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

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.

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

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

Metric and non-metric variation of Ainu

Am J Hum Biol. 2009 Jul 10.

Metric and nonmetric dental variation and the population structure of the Ainu.

Hanihara T.

Gene flow and genetic drift are important factors affecting geographic variations in human phenotypic traits. In the present study, the effects of gene flow from an outside source on the pattern of within- and among-group variation of the Ainu from Sakhalin Island and three local groups of Hokkaido are examined by applying an R-matrix approach to metric and nonmetric dental data. The comparative samples consist of their ancestral and neighboring populations, such as the Neolithic Jomon, the subsequent Epi-Jomon/Satsumon, the Okhotsk culture people who migrated from Northeast Asia to the northeastern part of Hokkaido during a period 1600-900 years B.P., and modern non-Ainu Japanese. The results obtained by using the census population sizes of the regional groups of the Ainu as an estimate of relative effective population size suggest the possibility of an admixture between the Okhotsk culture people and the indigenous inhabitants in Hokkaido, at least in the coastal region along the Sea of Okhotsk. Such gene flow from Northeast Asian continent may have exerted an effect on the genetic structure of the contemporary Ainu. The present findings indicate that the population structure, as represented by genetic drift and gene flow, tend to be obscured in the results obtained by standard statistical methods such as Mahalanobis' generalized distance and Smith's MMDs. The present extension of the R-matrix approach to metric and nonmetric dental data provide results that can be interpreted in terms of a genetically, archaeologically, and prehistorically suggested pattern of gene flow and isolation.

Link

Ancient mtDNA from Jomon skeletons

American Journal of Physical Anthropology doi: 10.1002/ajpa.20923

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American

Noburu Adachi et al.

Abstract

Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

Link

YAP in 25 ethnic groups from Yunnan China

YAP defines haplogroup DE of the human Y-chromosome phylogeny, which joins together the haplogroup E, found in Negroids and Caucasoids, with haplogroup D, found mainly among Mongoloids, including the archaic Ainu, but also non-Mongoloid populations such as the Andaman Islanders.

The YAP frequencies listed here are, in all probability mostly of haplogroup D.

Sci China C Life Sci. 2003 Apr;46(2):135-140.

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China.

Shi H, Dong Y, Li W, Yang J, Li K, Zan R, Xiao C.

The genetic polymorphisms of Y chromosome at YAP locus in 25 ethnic groups (33 populations) of China were analyzed in a total of 1294 samples. The average YAP+ frequency of the 33 populations was 9.2%, coinciding with published data of Chinese populations. Primi has the highest YAP+ frequency (72.3%), which is also the highest YAP+ among all the eastern Asian populations studied. The YAP+ occurred in 17 populations studied including Tibetan (36.0%), Naxi (37.5% and 25.5%), Zhuang (21.3%), Jingpo (12.5%), Miao (11.8%), Dai (11.4%, 10.0%, 3.3% and 2.0%), Yi (8.0%), Bai of Yunnan (6.7% and 6.0%), Mongol of Inner Mongolia (4.3%), Tujia of Hunan (2.6%), Yao (2.2%) and Nu (1.8%). The other 15 populations are YAP-including Lahu (2 populations), Hani, Achang, Drung, Lisu, Sui, Bouyei, Va, Bulang, Deang, Man and Hui and Mongol of Yunnan and Bai of Hunan. The YAP+ frequencies varied among the different ethnic groups studied, and even different among the same ethnic group living in different geographic locations. Using the genetic information, combined with the knowledge of ethnology, history and archaeology, the origin and prehistoric migrations of the ethnic groups in China, especially in Yunnan Province were discussed.

Link

Craniometry of the Ainu

American Journal of Physical Anthropology

Craniometric variation of the Ainu: An assessment of differential gene flow from Northeast Asia into Northern Japan, Hokkaido

Tsunehiko Hanihara et al.

Abstract

In and after the latest Neolithic period in Japan (B.P. 2,300 years), there were two distinct waves of migration from eastern Asia. One is well known as successive episodes in which indigenous inhabitants of main-island Japan were intruded on by new arrivals with advanced technology, and of a different genetic stock. Another migration of people and culture, identified as the Okhotsk culture, reached the northeastern part of Hokkaido. As opposed to main-island Japan, the morphological continuity from the Neolithic to recent inhabitants in Hokkaido (Ainu) is notable, so that the evidence of admixture easily could have escaped notice. In this study, the effects of gene flow from an outside source on the pattern of among-group variation of Hokkaido Ainu are examined by means of two models. One is the R-matrix model comparing observed and expected craniometric variation for estimating differential external gene flow into a region. The other is a simple simulation model that estimates admixture in a population with two parental populations. The two approaches give similar results. The results suggest the possibility of admixture between the migrants from Northeast Asia, the Okhotsk culture people, and the indigenous inhabitants in Hokkaido during the 5th to 12th centuries A.D., at least in northeastern Hokkaido. Such gene flow may have a certain degree of effect on the genetic structure of recent Ainu. The findings further suggest morphological heterogeneity in Northeast Asia during the Holocene that has relevance for understanding the morphological heterogeneity seen through time in the New World.

Link

AAPA 2008 abstracts

The 2008 meeting of the American Association of Physical Anthropologists will take place this April, and the book of abstracts for the conference is online in pdf format. As usual, there is a great variety of exciting research to be announced in the meeting; here is my sampling thereof:

A seemingly very important new piece of work on Central Anatolia:

O. Gokcumen et al., The Land of the Tired Ox: Ethnogenetic Insights into Rural Central Anatolian Population History

Excerpt: "For example, in one study area in the vicinity of Ankara, we have observed at least four distinct groups based on historical and ethnographic observations. Their self-claimed ancestries trace back to Afsar, Kurdish, Caucasian Cherkess, and Karaman groups. These groups came into the same area from different source regions and at different moments in history. Indeed, our data indicate that there were significant disparities between the paternal and maternal genetic diversity among these groups. These data also allow us to more accurately reconstruct the population history of the study area, as well as begin to provide new perspectives on the regional history of Central Anatolia in relation to historical Turkic invasions and perhaps the Neolithic transition. Finally, we discuss the utility of a more focal and detailed sampling approach for elucidating Anatolian population history."

I can only hope that more researchers will look into historical processes that have shaped modern populations. Too often I see research published which tries to infer human prehistory from modern populations, seemingly oblivious to the complex set of events in historical time that have shaped these populations. Anatolia, so often discussed in the context of the origin of the Neolithic is a prime example of this, as it contains multiple layers of population settlement and ethnic change.

M. C. Dulik et al. Y-chromosome variation in Altaian ethnic groups

Excerpt: "A large portion of all Altaian haplotypes belonged to haplogroup R. Differences in haplogroup frequency between the northern and southern Altaian populations were also observed, with more individuals from northern groups belonging to haplogroups N and Q, and haplogroup C being more prevalent in southern populations. In addition, there were village level patterns of NRY variation, while the overall diversity of NRY haplotypes suggested a significant cultural influence on the partitioning of genetic variation (i.e., patrilocality)."

The three elements involved in Siberian prehistory are indeed haplogroup R, in particular R1a1 which (in my opinion) represents the Western-derived Caucasoid element of likely Iranic affiliation, haplogroups N and Q which represent the Palaeo-Mongoloid element indigenous to Siberia and which has radiated from Siberia to the west (in the case of N) and to the east and into the Americas (in the case of Q), and the Mongoloid proper element which is associated with haplogroup C in this region, and which reflects the Eastern-derived movements of Mongoloid(-influenced) Altaic speakers such as the Mongols.

L. Pipes et al. Analysis of mtDNA in Mongolian Populations

J. Hawks. "Adaptive evolution of human hearing and the appearance of language"

Language requires not only a detailed anatomical and neurological system of language production, but also a highly adapted system of reception. Considering the frequency and amplitude range of human speech, the necessity of perceiving a large number of distinct speakers, the extended life history of humans, the need for children to learn phonemic distinctions at an early age, and the spatial distances covered by vocal communication in humans compared to other primates, it is likely that humans have distinctive auditory adaptations to language. This study tests the hypothesis of selection on the human auditory system, by interspecific genomic comparisons and genome-wide selection scans in living people. A set of hearing-related human genes shows clear signs of recurrent selected substitutions in humans compared to chimpanzees and macaques. These recurrent substitutions may have occurred at any time during human evolutionary history, but they were repeated with several selected variants for each gene. A smaller set of genes shows signs of significant population differentiation within the past 50,000 years, due to recent strong selection. Further, a relatively large set of hearing-related genes have segregating variants under recent strong selection in one or more human populations. These genes reflect continuing selection on hearing within the last 2000—3000 years. Together, these results suggest that human vocal communication exerted repeated selection pressures on the auditory system, that the system of human language continued to evolve during the Late Pleistocene, and that humans may still be adapting to language.

It seems that Hawks et al. paper on accelerated recent human evolution was just the beginning...

B.E. Hemphill. Are the inhabitants of Madaklasht an emigrant Persian population in northern Pakistan?: a dental morphometric investigation.

The answer: "Madaklasters share closest affinities to prehistoric Central Asians and more distant affinities to prehistoric inhabitants of the Iranian Plateau. Such results support the claim that the inhabitants of Madaklast are an intrusive population into Pakistan whose origins most likely may be found in northeastern Afghanistan and Tajikistan."

Someone should look at their genes. Human history is a giant jigsaw puzzle and it is populations that differ from their neighbors and came from somewhere else that allow us to catch a glimpse of the past (in this case prehistoric Central Asia).

N. Seguchi. "Re-analysis of the ainu-samurai hypothesis using population genetic analysis."

The conclusion: "The result shows that the Kamakura ties to the Ainu first, before it ties to the other ethnic Japanese. In addition, the Kamakura group shows more variability,indicating that the Kamakura group may have experienced significantly more gene flow. This indicates the Ainu-derived people who lived in East Japan at that time made a genetic contribution to the warrior class of Kamakura."

J. K. Rilling et al. "Abdominal depth as a principal determinant of human female attractiveness."

Excerpt: "Multiple linear regression analysis revealed that the depth of the lower torso at the umbilicus, or abdominal depth, was the strongest predictor of attractiveness, stronger than either BMI or WHR, and that its impact was significantly greater for video and side view stimuli in which it was clearly visible compared with front and back view stimuli. Women with shallow abdominal depth are more likely to be healthy, fertile and non-pregnant, suggesting that this may be an adaptive male preference that has been shaped by natural selection."

AAPA 2007 abstracts

The 2007 meeting of the American Association of Physical Anthropologists will be held in about a month. As in previous years, here are some interesting abstracts to be presented at the meeting (pdf).

(up to page 94)

Homo floresiensis Cranial and Mandibular Morphology
J.Y. Anderson, University of New Mexico
These results suggest the Flores material does not represent a population derived from Australomelanesians, and do not represent a non-pathological dwarfed population of Homo sapiens. These results do not completely rule out a representation of a microcephalic dwarfed population, at the same time it is suggested possible affinities to earlier hominin groups is equally parsimonious.

Do Qafzeh and Skhūl represent the ancestors of Upper Paleolithic modern humans? A dental perspective.
S.E. Bailey et al.
If these fossils represent the source of early Upper Paleolithic people, there is no need to invoke admixture with Neandertals to explain archaic dental features observed in some early Upper Paleolithic humans.

Ancient Cemetery Social Patterning Project: Ancient DNA in Tirup Cemetery.
L.E. Baker et al.

Reconstructing the settlement history of the central Andes from mitochondrial DNA analyses.
K. Batai et al.
We found that among central Andean ancient and modern population samples, haplogroup B frequencies increased through time, while haplogroup A frequencies declined. At this point, we do not yet have sufficient data to determine whether these patterns indicate different population histories between ancient coastal and modern highland populations, or a larger temporal trend in entire central Andes region

Analysis of Genetic Diversity in Ethnic Populations of Afghanistan
P. Bermudez et al.
The Middle East has the distinction of being a major crossroads of human migration. The genetic diversity of Afghanistan, however, has long remained a missing piece to this rich and complex puzzle. To explore both the diversity within Afghanistan and to understand the relative genetic contributions from various groups throughout the Eurasian continent, buccal swabs were collected from 252 unrelated Afghani men for mitochondrial DNA analysis. Each of these men hailed from
one of four major ethnic groups inhabiting the region: the Pashtun, Hazara, Tajik or
Nooristani. The Indo-Iranian speaking Pashtun represent the largest ethnic group in Afghanistan; the Tajiks have a complex genetic history that likely involves admixture between Turkic groups and smaller distinct ethnic groups within Afghanistan; the Hazara, on the other hand, are thought to represent remnants of Ghengis Khan’s army left behind as it expanded through Asia; and the Nooristani have biological links to populations in northern Pakistan and the
claim of descent from Alexander the Great’s army. All samples were analyzed for HVS1
and SNP variation. In all of these populations, Western Eurasian haplogroups (H, HV, R, J, I, U, X) were most common, with the highest frequency occurring in the Nooristanis, while the remaining East Eurasian haplogroups including D, G, and various other M types. The results of this study will be instrumental in expanding our knowledge of Afghani genetic history, in addition to broadening our understanding of population migrations throughout West and Central Asia.

Dental variation in Holocene Khoesan populations.
W. Black et al.

Are the Koh an indigenous population of the Hindu Kush? II: a dental morphology investigation.

S. Blaylock and B.E. Hemphill

Little is known about the population history of the ethnic groups in Chitral District, Pakistan, an area long been regarded as the “crossroads of Asia.” Some scholars emphasize that the Koh lifeway is the consequence of long-standing indigenous isolation. Others stress the equestrian
tradition among Koh villagers indicate they are descendants of Central Asians who emigrated across the Hindu Kush Mountains during the second millennium BC. To still others, an array of Persian linguistic inclusions indicates the Koh are more recent emigrants from the Iranian Plateau. This investigation tests these hypotheses for Koh origins through assessment of dental
morphology variations of the permanent dentition scored as 17 tooth-trait combination in accordance with the Arizona State University Dental Morphology System in a sample of 134 Kho school children from Chitral City. These data were contrasted with 17 additional samples. Comparisons are in two stages and include cluster analysis, multidimensional scaling and principal coordinates analysis. First, sex-pooled and sex-specific data compared Koh to six contemporary ethnic groups from India. Results indicate the Koh share equidistant affinities to Indo-European speaking west-Central Indian and Dravidianspeaking South Indian ethnic groups.
Second, sex-pooled data compared the Koh to 13 prehistoric samples from Neolithic to Early Iron Age sites located in the Indus Valley, Central Asia and the Iranian Plateau. Results indicate that the Koh share little affinity to prehistoric Indus Valley groups. Rather, the Koh share nearly equal affinities to prehistoric inhabitants of the Iranian Plateau and Central Asia.

A Howells grasp on prehistoric and recent Japan: A precursor to the Kennewick connection.
C. L. Brace, N. Seguchi.
Using many more samples, our results are compatible with what Howells showed for his Japanese comparisons, and,using the neighbor-joining technique, we can go on to show that Kennewick ties with the Ainu who are the descendants of the Jōmon.The Jōmon then are the probable ancestors of
the first inhabitants of the western hemisphere.

Admixture in Mexico City: implications for admixture mapping.
E. Cameron et al.
"The average proportions of Native American, European and West African admixture were estimated as 65%, 30% and 5% respectively."

"In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95% credible interval 3.8 – 22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is
paralleled, and possibly maintained, by socioeconomic stratification."

Intracontinental Distribution of Haplotype Variation: Implications for Human Demographic History.
M.C. Campbell et al.
"These results suggest that diverse African populations were more subdivided with lower levels of gene flow during human history."

Social stratification in a Christian cemetery? An assessment of stress indicators and social status at Anglo-Saxon Raunds.
E.F. Craig, J.L. Buckberry
"The occurrence of statistically more individuals with both cribra orbitalia and tibial periostitis in plain graves rather than graves with stone arrangements, and LEH in plain graves rather than graves with a cover or marker, suggests that individuals buried in more elaborate graves enjoyed better levels of health and may been of higher social status than those buried in plain graves."

Variability of the Stature of the Central European Population from the Neolithic Age to Present
M. Dobisíková, S. Katina, P. Velemínský
The aim of our contribution is to characterize the changes of the stature in adult populations that have lived in Central Europe from the Neolithic period up to the present. Our sample consisted of 802 male and 704 female skeletons. The evaluation was conducted taking into account the demographic structure of the groups studied. We confronted the findings with the living
conditions of the populations known to have a significant impact on human stature, in
addition to genetic factors. We thus considered the socioeconomic status of the populations that might have influenced the quality of nutrition. We focused our attention on the socioeconomic aspect of populations of the early Middle Ages and the recent population. We compared socially higher placed part of the society with socially poorer classes (agricultural groups) (177 male, 178 female) in the early-medieval population of Great Moravia. No statistically significant
differences were found among individual social groups. To calculate the stature of last populations we used the regression equations developed by Breitiger (1937) and Bach (1965). The
calculation was based only on the length of the femur that is directly involved in body length. The impact of the secular trend was evaluated in the recent population. We compared two autopsy skeletal samples from the beginning and ends of the 20th century (107 male, 53 female). Statistically significant differences between them was found. Finally, we proposed regression equations for calculating the stature of the contemporary Czech population usable in forensic practice.

A phylogeographic analysis of haplogroup D5 and its implications for the peopling of East Asia.
M.C. Dulik
While genetic studies have focused on the Altai region of South Siberia as a possible place of origin for Native Americans, it is also possible that it played a similarly significant role in the peopling of East Asia. A Siberian connection to other East Asian populations has already been proposed based on archaeological, linguistic and classical genetic marker evidence. In this study, we examined a rare and ancient haplogroup, D5c, in an effort to elucidate early population movements in East Asia. Previous studies suggested that D5 first emerged in China and
spread northwards from there. However,given the number of D5c individuals (12) and the range of variation in D5 from the Altai region, it is conceivable that this haplogroup instead originated in South Siberia and spread from there during the initial movements of Paleolithic peoples. To est this hypothesis, we obtained complete mtDNA sequences for individuals represented by aplogroups D4 and D5 and acquired additional sequences available through GenBank and published literature. We then analyzed the entire dataset with the reduced median network approach and
phylogeographic modeling. Our results suggest that Southern Siberia did play a
critical role in the spread of the D5 haplogroup. This focus on relatively unique
mtDNA lineages specific to certain populations allowed us to better understand
the processes of ancient settlement and subsequent population movements that helped shape the current genetic landscape of East Asia.

More than meets the eye: LB1, the transforming hominin.
R.B. Eckhard et al.

LB1 is not a microcephalic.
D. Falk1 et al.

Is there biological meaning to “Hispanic” in New Mexico?
H.J.H. Edgar, C.M. Willermet

Establishing the nature of the differences between skull samples from two populations.
S.P. Evans et al.
A sample of 1188 skulls from the Romano-British site at Poundbury shows differences from the 18th century sample of 822 skulls from Spitalfields. Both sites are in the south of England, but 1400 years apart in time. The differences between the sites could be due to immigrations over time and/or to adaptation to the environment. The aim of the study was to establish the nature of the differences, in particular the relative importance of genetic and acquired traits.
Frequencies of 22 selected non-metric traits in juvenile, female and male skulls were analysed. Initial logistic regression analyses established that there was a substantial difference between the two sites and between juveniles and adults, with some sexual dimorphism. The modified mean
measure of divergence, used to calculate overall distances between the groups, showed the juvenile groups to be closer to each other than to adults from their respective sites. Across sites, males were most distant from each other. The largest distance was between Spitalfields juveniles and males. Principal coordinate analysis, followed by a jackknife stability analysis, revealed a pattern indicating that this came about through growth and adaptation. Omitting traits in turn, procrustes methods were used to identify the most influential, all of which
were acquired through ageing or lifestyle. Without these traits there was no significant
difference between the two juvenile groups and no sexual dimorphism. These results show the importance of the behavioural environment in determining morphology, and the resilience of populations to genetic change.

Peopling of the Pacific: resolving the controversy.
J.S. Friedlaender et al.
"Our survey of mitochondrial DNA, Ychromosome, and over 600 short tandem repeat polymorphisms and 200 insertiondeletions from over 40 Pacific populations indicates Polynesians have their genetic
origins to both Melanesian and Taiwanese (Southeast Asian) populations in significant degrees. In Island Melanesia, there is a small but clear ancient genetic footprint in certain Oceanic-speaking populations (i.e., linguistically related to Polynesian). The survey results underscore the extraordinary diversity of Island Melanesian populations from one language group to another, and from island to island. This is the result of the small sizes of the populations and the very long extent of modern human settlement there (over 30,000 years)."

Multivariate studies of cranial form: the impact of Howells' research on defining Homo sapiens.
J.B. Gaines et al.

Demographic simulations of the admixture between foragers and farmers in central European Neolithic.
P. Galeta, J. Bruzek.

William White Howells: A physical anthropologist in the making.
E. Giles

The relationship of Nubians with their neighbors, the Egyptians.
By, K. Godde.

The Phylogeography of Haplogroup N1a
Gokcumen O et al.
Recent studies have revealed a complex geographic distribution of haplogroup N1a. This rare and distinctive lineage is widely distributed across Eurasia and Africa, but always found at very low frequencies. However, despite its rarity, the genetic diversity within N1a has remained relatively high (h=0.9605). The reduced median network of N1a haplotypes not only reflects
this level of diversity, but also exhibits several relatively well-defined branches. The
distribution of N1a is intriguing because of revealing previously unrecognized connections between populations. What makes N1a even more interesting is the prevalence of this lineage in ancient European populations. Haak et al. (2005) found that 25% of their European Neolithic
samples belonged to N1a and dated to ~5000 BCE, whereas the frequency of this lineage in contemporary Europeans is only ~0.2%. In addition, an Iron Age skeleton from Kazakhstan had an N1a haplotype, suggesting the existence of this lineage in the Altai Republic in ~500BCE (Ricaut et al. 2004). Indeed, we found several haplogroup N1a mtDNAs in indigenous Altaians and Altaian Kazakhs. To further elucidate the phylogeography of this lineage in Central Asia, we sequenced the whole mtDNA genomes of our N1a haplotypes, and analyzed the resulting data with several quantitative methods and simulation programs to estimate their expansion times and spatial
distribution in Eurasia. Our findings suggest that there are two well-defined sublineages
within N1a, and that the dispersal of this haplogroup could be associated with the Neolithic expansion and with prehistoric interactions between Central Asian and European populations.


Understanding human races: the retreat of neutralism.
Henry Harpending
Discussion and debate about human races has been dominated for decades by neutral theory and statistics. Since this literature never posed a real question, it has never produced an answer. Lewontin's 1972 paper with its claim that a value of 1/8 of a statistic like Fst is “small” and that this means that human race differences are insignificant is a staple of our textbooks. Recently geneticists have had a closer look and pointed out that Fst of 1/8 describes differences among sets of half sibs and few claim that half sibs are insignificantly related. Anthony Edwards has shown that the significance of differences is in the correlation structure of a large number of traits, again denying the Lewontin assertion that human differences are small. Alan Templeton in 1998 claimed that human races were less differentiated that races of some other large mammals, but he compared human nuclear DNA statistics with statistics from mtDNA in the other species. An appropriate comparison shows that human are more, not less, differentiated than other large mammal species. Since neutral differences are a passive
record of demographic history they are not very significant for issues of functional biology. Newly available data sources allow us to study the natural selection of race differences instead of their drift. It appears that there is a lot of ongoing evolution in our species and the loci under strong selection on different continents only partially overlap. Human race differences may be increasing rapidly.

Acceleration of adaptive evolution in modern humans.
J. Hawks and G. Cochran
Humans vastly increased in numbers during the past 40,000 years. Recent surveys of human genomic variation have suggested a large surplus of recent positive selection, indicated by excess linkage disequilibrium and skewed SNP frequency spectra. We applied estimates of prehistoric and historic population sizes to estimate the importance of population growth in explaining the number of recent adaptive mutations. Our estimates are consistent with genomic evidence in suggesting that the rate of generation of positively selected genes has increased as much as a hundredfold during the past 40,000 years.

Do skeletal features reflect this genomic evidence of selection? Under positive
selection, rapid appearance of new variants during the terminal Pleistocene and early
Holocene would cause maximal phenotypic change during the last 2000-4000 years. We compared original and published series of Holocene cranial data from Europe, Jordan, Nubia, South Africa, and China, in addition to Late Pleistocene samples from Europe and West Asia, to test the hypothesis that the genomic acceleration in positive selection correlates with phenotypic evolution during this time period. A constellation of features in the face and cranial vault, notably including endocranial volume, changed globally during this time period and documents common patterns of selection in different regions. Holocene changes were similar in pattern and chronologically faster than those at the archaic-modern transition, which themselves were rapid compared to earlier hominid evolution. In genomic and craniometric terms, the origin of modern humans was a minor event compared to more recent evolutionary changes.

Patterns of admixture in Mexican Americans assessed from 101,150 SNPs.
M.G. Hayes et al.
"No significant differences were observed between the 10 subsets, allowing us to average the admixture estimates across the subsets: 68% European, 27% Asian (as a proxy for Native American), and 6% African."

Gender, wealth, and status in Bronze Age Central Asia: a dental pathology investigation.
B.E. Hemphill.

Sahara passage: the post-glacial recolonisation of North Africa by mitochondrial L* haplotypes.
AD Holden. P Forster.

Secular trends of the European male facial skull from the Migration Period to the present.
E. Jonke et al.
We examined secular trends in the facial skull over three Central European samples spanning more than 13 centuries. Data are 43 conventional cephalometric landmark points for samples dating from 680–830 CE, from the mid-19th Century, and from living Austrian young adult males. Methods of geometric morphometrics demonstrate shape differences across the samples, and also
differences in allometry. There is a stronginteraction between these, so that group mean differences are different for small and large individuals (equivalently, allometry is
different from period to period). The oldest sample, from the Migration Period, exhibits
allometric features that may possibly be Turkic. There are implications for the
craniofacial biologist interested in growth trends or growth predictions in ethnically
mixed populations. There are also implications for the discussion concerning the morphology of the Avars (an ethnic group of probably Central Asian origin who conquered large parts of Central Europe during the Migration Period and who interbred with other incoming groups after their conquest by Charlemagne), and also the relation of these findings to current thinking on gnathic reduction trends.

Roman Gladiators - The Osseous Evidence.
F. Kanz, K. Grossschmidt

Paternal heritage for the Indonesian peoples.
T. M. Karafet et al.

Feeding the children: Isotopic evidence for weaning practices in the ancient Greek colony of Apollonia (5th-2nd centuries BC).
C. Kwok, A. Keenleyside.

Misconceptions about the postcranial skeleton of Homo floresiensis.
S.G. Larson et al.

A comparison of mitochondrial DNA and Y chromosome DNA variation on Manus Island.
K.E. Latham et al.

Dual origins of the Japanese

Very interesting paper on Y-chromosomal variation in Japan and neighboring regions. Haplogroup frequencies:


Japan 259; northeast Asia (NEA) 441; Southeast Asia (SEA) 683; central Asia (CAS) 419; south Asia (SAS) 496; Oceania (OCE) 209.

Interesting quote, which again confirms the East Asian origin of the NO clade:

Haplogroup N is the fourth most common haplogroup in Japan (1.5%) and is found only among mainland Japanese (Table 1). Clades N and O share a common node in the Y chromosome tree that is defined by marker M214. While NO* chromosomes are extremely rare, they are found in Japan at higher frequency than elsewhere in our survey, albeit only at 2.3%.

Also of interest is the detection of Caucasoid haplogroups I,J,G,R in some of the studied populations. In some cases these may represent recent admixture, but they may also represent older events, especially in the case of haplogroups J,G which are rare in most former European colonial powers.

J Hum Genet. 2005 Nov 18; [Epub ahead of print]

Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.

Hammer MF, Karafet TM, Park H, Omoto K, Harihara S, Stoneking M, Horai S.

Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning ~2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan ~20,000 and ~12,000 years ago, respectively, while haplogroup O-47z began its expansion only ~4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.

Link

Three phylogeographic anomalies

In the last few years, the phylogeography of many clades of the human mtDNA and Y-chromosome systems has been adequately resolved, but there still exist several big remaining puzzles.

The first one is that of mtDNA haplogroup X, which has been addressed in a recent paper. This is a very ancient clade, which is found at low frequencies almost everywhere, and is divided into two subclades: X1 is found mainly in eastern and northern Africa, whereas X2 is found in northern Africa and everywhere else, including Native Americans. It is interesting that the X2 seems to have spread after the Last Glacial Maximum, and the Native American clade, X2a was an "early split": today's Siberian X2 seem to be recently derived from Western Eurasia than those of the ancient trek which brought X2 into the New World. It is fascinating that X2 was brought into the New World by some ancient expansion that did not leave any traces in the genes of modern inhabitants of the likely routes.

The second great puzzle is mtDNA haplogroup M1 which occurs in East and North Africa, West Asia and Southern Europe, but not apparently anywhere else. M1 is a branch of the mainly Asian macrohaplogroup M, which is of great antiquity in Asia and likely originated there. According to a recent abstract, Holden et al. indicate that M1 is found at high frequencies in East and Northern Africa but not in Sub-Saharan Africa, and hint that it may be linked to the Afro-Asiatic language family. This suggestion is reasonable, and in my opinion the correspondence between M1 and Y-chromosome haplogroup E3b is quite remarkable throughout the broad peri-Mediterranean region, with E3b also reaching high frequencies in Afro-Asiatic speakers.

The third puzzle is that of Y-chromosome haplogroup DE defined by the YAP mutation. The E clade of YAP encompasses the great majority of African Y-chromosomes, and is clearly split into a subclade, E3b which has a peri-Mediterranean distribution similar to that of the aforementioned M1, and all the rest, almost exclusively limited to Sub-Saharan Africa. The "brother" of E, is haplogroup D, which is found in such peoples as the Andamanese, the Tibetans, and the Ainu. At present it seems reasonable that E originated somewhere in Africa, but the origin of D is far from certain, as it is now found in certain "fringe" populations, but also in low frequencies among many Asians. Perhaps, D had a much more prevalent distribution in the past, but the expansion of later successful lineages, such as O, the main haplogroup found in East Asians today overwhelmed those earlier Asian populations. What about YAP itself? Dit it originate in Asia, where its D descendants are located, or in Africa, where its E descendants are? As late as 2003, we don't know, and no new research has appeared to shed light on this problem.

mtDNA haplogroup M originated in Asia

The origin of mtDNA haplogroup M has been matter of some controversy. A reader alerts me to a new paper which conclusively demonstrates its Asian origin, by sequencing 24 full mitochondrial genomes, which allowed the researchers to reconstruct its phylogeny.

Haplogroup M is found mainly in Asia, and its various subclades make up the great majority of Mongoloid and Indian lineages. It is also found in the Near East, the Caucasus, Asia Minor and Southern Europe, in addition to Egypt, and Ethiopia. A particular clade of M, named M1 is the main one found in the "western" range of its range, and it was hypothesized that its high frequency and diversity in Ethiopia may indicate an East African origin for the entire M.

However, M1 is geographically limited in Africa, while it is very widespread in Asia. If M originated in Africa, then it must have done so at a very old time, because it would have to spread throughout Asia and the New World. However, it would be difficult to explain how M crossed such a vast distance and yet failed to reach other populations of Africa except Ethiopians, Egyptians and a few others.

The new study has dated the Indian clades of M and shown them to be very old. This clinches the argument in favor of the Asian origin.

Haplogroup M is one of those mtDNA lineages which does not correspond well to present-day racial groups, as it spans Mongoloid, Indian Caucasoid and Paleoindian, as well as Ethiopid and various Caucasoid groups in lesser frequency. This paper represents significant progress in our understanding of human prehistory.

Now, let's wait to see what the origin of other "peculiar" lineages turns out to be, such as the mysterious YAP (Y-chromosome haplogroup DE) clade which is found in peoples such as Greeks, East Africans, Andamanese, Tibetans and Ainu...

BMC Evolutionary Biology 2005, 5:26 doi:10.1186/1471-2148-5-26

Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages


Revathi Rajkumar et al.

Abstract (provisional)

Background

Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.

Results

The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.

Conclusions

This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M macrohaplogroup.

Link

Sexual dimorphism in 26 populations

Using the same data as before, I calculate the sexual dimorphism in 26 craniometric samples from around the world.

There are many ways to express sexual dimorphism, i.e., differences between men and women, which extend to both size and shape. I will limit myself to the simple measure of the average (over all traits) ratio of the male to the female mean (over all individuals).

Zulu 1.06
Egypt 1.06
Atayal 1.06
Zalavar 1.06
San 1.07
Hainan 1.07
Tasmanian 1.07
Moriori 1.07
Norse 1.07
Lake Alexandrina 1.07
Tolai 1.07
Dogon 1.08
Berg 1.08
Philippine 1.08
Yauyos 1.08
Teita 1.08
Buriat 1.08
Santa Cruz Island 1.08
North Kyushu 1.08
Ainu 1.09
Andaman Islands 1.09
Arikara 1.09
Hokkaido 1.09
Mokapu 1.09
Easter Island 1.09
Guam 1.09

So, it appears that these populations do not differ by much from each other in terms of sexual dimorphism. But, if we look at individual traits, the situation is much different. Men and women are most dimorphic (in decreasing order) in terms of their glabella projection (1.52), supraorbital projection (1.25), simotic subtense (1.2), mastoid breadth (1.18), mastoid height (1.16). So, it turns out that men and women can be quite different in terms of some traits, but not in terms of others.

Who is the most diverse of them all?

Here is the diversity ranking of Howells' 28 human populations based on 45 cranial measurements. The numbers are the average population standard deviation (for each population over all 45 measurements) as a percentage of the average human standard deviation (for all groups over all 45 measurements). In parentheses, the racial cluster of each population according to my previous analysis.

Guam 76.8 (Mongoloid)
Andaman Islands 76.8 (Andamanese)
Santa Cruz Island 76.9 (Americanoid)
Zalavar 77.0 (Caucasoid)
Yauyos 77.8 (Americanoid)
Easter Island 77.9 (Polynesoid)
Arikara 78.2 (Americanoid)
Moriori 78.2 (Polynesoid)
Tolai 78.3 (Australoid)
Lake Alexandrina 78.3 (Australoid)
Atayal 78.8 (Mongoloid)
Hainan 79.2 (Mongoloid)
Anyang 79.9 (Mongoloid)
Norse 80.1 (Caucasoid)
North Kyushu 80.6 (Mongoloid)
Mokapu 80.9 (Polynesoid)
Ainu 81.3 (Ainu)
Eskimo 81.6 (Eskimo)
Egypt 82.8 (Caucasoid)
Phillipine 84.2 (Mongoloid)
Dogon 84.5 (Negroid)
Teita 84.8 (Negroid)
Zulu 85.1 (Negroid)
Berg 85.3 (Caucasoid)
Tasmanian 85.3 (Australoid)
Hokkaido 85.5 (Mongoloid)
Buriat 87.0 (Mongoloid)
San 89.0 (Capoid)

Phylogenetic systematics and the existence of human "races"

In phylogenetic systematics one of the necessary preconditions for the recognition of a taxon is its monophyletic status. In other words, members of a taxon must share common descent, and not just relative similarity as in phenetics.

If three groups of organisms A, B, C are such that A and B are more similar to each other than they are to C, then phenetics would consider classifying A and B in one taxon and C in another. By contrast, phylogenetics would try to establish whether A and B share common characters derived from an ancestor that was not an ancestor of C. If it turns out e.g., that B and C have such an ancestor, then B and C should be grouped together, even though B is closer to A than to C.

It has long been established that human beings can be grouped into clusters corresponding to major "continental" populations. This has been achieved using cranial traits, classical polymorphisms, as well as more recently large numbers of microsatellites. Therefore, we are justified in thinking about the existence of human races in the phenetic sense.

However, recent advances in phylogeography, especially based on uniparentally transmitted markers on the Y chromosome and mtDNA have shown that human continental populations which correspond to phenetic races such as "Caucasoids", "Negroids", "Mongoloids", etc. do not correspond to monophyletic groups.

For example, almost 9 out of 10 Ainu trace their paternal lineage to an ancestor who has also fathered approximately 9 out of 10 Moroccans and South African Bantu. That man, who first carried the YAP mutation, lived either in Asia or Africa, and yet his descendants belong to three of the major human races.

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids).

Thus, despite the close proximity between, e.g., Spain and Morocco, and the genetic and phenotypic similarity of their inhabitants, who are considered to belong to the Caucasoid race, it is the case that phylogenetically, Spanish Basques and Mayan Indians share recent ancestry not shared by Moroccan Berbers, and conversely, Moroccan Berbers share recent ancestry with South African Bantu not shared by Basques.

Should we then acknowledge the existence of a "YAP race", or a "P race" on the basis of these observations? Not at all, since by examining other phylogenetically informative systems, e.g., mtDNA, it turns out that Basques and Moroccans are phylogenetically linked to the woman founder of mtDNA haplogroup N, while Ainu and Mayans are linked to a woman founder of mtDNA haplogroup M.

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies.

We may still however speak of human races as clusters of biological similarity, or as ecotypes, if we keep in mind the understanding that the commonly recognized races are not phylogenetically justified.

Racial Affinities of Prehistoric East Africans

Afrocentrists and Nordicists alike tend to assert that early East Africans were "Negroid". Since East Africa was the source of multiple migrations of early humans out of Africa, this allows the former to assert a "Negroid" stage in the evolution of Eurasians, or to postulate a later (mythological) stage of "Negroid" East African culture-bearers. Nordicists of the other hand, dissatisfied with the paucity to non-existence of genuine Sub-Saharan African genetic markers in Southeastern Europe have insinuated that Y-haplogroup E3b which originated in East Africa 26ky ago is "Negroid" or that mtDNA haplogroup M1 which according to some also originated in East Africa in Paleolithic times is also "Negroid".

W.W. Howells' study of world craniometric variation is especially relevant to the racial affinity of East Africans before the expansion of Negroids into the region. Howells studied some 2,500+ skulls from 28 populations of recent Homo sapiens based on 57 metric variables [1], including skulls from the Teita tribe of East Africa. These recent Teita tribesmen (and women) clustered with other Sub-Saharan Africans, indicating that (as is obvious) recent Kenyans belong primarily to the Negroid race.

Howells then studied prehistoric East Africans and other humans from around the world to determine whether or not they show any affinities with living races [2]. He did this to examine whether the morphological complexes of modern races can be discerned in remote times. Using the same multivariate approach he studied the Elmenteita, Nakuru and Willey's Kopje skulls from Kenya. His conclusion was that there is no racial continuity between recent Negroid East African skulls and these prehistoric remains, as the following passage illustrates ([2, p. 41]:

(...) The DISPOP [Dienekes: DISPOP is Howells' program] results here are not indicative of anything, except a general non-African nature for all these skulls. Display of POPKIN distances (infra) reinforces this and seems to find nearer neighbors among such more generalized populations as Peru, Guam, or Ainu, but also Europeans or even Easter Island.

Remembering that the Teita series (Bantu speakers of southeastern Kenya), and the recent East African skulls in table 4 above, do clearly exhibit African affiliations, it is fair to say, contra Rightmire, that there seems to be no clear continuity here in late prehistory. On the broad scale, looking at an "Out-of-Africa" scenario, one would expect that, in some region between southern and northeastern Africa, some differentiation would have been taking place within a Homo sapiens stock, evolving into something beginning to approximate later Sub-Saharan peoples on the one hand, and evolving in another direction on the other hand. East Africa would be a likely locale for appearance of the latter. So anyone is welcome to argue that this is what Elmenteita et al. are manifesting. The ensuing picture for East Africa, that is to say, would later have beeen changed through replacement by the expansion of Bantu or other "Negroid" tribes.

[1] Howells WW (1989) Skull shapes and the map: craniometric analyses in the dispersion of modern Homo. Peabody Museum Papers 79:1-189.
[2] Howells WW (1995) Who's Who in skulls: ethnic identification of crania from measurements. Peabody Museum Papers 82:1-108.