Human disturbance reduces genetic diversity of an endangered tropical tree, <Emphasis Type="Italic">Prunus africana</Emphasis> (Rosaceae)

Human activities such as fragmentation and selective logging of forests can threaten population viability by modification of ecological and genetic processes. Using six microsatellite markers, we examined the effects of forest fragmentation and local disturbance on the genetic diversity and structure of adult trees (N = 110) and seedlings (N = 110) of Prunus africana in Kakamega Forest, western Kenya. Taking samples of adults and seedlings allowed for study of changes in genetic diversity and structure between generations. Thereby, adults reflect the pattern before and seedlings after intensive human impact. Overall, we found 105 different alleles in the six loci examined, 97 in adults and 88 in seedlings. Allelic richness and heterozygosity were significantly lower in seedlings than in adults. Inbreeding increased from adult tree to seedling populations. Genetic differentiation of adult trees was low (overall F _ST = 0.032), reflecting large population sizes and extensive gene flow in the past. Genetic differentiation of seedlings was slightly higher (overall F _ST = 0.044) with all of the 28 pairwise F _ST-values being significantly different from zero. These results suggest that human disturbance in Kakamega Forest has significantly reduced allelic richness and heterozygosity, increased inbreeding and slightly reduced gene flow in P. africana in the past 80–100 years.     

Genetic diversity and gene flow in a Caribbean tree <Emphasis Type="Italic">Pterocarpus officinalis</Emphasis> Jacq.: a study based on chloroplast and nuclear microsatellites

We analysed the molecular diversity of Pterocarpus officinalis, a tree species distributed in Caribbean islands, South and Central America to quantify the genetic variation within island, to assess the pattern of differentiation and infer levels of gene flow; with the overall goal of defining a strategy of conservation. Two hundred two individuals of 9 populations were analysed using three chloroplast and six nuclear microsatellite markers. The observed heterozygosity varied markedly among the populations for nuclear (H _Onuc = 0.20–0.50) and chloroplast microsatellites (H _cp = 0.22–0.68). The continental population from French Guyana showed a higher value of H _Onuc than island populations, and the differences were significant in some cases. The fixation index F _IS ranged from −0.043 to 0.368; a significant heterozygote deficit was detected in 7 populations. The heterozygosity excess method suggested that two populations in Guadeloupe have undergone a recent bottleneck. Global and pairwise F _ST were high for both nuclear (F _STnuc = 0.29) and chloroplast microsatellites (F _STcp = 0.58). The neighbour-joining tree based on both markers, presented a differentiation pattern that can be explained by the seed dispersal by flotation and marine stream. The comparison of Bayesian approach and the method based on allelic frequency demonstrate a very limited number of migrants between populations.     

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 variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites

The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were F_IS = ?0.172, F_IT = ?0.082 and F_ST = 0.077, respectively. Furthermore, the pair‐wise F_IS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (F_ST = 0.041), and the highest one was between TC and Fat‐tailed Han (F_ST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

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.     

Moderately and Highly Polymorphic Microsatellites Provide Discordant Estimates of Population Divergence in Sockeye Salmon, Oncorhynchus nerka

Mutation rate can vary widely among microsatellite loci. This variation may cause discordant single-locus and multi-locus estimates of F_ST, the commonly used measure of population divergence. We use 16 microsatellite and five allozyme loci from 14 sockeye salmon populations to address two questions about the affect of mutation rate on estimates of F_ST: (1) does mutation rate influence F_ST estimates from all microsatellites to a similar degree relative to allozymes?; (2) does the influence of mutation rate on F_ST estimates from microsatellites vary with geographic scale in spatially structured populations? For question one we find that discordant estimates of F_ST among microsatellites as well as between the two marker classes are correlated with mean within-population heterozygosity (H_S) and thus are likely due to differences in mutation rate. Highly polymorphic microsatellites (H_S > 0.84) provide significantly lower estimates of F_ST than moderately polymorphic microsatellites and allozymes (H_S < 0.60). Estimates of F_ST from binned allele frequency data and R_ST provide more accurate measures of population divergence for highly polymorphic but not for moderately polymorphic microsatellites. We conclude it is more important to pool loci of like H_S rather than marker class when estimating F_ST. For question two we find the F_ST values for moderately and highly polymorphic loci, while significantly different, are positively correlated for geographically proximate but not geographically distant population pairs. These results are consistent with expectations from the equilibrium approximation of Wright's infinite island model and confirm that the influence of mutation on estimates of F_ST can vary in spatially structured populations presumably because the rate of migration varies inversely with geographic scale.     

Assessing the genetic consequences of flower-harvesting in Rhododendron decorum Franchet (Ericaceae) using microsatellite markers

Rhododendron decorum is widely distributed shrub in southwest China, and its flower is a favorite food of the local people. To investigate the impacts of harvesting, we genotyped 8 nuclear microsatellite loci in a total of 247 individuals from 10 natural populations and 4 flower-harvesting populations. No significant differences in allelic richness, effective number of alleles, private allelic richness, heterozygosity and effective population size were found among the natural and flower-harvesting populations. Differentiation between the 14 populations is relatively low (F_ST = 0.107). R. decorum showed high levels of intra-population genetic diversity. AMOVA analysis indicated that over 89% of the variation was contained within the populations, and that only 0.47% of the variation was attributed by human harvesting practices. Cluster analysis revealed two basic clusters related to the plants' geographical locations. Our results indicate that historical flower-harvesting practices do not lead to loss of genetic variation in R. decorum.     

Development of EST‐derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)

A set of expressed sequence tag–simple sequence repeat (EST‐SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di‐, tri‐, tetra‐ and pentanucleotide repeat motifs were identified and primers were designed to 24 EST‐SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (H_E) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST‐SSR loci, likely due to inbreeding (global F_IS = 0.151) and population structure (global F_ST = 0.246).     

Population structure of chum salmon and selection on the markers collected for stock identification

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single‐nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH‐3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2‐dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F _ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.     

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.     

Prediction of breed composition in an admixed cattle population

Swiss Fleckvieh was established in 1970 as a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Breed composition is currently reported based on pedigree information. Information on a large number of molecular markers potentially provides more accurate information. For the analysis, we used Illumina BovineSNP50 Genotyping Beadchip data for 90 pure SI, 100 pure RHF and 305 admixed bulls. The scope of the study was to compare the performance of hidden Markov models, as implemented in structure software, with methods conventionally used in genomic selection [BayesB, partial least squares regression (PLSR), least absolute shrinkage and selection operator (LASSO) variable selection)] for predicting breed composition. We checked the performance of algorithms for a set of 40 492 single nucleotide polymorphisms (SNPs), subsets of evenly distributed SNPs and subsets with different allele frequencies in the pure populations, using F_ST as an indicator. Key results are correlations of admixture levels estimated with the various algorithms with admixture based on pedigree information. For the full set, PLSR, BayesB and structure performed in a very similar manner (correlations of 0.97), whereas the correlation of LASSO and pedigree admixture was lower (0.93). With decreasing number of SNPs, correlations decreased substantially only for 5% or 1% of all SNPs. With SNPs chosen according to F_ST, results were similar to results obtained with the full set. Only when using 96 and 48 SNPs with the highest F_ST, correlations dropped to 0.92 and 0.90 respectively. Reducing the number of pure animals in training sets to 50, 20 and 10 each did not cause a drop in the correlation with pedigree admixture.     

Spatial and Temporal Genetic Variation of Green Mussel, Perna viridis in the Gulf of Thailand and Implication for Aquaculture

The culture of green mussel (Perna viridis) in the Gulf of Thailand depends on natural spat which are believed to come from spawning grounds adjacent to major river mouths. In the present paper, genetic diversity of spatial and temporal populations of green mussel in the Gulf of Thailand was investigated using five microsatellite loci. The results showed moderate genetic variation of all 11 populations (averaged number of alleles per locus, A = 10.4–12.2; effective number of alleles per locus, A _e = 5.36–6.59; mean allelic richness, A _r = 10.23–12.06; observed heterozygosity, H _o = 0.52–0.63, and expected heterozygosity, H _e = 0.66–0.73) without significant differences among populations. No sign of bottleneck or genetic disequilibrium was observed. Genetic differentiation among spatial populations was low (F _ST = 0.0046, CI_0.95 = 0.0020–0.0083 for the samples collected in January, 2007, and F _ST = 0.0088, CI_0.95 = 0.0010–0.0162 for the samples collected in July, 2007) while temporal variation was significant as revealed by the analysis of molecular variance. Multidimensional scaling separated temporal population groups with minor exception. The assignment test revealed that most of the recruits were from other populations.     

High population differentiation in the rock-dwelling land snail (<Emphasis Type="Italic">Trochulus caelatus</Emphasis>) endemic to the Swiss Jura Mountains

Understanding patterns of genetic structure is fundamental for developing successful management programmes for isolated populations of threatened species. Trochulus caelatus is a small terrestrial snail endemic to calcareous rock cliffs in the Northwestern Swiss Jura Mountains. Eight microsatellite loci were used to assess the effect of habitat isolation on genetic population structure and gene flow among nine populations occurring on distinct cliffs. We found a high genetic differentiation among populations (mean F _ST = 0.254) indicating that the populations are strongly isolated. Both allelic richness and effective population size were positively correlated with the size of the cliffs. Our findings support the hypothesis that T. caelatus survived on ice-free cliffs during the Pleistocene glacier advancements from the Alps. Due to the establishment of beech and pine forest under recent, temperate climate conditions, dispersal between cliffs is no longer possible for rock-dwelling snails such as T. caelatus. Our results provide basic data for developing a conservation action plan for this endangered gastropod species.     

Large‐scale connectivity,cryptic population structure,and relatedness in Eastern Pacific Olive ridley sea turtles (Lepidochelys olivacea)

Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial control region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (F_ST = 0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and preexisting microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (F_ST = 0.08, p < .001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (F_ST = 0.103, p < .001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p < .001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin‐wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life history, particularly in light of the natal‐homing paradigm.     

Ensuring effective restoration efforts with salt marsh grass populations by assessing genetic diversity

Smooth cordgrass (Spartina alterniflora) is a foundation species that naturally occurs along the Atlantic coast of North America and is often used in restoration due to its extensive rooting capacity and ability to halt erosion. Clonal species, such as S. alterniflora, are easy to rear for transplant, but using a predominantly asexual species for restoration may lead to genetically depauperate populations. We (1) identified if genetic diversity was maintained during restoration; (2) determined if genotypes from the native populations were genetically distinct from the restored populations; and (3) evaluated if current efforts limited the number of multiple copies of the same multilocus genotypes (MLG) within restoration sites along the shorelines of the Mosquito Lagoon (ML), Florida, United States. All objectives were addressed where only one representative of an identical MLG was retained within each population. We found that allelic richness (p = 0.618) and expected heterozygosity (p = 0.527) did not significantly differ between restored and natural populations. Furthermore, pairwise F_ST estimates between naturally occurring populations ranged from 0.021 to 0.178, while estimates ranged from approximately 0 to 0.084 among restored populations. When we evaluated differentiation between natural and restored populations, average F_ST was 0.087. Finally, we found that higher numbers of samples with multiple copies of the same MLG occurred in restored populations (31.4–55.9% of samples per population) compared to natural populations (0–11.8% of samples per population). Overall, we found that current restoration efforts in the ML are effective at maintaining natural levels of genetic diversity.     

Isolation of microsatellite markers in Cannabis sativa L. (marijuana)

We have identified 15 variable microsatellite loci in Cannabis sativa. In 48 samples from five fibre crop seed accessions, we detected an average of 10 alleles per locus (range 2–28) with mean heterozygosity of 0.68 (range 0.28–0.94). Significant genetic differentiation was found between accessions (F_ST = 0.12, P < 0.001). These markers have utility for characterizing genetic diversity in cultivated and naturalized Cannabis populations.     

Population genetics after fragmentation: the case of the endangered Spanish imperial eagle (Aquila adalberti)

The highly endangered Spanish imperial eagle, Aquila adalberti, has suffered from both population decline and fragmentation during the last century. Here we describe the current genetic status of the population using an extensive sampling of its current distribution range and both mitochondrial control region sequences and nuclear microsatellite markers. Results were evaluated in comparison to those obtained for the Eastern imperial eagle, Aquila heliaca, its nearest extant relative. Mitochondrial haplotype diversity was lower in the Spanish than in the Eastern species whereas microsatellite allelic richness and expected heterozygosity did not differ. Both allelic richness and expected heterozygosity were lower in the small Parque Nacional de Doñana breeding nucleus compared to the remaining nuclei. A signal for a recent genetic bottleneck was not detected in the current Spanish imperial eagle population. We obtained low but significant pairwise F_ST values that were congruent with a model of isolation by distance. F_ST and exact tests showed differentiation among the peripheral and small Parque Nacional de Doñana population and the remaining breeding subgroups. The centrally located Montes de Toledo population did not differ from the surrounding Centro, Extremadura and Sierra Morena populations whereas the latter were significantly differentiated. On the other hand, a Bayesian approach identified two groups, Parque Nacional de Doñana and the rest of breeding nuclei. Recent migration rates into and from Parque Nacional de Doñana and the rest of breeding nuclei were detected by assignment methods and estimated as 2.4 and 5.7 individuals per generation, respectively, by a Bayesian approach. We discuss how management strategies should aim at the maintenance of current genetic variability levels and the avoidance of inbreeding depression through the connection of the different nuclei.     

Polymorphic microsatellites in the African freshwater snail,Bulinus forskalii (Gastropoda,Pulmonata)

Eleven microsatellites were isolated in the freshwater snail Bulinus forskalii, intermediate host for the medically important trematode Schistosoma intercalatum. Characterization in 60 snails from three populations of B. forskalii from Cameroon revealed 4 to 18 alleles per locus. Low observed heterozygosity but higher expected heterozygosity, high F_IS estimates, significant departures from Hardy–Weinberg equilibrium and genotypic linkage disequilibria all indicate that B. forskalii is a preferential selfer. High F_ST estimates suggest that effective dispersal is limited and genetic drift is an important determinant of genetic structure. The potential utility of the microsatellite primers in other closely related Bulinus species was explored.     

Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin

Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea spawners, river spawners and lake spawners). To generate expected neutral distribution of F_ST and to evaluate whether highly variable microsatellite loci resulted in deflated F_ST estimates compared to less variable markers, we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (F_CT = 0.010) and within (F_ST = 0.014–0.041) ecotypes was rather low. The divergence in gill raker number, however, was substantially higher between sea and river spawners compared to observed microsatellite data and simulated neutral baseline (P_CT > F_CT). This suggests that the differences in gill raker number between sea and river spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill raker number among different populations of sea spawners (P_ST > F_ST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake spawners initially inferred from empirical microsatellite data was not supported by simulated F_ST distributions. This work provides a first formal test of divergent selection on gill raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for P_ST–F_ST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.