Founder effects and stochastic dispersal at the continental scale of the fungal pathogen of bananas Mycosphaerella fijiensis

The worldwide destructive epidemic of the fungus Mycosphaerella fijiensis on banana started recently, spreading from South-East Asia. The founder effects detected in the global population structure of M. fijiensis reflected rare migration events among continents through movements of infected plant material. The main objective of this work was to infer gene flow and dispersal processes of M. fijiensis at the continental scale from population structure analysis in recently invaded regions. Samples of isolates were collected from banana plantations in 13 countries in Latin America and the Caribbean and in Africa. The isolates were analysed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and microsatellite molecular markers. The results indicate that a high level of genetic diversity was maintained at the plantation and the plant scales. The loci were at gametic equilibrium in most of the samples analysed, supporting the hypothesis of the existence of random-mating populations of M. fijiensis, even at the plant scale. A low level of gene diversity was observed in some populations from the Africa and Latin America-Caribbean regions. Nearly half the populations analysed showed a significant deviation from mutation-drift equilibrium with gene diversity excess. Finally, a high level of genetic differentiation was detected between populations from Africa (FST = 0.19) and from the Latin America-Caribbean region (FST = 0.30). These results show that founder effects accompanied the recent invasion of M. fijiensis in both regions, suggesting stochastic spread of the disease at the continental scale. This spread might be caused by either the limited dispersal of ascospores or by movements of infected plant material.     

Plasmodium vivax Diversity and Population Structure across Four Continents

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (F _ST>0.2). Outside Central Asia F _ST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.     

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.     

Polymerase chain reaction–restriction fragment length polymorphism markers for the fungal banana pathogen Mycosphaerella fijiensis

Polymerase chain reaction–restriction fragment length polymorphism markers were developed to study populations of the fungal banana pathogen Mycosphaerella fijiensis. Twelve markers were defined, 11 in anonymous and single‐copy nuclear DNA sequences and one in the internal transcribed spacer and 5.8S rDNA sequence. The polymerase chain reaction products obtained with locus‐specific primer pairs were digested with restriction enzymes to reveal polymorphism. Between five and 12 markers were polymorph in M. fijiensis populations from different geographical origins (Papua New Guinea, the Philippines, Cameroon and Latin America). The mean of allele number and gene diversity (expected heterozygosity) per locus in the different geographical populations ranged between 1.4 and 2.7 and 0.17 and 0.45, respectively.     

Analysis of five y-Specific microsatellite loci in Asian and Pacific populations

We have analyzed five Y-specific microsatellite loci (DYS388, DYS390, DYS391, DYS394, DYS395) in 17 Asian and Pacific populations representing a broad geographical area and different linguistic families, with an emphasis on populations from mainland and insular Southeast Asia. Analysis of gene diversity indicates that several of the studied populations have experienced substantial genetic isolation, and a reduction in male effective sizes (viz. the Northeast Indian populations Nishi, Adi and the Taiwanese aboriginals). The average values of the F_ST and (_ST statistics indicate a high degree of genetic differentiation among these populations at the five Y-specific markers (F_ST =0.21 and (_ST = 0.33, based on individual loci; F_ST = 0.09 and (_ST = 0.36, based on haplotypes), which conform to the expectation of a fourfold smaller effective size of the Y-linked loci compared with the autosomal loci. Dendrogram and principal coordinates analysis, with few exceptions, show a major separation between mainland and insular populations. Among the mainland populations, the Tibeto-Burman speakers from Northeast India cluster in a well-defined group, supported by high bootstrap values. The Southern Chinese, Northern Thai, So, and Cambodian also are integral to this cluster. The other major cluster is rather heterogeneous and includes, among others, the Austronesian-speaking populations. The Samoans of the Pacific, with a distinctive pattern of allelic distributions, stand as an outlier in the tree and PC representations. Although trends of genetic affinities among ethnically and geographically related populations are evident from the Y-specific microsatellite data, microsatellites are not optimal for deciphering complex migratory patterns of human populations, which could possibly be clarified by using additional and more stable genetic markers. Am J Phys Anthropol 110: 1–16, 1999. © 1999 Wiley-Liss, Inc.     

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.     

Patterns of genetic diversity in population complexes of pacific chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum,from Asia and America,inferred from allozyme polymorphism data

Based on the data of Russian and foreign researchers, a database, consisting of 100 allozyme-coding loci examined in 288 chum salmon populations from Asia and Northern America, was constructed. Using G-test, genetic heterogeneity of Asian population samples of chum salmon was evaluated. Correlations between the frequencies of major alleles and geographic latitude of the mouths of native rivers were estimated. Using the methods of Nei and Cavalli-Sforza and Edwards, for different local chum salmon stock groups the genetic distances at the number of polymorphic enzyme loci were determined. Analysis of these distances made it possible to evaluate the patterns of genetic diversity in regional population groups from the Russian Far East, Japan, and North America. The proportions of genetic variation at each hierarchical level, identified in accordance with the geographical positions of the populations, were estimated through partitioning of variation in Asian populations into within and between-population components. It was demonstrated that intraspecific genetic structure of chum salmon corresponded geographic subdivision into regional population groups.     

Characterization of six microsatellite loci in the mangrove cricket Apteronemobius asahinai

The mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors in China, Southeast Asia and the Ryukyu archipelago (Amamiohsima, Okinawa, Miyako, Ishigaki and Iriomote Islands) of Japan. We developed six polymorphic microsatellite markers for the mangrove cricket from genomic DNA libraries enriched for CA, GA, AAG and ATG motifs. The M13‐tailed primer method was used in the process of screening of amplification and polymorphism of primers. A total of 64 specimens from two populations (one from Okinawa and the other from Iriomote) were genotyped for allelic diversity. The average number of alleles per locus was 4.67 and 6.67 for Okinawa and Iriomote populations, respectively. A significant genetic differentiation was detected between the two populations (pairwise F_ST 0.2404). These polymorphic microsatellite loci will be useful in ongoing studies of the population genetic structure of the mangrove cricket including several populations in the Ryukyu archipelago.     

Modeled distributions of Aedes japonicus japonicus and Aedes togoi (Diptera: Culicidae) in the United States,Canada, and northern Latin America

The Asian bush mosquito, Aedes japonicus japonicus, and the coastal rock pool mosquito, Aedes togoi, are potential disease vectors present in both East Asia and North America. While their ranges are fairly well‐documented in Asia, this is not the case for North America. We used maximum entropy modeling to estimate the potential distributions of Ae. togoi and Ae. j. japonicus in the United States, Canada, and northern Latin America under contemporary and future climatic conditions. Our results suggest suitable habitat that is not known to be occupied for Ae. j. japonicus in Atlantic and western Canada, Alaska, the western, midwestern, southern, and northeastern United States, and Latin America, and for Ae. togoi along the Pacific coast of North America and the Hawaiian Islands. Such areas are at risk of future invasion or may already contain undetected populations of these species. Our findings further predict that the limits of suitable habitat for each species will expand northward under future climatic conditions.     

Genetic diversity patterns in the SR-BI/II locus can be explained by a recent selective sweep

The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of European, African, East Asian (including Southeast Asian), Middle-Eastern as well as Amerindian descent. Nine of the 14 polymorphisms observed are new. Four of the five variants causing amino acid replacements, G2S, S229G, R484W, and G499R, are likely to affect protein structure and function. SR-BI/BII diversity is partitioned among 19 haplotypes; all but one interconnected by single mutation or a recombination event. Such tight haplotype network and the unusual geographic partitioning of this diversity, high not only in Africa but in East Asia as well, suggests its recent origin and possible effect of selection. Coalescent analysis infers a relatively short time to the most recent common ancestor and points to population expansion in Africa and East Asia. These two continents differ significantly in pairwise F(ST) values, differing as well from a single cluster formed by Europe, Middle East and America. In the context of findings for similarly analyzed other loci, we propose that a selective sweep at the origin of modern human populations could explain the low level of ancestral SR-BI/II diversity. The unusually deep split between Africa and Asia, well beyond the Upper Paleolithic when inferred under neutrality, is consistent with subsequent geographical and demographic expansion favoring the accumulation of new variants, especially in groups characterized by large effective population sizes, such as Asians and Africans. The relevance of such partitioning of SR-BI/II diversity remains to be investigated in genetic epidemiological studies which can be guided by the present findings.     

Body Mass Index and Cardiovascular Disease Risk Factors in Seven Asian and Five Latin American Centers: Data from the International Clinical Epidemiology Network (INCLEN)

We have tested the hypothesis that the relationship between body mass index (BMI) and other cardiovascular disease (CVD) risk factors as well as socioeconomic status is different in five Latin American populations (where BMI is high) and seven Asian populations (where BMI is low). Random samples of approximately 200 males aged between 35 and 65 years were selected from 12 general or industrial populations in Latin America and Asia. Standardized measures of height, weight, blood pressure, blood cholesterol, cigarette smoking, highest level of completed education, occupation and income were made. The mean BMI (kg/m₂) was 253 (SD 3.74) in the five Latin American populations (which were all urban), 22.2 (SD 3.24) in the four Asian urban populations and 21.4 (SD 3.33) in the three Asian rural populations. Despite the differences in mean BMI levels, statistically significant positive relationships of a similar magnitude were seen between BMI and blood pressure levels in Latin America and Asia. Similarly, there was a statistically significant positive relationship found between BMI and total cholesterol in both Latin American and Asian urban samples, but of a higher magnitude in Asian rural samples. Current cigarette smokers had significantly lower BMI than ex-smokers or never smokers in Latin America and Asia. In Asia, there were statistically significant positive associations between BMI and levels of education and income as well as with occupation — these relationships were stronger for education and occupation in rural than in urban samples. There were no statistically significant associations between BMI and these measures of socioeconomic status in Latin America. The similarities of the associations between BMI and blood pressure and cholesterol levels in the two groups suggest that efforts to reduce BMI in all populations is likely to be important in reducing risk of CVD. Preventing the future rise of BMI in populations tions where BMI is still relatively low is a high priority. The difference in association between BMI and socioeconomic status in the different population groups requires study of the way sociocultural factors influence behavior that determines BMI levels.     

Extended jurisdiction and the management of Pacific highly migratory species

Abstract

The Pacific region is the most important producer of tropical tuna in the world. Three subregions account for the production: Pacific Latin America, the Pacific Islands region, and Southeast Asia. Prior to the UN Third Conference on the Law of the Sea, the Tuna Fisheries in the subregions were the preserve of developed distant water fishing nations. The situation has now been entirely reversed, with coastal state jurisdiction and control being realized in all three subregions. It is argued that American opposition to coastal state jurisdiction over tuna resources acted as a goad to the coastal states in Pacific Latin America and the Pacific Islands region in their quest for greater control over tuna resources. There are prospects of cooperation developing among the three Pacific subregional tuna producers. It is argued further that American action may have inadvertently accelerated the progress toward cooperation.     

Invasive trees and shrubs: where do they come from and what we should expect in the future?

The global database of invasive trees and shrubs has been updated, resulting in a total of 751 species (434 trees and 317 shrubs) from 90 families (Rejmánek and Richardson 2013 Divers Distrib 19:1093–1094). This database is used to assess major trends in human-assisted exchanges of dendrofloras among 15 major geographical regions. Areas most invaded by non-native trees are Pacific Islands (136 species), Southern Africa (118), Australia (116), and North America (114). Areas most invaded by non-native shrubs are North America (98), Australia (87), Pacific Islands (71), and Europe (61). The most important sources of invasive trees are Asia (122–146 species, depending on how many Eurasian species are considered to have been introduced only from Europe), Australia (81), and South America (81). The most important sources of invasive shrubs are Asia (103–118), Europe (68), and South America (54). Mean number of native geographical regions for invasive trees is 1.64, while the mean number of invaded regions by trees is 2.51. The difference is smaller for shrubs: 1.60 versus 2.11. Asia is the major source of invasive Rosaceae shrubs, as well as invasive Arecaceae and Oleaceae species. South America and Australia are major sources of invasive Fabaceae trees. North America and Europe are major sources of invasive Pinaceae. Most of the invasive Salicaceae are of Eurasian origin. The identified trends will very likely continue in this century. Because of increasing interactions with many states in Asia, even more invasive woody species will be introduced from this part of the world.     

Archaic African and Asian lineages in the genetic ancestry of modern humans.

A 3-kb region encompassing the beta-globin gene has been analyzed for allelic sequence polymorphism in nine populations from Africa, Asia, and Europe. A unique gene tree was constructed from 326 sequences of 349 in the total sample. New maximum-likelihood methods for analyzing gene trees on the basis of coalescence theory have been used. The most recent common ancestor of the beta-globin gene tree is a sequence found only in Africa and estimated to have arisen approximately 800,000 years ago. There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained. Modest differences in levels of beta-globin diversity between Africa and Asia are better explained by greater African effective population size than by greater time depth. There may have been a reduction of Asian effective population size in recent evolutionary history. Characteristically Asian ancestry is estimated to be older than 200,000 years, suggesting that the ancestral hominid population at this time was widely dispersed across Africa and Asia. Patterns of beta-globin diversity suggest extensive worldwide late Pleistocene gene flow and are not easily reconciled with a unidirectional migration out of Africa 100,000 years ago and total replacement of archaic populations in Asia.     

普遍野生稻和亚洲栽培稻遗传多样性的研究

用 ４４个 ＲＦＬＰ标记对来自中国、印度、泰国等亚洲 １０个国家的普通野生稻（简称普野,下同）和来自多个国家的７５个栽培稻品种,从多态位点的比率、等位基因数、基因型数、平均杂合度及平均基因多样性等多个方面,比较了不同国家和不同地区的普通野生稻、栽培稻籼粳亚种及栽培稻与普野之间遗传多样性的差异。结果表明：中国普野的遗传多样性最大;其次是印度普野;南亚普野的平均基因多样性大于东南亚普野,而多态位点的比率、等位基因数及基因型数等却低于东南亚普野;栽培稻的遗传多样性明显小于普通野生稻。在所检测的４４个位点中,栽培稻的多态位点数仅为野生稻的３／４,等位基因数约为野生稻的６０％,基因型种类约为野生稻的１／２。栽培稻中籼稻的遗传多样性高于粳稻。在平均每个位点的实际杂合度上,以中国普野杂合度最高,普通野生稻是栽培稻的２倍。说明从野生稻演化成栽培稻的过程中,经过自然选择和人工选择,杂合度降低,等位基因减少,基因多样性下降。     

Zika virus: An emerging flavivirus

Zika virus (ZIKV) is a previously little-known flavivirus closely related to Japanese encephalitis, West Nile, dengue, and yellow fever viruses, all of which are primarily transmitted by blood-sucking mosquitoes. Since its discovery in Uganda in 1947, ZIKV has continued to expand its geographic range, from equatorial Africa and Asia to the Pacific Islands, then further afield to South and Central America and the Caribbean. Currently, ZIKV is actively circulating not only in much of Latin America and its neighbors but also in parts of the Pacific Islands and Southeast Asia. Although ZIKV infection generally causes only mild symptoms in some infected individuals, it is associated with a range of neuroimmunological disorders, including Guillain-Barré syndrome, meningoencephalitis, and myelitis. Recently, maternal ZIKV infection during pregnancy has been linked to neonatal malformations, resulting in various degrees of congenital abnormalities, microcephaly, and even abortion. Despite its emergence as an important public health problem, however, little is known about ZIKV biology, and neither vaccine nor drug is available to control ZIKV infection. This article provides a brief introduction to ZIKV with a major emphasis on its molecular virology, in order to help facilitate the development of diagnostics, therapeutics, and vaccines.     

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.     

Genetic diversity of donkey populations from the putative centers of domestication

Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mtDNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass (Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species.     

Extent of linkage disequilibrium between the androgen receptor gene CAG and GGC repeats in human populations: implications for prostate cancer risk

While studies have implicated alleles at the CAG and GGC trinucleotide repeats of the androgen receptor gene with high-grade, aggressive prostate cancer disease, little is known about the normal range of variation for these two loci, which are separated by about 1.1 kb. More importantly, few data exist on the extent of linkage disequilibrium (LD) between the two loci in different human populations. Here we present data on CAG and GGC allelic variation and LD in six diverse populations. Alleles at the CAG and GGC repeat loci of the androgen receptor were typed in over 1000 chromosomes from Africa, Asia, and North America. Levels of linkage disequilibrium between the two loci were compared between populations. Haplotype variation and diversity were estimated for each population. Our results reveal that populations of African descent possess significantly shorter alleles for the two loci than non-African populations (P<0.0001). Allelic diversity for both markers was higher among African Americans than any other population, including indigenous Africans from Sierra Leone and Nigeria. Analysis of molecular variance revealed that approx. 20% of CAG and GGC repeat variance could be attributed to differences between the populations. All non-African populations possessed the same common haplotype while the three populations of African descent possessed three divergent common haplotypes. Significant LD was observed in our sample of healthy African Americans. The LD observed in the African American population may be due to several reasons; recent migration of African Americans from diverse rural communities following urbanization, recurrent gene flow from diverse West African populations, and admixture with European Americans. This study represents the largest genotyping effort to be performed on the two androgen receptor trinucleotide repeat loci in diverse human populations.