Zebu Cattle Are an Exclusive Legacy of the South Asia Neolithic

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: Implications for the peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen fo

Y chromosome haplotypes reveal prehistorical migrations to the Himalayas

By using 19 Y chromosome biallelic markers and 3 Y chromosome microsatellite markers, we analyzed the genetic structure of 31 indigenous Sino-Tibetan speaking populations (607 individuals) currently residing in East, Southeast, and South Asia. Our results showed that a T to C mutation at locus M122 is highly prevalent in almost all of the Sino-Tibetan populations, implying a strong genetic affinity among populations in the same language family. Furthermore, the extremely high frequency of H8, a haplotype derived from M122C, in the Sino-Tibetan speaking populations in the Himalayas including Tibet and northeast India indicated a strong bottleneck effect that occurred during a westward and then southward migration of the founding population of Tibeto-Burmans. We, therefore, postulate that the ancient people, who lived in the upper-middle Yellow River basin about 10,000 years ago and developed one of the earliest Neolithic cultures in East Asia, were the ancestors of modem Sino-Tibetan populations.

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 125 and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus. (C) 2010 Published by Elsevier Ltd.

中国西部大气和雪冰黑碳及其传输过程研究

Glaciers in west China are the sources of the major great rivers in Asia, and the solid water resources are crucial to China and South Asia. Black carbon (BC) results in very complex climate effects not only in the atmosphere, but accelerates the melting after its deposit on the surface of snow/ice. As the main distributed area of glaciers in China, the Tibetan Plateau (TP) and Xinjiang region are abutted by South Asia, Central Asia, and Russia, and east China, and the atmospheric environment would be influenced by the BC emitted from these regions. Whereas, the BC’s temporal and spatial distributions for concentration in the mid and top troposphere in west China, its transport, and its radiative forcing after deposited on the snow/ice surface are not well understood at the present. In the field, we collected samples from surface snow, snow pits, ice core, and aerosol in the glaciers, analyzed BC content mainly by the thermo-oxidized method in the laboratory, and discussed temporal and spatial distributions for BC concentrations in glaciers, the transport, and its impacts on the environment. Several conclusions were derived as follows: 1_Spatial distribution and the impact on albedos for BC concentrations in snow/ice: the BC concentrations in the surface snow for the investigated glaciers could be placed in areas, the Tianshan Mountains ＞ the central TP ＞ the Pamirs ＞ the Qilian Mountians ＞ the Himalayas. This distribution could be attributed to the elevation of the glaciers, the topography of the TP, and more regional emissions. Probably significant impacts on the albedos of the glacier surface could be caused by BC deposits, and the estimated reduced albedos on the glaciers are 9.8% (the Zhadang glacier), 8.7% (the Miao’ergou Riverhead No.3 glacier), and 6.8% (the Kuitun River Haxilegen No.48 glacier), and 6.2% (the Dongkemadi glacier), and 5.3% (the La’nong glacier), and 4.2% (the Muztagata glacier), etc. 2_The temporal variance of BC concentrations in ice of the East Rongbuk Glacier (ERG) and its climatic implications: major cations and anions (e.g., SO42- and Ca2+) concentrations in aerosols during summer monsoon seasons showed their close relationships with the sources of air masses, in which the variance of SO42- concentrations suggested the atmospheric environment over the ERG was significantly influenced by the aerosols from South Asia. BC record based on an ice core suggested its deposit was dominantly transported by monsoons in summers and by westerlies in other seasons, and the BC from South Asia in summers dominated the varying trend of its concentrations in the ice core and caused higher concentrations in summers than those in other seasons. In the past 50 yrs, BC concentrations showed fluctuations, whereas showed an increasing tread in the most recent decade, and exceeded 50 μg kg-1 in the summer of 2001; correspondingly, the radiative forcing caused by BC showed an increasing trend since 1990s, and exceeded 4.5 W m-2 in the summer of 2001. 3_Cabonaceous aerosols in the Nam Co region: organic carbon (OC) concentration accounted for ～95% and BC for ～5% in the total carbonaceous aerosol concentration, which was significantly influenced by summer precipitations. OC was dominantly derived from fossil fuel burning and BC from both fossil fuel and biomass burning. Trajectory analysis and aerosol optical depth suggested the atmospheric environment in the Nam Co region was most probably influenced by the emissions from South Asia. The potential source regions of air pollutants in the Nam Co regions in summers might be Bangladesh and east India, and in winters might be the Indo-gangetic basin. The scavenging ratio of atmospheric BC by rainfalls was less than those at other sites. West China is a less-developed region for industry, where BC concentrations in the atmosphere and snow/ice could be significantly influenced by the emissions from the abutted regions with rising industries (South Asia, Central Asia, and Russia). For example, snow/ice BC concentrations in the glaciers of the Parmirs, the Tianshan Mountains, and the Qilian Mountains in the northeast margin of the TP might be more influenced by the emissions from Centrial Asia (transported by the westerlies), those in the glaciers of the Himalayas might be more influenced by the emissions from South Asia (transported by the monsoons and the westerlies), and atmospheric carbonaceous aerosols might also be more influenced by the emissions from South Asia (transported by the monsoons and the westerlies). The BC concentrations in some glaciers might cause significant impacts on the albedos for the glaciers, and therefore enhanced the radiative forcings, for example, the ERG. The research on the relationships among atmospheric and snow/ice BC and its radiative forcing, variance of snow cover, mass balance of glaciers, and climate forcing would be needed in future.

中国大陆及邻区地震活动背景、环境触发与地震预测研究

This dissertation that includes most of the P. PH.D research work during 2001~2002 covers the large-scale distribution of continental earthquakes in mainland China, the mechanism and statistic features of grouped strong earthquakes related to the tidal triggering, some results in earthquake prediction with correlativity analysis methods, and the flushes from the two strong continental earthquakes in South Asia in 2001. Mainland China is the only continental sub-plate that is compressed by collision boundaries at its two sides, within which earthquakes are dispersive and distributed as seismic belts with different widths. The control capability of the continental block boundaries on the strong earthquakes and seismic hazards is calculated and analyzed in this dissertation. By mapping the distribution of the 31282 ML:3s2,0 earthquakes, I found that the depth of continental earthquakes depend on the tectonic zonings. The events on the boundaries of relatively integrated blocks are deep and those on the new-developed ruptures are shallow. The average depth of earthquakes in the West of China is about 5km deeper than that in the east. The western and southwestern brim of Tarim Basin generated the deepest earthquakes in mainland China. The statistic results from correlation between the grouped M7 earthquakes and the tidal stress show that the strong events were modulated by tidal stress in active periods. Taking Taiwan area as an example, the dependence of moderate events on the moon phase angles (￡>) is analyzed, which shows that the number of the earthquakes in Taiwan when D is 50° ,50° +90° and 50° +180° is more than 2 times of standard deviation over the average frequency at each degree, corresponding to the 4th, 12th and 19th solar day after the new moon. The probability of earthquake attack to the densely populated Taiwan island on the 4th solar day is about 4 times of that on other solar days. On the practice of earthquake prediction, I calculated and analyzed the temporal correlation of the earthquakes in Xinjinag area, Qinghai-Tibet area, west Yunnan area, North China area and those in their adjacent areas, and predicted at the end of 2000 that it would be a special time interval from 2001 to 2003, within which moderate to strong earthquakes would be more active in the west of China. What happened in 2001 partly validated the prediction. Within 10 months, there were 2 great continental earthquakes in south Asia, i.e., the M7.8 event in India on Jan 26 and M8.1 event in China on Nov. 14, 2001, which are the largest earthquake in the past 50 years both for India and China. No records for two great earthquakes in Asia within so short time interval. We should speculate the following aspects from the two incidences: The influence of the fallacious deployment of seismic stations on the fine location and focal mechanism determination of strong earthquakes must be affronted. It is very important to introduce comparative seismology research to seismic hazard analysis and earthquake prediction research. The improvement or changes in real-time prediction of strong earthquakes with precursors is urged. Methods need to be refreshed to protect environment and historical relics in earthquake-prone areas.

珠穆朗玛峰东绒布冰川表层雪中的气候和环境记录

Snow chemistry research helps to found the basis of studying ice cores. Samples of fresh snow and snow pits were collected from East Rongbuk Glacier on the north slope of Mt. Qomolangma during October, 2002. Major soluble ions (Na~+, NH_4~+, K~+, Mg~(2+), Ca~(2+), Cl~-, NO_3~- and SO_4~(2-)) andδ~(18)O were detected for analysis. Source analysis showed that major sources contributing to the snow chemistry in Mt. Qomolangma region are remote Asian dust and salt lake dust, sea-salt aerosols from Indian monsoon, local rock-mineral dust, human activities and natural atmospheric procedures. Principal factor analysis indicated that high-concentration group was dominated by continental dust with little oceanic source, indicating continental or local precipitation, while the low group dominated by oceanic aerosols indicated oceanic precipitation. Local mineral dust was a minor a source characterized mainly by Ca~(2+), Mg~(2+) contribution. Ammonia related mainly with continental dusts and nitrogen-circulation processes in the atmosphere, it also had a peculiar source should be seasonal agriculture activities in the south Asia. Nitrate showed bad correlations with other ions for its special chemical characteristics. δ~(18)O and major soluble ions displayed obvious seasonal variations. The summer precipitation had very low ion loadings and relatively lower heavy oxygen isotope from the Indian Ocean with occasionally ion peaks formed by local evaporation. While the winter and spring precipitation had high ion loadings and δ~(18)O value for the great amount of continental dust and evaporated vapors. Frequent fluctuations of δ~(18)O and ion concentration occur during the transitional period, indicating alternated precipitations by various air mass types. Ion concentration in snow from the Qomolangma region is comparable with from the Antactica, representing relatively pure background of atmospheric environment on earth. While the high concentration is close to the glaciers' located near the major sources of Asian dust. Compared with the snow chemistry of South Slope of Mt. Qomolangma, the North Slope has lower sea-salt ion concentration during summer monsoon and higher concentration of all major ions during pre- and post-monsoon period due to it's special geophysical location.

Mitochondrial Cytochrome b Sequence Variations and Population Structure of Siberian Chipmunk (Tamias sibiricus) in Northeastern Asia and Population Substructure in South Korea

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we

Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal 'Out-of-Africa' route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started similar to 40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia similar to 15 KYA and finally made its way to the Americas. Journal of Human Genetics (2010) 55, 428-435; doi:10.1038/jhg.2010.40; published online 7 May 2010

Population structure and history in East Asia

Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.

Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea

Amblycipitidae Day, 1873 is an Asian family of catfishes (Siluriformes) usually considered to contain 28 species placed in three genera: Amblyceps (14 spp.), Liobagrus (12 spp.) and Xiurenbagrus (2 spp.). Morphology-based systematics has supported the monophyly of this family, with some authors placing Amblycipitidae within a larger group including Akysidae, Sisoridae and Aspredinidae, termed the Sisoroidea. Here we investigate the phylogenetic relationships among four species of Amblyceps, six species of Liobagrus and the two species of Xiurenbagrus with respect to other sisoroid taxa as well as other catfish groups using 6100 aligned base pairs of DNA sequence data from the rag1 and rag2 genes of the nuclear genome and from three regions (cyt b, COL ND4 plus tRNA-His and tRNA-Ser) of the mitochondrial genome. Parsimony and Bayesian analyses of the data indicate strong support for a diphyletic Amblycipitidae in which the genus Amblyceps is the sister group to the Sisoridae and a clade formed by genera Liobagrus and Xiurenbagrus is the sister group to Akysidae. These taxa together form a well supported monophyletic group that assembles all Asian sisoroid taxa, but excludes the South American Aspredinidae. Results for aspredinids are consistent with previous molecular studies that indicate these catfishes are not sisoroids, but the sister group to the South American doradoid catfishes (Auchenipteridae + Doradidae). The redefined sisoroid clade plus Bagridae, Horabagridae and (Ailia + Laides) make up a larger monophyletic group informally termed "Big Asia." Likelihood-based SH tests and Bayes Factor comparisons of the rag and the mitochondrial data partitions considered separately and combined reject both the hypothesis of amblycipitid monophyly and the hypothesis of aspredinid inclusion within Sisoroidea. This result for amblycipitids conflicts with a number of well documented morphological synapomorphies that we briefly review. Possible nomenclatural changes for amblycipitid taxa are noted.

Population genetic structure of crimson snapper Lutjanus erythropterus in East Asia, revealed by analysis of the mitochondrial control region

The population genetic structure of the crimson snapper Lutjanus erythropterus in East Asia was examined with a 427-bp hypervariable portion of the mtDNA control region. A total of 262 samples were collected and 75 haplotypes were obtained. Neutrality tests (Tajima's and Fu's) suggested that Lutjanus erythropterus in East Asia had experienced a bottleneck followed by population expansion since the late Pleistocene. Despite the low phylogeographic structures in mtDNA haplotypes, a hierarchical examination of populations in 11 localities from four geographical regions using analysis of molecular variance (AMOVA) indicated significant genetic differentiation among regions (Phi(CT) = 0.08564, p < 0.01). Limited gene flow between the eastern region (including a locality in the western Pacific Ocean and two localities in the East Sea) and three geographic regions of the South China Sea largely contributed to the genetic subdivision. However, comparisons among three geographic regions of the South China Sea showed little to no genetic difference. Populations of Lutjanus erythropterus in East Asia are inferred to be divided into two major groups: an eastern group, including populations of the western Pacific Ocean and the East Sea, and a South China Sea group, consisting of populations from northern Malaysia to South China. The results suggest that fishery management should reflect the genetic differentiation and diversity in East Asia. (c) 2006 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.

Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers

Crassostrea ariakensis is an important aquacultured oyster species in Asia, its native region. During the past decade, consideration was given to introducing C. ariakensis into Chesapeake Bay, in the United States, to help revive the declining native oyster industry and bolster the local ecosystem. Little is known about the ecology and biology of this species in Asia due to confusion with nomenclature and difficulty in accurately identifying the species of wild populations in their natural environment. Even less research has been done on the population genetics of native populations of C. ariakensis in Asia. We examined the magnitude and pattern of genetic differentiation among 10 wild populations of C. ariakensis from its confirmed distribution range using eight polymorphic microsatellite markers. Results showed a small but significant global theta (ST) (0.018), indicating genetic heterogeneity among populations. Eight genetically distinct populations were further distinguished based on population pairwise theta (ST) comparisons, including one in Japan, four in China, and three populations along the coast of South Korea. A significant positive association was detected between genetic and geographic distances among populations, suggesting a genetic pattern of isolation by distance. This research represents a novel observation on wild genetic population structuring in a coastal bivalve species along the coast of the northwest Pacific.