April 29, 2013

Okhotsk and Ainu: linguistic connection?

A genetic connection was hypothesized in the third of the following related links on the basis of ancient Jomon mtDNA that seemed to lack an element of the modern Ainu gene pool.

From the current paper:
If we accept a view that transmission of language may be gender-specific [50]–[52], then we are able to formulate at least two hypotheses for the specific processes of the Ainu language origin. Because Y-chromosome haplogroup D is thought to represent Jomon male ancestry, the predominance of that particular haplogroup in the Ainu (75–87.5%) implies that the majority of Ainu male ancestry is from the Jomon [53], [54], whereas a heavy mixture of mtDNA haplogroups indicates that a significant proportion of the Ainu female ancestry is from the Okhotsk (excluding 35.3% of mtDNA haplogroups that the Ainu share with other neighboring populations, 39.4% of the remaining female heritage is shared exclusively with the Okhotsk and the rest is a mixture of both Jomon and Okhotsk [18], [47], [54]). If we thus assume male-specific language transmission for the Ainu, the first hypothesis for the processes behind the Ainu language origin could be that proto-Ainu arose from a large number of Jomon males who intermarried with Okhotsk females in northern Hokkaido, and subsequently spread to the rest of region. Similarly, if we assume that the transmission of Ainu language corresponds with female ancestry, the second hypothesis could be that proto-Ainu was spoken by the incoming Okhotsk females who merged with the preexisting Jomon males. Based on these observations, we propose that one potential way of understanding how language change occurred for the Ainu is to estimate which gender was more influential when early Ainu people established family membership. This may be carried out indirectly by revealing the signature of historical post-marital residence pattern via estimating the degrees of genetic variation in their Y-chromosome and mtDNA [55] as well as reconstructing ancestral post-marital residence rules from regional cultural variation [56]. Investigating which model of language change [57] is relevant to the Ainu is a direction that deserves more attention, and acquiring an accurate description of how language change occurred for the Ainu would allow us to make further inferences about the deeper history of the human lineage that once thrived in northern Japan.
I would think that a fairly recent major event of Okhotsk+Jomon=Ainu would be detectable both by ancient DNA analysis and by the study of the modern Ainu. It is certainly fascinating that the Ainu rather than being a bona fide relic of the earliest inhabitants of Japan may actually have complex ancestry themselves, and in the very recent past at that.


  1. Craniometry of the Ainu
  2. Metric and non-metric variation of Ainu
  3. Ancient mtDNA of Hokkaido Jomon
  4. Ainu/Ryukyuan paper

Evolution of the Ainu Language in Space and Time

Sean Lee, Toshikazu Hasegawa

Languages evolve over space and time. Illuminating the evolutionary history of language is important because it provides a unique opportunity to shed light on the population history of the speakers. Spatial and temporal aspects of language evolution are particularly crucial for understanding demographic history, as they allow us to identify when and where the languages originated, as well as how they spread across the globe. Here we apply Bayesian phylogeographic methods to reconstruct spatiotemporal evolution of the Ainu language: an endangered language spoken by an indigenous group that once thrived in northern Japan. The conventional dual-structure model has long argued that modern Ainu are direct descendants of a single, Pleistocene human lineage from Southeast Asia, namely the Jomon people. In contrast, recent evidence from archaeological, anthropological and genetic evidence suggest that the Ainu are an outcome of significant genetic and cultural contributions from Siberian hunter-gatherers, the Okhotsk, who migrated into northern Hokkaido around 900–1600 years ago. Estimating from 19 Ainu language varieties preserved five decades ago, our analysis shows that they are descendants of a common ancestor who spread from northern Hokkaido around 1300 years ago. In addition to several lines of emerging evidence, our phylogeographic analysis strongly supports the hypothesis that recent expansion of the Okhotsk to northern Hokkaido had a profound impact on the origins of the Ainu people and their culture, and hence calls for a refinement to the dual-structure model.


April 24, 2013

Criticism of Y-chromosome Adam old age

... has just appeared on the arXiv. This refers to the paper by Mendez et al. announcing the basal clade A00 of the phylogeny and estimating a TMRCA for Y-chromosome Adam of 237-581ka.

The author argues that such an old age is inconsistent with neutral theory, although that assumes no population structure in the origin of modern humans; it may very well be that A00 introgressed into the modern human gene pool via an admixture event from a different African population.

The best evidence for the authors' of the original paper choice of mutation rate is their estimate that the common ancestor of all Eurasians being ~63ky vs. ~39ky using the faster rate. While a date between these two can be probably accommodated, the ~39ky age seems difficult to accept, given that Homo sapiens had arrived in various parts of Eurasia by the mid-40ky's and had been admixing with Neandertals 47-65ky BP; a higher date would also be more in line with age estimates of Eurasian mtDNA macro-haplogroups M and N.

In any case, it's probably a good idea to get a better handle on the mutation rate: Mendez et al. rely on the autosomal rate, adjusting for the Y-chromosome; while the faster rate derives from a single Chinese deep pedigree study.

arXiv:1304.6098 [q-bio.PE]

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al

Melissa A. Wilson Sayres (Submitted on 22 Apr 2013)

Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y haplotype is always exciting, and this haplotype, in particular, is unique in its basal position on the Y haplotype tree. However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya), with estimates from mtDNA (176.6 +- 11.3 kya, and 204.9 (116.8-295.7) kya) and with population genetic theory. The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors.


mtDNA haplogroup H and the origin of Europeans (Brotherton et al. 2013)

Panel b is particularly interesting, as it clearly shows the Iberian-ness of Bell Beaker mtDNA (BBC), and the South-Eastern-ness of LBK.

From the paper:
From around 2800 BC, the LNE Bell Beaker culture emerged from the Iberian Peninsula to form one of the first pan-European archaeological complexes. This cultural phenomenon is recognised by a distinctive package of rich grave goods including the eponymous bell-shaped ceramic beakers. The genetic affinities between Central Europe’s Bell Beakers and present-day Iberian populations (Fig. 2) is striking and throws fresh light on long-disputed archaeological models3. We suggest these data indicate a considerable genetic influx from the West during the LNE. These far-Western genetic affinities of Mittelelbe-Saale’s Bell Beaker folk may also have intriguing linguistic implications, as the archaeologically-identified eastward movement of the Bell Beaker culture has recently been linked to the initial spread of the Celtic language family across Western Europe39. This hypothesis suggests that early members of the Celtic language family (for example, Tartessian)40 initially developed from Indo-European precursors in Iberia and subsequently spread throughout the Atlantic Zone; before a period of rapid mobility, reflected by the Beaker phenomenon, carried Celtic languages across much of Western Europe. This idea not only challenges traditional views of a linguistic spread of Celtic westwards from Central Europe during the Iron Age, but also implies that Indo-European languages arrived in Western Europe substantially earlier, presumably with the arrival of farming from the Near East41.
It does seem increasingly likely that there was a major Out-of-Iberia episode which may very well have involved a population of relative newcomers (R1b males, undetected in Europe in the pre-5ka period) interacting with an "Iberian" matrilineal substratum and then exporting both R1b and the "Iberian" type of H into most of Western Europe with the Bell Beaker phenomenon. It's hard to think of the Bell Beakers as ultimately descended from the first farmers alone, both because of their distinctive physical type, and also because of the aforementioned absence of R1b in early farmers. More ancient DNA work will certainly help solve many of the remaining puzzles.

Also from the paper:
The demographic reconstruction, which is based on direct calibration points, has major implications for understanding post-glacial human history in Europe. Our new estimate is incompatible with traditional views that the majority of present-day hg H lineages were carried into Central, Northern and Eastern Europe via a post-glacial human population expansion before the Holocene (12 kya)13. Our data complement a recent study, based on present-day mt genomes, which describes a pronounced population increase at ~7000 BC (interpreted as a Neolithic expansion into Europe), but followed by a slow population growth until the present day26. By including ancient DNA data from across the critical time points in question, our skyride plot corrects for missing temporal data and suggests substantial growth of hg H from the beginning of the Neolithic and continuing throughout the entire Neolithic period. This emphasizes the role of farming practices and cultural developments in the demographic expansions inferred in subsequent time periods, which have not yet been explored genetically.
Nature Communications 4, Article number: 1764 doi:10.1038/ncomms2656

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Paul Brotherton et al.

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.


April 17, 2013

Y-chromosomes of Native South Americans (Roewer et al. 2013)

It would be useful to sequence these South American C3* Y-chromosomes to see how they are related to the C3b-P39 found in some native North Americans as well as other unresolved C3* from Asia. It would also be worthwhile to look at autosomal data from these populations, to see if they are wholly descended from First Americans, or have evidence of more recent gene flow from East Asia.

PLoS Genet 9(4): e1003460. doi:10.1371/journal.pgen.1003460

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

Lutz Roewer et al.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.


April 12, 2013

Haplotype that looks Neandertal-introgressed may reflect African population structure (Gokcumen et al. 2013)

From the paper:
Several scenarios can be envisioned to explain the unusual genetic variation observed at the NE1 locus: (1) recent Neandertal admixture exclusively with Eurasian populations, (2) back migration to Africa from Eurasia after Neandertal admixture with Eurasian populations, and (3) ancient African substructure maintained since before Human-Neandertal divergence (Figure 3A). 
The presence of African NE1 haplotypes does not support the first scenario of exclusive Neandertal admixture with Eurasian populations. Recent reports have suggested that Neandertals and Denisovans contributed their genetic material to present-day Eurasian populations and Melanesians, respectively [20], [21]. However, the variation that we observe at the NE1 locus is not consistent with direct archaic hominin admixture as discussed in these publications. We did not consider Neandertal admixture into ancient African populations because of paleoanthropological studies that only report interactions between Neandertals and modern humans outside of Africa [37].
Thinking about the last sentence, paleoanthropological studies only report interactions between Neandertals and modern humans in "parts of outside Africa", but the signal of Neandertal admixture exists all over "outside Africa". It is not incoceivable that Neandertal-admixed Eurasians back-migrated into Africa and introduced NE1 to African populations. Such hypothetical back-migrants would not appear Neandertaloid in tha paleoanthropological sense. The authors consider this possibility:
The second scenario assumes back migration into Africa from Eurasian populations after the admixture of Neandertal with Eurasian populations [38]. If such admixture occurred, the African NE1 haplotypes should represent a subset of Eurasian NE1 haplotypes. To test this, we again analyzed the phase 1 data of the 1000 Genomes Project, which includes 338 haplotypes from three African populations. Using this dataset, we found that variation within African NE1 haplotypes is significantly higher than variation within Asian and European NE1 haplotypes (p less than 10-15, Figure 3C, Figure S5). This result indicates that African NE1 haplotypes have a longer coalescence and, as such, the presence of the NE1 haplogroup among modern Africans cannot be explained by simple back migration and admixture of Eurasian haplotypes to African populations.
But, it is possible that the higher variation within African NE1 haplotypes may reflect introgression of short "Palaeoafrican" variants within the African NE1 haplotypes. Such variants would appear as excess variation, but would not be "provable" as introgression in the absence of a comparative archaic African genome. This is a recurring theme, that (part of?) the African-Eurasian diversity differential can be explained both in terms of loss of diversity in an Out-of-Africa bottleneck and a gain-of-diversity in In-Africa admixture events between divergent populations that must have lived in the large and ecologically diverse continent. Which brings us to scenario #3:

The third scenario represents the persistence of an old African substructure at the NE1 locus before the Human-Neandertal divergence (Figure 3A). This scenario explains the presence of NE1 haplotypes (that are similar to the Neandertal haplotype) among modern human populations as well as the deep, distinct lineages observed among African NE1 haplotypes. To corroborate this conclusion, we estimated the coalescence of NE1 haplotypes through network analysis (Figure S6) and found a coalescence time of between ~437 K and ~993 K years before present (YBP) for African NE1 haplotypes and ~134 K YBP and ~304 K YBP for European NE1 haplotypes. These observations collectively suggest that the most parsimonious explanation for the observed variation at the NE1 locus is that the NE1/nonNE1 haplogroups arose after the human-chimpanzee common ancestor, but before the Human-Neandertal split in Africa. As such, the variation at the NE1 locus has persisted within ancient African substructure and later spread to non-African populations.

  PLoS Genet 9(4): e1003404. doi:10.1371/journal.pgen.1003404

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

Omer Gokcumen et al.

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p less than 10-15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations.


April 10, 2013

Closed-access story about DIY analysis tools

I find it a little odd that this story about DIY analysis tools, which (apparently) includes some quotes by myself, has now appeared in a closed-access publication. Had I known that to be the case, I doubt that I would have offered any response. It's probably not too late to make that item open access. 

In any case here's what I had to say (in full) to the author of the piece:

I think that a plurality of tools from a number of different analysts is an unambiguously good thing, both for the creators of these tools and their users.

For the users it is good because they can obtain different assessments of their ancestry, so they learn to be skeptical of extraordinary or unexpected claims of any particular test, and also to be more convinced of results that recur across many different tests.

For the creators it is good because of both (i) the motivation to improve their tools driven by competition with other test creators, and also (ii) the feedback they get from users of their tests.

These tools are also good for science in general, because a plurality of eyes (test creators and users) examine genetic data trying to detect interesting patterns in them that might be missed by more narrowly-focused research. So, a whole ecosystem of ideas springs up from these tests, as people try to fit their results into a broader pattern of human history. This is complementary to academic research: less structured and more "noisy" in terms of ideas that don't pan out, but also more dynamic, fast-paced and democratic.

As for Dodecad, I have developed my calculators by utilizing standard population genetics software, as well as software developed by myself, making use of publicly accessible academic datasets together with data from volunteers; the latter is very useful, because it helps me fill in gaps in population coverage: either because some populations have not been sampled in the literature yet, or, if they have, because their data is not publicly accessible to everyone.

Pottery-using hunter-gatherer cooks from Japan

From an accompanying piece:
Pottery usage among hunter-gatherers was considered somewhat anomalous and counter-intuitive; fragile pots did not seem to have a place in the mobile lifestyles thought to characterize most human existence before the advent of farming villages during the Neolithic, from about 10,000 years ago in the eastern Mediterranean. But the discovery of lipids on ceramic vessels in East Asia dating from the Late Pleistocene, about 15,000–12,000 years ago, presented by Craig et al.2 in a paper published on Nature's website today, suggests that some hunter-gatherers used pots for cooking. The report also provides a demonstration of how science should be integral to our piecing together of history. 
Our knowledge that ceramic containers were being made and used by hunter-gatherers in the Late Pleistocene in various parts of East Asia — from Japan to far eastern Russia and north and south China — means that pottery usage among hunter-gatherers is no longer seen as anomalous in the Old World. In fact, there may be evidence for routes of the introduction of pottery into Europe that are not associated with the introduction of farming13.
From the paper itself:
From both the bulk stable isotope data and the more specific product identifications based on available lipid data, we suggest that aquatic products were the most frequently processed products in Incipient Jōmon pottery, through the fluctuating climate and across a range of environments, from Hokkaido in the north to Kyushu in the south. Whether ceramic vessels were integral to the processing of aquatic resources or, as is suggested by their rarity, were used only occasionally, perhaps ceremonially or as a prestige technology24, remains debatable.
Nature (2013) doi:10.1038/nature12109

Earliest evidence for the use of pottery 

O. E. Craig et al.

Pottery was a hunter-gatherer innovation that first emerged in East Asia between 20,000 and 12,000 calibrated years before present1, 2 (cal BP), towards the end of the Late Pleistocene epoch, a period of time when humans were adjusting to changing climates and new environments. Ceramic container technologies were one of a range of late glacial adaptations that were pivotal to structuring subsequent cultural trajectories in different regions of the world, but the reasons for their emergence and widespread uptake are poorly understood. The first ceramic containers must have provided prehistoric hunter-gatherers with attractive new strategies for processing and consuming foodstuffs, but virtually nothing is known of how early pots were used. Here we report the chemical analysis of food residues associated with Late Pleistocene pottery, focusing on one of the best-studied prehistoric ceramic sequences in the world, the Japanese Jomon. We demonstrate that lipids can be recovered reliably from charred surface deposits adhering to pottery dating from about 15,000 to 11,800?cal?BP (the Incipient Jomon period), the oldest pottery so far investigated, and that in most cases these organic compounds are unequivocally derived from processing freshwater and marine organisms. Stable isotope data support the lipid evidence and suggest that most of the 101 charred deposits analysed, from across the major islands of Japan, were derived from high-trophic-level aquatic food. Productive aquatic ecotones were heavily exploited by late glacial foragers3, perhaps providing an initial impetus for investment in ceramic container technology, and paving the way for further intensification of pottery use by hunter-gatherers in the early Holocene epoch. Now that we have shown that it is possible to analyse organic residues from some of the world’s earliest ceramic vessels, the subsequent development of this critical technology can be clarified through further widespread testing of hunter-gatherer pottery from later periods.


April 04, 2013

The role of Taiwan in the Austronesian expansion

Of interest:

It is of interest that only two of the Pacific populations,
NZA and NZEP, both from New Zealand, are
impacted by mainland Chinese groups in the admixture
proportions (Table 4). The fact that the NZA population
is of Asian descent is the likely explanation for its connection.
In contrast, all the Austronesian Pacific populations
studied (as well as Madagascar), exhibit
widespread influences from Taiwanese aborigines, these
influences are even greater, in most instances, than the
impact from populations more geographically proximal
(for example Indonesia). Notably, the three Taiwanese
aboriginal groups that seem largely responsible for the
aforementioned effects (Paiwan, Puyuma and Saisiyat)
have been largely understudied.
The Ami, which not
only is the largest tribe (population wise) within Taiwan
but the most represented in the literature, only affects
the New Zealand groups and Madagascar but not Samoa
and Tonga (Table 4), indicating that it is essential to
include a complete survey of these tribal groups when
ascertaining phylogenetic relationships.

Am J Phys Anthropol Volume 150, Issue 4, pages 551–564, April 2013

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Sheyla Mirabal et al.

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the “Out of Taiwan” hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.


Horse Y chromosomes

PLoS ONE 8(4): e60015. doi:10.1371/journal.pone.0060015

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

Barbara Wallner et al.

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.


April 03, 2013

Polynesian mtDNA in extinct Amerindians from Brazil

From the paper:
In 1808 the Portuguese Crown declared “Just War” (Bellumiustum) against all Indian tribes that did not accept European laws (23). The fierce Botocudo were targeted in such wars and, in consequence, became virtually extinct by the end of the 19th century (24). Their importance for the history of the peopling of the Americas was revealed by studies reporting that the Botocudo had cranial features that consistently were described as intermediate between the polar Paleoamerican and Mongoloid morphologies (25, 26). Multivariate analyses of the cranial measures of different Amerindian and Paleoamerican groups from Brazil indeed concluded that the Botocudo Indians presented sufficient similarities with the Lagoa Santa Paleoamericans to be considered candidates to be their possible descendants (27).
Possible explanations:

The first scenario, prehistoric, is related to the possibility of genetic continuity between the Paleoamericans from Lagoa Santa and Botocudo Indians (26, 27, 37), which indeed originally had motivated this study. 
Another imaginable pre-Columbian scenario involves opportunities for more recent direct contact between Polynesia and South America before the European arrival. Such possibility of a direct movement from Oceania across the Pacific Ocean to the Americas was raised by Cann (43) on a discussion of the origin of the Amerindian B haplogroup. This finding prompted Bonatto et al. (44) to evaluate the likelihood of a Polynesian-Amerindian contact having occurred and conclude against it, although they could rule out neither minor contact events nor nonmaternal genetic exchange. New evidence from human and nonhuman material has become available since then. For example, there were archeological findings of Polynesian chicken bones in the Arauco Peninsula, in Chile (45) and evidence has been found in Easter Island of pre-Columbian presence of sweet potato and bottle gourd, both typical of South America (46, 47). Independent of the plausibility or implausibility of the pre-Columbian arrival of Polynesians to the South American Pacific coast, there still would remain the need to explain how these migrants crossed the Andes and ended up in Minas Gerais, Brazil. We feel that such a scenario is too unlikely to be seriously entertained. 
The last scenario that we wish to assess is the possible arrival of Polynesian haplogroups to Brazil in modern times through the African slave trade from Madagascar, where 20% of the mtDNA lineages belong to the B4a1a1a haplogroup (29).

It may be of relevance that both Tianyuan (~40ka) and Boshan (~8ka) from China belong to mtDNA haplogroup B and that B belongs to the R (and N) clade of the mtDNA phylogeny, i.e., a different branch of Out-of-Africa than C (which belongs to M). I wager that interesting things were taking place in East Eurasia and the New World until fairly recent times, and hopefully ancient DNA will help us complete the picture.

PNAS doi: 10.1073/pnas.1217905110

Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

Vanessa Faria Gonçalves et al.

There is a consensus that modern humans arrived in the Americas 15,000–20,000 y ago during the Late Pleistocene, most probably from northeast Asia through Beringia. However, there is still debate about the time of entry and number of migratory waves, including apparent inconsistencies between genetic and morphological data on Paleoamericans. Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. The identification of these two Polynesian haplogroups was confirmed in independent replications in Brazil and Denmark, ensuring reliability of the data. Parallel analysis of 12 other Botocudo individuals yielded only the well-known Amerindian mtDNA haplogroup C1. Potential scenarios to try to help understand these results are presented and discussed. The findings of this study may be relevant for the understanding of the pre-Columbian and/or post-Columbian peopling of the Americas.


April 02, 2013

Direct dating of El Sidrón Neandertals: 48.4+/-3.2ky BP

I sometimes wonder what will be left of the "long co-existence between AMH and Neandertals in Europe" once all the radiocarbon redating dust settles. The more interesting question is: how did AMH wipe out the Neandertals? Love or War? If recent history of encounters between populations with a clear technology differential is any guide, probably a little bit of both.

Archaeometry Volume 55, Issue 1, pages 148–158, February 2013


R. E. WOOD et al.

Torres et al. (2010) published a series of radiocarbon, AAR, ESR and OSL dates from the site of El Sidrón, northern Spain, which is notable for the discovery of the partial remains of 12 Neanderthals. Whilst the non-radiocarbon methods suggested an age beyond 32 600–46 300 years, direct radiocarbon dates on the human fossils were inconsistent, ranging between 10 000 and 50 000 bp. This study uses the ultrafiltration pre-treatment protocol to obtain a date of 48 400 ± 3200 bp (OxA-21 776) on a bone fragment and confirm the antiquity of the Neanderthal assemblage. Moreover, it demonstrates the comparability of the ultrafiltration and ninhydrin bone radiocarbon pre-treatment protocols, and highlights the need for appropriate screening methods where valuable collections with poor biomolecular preservation are sampled for collagen extraction.


More asymmetric migration (Sundqvist et al. 2013)

A day after the paper by Peter and Slatkin, a new paper has appeared on the arXiv dealing with the problem of detecting directionaliy in human migration patterns. This seems to be purely methodological, so no new insights on human history to report.

arXiv:1304.0118 [q-bio.PE]

A new approach to estimate directional genetic differentiation and asymmetric migration patterns

Lisa Sundqvist, Martin Zackrisson, David Kleinhans

In the field of population genetics measures of genetic differentiation are widely used to gather information on the structure and the amount of gene flow between populations. These indirect measures are based on a number of simplifying assumptions, for instance equal population size and symmetric migration. Structured populations with asymmetric migration patterns, frequently occur in nature and information about directional gene flow would here be of great interest. Nevertheless current measures of genetic differentiation cannot be used in such systems without violating the assumptions. To get information on asymmetric migration patterns from genetic data rather complex models using maximum likelihood or Bayesian approaches generally need to be applied. In such models a large number of parameters are estimated simultaneously and this involves complex optimization algorithms. We here introduce a new approach that intends to fill the gap between the complex approaches and the symmetric measures of genetic differentiation. Our approach makes it possible to calculate a directional component of genetic differentiation at low computational effort using any of the classical measures of genetic differentiation. The approach is based on defining a pool of migrants for any pair of populations and calculating measures for genetic differentiation between the populations and the respective pools. The directional measures of genetic differentiation can further be used to calculate asymmetric migration. The procedure is demonstrated with a simulated data set with known migration pattern. A comparison of the estimation results with the migration pattern used for simulation suggests, that our method captures relevant properties of migration patterns even at low migration frequencies and with few marker loci.


April 01, 2013

Directionality index for detecting origin of range expansions

This appears to be an interesting methodology for detecting directionality in genetic datasets. I am not sure how it might perform in the presence of admixture, a topic that was not discussed. Interestingly, the San appear as the only human population that had positive directionality values with all others, suggesting -to the authors- that they are closest to the origin of humans. On the other hand, in Pakistan, they found the Makrani to be the most ancestral population, and I strongly suspect that this may be related to the African admixture found in that population and not in others from that country.

arXiv:1303.7475v1 [q-bio.PE]

Detecting range expansions from genetic data

Benjamin M Peter, Montgomery Slatkin

We propose a method that uses genetic data to test for the occurrence of a recent range expansion and to infer the location of the origin of the expansion. We introduce a statistic for pairs of populations $\psi$ (the directionality index) that detects asymmetries in the two-dimensional allele frequency spectrum caused by the series of founder events that happen during an expansion. Such asymmetry arises because low frequency alleles tend to be lost during founder events, thus creating clines in the frequencies of surviving low-frequency alleles. Using simulations, we further show that $\psi$ is more powerful for detecting range expansions than both $F_{ST}$ and clines in heterozygosity. We illustrate the utility of $\psi$ by applying it to a data set from modern humans and show how we can include more complicated scenarios such as multiple expansion origins or barriers to migration in the model.