Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture.

Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.

Unique characteristics of the Ainu population in Northern Japan.

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

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.

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.

Molecular systematics and evolution of the recently discovered "Parnassian" butterfly (Parnassius davydovi Churkin, 2006) and its allied species (Lepidoptera, Papilionidae).

The nucleotide sequence of 807 bp of the mtDNA-ND5 locus of Parnassius davydovi (Churkin, S. 2006. A new species of Parnassius Latreille, 1804, from Kyrgyzstan (Lepidoptera, Papilionidae). Helios (Moskow) 7,142-158), was determined. This butterfly was unexpectedly discovered recently in Kyrgyzstan, and we wished to shed light on its molecular phylogenetic relationship to other Parnassian butterflies, as well as to the related taxa in the subfamily Parnassiinae of the family Papilionidae. Using the ML method with the GTR+I+Gamma model, we inferred the phylogenetic tree for 60 Parnassius individuals together with materials of the related genera in the subfamily Parnassiinae (Hypermnestra, Archon, Luehdorfia, Bhutanitis, Allancastria, Zerynthia and Sericinus) with Papilio machaon as an out-group. It was found that P. davydovi is a distinct species most closely related to P. loxias in clade VI among the eight clades, or species groups of Parnassius. The morphological diversity in the form of sphragis, the attachment to the female abdomen formed by the male during copulation, is characteristic to this clade, and we inferred the order of emergence of the different sphragis forms during evolution. Attempts to estimate the divergence times between related taxa were also made. It was inferred that the relatively rapid radiation of Parnassian butterflies started at about 24 MYA BP, while P. davydovi diverged from P. loxias at about 10 MYA BP.

Characteristics of the beta-globin gene cluster haplotypes of three Han Chinese populations at Beijing, Xi'an, and Kunming as compared with those of other Asian populations.

Haplotype frequencies of the beta-globin gene cluster of Han Chinese at Beijing, Xi'an, and Kunming were estimated, and their mutual genetic relationships were examined and compared to those of Buryats, Khalkhs, Evenkis, Oroqens, Koreans, and Colombian Amerindians. A major 5' subhaplotype (5' to the delta-globin gene), a major 3' subhaplotype (in and 3' to the beta-globin gene), and a major haplotype (combination of 5' and 3' subhaplotypes) are represented as + - - - -, - +, and + - - - - - +, respectively, and found in all three Han Chinese. A rare 5' subhaplotype, - - - - -, which is one of the possible ancestral types, was found only in Han Chinese at Kunming at low frequency (0.013), and a rare 3' subhaplotype, - -, was also observed in all three Han Chinese at low frequencies (0.009-0.014). The present haplotype frequency study suggested that the highest genetic affinity was found between Han Chinese at Beijing and those at Xi'an; the next highest was between Han Chinese at Beijing and Koreans, followed by that between Han Chinese at Beijing and Khalkhs, then that between Han Chinese at Xi'an and those at Kunming or Khalkhs, and finally that between Han Chinese at Beijing and those at Kunming. A genetic boundary between northern and southern Han Chinese was not evident in the present study.

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

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 approximately 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 approximately 20,000 and approximately 12,000 years ago, respectively, while haplogroup O-47z began its expansion only approximately 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.

Beta-globin gene cluster haplotype frequencies in Khalkhs and Buryats of Mongolia.

Beta-globin gene cluster haplotype frequencies of 169 Khalkhs and 145 Buryats were estimated, and their characteristics were compared with those of Evenkis, Oroqens, Koreans, Japanese, and three Colombian Amerindian groups. The present study suggests that Colombian Amerindians diverged first from Asian populations and then Buryats diverged from other Asian populations.

Phylogeny and evolution of butterflies of the genus Parnassius: inferences from mitochondrial 16S and ND1 sequences.

Phylogenetic relationships among species of the genus Parnassius and its related taxa were analyzed by comparing nucleotide sequences of mitochondrial 16S ribosomal RNA (504 sites) and NADH-dehydrogenase subunit 1 (469 sites). In the phylogenetic trees, Parnassius was found to be most closely related to Hypermnestra helios, whereas Archon apollinus, which has been classified in the tribe Parnassiini together with Parnassius and Hypermnestra, was more closely related to members of the tribe Zerynthiini. Within the Parnassius clade, six major clades corresponding to species groups were well supported, although the phylogenetic relationships among them were not clear. Although the results of the present study were in agreement with those of a previous phylogenetic study based on mitochondrial NADH-dehydrogenase subunit 5 sequences, our study strongly supported a close relationship between Parnassius and Hypermnestra, which was not well supported in the previous study.

Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages.

The Ainu, a minority ethnic group from the northernmost island of Japan, was investigated for DNA polymorphisms both from maternal (mitochondrial DNA) and paternal (Y chromosome) lineages extensively. Other Asian populations inhabiting North, East, and Southeast Asia were also examined for detailed phylogeographic analyses at the mtDNA sequence type as well as Y-haplogroup levels. The maternal and paternal gene pools of the Ainu contained 25 mtDNA sequence types and three Y-haplogroups, respectively. Eleven of the 25 mtDNA sequence types were unique to the Ainu and accounted for over 50% of the population, whereas 14 were widely distributed among other Asian populations. Of the 14 shared types, the most frequently shared type was found in common among the Ainu, Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Moreover, analysis of genetic distances calculated from the mtDNA data revealed that the Ainu seemed to be related to both the Nivkhi and other Japanese populations (such as mainland Japanese and Okinawans) at the population level. On the paternal side, the vast majority (87.5%) of the Ainu exhibited the Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), which were distributed only in the Japanese Archipelago in this analysis. On the other hand, the Ainu exhibited no other Y-haplogroups (C-M8, O-M175*, and O-M122*) common in mainland Japanese and Okinawans. It is noteworthy that the rest of the Ainu gene pool was occupied by the paternal lineage (Y-haplogroup C-M217*) from North Asia including Sakhalin. Thus, the present findings suggest that the Ainu retain a certain degree of their own genetic uniqueness, while having higher genetic affinities with other regional populations in Japan and the Nivkhi among Asian populations.

Molecular systematics and evolution of the "Apollo" butterflies of the genus Parnassius (Lepidoptera: Papilionidae) based on mitochondrial DNA sequence data.

Sequences of 777 bp of mtDNA-ND5 locus were determined in order to shed light on the molecular systematics and evolution of the "Apollo" butterflies. Examined were nearly all of about 50 species of the genus Parnassius, together with seven species of the allied genera in the subfamily Parnassiinae (Papilionidae). The NJ and the MP phylogenetic trees show that the "Apollos" constitute a monophyletic group, comprising a number of cluster groups probably reflecting a relatively rapid radiation in evolution. The clusters of species-groups denoted I-VIII correspond to those species-groups recognized on the basis of morphological characters. Our findings will also help understand the biological relationships among several species or subspecies on which the classical taxonomy is in dispute. The unexpected finding is that among the samples of allied genera compared, Hypermnestra helios appears to be the most closely related to the "Apollos", despite morphological and behavioral dissimilarity. Furthermore, in contrast to the previous higher taxonomy, Archon apollinus which is classified in the tribe Parnassiini was found genetically closer to the tribe Zerynthiini, raising a taxonomic controversy.

Characteristic beta-globin gene cluster haplotypes of Evenkis and Oroqens in north China.

Haplotype frequencies of the beta-globin gene cluster were estimated for 114 Evenkis and 81 Oroqens from northeast China, and their characteristics were compared with those in Japanese, Koreans, and three Colombian Amerindian groups of South America (Wayuu, Kamsa, and Inga tribes). A major 5' subhaplotype (5' to the delta-globin gene) was + - - - - in Evenkis, whereas + - - - -, - + + - +, and - + - + + were the major subhaplotypes in Oroqens. One possible candidate for an ancestral 5' subhaplotype, - - - - -, was found in one Evenki (0.5%) and three Oroqen chromosomes (2.0%). They were observed as heterozygous forms for + ---- and -----. Major haplotypes were +-----+, + -----+-, and + - - - - + + in Evenkis, whereas they were +-----+,-++-+-+, +----+-, and -+-++-+ in Oroqens. The lowest Nei's genetic distance values of Evenkis or Oroqens based on the 5' subhaplotype frequency distributions were observed in relation to the Wayuu or Koreans, respectively, but those of Evenkis and Oroqens based on the haplotype frequency distributions were found in relation to Koreans.

Growth hormone binding protein, insulin-like growth factor-I and short stature in two pygmy populations from the Philippines.

The molecular basis and biochemical mediators of genetic growth propensity and adult height achievement in the general population are largely unknown. Pygmies represent one extreme of the height spectrum that may provide important clues regarding this issue. Previous studies in pygmies from Africa and Papua-New Guinea have shown decreased serum levels of growth hormone binding protein (GHBP), the circulating ectodomain of the growth hormone receptor (GHR). By inference, a similar limitation in tissue GHR expression has been assumed to be responsible for the partial growth hormone (GH) resistance observed in African pygmies. It is not clear how generalizable this concept is to other populations. To address this question, we studied two pygmy populations from the Philippines (Aeta and Mamanwa people) that are unrelated to the African pygmies. Serum GHBP and IGF-I levels were significantly decreased in both pygmy populations, compared to normal-statured Philippino controls. The results, together with previous observations in African and New Guinean pygmies, indicate that short stature is associated with low serum GHBP levels in pygmy populations of diverse origins and in different parts of the world. This strengthens the tentative postulate that the GHBP/GHR system plays an important role in the genetic and perhaps nutritional determination of adult stature in humans. Molecular genetic studies of the GHR gene in various pygmy populations may shed further light on the mystery of pygmy short stature.

Three major lineages of Asian Y chromosomes: implications for the peopling of east and southeast Asia.

DNA variation on the non-recombining portion of the Y chromosome was examined in 610 male samples from 14 global populations in north, east, and southeast Asia, and other regions of the world. Eight haplotypes were observed by analyses of seven biallelic polymorphic markers ( DYS257(108), DYS287, SRY(4064), SRY(10831), RPS4Y(711), M9, and M15) and were unevenly distributed among the populations. Maximum parsimony tree for the eight haplotypes showed that these haplotypes could be classified into four distinct lineages characterized by three key mutations: an insertion of the Y Alu polymorphic (YAP) element at DYS287, a C-to-G transversion at M9, and a C-to-T transition at RPS4Y(711). Of the four lineages, three major lineages (defined by the allele of YAP(+), M9-G, and RPS4Y-T, respectively) accounted for 98.6% of the Asian populations studied, indicating that these three paternal lineages have contributed to the formation of modern Asian populations. Moreover, phylogenetic analysis revealed three monophyletic Asian clusters, which consisted of north Asian, Japanese, and Han Chinese/southeast Asian populations, respectively. Coalescence analysis in the haplotype tree showed that the estimated ages for three key mutations ranged from 53,000 to 95,000 years, suggesting that the three lineages were separated from one another during early stages of human evolutionary history. The distribution patterns of the Y-haplotypes and mutational ages for the key markers suggest that three major groups with different paternal ancestries separately migrated to prehistoric east and southeast Asia.