POPULATION STRUCTURE IN AN INSHORE CETACEAN REVEALED BY MICROSATELLITE AND mtDNA ANALYSIS: BOTTLENOSE DOLPHINS (TURSIOPS SP.) IN SHARK BAY, WESTERN AUSTRALIA

We examined population substructure of bottlenose dolphins ( Tursiops sp). in Shark Bay, Western Australia, using 10 highly polymorphic microsatellite loci, and mitochondrial DNA (mtDNA). For microsatellite analysis, 302 different animals were sampled from seven localities throughout the bay. Analysis of genetic differentiation between sampling localities showed a significant correlation between the number of migrants ( Nm ) calculated from F _ST, R _ST and private alleles, and distance between localities–a pattern of isolation-by-distance. For mtDNA, 220 individuals from all seven localities were sequenced for a 351 base pair fragment of the control region, resulting in eight haplotypes, with two distinct clusters of haplotypes. Values of F _ST and (φ)_ST for mtDNA yielded statistically significant differences, mostly between localities that were not adjacent to each other, suggesting female gene flow over a scale larger than the sampled localities. We also observed a significant correlation between the number of female migrants calculated from F _ST and φ_ST and the distance of sampling localities. Our results indicate that dispersal in female dolphins in Shark Bay is more restricted than that of males.     

Microsatellite variation in cod Gadus morhua throughout its geographic range

Previous genetic studies using neutral markers such as allozymes, mtDNA and minisatellite loci have demonstrated varying amounts of population structure in cod Gadus morhua throughout the Atlantic. Microsatellite loci, which are potentially the most informative of presently available neutral genetic markers, have been applied extensively within western and eastern Atlantic areas but not on a range-wide basis. In the present study, six microsatellite DNA loci were used to screen cod samples from nine locations throughout the geographic range from the Scotian Shelf in the West Atlantic to the Barents and Baltic Seas in the east. Overall F _ST value was 0·03 ( P = < 0·001) across all samples. Statistically significant population differences over all loci combined were evident between more geographically distant samples, using either heterogeneity tests or F _ST analysis, with at least one locus showing significant differences between all samples (prior to Bonferroni correction). A significant correlation was observed between genetic and geographical distance, suggesting a higher level of historical and contemporary gene flow between adjacent populations than more distant populations. Samples from either end of the geographic range (Scotian Shelf and Baltic Sea) were particularly distinct when analysed using the STRUCTURE programme and also showed a high level of self-assignment when individuals of either the Scotian Shelf or Baltic Sea were tested against the entire data set. The present microsatellite study demonstrates a high level of geographic population structure between the western Atlantic, middle and eastern Atlantic and Baltic Sea, and thus, the findings should be useful in devising overall management and conservation strategies for the species.     

Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology

Comparative analyses of the genetic differentiation in microsatellite markers ( F _ST) and leaf morphology characters ( Q _ST) of Amphicarpaea edgeworthii Benth. were conducted to gain insight into the roles of random processes and natural selection in the population divergence. Simple sequence repeat analyses on 498 individuals of 19 natural populations demonstrate that a significant genetic differentiation occurs among populations (mean F _ST = 0.578), and A. edgeworthii is a highly self-fertilized species (mean selfing rate s  = 0.989). The distribution pattern of genetic diversity in this species shows that central populations possess high genetic diversity (e.g. population WL with H _E = 0.673 and population JG with H _E = 0.663), whereas peripheral ones have a low H _E as in population JD (0.011). The morphological divergence of leaf shape was estimated by the elliptical Fourier analysis on the data from 11 natural and four common garden populations. Leaf morphology analyses indicate the morphological divergence does not show strong correlation with the genetic differentiation ( R  = 0.260, P  = 0.069). By comparing the 95% confidence interval of Q _ST with that of F _ST, Q _ST values for five out of 12 quantitative traits are significantly higher than the average F _ST value over eight microsatellite loci. The comparison of F _ST and Q _ST suggests that two kinds of traits can be driven by different evolutionary forces, and the population divergence in leaf morphology is shaped by local selections.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 505–516.     

Genetic variability in Irish populations of the invasive zebra mussel, Dreissena polymorpha: discordant estimates of population differentiation from allozymes and microsatellites

1. The recent arrival and explosive spread of the zebra mussel, Dreissena polymorpha (Pallas), in Ireland provided a rare opportunity to study the population genetics of an invasive species.
2. Eight polymorphic allozyme loci ( ACO-1, ACO-2 , EST-D, GPI, IDH-2, MDH, OPDH and PGM ) were used to investigate genetic diversity and population structure in five Irish populations, and the results were compared with those from a previous microsatellite study on the same samples.
3. The mean number of alleles per locus (2.7 ± 0.1) was similar to the mean for the same loci in European populations, suggesting that Irish founder populations were large and/or multiple colonization events took place after foundation. A deficiency of heterozygotes was observed in all populations, but was uneven across loci.
4. Pairwise comparisons, using Fisher's exact tests and F _ST values, revealed significant genetic differentiation among populations. The overall multilocus F _ST estimate was 0.118 ± 0.045, which contrasted with an estimate of 0.015 ± 0.007 from five microsatellite loci on the same samples in a previous study.
5. Assuming that microsatellites can be used as a neutral baseline, the discordant results from allozymes and microsatellites suggest that selection may be acting on some allozyme loci, specifically ACO-1, ACO-2 , IDH-2 and MDH, which contributed most to the significant differentiation between samples.     

Genetic Variation and Clonal Diversity of the Two Divergent Types of Clonal Populations of Leymus chinensis Tzvel on the Song Liao Steppe in the West of Northeastern China

The genetic variation and clonal diversity of two divergent types (grey-green and yellow-green) of clonal populations of Leymus chinensis Tzvel at 14 loci were compared. Total gene diversity (HT) and the coefficient of genetic differentiation (GST) were all higher for the yellow-green type (HT = 0.270; GST =0.186) than for the grey-green type (HT = 0.250; GST = 0.157) of L. chinensis. Rare alleles usually occurred as heterozygotes rather than homozygotes and significant deviations from Hardy-Weinberg equilibrium were found only at a few loci. This indicated that these two types of populations were mainly out-crossing. Clonal diversity, evenness of clones, and mean clone size were not significantly different between the two types. We found that differences between the clone size and genetic variation of the yellow-green type of populations occurred with different climate and habitat population groups. However, for the grey-green type of populations, these genetic variations decreased under conditions of different climate and habitat population groups.     

RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance

R _ST, an analogue of F _ST, provides a convenient approach for estimating levels of genetic differentiation from microsatellite data. This paper examines current approaches for calculating estimates of R _ST and suggests a weighting scheme based on the transformation of allele sizes at loci across data sets. Combined within an analysis of variance framework this scheme yields an estimator of R _ST analogous to the θ estimator of F _ST. Software for the IBM-PC is described which carries out such calculations and assesses the significance of R _ST or Nm estimates using bootstrap and permutation tests.     

IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific

The Indo-West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum , is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: 'Least Concern' and 'Vulnerable'. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric F _ST analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.     

Genetic structure within and between island populations of the flightless cormorant (Phalacrocorax harrisi)

We assessed colony- and island-level genetic differentiation for the flightless cormorant ( Phalacrocorax harrisi ), an endangered Galápagos endemic that has one of the most limited geographical distributions of any seabird, consisting of only two adjacent islands. We screened 223 individuals from both islands and nine colonies at five microsatellite loci, recovering 23 alleles. We found highly significant genetic differentiation throughout the flightless cormorant's range on Fernandina and Isabela Islands (global F _ST = 0.097; P  < 0.0003) both between islands (supported by Bayesian analyses, F _ST and R _ST values) and within islands (supported only by F _ST and R _ST values). An overall pattern of isolation-by-distance was evident throughout the sampled range ( r =  0.4169, one-sided P  ≤ 0.02) and partial Mantel tests of this relationship confirmed that ocean is a dispersal barrier ( r =  0.500, one-sided P  ≤ 0.003), especially across the 5-km gap between the two islands. The degree of detected genetic differentiation among colonies is surprising, given the flightless cormorant's limited range, and suggests a role for low vagility, behavioural philopatry, or both to limit dispersal where physical barriers are absent. We argue that this population should be managed as at least two genetic populations to better preserve the species-level genetic diversity, but, for demographic reasons, advocate the continued conservation of all breeding colonies.     

Morphological and meristic evaluation of the population structure of Anguilla marmorata across its range

The population structure of the giant mottled eel Anguilla marmorata was evaluated using statistical analysis of 21 morphological characters among 13 representative localities across the Indo-Pacific region and as far north as Japan. There were no clear differences in 15 proportional and six vertebral characters using principal component analysis. The total number of vertebrae ( N _V) of A . marmorata at these localities had the widest variation among the morphological and meristic characters examined. A statistical analysis of the N _V of 1238 specimens from 14 localities that included previously published data found significant differences among Micronesia, French Polynesia and other localities, and between localities in the North Pacific and South Pacific regions. Few differences were detected between specimens from the Indian Ocean and the North Pacific or South Pacific regions. The differences in N _V among some regions and the population genetic studies of this species indicate that there are at least four populations of A. marmorata (North Pacific, Micronesia, Indian Ocean and South Pacific), which appear to include metapopulation structures in the Indian Ocean and South Pacific. This population structure is consistent with the ocean current patterns in each region and the evolution of migration loops of each spawning population.     

Genetic differentiation within and between isolated Algerian subpopulations of Barbary macaques (Macaca sylvanus): evidence from microsatellites

This study of wild-living Algerian Barbary macaques ( Macaca sylvanus ) was designed to examine genetic variability in subpopulations isolated in residual forest patches, in an attempt to obtain data on the effects of habitat fragmentation. The wild population of this species (estimated at a maximum of 15 000) is vulnerable and this study therefore has direct relevance for conservation measures. Data from five microsatellite loci were analysed for 159 individuals from nine different groups living in four isolates in Algeria. Genetic polymorphism was found to be relatively high (4–12 alleles per locus) compared with other genetic markers used in previous studies of this species; mean expected heterozygosity was 65%. The four isolates are all genetically distinct ( F _ST = 0; P < 0.001). Indeed, the results suggest that dispersal is limited even between some social groups within a single isolate. Genetic distances based on models not assuming stepwise mutation ( F _ST and chord distance) gave very similar results and are highly correlated with geographical distances within one isolate but not between isolates. This may indicate that isolation by distance exerts a significant influence within an isolate but that genetic drift prevails between the four isolates. After allowing for variation in sample size, we found no evidence of reduced allelic diversity within small isolates that may have been separated for 250 years or more. The surviving population of Algerian Barbary macaques taken as a whole still shows marked variability in microsatellite alleles, but maintenance of genetic variability over the long term will surely require effective protection of all isolates.     

Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki)

The genetic population structure of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in Washington state was investigated by analysis of variation in allele frequencies at six highly polymorphic microsatellite loci for 13 anadromous populations, along with one outgroup population from the Yellowstone subspecies ( O. clarki bouvieri) (mean heterozygosity = 67%; average number of alleles per locus = 24). Tests for genetic differentiation revealed highly significant differences in genotypic frequencies for pairwise comparisons between all populations within geographical regions and overall population subdivision was substantial ( F _ST = 0.121, R _ST = 0.093), with 44.6% and 55.4% of the among-population diversity being attributable to differences between streams ( F _SR = 0.054) and between regions ( F _RT = 0.067), respectively. Analysis of genetic distances and geographical distances did not support a simple model of isolation by distance for these populations. With one exception, neighbour-joining dendrograms from the Cavalli-Sforza and Edwards' chord distances and maximum likelihood algorithms clustered populations by physiogeographic region, although overall bootstrap support was relatively low (53%). Our results suggest that coastal cutthroat trout populations are ultimately structured genetically at the level of individual streams. It appears that the dynamic balance between gene flow and genetic drift in the subspecies favours a high degree of genetic differentiation and population subdivision with the simultaneous maintenance of high heterozygosity levels within local populations. Results are discussed in terms of coastal cutthroat trout ecology along with implications for the designation of evolutionarily significant units pursuant to the US Endangered Species Act of 1973 and analogous conservation units.     

Indo-Pacific population structure and evolutionary history of the coconut crab Birgus latro

Mitochondrial DNA variation was used to examine population structure in a widespread, marine-dispersed species, Birgus latro . Crabs were collected from eight locations throughout the species' Indo-Pacific distribution. Purified mtDNA from 160 individuals was cut with five restriction enzymes, revealing high haplotype diversity (0.96) and moderate nucleotide diversity (0.75%). Island populations from the Indian Ocean (Christmas I.) and Pacific Ocean were significantly different ( G _ST= 0.37) and had distinct mtDNA lineages with a net sequence divergence of 1.4%. Pacific island populations had diverged in a manner consistent with isolation by distance, with only the most peripheral populations being significantly different. The results for mtDNA are largely concordant with those from allozymes, although estimates of gene flow between the Indian and Pacific Oceans were much lower when based on mtDNA. The mtDNA phylogeny also permitted a deeper examination of the evolutionary and demographic history of Birgus latro . Long-term separation of populations is evident in the complete phylogenetic subdivision of mtDNA lineages between the Indian and Pacific Ocean populations sampled. The starlike phylogeny of alleles from the Pacific suggests a rapid population expansion in the Pacific during the Pleistocene. Including information about allele phylogeny, as well as distribution and frequency, obscured contemporary population structure, but provided unique insights into the evolutionary history of the species.     

Spatio-temporal population genetics of the Danish pine marten (Martes martes)

A spatio-temporal study of genetic variation in the Danish pine marten ( Martes martes ) populations from the Jutland peninsula and from the island of Sealand was performed using 11 microsatellite markers. Samples obtained from 1892 to 2003 were subdivided into historical (prior to 1970) and recent (from 1970) groups. As compared with the historical samples, there was a significant loss of genetic variation in the recent Jutland population, but not in Sealand. Effective population sizes were estimated using Bayesian-based software (TMVP). Historical effective population sizes were 5897 (90% highest probability density, HPD, limits: 1502–6849) in Jutland and 1300 (90% HPD limits: 224–5929) in Sealand, whereas recent effective population sizes were 14.7 (90% HPD limits: 10.9–23.5) in Jutland and 802 (90% HPD limits: 51.8–5510) in Sealand. Significant genetic differentiation ( F _ST) was found between the two historical samples, between the two recent samples, and between the historical and the recent sample in Jutland; whereas the F _ST value between the historical and the recent sample in Sealand was not significant. The significant genetic differentiation between the historical and the recent samples indicates changes in the genetic compositions over time, and the higher F _ST values between the two recent samples, as compared with the two historical samples, indicates that the populations in Sealand and Jutland have drifted apart within a short time span. No deviation from Hardy–Weinberg equilibrium was found within populations, indicating no further substructuring.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 457–464.     

Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites

To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides , 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F _ST, global amova , and genetic admixture analysis identified three clusters — the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations — indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals ( P _SAxy) analyses between the Sea of Japan and the other samples, P _SAxy was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P _SAxy data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P _SAxy data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P _SAxy were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.     

Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair-wise population differentiation ( F _ST-value) between the cohorts within a population and among three populations. Estimates of the effective population size ( N _e) based on maximum-likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size ( N _e/ N ) ranged from 0·004 to 0·023. These estimates of N _e/ N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of N _e/ N , similar to marine species with a pelagic life cycle.     

Multiple population structure of the giant mottled eel, Anguilla marmorata

The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (Tahiti, Fiji, New Caledonia, Papua New Guinea), eastern Indian Ocean (Sumatra), western Indian Ocean (Réunion, Madagascar), Ambon, and Guam regions were significantly different (Phi(ST) = 0.131-0.698, P < 0.05) while only a few differences were observed between localities within the South Pacific. These regions were roughly clustered in the neighbour-joining tree, although Ambon individuals were mainly divided into North and South Pacific groups. Analysis with eight microsatellite loci showed almost identical results to those of the control region, except no genetic difference was observed between the western and eastern Indian Ocean (F(ST) = 0.009, P > 0.05). The Bayesian cluster analysis of the microsatellite data detected two genetic groups. One included four North Pacific localities, and the other included eight localities in the South Pacific, Indian Ocean, and Guam, but Ambon individuals were evenly assigned to these two groups. These results showed that A. marmorata has four genetically different populations (North Pacific, South Pacific, Indian Ocean, Guam region). The North Pacific population is fully panmictic whereas the South Pacific and Indian Ocean populations have a metapopulation structure. Interestingly, Guam was suggested to be inhabited by a reproductive population restricted to that region, and the individuals from the North and South Pacific populations co-exist in Ambon.     

Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers

Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity ( H _E)=0.79; allozyme H _E=0.08; mtDNA restriction fragment length polymorphism (RFLP) H _E=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population ( R _ST/ F _ST=0.252/0.245; allozyme F _ST=0.536; mtDNA F _ST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population ( R _ST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.     

Invasion genetics of the Eurasian round goby in North America: tracing sources and spread patterns

The Eurasian round goby Neogobius melanostomus ( Apollonia melanostoma ) invaded the North American Great Lakes in 1990 through ballast water, spread rapidly, and now is widely distributed and moving through adjacent tributaries. We analyse its genetic diversity and divergence patterns among 25 North American ( N  = 744) and 22 Eurasian ( N  = 414) locations using mitochondrial DNA cytochrome b gene sequences and seven nuclear microsatellite loci in order to: (i) identify the invasion's founding source(s), (ii) test for founder effects, (iii) evaluate whether the invasive range is genetically heterogeneous, and (iv) determine whether fringe and central areas differ in genetic diversity. Tests include F _ST analogues, neighbour-joining trees, haplotype networks, Bayesian assignment, Monmonier barrier analysis, and three-dimensional factorial correspondence analysis. We recovered 13 cytochrome b haplotypes and 232 microsatellite alleles in North America and compared these to variation we previously described across Eurasia. Results show: (i) the southern Dnieper River population was the primary Eurasian donor source for the round goby's invasion of North America, likely supplemented by some alleles from the Dniester and Southern Bug rivers, (ii) the overall invasion has high genetic diversity and experienced no founder effect, (iii) there is significant genetic structuring across North America, and (iv) some expansion areas show reduced numbers of alleles, whereas others appear to reflect secondary colonization. Sampling sites in Lake Huron's Saginaw Bay and Lake Ontario significantly differ from all others, having unique alleles that apparently originated from separate introductions. Substantial genetic variation, multiple founding sources, large number of propagules, and population structure thus likely aided the goby's ecological success.     

The West Pacific diversity hotspot as a source or sink for new species? Population genetic insights from the Indo‐Pacific parrotfish Scarus rubroviolaceus

We used a population genetic approach to quantify major population subdivisions and patterns of migration within a broadly distributed Indo-Pacific parrotfish. We genotyped 15 microsatellite loci in Scarus rubroviolaceus collected from 20 localities between Africa and the Americas. A STRUCTURE model indicates the presence of four major populations: Eastern Pacific, Hawaii, Central-West Pacific and a less well-differentiated Indian Ocean. We used the isolation and migration model to estimate splitting times, population sizes and migration patterns between sister population pairs. To eliminate loci under selection, we used BayeScan to select loci for three isolation and migration models: Eastern Pacific and Central-West Pacific, Hawaii and the Central-West Pacific, and Indian Ocean and the Central-West Pacific. To test the assumption of a stepwise mutation model (SMM), we used likelihood to test the SMM against a two-phase model that allowed mutational complexity. A posteriori, minor departures from SMM were estimated to affect ≤2% of the alleles in the data. The data were informative about the contemporary and ancestral population sizes, migration rates and the splitting time in the eastern Pacific/Central-West Pacific comparison. The model revealed a splitting time ～17,000 BP, a larger contemporary N(e) in the Central-West Pacific than in the eastern Pacific and a strong bias of east to west migration. These characteristics support the Center of Accumulation model of peripatric diversification in low-diversity peripheral sites and perhaps migration from those sites to the western Pacific diversity hotspot.     

Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale

We have isolated specific microsatellite loci from a partial genomic library of brook charr Salvelinus fontinalis. Their usefulness was investigated by measuring intra- and inter-population genetic diversity at four loci among 20 individuals from each of five lakes located 3 to 22 km apart in La Mauricie national park (Canada). These markers were moderately to highly polymorphic. A total of five, six, 16 and 18 alleles per locus were detected, and their overall expected heterozygosity was 0.53, 0.58, 0.86 and 0.87. Strong inter-population diversity was detected. Highly significant differences in allelic frequencies were found in all but two pairwise χ² permutation tests between populations at all loci. Numerous population unique alleles were observed in all five lakes. Consequently, a highly significant component of total genetic diversity was due to interpopulation variance, as exemplified by G _ST values of 0.33, 0.42, 0.47 and 0.84 for each individual locus. Altogether, the results indicated that these loci should be valuable in addressing fine scale population genetics questions in brook charr. To our knowledge, they also represent the first available microsatellites developed in the genus Salvelinus.