Genetic diversity of Leishmania infantum field populations from Brazil

Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.     

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.     

Genetic relationship and genetic diversity among Typha taxa from East Asia based on AFLP markers

The genetic relationship and diversity among four Typha taxa in East Asia were evaluated using amplified fragment length polymorphism (AFLP) markers. Three AFLP selective primer combinations generated a total of 707 amplification products, of which 704 (99.6%) were polymorphic. The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram and principal component analysis (PCA) plot confirmed the taxonomic status of four separate species. East Asian Typha taxa separated into two groups: the first with Typha angustifolia and the second with T. orientalis, T. laxmanni, and T. latifolia with a high bootstrap value for UPGMA (93%) and a low first score for PCA (25%). The two clusters corresponded with two sections based on the bracteoles in the female flower: section Bracteolatae and section Ebracteolatae. T. angustifolia showed the highest genetic diversity among the four Typha taxa (percentage of polymorphic loci [PPL] = 71%, H_o = 0.157), whereas T. latifolia had the lowest genetic diversity (PPL = 40%, H_o = 0.117). Genetic diversity was related to the presence of the gap between male and female inflorescences. A positive correlation between genetic distance and geographic distance was clearly found in the two species with continuous inflorescences (T. latifolia and T. orientalis). This positive correlation was not observed in the other species with discontinuous spikes (T. angustifolia and T. laxmanni).     

Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

Aim  Middle East brown bears ( Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species.
Location  Middle East region of south-western Asia.
Methods  We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed.
Results  Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals.
Main conclusion  This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.     

亚欧美栗疫病菌群体的遗传多样性

从 12 0个随机引物中筛选出条带清晰、主带明显、重复性好的 9个引物 ,对来自不同地域和寄主的 7个群体的 14 2个栗疫病菌菌株进行 RAPD分析。 9个引物共扩增出条带 12 4条 ,其中多态性条带 111条 ,多态性比率为 89.5 2 %。利用 Popgen3.2软件对供试群体进行遗传多样性分析和 UPGMA聚类。结果表明 ,中国地区 4个群体间的遗传相似性较大 ,与美国、意大利和日本群体间的相似性较小 ;美国和意大利群体间的遗传相似性较大 ,且它们与日本群体间的相似性大于与中国群体间的相似性。病原菌群体的遗传变异率为 0 .2 35 1,其中在地区水平上 ,82 .34%由群体内的变异引起 ,17.6 6 %由群体间的差异引起 ,群体间的基因流动值为 2 .3311;而在寄主水平上 ,则 79.4 2 %由群体内的变异引起 ,2 0 .5 8%由群体间的差异引起 ,群体间的基因流动值为 1.92 97     

不同地理飞蝗种群的遗传多样性

用GenBank中飞蝗Locusta migratoriaL.的序列来设计微卫星引物,并对这些引物的有效性进行验证。结果表明,在所设计的3对引物中,只有1对为有效引物,可扩增出微卫星位点。序列分析表明本位点是一个不连续的重复微卫星位点。该多态微卫星位点含有14个等位基因,不同飞蝗地理种群的等位基因数目、大小和频率都存在较大的差异。对该位点各等位基因型进行χ2检验,基因型频率的观察和期望杂合度分别为0.4578和0.8836,该位点不属于Hardy-Weinberg平衡位点(χ2=733.12,P=0.0000)。该微卫星位点表现出高度的多态性说明是分析飞蝗种群遗传多样性的优良分子遗传标记。     

Genetic diversity and genetic structure of Northern Goshawk (Accipiter gentilis) populations in eastern Japan and Central Asia

Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks. In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in Central Asia. We used 11 newly developed microsatellite markers and also adopted six previously published markers. Genetic diversity was shown to be maintained with 0.58 as mean heterozygosity and 3.95 as mean allelic richness. The degree of genetic differentiation across all populations was low (Nei’s genetic differentiation index = 0.036, Wright’s genetic differentiation index = 0.039), possibly due to gene flow via adjacent regions (average number of migrants = 4.26; 0.68–20.30). However, it is possible that slight differentiation resulted from the short divergence time and/or inflow of escaping imported individuals. We recommend that goshawks in eastern Japan should be managed as a single unit. They do not appear to be under threat genetically at present, but there is the potential for rapid loss of genetic diversity. For future conservation, investigations of dispersal routes and actual conditions of gene flow are also recommended. To prevent further inflow of escaping goshawks into natural populations, it is desirable to reduce importation of goshawks and to enact a regulation obliging purchasers to register imported goshawks. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic relationship among several pig populations in East Asia analysed by blood groups and serum protein polymorphisms

The gene frequencies were calculated to investigate genetic variation apparent in blood group and serum protein systems in Asian native pigs. The results revealed that gene frequencies were generally similar in the nine pig populations, except in some systems. Differences of gene frequencies were recognized in HpY and Cpc detected on Taoyuan pigs of Taiwan and Ohmini pigs of Japan, respectively. TfC and AmC alleles were found in eight pig populations except Ohmini pigs. The overall genetic distances were calculated by gene frequencies of 13 loci and it was observed that Taoyuan pigs are closer to Ohmini pigs than to Short-ear pigs of Taiwan and other East Asian native pigs. However, the genetic distances between Asian native pigs and European or American breeds were larger than those among East Asian native pig populations.     

Genetic relationship among several pig populations in East Asia analysed by blood groups and serum protein polymorphisrns

The gene frequencies were calculated to investigate genetic variation apparent in blood group and serum protein systems in Asian native pigs. The results revealed that gene frequencies were generally similar in the nine pig populations, except in some systems. Differences of gene frequencies were recognized in Hp^Y and Cp^c detected on Taoyuan pigs of Taiwan and Ohmini pigs of Japan, respectively. Tf^C and Am^C alleles were found in eight pig populations except Ohmini pigs.
The overall genetic distances were calculated by gene frequencies of 13 loci and it was observed that Taoyuan pigs are closer to Ohmini pigs than to Short-ear pigs of Taiwan and other East Asian native pigs. However, the genetic distances between Asian native pigs and European or American breeds were larger than those among East Asian native pig populations.     

Colour-assortative mating among populations of Tropheus moorii, a cichlid fish from Lake Tanganyika, East Africa

The species flocks of cichlid fishes in the East African Lakes Tanganyika, Malawi and Victoria are prime examples of adaptive radiation and explosive speciation. Several hundreds of endemic species have evolved in each of the lakes over the past several thousands to a few millions years. Sexual selection via colour-assortative mating has often been proposed as a probable causal factor for initiating and maintaining reproductive isolation. Here, we report the consequences of human-mediated admixis among differentially coloured populations of the endemic cichlid fish Tropheus moorii from several localities that have accidentally been put in sympatry in a small harbour bay in the very south of Lake Tanganyika. We analysed the phenotypes (coloration) and genotypes (mitochondrial control region and five microsatellite loci) of almost 500 individuals, sampled over 3 consecutive years. Maximum-likelihood-based parenthood analyses and Bayesian inference of population structure revealed that significantly more juveniles are the product of within-colour-morph matings than could be expected under the assumption of random mating. Our results clearly indicate a marked degree of assortative mating with respect to the different colour morphs. Therefore, we postulate that sexual selection based on social interactions and female mate choice has played an important role in the formation and maintenance of the different colour morphs in Tropheus, and is probably common in other maternally mouthbrooding cichlids as well.     

Genetic diversity of Toll-like receptor 5 among pig populations

The Toll-like receptor 5 (TLR5) recognizes flagellin of Gram-positive and -negative bacteria and plays an important role in the host defense system. Here, we surveyed single nucleotide polymorphisms (SNPs) in the coding sequence of the porcine TLR5 gene in 83 individuals from five pig breeds, these including Chinese local populations and Western commercial pig breeds. A total of 19 medium polymorphic SNPs (0.25 < PIC < 0.5) were identified, three of which were missense mutations that clustered within the extracellular domain of TLR5. One of the non-synonymous SNPs fell within a 228-amino acid region which has been shown to be important for flagellin recognition. Four SNPs were only found with high frequencies in Oriental pig breeds. The 19 SNPs were found in 30 haplotypes, one of which segregated at high frequency in all samples. Compared with Western pig breeds, Chinese local populations had higher genetic diversity and more haplotypes. Tajima’s test showed no evidence for deviation from neutrality. The data provide useful information for future genetic marker characterization by means of disease association analysis and/or stimulating the mutation carrier with relevant ligands.     

Genetic diversity among geographically separated populations of Nepenthes mirabilis

The distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H _T) and inter-population genetic diversity (H _S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G _ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.     

Population prehistory of East Asia and the pacific as viewed from craniofacial morphology: The basic populations in East Asia,VII

Distance analyses were applied to 11 craniofacial measurements recorded in samples from East and Southeast Asia, Australia, Melanesia, Polynesia, and Micronesia for the purpose of assessing the biological affinities and possible origins of these populations. A clear separation between Australomelanesians and other populations from East and Southeast Asia and the Pacific is evident. The craniofacial variations suggest that the generalized Asian populations (Negritos, Dayaks, Lesser Sunda Islands, etc.) represent at least part of the morphological background of not only the majority of present Southeast Asians, but also the Neolithic Jomon people and their lineage in Japan, Polynesians, and western Micronesians. The original craniofacial features of Southeast Asians may have occurred as the result of convergent microevolution due to similar environmental conditions such as tropical rain forest. This supports the local-evolution hypothesis for modern Southeast Asian craniofacial features. © 1993 Wiley-Liss, Inc.     

Genetic differentiation among populations of the shortfinned eel Anguilla australis from East Australia and New Zealand

Variability at seven microsatellite loci was used to survey the genetic population structure of the shortfinned eel Anguilla australis . Samples were collected from six estuaries along the east coast of Australia and from three estuaries around New Zealand. Hierarchical analysis of molecular variance of the five loci with good fit to Hardy–Weinberg genotypic proportions detected highly significant differences among samples ( F _ST= 0·016, P < 0·001). The fixation index between countries ( F _CT= 0·012, P < 0·001) was more than double the index among samples within countries ( F _SC= 0·005, P < 0·05). An unweighted pair-group method with arithmetic mean (UPGMA) tree also supported the separation of Australian and New Zealand populations, as did assignment tests, which correctly assigned 80 and 84% of the individuals to Australia and New Zealand, respectively. Isolation-by-distance appeared among samples overall ( r = 0·807, P < 0·001), but not among samples within countries ( r = 0·027, P > 0·05 in Australia; r = 0·762, P > 0·05 in New Zealand). These findings indicate that populations of A. australis in East Australia and in New Zealand may be reproductively isolated from one another. Genetic differentiation among populations of A. australis was two- to 10-fold higher than that among populations of other temperate eels in the North Atlantic Ocean, suggesting that two group of A. australis may reflect sub-species. Anguilla australis in the two countries have different genetic structures and thus require separate management. Genetic isolation between Australian and New Zealand populations indicates that juveniles recruit independently into these two regions from geographically or temporally isolated spawning areas.     

Genetic diversity and differentiation of Gmelin larch Larix gmelinii populations from Evenkia (Central Siberia)

Within- and among-population diversity of Gmelin larch Larix gmelinii (Rupr.) Rupr. from Evenkia was inferred from data on 17 genes determining allozyme diversity of ten enzymes. More than 50% of the genes proved to be polymorphic. On average, each tree was heterozygous at 9.2% genes. Heterozygosity expected from the Hardy-Weinberg proportions was higher, 12.5%. A deficit of heterozygous genotypes was observed in all populations under study and attributed to inbreeding. With Wright's F statistics, average individual inbreeding was estimated at 26.6% relative to the population (F(IS)) and at 27.8% relative to the species (F(IT)). The greatest deficit of heterozygosity was observed for the youngest population. Within-population variation accounted for more than 98% of the total variation, while the contribution of among-population variation was 1.66%. Genetic distance between populations varied from 0.0025 to 0.0042, averaging 0.0035.     

Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.     

A New Species and New Records of the Genus Meharia Chretien, 1915 (Lepidoptera,Cossidae) from the Middle East and Central Asia

Entomological Review - A new species, Meharia rolandi Yakovlev, sp. n., is described from the United Arab Emirates. The new species is most closely related to M. acuta Wiltshire, 1982, and M....     

Genetic diversity,introgression and relationships among West/Central African cattle breeds

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups – African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.     

Genetic diversity among different species of the genus Leiurus (Scorpiones: Buthidae) in Saudi Arabia and the Middle East

The molecular phylogenetic relationship among two species of genus Leiurus, from Saudi Arabia with additional comparative sequence data available from Egypt, Oman and Turkey is presented. The molecular phylogeny was performed using maximum parsimony, neighbor joining and bayesian inference. Our results indicate a clear deep splitting between the Western clade, which represented by L. quinuestriatus sequences from Egypt and those from the Eastern clade which encompassing different Leiurus species from Saudi Arabia, Oman and Turkey was shown. Also, the phylogenetic relationship represents additional support for the taxonomic status of Arabian Leiurus species.