Deepest Neandertal mtDNA split

The authors interpret the new result from HST as placing a lower boundary on an introgression from Africans to Neandertals at more than 290kya, which explains why Africans are genomically closer to Neandertals than to Denisovans.

Of course, when one looks at the mitochondrial phylogeny, it has the form:

(Denisovans, (Neandertals, Modern Humans))

Within the Modern Humans, Eurasians are a branch of a tree which is mostly African. This has been interpreted for decades as evidence for the Out of Africa hypothesis for the origin of Modern Humans. But, within the phylogeny as a whole, Modern Humans are a branch of the Eurasian tree. This has not (why?) in general been interpreted as evidence for Out of Eurasia for the common ancestor of Modern Humans and Neandertals.

It seems to me that this hypothesis, that Modern Humans and Neandertals stem from a non-African ancestor (a non-African population of H. heidelbergensis, for example), has much to recommend it.

Eurasia has twice the size of Africa and has been home to hominins for ~1.8 million years. It was inhabited by diverse hominins, and thanks to blind luck we discovered that as late as a few tens of thousands years ago, it also sported two of the populations that split off before anyone else: first H. floresiensis, and second Denisovans.

While a North African source of modern humans is plausible, the data seems to favor a Eurasian origin of the (Modern Human, Neandertal) ancestor.

Nature Communications 8, Article number: 16046 (2017) doi:10.1038/ncomms16046

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Link

Mungo Man DNA revisited + first ancient mtDNA from Australia

The authors find that previously published mtDNA from earliest Australians was contamination, and one S2 mtDNA haplogroup in an undated sample of likely Holocene origin.

PNAS doi: 10.1073/pnas.1521066113

Ancient mtDNA sequences from the First Australians revisited

Tim H. Heupink et al.

The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537–542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the “Out of Africa” model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

Link

35,000 year old mtDNA haplogroup U6 from Romania

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

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

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

Scientific Reports 6, Article number: 25501 (2016)

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

M. Hervella et al.

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

Link

mtDNA from 55 hunter-gatherers across 35,000 years in Europe

The fact that UP Europeans had mtDNA haplogroup M really destroys any lingering justification for a coastal migration that first brought (M, N) to Asia and then a subset (N) into Europe.

Another justification for the "Asia-first" model was the presence of Y-haplogroup C in Australians and Asians. But, that too was found in UP Europeans (K14).

So, I think things are looking good for my theory that Eurasians came out of Arabia northwards, interbred with Neandertals, headed both west and east, populating both Europe and Asia. The inferred date for both M and N (55kya) is on the cusp of the 50kya technological transition.

The authors also propose a major turnover in Europe at 14.5kya that replaced (not necessarily completely) the previous occupants. The authors write:

In European hunter-gatherers, our model best explains this period of upheaval as a replacement of the post-LGM maternal population by one from another source. Although the exact origin for this later population is unknown, the inferred demographic history (Figure 3 and 2b in Figure S2) suggests that it descended from another, separate LGM refugium.

Where was this LGM refugium?

Exactly where this new population came from is still unclear, but it seems likely that they came from warmer areas further south. “The main hypothesis would be glacial refugia in south-eastern Europe,” says Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, who led the analysis.

Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.01.037

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

Cosimo Posth et al.

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.

Link

Rethinking the dispersal of Homo sapiens out of Africa

An excellent review which -among its other graces- demolishes the view that mtDNA haplogroup L3 provides a terminus post quem of 70 thousand years for the Out-of-Africa expansion, a question I've discussed in this blog before.

I think the evidence is overwhelming at this point that there were modern humans outside Africa before 100,000 years ago. The argument that they were a  failed expansion is shoddy and is based, as far as I can tell on things like the age of L3, the assumption that Y-chromosome haplogroup E is native to Africa and not derived from back-to-Africa migrants, the assumption that Out-of-Africa coincided with the Upper Paleolithic cultural efflorescence (disproven by the earlier dating of Neandertal admixture), or the failed hypothesis of a coastal route Out of Africa 60 thousand years ago that seems to be repeated in inverse proportion to the evidence for it. The halving of the human autosomal mutation rate relative to what was inferred before has certainly not helped either.

Evolutionary Anthropology: Issues, News, and Reviews Volume 24, Issue 4, pages 149–164, July/August 2015

Rethinking the dispersal of Homo sapiens out of Africa

Huw S. Groucutt, Michael D. Petraglia, Geoff Bailey, Eleanor M. L. Scerri, Ash Parton, Laine Clark-Balzan, Richard P. Jennings, Laura Lewis, James Blinkhorn, Nick A. Drake, Paul S. Breeze, Robyn H. Inglis, Maud H. Devès, Matthew Meredith-Williams, Nicole Boivin, Mark G. Thomas andAylwyn Scally

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.

Link and here

mtDNA from Xiaohe cemetery

BMC Genetics 2015, 16:78 doi:10.1186/s12863-015-0237-5

Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China

Chunxiang Li et al.

Abstract

Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

Link

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.

Abstract

Background

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.

Link

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.

Link

mtDNA of Alaskan Eskimos

AJPA DOI: 10.1002/ajpa.22750

Mitochondrial diversity of Iñupiat people from the Alaskan North Slope provides evidence for the origins of the Paleo- and Neo-Eskimo peoples 

Jennifer A. Raff et al.

ABSTRACT

Objectives:

All modern Iñupiaq speakers share a common origin, the result of a recent (∼800 YBP) and rapid trans-Arctic migration by the Neo-Eskimo Thule, who replaced the previous Paleo-Eskimo inhabitants of the region. Reduced mitochondrial haplogroup diversity in the eastern Arctic supports the archaeological hypothesis that the migration occurred in an eastward direction. We tested the hypothesis that the Alaskan North Slope served as the origin of the Neo- and Paleo-Eskimo populations further east.

Materials and Methods:

We sequenced HVR I and HVR II of the mitochondrial D-loop from 151 individuals in eight Alaska North Slope communities, and compared genetic diversity and phylogenetic relationships between the North Slope Inupiat and other Arctic populations from Siberia, the Aleutian Islands, Canada, and Greenland.

Results:

Mitochondrial lineages from the North Slope villages had a low frequency (2%) of non-Arctic maternal admixture, and all haplogroups (A2, A2a, A2b, D2a, and D4b1a–formerly known as D3) found in previously sequenced Neo- and Paleo-Eskimos and living Inuit and Eskimo peoples from across the North American Arctic. Lineages basal for each haplogroup were present in the North Slope. We also found the first occurrence of two haplogroups in contemporary North American Arctic populations: D2a, previously identified only in Aleuts and Paleo-Eskimos, and the pan-American C4.

Discussion:

Our results yield insight into the maternal population history of the Alaskan North Slope and support the hypothesis that this region served as an ancestral pool for eastward movements to Canada and Greenland, for both the Paleo-Eskimo and Neo-Eskimo populations

Link

Ancient mtDNA from cis-Baikal area

Russian Journal of Genetics: Applied Research January 2015, Volume 5, Issue 1, pp 26-32

Mitochondrial DNA diversity in the gene pool of the Neolithic and Early Bronze Age Cisbaikalian human population R. O. Trapezov, A. S. Pilipenko, V. I. Molodin

This paper presents the results of a study of a mitochondrial DNA sample (N = 15) from the remains of representatives of the Neolithic and Early Bronze Age (VI–III millennia BC) Cisbaikalian human population. It was found that the mitochondrial gene pool of the ancient population under study contains lineages of East Eurasian haplogroups D, G2a C, Z, and F1b. The results of the comparative analysis of the group under study with ancient and modern Eurasian populations suggest that the development of autochtonous East Eurasian genetic components was the main mechanism of the formation of the population of the Baikal region. Genetic contacts with populations of neighboring regions of Central Asia also contributed to the formation of the gene pool of the Cisbaikalian population.

Link

mtDNA from Lengyel culture in Poland

PLoS ONE 10(2): e0118316. doi:10.1371/journal.pone.0118316

Between the Baltic and Danubian Worlds: The Genetic Affinities of a Middle Neolithic Population from Central Poland

Wiesław Lorkiewicz et al.

For a long time, anthropological and genetic research on the Neolithic revolution in Europe was mainly concentrated on the mechanism of agricultural dispersal over different parts of the continent. Recently, attention has shifted towards population processes that occurred after the arrival of the first farmers, transforming the genetically very distinctive early Neolithic Linear Pottery Culture (LBK) and Mesolithic forager populations into present-day Central Europeans. The latest studies indicate that significant changes in this respect took place within the post-Linear Pottery cultures of the Early and Middle Neolithic which were a bridge between the allochthonous LBK and the first indigenous Neolithic culture of north-central Europe—the Funnel Beaker culture (TRB). The paper presents data on mtDNA haplotypes of a Middle Neolithic population dated to 4700/4600–4100/4000 BC belonging to the Brześć Kujawski Group of the Lengyel culture (BKG) from the Kuyavia region in north-central Poland. BKG communities constituted the border of the “Danubian World” in this part of Europe for approx. seven centuries, neighboring foragers of the North European Plain and the southern Baltic basin. MtDNA haplogroups were determined in 11 individuals, and four mtDNA macrohaplogroups were found (H, U5, T, and HV0). The overall haplogroup pattern did not deviate from other post-Linear Pottery populations from central Europe, although a complete lack of N1a and the presence of U5a are noteworthy. Of greatest importance is the observed link between the BKG and the TRB horizon, confirmed by an independent analysis of the craniometric variation of Mesolithic and Neolithic populations inhabiting central Europe. Estimated phylogenetic pattern suggests significant contribution of the post-Linear BKG communities to the origin of the subsequent Middle Neolithic cultures, such as the TRB.

Link

Ancient mtDNA from collective burials in Germany

Journal of Archaeological Science Volume 51, November 2014, Pages 174–180

Collective burials among agro-pastoral societies in later Neolithic Germany: perspectives from ancient DNA

Esther J. Lee et al.

Ancient DNA research has focused on the genetic patterns of the earliest farmers during the European Neolithic, especially with regards to the demographic changes in the transition from hunting and gathering to agriculture. However, genetic data is relatively lacking after this earliest transition period, when societies had fully adapted to new agrarian lifestyles specific to their local environment. During the later central European Neolithic (ca. 3600–2800 cal BC), large-scale collective burials and monumental architecture appeared within the landscape of many agricultural societies. This phenomenon has been argued to represent the emergence of a “collective” identity. With the aim of exploring genetic-based relations among individuals collectively buried, we obtained human skeletal remains of nearly 200 individuals from four later Neolithic collective burial sites in Germany: Calden, Odagsen, Groβenrode, and Panker. We successfully reproduced reliable mitochondrial DNA (mtDNA) haplotypes from eight Neolithic individuals, which were assigned to haplogroups H, HV0, and X2. Shared haplotypes observed among individuals within Calden and Odagsen suggest that genetic relations may have shaped the arrangement of the deceased within later Neolithic agricultural groups.

Link

Western Eurasian mtDNA in modern Siberians

The eastern European mtDNA discussed in this article might be a remnant of the population of Proto-Europeoids that occupied Siberia even in Upper Paleolithic times (as the genome of the Mal'ta Upper Paleolithic Siberian has shown). However, the authors write:

Overall, the phylogeographic analysis strongly implies that the western Eurasian founders, giving rise to Siberian specific subclades, trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of LGM. Importantly, we have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions, that originated from the Upper Paleolithic industries present both in the southern Siberia and Siberian Arctic, and that date back to ~30 kya, well before the LGM [43]–[45].

If this is true, then probably the mysterious Mal'ta-like population did not have a lasting impact in Siberia.

The western Asia/Caucasus migration can't be attributed to farming expansions (because Siberia didn't have those), so it may very well be a genetic signature of the Bronze Age expansion of Indo-European languages (assuming it did not go there with occasional trade and intermarriage with later Eastern Europeans and Central Asians).

BMC Evolutionary Biology 2014, 14:217 doi:10.1186/s12862-014-0217-9

Western Eurasian ancestry in modern Siberians based on mitogenomic data

Miroslava Derenko et al.

Abstract

Background

Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians.

Results

We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate).

Conclusions

The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions.

Link

Ancient DNA from Di-qiang populations in the Xinjiang

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22690

Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age

Shi-Zhu Gao et al.

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.

Link

Remains of Richard III identified

From the paper:

Four of the modern relatives were found to belong to Y-haplogroup R1b-U152 (x L2, Z36, Z56, M160, M126 and Z192)13, 14 with STR haplotypes being consistent with them comprising a single patrilinear group. One individual (Somerset 3) was found to belong to haplogroup I-M170 (x M253, M223) and therefore could not be a patrilinear relative of the other four within the time span considered, indicating that a false-paternity event had occurred within the last four generations. 

... 

In contrast to the Y-haplotypes of the putative modern relatives, Skeleton 1 belongs to haplogroup G-P287, with a corresponding Y-STR haplotype. Thus, the putative modern patrilinear relatives of Richard III are not genetically related to Skeleton 1 through the male line over the time period considered. However, this is not surprising, given an estimated average false-paternity rate of ~1–2% (refs 12, 17, 18). The putative modern relatives and Richard III are related through a male relative (Edward III) four generations up from Richard III (Fig. 1a and Supplementary Fig. 2), and a false-paternity event could have happened in any of the 19 generations separating Richard III and the 5th Duke of Beaufort, on either branch of the genealogy descending from Edward III. Indeed, even with a conservative false-paternity rate18 (see Supplementary Methods) the chance of a false-paternity occuring in this number of generations is 16%.

Nature Communications 5, Article number: 5631 doi:10.1038/ncomms6631

Identification of the remains of King Richard III

Turi E. King et al.

Abstract

In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard’s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.

Link

High coverage genome from 45,000-year old Siberian (Ust'-Ishim)

This is the oldest full genome of a modern human published to date and it also comes from a time (45 thousand years ago) that coincides with the Upper Paleolithic revolution in Eurasia.

45 thousand years ago is probably close to when Eurasians started diverging from each other as they spread in all directions. So, we expect that a human from that time would be "undifferentiated Eurasian" and indeed this seems to be the case.

First the Y-chromosome:

The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today6 (Supplementary Information section 9).

and mtDNA:

The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia (Supplementary Information section 8).

It is clear that this was a Eurasian individual:

Based on genotyping data for 87 African and 108 non-African individuals (Supplementary Information section 11), the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans (|Z| = 41–89), consistent with the principal component analysis, mtDNA and Y chromosome results.

It was also more like East Asians than Europeans:

Among the non-Africans, the Ust’-Ishim genome shares more derived alleles with present-day people from East Asia than with present-day Europeans (|Z| = 2.1–6.4).

But, when they compared East Asians with La Brana and MA-1 they didn't see a difference:

However, when an ~8,000-year-old genome from western Europe (La Braña)9 or a 24,000-year-old genome from Siberia (Mal’ta 1)10 were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (|Z| < 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000- to 24,000-year-old individuals from western Eurasia, but not to present-day Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia11.

So it seems that the Ust'-Ishim individual belonged to the same branch as Asians and WHG/ANE and modern Europeans are less like it because they also have "Basal Eurasian" admixture which they inherited via the EEF in the model of Lazaridis et al.

The authors could also get estimates of the mutation rate because this is a 45,000 year old individual that hasn't experienced 45,000 years worth of mutations:

Assuming that this corresponds to the number of mutations that have accumulated over around 45,000 years, we estimate a mutation rate of 0.43 × 10−9 per site per year (95% CI 0.38 × 10−9 to 0.49 × 10−9) that is consistent across all non-African genomes regardless of their coverage (Supplementary Information section 14). This overall rate, as well as the relative rates inferred for different mutational classes (transversions, non-CpG transitions, and CpG transitions), is similar to the rate observed for de novo estimates from human pedigrees (~0.5 × 10−9 per site per year14, 15) and to the direct estimate of branch shortening (Supplementary Information section 10). As discussed elsewhere14, 16, 17, these rates are slower than those estimated using calibrations based on the fossil record and thus suggest older dates for the splits of modern human and archaic populations.

This is a very direct confirmation of the "slow" autosomal rate of ~1.2x10-8 mutations/generation/bp using a technology much different than those used before to estimate this. The slower mutation rate implies that major splits in human history (such as the Out-of-Africa event) took place much earlier than the Upper Paleolithic revolution and the spread of humans across Eurasia. Modern humans probably established an early presence in the Levant/Arabia (consistent with Out-of-Arabia), and invented the Upper Paleolithic-related tools/behaviors there much later, and only then spread across Eurasia.

The authors write:

we estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East.

This clinches the hypothesis of Neandertal introgression in Eurasians, as Ust'-Ishim has longer Neandertal segments than modern humans, as one might expect from an individual who experienced this admixture more recently in its evolutionary past than modern humans did. It's probably in the Middle East that the Levantine/Arabian modern humans that expanded Out-of-Africa more than 100 thousand years ago came into contact with Neandertals, admixed with them and later carried this ancestry to the rest of Eurasia. I tend to think that the AMH "colony" was first limited to Arabia and only later (post-70kya) expanded north as the climate deteriorated there. The authors estimate the common ancestor of non-African Y-chromosomes (including E, which is probably a back-migration to Africa) to around 70 thousand years ago which may coincide with the Arabian Exodus event.

Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810

Genome sequence of a 45,000-year-old modern human from western Siberia

Qiaomei Fu et al.

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.

Link

Ancient mtDNA from southern Africa related to San

Genome Biol Evol (2014) doi: 10.1093/gbe/evu202

First Ancient Mitochondrial Human Genome from a Pre-Pastoralist Southern African

Alan G. Morris et al.

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of Southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semi-desert regions of Namibia and Botswana, while archeological, historical and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. Today extinct, no genetic data has been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa pre-pastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330 year old male skeleton, confirmed via osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that pre-pastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

Link

Y chromosomes and mtDNA of early farmers from Hungary

A new preprint has just appeared on the bioRxiv. It's free to read so I'll just summarize some results. First:

The haplotype of the Mesolithic skeleton from the Croatian Island Korčula belongs to the mtDNA haplogroup U5b2a5 (Dataset S3). The sub-haplogroup U5b has been shown to be frequent in pre-Neolithic hunter-gatherer communities across Europe [28–30,32,33,45,46]. 

But:

Contrary to the low mtDNA diversity reported from hunter-gatherers of Central/North Europe [28–30], we identify substantially higher variability in early farming communities of the Carpathian Basin  including the haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4, and U5a (Table 1). Previous studies have shown that haplogroups N1a, T2, J, K, HV, V, W and X are most characteristic for the Central European LBK and have described these haplogroups as the mitochondrial ʻNeolithic packageʼ that had reached Central Europe in the 6th millennium BC [36,37]. Interestingly, most of these haplogroups show comparable frequencies between the STA, LBKT and LBK,

N1a is the "signature group" of the LBK based on previous publications and now it seems that it was also found in the Starcevo culture of Hungary. The mtDNA PCA plot (right) shows clearly that the Hungarian farmers are very similar to the German ones so it seems that the LBK is a direct outgrowth of the Carpathian Neolithic; some earlier models of "demic diffusion" argued that Neolithic farmers spread slowly across Europe, picking up hunter-gatherer ancestry as they went along, but now it seems that at least in the Hungary->Germany part of this journey interaction with hunter-gatherers was minimum.

mtDNA change over time in Europe is pictured in Figure 3 (left) showing a shared haplotype analysis. The Y-chromosome data genetic distance is shown on the right and shows the Balkan-Anatolian-Caucasian-Mesopotamian relationship of the early farmer Y-chromosomes. Practically, this is due to haplogroup G2a (and especially G2a2b), which has turned up in lots of ancient European farmers (including the famous Iceman):

Three STA individuals belong to the NRY haplogroup F* (M89) and two specimens can be assigned to the G2a2b (S126) haplogroup, and one each to G2a (P15) and I2a1 (P37.2) (Dataset S3, S5). The two investigated LBKT samples carry haplogroups G2a2b (S126) and I1 (M253). Furthermore, the incomplete SNP profiles of eight specimens potentially belong to the same haplogroups; STA: three G2a2b (S126), two G2a (P15), and one I (M170); LBKT: one G2a2b (S126) and one F* (M89) (Dataset S5).

I believe this is the first ancient finding of haplogroup I1 which attains a peak in modern Swedes. This might be useful to those who have tied this to Germanic migrations because of this, as it was already in Central Europe with the earliest farmers.

Interestingly:

Surprisingly, Y chromosome haplogroups, such as E1b1b1 (M35), E1b1b1a1 (M78), E1b1b1b2a (M123), J2 (M172), J1 (M267), and R1b1a2 (M269), which were claimed to be associated with the Neolithic expansion [23–25], have not been found so far in the 6th millennium BC of the Carpathian Basin and Central Europe. Intriguingly, R1a and R1b, which represent the most frequent European Y chromosome haplogroups today, have been reported from cultures that emerged in Central Europe during the 3rd/2nd millennium BC, while a basal R type has been reported from a Palaeolithic sample in Siberia [60] in agreement with a proposed Central Asian/Siberian origin of this lineage. In contrast, G2a has not been detected yet in late Neolithic cultures [42,43]. This suggests further demographic events in later Neolithic or post-Neolithic periods.

A cautionary tale against over-reliance on modern distributions to trace ancient origins.

Also:

Considering the entire set of 32 published NRY records available for Neolithic Europe thus far, the low paternal diversity is indeed quite remarkable: G2a is the prevailing haplogroup in the Central European and Carpathian Basin Neolithic, and in French and Iberian Neolithic datasets [36,40,41]. There are only two exceptions, namely one E1b1b (V13) [41] individual from the Avellaner cave in Spain (~5,000-4,500 BC), and two I2a [40] individuals from Treilles, France (~3,000 BC).

biorxiv http://dx.doi.org/10.1101/008664

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

Anna Szécsényi-Nagy et al.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis has not been revealed yet. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (7th/6th millennium BC) from the Carpathian Basin and south-eastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early farming south-eastern European and Carpathian Basin cultures on Central European populations of the 6th-4th millennium BC. Our comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through south-eastern Europe and the Carpathian Basin into Central Europe. Our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting patrilineal descent system and patrilocal residential rules among the early farmers.

Link

mtDNA from Chalcolithic Iberia (El Mirador cave)

A very exciting new study from Chalcolithic Iberia. The authors compare their mtDNA data with those from the Brandt et al. (2013) paper which includes German samples from the same time.

The following plot seems quite useful. From its caption:

This study: El Mirador (MIR). Published prehistoric cultures [21]: Hunter-gatherer central (HGC), Linear Pottery culture (LBK), Rössen culture (RSC), Schöningen group (SCG), Baalberge culture (BAC), Salzmünde culture (SMC), Bernburg culture (BEC), Corded Ware culture (CWC), Bell Beaker culture (BBC), Unetice culture (UC), Funnel Beaker culture (FBC), Pitted Ware culture (PWC), Hunter-Gatherer south (HGS), (Epi) Cardial (CAR), Neolithic Portugal (NPO), Neolithic Basque Country and Navarre (NBQ), Treilles culture (TRE), Hunter-gatherer east (HGE), Bronze Age Siberia (BAS), Bronze Age Kazakhstan (BAK).

From the paper:

In none of the analyses El Mirador sample shows close genetic affinities with a contemporaneous Bell Beaker population of 29 specimens gathered from three sites in Germany. The Bell Beaker mtDNA signal is characterized by high frequencies (around 50%) of H haplogroup that in El Mirador only reaches 26%. This heterogeneity in the genetic composition of geographically close populations adds further complexity to future reconstructions of these ancient expansions and correlates with the existence of contemporaneous groups with and without the typical Bell Beaker burial kit.

mtDNA may not be the best tool for studying the spread of Bell Beakers (if this involved men), but this shows that the high frequency of H in Bell Beakers of Germany (observed by Brandt et al.) is not due to an even higher frequency of H in Iberia.

PLoS ONE 9(8): e105105. doi:10.1371/journal.pone.0105105

Mitochondrial DNA from El Mirador Cave (Atapuerca, Spain) Reveals the Heterogeneity of Chalcolithic Populations

Daniel Gómez-Sánchez,Iñigo Olalde et al.

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

Link

New estimates of human mtDNA node dates and substitution rates (Rieux et al. 2014)

This is a quite useful paper as it compares different methods of obtaining mutation rate estimates, either using "archaeological calibration" based on known migration events or ancient mtDNA genomes (with known archaeological dates). The authors write:

Our estimate of 143 Kya [112-180 95% HPD] for the TMRCA of all modern human mtDNA is slightly younger but highly consistent with the 157 Kya [120-197 95% HPD] value obtained by Fu et al. (2013b). We stimate the coalescence of the L3 haplogroup (the lineage from which all non-African mtDNA haplogroups descend), often used to date the “out-of-Africa” event, to 72 Kya [54-93 95%HPD], a value also onsistent with Fu et al. (2013b) estimation of 78 Kya [62-95 95%HPD]. This estimation rather places a conservative upper bound of 93 kya for the time of the last major gene exchange between non-African nd sub-Saharan African populations. As pointed out by Fu et al. (2013b), it is important to recognize that this divergence time may merely represent the most recent gene exchanges between the ancestors f non-Africans and the most closely related sub-Saharan Africans and thus may reflect only the most recent population split in a long, drawn-out process of population separation (Scally and Durbin 2012).

The 72kya date would agree quite well with my postulated Out-of-Arabia event circa 70 thousand years ago.

It should be fairly easy to pick out the common ancestor of Eurasian mtDNA (the common ancestor of M+N). I am reasonably sure that the two African red dots to the right of event "8" in the figure are African L3's, and this would place them within the Eurasian variation, and in particular as a relative of Eurasian M.

A similar observation could be found in Supplementary Figure 14 of the Lippold et al. (2014) preprint, with African L3 lineages clearly related to Eurasian M (and nested within the Eurasian phylogeny).

In any case, I don't see any evidence at all from this phylogeny that the date of L3 corresponds to an Out-of-Africa event. Unfortunately I couldn't see an estimate for the split of L3 from the rest of the phylogeny; my eyeball estimate from the figure is that it's about 20ky earlier. Hopefully, someone sooner or later will deal with the question of L3 phylogeny, because the "conventional wisdom" that Eurasian M, N are nested within African L3 variation does not appear to be quite right.

Mol Biol Evol (2014) doi: 10.1093/molbev/msu222

Improved calibration of the human mitochondrial clock using ancient genomes

Adrien Rieux et al.

Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g. the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g. first entry into the Americas). The recent availability of ancient mtDNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analysed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive dataset of 350 ancient and modern human complete mtDNA genomes, among which 146 were generated for the purpose of this study, and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same dataset, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.

Link