Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn,Penaeus monodon

Surveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo-West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (pi) was greatest in Indonesia (pi averaged 0.05), less in the Philippines and Australia (pi averaged 0.01), and markedly less in the southeast African and the West Australian populations (pi averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo-West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.     

Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from Southeast Asia

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.     

The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India

A 9-base-pair (bp) deletion located between the lysine tRNA (MTTK) and COII (MTCOX*2) genes in the human mitochondrial genome is a valuable marker for tracing population relationships. Previous research has shown that the 9-bp deletion is associated with two major clusters of control region sequences; one occurs in sub-Saharan Africa, while the other is associated with Asian populations and populations of Asian origin. We surveyed 898 individuals from 16 tribal populations in India and found 6 individuals with the 9-bp deletion. Sequences of the first hypervariable segment (HV1) of the mtDNA control region from these 9-bp deletion-bearing mtDNAs were compared to those previously reported from Asian and African populations. Phylogenetic analysis indicates three distinct clusters of tribal Indian 9-bp deletion mtDNA types. One cluster, found in northeast India, includes southeast Asian and Indonesian mtDNA types. The remaining two clusters appear to have unique origins in southern India. These data provide further evidence of past migrations from Asia into the northeast corner of the Indian subcontinent.     

Duffy blood groups and malaria in the Ao Nagas in Nagaland, India.

Blood samples from 324 malarial patients and 384 healthy individuals belonging to the Ao tribal community have been examined for Duffy blood group systems. The complete absence of Duffy-negative individuals among the Ao Nagas suggests that selection for resistance to vivax malaria by means of the Duffy-negative phenotype has not been available in the southeast Asian regions including the Ao Nagas.     

Haplotype diversity and distribution pattern of Oecophylla smaragdina (Fabricius) (Hymenoptera,Formicidae) in Bangladesh based on mitochondrial COI genes

Climatic oscillation often have influenced the present distribution and intraspecific genetic diversity Oecophylla smaragdina through its wide range of geographical distribution. Previous phylogeographic study of Asian weaver ant population denotes the evidence of distribution of Indian types in Indian, Sri Lanka and SE Asian types in South Asian countries including Bangladesh. However, recent phylogenetic analysis reveals the overlapping distribution of the Indian and South East Asian clades of O. smaragdina in Bangladesh. The present study aims to identify the haplotypes and it’s networking in Bangladesh based on extensive materials. Sampling was executed according to zonation of 5 areas, demarcated by 3 main rivers during the years 2013 to 2018. Adult O. smaragadina workers were collected from 71 colonies of 67 localities belonging to 47 districts of Bangladesh. A total of 25 haplotypes were identified in Bangladesh comprises 13 and 12 of Indian and SE Asian types, respectively from 93 sequences of Cytochrome c oxidase subunit I (COI) gene of 639 bp. The geographical distribution of this haplotype reveals that the Indian haplotypes are mostly located at the western part of Bangladesh while SE Asian haplotypes were dominated in the Eastern part of the country. Central part of Bangladesh has overlapped with the mixture of both Indian and SE Asian haplotypes. The results of the haplotype network give the evidence of recent expansion of O. smaragdina population in Bangladesh and clarify the evidence of presence of many missing haplotypes in refugee.     

Investigating Cultural Evolution Using Phylogenetic Analysis: The Origins and Descent of the Southeast Asian Tradition of Warp Ikat Weaving

The warp ikat method of making decorated textiles is one of the most geographically widespread in southeast Asia, being used by Austronesian peoples in Indonesia, Malaysia and the Philippines, and Daic peoples on the Asian mainland. In this study a dataset consisting of the decorative characters of 36 of these warp ikat weaving traditions is investigated using Bayesian and Neighbornet techniques, and the results are used to construct a phylogenetic tree and taxonomy for warp ikat weaving in southeast Asia. The results and analysis show that these diverse traditions have a common ancestor amongst neolithic cultures the Asian mainland, and parallels exist between the patterns of textile weaving descent and linguistic phylogeny for the Austronesian group. Ancestral state analysis is used to reconstruct some of the features of the ancestral weaving tradition. The widely held theory that weaving motifs originated in the late Bronze Age Dong-Son culture is shown to be inconsistent with the data.     

Soybean germplasm pools in Asia revealed by nuclear SSRs

Soybean was domesticated in East Asia, where various kinds of landraces have been established as a result of adaptation to different environments and the diversification of food cultures. Asia is thus an important germplasm pool of soybean. In order to evaluate the genetic structure of the Asian soybean population, we analyzed allelic profiles at 20 simple-sequence repeat (SSR) loci of 131 accessions introduced from 14 Asian countries. The SSR loci produced an average of 11.9 alleles and a mean gene diversity of 0.782 in the accessions tested. Quantification theory III analysis and cluster analysis with the UPGMA method clearly separated the Japanese from the Chinese accessions, suggesting that the Japanese and Chinese populations formed different germplasm pools. The Korean accessions were involved in both germplasm pools, whereas most of the accessions from southeast and south/central Asia were derived from the Chinese pool. Relatively high genetic diversity and the absence of region-specific clusters in the southeast and south/central Asian populations suggest that soybean in these areas has been introduced repeatedly and independently from the diverse Chinese germplasm pool. The present study indicates that the two germplasm pools can be used as exotic genetic resources to enlarge the genetic bases of the respective Asian soybean populations.     

Genetic origins of the Japanese: A partial support for the dual structure hypothesis

Based on the morphological characteristics of the skull and teeth, Hanihara ([1991] Japan Review 2:1–33) proposed the “dual structure model” for the formation of modern Japanese populations. We examine this model by dividing it into two independent hypotheses: 1) the Upper Paleolithic population of Japan that gave rise to the Neolithic Jomon people was of southeast Asian origin, and 2) modern Ainu and Ryukyuan (Okinawa) populations are direct descendants of the Jomon people, while Hondo (Main Island)-Japanese are mainly derived from the migrants from the northeast Asian continent after the Aeneolithic Yayoi period. Our aim is to examine the extent to which the model is supported by genetic evidence from modern populations, particularly from Japan and other Asian areas. Based on genetic distance analyses using data from up to 25 “classic” genetic markers, we find first that the three Japanese populations including Ainu and Ryukyuan clearly belong to a northeast Asian cluster group. This negates the first hypothesis of the model. Then, we find that Ainu and Ryukyuans share a group contrasting with Hondo-Japanese and Korean, supporting the second hypothesis of the model. Based on these results, we propose a modified version of the dual structure model which may explain the genetic, morphological, and archaeological evidence concerning the formation of modern Japanese populations. Am J Phys Anthropol 102:437–446, 1997. © 1997 Wiley-Liss, Inc.     

Asian weaver ants,Oecophylla smaragdina,and their repelling of pollinators

The Asian weaver ant, Oecophylla smaragdina, is known to have outstanding predatory power. This ant can protect the host plants from attacks of phytophagous insects and therefore has been used for biological control in the tropics. We present evidence for a possible negative effect of Oecophylla on the performance of host plants. Our observation in a fruit orchard of rambutan in Sumatra suggested that the presence of Oecohylla nests on the trees statistically significantly lowered the flower-visiting rate of flying insects, involving the major pollinator Trigona minangkabau. The visiting rate of Oecophylla workers to each flower shoot of rambutan significantly negatively correlated with the visiting rate of flying insects. Empirical evidence of such an inhibitory effect on flower-visiting of pollinators cased by aggressive ants has been scarce so far.     

Early Eocene Primates from Gujarat, India

The oldest euprimates known from India come from the Early Eocene Cambay Formation at Vastan Mine in Gujarat. An Ypresian (early Cuisian) age of ∼53 Ma (based on foraminifera) indicates that these primates were roughly contemporary with, or perhaps predated, the India-Asia collision. Here we present new euprimate fossils from Vastan Mine, including teeth, jaws, and referred postcrania of the adapoids Marcgodinotius indicus and Asiadapis cambayensis. They are placed in the new subfamily Asiadapinae (family Notharctidae), which is most similar to primitive European Cercamoniinae such as Donrussellia and Protoadapis. Asiadapines were small primates in the size range of extant smaller bushbabies. Despite their generally very plesiomorphic morphology, asiadapines also share a few derived dental traits with sivaladapids, suggesting a possible relationship to these endemic Asian adapoids. In addition to the adapoids, a new species of the omomyid Vastanomys is described. Euprimate postcrania described include humeri, radii, femora, calcanei, and tali, most of which show typical notharctid features and are probably attributable to asiadapines. Anatomical features of the limb elements indicate that they represent active arboreal quadrupedal primates. At least one calcaneus is proximally shorter and distally longer than the others, resembling eosimiids in this regard, a relationship that, if confirmed, would also suggest an Asian or southeast Asian faunal connection. Isolated teeth from Vastan Mine recently attributed to a new eosimiid, Anthrasimias gujaratensis, appear to provide that confirmation. However, their attribution to Eosimiidae is equivocal. They are similar to teeth here tentatively referred to Marcgodinotius, hence A. gujaratensis may be a junior synonym of M. indicus. Corroboration of eosimiids at Vastan requires more compelling evidence. Although definitive conclusions are premature, available evidence suggests that the Vastan adapoids, at least, were derived from western European stock that reached India near the Paleocene-Eocene boundary.     

Contraceptive practices and fertility among Southeast Asian, black, and white mothers attending a maternal infant care program

The purpose of this analysis was to determine if there were differences in selected fertility characteristics including parity, pregnancy spacing, age at 1st pregnancy, age of menarche, breastfeeding postpartum, and contraceptive practices among white, black, Hmong, and other Southeast Asian mothers attending a maternal infant care program in Minneapolis, Minnesota, during 1980-1982. White and black mothers were younger than the Hmong and other Asian mothers. The lowest mean age of 1st pregnancy was among blacks. Ages of 1st pregnancy were similar for whites, Hmong, and other Asians, although the mean age of menarche was approximately 2 years later for Hmong and other Southeast Asian mothers compared to the white and black mothers. Based on self reports at the 1st postpartum visit 1 month after delivery, 39% of the whites and 25% of the blacks were breastfeeding. In comparison 8.7% of the Hmong and 17% of the other southeast Asian mothers were breastfeeding. Maternal aged age at 1st pregnancy were significant predictors of parity for whites, blacks, Hmong, and other Southeast Asians. Ever-use of contraception was significant predictor of parity only for Hmong. The highest proportion of ever-users of contraception was among the white mothers (80%) followed by the blacks (69.3%) and other Asian mothers (34.85). Hmong mothers had the lowest proportion having used contraception (17.1%).     

Microsatellite markers reveal population structure and low gene flow among collections of Bactrocera cucurbitae (Diptera: Tephritidae) in Asia

The melon fruit fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), is widespread agricultural pest, and it is known to have the potential to establish invasive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the population genetics of this pest have remained relatively unexplored in Asia, the main area for distribution of this pest. The goals for this study were to employ nuclear markers to examine geographic collections for population genetic structure and quantify the extent of gene flow within these Southeast Asian and Chinese populations. To achieve these goals, we used 12 polymorphic microsatellite markers. A low level of genetic diversity was found among collections from China and higher levels were seen in Southeast Asia collections. Three genetically distinct groups, Southeast Asia, southwest China, and southeast China, were recovered by Bayesian model-based clustering methods, the phylogenetic reconstruction and the principal coordinate analysis. The Mantel test clearly shows geographical distance contributed in the genetic structuring of B. cucurbitae's populations. No recent bottlenecks for any of the populations examined. The results of clustering, migration analyses, and Mantel test, strongly suggest that the regional structure observed may be due to geographical factors such as mountains, rivers, and islands. We found a high rate of migration in some sites from the southwest China region (cluster 1) and the southeast China region (cluster 2), suggesting that China-Guangdong-Guangzhou (GZ) may be the center of melon fruit fly in the southeast China region.     

Colonization patterns of the invasive Brazilian peppertree, Schinus terebinthifolius, in Florida

Invasive species are believed to spread through a process of stratified dispersal consisting of short-distance diffusive spread around established foci and human mediated long-distance jumps. Brazilian peppertree (Schinus terebinthifolius), native to South America, was introduced twice as an ornamental plant into Florida, USA, just over 100 years ago. A previous study indicated that these two introductions were from genetically differentiated source populations in the native range. In this study, we took advantage of these contrasting genetic signatures to study the spatial spread of Brazilian peppertree across its entire range in Florida. A combination of spatial genetic and geostatistical analyses using chloroplast and nuclear microsatellite markers revealed evidence for both diffusive dispersal and long-distance jumps. Chloroplast DNA haplotype distributions and extensive bands of intra-specific hybridization revealed extensive dispersal by both introduced populations across the state. The strong genetic signature around the original introduction points, the presence of a general southeast to northwest genetic cline, and evidence for short-distance genetic spatial autocorrelation provided evidence of diffusive dispersal from an advancing front, probably by birds and small mammals. In the northernmost part of the range, there were patches having a high degree of ancestry from each introduction, suggesting long-distance jump dispersal, probably by the movement of humans. The evidence for extensive movement throughout the state suggests that Brazilian peppertree will be capable of rapidly recolonizing areas from which it has been eradicated. Concerted eradication efforts over large areas or the successful establishment of effective biocontrol agents over a wide area will be needed to suppress this species.     

Further evidence of an oriental origin for Nosema ceranae (Microsporidia: Nosematidae)

Although Nosema ceranae was first isolated from the Asian honeybee (Apis cerana) in Asia and then subsequently recognized as a widespread gut parasite of the Western honeybee (Apis mellifera), its origins and primary host are yet to be accurately established. In this study we examined the possibility of an Asian origin for the parasite by looking for evidence of its ongoing spread out of Asia. To do this, we surveyed for the presence of N. ceranae in A. cerana and A. mellifera on isolated islands of the Solomon Islands (Pacific region), most of which were inhabited with A. mellifera that had been introduced from Australia and New Zealand at a time when N. ceranae was not present in either country, but on which some had also recently become inhabited with invasive A. cerana that originated from Asia with no prior history of contact with A. mellifera infected with N. ceranae. We also sought to verify previous findings that N. ceranae was widespread in Asian honeybees by surveying for its presence in isolated populations of the Asian honeybees, A. cerana, A. koschevnikovi, A. nigrocincta and A. florea. We obtained evidence that A. cerana introduced N. ceranae to A. mellifera in the Solomon Islands and also confirmed the widespread occurrence of the parasite in Asian honeybees, even reporting it for the first time in A. koschevnikovi from Borneo. Our findings provide further support for the hypothesis that N. ceranae has only recently emerged from Asia to become a parasite of A. mellifera.     

现代人出现和演化的化石证据

近年来,新材料的发现、新测年结果的更新以及分子生物学的加入,刷新了关于现代人在各主要区域出现时间、在迁徙扩散中与古老人群的交流模式、晚更新世晚期现代人演化复杂场景等方面的认识。本文梳理了关于现代人出现和演化路径的主要化石证据和研究成果。目前化石证据显示：非洲准现代人的出现时间最早可到MIS 9阶段,非洲现代人在中更新世晚期到晚更新世化石证据连续;欧亚大陆现代人的出现时间可追溯到MIS 6阶段,在MIS 5a-MIS 4阶段经历“瓶颈期”,在MIS 3阶段开始广泛分布。从已有证据来看,MIS 3和MIS 2阶段,欧亚大陆不同区域的现代人演化链条并非单一线性,而是呈现有断点的“网状”演化模式。     

利用HPA-1～3,5和15系统多态性估算中外不同人群遗传距离

依据血小板同种抗原5个系统的遗传多态性, 采用聚合酶链反应序列特异性引物技术, 对1 000名中国汉族无关献血者HPA-1~3, 5和15系统进行基因分型, 计算基因频率。使用DISPAN软件及PHYLIP软件计算不同群体间遗传距离并绘制系统树。系统树显示, 亚洲人群先与欧洲人群相聚, 之后再与非洲人群相聚, 非洲人群位于系统发生树的最顶部; 印度人群处于亚洲人群与欧洲人群之间; 南美洲巴西白人与欧洲人群聚在一起; 大洋洲的波利尼西亚人与亚洲人群聚在一起。此研究从一个侧面证明了人类“非洲起源说”, 印证亚洲人群由南亚向东南亚再向东亚迁徙的路线, 并推断出欧洲人群由南欧向北欧、西欧迁徙的线路。HPA能有效估算不同人群间遗传距离, 分析人类迁徙过程, HPA可作为遗传标记应用于人类进化的研究。     

Contraceptive practices and fertility among Southeast Asian,black, and white mothers attending a maternal infant care program

Abstract

The purpose of this analysis was to determine if there were differences in selected fertility characteristics including parity, pregnancy spacing, age at first pregnancy, age of menarche, breastfeeding postpartum, and contraceptive practices among white, black, Hmong, and other Southeast Asian mothers attending a maternal infant care program in Minneapolis, Minnesota, during 1980–82.

White and black mothers were younger than the Hmong and other Asian mothers. The lowest mean age of first pregnancy was among blacks. Ages of first pregnancy were similar for whites, Hmong, and other Asians, although the mean age of menarche was approximately two years later for Hmong and other Southeast Asian mothers compared to the white and black mothers.

Based on self reports at the first postpartum visit one month after delivery, 39 per cent of the whites and 25 per cent of the blacks were breastfeeding. In comparison 8.7 per cent of the Hmong and 17 per cent of the other southeast Asian mothers were breastfeeding.

Maternal age and age at first pregnancy were significant predictors of parity for whites, blacks, Hmong, and the other Southeast Asians. Ever‐use of contraception was a significant predictor of parity only for Hmong.

The highest proportion of ever‐users of contraception was among the white mothers (80 per cent) followed by the blacks (69.3 per cent) and other Asian mothers (34.8 per cent). Hmong mothers had the lowest proportion having used contraception (17.1 per cent).     

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.     

Kamala tree as an indicator of the presence of Asian elephants during the dry season in the Shivalik landscape of northwestern India

The availability of forage resources during the dry season is often a critical factor in determining the distribution and movement of large herbivores. It has long been suspected that the Kamala tree (Mallotus philippinensis) can serve as an indicator of the distribution for Asian elephants during the dry season in northwestern India. However, there is little direct evidence in support of this speculation, especially at a large landscape scale. Here, we predicted the distribution of Kamala trees in the Shivalik landscape of northwestern India based on topographic and bioclimatic variables, as well as satellite-derived vegetation indices and forest canopy height data using a presence-only ecological niche model. We used the area under the receiver operating characteristic curve (AUC) and true skill statistic (TSS) to validate the model. We then examined the relationship between the occurrence probability of Kamala trees and the presence of Asian elephants with data collected during dry seasons between 2010 and 2014 using logistic regression models. Our results showed that the probability of occurrence of Kamala trees was predicted with good accuracy (AUC = 0.88 and TSS = 0.51). The logistic regression models showed that the presence of Asian elephants can be adequately predicted by the occurrence probability of Kamala trees. This result suggests that the distribution of Kamala trees is a good indicator of the presence of Asian elephants during the dry season in the Shivalik landscape. These findings may have major implications for the conservation of Asian elephants, especially in designing wildlife corridors and mitigating human-elephant conflicts.     

Placental endogenous retrovirus (ERV): structural,functional, and evolutionary significance

That endogenous retrovirus (ERV) is present within the placenta of humans and other mammals has been known for the past 25 years, but the significance of this observation is still not fully understood. Much molecular biological data have emerged in recent years to support the earlier electron microscopic data on the presence of placental ERV. The evidence for ERV in animal and human placental tissue is presented, then integrated with data on the the presence of ERV in a range of other tissues, in particular teratocarcinoma cells. Placental invasiveness and maternal immunosuppression are then discussed in relation to metalloproteinase secretion, the immunosuppressive potential of retroviruses, and placental growth factors, while the evidence for a functional link between placental proto-oncogenes and trophoblast malignancy is reviewed. Finally, placental development, structure, and life span are discussed within an evolutionary context. The hypothesis that one or more ancient trophoblastic ERVs could have played a role in the evolution and divergence of all placental mammals is evaluated. BioEssays 20: 307-316, 1998. © 1998 John Wiley & Sons, Inc.