Multiple origins of Tibetan Y chromosomes

The genetic origin of Tibetans was investigated using Y chromosome markers. A total of three populations were studied, two from central Tibet speaking central Tibetan and one from Yunnan speaking Kham. Two dominant paternal lineages (>80%) were identified in all three populations with one possibly from central Asia (YAP+) and the other from east Asia (M122C). We conclude that Tibetan Y chromosomes may have been derived from two different gene pools, given the virtual absence of M122C in central Asia and YAP+ in east Asia, with drift an unlikely mechanism accounting for these observations.     

Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes

Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.     

African and Levantine origins of Pakistani YAP+ Y chromosomes.

We surveyed 9 Pakistani subpopulations for variation on the nonrecombining portion of the Y chromosome. The polymorphic systems examined were the Y-chromosome Alu insertion polymorphism (YAP) at DYS287, 5 single nucleotide polymorphisms, and the tetranucleotide microsatellite DYS19. Y chromosomes carrying the YAP element (YAP+) were found in populations from southwestern Pakistan at frequencies ranging from 2% to 8%, whereas northeastern populations appeared to lack YAP+ chromosomes. In contrast to other South Asian populations, several Pakistani subpopulations had a high frequency of the DYS19*B allele, the most frequent allele in West Asian, North African, and European populations. The combination of alleles at all polymorphic sites gave rise to 9 YAP-DYS19 combination haplotypes in Pakistani populations, including YAP+ haplotypes 4-A, 4-B, 5-C, and 5-E. We hypothesize that the geographic distributions of YAP+ haplotypes 4 and 5 trace separate migratory routes to Pakistan: YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East. These inferences are consistent with ethnohistorical data suggesting that Pakistan's ethnic groups have been influenced by migrations from both African and Levantine source populations.     

Early origins of the X and Y chromosomes: lessons from tilapia

Differentiated sex chromosome pairs in diverse species display certain common characteristics, normally comprising one largely heterochromatic genetically inactive chromosome and one euchromatic genetically active chromosome (e.g. the mammalian Y and X respectively). It is widely accepted that dimorphic sex chromosomes evolved from homologous pairs of autosomes. Although the exact mechanisms through which the pair diverged are not fully understood, an initial suppression of recombination in the sex-determining region is required by all of the major theories. Here we address the question of the mechanism by which this initial suppression of recombination occurs. Our model postulates that the stochastic, de novo accumulation of heterochromatin in the sex determining region can delay pairing of the sex chromosomes in meiosis, resulting in a decrease in recombination. Data to support this model is presented from the cichlid fish, Oreochromis niloticus. Although such a decrease would in most circumstances be evolutionarily disadvantageous, if the region concerned included the major sex determining gene and other gene(s) with sex-specific functions, then this would be selectively advantageous and could trigger the process(es) which, ultimately, lead to the differentiation of the sex chromosomes.     

Phylogenetic Patterns of the Southeast Asian Tree Frog Chiromantis hansenae in Thailand

Although landscape features such as mountains and rivers are recognized often as limiting factors to amphibian dispersal and gene flow, a limited number of studies have investigated such patterns across Southeast Asia. A perfect example of this is Thailand, located in one of the world＇s biodiversity hotspot regions. Thailand represents the corridor between mainland Asia and the Sunda Shelf, a famous and widely recognized biogeographic region, and yet there are few studies on the genetic structure among populations of amphibian species distributed across Thailand. The Southeast Asian tree frog, Chiromantis hansenae has been reported to possess a geographic range that is restricted to Thailand and, presumably, Cambodia~ Here, we investigate phylogenetic relationships among C. hansenae populations using partial sequences of the mitochondrial 16S rRNA gene and nuclear POMC gene. Our results reveal two distinct evolutionary lineages within C. hansenae populations in Thailand. The genetic divergence among populations between these two clades is considerable, and results support inter-population divergence, and high genetic differentiation （pairwise FsT = 0.97）, between two localities sampled in western Thailand （TK1 and TK2）, separated from each other by 40 kilometers only. The results suggest that landscape features across Thailand may have a profound impact on patterns of diversification in the country, underscoring the urgent need for fine-scale investigations of genetic structure of endemic and ＂widespread＂ species.     

Hemoglobin Constant Spring among Southeast Asian Populations: Haplotypic Heterogeneities and Phylogenetic Analysis

Background

Hemoglobin Constant Spring (Hb CS) is an abnormal Hb caused by a mutation at the termination codon of α2-globin gene found commonly among Southeast Asian and Chinese people. Association of Hb CS with α°-thalassemia leads to a thalassemia intermedia syndrome commonly encountered in the region. We report chromosome background and addressed genetic origins of Hb CS observed in a large cohort of Hb CS among Southeast Asian populations.

Materials and Methods

A study was done on 102 Vietnamese (aged 15–49 year-old) and 40 Laotian (aged 18–39 year-old) subjects with Hb CS and results compared with 120 Hb CS genes in Thailand. Hematological parameters were recorded and Hb analysis was performed using capillary electrophoresis. Hb CS mutation and thalassemia genotypes were defined by DNA analysis. Six DNA polymorphisms within α-globin gene cluster including 5’Xba I, Bgl I, Inter-zeta HVR, AccI, RsaI and αPstI 3’, were determined using PCR-RFLP assay.

Results

Nine different genotypes of Hb CS were observed. In contrast to the Thai Hb CS alleles which are mostly linked to haplotype (+—S + + -), most of the Vietnamese and the Laotian Hb CS genes were associated with haplotype (+—M + + -), both of which are different from that of the European Hb CS.

Conclusions

Hb CS is commonly found in combination with other thalassemias among Southeast Asian populations. Accurate genotyping of the cases requires both hematologic and DNA analyses. At least two independent origins are associated with the Hb CS gene which could indirectly explain the high prevalence of this Hb variant in the region.     

Phylogenetic evolution and biogeography of Southeast Asian shrews (genus Crocidura: Soricidae)

Genetic variation of 20 species of shrews from the Malay peninsula, Sumatra, Java, Borneo, the Philippines and Sulawesi was assessed by allozyme electrophoresis at 32 loci. According to Mantel's tests, the genetic differentiation of these species of shrews is not a function of the geographic distance separating them (r = 0.09, NS), but is correlated to the water depth surrounding the islands where they live (r = 0.49, P < 0.01). The results are just the reverse if the correlations are computed for the Sunda Shelf taxa only. In this case, the sampled populations show an isolation-by-distance relationship (r = 0.32; P < 0.01), while no significant correlation with water depth was detected (r = 0.20; P - 0.07). Qualitative predictions based on eustatic sea level variation and water depth were formulated as a model of historic connections between the islands. This palaeogeographic model was tested through Brooks Parsimony Analysis. The assumption of a simple vicariant evolution of the shrews was rejected, but several concordant patterns indicate that the phytogeny of these mammals was indeed shaped by these events. Homoplasies demonstrated that the SE Asian species of Crocidura include composite zoogeographic histories. Sulawesi, for example, supports at least six species, five of which are closely related, while the last one, C. nigripes, is more closely related to a Bornean taxon. This pattern was interpreted as the result of a first wave of colonizers which subsequently radiated, followed by a more recent, second colonization event from Borneo. The overall small genetic distance found within the assemblage of the five old endemics (D_N= 0.151 pL 0.041) suggests that the radiation was not accompanied by extensive differentiation, although from a karyological point of view, they exhibit unusual variations when compared to other Indomalayan Crocidura. By contrast, the four species found on Sumatra are more differentiated (D_N= 0.221 pL 0.063) and never form sister-group relationships in any phylogenetic reconstruction; each one is more closely related to different taxa living outside Sumatra. This suggests that they are probably remnants of an important centre of dispersal for the entire Malay Archipelago. The standard genetic distance averaged among all Southeast Asian species (D_N= 0.235 pL 0.094) is about half that measured within Palearctic or African taxa. Such an overall lower mean level of genetic variability is consistent with the hypothesis of a relatively recent colonization of the Malay Archipelago by shrews of the genus Crocidura.     

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.     

Mitochondrial DNA D‐loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens

This study sought to assess mitochondrial DNA (mtDNA) diversity and phylogeographic structure of chickens from five agro‐ecological zones of Zimbabwe. Furthermore, chickens from Zimbabwe were compared with populations from other geographical regions (Malawi, Sudan and Germany) and other management systems (broiler and layer purebred lines). Finally, haplotypes of these animals were aligned to chicken sequences, taken from GenBank, that reflected populations of presumed centres of domestication. A 455‐bp fragment of the mtDNA D‐loop region was sequenced in 283 chickens of 14 populations. Thirty‐two variable sites that defined 34 haplotypes were observed. In Zimbabwean chickens, diversity within ecotypes accounted for 96.8% of the variation, indicating little differentiation between ecotypes. The 34 haplotypes clustered into three clades that corresponded to (i) Zimbabwean and Malawian chickens, (ii) broiler and layer purebred lines and Northwest European chickens, and (iii) a mixture of chickens from Zimbabwe, Sudan, Northwest Europe and the purebred lines. Diversity among clades explained more than 80% of the total variation. Results indicated the existence of two distinct maternal lineages evenly distributed among the five Zimbabwean chicken ecotypes. For one of these lineages, chickens from Zimbabwe and Malawi shared major haplotypes with chicken populations that have a Southeast Asian background. The second maternal lineage, probably from the Indian subcontinent, was common to the five Zimbabwean chicken ecotypes, Sudanese and Northwest European chickens as well as purebred broiler and layer chicken lines. A third maternal lineage excluded Zimbabwean and other African chickens and clustered with haplotypes presumably originating from South China.     

Multiple origins of Ashkenazi Levites: Y chromosome evidence for both Near Eastern and European ancestries

Previous Y chromosome studies have shown that the Cohanim, a paternally inherited Jewish priestly caste, predominantly share a recent common ancestry irrespective of the geographically defined post-Diaspora community to which they belong, a finding consistent with common Jewish origins in the Near East. In contrast, the Levites, another paternally inherited Jewish caste, display evidence for multiple recent origins, with Ashkenazi Levites having a high frequency of a distinctive, non-Near Eastern haplogroup. Here, we show that the Ashkenazi Levite microsatellite haplotypes within this haplogroup are extremely tightly clustered, with an inferred common ancestor within the past 2,000 years. Comparisons with other Jewish and non-Jewish groups suggest that a founding event, probably involving one or very few European men occurring at a time close to the initial formation and settlement of the Ashkenazi community, is the most likely explanation for the presence of this distinctive haplogroup found today in >50% of Ashkenazi Levites.     

Multiple origins of parthenogenesis,and a revised species phylogeny for the Southeast Asian butterfly lizards,Leiolepis

Hybridization often occurs in areas of secondary contact between closely related species. In some cases these hybridization events can create hybrid offspring that are reproductively viable as new parthenogenetic species. The genus Leiolepis contains nine species that collectively range throughout continental Southeast Asia. Of these, four are unisexual (some diploid and some triploid). We analyzed a multi‐locus dataset within a multi‐lineage coalescent framework to infer the origins of these parthenogenetic hybrid species. Our results provide evidence that repeated hybridization events between L. reevesii and L. guttata have led to the formation of all four distinct parthenogenetic species. Our data further suggest there have been low levels of mitochondrial introgression between L. belliana and L. reevesii at their contact zone in southern Cambodia. This work addresses contentious species boundaries and provides the first taxon‐complete hypothesis of relationships for the butterfly lizards. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1080–1093.     

Phylogenetic relationships among Southeast Asian climbing bamboos (Poaceae: Bambusoideae) and the Bambusa complex

A phylogenetic analysis of Bambusa and allies based on the plastid DNA non-coding regions rps16-trnQ, trnC-rpoB, trnH-psbA and trnD-T, and a partial nuclear GBSSI gene, was carried out. This included representatives from all four Bambusa subgenera (including type species), a group of segregate Southeast Asian genera distinctive by their climbing–scrambling culms (Dinochloa, Holttumochloa, Kinabaluchloa, Maclurochloa, Soejatmia, Sphaerobambos), and two other Bambusinae genera (Dendrocalamus, Gigantochloa). The results do not support the present subgeneric classification of Bambusa. The climbing Southeast Asian genera, all of which include species previously placed in Bambusa, are distinct from the “core Bambusa group” (type species and alliance) and the Bambusa complex generally.     

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.     

The state and conservation of Southeast Asian biodiversity

Southeast Asia is a region of conservation concern due to heavy losses of its native habitats. In this overview, we highlight the conservation importance of Southeast Asia by comparing its degree of species endemism and endangerment, and its rate of deforestation with other tropical regions (i.e., Meso-America, South America, and Sub-Saharan Africa). Southeast Asia contains the highest mean proportion of country-endemic bird (9%) and mammal species (11%). This region also has the highest proportion of threatened vascular plant, reptile, bird, and mammal species. Furthermore, not only is Southeast Asia’s annual deforestation rate the highest in the tropics, but it has also increased between the periods 1990–2000 and 2000–2005. This could result in projected losses of 13–85% of biodiversity in the region by 2100. Secondary habitat restoration, at least in certain countries, would allow for some amelioration of biodiversity loss and thus potentially lower the currently predicted extinction rates. Nonetheless, urgent conservation actions are needed. Conservation initiatives should include public education, sustaining livelihoods, and ways to enhance the sustainability of agriculture and increase the capacity of conservation institutions. Furthermore, these actions should be country-specific and not ignore areas heavily populated by humans, as they can also harbour high numbers of threatened species. We urge that cooperative conservation initiatives be undertaken and support (e.g., capacity-building) be given by more developed countries in the region and beyond.     

Cervical cancer screening in Middle Eastern and Asian migrants to Australia: A record linkage study

Background. Australia's organized cervical screening program recommends two-yearly screening for women aged 18–69 years and reminder letters are sent at 27 months. Cervical screening registers hold comprehensive information on screening, but not country of birth. A linkage study was performed in order to assess cervical screening behavior in migrants. Methods. To assess screening participation, we linked year 2000 records for 12,541 Middle Eastern/Asian-born women 20–54 years of age, and an age and area matched random sample of 12,143 Australian-born women in the New South Wales (NSW) Midwives Data Collection (MDC), which records country of birth, to screening register records. Screening behavior after 2000 was assessed in women without a recorded prior cervical abnormality. Results. The odds ratios for being screened at least once within a 3 year period, with reference to Australian-born women and adjusted for age, parity, socioeconomic status and smoking, were 0.88 (95% CI: 0.81–0.97) and 0.74 (95% CI: 0.70–0.79) in women born in the Middle East and Asia, respectively. Screening increased with increasing socioeconomic status (SES), absence of smoking and greater parity in Australian-born women but little, if at all, in migrant women. In a sensitivity analysis in which hospital admitted patients were the source of population samples, some patterns were sufficiently different to suggest that selection for illness can affect the strength and direction of associations in linked data. Conclusion. Migrant women from Asian and Middle-eastern countries are less likely than Australian-born women to participate in cervical screening at the recommended interval. Their likelihood of screening is also less related to socioeconomic status, smoking and parity than that in Australian-born women.     

Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members

Mammalian DNA polymerase (pol) β is the founding member of a large group of DNA polymerases now termed the X-family. DNA polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. Accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the X-family of DNA polymerases. The bacterial X-family DNA polymerases, Saccharomyces cerevisiae pol IV, and four mammalian X-family polymerases appear to be directly related. These enzymes originated from an ancient common ancestor characterized in two Bacillus species. Understanding distinct functions for each of the X-family polymerases, evolving from a common bacterial ancestor is of significant interest in light of the specialized roles of these enzymes in DNA metabolism.     

Differential condensation of human chromosomes 9 and Y

Some differences were observed in the mitotic condensation of regions composing human chromosomes 9 and Y: regions 9p, 9h and Y nf are characterized by an intense condensation by the end of the spiralization interval studied (the length of the repair chromosome 3 varying from 5.4 to 2.9 mkm). At the same time, the condensation of regions 9q-h (region 9q without heterochromatic block) is slowing in the initial spiralization interval (the length of chromosome 3 varying from 16.6 to 5.5 mkm). The Yf-block of Y-chromosome is condensing faster than nf-region. The condensation parameters of Q-heterochromatic blocks are most variable while the euchromatic regions are most stable. The dynamics of 9h and of f-block condensation are independent within one karyotype. Based on the data obtained we doubt the correctness of studies on linear dimensions of the constitutive heterochromatin blocks for the evaluation of its quantity in the karyotype. A possible association of differential mitotic condensation with the chromosome segregation disturbances is discussed.