Genetic Heterogeneity of the Blue Swimming Crab (Portunus pelagicus) in Thailand Determined by AFLP Analysis

Genetic diversity and population differentiation of the blue swimming crab (Portunus pelagicus) in Thailand, originating from Ranong and Krabi located in the Andaman Sea (west) and Chanthaburi, Prachuap Khiri Khan, and Suratthani located in the Gulf of Thailand (east), were examined by AFLP analysis. High genetic diversity of P. pelagicus in Thai waters was found (N=72). The four primer combinations generated 227 AFLP fragments, and the percentage of polymorphic bands in each geographic sample was 66.19-94.38%. The mean genetic distance between pairs of samples was 0.1151-0.2440. Geographic heterogeneity analyses using the exact test and FST-based statistics between all pairwise comparisons were statistically significant (P<0.01), indicating a fine-scale level of intraspecific population differentiation of Thai P. pelagicus. The estimated number of migrants per generation (Nem) was 0.26-0.76, suggesting restricted gene flow levels of P. pelagicus in Thai waters.     

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

Genetic variation at 19 allozyme (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 over the allozyme loci, per broodline, were on average 0.43% (GST), while over the microsatellite loci it was 0.26% (the theta(ST) coefficient, F-statistics based on the allele frequency variance), and 0.90% (the rho(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 Island. Multivariate 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 theta(ST) values were substantially lower than in terms of rho(ST) values. Regional genetic differentiation, mostly expressed at the allozyme loci among the populations from the northern and southern parts of the Sea of Okhotsk (i.e., between the Sakhalin and Kuril 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 genetic 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 and colonization of the range.     

Microgeographic genetic variation in the apple maggot rhagoletis pomonella

We examined electrophoretic variability at five enzyme loci in the apple maggot fly, Rhagoletis pomonella, on a microgeographic scale. Treating flies from individual hawthorn trees as separate populations, we estimated F(ST) values from allele frequencies. The results indicate that there is significant allele frequency heterogeneity among fly populations over a small spatial scale at some loci but not at others. This variation among loci in degree of differentiation is itself statistically significant, casting doubt on the role of genetic drift in maintaining the heterogeneity. There is also heterogeneity between years in flies from a given tree. These data provide a baseline with which future work on genetic differentiation among apple maggot populations associated with different species of host plants may be compared.     

The population genetic diversity and pattern of Pteroceltis tatarinowii,a relic tree endemic to China,inferred from SSR markers

Pteroceltis tatarinowii (Cannabaceae), a relic tree endemic to China, is mainly distributed in limestone mountains and has a wide geographical range. In this study, 12 microsatellite primer pairs were assayed to analyse the genetic pattern and gene flow among 461 individuals sampled from 23 wild populations of P. tatarinowii. A high level of genetic diversity was detected based on high values of total alleles (159), the number of alleles (N_A = 6.373), expected heterozygosity (H_E = 0.696) and observed heterozygosity (H_O = 0.679). The high genetic diversity in this species may be attributed to its long‐life history, wide geographical distribution and wind dispersal. Only low genetic differentiation (G_ST = 0.137, F_ST = 0.138) was found among populations. Gene flow (migrants per generation, N_m) was estimated to be 1.56. This moderate level of gene flow possibly decrease interpopulation differentiation by buffering against genetic drift and improving gene exchange. However, spatial genetic structure was detected throughou the sampled range of the species (r = 0.311, p < 0.05) as well as in southern China (r = 0.453, p < 0.05), and may be related to terrain heterogeneity and the demographic history of P. tatarinowii. The east‐west high mountains of southern China might serve as physical barriers to seed and pollen flow. The isolation and local adaptation of different refugia may further limit gene flow. In addition, geographically remote populations might fail to effectively disperse pollen and seeds. Based on the above‐mentioned results, some suggestions for the conservation of the species are presented.     

A genetic metapopulation model for reef fishes in oceanic islands: the case of the surgeonfish,Acanthurus triostegus

Allozyme data on a surgeonfish, Acanthurus triostegus, were analysed from 10 islands in French Polynesia. We compared estimates of gene flow according to the hypothesis of an equilibrium between genetic drift and migration, and estimated genetic divergence times assuming complete genetic isolation without gene flow since foundation. The significant correlation between genetic divergence and geographic distance, at the within-archipelago level (r = 0.709, P = 0.024) indicates exchange of individuals mainly between neighbouring populations. The correlation was, however, not significant at the among-archipelagoes level (r = 0.325, P = 0.330), suggesting that long distance migrations are more sporadic. This addresses the problem of scale in population biology. According to the spatial scale of analysis, results can change from an island model, with no relation between genetic differentiation and geographical distances between archipelagos, to an isolation-by-distance model within an archipelago. These factors lead us to propose a “patchy population” model, in which all patches are occupied and reproductively active, though with few successful migrations between neighbouring populations. This model describes a subdivided population that is stable through time, with an amount of gene flow small enough to allow significant local differentiation in neutral gene frequency, but high enough to prevent differential fixation in the long term, and therefore preserving the genetic cohesion of the species.     

Spatiotemporal genetic structure of anadromous Arctic char (<Emphasis Type="Italic">Salvelinus alpinus</Emphasis>) populations in a region experiencing pronounced climate change

We examined spatio-temporal genetic variation at 53 single nucleotide polymorphisms in anadromous Arctic char populations from Western Greenland, a region experiencing pronounced climate change. The study was based on contemporary and historical samples, the latter represented by DNA extracted from otoliths and scales from the 1950s–1960s. We investigated whether genetic population structure was temporarily stable or unstable, the latter due to relatively small spawning and nursery areas combined with a harsh Arctic environment. Furthermore, in order to evaluate the potential for adaptive responses and local adaptation we estimated effective population size (N_e) and migration rate (m). Temporal stability of genetic population structure was suggested, based on a hierarchical analysis of genetic differentiation showing much higher differentiation among samples from different populations (F_CT = 0.091) than among temporal samples from the same populations (F_SC = 0.01). This was further supported by a neighbor-joining tree and assignment of individuals that showed high contingency between historical and contemporary samples. Estimates of N_e were high (>?500) in three out of four populations, with a lower estimate in one population potentially reflecting fishing pressure or suboptimal environmental conditions. Estimates of m were in most cases low, ≤ 0.01. N_e and m estimates suggest a potential for adaptive responses and local adaptation. However, long generation time may also cause adaptive responses by microevolution to be unable to track climate change, especially considering the low migration rates that reduce potential evolutionary rescue by gene flow from populations better adapted to the altered environments.     

Genetic diversity and differentiation between the two remaining populations of the critically endangered Mediterranean monk seal

The Mediterranean monk seal Monachus monachus , is a critically-endangered species of which only two populations, separated by c . 4000 km, remain: the eastern Mediterranean (150–300 individuals) and the Atlantic/western Sahara populations (100–130 individuals). We measured current levels of nuclear genetic variation at 24 microsatellite loci in 12 seals from the eastern Mediterranean and 98 seals from the western Sahara population and assessed differences between them. In both populations, genetic variation was found to be low, with mean allelic richness for the loci polymorphic in the species of 2.09 and 1.96, respectively. For most loci, the observed allele frequency distributions in both populations were discontinuous and the size ranges similar. The eastern Mediterranean population had 14 private alleles and the western Sahara had 18, but with a much larger sample size. Highly significant differences in allele frequencies between the two populations were found for 14 out of 17 loci. F _ST between the two populations was 0.578 and the estimated number of migrants per generation was 0.046, both clearly indicating substantial genetic differentiation. From a conservation perspective, these results suggest that each population may act as a source for introducing additional genetic variation into the other population.     

Novel tetranucleotide microsatellite DNA markers for the wood frog,Rana sylvatica

Fifteen tetranucleotide microsatellite loci were identified and characterized for wood frogs (Rana sylvatica) collected from three vernal pools in the southeastern US. These markers revealed a high degree of genetic diversity (nine to 34 alleles per locus), heterozygosity (30.6–92.3%) and allelic heterogeneity (69% of comparisons were statistically significant). Considerable differentiation among populations was observed as genetic distances (chord) ranged between 0.40 and 0.55 and all F_ST values (0.02–0.05) were statistically significant. Genotypic assignment tests correctly classified 103 of 113 individuals to their respective collection. These markers should prove useful for investigating fine‐scale population structure and metapopulation dynamics.     

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     

Temporal changes in allele frequencies but stable genetic diversity over the past 40 years in the Irish Sea population of thornback ray, Raja clavata

Rays and skates are an unavoidable part of the by-catch in demersal fisheries. Over the past 40 years, the thornback ray (Raja clavata) has decreased in numbers and even disappeared in some areas, leading to concerns about genetic risk. For this reason, the effective population size (N(e)), the migration rate (m) and temporal changes in the genetic diversity were estimated for the population of thornback rays in the Irish Sea and Bristol Channel. Using genotyped, archived and contemporary samples (1965 and 2003-2004), N(e) was estimated at 283 individuals (95% CI=145-857), m at 0.1 (95% CI=0.03-0.25) and the N(e)/N ratio between 9 x 10(-5) and 6 x 10(-4). Although these results must be treated with caution, due to the small sample sizes, this is the first attempt to estimate N(e) in an elasmobranch species. The low N(e)/N ratio suggests that relatively few individuals contribute to the next generation. The combined effect of sex bias, inbreeding, fluctuations in population size and, perhaps most important, the variance in reproductive success may explain the low N(e)/N ratio. In addition, the relatively high gene flow between Irish Sea population and other source populations is likely to have had an impact on our estimate, which may be more relevant at the metapopulation scale. No significant loss of genetic diversity was found over the 40-year timeframe and long-term maintenance of the genetic diversity could be due to gene flow.     

Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis)

Population genetic structure can be shaped by multiple ecological and evolutionary factors, but the genetic consequences of these factors for multiple species inhabiting the same environment remain unexplored. We used microsatellite markers to examine the population structures of two coexisting species of garter snake, Thamnophis elegans and Thamnophis sirtalis, to determine if shared landscape and biology imposed similar population genetic structures. These snakes inhabit a series of ponds, lakes and flooded meadows in northern California and tend to converge on prey type wherever they coexist. Both garter snakes had comparable effective population sizes and bidirectional migration rates (estimated using a maximum-likelihood method based on the coalescent) with low but significant levels of genetic differentiation (F(ST) = 0.024 for T. elegans and 0.035 for T. sirtalis). Asymmetrical gene flow revealed large source populations for both species as well as potential sinks, suggesting frequent extinction-recolonization and metapopulation dynamics. In addition, we found a significant correlation between their genetic structures based on both pairwise F(ST)s for shared populations (P = 0.009) and for bidirectional migration rates (P = 0.024). Possible ecological and evolutionary factors influencing similarities and differences in genetic structure for the two species are discussed. Genetic measures of effective population size and migration rates obtained in this study are also compared with estimates obtained from mark-recapture data.     

Allozyme analyses of the genus Trisopterus: taxonomic status and population structure of the poor cod

Genetic analysis of the four Trisopterus (Gadidae) taxa suggests that the interrelationships of the two morphs of poor cod ( T. minutus minutus in the Atlantic and T. minutus capelanus in the Mediterranean) should be reconsidered. The Mediterranean poor cod T. m. capelanus is more closely related to bib T. luscus than to the Atlantic poor cod, so the population structure in the Atlantic and Mediterranean poor cod must be considered separately. Among 635 Atlantic individuals there was some evidence of poor cod population differentiation (allele frequency heterogeneity test P <0·0005; F _ST=0·0135, P ≤0·0005). Levels of genetic variation were similar to those reported for related gadoid species. Some differentiation was present on the Norwegian coast (samples from Trondheimsfjord) and between the Faeroe Islands (Faeroe Bank) and the adjacent European coastal location. In contrast no statistically significant population differentiation was evident in Mediterranean poor cod, but fewer samples and individuals were screened.     

Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.     

Isolation and characterization of novel tetranucleotide microsatellite DNA markers for the spotted salamander,Ambystoma maculatum

Fifteen tetranucleotide microsatellite loci were identified and characterized for spotted salamanders (Ambystoma maculatum) collected from three vernal pools in the south‐eastern USA. These markers revealed a high degree of genetic diversity (7–32 alleles per locus), heterozygosity (31.6–86.3%) and allelic heterogeneity (91% of comparisons were statistically significant). Considerable differentiation among populations was observed as genetic distances (chord) ranged between 0.50 and 0.65, and all F_ST values (0.08–0.14) were statistically significant. Moreover, genotypic assignment tests correctly classified all individuals to their respective collection. These markers should prove useful for investigating fine‐scale population structure and mating system.     

Vocal dialects, sex-biased dispersal, and microsatellite population structure in the parrot Amazona auropalliata

Geographic variation in microsatellite allele frequencies was assessed at nine sites in two regional vocal dialects of the parrot Amazona auropalliata (yellow-naped amazon) to test for correspondence between dialects and population structure. There was no relationship between the genetic distances between individuals and their dialect membership. High rates of gene flow were estimated between vocal dialects based on genetic differentiation. In addition, 5.5% of pairs of individuals compared across the dialect boundary were estimated to be related at the level of half siblings, indicating that dispersal is ongoing. The number of effective migrants per generation between dialects estimated with the microsatellite data was roughly one-seventh the number estimated with mitochondrial control region sequence data from the same individuals, suggesting that gene flow may be female-biased. Together, these results suggest that the observed mosaic pattern of geographic variation in vocalizations is maintained by learning of local call types by immigrant birds after dispersal. We found no evidence that ongoing habitat fragmentation has contributed to cryptic population structure.     

Genetic monitoring of northern sea of Okhotsk populations of pink salmon (<Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis>)

Results from the 1993–2004 genetic monitoring of pink salmon populations reproducing in the rivers of Tauy Bay on the Sea of Okhotsk are analyzed. A statistically significant heterogeneity of samples as determined by gene frequencies is found only in the pink salmon generations of even years. The genetic differentiation of samples from even years (G_ST = 1.39 ± 0.41) is higher than that of odd years (G_ST = 0.740.09). The pattern for the indicator of genetic variability (heterozygosity) is exactly the opposite (0.076 ± 0.02564 vs. 0.8760 ± 0.01950). Consequently, the lower-heterozygosity samples of lines from even years are on average more genetically distinct than the analogous indicator for odd years. In addition, the interpopulation ratio in the general value of genetic diversity is almost always smaller than both the intraannual and interannual ratios, leading to a low level of interpopulation genetic differences. Cluster analysis reveals that most 2001–2004 samples are grouped separately from samples collected prior to 2000. In our opinion, the reason for this could be the turnover of a numerically dominant generation of northern Sea of Okhtosk pink salmon and the change in gene frequencies accompanying it.     

Development of genetic differentiation and postzygotic isolation in experimental metapopulations of spider mites

We studied the development of genetic differentiation and postzygotic isolation in experimental metapopulations of the two-spotted spider mite, Tetranychus urticae Koch. A genetically diverse starter population was made by allowing six inbred sublines to interbreed. Then three migration patterns were tested: no migration, or one or three immigrants per subpopulation per generation. Variations in four traits were investigated: allozymes, acaricide resistance, diapause, and hatchability. In the allozymes, acaricide resistance, and diapause, genetic variation among subpopulations became high in metapopulations with no migration, but not in the others, which showed that one immigrant is enough to prevent genetic differentiation. Hatchability, which was decreased by interbreeding among the six sublines, gradually recovered in succeeding generations. In metapopulations with no migration, hatchability was reduced again after in-migration at the 15th generation. Different karyotypes or coadapted gene complexes can survive in different subpopulations by genetic drift, and both Wolbachia-infected and -noninfected subpopulations may be selected, which would lead to postzygotic isolation between isolated subpopulations. Our results indicate that sampling effects such as genetic drift or stochastic loss of Wolbachia produce postzygotic isolation in laboratory populations of spider mite.     

Habitat related allozyme variation on a microgeographic scale in the marine snail Littorina mariae (Prosobranchia: Littorinacea)

The marine snail Littorina mariae Sacchi & Rastelli occurs in high numbers in the littoral zone on fucoid macro-algae. The eggs are laid on the seaweed and d e velopment to miniature snails takes place without any pelagic larval stage. We have mapped the genetic variation of 30 enzyme loci in populations from eight small islands within 15 km of each other on th swedish west coast. The original intention was to investigate the magnitude of gene flow within and between islands. However, we soon realized that our basic assumption of neutral genetic variation was forcefully violated in at least one locus, arginine kinase ( Ask ). Allele frequencies of Ark were strongly associated with type of habitat. Therefore the main part of this study focused on allele frequency distribution in different habitats. Eight of the 30 loci screened were polymmorphic but we mainly considered the four most polymorphic ones (total heterozygosity between 0.32 and 0.57). All four showed significant heterogeneity between subpopulations, Ask especially so; 42% of the total variation of Ark was explained by differentiation between samples, and 90% of this variation was attributed to differences between different types of habitats (more or less exposed to wave action). In contrast, peptidase ( Pep-1 ) and phosphoglucomutase ( Pgm-2 ) varied in a way predicted by neutral theory; between sample variation being mainly attributed to differentiation bvetween islands. The variation in phosphoglucose isomerase ( Pgi ) was less consistent. In some islands there w as an obvious difference between different habitats, but on other islands we found no significant difference.Not taking into account the extreme, presumably sclected, variation in Ark , we concluded that the metapopulation of Littoriana mariae that we studied was divided into semi-isolated populations, between which the average rate of migration was in the range of a fe w individuals per generation.     

A program to compare genetic differentiation statistics across loci using resampling of individuals and loci

Comparisons of genetic differentiation across populations based on different loci can provide insight into the evolutionary patterns acting on various regions of genomes. Here, we develop a program to statistically compare population genetic differentiation statistics (F(ST) or G'(ST) ) calculated from different loci. The program employs a routine that resamples either or both of individuals and loci and calculates a bootstrap confidence interval in the statistics. Resampling individuals is important when fewer than 25 individuals are sampled per population and when confidence intervals are required for individual loci. Resampling loci provides confidence intervals for sets of loci, such as a set presumed to be neutral, but can be anticonservative if fewer than 20 loci are analysed. We demonstrate the program using previously published data on the genetic differentiation at a major histocompatibility complex locus and at microsatellite loci across 10 populations of the guppy (Poecilia reticulata).