Population structure and colour variation of the cichlid fishes Labeotropheus fuelleborni Ahl along a recently formed archipelago of rocky habitat patches in southern Lake Malawi

Extremely fine-scale genetic partitioning has recently been detected among populations of Lake Malawi''s rock-dwelling cichlids through the study of microsatellite loci. Understanding the mechanisms of genetic differentiation that operate in this rapidly speciating group requires further investigation of the geographic patterns of gene flow and the congruence between morphological and genetic divergence. In pursuit of this goal, genetic variation at four microsatellite loci and variation in male breeding coloration were examined in several populations of Labeotropheus fuelleborni from southern Lake Malawi. Significant genetic differentiation exists among populations (overall F_ST = 0.063; p = 0.0002). While migration appears unrestricted within continuous rocky patches, deep waters and sandy bays more than 2 km wide act as strong barriers to gene flow. Dispersal of L. fuelleborni appears to follow a stepping-stone model in which the distribution of habitats often constrains migration to one dimension. It is hypothesized that clinal colour variation in the study area has resulted from the secondary contact of divergent lineages, although reproductive isolation between colour variants is not apparent. Relative to shoreline populations, reduced levels of gene flow among populations inhabiting isolated, deep-water islands provides greater opportunities for drift, adaptation to local conditions, or sexual selection to effect genetic differentiation in this species.     

Local human pressures influence gene flow in a hybridizing Daphnia species complex

Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members of the Daphnia longispina species complex were reconstructed over the last 100 years for three large temperate lakes under strong anthropogenic pressures via palaeogenetic analyses of resting egg banks. Drastic changes in the genetic structure of the Daphnia community, associated with hybridization events between D. longispina and D. galeata and subsequent introgression, were detected in Lakes Geneva and Bourget. In Lake Bourget, these changes were induced by the successful establishment of D. galeata with rising phosphorus levels and reinforced by the sensitivity of D. longispina to fish predation pressure. In Lake Geneva, the pattern of hybridization during eutrophication is more likely a function of the original taxonomic composition of the species complex in this lake. Lakes seem to require at least a meso‐oligotrophic status to allow D. galeata populations to establish and accordingly no D. galeata genotypes were found in the egg bank of oligotrophic Lake Annecy. In contrast to the generally assumed pattern of unidirectional hybridization in this species complex, bidirectional hybridization was recorded in Lakes Geneva and Bourget. Our results also demonstrate complex genetic trajectories within this species complex and highlight the irreversibility of changes in the genotypic architecture of populations driven by local human pressures. Finally, we show that extensive hybridization and introgression do not necessarily result in a large and homogenous hybrid swarm.     

千岛湖社鼠种群遗传现状及与生境面积的关系

以千岛湖地区13个岛屿上的社鼠(Niviventer confucianus)种群为研究对象,利用13个微卫星位点分析了13个社鼠种群的遗传现状,并探讨了种群遗传现状与岛屿面积大小之间的关系。研究结果显示,13个社鼠种群的平均观测等位基因数(Na)与平均有效等位基因数(Ne)分别为7.385,5.952,平均期望杂合度(He)与平均观测杂合度(Ho)分别为0.819,0.930,平均多态信息含量(PIC)为0.760,说明13个社鼠种群均具有较高的遗传多样性。13个种群间的分化系数(Fst)为0.053,表明种群间的遗传分化较小。3个面积较大且相近岛屿上社鼠种群,即高仙阁种群 (Gaoxiange Island,G);乌石T岛种群 (Wushi T Island,WT);东门岛种群 (Dongmen Island,DM)间的Fst值均小于0.05,表明种群间无分化,而小岛种群与大岛种群间的分化却比较明显。此外,一元回归结果显示,多态信息含量(PIC)和Shannon多样性指数(I)与岛屿面积大小之间均存在显著地正相关关系。以上结果说明,在社鼠种群进化过程中,生境面积的缩小可能使种群的遗传结构发生改变,并有可能导致种群的快速进化。     

Genetic diversity in the Churra tensina and Churra lebrijana endangered Spanish sheep breeds and relationship with other Churra group breeds and Spanish mouflon

The aim of the present study was to estimate the genetic intra-breed variability of Churra tensina and Churra lebrijana endangered breeds and to establish genetic relationships with Churra, Latxa and Merino breeds, as well as Spanish mouflon, by using 28 microsatellite markers, to provide useful information for their conservation. Allele frequencies and heterozygosity revealed high genetic variation in the two endangered breeds despite their small population size. Estimates of inbreeding coefficient (F_IS) were significant for all breeds studied, except for Churra lebrijana breed. The highest inbreeding coefficient (F_IS = 0.143) was found in the Spanish mouflon. Genetic differentiation tests (F_ST = 0.121) and assignment of individuals to populations indicated the existence of defined breed populations, and low genetic flow between these breeds. The highest pairwise Reynolds distance (D_R) values were observed between Mouflon and the domestic sheep breeds. Considering only domestic sheep breeds, the Churra lebrijana breed showed the highest pairwise D_R values_. The lowest values were found between Latxa and the other domestic sheep, except for Churra lebrijana. Results of pairwise D_R values, as well as phylogenetic tree and bottleneck analysis showed an important genetic isolation of the Churra lebrijana breed from the other Churra types, and genetic signatures of a demographic bottleneck. Finally, structure analysis of populations detected a population subdivision in the Latxa sheep breed. In conclusion, this study presents valuable insight into the existing genetic variability of two Spanish endangered breeds, as well as the first study in Spanish mouflon based on microsatellite analysis. The high degree of variability demonstrated in Churra tensina and Churra lebrijana implies that these populations are rich reservoirs of genetic diversity.     

Genetic structure, subdivision, and differentiation in stankewiczii pine (Pinus stankewiczii (Sukacz.) Fomin) populations from mountainous Crimea

In order to analyze the genetic structure, subdivision and differentiation within and between two small isolated populations of the Crimea relict endemic, Pinus stankewiczii (Sukacz.) Fomin, electrophoretic analysis of the isozyme variation at nine enzymatic systems was carried out using 183 oldest trees. It was demonstrated that in populations of P. stankewiczii, 80% of the genes were in polymorphic state. Each tree was heterozygous at 19.1% loci, and at 21.6% loci in artificial 50-year-old plantation. The genetic structure of two populations was less differentiated (D _N = 0.006), compared to their individual localities (D _N = 0.008?0.009). Within-population subdivision of the diffusely dispersed populations was higher (F _ST -G _ST = 1.8–2.0%) than that of the populations themselves (0.8%).     

Genetic structure and differentiation of populations of the tetraploid species <Emphasis Type="Italic">Oxytropis chankaensis</Emphasis> (Fabaceae)

The population genetic variation of the tetraploid species Oxytropis chankaensis Jurtz. (Fabaceae), a local endemic of the western coast of Khanka Lake (Primorye), was examined. Five populations were analyzed using 28 isozyme loci encoding 16 enzyme systems. Significant allelic heterogeneity among the populations was found for six out of twelve polymorphic loci. The heterozygosity of the samples (total sample size 294 plants) H _e = 0.301 was considerable higher than the mean values in populations of endemic species (0.076). Based on the results of this study, we identified two groups of O. chankaensis populations (southern and northern), in spite of the absence of marked hiatus between them. Of special interest is the population from Przhewalski Spit, which is a natural reserve of genetic diversity of the species and the putative center of formation of the autotetraploid O. chankaensis.     

Genetic Structure of Daphnia galeata Populations in Eastern China

This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes.     

High genetic similarity between Polish and North European Scots pine (Pinus sylvestris L.) populations at nuclear gene loci

Nucleotide polymorphisms in a set of 32 nuclear genes were studied in 19 mountain, peatbog and lowland populations of Scots pine representing known phenotypic races and populations of presumably relict character for the species in Poland. At 29 genes, the pattern of genetic variation was compared to 11 reference populations from Northern, Western and Southern Europe. Similar levels of nucleotide polymorphism and excess of low-frequency mutations were observed in Polish populations (π _tot?=?0.0055, D?=??0.308) and as compared to the reference samples (π _tot?=?0.0054, D?=??0.170). Bayesian assignment and conventional frequency-based statistics indicate that Polish populations share the same genetic background at the analysed nuclear gene markers. However, the populations showed a much closer genetic relationship with North European samples than other regional groups of populations. Across the very uniform genetic background of the populations, we identified several genes with outlier patterns of haplotype, polymorphism frequency variation and departures from compound neutrality tests. Our data indicate that the Central and North European parts of the Scots pine distribution seem particularly suitable for association genetic studies to link phenotypic and genetic variation at a large geographical scale.     

Genetic characterization and management of the endangered Mohave tui chub

The Mohave tui chub (Siphateles bicolor mohavensis) is the only fish native to the Mojave River, California. The fish were displaced by introduced arroyo chubs (Gila orcutti) throughout most of their range, starting in the 1930s. Two potentially relictual populations and two transplanted populations were genetically characterized using 12 microsatellite DNA loci, along with contemporary cyprinid populations in the Mojave River. We found only un-hybridized Mohave tui chubs in the refuge populations, and only un-hybridized arroyo chubs in the Mojave River. The two largest Mohave tui chub populations (Lake Tuendae and China Lake) exhibit similar, comparatively high genetic variation. Another large population (Camp Cady) with low genetic diversity shows the effect of a bottleneck of ten individuals during the historic founding event. The fourth population (MC Spring) has the fewest alleles, lowest heterozygosity, and is the most divergent, suggesting that genetic drift from a persistently low effective population size has reduced genetic diversity since its apparent isolation in 1934. We recommend instituting artificial gene flow to rebuild genetic variation in Camp Cady from both Lake Tuendae and China Lake, and the establishment of new populations with founders from both Lake Tuendae and China Lake. Additionally, we comment on the infeasibility of restoring populations of Mohave tui chub in their historic habitats.     

Genetic diversity of nine faba bean (Vicia faba L.) populations revealed by isozyme markers

Seven isozyme systems (Sod, 6-Pgd, Me, Est, Skdh, Fdh and Gdh) representing nine loci were used to study the genetic diversity of nine faba bean populations. Seven loci revealed polymorphic bands and showed the same quaternary structure as that found in several species. They revealed a high number of phenotypes. Indeed, from 3 to 9 phenotypes per locus were investigated in this study. The percentage of polymorphic loci (P = 59.3 %) was higher than that mentioned in the autogamous species (P = 20.3 %) and less than the optimum (P=96 %) indicated for allogamous plants. Total genetic diversity (H _T) and within population genetic diversity (H _S) were estimated with the isozyme markers. The contribution of among population genetic diversity (D _ST) to total genetic diversity was 22%. Enzyme markers pointed out an average inbreeding level for whole population (F _IT) and within population (F _IS). Within population genetic diversity represents 78% of total diversity. Intra-population genetic diversity (H _S = 0.206) was ranged with the respect of allogamous species and was clearly higher than that of among population genetic diversity (D _ST = 0.057) indicating an out-crossing predominance in the studied populations. The expected heterozygosity was higher than that observed heterozygosity at the allogamous species was confirmed in this study. Although, the mean estimated gene flow was less than 1(Nm=0.814), the dendrogram based on Nei’s genetic distance of the 9 populations using UPGMA method showed some genetic drift between populations.     

Genetic analysis of potential postglacial watershed crossings in Central Europe by the bullhead (Cottus gobio L.)

Natural colonizations across watersheds have been frequently proposed to explain the present distributions of many freshwater fish species. However, detailed studies of such potential watershed crossings are still missing. Here, we investigated potential postglacial watershed crossings of the widely distributed European bullhead (Cottus gobio L.) in two different areas along the Rhine–Rhône watershed using detailed genetic analysis. The main advantage of studying bullheads vs. other freshwater fish species is that their distribution has been lightly influenced by human activities and as such, interpretations of colonization history are not confounded by artificial transplantations. The genetic analyses of eight microsatellite loci revealed strong genetic similarities between populations of both sides of the Rhine–Rhône watershed in the Lake Geneva area, giving strong evidence for a natural watershed crossing of bullheads from the upper Rhine drainage into the Rhône drainage in the Lake Geneva area likely facilitated by the retreat of the glaciers after the last glacial maximum some 20 000 years ago. Populations from the Lake Geneva basin were genetically more similar to populations from across the watershed in the upper Rhine drainage than to populations further downstream in the lower Rhône. In contrast, populations from Belfort, an area, which was not covered by ice during the last glacial maximum, showed strong genetic differentiation between populations of the upper Rhine and Rhône drainages. Based on our results on the bullhead, we propose that glacial retreat may have eased the dispersal of numerous European freshwater fish species across several geological boundaries.     

Population Genetic Structure of the Endangered Kaiser’s Mountain Newt,Neurergus kaiseri (Amphibia: Salamandridae)

Species often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in an endemic and critically endangered stream breeding mountain newt, Neurergus kaiseri, within its entire range in southwestern Iran. We identified two geographic regions based on phylogenetic relationships using Bayesian inference and maximum likelihood of 779 bp mtDNA (D-loop) in 111 individuals from ten of twelve known breeding populations. This analysis revealed a clear divergence between northern populations, located in more humid habitats at higher elevation, and southern populations, from drier habitats at lower elevations regions. From seven haplotypes found in these populations none was shared between the two regions. Analysis of molecular variance (AMOVA) of N. kaiseri indicates that 94.03% of sequence variation is distributed among newt populations and 5.97% within them. Moreover, a high degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θ_CT = 0.94, P = 0.002). The positive and significant correlation between geographic and genetic distances (r = 0.61, P = 0.002) following controlling for environmental distance suggests an important influence of geographic divergence of the sites in shaping the genetic variation and may provide tools for a possible conservation based prioritization policy for the endangered species.     

Latitudinal variability of Drosophila melanogaster: Allozyme frequencies divergence between European and Afrotropical populations

Allelic frequencies at five polymorphic loci were determined in seven European and six Afrotropical populations of Drosophila melanogaster. African populations, which may be considered as ancestral for the species, showed a greater genetic diversity as measured by the number of alleles found. Within each geographic group (Europe or tropical Africa) genetic distances between local populations were very small (D=0.027). By contrast, the average distance between European and African populations (D=0.389) was more than 12 times bigger. It was previously known that various morphological or physiological differences, which probably reflect genetic adaptations to different environments, exist between these temperate and tropical populations. Data presented here suggest that the divergence in allozyme frequencies also reflects some selective mechanisms.     

Comparative ecotoxicity of suspended sediment in the lower Rhone River using algal fractionation,Microtox® and Daphnia magna bioassays

The toxicity associated with suspended sediments from the Rhone River (Switzerland-France) was determined with three acute bioassays. Large volume water samples were centrifuged for recovery of suspended solids in November 1989; one sample was taken as a control upstream from Lake Geneva and the 9 remainder downstream from Geneva to the Mediterranean Sea, with a single sample of the major tributary the Saône at Lyon. Heavy metals (Hg, Cd, Cr, Cu, Ni, Pb, Zn) and organic contaminants (OCs, PCBs, PAHs) bound to sediment were analysed and extracted by elutriation with filtered lake water and by organic solvent (dichloromethane). Sediment water elutriates were tested with algal fractionation bioassays (AFB) using Lake Geneva ambient phytoplankton, with Daphnia magna and Microtox® acute toxicity tests, whereas organic extracts were utilized in the latter two bioassays to evaluate the potential sediment toxicity.The bulk analyses of the sediment together with elutriate metal concentrations indicated the highest contamination of sediment downstream of Lyon. Medium contamination appeared for the stations downstream of Geneva, in the Saône River and at the Rhone River mouth. The station upstream of Lyon had low concentrations, comparable to the values in the Upper Rhone. Organic contaminants are mainly observed downstream of Lyon and their concentrations decline onwards to the sea. The bioassays Microtox® on organic extracts and AFB on the elutriates show a similar toxicity trend, but differ in that Microtox was more sensitive to organics whereas the algal test responded predominantly to metals. This difference is believed to be due to the different extraction procedures used, rather than to the tests themselves. Daphnia magna was the least sensitive and appeared to give a broader band response to the observed contaminants in the sediment. The bioassay results when integrated confirm that the biotoxicity trends relate well to the composition of the sediment, a factor which emphasizes the need for battery testing in ecotoxicological assessment.     

Pronounced genetic differentiation of small,isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya

Lake Magadi, an alkaline hypersaline lake in Kenya, is one of the most extreme water bodies known. Although its water temperatures often exceed 40°C, a particular lineage of ‘dwarf’ tilapia, Alcolapia grahami, has evolved remarkable adaptations to survive in this hostile environment. Magadi tilapia exists in small fragmented populations in isolated lagoons within Lake Magadi and its satellite Lake, Little Magadi. In spite of the potential this tilapia holds for understanding evolutionary processes in stressful environments, few genetic studies have focused on this species. We examined the genetic diversity and spatial genetic relationships of Magadi tilapia populations using microsatellite and mitochondrial markers. High levels of genetic variation were found to be supporting the hypothesis that A. grahami populations represent remnants of a much larger fish population that inhabited paleo-lake Orolonga. In contrast to previous studies, we found a well-supported genetic structure of A. grahami consisting of three differentiated genetic clusters (a) Little Magadi, (b) Fish Spring Lagoon and (c) Rest of Magadi. Given the importance of this species to the Magadi ecosystem and its potential evolutionary significance, the three genetic clusters should be considered as separate gene pools and conservation strategies aimed at protecting the species based on these clusters are recommended.     

Genetic Relationships of Ethnic Minorities in Southwest China Revealed by Microsatellite Markers

Population migrations in Southwest and South China have played an important role in the formation of East Asian populations and led to a high degree of cultural diversity among ethnic minorities living in these areas. To explore the genetic relationships of these ethnic minorities, we systematically surveyed the variation of 10 autosomal STR markers of 1,538 individuals from 30 populations of 25 ethnic minorities, of which the majority were chosen from Southwest China, especially Yunnan Province. With genotyped data of the markers, we constructed phylogenies of these populations with both D_A and D_C measures and performed a principal component analysis, as well as a clustering analysis by structure. Results showed that we successfully recovered the genetic structure of analyzed populations formed by historical migrations. Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation.     

Population genetics of introduced bullfrogs, Rana (Lithobates) catesbeianus, in the Willamette Valley, Oregon, USA

The American bullfrog, Rana (Lithobates) catesbeianus, is endemic to eastern North America, but has been introduced to approximately 40 countries on four continents and is considered one of the hundred worst invasive alien species in the world. Here, we investigated the genetics of invasive bullfrogs in the Willamette Valley, Oregon, USA, where bullfrogs are widespread and abundant to determine: (1) the minimum number of bullfrog introductions; (2) the native source population(s); and (3) whether genetic variation is reduced compared to source populations. To answer these questions, we analyzed partial sequences of the mitochondrial cytochrome b gene for 251 bullfrogs from the Willamette Valley and the native range. We found that bullfrogs from the Mississippi River basin and Great Lakes region were introduced at least once to the Willamette Valley. Genetic variation measured as haplotype diversity (h) and nucleotide diversity (?? _n ) was not significantly different between Willamette Valley and source populations. Our results were in contrast to a recent genetic analysis of invasive bullfrog populations in Europe, which found that genetic variation in European bullfrog populations was much lower than in source populations. European bullfrogs also originated from different source populations than Willamette Valley bullfrogs. The difference in genetic composition between Willamette Valley and European bullfrogs is likely due to differences in their invasion histories and may have implications for the potential of bullfrogs in these different regions to adapt and expand.     

Sequence-related amplified polymorphism (SRAP) of wild emmer wheat (Triticum dicoccoides) in Israel and its ecological association

Genetic diversity and population structure of 15 wild emmer wheat (Triticum dicoccoides) populations from Israel were detected by 30 sequence-related amplified polymorphism (SRAP) primer pairs. Two hundred and forty four fragments out of 438 were polymorphic. The proportion of polymorphic loci (P), the genetic diversity (He), and Shannon's information index were 0.557, 0.198, and 0.295, respectively. The population Amirim had the highest genetic variation, whereas the population of Tabigha had the lowest genetic variation. The hierarchical analysis of molecular variance (AMOVA) revealed that most of the variation was presented within populations. The value of genetic distance (D) between the populations varied from 0.027 to 0.165 with an average of 0.079, and the estimates of genetic distance were geographically independent based on the Mantel test (r = 0.105, P = 0.168). A total of 30 significant (P < 0.05) correlations were detected between 14 SRAP loci and 12 ecogeographic factors.     

广东省五节芒遗传多样性的ISSR分析

采用ISSR分子标记技术,对广东省内分布的能源植物五节芒(Miscanthus floridulus)13个野生居群共215个个体的遗传多样性进行了研究.9个ISSR引物共扩增到了81个位点,其中76个是多态性位点.结果表明,广东五节芒的遗传多样性水平很高,物种水平上,多态位点百分率(PPB)为93.83％,Nei's...     

Population structure and genetic variation in the genus Dipteronia Oliv. (Aceraceae) endemic to China as revealed by cpSSR analysis

The genus Dipteronia Oliv. endemic to central and southern China consists of two species, D. sinensis Oliv. and D. dyerana Henry, both of them are rare and endangered. In the present study, genetic variation in 17 populations of D. sinensis and four populations of D. dyerana was estimated using ten polymorphic chloroplast microsatellite loci (cpSSR). Forty-nine chloroplast haplotypes were identified from 204 individuals analyzed. Thirty-nine haplotypes were found in D. sinensis, while ten in D. dyerana. No haplotype was shared between the species. AMOVA analysis revealed that the majority of the genetic variation was partitioned among populations within D. sinensis (F _ST = 0.7980) and D. dyerana (F _ST = 0.654). Cluster analysis grouped the 21 populations into two groups according to their species delimitation. The populations of D. sinensis were further divided into two subgroups corresponding to their geographical distributions. Correlation analysis revealed significant correlation between geographical distance and genetic distance of these populations (r = 0.326, p < 0.01 for D. sinensis vs. r = 0.777, p < 0.05 for D. dyerana). Genetic structure of these populations and a calculated pollen-to-seed flow ratio of (3.2:1 vs. 0.6:1) within the species suggested that little gene flow has occurred among the populations over an extended period. Thus, it implies that the genus Dipteronia might have experienced a genetic bottleneck and limited expansion during its evolutionary history.