Human admixture common in human history (Hellenthal et al. 2014)

A string of recent papers argued for admixture in human populations at time scales from the Middle Pleistocene to recent centuries. A new paper in Science makes the point convincingly for extensive admixture in humans over the last few thousand years. The authors include the creators of Chromopainter/fineStructure software; the new "Globetrotter" method appears to be a natural extension of that method that seemed to work wonderfully well except for the limitation of producing only a tree of the studied populations.

The paper has a companion website in which you can look up the admixture history of individual populations.

While reading this study, it is important to remember its limitations. Two are immediately obvious: (i) admixture events can only be detected for the last few thousand years, as this method depends on pattern of linkage disequilibrium which decays exponentially with time due to recombination, and (ii) detection of admixture seems to depend on the presence of maximally differentiated populations from the edges of the human geographical range; for example, the Japanese appear unadmixed even though they are clearly of dual Jomon/Yayoi ancestry. On the other hand, the method does detect the admixture present in the San at a similar time scale.

The case of Northwestern Europe appears especially striking as none of the populations from the region show evidence of admixture. This may be because the mixtures taking place there (e.g., between "Celts" and "Anglo-Saxons" in Great Britain) involved populations that were not strongly differentiated. Alternatively, population admixture history may have preceded the last few thousand years and is thus beyond the temporal scope of this method.

An exception to the rule that populations at the edges of the human range appear to be unadmixed are the Armenians who appear to be the only * between the Atlantic and Pacific in Figure 2D (shown at the beginning of this post). The companion site lists their status as "uncertain".

Other results are more questionable; for example, the authors assert that Sardinians are an admixed population with one side being "Egyptian-like" and the other "French-like" whereas the ancient DNA evidence as it stands would rather indicate that Sardinians are the best approximation of Neolithic Europeans currently in existence and so are more likely to (mostly) possess a gene pool that traces back to ~8-9 thousand years in Europe. It will be quite the surprise if so many Europeans from 5kya or earlier look like modern Sardinians and ancient Sardinians don't!

The analysis of Eastern Europe is particularly interesting as it documents three way admixture (Northern/Southern/NE Asian) in most populations but two way admixture (Northern/Southern) in Greeks, estimated at ~37%. The authors claim that this is related to the Slavs, which seems reasonable given the 1,054AD age estimate. On the other hand, according to the companion website, the southern element in Greeks is inferred to be Cypriot-like and it's far from clear that the pre-Slavic population of Greece was Cypriot-like or indeed represented by any of the populations in the authors' dataset.

The three-way admixture in much of eastern Europe is not particularly surprising as history furnishes ample evidence for groups of steppe origin in the region during historical times. Some bequeathed their both language and name (e.g., Magyars), others only their name (e.g., Bulgarians) on the local Europeans, but records indicate a widespread presence of "eastern" groups in Europe from the time of the Huns to that of the Ottomans. A study of late Antique eastern Europeans from the Baltic to the Aegean may help better document how the twin phenomena of the eastern invasions and the spread of the Slavs shaped the present-day genetic diversity of the region.

I suspect that a few ancient samples will be far more informative for understanding the recent history of our species than the most sophisticated modeling of modern populations. Nonetheless, it's great to have a new method that maximizes what can be learned about the past from the messy palimpsest of the present.

Science 14 February 2014: Vol. 343 no. 6172 pp. 747-751 DOI: 10.1126/science.1243518

A Genetic Atlas of Human Admixture History

Garrett Hellenthal et al.

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

Link

SMBE 2013 abstracts

Some abstracts from the SMBE 2013 conference that will take place next week. 

Legacy of Early Migrants in Neolithic East Asian Hunter-Gatherer from Fukushima, Japan

K.K. Hideaki et al.   

Clarifying the genetic relationship between Neolithic East Asian Hunter-Gatherer, Jomon people, and modern human populations is one of the Keystones to understand the controversial history of modern East Asian populations. Jomon people inhabited in the Japanese archipelago from 16,000 years ago, and their origin and the relationship with modern humans have been debated for a long time. To solve these questions, we obtained 20 million base pairs of genomic DNA from a ~4,000-year-old Jomon male tooth, excavated in Sanganji shell mound, Fukushima, Japan. We compared his genetic components with the data of modern worldwide populations. Our major findings are: (1) Sanganji Jomon was very similar with modern East Asians when we compared the worldwide populations in the PCA plot; (2) when only East Asians were compared, Sanganji Jomon was distant from both modern Northeast and Southeast Asians, indicating that Sanganji Jomon people were already isolated from other continental populations for a long time; (3) the Sanganji Jomon male shared more SNP alleles with southern and northern minorities in China than geographically close Han Chinese, implying a complex history of people in China after the divergence between Jomon ancestors and Eurasian continent people; (4) Sanganji Jomon is genetically closer to modern mainland Japanese than continental populations, indicating that some of their components were transmitted to modern Japanese; (5) within Japanese archipelago, Ainu and Ryukyuan (the populations of northern and southern edges of the Japanese archipelago) have more Jomon components than mainland Japanese, indicating that the genetic effect of agricultural people who migrated from the Eurasian continent in and after the Yayoi period is stronger in Mainland Japanese than Ainu and Ryukyuan.

Extensive Gene Gain in Human Brain Evolution

Yong E. Zhang et al.
The genetic changes contributing to the evolution of the human brain have always attracted wide interest. A emerging consensus view is that while there have been no major patterns of genome-wide changes to the coding regions of brain-related genes, cis-regulatory changes of these genes have played a key role. Here, motivated by anecdotal studies of primate-specific genes implicated in brain function, we identified thousands of lineage-specific (primate-specific or rodent-specific) genes by mining syntenic vertebrate genomic alignments and examined the expression profile of these genes in both fetal and adult brains of human and mouse across different transcriptome profiling platforms. We found that an excess of lineage-specific genes are expressed in the early (fetal or infant) developing human brain compared with those in mouse brain. Expression data covering numerous subregions of the developing brain further demonstrate that these young genes are mainly transcribed in the neocortex. They originated in the evolutionary period during which the neocortex was expanding, suggesting the functional association of new genes with this newly evolving brain structure. Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination and also via evolution of regulatory networks, as hinted by the enrichment of primate-specific transcriptional regulators in our dataset. More than that, these ?ndings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach based on functional and evolutionary genomic methods to better annotate these non-conserved genes.

Recent Human Demography Impacts the Architecture of Genetic Disease in Populations but Not Individual Genetic Load

Yuval Simons et al.
Human populations have undergone dramatic changes in population sizes in the past 100,000 years, including a severe bottleneck of non-African populations and recent explosive population growth. There is currently great interest in how these demographic events may have affected the burden of deleterious mutations in individuals and the allele frequency spectrum of disease mutations in populations. Here we use population genetic models to show that--contrary to previous conjectures--recent human demography likely had very little impact on the average burden of deleterious mutations carried by individuals. This prediction is supported by exome sequence data showing that African American and European American individuals carry very similar burdens of damaging mutations. We next considered whether recent population growth has increased the importance of very rare mutations in disease. Our analysis predicts that, even given recent growth, it is unlikely that very rare mutations contribute a large fraction of disease heritability except for diseases that are largely due to strongly deleterious mutations. In summary, demographic history has dramatically impacted patterns of variation in different human populations, but these changes likely had little impact on either genetic load or on the importance of rare variants in most complex traits.

Functional and Population Genetic Analyses of a High-Coverage Neandertal Genome

Fernando Racimo et al.
We have sequenced the genome of a Neandertal from the Altai mountains in Siberia at 50-fold coverage. This Neandertal was located in the same cave as the Denisovan individual, but is phylogenetically closer to Neandertals from Western Eurasia. To avoid confusion, we call this individual the Altai Neandertal. Here we show an assessment of genome data quality and functional and population genetic comparisons with the Denisovan genome and a set of 25 high-coverage modern human genomes. We present an analysis of genes with recent changes in either the modern human lineage or the archaic human lineage (Neandertal+Denisova). We find enrichment for nonsynonymous changes in genes associated with melanosomes in the modern human lineage, and genes associated with particular muscoskeletal morphologies in the archaic human lineage. We utilize a compound deleteriousness scoring that allows us to combine a variety of conservation, regulatory and expression data to rank all modern and archaic-specific single-nucleotide changes and InDels across the genome, and predict which are those that could have been most disruptive in our evolutionary history. Furthermore, we overlap the modern-specific catalog with the top regions of a screen for selective sweeps exclusive to the modern human lineage, and observe enrichments for changes in genes related to ion channel activity, muscle contraction and membrane transport. Finally, we note an excess of ancestral alleles in the Denisovan individual relative to the Altai Neandertal individual, which is strongest at sites where modern humans are fixed derived. We develop an approximate Bayesian computation approach that allows us to test different models, and conclude that gene flow between the Denisovan individual and a more anciently diverged human lineage is most consistent with the patterns observed.

Multiple Episodes of Population Mixture in Southern African History

Joseph K. Pickrell et al.
The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved temporarily or permanently into the region. The influence of these interactions on the genetic structure of current populations remains unclear. Here, using patterns of linkage disequilibrium, we show that there are at least two admixture events in the genetic history of southern African hunter-gatherers and pastoralists: one involving populations related to Niger-Congo-speaking African populations, and one which introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We estimate that at least a few percent of ancestry in the Khoisan is derived from this latter admixture event, which occurred on average 1,200-1,800 years ago. We show that a similar signal of west Eurasian ancestry is present throughout eastern Africa; in particular, we also find evidence for two admixture events in the genetic history of several Kenyan, Tanzanian, and Somali populations, the earliest of which involved populations related to southern Europeans and which we date to approximately 2700 - 3300 years ago. We thus suggest that west Eurasian ancestry entered southern Africa indirectly through eastern Africa. These results demonstrate how large-scale genomic datasets can inform complex models of population movements, and highlight the genomic impact of largely uncharacterized back-to-Africa migrations in human history.

Mechanistic Models of Admixture and Approximate-Approximate-Bayesian Computation 

Noah Rosenberg et al.   

Investigations of the history of migrations that underlie admixed populations often use nonmechanistic admixture models rather than a modeling perspective that incorporates a population-genetic history of admixture built from first principles. We build a general model of admixture that mechanistically accounts for complex admixture processes, considering two source populations that contribute to the ancestry of a hybrid population, potentially with variable contributions across generations. For a random individual in the hybrid population at a given point in time, we study the fraction of admixture originating from a specific one of the source populations. Quite different admixture processes can produce identical mean admixture across individuals, but such processes typically produce different values for the variance of admixture. Interestingly, even without considering sex chromosomes, the variance of admixture for autosomes captures information about sex-specific migration in the contributions of the source populations to the admixed group. To perform inference under the model, we use approximate-approximate-Bayesian computation (AABC), a modification of approximateBayesian computation well-suited to estimation under complex mechanistic models that are computationally intensive to simulate. The model and inference method can contribute to an understanding of the theory and analysis of the history of admixed populations.

Inferring Human Population History and Migration Patterns from Multiple Genome Sequences

Stephan Schiffels, Richard Durbin
The availability of human genomes from populations across the world has given rise to new inference methods that exploit high-coverage sequence data. Among the most influential recent developments is the Pairwise Sequentially Markovian Coalescenct (PSMC) by Li and Durbin, 2011. While PSMC infers the demographic history for times between 20kya and 2mya with high resolution, neither the more recent evolutionary history nor migration patterns across populations can be adressed. Here we present a new method that overcomes both of these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) infers the recent evolutionary history within and across populations only a few thousand years ago and younger. MSMC models the pattern of mutations in multiple genome sequences under the coalescent with recombination. It fits local genealogical trees to the observed pattern, focussing on the first coalescence among any two individuals. We apply our method to the genome sequences from several family trios from the 1000 Genomes project with African, European, Asian and SouthAmerican ancestry. We infer population sizes and migration rates as a function of time with high resolution. In particular, our method resolves the more recent evolutionary history of non-African populations after the out-of-Africa event, such as the peopling of the Americas.

Ancient mtDNA of Tohoku district Jomon

Anthropological Science

Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

Hideaki KANZAWA-KIRIYAMA et al.

Abstract We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

Link

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.

Related:

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.

Link

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.

Link

Body form variation of prehistoric Jomon (Fukase et al. 2012)

Am J Phys Anthropol DOI: 10.1002/ajpa.22112
 
Geographic variation in body form of prehistoric Jomon males in the Japanese archipelago: Its ecogeographic implications 

Hitoshi Fukase et al.

Diversity of human body size and shape is often biogeographically interpreted in association with climatic conditions. According to Bergmann's and Allen's rules, populations in regions with a cold climate are expected to display an overall larger body and smaller/shorter extremities than those in warm/hot environments. In the present study, the skeletal limb size and proportions of prehistoric Jomon hunter-gatherers, who extensively inhabited subarctic to subtropical areas in the ancient Japanese archipelago, were examined to evaluate whether or not the inter-regional differences follow such ecogeographic patterns. Results showed that the Jomon intralimb proportions including relative distal limb lengths did not differ significantly among five regions from northern Hokkaido to the southern Okinawa Islands. This suggests a limited co-variability of the intralimb proportions with climate, particularly within genealogically close populations. In contrast, femoral head breadth (associated with body mass) and skeletal limb lengths were found to be significantly and positively correlated with latitude, suggesting a north-south geographical cline in the body size. This gradient therefore comprehensively conforms to Bergmann's rule, and may stem from multiple potential factors such as phylogenetic constraints, microevolutionary adaptation to climatic/geographic conditions during the Jomon period, and nutritional and physiological response during ontogeny. Specifically, the remarkably small-bodied Jomon in the Okinawa Islands can also be explained as an adjustment to subtropical and insular environments. Thus, the findings obtained in this study indicate that Jomon people, while maintaining fundamental intralimb proportions, displayed body size variation in concert with ambient surroundings. 

Link

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

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. 

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.

ALDER paper and software (Loh et al. 2012)

A new paper has appeared on the arXiv that introduces ALDER, a method for testing for admixture and inferring its parameters (when it happened and the proportions of the two mixing populations). You can get the software from here.

I have already tried it and I can confirm two claims in the paper (i) it's extremely fast, and (ii) it is conservative in the sense that it's test fails even when an f3 test of admixture indicates admixture. Here is a plot of one case where it detected admixture, ASW as CEU+YRI, I got the output on the right, which shows a very clear pattern of exponential decay. I also tried a different experiment using Mozabites as the admixed population. The results are quite interesting:

Test SUCCEEDS (z=10.39, p=2.7e-25) for Mozabite with {CEU30, YRI30} weights

DATA: success (warning: decay rates inconsistent) 2.7e-25 Mozabite CEU30 YRI30 10.39 6.75 11.39 55%  17.45 +/- 1.68 0.00037417 +/- 0.00003187 28.63 +/- 3.84 0.00005311 +/- 0.00000787 16.21 +/- 1.42 0.00023789 +/- 0.00001752

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

Notice that the 1-reference decay using CEU is 28.63 and with YRI it is 16.21, while the 2-reference (both CEU and YRI) is an intermediate 17.45. I believe that this is capturing the same behavior as Jin et al. (2012), according to which:

There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 

This is also what ALDER is telling us, since the decay using CEU is more "abrupt" (hence lack of long segments of admixture that might indicate recent admixture), while that using YRI is less so (and hence recent Sub-Saharan admixture has contributed longer segments).

In any case, enough with my own preliminary experiments. From the paper itself, there are interesting applications of the new methodology for Sardinians, Japanese, and Central African Pygmies:

Both Central African Pygmy populations in the HGDP, the Mbuti and Biaka, show evidence of admixture (Table 1), about 28 +/- 4 generations (800 years) ago for Mbuti and 38 +/- 4 generations (1100 years) ago for Biaka, estimated using San and Yoruba as reference populations (Figure 2A,C). The intra-population heterogeneity is low, as demonstrated by the negligible affine terms. In each case, we also generated weighted LD curves with the Pygmy population itself as one reference and a variety of second references. We found that using populations French, Han, or Yoruba as the second reference gave very similar amplitudes, but the amplitude was significantly smaller with the other Pygmy population or San as the second reference (Figure 2B,D). Using the amplitudes with Yoruba, we estimated mixture fractions of at least 15.9 +/- 0.9% and 28.8 +/- 1.4% Yoruba-related ancestry for Mbuti and Biaka, respectively. 

For Sardinians:

We detect a very small proportion of Sub-Saharan African ancestry in Sardinians, which our ALDER tests identified as admixed (Table 1; Figure 3A). To investigate further, we computed weighted LD curves with Sardinian as a test population and all pairs of the HapMap CEU, YRI and CHB populations as references (Table 2). We observed an abnormally large amount of shared long-range LD in chromosome 8, likely do to an extended inversion segregating in Europeans (PRICE et al. 2008), so we omitted it from these analyses. The CEU–YRI curve has the largest amplitude, suggesting both that the LD present is due to admixture and that the small non- European ancestry component, for which we estimated a lower bound of 0.6+/-0.2%, is from Africa. The existence of a weighted LD decay curve with CHB and YRI as references provides further evidence that the LD is not simply due to a population bottleneck or other non-admixture sources, as does the fact that our estimated dates from all three reference pairs are roughly consistent at about 40 generations (1200 years). Our findings thus confirm the signal of African ancestry in Sardinians reported in MOORJANI et al. (2011). The date, small mixture proportion, and geography are consistent with a small influx of migrants from North Africa, who themselves traced only a fraction of their ancestry ultimately to Sub-Saharan Africa, consistent with the findings of DUPANLOUP et al. (2004).

Moorjani et al. (2011) had estimated 2.9% admixture in Sardinians occurring at 71 +/- 28 generations, so the new results appear to be different, perhaps on account of the the treatment of the chromosome 8 inversion or the ability of ALDER to pick the distance threshold (hard-set at 0.5cM in rolloff) adaptively. Also, note that ALDER is able to estimate admixture proportions based on the amplitude of the weighted LD, whereas in the previous test the proportions were calculated using an F4 ratio test which did not take into account East Eurasian-like gene flow into the CEU population, and considered both CEU and Sardinians as having experienced no Asian-related gene flow.

So it appears that the African admixture in Sardinians is real, but may be both lower and later than previously estimated. In a recent experiment, I "scrubbed" possible segments of African ancestry in Sardinians, and this diminished their African ancestry from 3.1% to 1.8%. If we consider the 1.8% to be the spurious admixture due to Asian-related gene flow into northern Europe, then African admixture in Sardinians will be the remainder 1.3%, and perhaps lower due to the very "intensive" nature of the scrubbing procedure.

globe4 estimates African admixture in Sardinians as 0.8%, with some heterogeneity in its apportionment in 28 different individuals (left), with three individuals appearing as outliers and the remainder randomly distributed around the 0.8% median. The outlier individuals are HGDP01062, HGDP01076, and HGDP01071; the last of these is not included in the curated version of HGDP released by Patterson et al. (2012). ALDER includes a facility for detecting heterogeneity in admixture, but I did not see this particularly discussed in my first scan of the paper. In any case, it now appears that different methods converge on a small African admixture in Sardinians, and the 1200-year old age estimate seems consistent with medieval history.


The paper also deals with the Japanese: 

Genetic studies have suggested that present-day Japanese are descended from admixture between two waves of settlers, responsible for the Jomon and Yayoi cultures (HAMMER and HORAI 1995; HAMMER et al. 2006; RASTEIRO and CHIKHI 2009). We also observed evidence of admixture in Japanese (Table 1), and while our ability to learn about the history is limited by the absence of a close surrogate for the original Paleolithic mixing population, we were able to take advantage of the one-reference inference capabilities of ALDER. We observed a clear weighted LD curve using HapMap JPT as the test population and JPT–CHB weights (Figure 3B). This curve yields an estimate of 45 +/- 6 generations, or about 1,300 years, as the age of admixture. To our knowledge, this is the first time genome-wide data have been used to date admixture in Japanese. As with previous estimates based on coalescence of Y-chromosome haplotypes (HAMMER et al. 2006), our date is consistent with the archaeologically attested arrival of the Yayoi in Japan roughly 2300 years ago (we suspect that our estimate is from later than the initial arrival because admixture may not have happened immediately). Based on the amplitude of the curve, we also obtain a (likely very conservative) genome-wide lower bound of 41 +/- 3% “Yayoi” ancestry using formula (12) (under the reasonable assumption that Han Chinese are fairly similar to the Yayoi population). It is important to note that observation of a single-reference weighted LD curve is not sufficient evidence to prove that a population is admixed, but we did find a pair of references with which the ALDER test identified Japanese as admixed, which, combined with previous work and the lack of any signal of reduced population size, makes us confident that our inferences are based on true historical admixture.

This is a useful application of the idea that you don't need both reference populations to estimate admixture. If a population A experiences gene flow from another B, then A will become more like B over time, and allele frequency differences between A and B will diminish but will continue to reflect differences between the local and introgressing element. This idea was first used by Pickrell et al. (2012), and a new variation of it is used in the current paper.

According to Wikipedia, Japanese skeletons of the Kofun period resemble those of modern Japanese, so perhaps the age estimate is a little younger than the actual period of admixture. In any case, perhaps admixture between populations carrying varying amounts of Yayoi/Jomon ancestry was not instantaneous, so ALDER is not picking up the beginning of a continuous process that lasted for several centuries.

Finally, there is a reference to another paper currently in submission: "MOORJANI, P., N. PATTERSON, P. LOH, M. LIPSON, and OTHERS, 2012 Reconstructing Roma history from genome-wide data. In submission." Given that the Roma likely possess really old West Eurasian admixture related to "Ancestral North Indians", as well as really recent European admixture after they migrated to Europe, and perhaps even intermediate West/Central Asian admixture as they made their way from India to the west, this seems like a very complicated case, involving admixture at different time scales, and between different but related populations, so it will be interesting to see how it will all fit together.

To conclude, ALDER seems like a very practical tool for studying admixture in human populations, so I'm sure it will prove quite useful in the future.

arXiv:1211.0251 [q-bio.PE]

Inference of Admixture Parameters in Human Populations Using Weighted Linkage Disequilibrium

Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K. Pickrell, David Reich, Bonnie Berger

Abstract

Long-range migrations and the resulting admixture between populations have been an important force shaping human genetic diversity. Most existing methods for detecting and reconstructing historical admixture events are based on allele frequency divergences or patterns of ancestry segments in chromosomes of admixed individuals. An emerging new approach harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. Here, we comprehensively develop LD-based inference into a versatile tool for investigating admixture. We present a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods. We de?ne an LD-based three-population test for admixture and identify scenarios in which it can detect admixture that previous formal tests cannot. We further show that we can discover phylogenetic relationships between populations by comparing weighted LD curves obained using a suite of references. Finally, we describe several improvements to the computation and fitting of weighted LD curves that greatly increase the robustness and speed of the computation. We implement all of these advances in a software package, ALDER, which we validate in simulations and apply to test for admixture among all populations from the Human Genome Diversity Project (HGDP), highlighting insights into the admixture history of Central African Pygmies, Sardinians, and Japanese.

Link

1000 Genomes Project Community meeting video

can be found here.

I fast forwarded through a few of the talks. Some interesting tidbits:

1) John Novembre reports on the human autosomal mutation rate on the basis of a very large sample sequenced in a small number of regions; he is using an approach that simultaneously estimates effective size and mutation rate: he gets a median of 1.38x10^-8 per bp per gen. This tends to agree with previously published pedigree estimates, and seems to also be quite lower than a widely used value of 2.5x10^-8 that assumed an ancestral effective population size and an age for the human-chimp divergence. Adoption of the slower rates has implications: if people start using the lower rates that come out of sequencing, population splits will probably have to be redated.

2) Jay Shendure speaks about the future of sequencing; we are now at around $3,500; he expects costs to continue to decline, but we shouldn't be overly optmistic due to technology limits+market forces. I think that the latter may be significant: when a company can offer a better deal than any of its competitors, it has no incentive to drop prices further, even if its own costs are dropping; moreover, demand is going to surge as prices approach the magical $1,000 mark: I know I'll be very tempted to buy at that point myself.

3) Alexander Platt talks about inferring population history using haplotypes. Of interest: during the last 1,000 generations there are more coalescences between Beijing Chinese and Japanese rather than Beijing Chinese and southern Chinese; in more recent times, there are more coalescences between Chinese groups. This makes some sense, if we suppose that -as seems likely- Mongoloids spread north-to-south across China during prehistory; the Japanese are thus linked -in older times- with northern Chinese, both of which are mostly descended from the northern Mongoloids; in more recent times, especially after the emergence of a uniquely Chinese polity and culture, the Chinese tend to marry other Chinese, hence they share more recent common ancestors within the country itself.

Quantifying Yayoi and Jomon ancestry in Japanese

This paper attempts a difficult task: quantifying the relative influence of Yayoi agriculturalists and Jomon hunter gatherers on the population of Japan. While relatives to the early farmers of Japan can be traced to Korea or China, there are no known relatives of the Jomon people. This is different from the case of Latin Americans, where Amerindians have been largely absorbed in the Mestizo population, but populations with minimal European or African admixture persist. It is also different from the case of Indians, where the Ancestral South Indians have also been largely absorbed but their distant relatives in the Andaman Islands still exist.

This is an issue that will come up time and again: in Europe, for example, the hunter-gatherers disappeared thousands of years ago, and the extant population is apparently a mix of the two in proportions that remain to be determined. And, there were probably older, pre-Neolithic, episodes of admixture, as well, when different groups of modern humans expanded across the globa and mixed with older groups of modern humans, or, as it seems increasingly likely, with archaic humans as well.

It is sometimes possible to obtain ancient DNA from pre-contact individuals and determine their contribution to modern populations directly. However, there is still value in trying to extract this signal in the absence of ancient DNA, as was attempted for archaic Africans, and, in the current paper for the pre-agricultural Japanese. Hopefully, the latter can be eventually studied directly, and their genetic makeup can then be compared with their reconstruction in this paper.


The authors link the Jomon to modern Altaic populations of Siberia. There has already been ancient mtDNA work on the Jomon tying them to Siberia. On the other hand, the link to Altaic populations is intriguing, and I am wondering whether the authors' model (which uses Chinese and Koreans as farmer representatives) may not be actually representing as a substratum of the farmers, what may in fact be -at least partially- an Altaic superstratum.

Scientific Reports 2, Article number: 355 doi:10.1038/srep00355

Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data 

Yungang He et al.

The genetic origins of Japanese populations have been controversial. Upper Paleolithic Japanese, i.e. Jomon, developed independently in Japanese islands for more than 10,000 years until the isolation was ended with the influxes of continental immigrants about 2,000 years ago. However, the knowledge of origin of Jomon and its contribution to the genetic pool of contemporary Japanese is still limited, albeit the extensive studies using mtDNA and Y chromosomes. In this report, we aimed to infer the origin of Jomon and to estimate its contribution to Japanese by fitting an admixture model with missing data from Jomon to a genome-wide data from 94 worldwide populations. Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin.

Link

Japanese population substructure (Nishiyama et al. 2012)

PLoS ONE 7(4): e35000. doi:10.1371/journal.pone.0035000

Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

Takeshi Nishiyama et al.

Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating FST among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study.

Link

Chinese, Korean, Japanese (genetic edition)

My 2006 post on facial composites of Chinese, Korean, and Japanese women is, surprisingly, the most widely read single entry of this blog. People still occasionally guess "who is who" in that post, five years later.

As I was going through the list of the Dodecad populations, I realized that there are 5+ participants in each of the Korean, Japanese, and Chinese groups. So, it seemed like a simple exercise to see whether the relatively high success rate of people's guesses could be corroborated using the DNA data.

Below is the MDS plot; there are 9 Chinese, 5 Japanese, 5 Koreans in the Dodecad Project; I have also added 30 HapMap Chinese (CHB) and Japanese (JPT):

Only the first MDS dimension showed deviation from normality according to a Shapiro-Wilk test. Using MCLUST, that dimension was enough (as can be seen from the above figure) to infer the presence of 3 clusters which corresponded to the 3 groups, with 100% correct assignments.

Interestingly, when I did not use the extra HapMap individuals, MCLUST did not split Koreans from Chinese. This goes to show that the absence of apparent structure does not imply absence of structure. The extra Chinese and Japanese individuals helped flesh out the existing structure in these East Asian groups.

Below is the list of the Dodecad populations that are below the 5-individual limit:

Algerian_D	4		East_African_Various_D	3		Greek_Italian_D	2		Belgian_D	1
North_African_Jews_D	4		Danish_D	3		Swiss_German_D	2		Latvian_D	1
Slovenian_D	4		Tunisian_D	3		Szekler_D	2		Estonian_D	1
Mixed_Scandinavian_D	4		Austrian_D	3		Mandaean_D	2		Bangladesh_D	1
Moroccan_D	4		Saudi_D	3		Azeri_D	2		Yemenese_D	1
Serb_D	4		Pakistani_D	3		Czech_D	2		Sri_Lanka_D	1
			Tatar_Various_D	3		Georgian_D	2		Hungarian_D	1
			Palestinian_D	3		Kazakh_D	2		Basque_D	1
			Romanian_D	3					Udmurt_D	1
									Ukrainian_D	1
									Egyptian_D	1

If you belong to one of the above groups (all 4 grandparents) and have tested with either 23andMe or Family Finder, you are especially invited to contact me at dodecad@gmail.com (but do not send data right away!), about possible inclusion in the project. 

For example, in the most recent Clusters Galore analysis, there was a generic "Balkan" cluster. Does this imply that Balkan ethnic groups cannot be distinguished from each other, or that sample sizes are simply not yet sufficient to make manifest the existing structure?

Ancient mtDNA of Hokkaido Jomon

This is a very good paper that I don't have time right now to write a long post about; I will update this entry with some excerpts and/or additional thoughts when I can.

The gist of it is that the prehistoric Jomon people of Japan belonged to mtDNA haplogroups tying them to southeastern Siberia, but some haplogroups present there today were lacking in them. Then, the Ainu seem to have inherited the Jomon gene pool, but their major lineages tie them to the Okhotsk people. So, it seems that the deepest ancestry of Japan is not peculiar to it, but rather an extension of ancient Siberian variation with different population strata attributed to the Jomon, the Ainu, and (probably) the modern Japanese.

AJPA DOI: 10.1002/ajpa.21561

Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia

Noboru Adachi et al.

To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.

Link

The reality of the Altaic language family

Personally I'm not surprised by this; my own look at genomic data has identified an "Altaic" component which peaks at the Turkic Yakut and Tungusic Evenk, and is shared by every Turkic, Mongolic, and Tungusic population available to me. The same component also occurs to some extent among all the Japanese (5) and Korean (4) members of the Dodecad Project, while it is lacking in all the Chinese ones (8).

Of particular interest is the degree of CCM between Indo-European and Semitic languages (Tables 2 and 3). In many of the most geographically distant languages these are less than 10; by comparison, among Semitic languages the are all greater than 20. This seems to be quite in agreement with the idea that Semitic is a Bronze Age language family, Indo-European a Neolithic one.

This impression is strengthened by the fact that CCM between reconstructed proto-languages (e.g. Proto-Iranian and Proto-Slavic = 20) are much higher. Since these proto-languages are a few thousand years closer to the root of PIE than present-day languages, and differences between them are similar to those of Semitic languages, the notion that PIE is a few thousand years older than Proto-Semitic seems quite consistent with the evidence.

Journal of Language Relationship • Вопросы языкового родства • 3 (2010) • Pp. 117–126 • © Turchin P., Peiros I., Gell-Mann M., 2010

Analyzing genetic connections between languages by matching consonant classes

Peter Turchin (University of Connecticut)
Ilia Peiros (Santa Fe Institute)
Murray Gell-Mann (Santa Fe Institute)

The idea that the Turkic, Mongolian, Tungusic, Korean, and Japanese languages are genetically related (the “Altaic hypothesis”) remains controversial within the linguistic community. In an effort to resolve such controversies, we propose a simple approach to analyzing genetic connections between languages. The Consonant Class Matching (CCM) method uses strict phonological identification and permits no changes in meanings. This allows us to estimate the probability that the observed similarities between a pair (or more) of languages occurred by chance alone. The CCM procedure yields reliable statistical inferences about historical connections between languages: it classifies languages correctly for well-known families (Indo-European and Semitic) and does not appear to yield false positives. The quantitative patterns of similarity that we document for languages within the Altaic family are similar to those in the non-controversial Indo-European family. Thus, if the Indo-European family is accepted as real, the same conclusion should also apply to the Altaic family.

Link (pdf)

Dating the origin of Japanese languages with Bayesian phylogenetics

One more success story in the application of Bayesian phylogenetics to language studies. As Nicholas Wade reports:

Researchers studying the various dialects of Japanese have concluded that all are descended from a founding language taken to the Japanese islands about 2,200 years ago. The finding sheds new light on the origin of the Japanese people, suggesting that their language is descended from that of the rice-growing farmers who arrived in Japan from the Korean Peninsula, and not from the hunter-gatherers who first inhabited the islands some 30,000 years ago.

I think it's absolutely fascinating how closely the authors' date for Japonic languages corresponds to the Yayoi period. The Quentin & Atkinson way of doing language age estimation was initially met with derision by the linguistic establishment: part of it was that they did not understand it, part of it that it was introduced with a very controversial topic (Indo-European), and part of it that it triggered a deep-seated skepticism against the application of biologically-inspired methods to the study of culture.

Nonetheless, the method keeps on bringing reasonable results every time it has been applied, and it has now been adopted by many researchers of a quantitative inclination.

From the paper:

Fortunately, recent progresses in phylogenetic methods and their application in studying languages were found to provide adequate solutions for these problems [6]. Accumulating empirical evidence suggests that languages have, astonishingly, gene-like properties in numerous aspects and they also evolve by a process of descent with modification (for review, see [7]). This implies that once the shared innovations among languages are revealed by converting linguistic signals (i.e. presence or absence of homologous words) into discrete binary characters, various stochastic phylogenetic techniques for modelling biological evolution can be used to adequately reconstruct the history of language evolution. During the last decade, therefore, these techniques were quickly adopted to critically examine, and subsequently corroborate, instances of farming/language co-dispersal for Bantu [8], Indo-European [9] and Austronesian speakers [10].

What I find fascinating is the widely different manifestations of the farming/language dispersal phenomenon: the earliest attested one is the expansion of Indo-European languages from Asia Minor ~9,000 years ago, and the latest one the expansion of Japonic languages from mainland Asia ~2,400 years ago. Bantu, Austronesian, Semitic languages fill the void between these two dates. The law-like regularity with which farmers fill lands, transform the landscape, grow in numbers, and start diverging linguistically as they do so is a rare instance of mathematical regularity manifesting itself in the recent history of our species.

But, lest we get too much carried away by admiration for the farming phenomenon, let's tip our sugegasa to the Jomon hunter-gatherers of Japan, who were the partial ancestors of the modern Japanese people, and whose genetic legacy is best preserved among the Ainu (left). Again, from the paper:

If our results are correct, one surprising aspect of prehistoric Japan becomes apparent; the hunter–gatherer population, which settled in Japan around 12 000–30 000 YBP, managed to fend off the farmers for thousands of years until being abolished suddenly and dramatically with the arrival of proto-Japonic-speaking farmers around 2400 YBP. To place this in perspective, it should be noted that the hunter–gatherer societies and their languages in Europe began to be abolished by those of the farmers as early as 8500 YBP [9]. Even some of Japan's closest neighbours such as China had started agriculture since 9000 YBP [1], which progressively brought about fully fledged kingdoms equipped with metal tools fighting each other for political unification. During all this transition outside, the hunter–gatherers of Japan continued to prosper by using simple stone tools and without adopting full-scale agriculture, despite knowledge of cultivation of many crops [12]. There are probably two reasons that explain their unusually long survival. First, the population size of the hunter–gatherers may have been too large to be invaded by nearby farmers. The hunter–gatherer of Japan was perhaps one of the most affluent hunter–gatherers known to humankind, endowed with a large range of plants, animals and sea foods [46]. This vast availability of food resources is probably related to the fact that the world's oldest known pottery was made by the hunter–gatherers of Japan [47]. The development of pottery meant that unlike other hunter–gatherers around the world, they had a means to cook and store the foods that were available abundantly in their environment, and such could have triggered a population explosion to the extent that it prevented the farmers asserting any force over the hunter–gatherers for a long time. The second reason behind their long survival could be that it probably took a few thousand years for the farmers to modify rice, one of their main food sources, to grow in cold climate [48]. The archaeological evidence suggest it was not until around 3500 YBP that rice farming of warm southern China spread to the much colder Korean Peninsular [49], which is thought to be the most recent homeland of proto-Japonic-speaking farmers. A combination of these two factors might have contributed to the unusually long occupation of the hunter–gatherers in Japan.

Proceedings of the Royal Society B doi: 10.1098/rspb.2011.0518

Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages

Sean Lee and Toshikazu Hasegawa

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.

Link