Paleolithic European mtDNA

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe (free full text):

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

The ancestry and affiliations of Kennewick Man

Kennewick Man ancient DNA. The paper is openly accessible. Results pretty much as I expected.

We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide.

The paper is marred by strained, politically-motivated attempts to tie Kennewick Man specifically to "the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man". So those interested in aboriginal American population structure are probably better off ignoring much of the authors's narrative and looking directly at the data.

Near Eastern admixture in Tuscany: signal of Etruscans, or medieval slaves?

Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans

Background

Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000).

Results

Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.

Conclusions

Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

Something I never see mentioned in these papers attempting to make inferences about the origins of Etruscans based on genetic variation in modern Tuscans:

Until recently, slaves have been invisible in the literature on medieval Tuscany, leading scholars to overlook them as a means of contact with the east. Historians abandoned this assumption when Giulio Prunai and Iris Origo documented the importation of hundreds of slaves to the region, conclusively demonstrating that the institution was widespread in medieval Tuscany.

[Michael P. Kucher. The Water Supply System of Siena, Italy: The Medieval Roots of the Modern Networked Cities.]

THE DOMESTIC ENEMY: THE EASTERN SLAVES IN TUSCANY IN THE FOURTEENTH AND FIFTEENTH CENTURIES:

Introduction. Among the unfamiliar minor episodes of history - those shadowy backwaters which so often repay exploration - there is one that is little known even by students of mediaeval Florence: the story of the slaves brought to Tuscany from the Black Sea and from Africa, during the fourteenth and fifteenth centuries, who came to form no inconsiderable proportion of the Florentine population. A traveller arriving in Tuscany at this time might well have been startled by the appearance of the serving-maids and grooms of the Florentine ladies. Mostly small and squat, with yellow skins, black hair, high cheek-bones and dark slanting eyes, many of them deeply marked by smallpox and by scars or tattooed patterns on their faces, they certainly seemed to belong to a different race from the Florentine. Sometimes, too, a lady would be attended by a negro, or by a taller, fair-haired woman, white-skinned, but also unmistakably foreign; and if the traveller had friends in one of the Florentine palazzi and went to call, he found several other exotic figures there, too: swarthy or yellow little girls of eleven or twelve, and sometimes a small Moorish boy, acting as nursemaids or playmates for the little Florentine merchant-princes.

All these were slaves: most of them Tartars, but some also Russian, Circassian or Greek, Moorish or Ethiopian. Every prosperous noble or merchant had at least two or three of them; many had more. Even a notary's wife, or a small shopkeeper's, would have at least one, and it was far from uncommon to find one among the possessions of a priest or nun. [. . .]

Where had they all come from? Who were they? And - we may add - what was the part they played in the domestic life of Tuscany? The answer to these questions forms a curious story. It may be pieced together from deeds of sale and enfranchisements and wills, from the ledgers of foundling hospitals, from the bills of lading of trading-ships, from court records and judgments and city stat- utes, from private letters and diaries and account-books. Out of all these docu- ments a picture emerges of a whole underworld of alien, uprooted creatures - the "displaced persons" of their time. Sometimes a few of them succeeded in escaping from servitude - but often only to form the dregs of the predatory population of outlaws who lived by robbery on the Tuscan roads, or who swelled the crowd during bread riots or political tumults. And by far the greater number of them remained (often even after enfranchisement), in their masters' houses, the necessary background of every domestic scene, speaking a curious half-in- comprehensible jargon, waiting at every table, listening at every door, and mingling (as to this, the records leave us no doubt) their blood with that of their Tuscan hosts. Domestici hostes, domestic enemies - that was Petrarch's name for these inmates of every household, so alien and yet so close, and the author of a treatise of domestic economy in Sicily, Caggio, held the same opinion. "We have," he wrote, "as many enemies as we have slaves."

The interest of this forgotten episode of history is a double one - social and ethnical. On the one hand it is curious to discover that Florentine society during the last centuries of the Middle Ages depended, even if to a lesser degree than that of Athens and Rome, on services of men who were un-free. Beneath the co- operative associations of the guilds - the Arti Maggiori e Minori - beneath even the oppressed, hungry rabble of the popolo minuto, the Tuscan cities held another class- made up of men and women without human or legal rights, without families of their own, without any recognized ties between them, with- out even a name, save that given to them by their master: the slaves.

Moreover, and perhaps this is the most interesting point- they came to form a sufficiently large proportion of the population to affect, by this strong alien infiltration, the Tuscan stock- and, perhaps, the Tuscan character. Many widely different strains had already contributed to the formation of the Tuscan people: Etruscan, Roman, Lombard, Frankish. And now there came this new blood from the East and, later on, from Africa - vigorous and vital, di genteferigna.* From the cities it spread - since slaves, as we shall see, were kept even in remote country villages - throughout the whole of Tuscany. We may see their features in many of the pictures of the time. To this day, if you watch a group of children squatting in a semicircle in the dust of a village street, their voices and hands upraised in the old Mediterranean game of morra, you will some- times see among them the crisp black curls, the dark skin and flashing eyes of an Arab boy, or the high cheek-bones and slanting eyes of a little Tartar.

[Iris Origo. The Domestic Enemy: The Eastern Slaves in Tuscany in the Fourteenth and Fifteenth Centuries. Speculum / Volume 30 / Issue 03 / July 1955, pp 321-366.]

SMBE 2014: Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe

Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe

David Reich ^{1 ,2}, Nadin Rohland^{1 ,2}, Swapan Mallick^{1 ,2}, Iosif Lazaridis¹, Eadaoin Harney¹, Susanne Nordenfelt¹, Qiaomei Fu³, Matthias Meyer³, Dorcas Brown⁴, David Anthony⁴, Nick Patterson^2
1Harvard Medical School, Boston, MA, USA, ²Broad Institute of Harvard and MIT, Cambridge, MA, USA, ³Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, ⁴Hartwick College, Oneonta, NY, USA

 A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals.  We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

• Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
• The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
• Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.

[Via Greg Cochran.]

ESHG 2014: A mitogenomic phylogeny of haplogroups U2e and U3: revealing the phylogenetic signals for population expansions in the Slavs prehistory

Title: J17.66 - A mitogenomic phylogeny of haplogroups U2e and U3: revealing the phylogenetic signals for population expansions in the Slavs prehistory
Keywords: mitochondrial DNA; molecular phylogeography; molecular evolution
Authors: B. Malyarchuk1, M. Derenko1, T. Grzybowski2, M. Perkova1, G. Denisova1, A. Litvinov1, U. Rogalla2, K. Skonieczna2; 1Institute of Biological Problems of the North, Magadan, Russian Federation, 2Institute of Forensic Medicine, Nicolaus Copernicus University, Bydgoszcz, Poland.

Abstract: To resolve the phylogeny of some uncommon and poorly studied West Eurasian mitochondrial DNA (mtDNA) haplogroups, we sequenced 32 U2e and 19 U3 complete mitogenomes of Central and Eastern Europeans (Czechs, Slovaks, Poles, Russians, Ukrainians and Belarusians) and re-analysed the available at the present time data on 74 U2e and 80 U3 complete mtDNAs. Molecular dating suggests that the coalescence time estimates are ~21 and ~35 thousand years (ky) for haplogroups U2e and U3, respectively. Detailed analysis of about 500 Slavic complete mitogenomes belonging to different haplogroups allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (U3b1b, U4a2a1, U5a2a1c, U2e1b1a, U2e1b1, U3a1a, H5a1f, U5a1a1a1, U5a1c1, U2e2a1a, U4a2a, H5a2, U2e2a1d and U5a1b1b). These subhaplogroups consist of similar haplotypes revealed in different ethnic groups of modern Slavs, thereby proving the existence of ethnolinguistic community of Slavs through DNA testing. Evolutionary age of Slavic-specific subhaplogroups is calculated to approximately 3.9 ky (from 2.3 to 5.9 ky, according to the mutation rate proposed by Soares et al. (2009) for the entire mtDNA molecule). This indicates that the ancestors of modern Slavs inhabited areas of Central and Eastern Europe from the times of Bronze and Iron Ages, i.e. earlier than it was estimated on the basis of archaeological, historical and linguistic data. This study was supported by Russian Foundation for Basic Research (grant 14-04-00131) and the Program of Presidium of Russian Academy of Sciences (grant 12-I-P30-12).

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Making of Europe unlocked by DNA

But, from the Middle Neolithic onwards, DNA patterns more closely resembled those of people living in the area today, pointing to a major - and previously unrecognised - population upheaval around 4,000 BC.

Co-author Prof Alan Cooper, from the University of Adelaide in Australia, said: "What is intriguing is that the genetic markers of this first pan-European culture, which was clearly very successful, were then suddenly replaced around 4,500 years ago, and we don't know why.

"Something major happened, and the hunt is now on to find out what that was." [. . .]

A significant contribution appears to have been made in the Late Neolithic, by populations linked to the so-called Bell Beaker archaeological culture. Sub-types of haplogroup H that are common today first appear with the Beaker people and the overall percentage of individuals belonging to the H clan jumps sharply at this time.

The origins of the "Beaker folk" are the subject of much debate. Despite having been excavated from the Mittelelbe Saale region of Germany, the Beaker individuals in this study showed close genetic similarities with people from modern Spain and Portugal.

Other remains belonging to the Late Neolithic Unetice culture attest to links with populations further east.

"We have established that the genetic foundations for modern Europe were only established in the Mid-Neolithic, after this major genetic transition around 4000 years ago," said co-author Dr Wolfgang Haak.

"This genetic diversity was then modified further by a series of incoming and expanding cultures from Iberia and Eastern Europe through the Late Neolithic."

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

Polynesian mtDNA in C19 Brazilian Amerindians

DNA study links indigenous Brazilians to Polynesians

One broad group of these Palaeoamericans — the Botocudo people, who lived in inland regions of southeastern Brazil — stands out, having skull shapes that were intermediate between those of other Palaeoamericans and a presumed ancestral population in eastern Asia.

Now, a genetic analysis sheds light on the possible heritage of the Botocudo. Pena and his colleagues studied short stretches of mitochondrial DNA (mtDNA) in samples drilled from teeth in 14 Botocudo skulls kept in a museum collection in Rio de Janeiro. By analysing material from inside the teeth, the team minimized the possibility of contamination with DNA from the numerous people who have probably handled the skulls since they arrived at the museum in the late 1800s.

The mtDNA from 12 of the skulls matched a well-known Palaeoamerican haplogroup. But mtDNA from two of the skulls included a haplogroup commonly found in Polynesia, Easter Island and other Pacific island archipelagos, the researchers report today in Proceedings of the National Academy of Sciences1. A separate lab confirmed the result with samples from one of the skulls, indicating that the ‘Polynesian haplogroup’ did not result from contamination, the researchers contend.

The researchers say that it is possible — but unlikely — that the DNA could have come from Polynesians who voyaged from remote islands to the western coast of South America. [. . .]

The researchers also entertain scenarios in which the haplogroup arrived in South America via the slave trade. Around 2,000 Polynesians were brought to Peru in the 1860s, and some could have ended up in Brazil, although the researchers say that they are not aware of any evidence that this occurred. And between 1817 and 1843, approximately 120,000 slaves were shipped from Madagascar to Brazil — and some of them were probably transported to areas where the Botocudo also lived. Although the researchers consider the latter scenario to be the most probable, Pena says: “We currently don’t have enough evidence to definitively reject any of these scenarios.”

“This is a pretty exciting initial result,” says Alice Storey, an archaeologist at the University of New England in Armidale, Australia. Further studies of genetic material from the skulls, including detailed analyses of nuclear DNA (which contains much longer genetic sequences than mtDNA), could offer more insight into the mysterious ancestry of the Botocudo, she says.

The paper: Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

Mitochondrial DNA tree calibrated with ancient DNA

Clocking the Human Exodus Out of Africa

The team analyzed 10 well-dated fossils, including a medieval man who lived in France 700 years ago; the 4550-year-old Iceman; two 14,000-year-old skeletons from the tombs of Oberkassel in Germany; three related, modern humans from 31,000 years ago in Dolni Vestonice in the Czech Republic; and an early modern human from 40,000 years ago in Tianyuan, China. [. . .]

The team's method for checking the mutation rate is clever, says geneticist Aylwyn Scally of the Wellcome Trust Sanger Institute in Hinxton, U.K., co-author of one of the studies that calculated the slower mutation rate in living humans. "It's excellent that they have been able to get a better baseline for calibrating the mtDNA mutation rate by looking at ancient DNA."

However, Scally notes, mtDNA is a single genetic lineage, which is not typical of the genome, partly because the mutation rate of mtDNA could be higher because it has a higher proportion of genes under selection than the entire nuclear genome. Krause and one of his collaborators, paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, agree that future work will be needed to resolve the differences in mutation rates in the mtDNA and nuclear genomes. "It is possible that there are things we do not understand about mitochondrial inheritance and mutation patterns," Pääbo says. [. . .]

And that matters, Krause says, because a sense of timing is critical in human evolution. Knowing when modern humans spread out of Africa and into Europe and Asia, for example, allowed Krause and his collaborators to show that the same modern humans were in Europe before and after the glaciers covered that continent—and had the ability to adapt to changing climates. They found that modern humans before and after the last major ice age in Europe share the same mtDNA lineage, making them direct descendants of the same linage. "Out of Africa is one of the major events within human evolution," Krause says. "We need to know when it happened."

The paper:

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

Qiaomei Fu, Alissa Mittnik, Philip L.F. Johnson, Kirsten Bos, Martina Lari, Ruth Bollongino, Chengkai Sun, Liane Giemsch, Ralf Schmitz, Joachim Burger, Anna Maria Ronchitelli, Fabio Martini, Renata G. Cremonesi, Jir(í Svoboda, Peter Bauer, David Caramelli, Sergi Castellano, David Reich, Svante Pääbo, Johannes Krause

Background

Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Results

Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.

Conclusions

Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome. [. . .]

We were able to reconstruct three complete and six nearly complete mitochondrial genomes from ancient human remains that were found in Europe and Eastern Asia and span 40,000 years of human history. All Paleolithic and Mesolithic European samples belong to mtDNA hg U, as was previously suggested for pre-Neolithic Europeans [15]. Two of the three individuals from the Dolni Vestonice triple burial associated with the pre-ice age Gravettian culture, namely, 14 and 15, show identical mtDNAs, suggesting a maternal relationship. Furthermore, both individuals display a mitochondrial sequence that falls basal in a phylogenetic tree compared to the post-ice age hunter-gatherer samples from Italy and central Europe, as well as the contemporary mtDNA hg U5 (Figure 1). It has been argued that hg U5 is the most ancient subhaplogroup of the U lineage, originating among the first early modern humans in Europe [18]. Our results support this hypothesis because we find that the two Dolni Vestonice individuals radiocarbon dated to 31.5 kya carry a type of mtDNA that is as yet uncharacterized, sits close to the root of hg U, and carries two mutations that are specific to hg U5. With our recalibrated molecular clock, we date the age of the U5 branch to approximately 30 kya, thus predating the LGM. Because the majority of late Paleolithic and Mesolithic mtDNAs analyzed to date fall on one of the branches of U5 (see also [15]), our data provide some support for maternal genetic continuity between the pre- and post-ice age European hunter-gatherers from the time of first settlement to the onset of the Neolithic. U4, another hg commonly found in Mesolithic hunter-gatherers [15], has so far not been sequenced in a Paleolithic individual, and we find hgs U8 and U2 in pre-LGM individuals but not in later hunter-gatherers. At present, the genetic data on Upper Paleolithic, and especially pre-ice age, populations are too sparse to comment on whether or not this is representative of a change in the genetic structure of the population, perhaps caused by a bottleneck during the LGM and a subsequent repopulation from glacial refugia.

"Huge" Genographic Project ancient DNA study underway?

A reader forwards a comment posted to a mailing list yesterday by a project administrator attending FamilyTreeDNA's Houston conference:

Report from the mixer -- Spencer Wells was there and spoke enticingly of a huge ancient DNA research project that's been underway for some time, in which, instead of a simple replacement by incoming Neolithic populations, they are seeing wave after wave of peoples coming over thousands of years, each wave adding a stratum superimposed on those before it. The set of haplogroups seen in the earlier strata were not like the ones we see today. In particular he says mtDNA H was not there until a fairly recent, post-Neolithic date.

It's clear from already-published ancient DNA results that at least some sublineages of H were present in Neolithic Europe -- but H does seem to have become much more common since then.

He is still apparently clinging to a rather old date for R1b, though. He seems to think it had a major expansion about 10,000 years ago. Haven't genetic genealogists mostly been arguing for a considerably more recent time frame? I hope to see some R1b experts engage him in dialog on that point.

That's a 20,000 year step in the right direction. I won't begrudge him the other 5,000 years for now. I just hope the "huge" ancient DNA effort underway includes Y chromosomes. Another comment from the FTDNA conference:

Katherine, Emily, Joan and Bonnie are already tweeting from the FTDNA conference. Their Twitter accounts are: @khborges, @Genealem, @Luxegen and @Greenleafy

You can also follow the hashtag #FTDNA2011 though not all the tweets are going out with the hashtag. [. . .]

FTDNA has tested over 600,000 people.

The Genographic Project has 450,000 public participation samples and 75,000 indigenous samples.

The Genographic Project has two Basque papers going into journals this week and another paper which includes mtDNA haplogroup U5 is due out next year.

And a few more twitter comments:

khborges Katherine H. Borges SW-Phase 1 of Geno is wrapping up. Phase 2 to begin #FTDNA2011

khborges Katherine H. Borges #FTDNA2011 #Genographic SW- 1 in 17 men in Med are descended from Phoenician traders

khborges Katherine H. Borges #FTDNA2011 #Genographic SW-East Asian human migration patterns follow the rivers

khborges Katherine H. Borges #FTDNA2011 #Genographic SW-10 papers are going off to the journals next week and about a dozen more in the pipeline

Luxegen Joan Miller SW - teaser - big announcement coming in Genographic project next year. #FTDNA2011

Haplogroup C mtDNA in Caucasoids does not necessarily indicate "Mongoloid" admixture

Dienekes writes:

Jean M links to a Master's thesis, which discovered the following:

While most of our samples possessed mtDNA haplotypes that can be linked to European and Near Eastern populations, three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe. Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans. In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia. This implies the demographic history for the European gene pool is more complex than previously considered and also has significant implications regarding the origin of Kurgan populations.

[. . .] The Dnieper-Donets population was described as robust Europeoid by Soviet anthropologists as was the Andronovo/Afanasevo tradition further east. It is interesting that Mongoloid admixture has been detected in both groups. I would not have guessed that this would have extended that far west and south. It seems that M. G. Levin may have been right when he stated that the Mongoloid elements penetrated far into eastern Europe.

I see no reason to believe the presence of haplogroup C indicates a "Mongoloid component". Stephen Oppenheimer sees C/Z mtDNA entering Mongoloids as part of an "intrusive" element "likely to have arrived from farther west in Asia, along with the eastern spread of the Upper Palaeolithic technology that appeared in Kara Bom in the Russian Altai 43,000 years ago." If this is correct, the presence of C in robust steppe Caucasoids would not be surprising. Oppenheimer has C/Z originating in western South Asia and entering Central Asia "round the western end of the Himalayas" 40-50,000 years ago, whereas Mongoloids (and "real" East Eurasian haplogroups) ultimately originate in SE Asia. Rather than indicating Mongoloid admixture "penetrated far into Eastern Europe", the presence of C mtDNA this early and this far west means one can't simply write off C and Z lineages in more easterly ancient Caucasoids (like some of those those buried at Xiaohe) -- or in Icelanders, for that matter -- as the product of Mongoloid admixture.

From Oppenheimer's Out of Eden:

Elite Afr-Am sprinters more admixed than Afr-Am non-athletes?

Though hardly definitive, this study certainly lends no support to the notion that black dominance of short sprints in the US can be explained purely as a consequence of West African DNA.

The purpose of this study was to compare the mtDNA haplogroup data of elite groups of Jamaican and African-American sprinters against respective controls to assess any differences in maternal lineage. The first hypervariable region of mtDNA was haplogrouped in elite Jamaican athletes (N=107) and Jamaican controls (N=293), and elite African-American athletes (N=119) and African-American controls (N=1148). Exact tests of total population differentiation were performed on total haplogroup frequencies. The frequency of non-sub-Saharan haplogroups in Jamaican athletes and Jamaican controls was similar (1.87% and 1.71%, respectively) and lower than that of African-American athletes and African-American controls (21.01% and 8.19%, respectively). There was no significant difference in total haplogroup frequencies between Jamaican athletes and Jamaican controls (P=0.551 ± 0.005); however, there was a highly significant difference between African-American athletes and African-American controls (P<0.001). The finding of statistically similar mtDNA haplogroup distributions in Jamaican athletes and Jamaican controls suggests that elite Jamaican sprinters are derived from the same source population and there is neither population stratification nor isolation for sprint performance. The significant difference between African-American sprinters and African-American controls suggests that the maternal admixture may play a role in sprint performance.
[. . .]
Among African Americans, no individual haplogroup produced significant findings for Bonferroni-adjusted critical a of 0.003, presented in Table 3. Interestingly, the nonsub- Saharan paragroup was highly significant in overrepresentation within athletes. This may indicate an advantage possessed by more admixed individuals. While maternal admixture contributing any environmental and social advantages with regard to athletic training and development cannot be ruled out, further investigation into the amount of admixture in the autosomal genome is required to assess the overall non-African genomic component. In addition to assessing differences between athletes and controls in either group, the haplogroup distributions of Jamaican controls and African-American controls were also compared. These two populations were found to have significantly different haplogroup distributions (Po0.001), providing further mitochondrial evidence of different population histories. The matrilineal distribution of both athlete populations differs significantly, suggesting no discernable distribution of lineages indicative of elite sprinting in these genetically distinct groups of West African descent.

Reference: Deason et al. Scand J Med Sci Sports. 2011 Mar 16. doi: 10.1111/j.1600-0838.2010.01289.x. [Epub ahead of print]

The Denisova hominin need not be an out of Africa story

I had a similar reaction when the original article was published, but this piece in the Journal of Human Evolution makes a much more extensive and better-argued case:

The recent retrieval of a complete mitochondrial (mt) DNA sequence from a 48–30 ka human bone from Denisova (Siberia) (Krause et al., 2010) is a remarkable achievement fully deserving international acclaim. Without wishing to detract from this feat, however, we wish to challenge their conclusion that the Denisova hominin “derives from a hominin migration out of Africa [ca. 1.0 Ma] distinct from that of the ancestors of Neanderthals and of modern humans” (Krause et al., 2010: 894). In addition, we challenge their assumption that the ancestors of the Neanderthals left Africa between 500–300 ka. In our view, alternative interpretations of the evidence are available and should be considered.

Longer excerpts below:

Icelandic C1 distinct from Amerindian and Asian subclades

A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?

Although most mtDNA lineages observed in contemporary Icelanders can be traced to neighboring populations in the British Isles and Scandinavia, one may have a more distant origin. This lineage belongs to haplogroup C1, one of a handful that was involved in the settlement of the Americas around 14,000 years ago. Contrary to an initial assumption that this lineage was a recent arrival, preliminary genealogical analyses revealed that the C1 lineage was present in the Icelandic mtDNA pool at least 300 years ago. This raised the intriguing possibility that the Icelandic C1 lineage could be traced to Viking voyages to the Americas that commenced in the 10th century. In an attempt to shed further light on the entry date of the C1 lineage into the Icelandic mtDNA pool and its geographical origin, we used the deCODE Genetics genealogical database to identify additional matrilineal ancestors that carry the C1 lineage and then sequenced the complete mtDNA genome of 11 contemporary C1 carriers from four different matrilines. Our results indicate a latest possible arrival date in Iceland of just prior to 1700 and a likely arrival date centuries earlier. Most surprisingly, we demonstrate that the Icelandic C1 lineage does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. Rather, it is presently the only known member of a new subclade, C1e. While a Native American origin seems most likely for C1e, an Asian or European origin cannot be ruled out. Am J Phys Anthropol, 2010.

The logic and evidence behind the authors' assertion that "a Native American origin seems most likely" is wanting; I find it much more likely C1 entered Iceland via Europe. Scientists will need to look elsewhere to explain Björk.

The 11 mutations that differentiate the Icelandic C1 sequences from the C1 root are in the upper range of mutation counts that differentiate the other C1 sequences from the root. [. . .]

A simple [polite way of saying retarded] argument in favor of a Native American origin of C1e is the fact that three of the four previously characterized C1 subclades are associated with these groups and the vast majority of C1 sequences in the literature have been sampled from individuals of Native American ancestry. [. . .]

The German sequence (Pfeiffer et al., 2001) represents a perfect match to the Icelandic C1e for the short HVS1 fragment spanning sites 16024–16365. This raises the intriguing, but perhaps unlikely, hypothesis that C1e is a European-specific subclade of C1, following the precedent of the European and Native American subclades of mtDNA haplogroup X2 (Brown et al., 1998; Reidla et al., 2003). However, given the dense sampling of mtDNA variation in European populations, it is clear that C1e is exceedingly rare, a fact that weighs against a hypothesis of antiquity in Europe.

The frequency of C1 in a sample of 1538 Icelandic mtDNA sequences was 0.26%. Coincidentally, another abstract that recently appeared in PubMed is that of a Russian publication reporting:

The role of natural selection in the evolution of human populations from Northeastern Eurasia was studied. Selection for the regions-specific haplogroup C was demonstrated.

Amerindian admixture in Gaspesia (Franch Canadia)

When Genetics and Genealogies Tell Different Stories-Maternal Lineages in Gaspesia

Data from uniparentally inherited genetic systems were used to trace evolution of human populations. Reconstruction of the past primarily relies on variation in present-day populations, limiting historical inference to lineages that are found among living subjects. Our analysis of four population groups in the Gaspé Peninsula, demonstrates how this may occasionally lead to erroneous interpretations. Mitochondrial DNA analysis of Gaspesians revealed an important admixture with Native Americans. The most likely scenario links this admixture to French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century. However, in contrast to genetic data, analysis of genealogical record shows that Native American maternal lineages were brought to Gaspesia in the 18th century by Acadians who settled on the south-western coast of the peninsula. Intriguingly, within three generations, virtually all Métis Acadian families separated from their nonadmixed relatives and moved eastward mixing in with other Gaspesian groups, in which Native American maternal lines are present in relatively high frequencies. Over time, the carriers of these lines eventually lost memory of their mixed Amerindian-Acadian origin. Our results show that a reliable reconstruction of population history requires cross-verification of different data sources for consistency, thus favouring multidisciplinary approaches.

I haven't read the article, so I have no idea on what basis the authors assert DNA results specifically pointed to "French-Canadians from the St. Lawrence Valley who moved to Gaspesia in the 19th century" as the most likely source of the admixture; but I'm all in favor of integrating DNA results with genealogical records in studies of this sort.

Sub-Saharan mtDNA and malaria in Portugal

Genetic characterization of uniparental lineages in populations from Southwest Iberia with past malaria endemicity:

Malaria endemicity in Southwest Iberia afforded conditions for an increase of sickle cell disease (SCD), which in the region follows a clinal pattern toward the south, where foci of high prevalence were found. SCD distribution is associated with specific geographical areas, and therefore, its introduction into Iberia may be related to the migration of different populations. We have analyzed the variation of uniparental markers in Portuguese populations with high frequency of SCD-Coruche, Pias, and Alcacer do Sal-to evaluate if their present-day pattern of neutral diversity could provide evidence about people inhabiting the area over different time periods. Two hundred and eighty-five individuals were sampled in Coruche, Pias, and Alcacer do Sal. All were analyzed for the control region of mitochondrial DNA (mtDNA); males were additionally examined for Y-chromosome markers. Results were then compared with data from other Portuguese and non-Portuguese populations. In Coruche, the genetic profile was similar to the profile usually found in Portugal. In Alcacer do Sal, the frequency of sub-Saharan mtDNA L lineages was the highest ever reported (22%) in Europe. In Pias, mtDNA diversity revealed higher frequencies of Mediterranean haplogroups I, J, and T than usually found in surrounding populations. The presence of Sub-Saharan maternal lineages in Alcacer do Sal is likely associated with the influx of African slaves between the 15th and 19th centuries, whereas in Pias, the Mediterranean influence might be traced to ancient contacts with Greeks, Phoenicians, and Carthaginians, who established important trading networks in southern Iberia. Am. J. Hum. Biol. 22:588-595, 2010.

Women selling seafood in Alcácer do Sal.

Ancient French megalithic mtDNA

Sample size is three:

We reproducibly retrieved partial HVR-I sequences (nps 16,165 to 16,390) from three human remains (Prisse´ 1, 2, and 4, Table 1), one adult and two children deposited during different stages of use of the burial chamber. Corresponding sequences could be unambiguously assigned to haplogroups X2, U5b, and N1a

Marie-France Deguilloux et al. News from the west: Ancient DNA from a French megalithic burial chamber. American Journal of Physical Anthropology DOI: 10.1002/ajpa.21376.

Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.

Ancient Scandinavian mtDNA

Genetic Diversity among Ancient Nordic Populations:

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. [. . .] The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (~2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

Dating sub-Saharan admixture in North Africa

From a paper published today in BMC Evolutionary Biology, "The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages":

The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool for the time of its settlement, some 40,000 years ago.

Ancient DNA from Syria and Iberia

A post from Jean M brought to my attention a 2005 doctoral thesis by Eva Fernández Domínguez featuring ancient DNA results for samples from the Middle East and Iberia. The "surprising conclusion":

Haplotype and haplogroup frequencies in the ancient samples from Middle East and the Iberian Peninsula are clearly different from those present nowadays in the same geographical regions. Haplogroups related to neolithic expansion to Europe - J, U3, W and X - are absent in ancient Middle Eastern samples.

Mitochondrial DNA haplogroups represented in the Neolithic Syrian sample: H, H5, R, HV, and L2a1. Fernández reports other interesting results not mentioned by Jean M, such as 50% sub-Saharan lineages across two Chalcolithic Iberian sites; from the conclusion:

37. La presencia de casi un 50% de linajes subsaharianos L1b, L2 y L3 en los yacimientos calcolíticos de Abauntz y Tres Montes, en Navarra, sugiere la existencia en el pasado de un flujo genético importante desde África hacia esta región geográfica. La baja frecuencia de estos linajes en la población actual española apunta a que se ha producido un recambio genético desde el Calcolítico. La entrada de linajes africanos pudo darse durante el Paleolítico, durante el Neolítico, o durante ambos períodos. La presencia de secuencias filogenéticamente relacionadas en yacimientos calcolíticos de la Península Ibérica y en muestras neolíticas y calcolíticas de Oriente Próximo apunta al Neolítico como momento más probable de entrada en la península de estos linajes.

Update: Jean M comments that "it looks as though the reported L3 is actually R or H20 on the present tree".

Ancient DNA from Small River Cemetery Number 5

Someone asked about the reference to Siberian admixture in the NYT article on Ordek's necropolis. According to the paper reporting the DNA results, the majority of individuals tested belonged to a branch of haplogroup C4 that shows some similarities to one found among "Evenks and Udegeys of southeastern Siberia". Other mtDNA lineages detected include H and K. All Y chromosomes tested belonged to haplogroup R1a1a.

The shared sequences of the Xiaohe C haplotype (S1) were distributed in southeastern Siberia. It implies that the east Eurasian component in the Xiaohe people originated from the Siberian populations, especially the southern or eastern Siberian populations.

The mtDNA haplogroup H is the most common mtDNA haplogroup in Europe, especially in northwestern Europe, and its frequency can be as high as 65% in Iberia. Frequencies gradually decrease from the northwest to the southeast of Europe. By contrast, the frequency of haplogroup H rises to only 20% in the Near East, and to less than10% in Central Asia, and is very low in East Asia [33,34]. All of the shared sequences of the Xiaohe H haplotype, however, were distributed in Western Europe. Haplogroup K is also common in Europe, particularly around the Alps and the British Isles. It is found with less frequency in North Africa, the Middle East, and South Asia [21,35-37]. Considering the presence of haplogroups H and K in the Xiaohe people and the geographical distribution of shared sequences, we conclude that the west Eurasian component observed in the Xiaohe people originated from western European, and maternal ancestry of the Xiaohe people might have close relationship with western European.

Regarding the Y chromosomal DNA analyses, the seven males identified all belonged to haplogroup R1a1a. It is most frequently found in Eastern Europe, South Asia and Siberia. In contrast, it is relatively uncommon in Middle Easterners and rare in East Asian [22-24]. It is thought to be a trace of the migration events of early Indo-European [38,39]. The presence of haplogroup R1a1a in the ancient Xiaohe people implies that the parental ancestry of the Xiaohe people originated from somewhere in Siberia or Europe, which is consistent with the origin of maternal ancestry.

[Chunxiang Li et al. Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age. BMC Biology 2010, 8:15doi:10.1186/1741-7007-8-15.]