Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction‐site‐associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F_ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half‐ and full‐siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual‐level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual‐level genotype information, such as quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.     

Genetic differentiation between collections of hatchery and wild masu salmon (<Emphasis Type="Italic">Oncorhynchus masou</Emphasis>) inferred from mitochondrial and microsatellite DNA analyses

There has been very little effort to understand genetic divergence between wild and hatchery populations of masu salmon (Oncorhynchus masou). In this study, we used mitochondrial (mt) NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic nuclear microsatellite DNA loci to compare the genetic variability in three hatchery broodstocks of masu salmon with the variability in eight putative wild masu populations sampled in five rivers including one known source river for the hatchery broodstocks. Both ND5 and microsatellites showed no significant genetic divergence (based on F_ST estimates) between four annual collections from the source river population, suggesting no change in genetic diversity over this time period. The F_ST estimates, an analysis of molecular variance (AMOVA), and a neighbor-joining tree using both DNA markers suggested significant differentiation between the three hatchery and all eight putative wild populations. We conclude that genetic diversity of hatchery populations are low relative to putative wild populations of masu salmon, and we discuss the implications for conservation and fisheries management in Hokkaido.     

Genetic diversity and integrity of German wildcat (Felis silvestris) populations as revealed by microsatellites,allozymes, and mitochondrial DNA sequences

As a consequence of persecution and habitat fragmentation, wildcats (Felis silvestris silvestris) in Western Europe have experienced a severe reduction in population numbers and sizes. The remaining wildcat populations are considered to be endangered by losses of genetic variability and by hybridisation with free-ranging domestic cats. To investigate genetic diversity within and among wild and domestic cat populations in Germany and to estimate the extent of gene flow between both forms, we analysed a total of 266 individuals. PCR-amplification and sequencing of 322 base pairs of a highly variable part of the mitochondrial control region (HV1) of 244 specimens resulted in 41 haplotypes with 31 polymorphic sites. Additionally, eight microsatellite loci were examined for those 244 cats. Moreover, a total of 46 wildcats and 22 domestic cats could be genotyped for 13 polymorphic out of 31 enzyme loci. Genetic variability in both groups was generally high. Variability in domestic cat populations was higher than in wildcat populations. Almost no differentiation between domestic cat populations could be found (F_ST for microsatellites=3%). In contrast, wildcat populations differed significantly from one another (F_ST for microsatellites=9.55%) Within the smaller wildcat populations, a reduction of genetic diversity was detectable with regard to the nuclear DNA. Wildcat and domestic cat mitochondrial haplotypes were separated, suggesting a very low level of maternal gene flow between both forms. In microsatellites and to a somewhat lesser extent in allozymes, wildcats and domestic cats showed distinct differentiation, suggesting an only low extent of past hybridisation in certain populations. The microsatellite data set indicated a significantly reduced effective population size (bottleneck) in the recent past for one German wildcat population.     

Estimates of population differentiation in pink salmon Oncorhynchus gorbuscha with using of the microsatellite markers may be underestimated due to high population sizes

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.     

Population Genomics of the Euryhaline Teleost Poecilia latipinna

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative F_ST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant F_ST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive F_ST values that could indicate adaptive divergence.     

Microsatellite Variation in Two Populations of Free-Ranging Yellow Baboons (Papio hamadryas cynocephalus)

We investigated genetic variation at six microsatellite (simple sequence repeat) loci in yellow baboons (Papio hamadryas cynocephalus) at two localities: the Tana River Primate Reserve in eastern Kenya and Mikumi National Park, central Tanzania. The six loci (D1S158, D2S144, D4S243, D5S1466, D16S508, and D17S804) were all originally cloned from and characterized in the human genome. These microsatellites are polymorphic in both baboon populations, with the average heterozygosity across loci equal to 0.731 in the Tana River sample and 0.787 in the Mikumi sample. The genetic differentiation between the two populations is substantial. Kolmogornov–Smirnov tests indicate that five of the six loci are significantly different in allele frequencies in the two populations. The mean F _ST across loci is 0.069, and Shriver's measure of genetic distance, which was developed for microsatellite loci (Shriver et al., 1995), is 0.255. This genetic distance is larger than corresponding distances among human populations residing in different continents. We conclude that (a) the arrays of alleles present at these six microsatellite loci in two geographically separated populations of yellow baboons are quite similar, but (b) the two populations exhibit significant differences in allele frequencies. This study illustrates the potential value of human microsatellite loci for analyses of population genetic structure in baboons and suggests that this approach will be useful in studies of other Old World monkeys.     

Does GST underestimate genetic differentiation from marker data?

The widely applied genetic differentiation statistics F_ST and G_ST have recently been criticized for underestimating differentiation when applied to highly polymorphic markers such as microsatellites. New statistics claimed to be unaffected by marker polymorphisms have been proposed and advocated to replace the traditional F_ST and G_ST. This study shows that G_ST gives accurate estimates and underestimates of differentiation when demographic factors are more and less important than mutations, respectively. In the former case, all markers, regardless of diversity (H_S), have the same G_ST value in expectation and thus give replicated estimates of differentiation. In the latter case, markers of higher H_S have lower G_ST values, resulting in a negative, roughly linear correlation between G_ST and H_S across loci. I propose that the correlation coefficient between G_ST and H_S across loci, r_GH, can be used to distinguish the two cases and to detect mutational effects on G_ST. A highly negative and significant r_GH, when coupled with highly variable G_ST values among loci, would reveal that marker G_ST values are affected substantially by mutations and marker diversity, underestimate population differentiation, and are not comparable among studies, species and markers. Simulated and empirical data sets are used to check the power and statistical behaviour, and to demonstrate the usefulness of the correlation analysis.     

Genetic differentiation of pink salmon Oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 enzyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd-and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation for the allozyme loci, per broodline, were on average 0.43% (G _ST), while over the microsatellite loci it was 0.26% (the ?_ST coefficient, F-statistics based on the allele frequency variance), and 0.90% (the ρ_ST coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of southern Sakhalin. Multidimensional scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of ?_ST values were substantially lower than in terms of ρ_ST values. Regional genetic differentiation, mostly expressed at the allozyme loci between the populations from the northern Sea of Okhotsk and the Sakhalin and Kuril group of populations, was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the gene migration coefficient inferred from the “private” allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization of the range     

Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci

The population genetic structure of the Anopheles gambiae in western Kenya was studied using length variation at five microsatellite loci and sequence variation in a 648-nt mtDNA fragment. Mosquitoes were collected from houses in villages spanning up to 50 km distance, The following questions were answered, (i) Are mosquitoes in a house more related genetically to each other than mosquitoes between houses? (ii) What degree of genetic differentiation occurs on these geographical scales? (iii) How consistent are the results obtained with both types of genetic markers? At the house level, no differentiation was detected by F_ST and R_ST, and the band sharing index test revealed no significant associations of alleles across loci. Likewise, indices of kinship based on mtDNA haplotypes in houses were even lower than in the pooled sample. Therefore, the hypothesis that mosquitoes in a house are more related genetically was rejected. At increasing geographical scales, microsatellite allele distributions were similar among all population samples and no subdivision of the gene pool was detected by F_ST or R_ST. Likewise, estimates of haplotype divergence of mtDNA between populations were not higher than the within population estimates, and mtDNA-based F_ST values were not significantly different from zero. That sequence variation in mtDNA provided matching results with microsatellite loci (while high genetic variation was observed in all loci), suggested that this pattern represents the whole genome. The minimum area associated with a deme of A. gambiae in western Kenya is therefore larger than 50 km in diameter.     

Low levels of quantitative and molecular genetic differentiation among natural populations of Medicago ciliaris Kroch. (Fabaceae) of different Tunisian eco-geographical origin

In this paper, we analyze the genetic variability in four Tunisian natural populations of Medicago ciliaris using 19 quantitative traits and six polymorphic microsatellite loci. We investigated the amplification transferability of 30 microsatellites developed in the model legume M. truncatula to M. ciliaris. Results revealed that about 56.66% of analyzed markers are valuable genetic markers for M. ciliaris. The most genetic diversity at quantitative traits and microsatellite loci was found to occur within populations (>80%). Low differentiations among populations at quantitative traits Q _ST  = 0.146 and molecular markers F _ST  = 0.18 were found. The majority of measured traits exhibited no significant difference in the level of Q _ST and F _ST . Furthermore, significant correlations established between these traits and eco-geographical factors suggested that natural selection should be invoked to explain the level of phenotypic divergence among populations rather than drift. There was no significant correlation between population differentiation at quantitative traits and molecular markers. Significant spatial genetic structure consistent with models of isolation by distance was detected within all studied populations. The site-of-origin environmental factors explain about 9.07% of total phenotypic genetic variation among populations. The eco-geographical factors that influence more the variation of measured traits among populations are the soil texture and altitude. Nevertheless, there were no consistent pattern of associations between gene diversity (He) and environmental factors.     

Microsatellite polymorphism and genetic differentiation in three Norwegian populations of Elymus alaskanus (Poaceae)

 Variation at seven microsatellite loci was investigated in three local E. alaskanus populations from Norway and microsatellite variation was compared with allozyme variation. The percentage of polymorphic loci was 81%, the mean number of alleles per polymorphic locus was 5.7 and expected heterozygosity was 0.37. An F-statistic analysis revealed an overall 48% deficit of heterozygotes over Hardy-Weinberg expectations. Gene diversity is mainly explained by the within population component. The averaged between population differentiation coefficient, F _st , over 7 loci is only 0.13, which accounts for only 13% of the whole diversity and was contrary to allozyme analysis. The mean genetic distance between populations was 0.12. However, a χ² -test showed that allele frequencies were different (p < 0.05) among the populations at 5 of the 7 loci. In comparison with the genetic variation detected by allozymes, microsatellite loci showed higher levels of genetic variation. Microsatellite analysis revealed that population H10576 possesses the lowest genetic variation among the tested three populations, which concur with allozyme analysis. The dendrogram generated by microsatellites agreed very well with allozymic data. Our results suggest that natural selection may be an important factor in shaping the genetic diversity in these three local E. alaskanus populations. Possible explanations for deficit heterozygosity and incongruence between microsatellites and allozymes are discussed. Received November 6, 2001; accepted April 24, 2002 Published online: November 14, 2002 Addresses of the authors: Genlou Sun (e-mail: Genlou.sun@STMARYS.CA), Biology Department, Saint Mary's University, Halifax. Nova Scotia, B3H 3C3, Canada. B. Salomon, R. von Bothmer, Department of Crop Science, The Swedish University of Agricultural Sciences, P.O. Box 44, SE-230 53, Alnarp, Sweden.     

Comparative allozyme and microsatellite population structure in a narrow endemic plant species, Centaurea corymbosa Pourret (Asteraceae)

Centaurea corymbosa Pourret (Asteraceae) is a narrow endemic species known only from six populations located in a 3-km2 area in the south of France. Earlier field experiments have suggested that pollen and seed dispersal were highly restricted within and among populations. Consistent with the field results, populations were highly differentiated for five allozyme loci and among-population variation fitted an isolation-by-distance model. In the present study, we investigated the genetic structure of C. corymbosa using six microsatellite loci. As with allozymes, microsatellites revealed no within-population structure and a large differentiation among populations. However, allozyme loci were less powerful than microsatellites in detecting the extent of gene flow assessed by assignment tests. The patterns of structuration greatly varied among loci for both types of marker; we suggest that differences in single-locus pattern could mainly be an effect of stochastic variation for allozymes and an effect of variation in mutation rate for microsatellites. In contrast to the multilocus results, the two most polymorphic microsatellite loci did not show any isolation-by-distance pattern. Our results suggest that highly variable loci might not always be the best suited markers to quantify levels of gene flow among populations.     

Genetic variation in two populations of the rough‐skinned newt (Taricha granulosa) assessed using novel tetranucleotide microsatellite loci

Seven novel tetranucleotide microsatellite loci were identified from a partial genomic DNA library, enriched for GATA‐motif microsatellites, from the rough‐skinned newt (Taricha granulosa). All loci were polymorphic, and one displayed a high frequency null allele. A related species, T. rivularis, displays strong site fidelity and detectable population structure over small spatial scales, so we assessed genetic variation in two samples of T. granulosa separated by 16 km. Distributions of allele frequencies differ significantly between our two sites, but small values of F_ST and Rho_ST suggest that the populations are linked by a large amount of gene flow.     

Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with Q _ST = 0.47, and F _ST = 0.47 for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of Q _ST and F _ST . Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P₂0₅) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, H _e , were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.     

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 selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non‐neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of F_ST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations.     

Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers

This study presents a comprehensive genetic analysis of stock structure for leatherback turtles (Dermochelys coriacea), combining 17 microsatellite loci and 763 bp of the mtDNA control region. Recently discovered eastern Atlantic nesting populations of this critically endangered species were absent in a previous survey that found little ocean-wide mtDNA variation. We added rookeries in West Africa and Brazil and generated longer sequences for previously analyzed samples. A total of 1,417 individuals were sampled from nine nesting sites in the Atlantic and SW Indian Ocean. We detected additional mtDNA variation with the longer sequences, identifying ten polymorphic sites that resolved a total of ten haplotypes, including three new variants of haplotypes previously described by shorter sequences. Population differentiation was substantial between all but two adjacent rookery pairs, and F _ST values ranged from 0.034 to 0.676 and 0.004 to 0.205 for mtDNA and microsatellite data respectively, suggesting that male-mediated gene flow is not as widespread as previously assumed. We detected weak (F _ST = 0.008 and 0.006) but significant differentiation with microsatellites between the two population pairs that were indistinguishable with mtDNA data. POWSIM analysis showed that our mtDNA marker had very low statistical power to detect weak structure (F _ST < 0.005), while our microsatellite marker array had high power. We conclude that the weak differentiation detected with microsatellites reflects a fine scale level of demographic independence that warrants recognition, and that all nine of the nesting colonies should be considered as demographically independent populations for conservation. Our findings illustrate the importance of evaluating the power of specific genetic markers to detect structure in order to correctly identify the appropriate population units to conserve.     

Isolation and characterization of microsatellite loci in the flour mite Acarus siro

Thirteen microsatellites with dinucleotide repeats were isolated from genomic DNA in solution by hybridization capture. Eleven were evaluated against Acarus siro using a multiple‐tube approach to assess polymorphism and reliability of the results. The multiple‐tube method demonstrated the presence of null alleles due to low levels of DNA. Seven of the 11 microsatellite loci were polymorphic and six produced reliable amplification products, if results only from individuals that scored at all six loci were used in the analysis. These were evaluated in eight strains of A. siro. Two of the samples showed some genetic divergence using F_ST values.     

Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus—a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP data set (16 tortoises from four populations sequenced at 17 901 SNPs) to two microsatellite data sets, a full data set of 101 tortoises and a partial data set of 16 tortoises previously genotyped at 10 microsatellites. For the full microsatellite data set, observed heterozygosity, expected heterozygosity and F_ST were correlated between SNPs and microsatellites; however, allelic richness was not. The same was true for the partial microsatellite data set, except that allelic richness, but not observed heterozygosity, was correlated. The number of clusters estimated by structure differed for each data set (SNPs = 2; partial microsatellite = 3; full microsatellite = 4). Principle component analyses (PCA) showed four clusters for all data sets. More than 800 SNPs were needed to correlate with allelic richness, observed heterozygosity and expected heterozygosity, but only 100 were needed for F_ST. The number of SNPs typically obtained from next‐generation sequencing (NGS) far exceeds the number needed to correlate with microsatellite parameter estimates. Our study illustrates that diversity, F_ST and PCA results from microsatellites can mirror those obtained with SNPs. These results may be generally applicable to small populations, a defining feature of endangered and threatened species, because theory predicts that genetic drift will tend to outweigh selection in small populations.     

Identification and characterization of microsatellite markers for the population genetic structure in endemic red-tailed barb,Gonoproktopterus curmuca

Gonoproktopterus curmuca is an endangered red tailed barb found in Southern part of Western Ghat, India. As a part of stock-specific, propagation assisted rehabilitation and management program, polymorphic microsatellites markers were used to study the genetic diversity and population structure of this species from the three River systems of Southern Western Ghats, such as Periyar River, the Chalakkudy River, and the Chaliyar River. From selected eight polymorphic microsatellite markers, the number of alleles per locus ranged from 2 to 8, and the average number of alleles among 3 populations ranged from 5.0 to 5.75. The mean observed (H_ob) and expected (H_ex) heterozygosity ranged from 0.5148 to 0.5360 and from 0.5996 to 0.6067, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci (except Gcur MFW72 and Gcur MFW19) and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance indicates that the percent of variance among populations and within populations were 6.73 and 93.27, respectively. The pairwise F_ST values between populations indicate that there were significant deviations in genetic differentiations for the red-tailed barb populations from these three Rivers of the Western Ghats, India. The microsatellites methods reported a low degree of gene diversity and lack of genetic heterogeneity in the population of G. curmuca, which strongly emphasize the need of fishery management, conservation and rehabilitation of G. curmuca.