and CF migrated out of Africa separately; 2) the single common ancestor of CF and DE migrated out of Africa followed by a back-migration of E to Africa. From this study, the short interval between CF/DE and C/F divergences weakens the possibility of multiple independent migrations (CF, D, and DE*) out of Africa, and thus supports the latter hypothesis 63 (Fig. S2 a).
I have argued for haplogroup E back-migration into Africa before in this blog, so it's nice to see that this idea is gaining some supporters.

arXiv:1310.3897v1 [q-bio.PE]

Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers

Shi Yan et al.

Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.


October 14, 2013

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)

October 12, 2013

Ancient Y chromosomes of West Liao River valley

I added the results in my compendium.

BMC Evolutionary Biology 2013, 13:216 doi:10.1186/1471-2148-13-216

Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China

Yinqiu Cui et al.



The West Liao River valley in Northeast China is an ecologically diverse region, populated in prehistory by human populations with a wide range of cultures and modes of subsistence. To help understand the human evolutionary history of this region, we performed Y chromosome analyses on ancient human remains from archaeological sites ranging in age from 6500 to 2700 BP.


47 of the 70 individuals provided reproducible results. They were assigned into five different Y sub-haplogroups using diagnostic single nucleotide polymorphisms, namely N1 (xN1a, N1c), N1c, C/C3e, O3a (O3a3) and O3a3c. We also used 17 Y short tandem repeat loci in the non-recombining portion of the Y chromosome. There appears to be significant genetic differences between populations of the West Liao River valley and adjacent cultural complexes in the prehistoric period, and these prehistoric populations were shown to carry similar haplotypes as present-day Northeast Asians, but at markedly different frequencies.


Our results suggest that the prehistoric cultural transitions were associated with immigration from the Yellow River valley and the northern steppe into the West Liao River valley. They reveal the temporal continuity of Y chromosome lineages in populations of the West Liao River valley over 5000 years, with a concurrent increase in lineage diversity caused by an influx of immigrants from other populations.


October 10, 2013

Ancient central European mtDNA across time (Brandt, Haak et al. and Bollongino et al.)

Two important new papers appeared in Science today. In the first one (Brandt, Haak et al.), researchers compiled mtDNA results from 364 prehistoric central Europeans from the early Neolithic to the early Bronze Age, spanning about four millennia of history. Importantly they uncover not a smooth transition between early Neolithic farmers and modern Europeans, but a punctuated series of haplogroup frequency changes that cannot really be explained by genetic drift in a single European population evolving over time. Hopefully this kind of research can be repeated in other parts of the world, as it provides a way to see evolution and migration as it happens.

Earlier work has disproved the hypothesis that modern Europeans are simply "acculturated" hunter-gatherers, and this newer research disproves the idea that they are simply the descendants of early farmers, little modified since the beginning of the Neolithic.

I am sure that myself and others will spend some time trying to digest the wealth of information present in the paper and its supplementary materials. Yet, one conclusion can already be made, that migrationism is alive and well. Anyone adhering to a "pots not people" paradigm will find difficult to explain the sharp discontinuities found in the genetic record. European foragers contrast with the earliest farmers, who, in turn, contrast with and the Late Neolithic copper cultures that supplanted them a few thousand years later and spawned the Bronze Age world. If pots aren't people, it's strange that archaeological cultures defined largely by pots (right) also appear to mark genetic contrasts.

These discontinuities are most evident in Figure 3 from the paper:

You may follow the grey line to see how central Europe, once populated exclusively by hunter-gatherers, experienced a virtual disappearance of their matrilineages for almost two thousand years after the advent of farming.  Then, between the Middle to Late Neolithic, around five thousand year ago, the hunter-gatherers make their re-appearance before their lineages converge to their modern (minority) frequency. The authors present a model of migration to explain these events, illustrated in a movie in the supplementary material, and also in the figure on the left.

Of particular interest is a set of haplogroups marked by the yellow line (I, U2, T1, R) and are most strongly represented in the Unetice and Corded Ware samples before reverting to a small minority in the present-day. These may be potentially very informative to understand the c. 5,000-year old ago upheaval. I reproduce below three of the genetic distance maps from the supplement for the three latest cultures (CWC: Corded Ware; BBC: Bell Beaker; and UC: Unetice):

I note the European-ness of Bell Beaker (probably due to elevated frequencies of haplogroup H) and the eastern European-ness/west Asian-ness of Corded Ware/Unetice.

Moving on to the next shorter paper by Bollongino et al. which produces evidence for an interesting hypothesis: that hunter-gatherers did not disappear in central Europe after the introduction of farming, but some of their descendants persisted for at least two thousand years afterwards:
In summary, the results of 14C and stable isotope analysis, together with the DNA evidence, suggest that the Blätterhöhle individuals are sampled from three distinct populations: (i) Mesolithic hunter-gatherers, (ii) Neolithic farmers, and (iii) Neolithic fisher-hunter-gatherers (special-izing in freshwater fish). The latter two notably date to the fourth mil-lennium BC, which is around 2000 years after the introduction of farming to Central Europe.
I was reminded of an older paper about first contact between farmers and hunter-gatherers. An important consequence of the second paper is that hunter-gatherer lineages in modern Europeans may have come not only from outlying areas where foragers persisted in greater numbers, but also from within the farming realm itself.

Science 11 October 2013: Vol. 342 no. 6155 pp. 257-261 DOI: 10.1126/science.1241844

Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity 

Guido Brandt, Wolfgang Haak et al.

The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.


Science DOI: 10.1126/science.1245049

2000 Years of Parallel Societies in Stone Age Central Europe

Ruth Bollongino et al.

Debate on the ancestry of Europeans centers on the interplay between Mesolithic foragers and Neolithic farmers. Foragers are generally believed to have disappeared shortly after the arrival of agriculture. To investigate the relation between foragers and farmers, we examined Mesolithic and Neolithic samples from the Blätterhöhle site. Mesolithic mitochondrial DNA sequences were typical of European foragers, whereas the Neolithic sample included additional lineages that are associated with early farmers. However, isotope analyses separate the Neolithic sample into two groups: one with an agriculturalist diet and one with a forager and freshwater fish diet, the latter carrying mitochondrial DNA sequences typical of Mesolithic hunter-gatherers. This indicates that the descendants of Mesolithic people maintained a foraging lifestyle in Central Europe for more than 2000 years after the arrival of farming societies.

October 09, 2013

House of Bourbon belonged to Y-haplogroup R1b1b2a1a1b* (R-Z381*)

Thus concludes a new study which conflicts with the identification of blood from a handkerchief presumed to be from the execution of Louis XVI and the presumed head of Henri IV.

It is nice that this study was made possible by the co-operation of three patrilineal Bourbon descendants. I've mentioned before that the European nobility is an untapped resource for historical/genetic studies, as they can often document much longer lines of descent than most others, so it's good to see that at least some descendants of kings are willing to contribute to this kind of research.

European Journal of Human Genetics advance online publication 9 October 2013; doi: 10.1038/ejhg.2013.211

Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings

Maarten H D Larmuseau et al.

Genetic analysis strongly increases the opportunity to identify skeletal remains or other biological samples from historical figures. However, validation of this identification is essential and should be done by DNA typing of living relatives. Based on the similarity of a limited set of Y-STRs, a blood sample and a head were recently identified as those belonging respectively to King Louis XVI and his paternal ancestor King Henry IV. Here, we collected DNA samples from three living males of the House of Bourbon to validate the since then controversial identification of these remains. The three living relatives revealed the Bourbon’s Y-chromosomal variant on a high phylogenetic resolution for several members of the lineage between Henry IV and Louis XVI. This ‘true’ Bourbon’s variant is different from the published Y-STR profiles of the blood as well as of the head. The earlier identifications of these samples can therefore not be validated. Moreover, matrilineal genealogical data revealed that the published mtDNA sequence of the head was also different from the one of a series of relatives. This therefore leads to the conclusion that the analyzed samples were not from the French kings. Our study once again demonstrated that in order to realize an accurate genetic identification of historical remains DNA typing of living persons, who are paternally or maternally related with the presumed donor of the samples, is required.


October 08, 2013

Ashkenazi Jewish matrilineages mainly of European origin

From the paper:
If we allow for the possibility that K1a9 and N1b2 might have a Near Eastern source, then we can estimate the overall fraction of European maternal ancestry at ~65%. Given the strength of the case for even these founders having a European source, however, our best estimate is to assign ~81% of Ashkenazi lineages to a European source, ~8% to the Near East and ~1% further to the east in Asia, with ~10% remaining ambiguous (Fig. 10; Supplementary Table S9). Thus at least two-thirds and most likely more than four-fifths of Ashkenazi maternal lineages have a European ancestry.
Nature Communications 4, Article number: 2543 doi:10.1038/ncomms3543

A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages 

Marta D. Costa et al.

The origins of Ashkenazi Jews remain highly controversial. Like Judaism, mitochondrial DNA is passed along the maternal line. Its variation in the Ashkenazim is highly distinctive, with four major and numerous minor founders. However, due to their rarity in the general population, these founders have been difficult to trace to a source. Here we show that all four major founders, ~40% of Ashkenazi mtDNA variation, have ancestry in prehistoric Europe, rather than the Near East or Caucasus. Furthermore, most of the remaining minor founders share a similar deep European ancestry. Thus the great majority of Ashkenazi maternal lineages were not brought from the Levant, as commonly supposed, nor recruited in the Caucasus, as sometimes suggested, but assimilated within Europe. These results point to a significant role for the conversion of women in the formation of Ashkenazi communities, and provide the foundation for a detailed reconstruction of Ashkenazi genealogical history.


October 07, 2013

Migration from Sweden to Poland during the Early Bronze Age

Proof of human migration from Sweden to Poland during the Early Bronze Age
During the Early Bronze Age there was a very high level of territorial mobility of the Únětice culture in Silesia, a large community inhabiting the south western territories of Poland approximately 4 000 years ago. This is found in a new doctoral thesis from the University of Gothenburg which also conclusively confirms the first case of human long-distance overseas journey to Silesia from Scandinavia, probably from southern Sweden.

'Over 3800 years ago, a young male, possibly born in Skåne, made a journey of over 900 kilometers south, to Wroclaw in Poland. He died violently in Wroclaw, killed by Úněticean farmers, possibly due to romance with two local females, who were murdered together with him. This 'Bronze Age love story', with no happy end today is the first case of Swedish-Polish contacts in history ever', concludes archaeologist Dalia Pokutta, author of the thesis.
Here is the thesis, titled:  Population Dynamics, Diet and Migrations of the Únětice Culture in Poland.

October 01, 2013

Neolithic boom followed by later collapse (Shennan et al. 2013)

From the paper:
It is particularly important to note that the bust following the initial farming boom is found in two historically separate agricultural expansions, the first into Central Europe c. 7,500 years ago and the second into Northwest Europe 1,500 years later. It is possible that some of these regional declines represent out-migration to neighbouring areas rather than a real decline in numbers, for example, from the Paris Basin into Britain, but, in some cases, for example, Ireland, Scotland and Wessex, it is very clear that the rising and falling trends are roughly synchronous with one another—there is little indication of one going up as the others go down. On present evidence the decline in the initially raised population levels following the introduction of agriculture does not seem to be climate-related, but of course this still leaves open a variety of possible causes that remain to be explored in the future. One possibility is disease, as the reference to the Black Death above implies, although this would have to be occurring on multiple occasions at different times in different places, given the patterns shown. It is perhaps more likely that it arose from endogenous causes; for example, rapid population growth driven by farming to unsustainable levels, soil depletion or erosion arising from early farming practices, or simply the risk arising from relying on a small number of exploitable species32. However, these suggestions remain speculative and an autocorrelation analysis of the demographic data did not find evidence of a cyclical pattern, which would be one indicator of the operation of endogenous processes (Supplementary Fig. S7). Regardless of the cause, collapsing Neolithic populations must have had a major impact on social, economic and cultural processes.

Nature Communications 4, Article number: 2486 doi:10.1038/ncomms3486

Regional population collapse followed initial agriculture booms in mid-Holocene Europe

Stephen Shennan et al.

Following its initial arrival in SE Europe 8,500 years ago agriculture spread throughout the continent, changing food production and consumption patterns and increasing population densities. Here we show that, in contrast to the steady population growth usually assumed, the introduction of agriculture into Europe was followed by a boom-and-bust pattern in the density of regional populations. We demonstrate that summed calibrated radiocarbon date distributions and simulation can be used to test the significance of these demographic booms and busts in the context of uncertainty in the radiocarbon date calibration curve and archaeological sampling. We report these results for Central and Northwest Europe between 8,000 and 4,000 cal. BP and investigate the relationship between these patterns and climate. However, we find no evidence to support a relationship. Our results thus suggest that the demographic patterns may have arisen from endogenous causes, although this remains speculative.