500 thousand year old spear tips

I'll add the abstract when I see it on the Science website.

Archaeologists identify spear tips used in hunting a half-million years ago

TORONTO, ON – A University of Toronto-led team of anthropologists has found evidence that human ancestors used stone-tipped weapons for hunting 500,000 years ago – 200,000 years earlier than previously thought. 

"This changes the way we think about early human adaptations and capacities before the origin of our own species," says Jayne Wilkins, a PhD candidate in the Department of Anthropology at the University of Toronto and lead author of a new study in Science. "Although both Neandertals and humans used stone-tipped spears, this is the first evidence that the technology originated prior to or near the divergence of these two species," says Wilkins. 

... 

Wilkins and colleagues from Arizona State University and the University of Cape Town examined 500,000-year-old stone points from the South African archaeological site of Kathu Pan 1 and determined that they had functioned as spear tips.

Science 16 November 2012: Vol. 338 no. 6109 pp. 942-946 DOI: 10.1126/science.1227608

Evidence for Early Hafted Hunting Technology

Jayne Wilkins1 et al.

ABSTRACT

Hafting stone points to spears was an important advance in weaponry for early humans. Multiple lines of evidence indicate that ~500,000-year-old stone points from the archaeological site of Kathu Pan 1 (KP1), South Africa, functioned as spear tips. KP1 points exhibit fracture types diagnostic of impact. Modification near the base of some points is consistent with hafting. Experimental and metric data indicate that the points could function well as spear tips. Shape analysis demonstrates that the smaller retouched points are as symmetrical as larger retouched points, which fits expectations for spear tips. The distribution of edge damage is similar to that in an experimental sample of spear tips and is inconsistent with expectations for cutting or scraping tools. Thus, early humans were manufacturing hafted multicomponent tools ~200,000 years earlier than previously thought.

Link

Swat valley cemetery

A lost civilisation: 3,000-year-old cemetery discovered in Swat

The Italian Archaeological Mission on Wednesday discovered an ancient cemetery dating back thousands of years at Odigram, Swat — a site experts believe was built between 1500 BC to 500 BC.

...

A total of 23 graves have been excavated at the site that seems to be an ancient cemetery, indicating that they belonged to the pre-Buddhist era.

...

“It clearly indicates that Swat Valley was thickly populated at that time. Most probably they were the Dards (a group of people defined by linguistic similarities and not a common ethnic origin, predominantly found in Eastern Afghanistan) and in my view these Dards were somehow linked culturally to the people presently living in Kohistan and Kalash valleys,” revealed Massimo Vidale, a professor of Archaeology at University of Padua. “They probably spoke the Indo-European languages. We can say that the present culture of Kalash and Kohistan in Chitral valley can be linked with the ancient culture of Swat,” Vidale explained.

Pig genome + admixture into European wild boars

Of interest: 

The domestic pig (Sus scrofa) is a eutherian mammal and a member of the Cetartiodactyla order, a clade distinct from rodent and primates, that last shared a common ancestor with humans between 79 and 97 million years (Myr) ago1,2 (http://www.timetree.net). Molecular genetic evidence indicates that Sus scrofa emerged in South East Asia during the climatic fluctuations of the early Pliocene 5.3–3.5 Myr ago. Then, beginning ~10,000 years ago, pigs were domesticated in multiple locations across Eurasia3 (Frantz, L. A. F. et al., manuscript submitted).

also:

We found a clear signal for admixture between North Chinese and European populations of wild boars that we interpret as migrations across Eurasia during the later stage of the Pleistocene (Supplementary Table 24). Moreover, this hypothesis is further supported by the high value of concordance factor on the X chromosomes (Supplementary Table 20). The demographic analysis shows that the last glacial maximum (LGM)-induced bottleneck had similar magnitude in Europe and North China (Figure 2, main text). Together, these evidences suggest the existence of another (besides Asian + European) biogeographic zone for pigs, extending across North Eurasia. 

... 

There was a strong signal for admixture from Asian into European breeds. We found that European domestic breeds such as Landrace and Large White have a significant amount of Asian genetic material (Supplementary Table 24). This admixture is likely to be due to importation of Chinese breeds into Europe (especially UK) at the onset of the 'agricultural' revolution in the late 18th and 19th century.

Nature 491, 393–398 (15 November 2012) doi:10.1038/nature11622

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A. M. Groenen et al.

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Link

High altitude adaptation in Ethiopia

The anthropometric characteristics on pp. 49-50 may also be of interest. It seems Amhara highlanders are shorter, thinner, and  lighter than their co-ethnic lowlanders. Oromo highlanders, on the other hand, appear to be heavier and less thin. (for males).

arXiv:1211.3053 [q-bio.PE]

The genetic architecture of adaptations to high altitude in Ethiopia

Gorka Alkorta-Aranburu, Cynthia M. Beall, David B. Witonsky, Amha Gebremedhin, Jonathan K. Pritchard, Anna Di Rienzo

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

Link

Hawaiian origins (Kim et al. 2012)

PLoS ONE 7(11): e47881. doi:10.1371/journal.pone.0047881

Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study

Sung K. Kim et al.

The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

Link

Dynamics of genetic and morphological variability within Neandertals (Hawks 2012)

A useful quote:

A problematic aspect of the idea of Levantine  Neandertals is that the very features that distinguish them from European Neandertals tend to  align them with modern humans. For example,  the Amud skeleton has stature and limb proportions that set it apart from European Neandertals,  but that fall within the range of variability of the  Skhul and Qafzeh skeletal remains. Trinkaus  (1995) considered the Near East, including  Shanidar and the Levantine samples, to include  two forms of hominins: “late archaic” and “modern” forms. He argued that the late archaic forms  in the Near East have no close connection to  European Neandertals, and that similar features  reflect mosaicism or generalized archaic morphology in both evolving populations 

Journal of Anthropological Sciences Vol. 90 (2012), pp. 1-17

Dynamics of genetic and morphological variability within Neandertals

John Hawks

Summary - Paleogenomics may suggest changes to the way anthropologists have discussed the dynamics and morphological diversity among Neandertals. Genetic comparisons show that later Neandertals had relatively low autosomal genetic variation compared to recent humans. The known mitochondrial sample from Neandertals covers a broader geographic and temporal range, and shows greater diversity. This review addresses how genetic data compare to morphological and archaeological evidence about Neandertal variation and dynamics. Traditional views emphasized the morphological differences between western and eastern Neandertal populations, and between early and later Neandertals. Genomes broadly support these groupings, without resolving the outstanding question of the affinities of specimens from southwest Asia. However, the pattern of genetic variation appears to reject a long, in situ transformation of Neandertal groups over time, suggesting instead a more rapid process of regional dispersal and partial population replacement. Archaeological indicators sample dynamics on a much finer timescale than morphological or genetic evidence, and point to dispersal and turnover among Neandertals on a regional scale. In this way, genetic evidence may provide a bridge between the timescales relevant to morphological and archaeological comparisons. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.

Link (pdf)

Ainu/Ryukyuan paper

The paper I had mentioned earlier is online (and open access!) at the Journal of Human Genetics. From the paper:

The SNP genotype data determined in this study are available upon requests to corresponding authors, under the conditions of collaboration with us and with an appropriate approval of human genomic DNA research ethics committee of institutions to which researchers involved in the data analyses belong.

I guess that means that I won't be able to use this data, but hopefully it will be made available to academic researchers who can use it for different analyses than those presented in this paper, some of which I have suggested here.

For example, in my review of MULTIMIX, I noted that populations that have 100% of one component in ADMIXTURE analysis (which has the same model as frappe used here) are not necessarily unadmixed. So, for example, the frappe analysis shown at the top left shows some Ainu individuals fully on the "blue" Ainu cluster, and others having evidence of admixture. But, are the "100% Ainu" really unadmixed? Using either the aforementioned MULTIMIX or ALDER, it may be possible to show if even they have some admixture. And, using the methodology introduced in a recent Mexican admixture study it may be possible to create "virtual" unadmixed Ainu genomes.

Journal of Human Genetics advance online publication 8 November 2012; doi: 10.1038/jhg.2012.114

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Japanese Archipelago Human Population Genetics Consortium*: Timothy Jinam1,18, Nao Nishida2,19, Momoki Hirai3,19, Shoji Kawamura3,19, Hiroki Oota4,19, Kazuo Umetsu5,19, Ryosuke Kimura6,19, Jun Ohashi7,19, Atsushi Tajima8,19, Toshimichi Yamamoto9,19, Hideyuki Tanabe10,19, Shuhei Mano11,19, Yumiko Suto12,19, Tadashi Kaname13, Kenji Naritomi13, Kumiko Yanagi13, Norio Niikawa14, Keiichi Omoto15,19, Katsushi Tokunaga2,19 and Naruya Saitou1,16,17,19

Abstract

The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

Link

A00 at FTDNA2012: history in the making?

I've been following the #FTDNA2012 tag on twitter where Dr. Mike Hammer has been  talking about A00, the new most basal clade of the human Y-chromosome phylogeny. Apparently, 338ky old Y-chromosome ancestor for modern humans, at 98% confidence, with most basal clade found in western Cameroon and in African Americans separated by ~500 years from Cameroonian chromosome.

Root of human Y-chromosome phylogeny is now much older than both mtDNA Eve and first modern human fossils.

Conference attendees feel free to correct/supplement my understanding of what was said.

UPDATE: With respect to the confidence interval, Bonnie Schrack says:

The 338,000 years ago figure was the median (middle) of the confidence interval, which I believe was 95%, and not 98%. The lower limit of the confidence interval was still a bit over 200,000, I think -- that is, still before the time when fossils have been found showing fully anatomically modern features. Mike specifically said that even if the true age of A00 varied by 10 or 20% from the estimate, it would still be before the time when anatomically modern humans are thought to have appeared. I don't remember the upper limit too clearly, but as I recall, it was over 500,000 ybp.

UPDATE II: There is some uncertainty about the level of significance, with different people remembering anything from 90-98%. Some newer information from Tim Janzen:

Michael gave a TMRCA estimate of 338,000 years with a confidence interval range of 246,000 and 563,000 years for the A00/A0 node. He gave a TMRCA estimate of 202,000 years with a confidence interval range of 133,000 to 366,000 years for the A0/R-M269 node.

I guess we will have to wait for the publication to see the exact numbers, but it certainly appears that A00 branched off from the rest of mankind at an age that is much earlier than the next most basal clade (A0).

Iron Age Pazyryk mtDNA

The term "Scythian" is often used to describe a whole host of unrelated peoples across time periods, a practice that is not new but was also applied by the classical writers who were not well acquainted with the world of Eurasian nomads.

The distinction between "west" and "east" in terms of genetics and geography was not always very concordant. East Eurasian mtDNA has been uncovered as far west as Ukraine, and West Eurasian mtDNA well to the east of Europe, in Siberia and eastern Central Asia. The former was extended in the boreal zone of north Eurasian hunter-gatherers, while the latter in the intermediate steppe zone. The results of this paper might suggest that the Europeoid zone extended only up to the Altai, but a previous study discovered mtDNA U5a in Lake Baikal, well to the east of this region. A temporal transect of a particular region, such as the one reported here may help  elucidate not only the mixing of west/east types --which seems to be ancient across the northern parts of Eurasia-- but also the kinds of elements involved. For example, haplogroups K and J which are well-represented in the Iron Age results presented in this paper (especially the former), made their first appearance in the transition to the Iron Age in the Baraba forest-steppe zone to the west during the same time. The picture is still muddy, but a few patterns have begun to emerge: first U's, followed by T's during Andronovo horizon, followed by a wide assortment of lineages during the "Scythian" Iron Age. As I've written before, I strongly suspect that the last stratum originated in the area east of the Caspian sea, where the likely Proto-Indo-Iranian homeland existed, and where a segment of the BMAC population "went nomad" after the desiccation of their homeland.

PLoS ONE 7(11): e48904. doi:10.1371/journal.pone.0048904

Tracing the Origin of the East-West Population Admixture in the Altai Region (Central Asia)

Mercedes González-Ruiz et al.

Abstract

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

Link

Investigating East Asian admixture in Balkans/Anatolia/Caucasus

I used ALDER with a dataset of populations from the Balkans, Anatolia, and Caucasus, using the She, Japanese, Miaozu, and Dai as East Asian references. A few caveats for this analysis:

1. Some populations may possess "South Asian" admixture which may be mistaken for East Asian
2. Populations differ in the number of SNPs used in the analysis; for example, the Armenian_D sample includes mostly Family Finder data which has a smaller overlap with the SNP set used
3. Populations differ in the number of individuals used, from a low of 5 (e.g., Turkish_Cypriot) to a high of 45 (Armenian_D)

I have also added the HGDP Europeans to the analysis. The results can be seen below; I have made bold those rows where all estimates are at least one standard error above zero, and bold/big those where the estimates are they are two standard errors above zero. I consider the latter to be the most reliable.

I have already discussed the Turkish signal of admixture at length elsewhere. I will note that the Iranian_D sample produces similar or younger admixture dates, which would make sense, given the fact that the Iranians came under control of the Mongols, while the successes of the latter in Anatolia were short-lived.

A very interesting signal is that of the North Ossetians which show admixture ~9-10 centuries ago. This seems to have occurred a little after the foundation of the kingdom of Alania, and I think it makes excellent sense to view it as the signal of Eurasian nomads (who must have carried some East Asian admixture at that time) intermingling with pre-Iranic local Caucasus populations, Two other populations from the Caucasus, the Georgians and Lezgins (and also the Abkhaz and Chechens) show earlier admixture signals that could very well date to the period of east-west Eurasian migrations inaugurated by the Huns, although a possible Sassanian origin of such influence cannot be overlooked.

The Kurds are another interesting case where the Dodecad sample and the Yunusbayev et al  sample produce very different dates. The different number of SNPs may be at play here, or it may be that some Dodecad participants have recent Turkish ancestry that cause the admixture date average to appear lower, although the globe13 analysis suggests that the "East Asian" found here may be in fact "South Asian".

It seems to me that with large, dense, and well-curated sample sets from several of these populations, their admixture dynamics will become more distinct.

Multiway Admixture Deconvolution with MULTIMIX

The software will appear here. This has already been used in the recent 1000 Genomes paper. Below is the analysis of the MEX data:

I ran a small CEU/YRI/MEX K=3 analysis using ADMIXTURE on 30 random individuals from each population.

Notice that ADMIXTURE assigns 100% "American" ancestry to the most Amerindian-admixed individuals. MULTIMIX, on the other hand, has correctly not assigned any Mexicans 100% to the Amerindian component, because it makes use of LD to infer the ancestry of individual segments.

A couple advantages of the new method is that it is not limited to two ancestral populations, and does not require phased data as input, although phased data may provide some accuracy benefit, if available.

I'm eager to try the new software when it becomes available. I am not sure how it will scale (CPU/Memory-wise) with more individuals/components, so it'll be fun to experiment with.

Genet Epidemiol. 2012 Nov 7. doi: 10.1002/gepi.21692. [Epub ahead of print]

Multiway Admixture Deconvolution Using Phased or Unphased Ancestral Panels. 

Churchhouse C, Marchini J.

Abstract

We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model-Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported.

Link

Report on Sardinian-like ancient Europeans from ASHG 2012

Tia Ghose reports from ASHG2012: 

To answer that question, Sikora's team sequenced Ötzi's entire genome and compared it with those from hundreds of modern-day Europeans, as well as the genomes of a Stone Age hunter-gatherer found in Sweden, a farmer from Sweden, a 7,000-year-old hunter-gatherer iceman found in Iberia, and an Iron Age man found in Bulgaria. 

The team confirmed that, of modern people, Sardinians are Ötzi's closest relatives. But among the prehistoric quartet, Ötzi most closely resembled the farmers found in Bulgaria and Sweden, while the Swedish and Iberian hunter-gatherers looked more like present-day Northern Europeans.
...

The findings add to a growing body of evidence showing that farming played a major role in shaping the people of Europe, said Chris Gignoux, a geneticist at the University of California San Francisco, who was not involved in the study.

"I think it's really intriguing," Gignoux said. "The more that people are sequencing these ancient genomes from Europe, that we're really starting to see the impact of farmers moving into Europe."

Any ASHG attendees want to add any interesting details from the presentation? Comment away or e-mail me.

Deep structure in Y-chromosome phylogeny (Scozzari et al. 2012)

The following two figures summarize the new phylogenetic information:

The discovery of new haplogroup C7 in Italian is potentially important, since it may mean that haplogroup C --for which region-specific clades covering East Asia (with an American twig), South Asia, Australasia are known-- may have also been present natively in Europe. It will certainly be interesting to resolve occasional C chromosomes that have been occasionally found in West Eurasia at a finer level, and do some whole-Y sequencing on the different C clades to figure out exactly how they are phylogenetically related.

It is also interesting to note that the geographical origin of the human Y-chromosome phylogeny (NW Africa) is discordant with that of mtDNA (apparently in the Khoe-San of South Africa). This underscores the futility of trying to determine "where" modern humans originated in a geographically circumscribed area.

PLoS ONE 7(11): e49170. doi:10.1371/journal.pone.0049170

Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree

Rosaria Scozzari et al.

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

Link

Okinawans and admixture in East Asia

I don't use the Pan-Asian SNP Consortium data much, but the upcoming paper on the Ainu spurred me to give it a look, because it contains an Okinawan sample (JP-RK). I calculated all f3-statistics that involved this sample, and report the lowest f3-statistic for all populations in this set that appear to be admixed:

Several of these are interesting:

• A set of Indonesian populations (ID prefix; Lamaholot, Lembata, Kambera, Manggarai) are mixed with Melanesians (AX-ME)
• A set of Indian populations appear admixed (IN prefix). It seems that the Okinawan sample acts as a surrogate for "Asian" ancestry 
• Filipino populations PI-UI and PI-UN (listed as Visaya, Chabakano and Tagalog) are seen as mixtures of Okinawans and PI-UB (Ilocano)
• The three Singaporean populations (SG prefix) are seen as mixtures with Caucasoids (the SG-ID Tamil Indians with CEU), with Sunda Indonesians (SG-ML Malay with ID-SU), with Zhuang Chinese (SG-CH Singaporean Chinese with CN-CC Zhuang, northern)
• Tai Yuan from Thailand with Mlabri (TH-TU with TH-MA)
• Taiwanese (Hakka TW-HA and Minnan TW-HB) with CN-CC (Zhuang) and Jiamao (CN-JI)
• Cantonese CN-GA  with Jiamao (CN-JI)
• Uygur CN-UG with West Eurasians (CEU)

And, of course JPT and JP-ML (Japanese) are seen as a mixture of Okinawans and Mandarin Han (CN-SH) and Beijing Chinese (CHB).

An interesting question is whether the mainland East Asian Yayoi element in Japanese is more similar to Han (as the f3 statistic suggests) or to Koreans. Interestingly, Koreans themselves (KR-KR) appear admixed between Han (CN-SH) and Okinawans. So, it seems that whatever this Okinawan element represents was not limited to the isles of Japan.

I also calculated the D-statistic:

D(CN-SH      KR-KR  :      JP-RK        YRI) =      -0.0154   (Z = -14.779)

which suggests indeed, that there is an excess of "Okinawan"-like ancestry in Koreans compared to the Chinese. This is very interesting, because it suggests that similarity between Koreans and Japanese is due to a common substratum in the two populations. 

71,000-year old South African microliths

Press release, Nature News, and podcast.

Nature (2012) doi:10.1038/nature11660

An early and enduring advanced technology originating 71,000 years ago in South Africa

Kyle S. Brown et al.

There is consensus that the modern human lineage appeared in Africa before 100,000 years ago1, 2. But there is debate as to when cultural and cognitive characteristics typical of modern humans first appeared, and the role that these had in the expansion of modern humans out of Africa3. Scientists rely on symbolically specific proxies, such as artistic expression, to document the origins of complex cognition. Advanced technologies with elaborate chains of production are also proxies, as these often demand high-fidelity transmission and thus language. Some argue that advanced technologies in Africa appear and disappear and thus do not indicate complex cognition exclusive to early modern humans in Africa3, 4. The origins of composite tools and advanced projectile weapons figure prominently in modern human evolution research, and the latter have been argued to have been in the exclusive possession of modern humans5, 6. Here we describe a previously unrecognized advanced stone tool technology from Pinnacle Point Site 5–6 on the south coast of South Africa, originating approximately 71,000 years ago. This technology is dominated by the production of small bladelets (microliths) primarily from heat-treated stone. There is agreement that microlithic technology was used to create composite tool components as part of advanced projectile weapons7, 8. Microliths were common worldwide by the mid-Holocene epoch, but have a patchy pattern of first appearance that is rarely earlier than 40,000 years ago9, 10, and were thought to appear briefly between 65,000 and 60,000 years ago in South Africa and then disappear. Our research extends this record to ~71,000 years, shows that microlithic technology originated early in South Africa, evolved over a vast time span (~11,000 years), and was typically coupled to complex heat treatment that persisted for nearly 100,000 years. Advanced technologies in Africa were early and enduring; a small sample of excavated sites in Africa is the best explanation for any perceived ‘flickering’ pattern.

Link

Major new Ainu genetic study forthcoming

Genetic kinship found between Ainu and native Okinawans (The Asahi Shimbun):

The researchers examined and compared the DNA of 36 Ainu, 35 native Okinawans, and 243 people living in Honshu and elsewhere in Japan. They also studied the DNA of ethnic Han Chinese living in Beijing. The Ainu DNA was from stored samples that had been collected about 30 years ago.

The analysis found that the DNA of the Ainu bore closest similarity to people who had lived for generations in Okinawa. There was increasing dissimilarity with--in this order--those from Honshu, South Koreans and Chinese.
Meanwhile, the researchers found that the DNA of people living in Honshu showed similarities with that of South Koreans and Chinese.

The findings were to be published Nov. 1 in the Journal of Human Genetics.

I don't see the paper on the journal site yet. Loh et al. (2012) were able to infer that admixture in the Japanese occurred 45 +/- 6 generations ago, and involved at least 41 +/- 3% Yayoi ancestry. Another recent paper (He et al. 2012) estimated 23.1∼39.5% "Paleolithic" ancestry in mainland Japanese. But both studies lacked an Ainu genetic sample, which will apparently now become available (and I hope publicly so).

It will now be possible both to do a 2-reference text of admixture with software like ALDER for the Japanese, but also, and perhaps more importantly, to do a 1-ref test of admixture for the Ainu themselves! It is important to remember that the Ainu are not unmodified descendants of the Jomon, and their own ancestry is likely to be complex.

And, there will now be a second population of Y-haplogroup D descendants (the Ainu) to complement the Andamanese islanders genotyped by Reich et al. (2009). It is not clear to me whether there will be any autosomal signal left to link these peoples together, but the issue can now be investigated.

Finally, there is the whole issue of the relationship of the Ainu with West Eurasians; while research has not been supportive of that notion, it may still be useful to see whether the hirsuteness of the Ainu and other phenotypic similarities with Europeans have the same genetic aetiology or not. A link of a different kind that might be useful to investigate is the East Eurasian/Amerindian-like gene flow into Europe which seems to be more pronounced for Amerindians: will the signal also be present for the Ainu, and how strong will it be? And, of course there is that whole other issue of levels of affinity to Eurasian archaic hominins...

It is great that the last few gaps in our sampling of world genetic variation are being filled. Time and again we have discovered that at the "edges of variation" we often find the most interesting nuggets of information about our prehistoric past (e.g., Sardinians re: prehistoric Europe, Australo-Melanesians re: Denisovan admixture, Amerindians re: North Eurasian admixture in Europe, Khoe-San re: earliest divergences in the human family). The Ainu are likely to offer us new insight not only about their own origins, and those of the Japanese, but also about events taking place much further from the isles of Japan.