June 24, 2015

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.


June 20, 2015

DNA from hot climates technically feasible

From the paper:
Ten petrous bones were selected from archaeological specimens, representing a wide range of geographical locations and climatic contexts (Table 1, for repository information see S1 File). The specimens were selected from Central Europe, Central Asia, Southeast Asia, the Levant, Anatolia, and North Africa. The specimens are from Holocene archaeological contexts dated to between 10,000–1,800 calibrated years before present (cal. BP). The samples from Nubia, Jordan and Turkmenistan are from hot and arid regions. The sample from Turkey is from the Eastern Mediterranean (northwestern Turkey); the samples from Hungary and Serbia are from the Carpathian Basin/Southeast Europe, while the two samples from Cambodia and Vietnam are from tropical/subtropical Southeast Asia. We also included a metatarsal bone for one Neolithic individual from Hungary (Polgár Ferenci hát, PF280-443) as a control to confirm the differences between petrous and non-petrous reported in the previous study [8].
It has recently been demonstrated [8] that petrous bone samples yield exceptionally high percentages of endogenous ancient DNA. Here we have shown that both the total amount of endogenous DNA that can be recovered as well as the percentage of all reads that represents endogenous DNA vary substantially for different parts of the petrous bone. Our results have several implications for aDNA studies. The results support the hypothesis that dense bone parts are especially suitable for ancient DNA research, with the densest part of the petrous bone, that which composes the otic capsule, providing the best results. For our samples the yields obtained for this part (part C) exceed those obtained for part B (i.e. dense bone part of the petrous outside the otic capsule) by up to 65-fold and those from part A by up to 177-fold. It is therefore apparent that while high endogenous yields can be obtained from part B, and hence from any dense part in the petrous, optimal yields should be obtained from bone sample taken directly from the otic capsule.
Finally, our results show that endogenous yields from the five samples which originated from hot (either arid or humid) regions were always lower than 1% including extractions from part C of the petrous bone. However, deamination patterns suggest for two (Ain Ghazal and Vat Komnou) of the three samples for which we obtained sufficient numbers of reads that the obtained sequences are likely endogenous to the bones (S3 Fig). In contrast, the deamination pattern for the third sample, Man Bac, suggests that the human reads obtained are more likely to represent contamination than endogenous ancient DNA. These results suggest that it may be possible to obtain endogenous DNA from part C also for samples with relatively low amounts of endogenous DNA from hot environments, although extreme caution will be necessary in the interpretation of the results obtained from such samples.

PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

Ron Pinhasi et al.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.


June 18, 2015

Kennewick Man was a Native American

Nature (2015) doi:10.1038/nature14625

The ancestry and affiliations of Kennewick Man

Morten Rasmussen, Martin Sikora, Anders Albrechtsen, Thorfinn Sand Korneliussen, J. Víctor Moreno-Mayar, G. David Poznik, Christoph P. E. Zollikofer, Marcia S. Ponce de León, Morten E. Allentoft, Ida Moltke, Hákon Jónsson, Cristina Valdiosera, Ripan S. Malhi, Ludovic Orlando, Carlos D. Bustamante, Thomas W. Stafford Jr, David J. Meltzer, Rasmus Nielsen & Eske Willerslev

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (BP)1. His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted2. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans2. In order to resolve Kennewick Man’s ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.


June 13, 2015

Into, out of, and across the Eurasian steppe

A new paper in Nature adds to the earlier study in the same journal by presenting data from 101 ancient Eurasians. The year is not yet halfway over, but it seems that the ancient DNA field is moving towards a new norm of studying dozens of individuals at a time and comprehensively tackling the "big problems" that have vexed archaeologists, linguists, and historians for decades if not centuries.

The first conclusion of the new study is the detection of the migration from the steppe to Europe that was the title piece of the earlier study. The authors do not present quantitative estimates of the amount of demographic replacement effected by the Yamnaya-to-Corded Ware migration, so it will be interesting to see if there are any minor significant differences in these. But, the two papers have different Yamnaya and Corded Ware samples, and yet arrive at qualitatively similar conclusions, so at least this part of the story should be considered firmly "settled".

The second conclusion is the migration from the European steppe to the Afanasievo culture of the Altai. This has been long-hypothesized based on the physical type of the Afanasievo people and their possession of a similar pastoralist/wheeled vehicle toolkit that would have allowed them to cover the huge difference between Europe and the Altai. This confirms movement #2 of the Anthony/Ringe model, although I doubt that this migration had anything to do with Tocharians as detailed below. But, it did happen.

The third conclusion is that the later steppe cultures of the Sintashta and Andronovo (putative Indo-Iranians according to some), were not a continuation of the Yamnaya-Afanasievo people, but had extra Neolithic farmer ancestry. So, it seems that Neolithic farmers entered the steppe, and the development of steppe cultures did not happen in isolation. Whether this involved migration of Corded Ware people (as the authors prefer), who were already a mixture of Yamnaya and Neolithic farmers, or some other mixture of Neolithic farmers with steppe populations (e.g., Tripolye plus Yamnaya) remains to be seen.

The fourth conclusion of the paper is that these steppe cultures were also later replaced by people of at least partial East Asian or "Native American"-like ancestry.  So, it seems that movements into the steppe happened both on the western end (as the incursion of Neolithic farmer ancestry into the Sintashta proves), but also on the eastern end, with the Europeoid populations of western origin receiving admixture from the eastern periphery of the Eurasian steppe.

As for the Yamnaya, the authors do not find a very strong signal of admixture (as did the earlier study), which they attribute quite plausibly to the lack of eastern hunter-gatherers in their dataset. On the other hand, they claim that the "Caucasus" genetic component in the steppe populations was of steppe ancestry rather than Near Eastern/Caucasian origin as was claimed in the earlier paper. This is based on the statistic D(Yoruba, Armenia BA; Yamnaya, Corded Ware) that is not significantly different from zero. However, Corded Ware is a mixture of Yamnaya and European Neolithic, so the sign of this statistic is determined by the sign of the statistic D(Yoruba, Armenia BA; Yamnaya, European Neolithic). If Yamnaya was simply a steppe population, descendants of local people without ancestry from the Middle East/Caucasus, then this statistic would be positive because of the shared Middle Eastern ancestry of Armenia BA and European Neolithic. Whereas, if Yamnaya is a mixture of a steppe population and a Middle Eastern/Caucasian one, then the statistic would be positive/negative for the respective parts, which would be consistent with an average not different from zero. I am sure that when the new data is re-analyzed together with the eastern hunter-gatherers it will be clear that the Yamnaya are not a pure steppe population.

Nonetheless, I am quite glad to read a sentence such as this:
Populations in northern and central Europe were composed of a mixture of the earlier hunter-gatherer and Neolithic farmer10 groups, but received ‘Caucasian’ genetic input at the onset of the Bronze Age (Fig. 2).
It seems that my prediction the the West_Asian component would appear in post-5ka Europeans and was related to Indo-Europeans has been adequately confirmed by the last two papers.

Speaking of the Caucasus/Middle East, it seems clear as a first approximation that the Bronze Age Armenians are quite similar to modern Armenians. Whether the genetic continuity of Armenians extends beyond the Bronze Age, or Armenians were formed by mixture in the Bronze Age remains to be seen. The question of Armenian linguistic origins is of course separate as it is commonly understood that the Armenian language is unrelated to Anatolian languages and may have arrived in Armenia from the Balkans at around the Bronze Age-Iron Age transition.

The authors also study some phenotypic traits such as lactase peristence (Yamnaya had some, but overall prevalence was much lower than modern Europeans, hence lots of selection to the present), and skin eye pigmentation. Like Wilde et al., and Mathieson et al., the steppe populations seem to have had brown eyes. Given that so did Neolithic Europeans, and (presumably) ancient Middle Easterners/Caucasians, I think it's a good bet that Proto-Indo-Europeans (whatever solution to the PIE urheimat one accepts) were a brown-eyed people, or in the very least far from the blue-eyed "Aryans" of racial mythology. Even the Bronze Age and Iron Age Asians seem to have been a predominantly brown-eyed people, although the derived HERC2 allele seems to be at a higher frequency in them than in the steppe Europeans.

The story of the Y-chromosomes seems very interesting, although these are not resolved to fine detail. The most interesting aspect of this part of the work is the appearance of haplogroup J in Iron Age samples from Russia, Armenia, and the Altai. This may tie in to the question of the Tocharian origins, which I have claimed were associated with R1b, rather than R1a (as the Indo-Iranians were). The modern Uygurs (who are partially of Tocharian origin) have both J2 and R1b, so were the recipients of West Eurasian elements other than the R1a that so seem to have dominated the eastern steppe, including the Afanasievo. I continue to think there's no evidence that the Afanasievo is Proto-Tocharian, as it's in the wrong place and 3,000 years before the attestation of Tocharian. 

Overall this is an amazing study which adds a lot to what we know about Bronze Age Eurasia. Hopefully there is more to come in the second half of 2015, but for the time being there is plenty to chew on.

Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Population genomics of Bronze Age Eurasia

Morten E. Allentoft, Martin Sikora, Karl-Göran Sjögren, Simon Rasmussen, Morten Rasmussen, Jesper Stenderup, Peter B. Damgaard, Hannes Schroeder, Torbjörn Ahlström, Lasse Vinner, Anna-Sapfo Malaspinas, Ashot Margaryan, Tom Higham, David Chivall, Niels Lynnerup, Lise Harvig, Justyna Baron, Philippe Della Casa, Paweł Dąbrowski, Paul R. Duffy, Alexander V. Ebel, Andrey Epimakhov, Karin Frei, Mirosław Furmanek, Tomasz Gralak, Andrey Gromov, Stanisław Gronkiewicz, Gisela Grupe, Tamás Hajdu, Radosław Jarysz, Valeri Khartanovich, Alexandr Khokhlov, Viktória Kiss, Jan Kolář, Aivar Kriiska, Irena Lasak, Cristina Longhi, George McGlynn, Algimantas Merkevicius, Inga Merkyte, Mait Metspalu, Ruzan Mkrtchyan, Vyacheslav Moiseyev, László Paja, György Pálfi, Dalia Pokutta, Łukasz Pospieszny, T. Douglas Price, Lehti Saag, Mikhail Sablin, Natalia Shishlina, Václav Smrčka, Vasilii I. Soenov, Vajk Szeverényi, Gusztáv Tóth, Synaru V. Trifanova, Liivi Varul, Magdolna Vicze, Levon Yepiskoposyan, Vladislav Zhitenev, Ludovic Orlando, Thomas Sicheritz-Pontén, Søren Brunak, Rasmus Nielsen, Kristian Kristiansen & Eske Willerslev

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.


June 10, 2015

101 ancient genomes from Bronze Age Eurasia

New data has been posted online. This seems related to this earlier post. Hopefully the study linked to this data will appear soon, but genome bloggers can get to it thanks to the early data release.

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. 

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.


June 09, 2015

Nilo-Saharan component

Scientific Reports 5, Article number: 9996 doi:10.1038/srep09996

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Begoña Dobon et al.

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.


May 30, 2015

Out of Egypt or Out of Ethiopia?

I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.

For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.

For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.

AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Luca Pagani et al.

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.


May 21, 2015

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.

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.


May 13, 2015

Neandertal in the (immediate) family tree

Early European may have had Neanderthal great-great-grandparent
One of Europe’s earliest known humans had a close Neanderthal ancestor: perhaps as close as a great-great-grandparent.

The finding, announced on 8 May at the Biology of Genomes meeting in Cold Spring Harbor, New York, questions the idea that humans and Neanderthals interbred only in the Middle East, more than 50,000 years ago.

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone's genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

May 12, 2015

mtDNA haplogroup A10 in Bronze Age West Siberia

PLoS ONE 10(5): e0127182. doi:10.1371/journal.pone.0127182

MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population

Aleksandr S. Pilipenko et al.



The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history.

Results and Conclusion

We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V—I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages’ phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.


May 07, 2015

2,500-year old Etruscans

From a Biology of Genomes poster (pdf) on "Assessment of Whole-Genome capture methodologies on single- and double-stranded ancient DNA libraries from Caribbean and European archaeological human remains" by Ávila-Arcos et al.

All that can be said based on this is that they seem broadly southern European and not particularly Tuscan.

May 04, 2015

Ancient mtDNA from Neolithic France

PLoS ONE 10(4): e0125521. doi:10.1371/journal.pone.0125521

When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin

Maïté Rivollat et al.

An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.


Facial reconstruction of Lord of Moken

I wonder when we will start seeing facial reconstructions that make use of ancient DNA. Ancient DNA isn't very good for reconstructing facial features, but it should be quite good at reconstructing pigmentation.

Facial reconstruction for 1,400-year-old 'Lord of Morken'
The man's remains were discovered in 1955 in a Franconian burial ground in Morken, near Cologne. He had been interred around the year 600 AD in a royal burial chamber there. The precious goods within the grave, especially the materials used for his weapons, suggest that the man enjoyed a special status in the population, Elke Nieveler a specialist for the early Middle Ages at the Rheinisches Landesmuseum said.

May 03, 2015

Modern humans, not Neandertals made the Proto-Aurignacian

Science DOI: 10.1126/science.aaa2773

The makers of the Protoaurignacian and implications for Neandertal extinction

S. Benazzi et al.

The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in Western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into Southern Europe. Because the last Neandertals date to 41,030 to 39,260 calendar years before the present, we suggest that the Protoaurignacian triggered the demise of Neandertals in this area.


Structure of Y-haplogroup N

arXiv:1504.06463 [q-bio.PE]

The dichotomy structure of Y chromosome Haplogroup N

Kang Hu et al.

Haplogroup N-M231 of human Y chromosome is a common clade from Eastern Asia to Northern Europe, being one of the most frequent haplogroups in Altaic and Uralic-speaking populations. Using newly discovered bi-allelic markers from high-throughput DNA sequencing, we largely improved the phylogeny of Haplogroup N, in which 16 subclades could be identified by 33 SNPs. More than 400 males belonging to Haplogroup N in 34 populations in China were successfully genotyped, and populations in Northern Asia and Eastern Europe were also compared together. We found that all the N samples were typed as inside either clade N1-F1206 (including former N1a-M128, N1b-P43 and N1c-M46 clades), most of which were found in Altaic, Uralic, Russian and Chinese-speaking populations, or N2-F2930, common in Tibeto-Burman and Chinese-speaking populations. Our detailed results suggest that Haplogroup N developed in the region of China since the final stage of late Paleolithic Era.


Southern origins and recent admixture of Siberian populations

bioRxiv http://dx.doi.org/10.1101/018770

The complex admixture history and recent southern origins of Siberian populations

Irina Pugach , Rostislav Matveev , Viktor Spitsyn , Sergey Makarov , Innokentiy Novgorodov , Vladimir Osakovsky , Mark Stoneking , Brigitte Pakendorf

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, since commonly used methods assume a tree-like population history and at most single admixture events. We therefore developed a new method based on the covariance of ancestry components, which we validated with simulated data, in order to investigate this potentially complex admixture history and to distinguish the effects of shared ancestry from prehistoric migrations and contact. We furthermore adapted a previously devised method of admixture dating for use with multiple events of gene flow, and applied these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have indeed been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations, and with the earliest events dated to not more than 4500 years ago. Furthermore, most of the populations of Siberia included here, even those settled far to the north, can be shown to have a southern origin. These results provide support for a recent population replacement in this region, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyse multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.