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1.
Studies linking genetic structure in amphibian species with ecological characteristics have focused on large differences in dispersal capabilities. Here, we test whether two species with similar dispersal potential but subtle differences in other ecological characteristics also exhibit strong differences in genetic structure in the same landscape. We examined eight microsatellites in marbled salamanders (Ambystoma opacum) from 29 seasonal ponds and spotted salamanders (Ambystoma maculatum) from 19 seasonal ponds in a single geographic region in west-central Massachusetts. Despite overall similarity in ecological characteristics of spotted and marbled salamanders, we observed clear differences in the genetic structure of these two species. For marbled salamanders, we observed strong overall genetic differentiation (F ST = 0.091, F′ ST = 0.375), three population-level clusters of populations (K = 3), a strong pattern of isolation by distance (r = 0.58), and marked variation in family-level structure (from 1 to 23 full-sibling families per site). For spotted salamanders, overall genetic differentiation was weaker (F ST = 0.025, F′ ST = 0.102), there was no evidence of population-level clustering (K = 1), the pattern of isolation by distance (r = 0.17) was much weaker compared to marbled salamanders, and there was less variation in family-level structure (from 10 to 36 full-sibling families per site). We suspect that a combination of breeding site fidelity, effective population size, and generation interval is responsible for these marked differences. Our results suggest that marbled salamanders, compared to spotted salamanders, are more sensitive to fragmentation from various land-use activities and would be less likely to recolonize extirpated sites on an ecologically and conservation-relevant time frame.  相似文献   

2.
3.
In studying the variation of the taxa group Pseudopleuronectes yokohamae and P. schrenki from various areas in the Sea of Japan, significant differences in the combination of morphometric and meristic characters were not revealed. It was found that typical characters such as fin coloration from the blind side of the body, number of rays in the fins, number of scales in the lateral line, etc. that are used by most authors to distinguish P. yokohamae and P. shrenki strongly vary and are not adequate for assigning individuals to a certain taxon. A conclusion of the absence of differences and, hence, the homogeneity of the group studied is supported by genetic-biochemical studies, as well as by analysis of the lateral line system of these two groups of flatfish. Considering the results obtained and literature data on the morphology and ecology of flatfish taxa considered in the paper, it is justifiable to consider the P. yokohamae + P. schrenki group as one polymorphic species Pseudopleuronectes yokohamae Günther, 1877. The second taxon, P. shrenki, as a later species, should be considered a synonym of the species P. yokohamae.  相似文献   

4.
We provide initial information regarding the population structure and genetic diversity of Stenella frontalis from the Caribbean and southeastern Brazil from analyses of mitochondrial control region sequences and sequences from the first intron of the α-lactalbumin gene. Comparisons with previously described S. frontalis sequences showed a high number of haplotypes shared between populations throughout their distribution range. High diversity was found for southeastern Brazil and Caribbean samples, and population structure analyses indicate significant differentiation among population units at the FST level, but not at the ΦST level. Significant differentiation at the FST level was found between the Caribbean population unit and all other populations units. These results suggest historical or present connectivity between the Azores and Madeira and the southeastern Brazil groups and population differentiation between the Caribbean and southeastern Brazil, supporting the notion of two separate stocks in the waters around the Atlantic coast of South America.  相似文献   

5.
Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based F ST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the F ST-outlier methods detected together 11 F ST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with F ST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation.  相似文献   

6.
Genetic variation and population structure of hair crab (Erimacrus isenbeckii) were examined using nucleotide sequence analysis of 580 base pairs (bp) in the 3′ portion of the mitochondrial cytochrome c oxidase subunit I gene (COI) of 20 samples collected from 16 locales in Japan (the Hokkaido and Honshu Islands) and one in Korea. A total of 27 haplotypes was defined by 23 variable nucleotide sites in the examined COI region. Pairwise population F ST estimates and neighbor-joining tree inferred distinct genetic differentiation between the representative samples from the Pacific Ocean off the Eastern Hokkaido Island and the Sea of Japan, while others were intermediate between these two groups. AMOVA also showed a weak but significant differentiation among these three groups. The present results suggest a moderate population structure of hair crab, probably influenced by high gene flow between regional populations due to sea current dependent larval dispersal of this species.  相似文献   

7.
Halacsya and Paramoltkia are two monotypic genera of the Balkan ultramafic outcrops, both classified as paleoendemics. They show close phylogenetic relationship, similar ecology and partially sympatric range, but contrasting life-history traits, patterns of distribution and chromosomal features. We performed a study to compare their infraspecific genetic structure using AFLP fingerprinting. Within-population heterozygosity (HS) and total heterozygosity (HT) were lower in diploid H. sendtneri than in polyploid P. doerfleri (0.121 and 0.142 vs. 0.165 and 0.178, respectively). Number of polymorphic loci was also higher in the latter species. Halacsya showed significant levels of among-population variation (14.5%) and population differentiation (FST = 0.145), as well as a structuring in four main geographic groups connected by low gene flow. Combined with inability for long-distance dispersal, these data suggest that present-day range fragmentation in this species is the result of historical losses of intervening populations and support its status of paleoendemic surviving in refugial serpentine “islands”. Populations of P. doerfleri were instead genetically very close (FST = 0.049), and variation was partitioned almost exclusively among individuals (95.1%). Lack of population groupings and higher levels of gene flow suggested a single, panmictic group, fitting more a metapopulation than a “classical” paleoendemic model.  相似文献   

8.
Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.  相似文献   

9.
Fasciola hepatica, the liver fluke, is a trematode parasite that causes disease of economic importance in livestock. As a zoonosis this parasite also poses a risk to human health in areas where it is endemic. Population genetic studies can reveal the mechanisms responsible for genetic structuring (non-panmixia) within parasite populations and provide valuable insights into population dynamics, which in turn enables theoretical predictions of evolutionary dynamics such as the evolution of drug resistance. Here we genotyped 320 F. hepatica collected from 14 definitive hosts from four provinces in Argentina. STRUCTURE analysis indicated three population clusters, and principal coordinate analysis confirmed this, showing population clustering across provinces. Similarly, pairwise FST values amongst all four provinces were significant, with standardised pairwise FST (F′ST) ranging from 0.0754 to 0.6327. Therefore, population genetic structure was evident across these four provinces in Argentina. However, there was no evidence of deviation from Hardy–Weinberg equilibrium, so it appears that within these sub-populations there is largely random mating. We identified 263 unique genotypes, which gave a clonal diversity of 82%. Parasites with identical genotypes, clones, accounted for 26.6% of the parasites studied and were found in 12 of the 14 hosts studied, suggesting some clonemate transmission.  相似文献   

10.

Introduction

The importance of Plasmodium vivax in malaria elimination is increasingly being recognized, yet little is known about its population size and population genetic structure in the South Pacific, an area that is the focus of intensified malaria control.

Methods

We have genotyped 13 microsatellite markers in 295 P. vivax isolates from four geographically distinct sites in Papua New Guinea (PNG) and one site from Solomon Islands, representing different transmission intensities.

Results

Diversity was very high with expected heterozygosity values ranging from 0.62 to 0.98 for the different markers. Effective population size was high (12′872 to 19′533 per site). In PNG population structuring was limited with moderate levels of genetic differentiation. F ST values (adjusted for high diversity of markers) were 0.14–0.15. Slightly higher levels were observed between PNG populations and Solomon Islands (F ST = 0.16).

Conclusions

Low levels of population structure despite geographical barriers to transmission are in sharp contrast to results from regions of low P. vivax endemicity. Prior to intensification of malaria control programs in the study area, parasite diversity and effective population size remained high.  相似文献   

11.
The population structure of Labeo calbasu from 11 rivers belonging to the Indus, Ganges, Bhima, Mahanadi, and Godavari basins was investigated using allozyme marker systems. Seven out of 20 allozyme loci (35%) were polymorphic (P < 0.99). Both probability and score tests indicated significant deviation of genotype proportions from Hardy–Weinberg expectations at two loci, XDH* (Mahanadi, Bhima, and Godavari) and G6PDH* (Mahanadi). A pairwise genetic homogeneity test and F ST values indicated a low-to-moderate level (0.0515) of genetic structuring in the wild population of L. calbasu. AMOVA analysis also indicated moderate differentiation among the samples from different river basins. Analysis for genetic bottleneck was performed under the infinite allele model. The study revealed nine genetic stocks of L. calbasu from the natural population across Indian rivers. Evidence of genetic bottlenecks in some rivers was also revealed.  相似文献   

12.
Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase F ST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. F ST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.  相似文献   

13.
Understanding the factors that influence larval dispersal and connectivity among marine populations is critical to the conservation and sustainable management of marine resources. We assessed genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of inlets in five replicate sounds on the west coast of Vancouver Island, British Columbia, using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031, < 0.001), but consistently higher between paired coast and head of inlet sites (mean FST = 0.047, < 0.001) compared to among the five coast sites (mean FST = ?0.001, > 0.5) or among the five head of inlet sites (mean FST = 0.026, < 0.001). Heterozygosity, allelic richness and estimates of effective population size were also lower in head of inlet sites than in coast sites. Bayesian analysis identified two genetic groups across all samples, a single genetic group among only coast samples, two genetic groups among head of inlet samples and two genetic groups within each sound analysed separately. Head of inlet copper rockfish tended to be shorter with lower condition factors and grew more slowly than coast sites fish. Reduced physical connectivity and selection against immigrants in contrasting outer coast–head of inlet environments likely contribute to the evolution of population structure of copper rockfish. Based on genetic connectivity, coast sites appear to be better served by existing marine protected areas than are head of inlet sites.  相似文献   

14.
Data on the variation at eight microsatellite loci in the Far East salmon Oncorhynchus gorbuscha samples caught in 1984–1985 and 2001–2006 are analyzed. F-statistics indices at all levels of the hierarchical spatial structures are very small. At the same time, the differentiation between populations (according to F ST estimates) in the odd-year broodline of pink salmon does not exceed the temporal variation within populations. In the even-year broodline, the F-statistics indices at the interregional and intraregional levels are significantly greater than those in the odd-year broodline. F ST estimates (averaged over the same set of loci) vary widely within the range: the highest values are observed in populations of the coast of North America (except Alaska) and in the new range in the European North of Russia, whereas in the populations of the Asian part of the range and Alaska they are one order of magnitude smaller. The causes of the heterogeneity of the estimates of genetic differentiation within the range and between the broodlines of odd and even years are discussed. Since the mean population size estimates were correlated with the F ST values, it was assumed that the effect of random genetic drift, the main factor of population divergence in selectively neutral loci, weakens with an increase in the population size. Because of the greater population sizes in pink salmon compared to other salmon species, as well due to the uneven distribution of populations of different size, the usage of microsatellite markers may lead to an underestimation of the true divergence of populations and their regional groups and, consequently, to an overestimation of genetic migration.  相似文献   

15.
Ma Y  Yang M  Fan Y  Wu J  Ma Y  Xu J 《PloS one》2011,6(7):e22219

Background

Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet.

Methodology/Principal Findings

This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy–Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F ST = 0.156). Pairwise differentiation between populations were lower within clusters (F ST = 0.008–0.028 in cluster I and F ST = 0.004–0.048 in cluster II) than between clusters (F ST = 0.120–0.201). A reduced gene flow (Nm = 1–1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations.

Conclusions/Significance

Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The structured populations may limit the migration of genes under pressures/selections, such as insecticides and immune genes against malaria.  相似文献   

16.
The black tiger shrimp (Penaeus monodon), a commercially important penaeid species, is widely distributed across the Indo-Pacific region. Genetic diversity in P. monodon collected from eight geographical regions in Southwest, East and Andaman coastal waters of India (N = 418) was investigated using 10 polymorphic microsatellite loci. Average observed heterozygosity at sampled loci were high, ranging from 0.643 (Coromandel Coast) to 0.753 (South Andaman). Pairwise FST (ranged from 0.005 to 0.078) and RST (ranged from 0.005 to 0.171) estimates revealed surprisingly strong and statistically significant genetic structure among tiger shrimp populations. A synthetic map generated by multidimensional scaling shows an apparent cline in allele frequencies paralleling the roughly circular flow of surface currents in the Bay of Bengal. Significant heterozygote deficiencies were noted in most population samples at most loci. Andaman Island sites showed the highest diversity. Recognition of high genetic diversity and distinct population structuring of P. monodon in Indian seas has important implications for future domestication of this species in India, for two reasons: identification of the best wild founding stocks for aquaculture and, subsequently, the potential impacts of release of domesticates to the wild, either accidentally or deliberately (i.e. for stock enhancement).  相似文献   

17.
To evaluate the effects of landscape and demographic history on genetic variation in Picea glehnii at a regional scale we have investigated the genetic diversity and genetic differentiation of P. glehnii populations in the Furano region, central Hokkaido, Japan, using seven simple sequence repeat (SSR) markers. We found significant correlations between elevation and genetic diversity parameters. The value of A [46] increased and the value of F IS decreased with increasing elevation, while F IS values were not significantly different from 0 in any of the populations. Significant recent bottlenecks were detected for isolated populations at low-elevation sites and for relatively large populations at moderate- and high-elevation sites. Evolutionary events pre-dating the Holocene should be taken into consideration, as elevational gradients should be with respect to locally adapted traits such as flowering phenology, However, the palynological data from the Holocene in this region suggest that the distribution pattern of genetic diversity of P. glehnii detected here may have been influenced by past demographic history related to the elevation shifts in this species’ distribution associated with climate change during this period. Population differentiation was low, with F ST and GST values of 0.022 and 0.065, respectively. However, genetic boundaries were detected around one swamp population (C13). Therefore, significant isolation by distance (IBD) was not detected when all populations were considered, but there was significant IBD when the C13 population was excluded. Information on genetic diversity and genetic differentiation at the regional scale may be useful for selecting seed sources for afforestation programs for P. glehnii.  相似文献   

18.

Background and Aims

Allozyme and reproductive data sets for the Canarian flora are updated in order to assess how the present levels and structuring of genetic variation have been influenced by the abiotic island traits and by phylogenetically determined biotic traits of the corresponding taxa; and in order to suggest conservation guidelines.

Methods

Kruskal–Wallis tests are conducted to assess the relationships of 27 variables with genetic diversity (estimated by A, P, Ho and He) and structuring (GST) of 123 taxa representing 309 populations and 16 families. Multiple linear regression analyses (MLRAs) are carried out to determine the relative influence of the less correlated significant abiotic and biotic factors on the genetic diversity levels.

Key Results and Conclusions

The interactions between biotic features of the colonizing taxa and the abiotic island features drive plant diversification in the Canarian flora. However, the lower weight of closeness to the mainland than of (respectively) high basic chromosome number, partial or total self-incompatibility and polyploidy in the MLRAs indicates substantial phylogenetic constraint; the importance of a high chromosome number is feasibly due to the generation of a larger number of linkage groups, which increase gametic and genotypic diversity. Genetic structure is also more influenced by biotic factors (long-range seed dispersal, basic chromosome number and partial or total self-incompatibility) than by distance to the mainland. Conservation-wise, genetic structure estimates (FST/GST) only reflect endangerment under intensive population sampling designs, and neutral genetic variation levels do not directly relate to threat status or to small population sizes. Habitat protection is emphasized, but the results suggest the need for urgent implementation of elementary reproductive studies in all cases, and for ex situ conservation measures for the most endangered taxa, even without prior studies. In non-endangered endemics, multidisciplinary research is needed before suggesting case-specific conservation strategies. The molecular information relevant for conservation should be conserved in a standardized format to facilitate further insight.  相似文献   

19.
Wild cherry (Prunus avium L.) is a widespread, partially asexual, noble hardwood European species characterized by a scattered distribution, small population sizes, and human exploitation for its valuable wood. These characteristics, especially at the southern limits of the species natural distribution where additional varying stresses may occur, render P. avium populations prone to potential stochastic, genetic, and demographic events. In this study, we used dominant inter simple sequence repeat (ISSR) and codominant simple sequence repeat (SSR) markers to infer the genetic structure of P. avium. Five populations from northern Greece were evaluated based on 46 ISSR and 11 SSR loci. Populations presented a relatively high level of genetic variation, with a mean genetic diversity of H e?=?0.166 and H e?=?0.740 regarding ISSR and SSR analysis, respectively. We observed moderate population differentiation for ISSR (G ST?=?0.113) and SSR (F ST?=?0.097) markers. AMOVA also detected significant differentiation among populations for ISSRs (?? ST?=?0.338) and SRRs (?? ST?=?0.162). According to linkage disequilibrium analysis, estimates of effective population size were generally sufficient for maintaining extant genetic variability and evolutionary potential. A possible bottleneck was detected for only one population. In general, it appears that despite the particular characteristics of the P. avium populations studied, genetic stochasticity events were not apparent. The studied populations, located at the rear edge of the species European distribution, reveal a wealth of genetic variation that is very valuable for the genetic conservation of local adaptive gene complexes, especially under contemporary climatic change scenarios.  相似文献   

20.
Effective population size, levels of genetic diversity, gene flow, and genetic structuring were assessed in 205 colonial Roseate spoonbills from 11 breeding colonies from north, central west, and south Brazil. Colonies and regions exhibited similar moderate levels of diversity at five microsatellite loci (mean expected heterozygosity range 0.50–0.62; allelic richness range 3.17–3.21). The central west region had the highest Ne (59). F ST values revealed low but significant genetic structuring among colonies within the north and within the south regions. Significant global genetic structuring was found between the northern and central western populations as well as between the northern and southern populations. An individual-based Bayesian clustering method inferred three population clusters. Assignment tests correctly allocated up to 64% of individuals to their source regions. Collectively, results revealed complex demographic dynamics, with ongoing gene flow on a local scale, but genetic differentiation on a broader scale. Populations in the three regions may all be conserved, but special concern should be given to central western ones, which can significantly contribute to the species’ gene pool in Brazil.  相似文献   

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