The Emerging Limbs and Twigs of the East Asian mtDNA Tree

Toomas Kivisild, Helle-Viivi Tolk, Jüri Parik, Yiming Wang,Surinder S.     

A reappraisal of complete mtDNA variation in East Asian families with hearing impairment

In a number of recent studies, we summarized the obvious errors and shortcomings that can be spotted in many (if not most) mitochondrial DNA (mtDNA) data sets published in medical genetics. We have reanalyzed here the complete mtDNA genome data published in various recent reports of East Asian families with hearing impairment, using a phylogenetic approach, in order to demonstrate the persistence of lab-specific mistakes in mtDNA genome sequencing in cases where those caveats were (deliberately) neglected. A phylogenetic reappraisal of complete mtDNAs with mutation A1555G (or G11778A) indeed supports the suggested lack of association between haplogroup background and phenotypic presentation of these mutations in East Asians. In contrast, the claimed pathogenicity of mutation T1095C in Chinese families with hearing impairment seems unsupported, basically because this mutation is rather basal in the mtDNA phylogeny, being specific to haplogroup M11 in East Asia. The roles of other haplogroup specific or associated variants, such as A827G, T961C, T1005C, in East Asian subjects with aminoglycoside-induced and non-syndromic hearing loss are also unclear in view of the known mtDNA phylogeny.     

East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis

Understanding the complex origin of domesticated populations is of vital importance for understanding, preserving and exploiting breed genetic diversity. Here, we aim to assess Asian contributions to European traditional breeds and western commercial chickens for mitochondrial genetic diversity. To this end, a 365‐bp fragment of the chicken mtDNA D‐loop region of 16 Dutch fancy breeds (113 individuals) was surveyed, comprising almost the entire breed diversity of The Netherlands. We also sequenced the same fragment for 160 commercial birds representing all important commercial types from multiple commercial companies that together represent more than 50% of the worldwide commercial value. We identified 20 different haplotypes. The haplotypes clustered into five clades. The commonest clade (E‐clade) supposedly originates from the Indian subcontinent. In addition, both in commercial chicken and Dutch fancy breeds, many haplotypes were found with a clear East Asian origin. However, the erratic occurrence of many different East Asian mitochondrial clades indicates that there were many independent instances where breeders used imported exotic chickens for enhancing local breeds. Nucleotide diversity and haplotype diversity analyses showed the influence of the introgression of East Asian chicken on genetic diversity. All populations that had haplotypes of multiple origin displayed high inferred diversity, as opposed to most populations that had only a single mitochondrial haplotype signature. Most fancy breeds were found to have a much lower within‐population diversity compared to broilers and layers, although this is not the case for mitochondrial estimates in fancy breeds that have multiple origin haplotypes.     

mtDNA polymorphism in East Asian Populations,with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.     

Harvesting the fruit of the human mtDNA tree

Human mitochondrial DNA (mtDNA) studies have entered a new phase since the blossoming of complete genome analyses. Sequencing complete mtDNAs is more expensive and more labour intensive than restriction analysis or simply sequencing the control region of the molecule. But the efforts are paying off, as the phylogenetic resolution of the mtDNA tree has been greatly improved, and, in turn, phylogeographic interpretations can be given correspondingly greater precision in terms of the timing and direction of human dispersals. Therefore, despite mtDNA being only a fraction of our total genome, the deciphering of its evolution is profoundly changing our perception about how modern humans spread across our planet. Here we illustrate the phylogeographic approach with two case studies: the initial dispersal out of Africa, and the colonization of Europe.     

The Anthropology of Korea: East Asian Perspectives

The Anthropology of Korea: East Asian Perspectives. Mutsuhiko Shima and Roger L. Janelli. eds. Osaka: National Museum of Ethnology, 1998. 237 pp.     

Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution

In the past decade, mitochondrial DNA (mtDNA) of 826 representative East Asians and Papuans has been typed by high-resolution (14-enzyme) restriction fragment length polymorphism (RFLP) analysis. Compared with mtDNA control region sequencing, RFLP typing of the complete human mitochondrial DNA generally yields a cleaner phylogeny, the nodes of which can be dated assuming a molecular clock. We present here a novel star contraction algorithm which rigorously identifies starlike nodes (clusters) diagnostic of prehistoric demographic expansions. Applied to the Asian and Papuan data, we date the out-of-Africa migration of the ancestral mtDNA types that founded all Eurasian (including Papuan) lineages at 54,000 years. While the proto-Papuan mtDNA continued expanding at this time along a southern route to Papua New Guinea, the proto-Eurasian mtDNA appears to have drifted genetically and does not show any comparable demographic expansion until 30,000 years ago. By this time, the East Asian, Indian, and European mtDNA pools seem to have separated from each other, as postulated by the weak Garden of Eden model. The east Asian expansion entered America about 25,000 years ago, but was then restricted on both sides of the Pacific to more southerly latitudes during the Last Glacial Maximum around 20,000 years ago, coinciding with a chronological gap in our expansion dates. Repopulation of northern Asian latitudes occurred after the Last Glacial Maximum, obscuring the ancestral Asian gene pool of Amerinds.     

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.     

Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.     

The future of South East Asian rainforests in a changing landscape and climate

With a focus on the Danum Valley area of Sabah, Malaysian Borneo, this special issue has as its theme the future of tropical rainforests in a changing landscape and climate. The global environmental context to the issue is briefly given before the contents and rationale of the issue are summarized. Most of the papers are based on research carried out as part of the Royal Society South East Asia Rainforest Research Programme. The issue is divided into five sections: (i) the historical land-use and land management context; (ii) implications of land-use change for atmospheric chemistry and climate change; (iii) impacts of logging, forest fragmentation (particularly within an oil palm plantation landscape) and forest restoration on ecosystems and their functioning; (iv) the response and resilience of rainforest systems to climatic and land-use change; and (v) the scientific messages and policy implications arising from the research findings presented in the issue.     

Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations.

Central Asia is a vast region at the crossroads of different habitats, cultures, and trade routes. Little is known about the genetics and the history of the population of this region. We present the analysis of mtDNA control-region sequences in samples of the Kazakh, the Uighurs, the lowland Kirghiz, and the highland Kirghiz, which we have used to address both the population history of the region and the possible selective pressures that high altitude has on mtDNA genes. Central Asian mtDNA sequences present features intermediate between European and eastern Asian sequences, in several parameters-such as the frequencies of certain nucleotides, the levels of nucleotide diversity, mean pairwise differences, and genetic distances. Several hypotheses could explain the intermediate position of central Asia between Europe and eastern Asia, but the most plausible would involve extensive levels of admixture between Europeans and eastern Asians in central Asia, possibly enhanced during the Silk Road trade and clearly after the eastern and western Eurasian human groups had diverged. Lowland and highland Kirghiz mtDNA sequences are very similar, and the analysis of molecular variance has revealed that the fraction of mitochondrial genetic variance due to altitude is not significantly different from zero. Thus, it seems unlikely that altitude has exerted a major selective pressure on mitochondrial genes in central Asian populations.     

Nuclear and mtDNA phylogenies of the Trimeresurus complex: implications for the gene versus species tree debate

Phylogenies based on mitochondrial DNA (mtDNA) may represent gene trees that may not be congruent with the equivalent species tree. One solution to this problem is to include additional, independent loci from the nuclear genome. Sequence data from the seventh intron of the beta-fibrinogen gene were generated for 25 specimens of vipers, including 8 nominal species of the Trimeresurus complex of Asian pit vipers. Phylogenetic trees were generated using maximum-parsimony and maximum-likelihood methods. The taxonomic level at which the intron provided significant phylogenetic information was examined and the trees were compared to those produced from previously obtained mtDNA cytochrome b sequences. A variety of different approaches (separate analyses, conditional data combination, and consensus) were used in an attempt to provide a sound organismal phylogeny based on both nuclear and mtDNA data sets. We discuss the implications for the gene tree-species tree debate and its particular relevance to medically important organisms.     

Growing-season precipitation since 1872 in the coastal area of subtropical southeast China reconstructed from tree rings and its relationship with the East Asian summer monsoon system

Tree rings from temperate zones of the world have provided abundant palaeo- ecological and paleo-hydroclimatic information. However, tree rings from subtropical to tropical regions remain relatively scarce, which greatly limit our fully understanding about the climate change issues. In the present work, tree-ring-width (TRW) measurements of Masson pine from Fujian province, the coastal area of subtropical southeast China were successfully crossdated and a TRW STD chronology was developed from 1854 to 2012. Significantly positive correlation was identified between the tree rings and April–November total precipitation (r = 0.71, p < 0.01). The reconstructed April–November precipitation exhibited two comparatively wet (1876–1886 and 1957–1962) and one comparatively dry (1986–2004) periods. An evident drying trend since 1959 was seen and it was mitigated after 1993. Most of the extreme low-precipitation years in the reconstruction were supported by the historical records. As revealed by the spatial correlation patterns, our precipitation reconstruction was also consistent with other hydroclimatic records along the coastal areas of southeast China, proving its ability to capture the large-scale hydrological signal in southeast China (mainly refers to the south of the middle-lower reaches of Yangtze River). The reconstructed precipitation showed significant correlation with the East Asian summer Monsoon (EASM) index. Moreover, it also indicated simultaneous variation with the monsoon precipitation in North China on a decadal scale, implying that growing season precipitation variations in both regions were influenced by the EASM strength. This work highlights the potential of using tree-ring width to reconstruct precipitation in subtropical southeast China, while the relevant issues about precipitation variation in this region is far from resolved.     

The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs.

Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged approximately 50,000 years ago.     

Law of the Sea Issues Between the United States and East Asian States

The United States is the sole superpower in the contemporary world and its role in the development of the law of the sea cannot be ignored. Although having not yet acceded to the U.N. Convention on the Law of the Sea, the United States has contributed to the development of the international law of the sea in numerous ways, including responding to the so-called excessive maritime claims in East Asia and creating new rules of maritime enforcement. This article assesses this recent U.S. practice.