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.     

Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphytic orchid

Populations of many species are isolated within narrow elevation bands of Neotropical mountain habitat, and how well dispersal maintains genetic connectivity is unknown. We asked whether genetic structure of an epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa Rican mountain ranges, and how these gaps influence pollen and seed flow. We predicted that significant genetic structure exists among mountain ranges due to different colonization histories and limited gene flow. Furthermore, we predicted that pollen movement contributes more to gene flow than seeds because seeds are released into strong winds perpendicular to the narrow northwest–southeast species distribution, while the likely pollinators are strong fliers. Individuals from 12 populations and three mountain ranges were genotyped with nuclear microsatellites (nDNA) and chloroplast sequences (cpDNA). Genetic diversity was high for both markers, while nDNA genetic structure was low (F_STn = 0.020) and cpDNA structure was moderate (F_STc = 0.443). Significant cpDNA barriers occurred within and among mountain ranges, but nDNA barriers were not significant after accounting for geographic distance. Consistent with these contrasting patterns of genetic structure, pollen contributes substantially more to gene flow among populations than seed (m_p/m_s = 46). Pollinators mediated extensive gene flow, eroding nDNA colonization footprints, while seed flow was comparatively limited, possibly due to directional prevailing winds across linearly distributed populations. Dispersal traits alone may not accurately inform predictions about gene flow or genetic structure, supporting the need for research into the potentially crucial role of pollinators and landscape context in gene flow among isolated populations.     

Patterns of genetic diversity and differentiation in the tsetse fly <Emphasis Type="Italic">Glossina morsitans morsitans</Emphasis> Westwood populations in East and southern Africa

Genetic diversity and differentiation within and among nine G. morsitans morsitans populations from East and southern Africa was assessed by examining variation at seven microsatellite loci and a mitochondrial locus, cytochrome oxidase (COI). Mean COI diversity within populations was 0.63 ± 0.33 and 0.81 taken over all populations. Diversities averaged over microsatellite loci were high (mean number of alleles/locus ≥7.4; mean H _E ≥ 65%) in all populations. Diversities averaged across populations were greater in East Africa (mean number of alleles = 22 ± 2.6; mean h _e = 0.773 ± 0.033) than in southern Africa (mean number of alleles = 18.7 ± 4.0; mean h _e = 0.713 ± 0.072). Differentiation among all populations was highly significant (R _ST = 0.25, F _ST = 0.132). Nei’s G _ij statistics were 0.09 and 0.19 within regions for microsatellites and mitochondria, respectively; between regions, G _ij was 0.14 for microsatellites and 0.23 for mitochondria. G _ST among populations was 0.23 for microsatellite loci and 0.40 for mitochondria. The F, G and R statistics indicate highly restricted gene flow among G. m. morsitans populations separated over geographic scales of 12–917 km.     

Chloroplast microsatellite variation in <Emphasis Type="Italic">Abies nordmanniana</Emphasis> and simulation of causes for low differentiation among populations

Fifteen populations of Abies nordmanniana, originating from all main parts of its distributional area in the Caucasian region, were genotyped for three chloroplast microsatellites as well as one mitochondrial marker. The chloroplast microsatellites were highly variable, resulting in a total of 111 haplotypes in 361 analysed individuals, while the mitochondrial marker showed no variation. Analysis of molecular variance attributed 2.1% of the variation in the microsatellites to be among populations, and no correlation between geographic distribution and genetic distances among populations could be observed. A simulation study was conducted to investigate to what extent the low genetic differentiation among populations could be a result of size homoplasy in the applied microsatellites. However, the simulations indicated that the low differentiation more likely is caused by high gene flow among populations.     

Global warming will affect the genetic diversity and uniqueness of Lycaena helle populations

The climate warming of the postglacial has strongly reduced the distribution of cold‐adapted species over most of Central Europe. Such taxa have therefore become extinct over most of the lowlands and shifted to higher altitudes where they have survived to the present day. The lycaenid butterfly Lycaena helle follows this pattern of former widespread distribution and later restriction to mountain areas such as the European middle mountains. We sampled 203 individuals from 10 populations representing six mountain ranges (Pyrenees, Jura, Massif Central, Morvan, Vosges and Ardennes) over the species' western distribution. Allozyme and microsatellite polymorphisms were analysed to study the genetic status of these highly fragmented populations. Both molecular marker systems revealed a strong genetic differentiation among the analysed populations, coinciding with the orographic structure and highly restricted gene flow among them. The large‐scale genetic differentiation is more pronounced in allozymes (F_CT: 0.326) than in microsatellites (R_CT: 0.113), but microsatellites show a higher resolution on the regional scale (R_SC: 0.082) compared with allozymes (F_SC: n.s.). For both analytical tools, we found private alleles occurring exclusively in a single mountain area. The highly fragmented and isolated occurrence of populations is supported by the distribution pattern of potentially suitable climate suggested by species distribution models. Model projections under two climate warming scenarios predict a decline of climatically suitable areas, which will result in the extinction of most of the populations showing unique genetic characteristics.     

Comparisons of microsatellite variability and population genetic structure of two endangered wild rice species, <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and <Emphasis Type="Italic">O. officinalis</Emphasis>, and their conservation implications

Conserving endangered wild rice species requires a thorough understanding of their population genetic structure and appropriate approaches. We applied six and seven microsatellite loci to study the genetic structure of six populations throughout the range of Chinese Oryza rufipogon and Oryza officinalis, respectively. The results showed that O. rufipogon possesses higher levels of genetic diversity but lower differentiation (R_S = 3.2713, P = 100.0%, H_O = 0.1401, H_S = 0.5800, F_ST = 0.271) than O. officinalis (R_S = 2.0545, P = 57.14%, H_O = 0.0470, H_S = 0.2830, F_ST = 0.554). Mean population F_IS was slightly larger for O. officinalis (F_IS = 0.844) than that for O. rufipogon (F_IS = 0.755), indicating that O. officinalis has slightly higher departures from Hardy–Weinberg expectations and heterozygosity deficits than O. rufipogon. In addition to different origins and evolutionary histories, O. officinalis has restricted gene flow, high inbreeding, isolated small populations and fewer opportunities of hybridization with other taxa, which may determine major differences in population genetic structure from O. rufipogon. Our results suggest the adoption of a plan of involving fewer populations but more individuals within populations for O. rufipogon, while both the number of populations and the individuals for a sampled population should be almost equally considered for O. officinalis. The known high degree of inbreeding in the populations of both species implies that conservation and restoration genetics should particularly focus on the maintenance of historically significant processes such as high levels of outbreeding, gene flow and large effective population sizes. We finally proposed to further estimate the role of rice gene flow in the conservation of O. rufipogon, and to perform detailed analysis of mating systems in both species for better conservation perspectives of their ecological and evolutionary processes.     

Selection on life‐history traits and genetic population divergence in rotifers

A combination of founder effects and local adaptation – the Monopolization hypothesis – has been proposed to reconcile the strong population differentiation of zooplankton dwelling in ponds and lakes and their high dispersal abilities. The role genetic drift plays in genetic differentiation of zooplankton is well documented, but the impact of natural selection has received less attention. Here, we compare differentiation in neutral genetic markers (F_ST) and in quantitative traits (Q_ST) in six natural populations of the rotifer Brachionus plicatilis to assess the importance of natural selection in explaining genetic differentiation of life‐history traits. Five life‐history traits were measured in four temperature × salinity combinations in common‐garden experiments. Population differentiation for neutral genetic markers – 11 microsatellite loci – was very high (F_ST = 0.482). Differentiation in life‐history traits was higher in traits related to sexual reproduction than in those related to asexual reproduction. Q_ST values for diapausing egg production (a trait related to sexual reproduction) were higher than their corresponding F_ST in some pairs of populations. Our results indicate the importance of divergent natural selection in these populations and suggest local adaptation to the unpredictability of B. plicatilis habitats.     

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

Background and Aims

The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest.

Methods

Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers.

Key Results

For nuclear microsatellites, allelic richness (R) and heterozygosity (H_e,nuc) differed between types of forest: R = 7·36 and R = 9·55, H_e,nuc = 0·64 and H_e,nuc = 0·80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N_a,nuc) and the fixation index F_IS differed significantly: N_a,nuc = 9·41 and N_a,nuc = 13·18, F_IS = 0·06 and F_IS = 0·15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F_ST,nuc = 0·08) and moderate for chloroplast microsatellites (F_ST,cp = 0·49). A clear relationship was observed between genetic and geographic distance (r = 0·42 P < 0·01 and r = 0·42 P = 0·03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations.

Conclusions

Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.     

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.     

Causes of Size Homoplasy Among Chloroplast Microsatellites in Closely Related <Emphasis Type="Italic">Clusia</Emphasis> Species

Chloroplast DNA sequences and microsatellites are useful tools for phylogenetic as well as population genetic analyses of plants. Chloroplast microsatellites tend to be less variable than nuclear microsatellites and therefore they may not be as powerful as nuclear microsatellites for within-species population analysis. However, chloroplast microsatellites may be useful for phylogenetic analysis between closely related taxa when more conventional loci, such as ITS or chloroplast sequence data, are not variable enough to resolve phylogenetic relationships in all clades. To determine the limits of chloroplast microsatellites as tools in phylogenetic analyses, we need to understand their evolution. Thus, we examined and compared phylogenetic relationships of species within the genus Clusia, using both chloroplast sequence data and variation at seven chloroplast microsatellite loci. Neither ITS nor chloroplast sequences were variable enough to resolve relationships within some sections of the genus, yet chloroplast microsatellite loci were too variable to provide any useful phylogenetic information. Size homoplasy was apparent, caused by base substitutions within the microsatellite, base substitutions in the flanking regions, indels in the flanking regions, multiple microsatellites within a fragment, and forward/reverse mutations of repeat length resulting in microsatellites of identical base composition that were not identical by descent.     

Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide‐spread African tree with high colonization capacity,Milicia excelsa (Moraceae)

The impact of the Pleistocene climate oscillations on the structure of biodiversity in tropical regions remains poorly understood. In this study, the forest refuge theory is examined at the molecular level in Milicia excelsa, a dioecious tree with a continuous range throughout tropical Africa. Eight nuclear microsatellites (nSSRs) and two sequences and one microsatellite from chloroplast DNA (cpDNA) showed a deep divide between samples from Benin and those from Lower Guinea. This suggests that these populations were isolated in separate geographical regions, probably for several glacial cycles of the Pleistocene, and that the nuclear gene pools were not homogenized despite M. excelsa’s wind‐pollination syndrome. The divide could also be related to seed dispersal patterns, which should be largely determined by the migration behaviour of M. excelsa’s main seed disperser, the frugivorous bat Eidolon helvum. Within Lower Guinea, a north–south divide, observed with both marker types despite weak genetic structure (nSSRs: F_ST = 0.035, cpDNA: G_ST = 0.506), suggested the existence of separate Pleistocene refugia in Cameroon and the Gabon/Congo region. We inferred a pollen‐to‐seed dispersal distance ratio of c. 1.8, consistent with wide‐ranging gene dispersal by both wind and bats. Simulations in an Approximate Bayesian Computation framework suggested low nSSR and cpDNA mutation rates, but imprecise estimates of other demographic parameters, probably due to a substantial gene flow between the Lower Guinean gene pools. The decline of genetic diversity detected in some Gabonese populations could be a consequence of the relatively recent establishment of a closed canopy forest, which could negatively affect M. excelsa’s reproductive system.     

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Mare to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautes, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci-population combinations (per population FIS = 0-0.03 on Grande-Terre and Ile des Pins, and 0-0.67 on Loyautes). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyaute and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.     

Patterns of genetic variation in the Chinese endemic Psilopeganum sinense (Rutaceae) as revealed by nuclear microsatellites and chloroplast microsatellites

Psilopeganum sinense is a perennial herb endemic to Three-Gorges Reservoir Area (TGRA) in China. Genetic diversity of this endangered species was assessed by using 11 nuclear microsatellites and three chloroplast microsatellite (cpSSR) markers. A total of 8 haplotypes were identified in a survey of 212 individuals sampled from nine populations encompassing most of the natural range of the species. A low level of genetic diversity was detected: H_E = 0.301 for SSR and H_E = 0.28 for cpSSR. Populations were highly differentiated from one another: an AMOVA analysis that showed that 56.3% and 68.2% genetic variation resided between populations based on SSR and cpSSR analysis, respectively, and F_ST and F_STc (0.467 for SSR and 0.644 for cpSSR, respectively) were high. Significant differences were found between estimates of haplotypic differentiation calculated by using unordered alleles (G_STc = 0.857) and ordered alleles (N_STc = 0.728), which indicated the existence of phylogeographical structure in P. sinense. The indirect ratio of pollen flow/seed flow derived from estimates of haplotypic and nuclear DNA differentiation indicated that gene flow via pollen is less efficient than via seed. Two distinct evolutionary lineages (evolutionary significant units, ESUs) were recognized for P. sinense on the basis of both the PCoA and NCA analysis. Sampling strategies for conserving this endangered plant were discussed.     

Genetic diversity and differentiation of the endangered Japanese endemic tree Magnolia stellata using nuclear and chloroplast microsatellite markers

Genetic diversity and differentiation were analyzed in 11 populations of Magnolia stellata (Sieb. and Zucc.) Maxim. (Magnoliaceae) in the Tokai district, Japan. Variation at four nuclear microsatellite (nSSR) loci was examined, three chloroplast microsatellite (cpSSR) markers were developed and 13 haplotypes identified. The 11 populations were divided into three groups (A, B and C). Each population within the group was separated less than 40 km. Group B harbored the highest gene diversity (H) and allelic richness (Ar) for nSSR (H=0.74 and Ar=8.02). Group C had the highest diversity of chloroplast haplotypes (H=0.79 and Ar=6.8): 2.5 times more haplotypes than the other groups. Each population contributed differently to the total diversity, with respect to nSSR and cpSSR. AMOVA revealed that 58% of haplotypic and 15% of nSSR variation was partitioned among populations within groups. A Mantel test revealed significant correlations between population pairwise geographic ln(distance) and F_ST/(1−F_ST) for both nSSR (r=0.479; P=0.001) and cpSSR (r=0.230; P=0.040). Dendrograms of populations for nSSR, based on Nei’s genetic distance, were constructed using UPGMA and the neighbor-joining method. These results suggest that populations in group C have diverged from the other populations, while those in group B are similar to each other. For group B, fragmentation between populations should be avoided in order to maintain gene flow. For group C, the uniqueness of each population should be given the highest priority when planning genetic conservation measures for the species.     

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

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

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

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

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

Size differentiation in Finnish house sparrows follows Bergmann's rule with evidence of local adaptation

Bergmann's rule predicts that individuals are larger in more poleward populations and that this size gradient has an adaptive basis. Hence, phenotypic divergence in size traits between populations (P_ST) is expected to exceed the level of divergence by drift alone (F_ST). We measured 16 skeletal traits, body mass and wing length in 409 male and 296 female house sparrows Passer domesticus sampled in 12 populations throughout Finland, where the species has its northernmost European distributional margin. Morphometric differentiation across populations (P_ST) was compared with differentiation in 13 microsatellites (F_ST). We find that twelve traits phenotypically diverged more than F_ST in both sexes, and an additional two traits diverged in males. The phenotypic divergence exceeded F_ST in several traits to such a degree that findings were robust also to strong between‐population environmental effects. Divergence was particularly strong in dimensions of the bill, making it a strong candidate for the study of adaptive molecular genetic divergence. Divergent traits increased in size in more northern populations. We conclude that house sparrows show evidence of an adaptive latitudinal size gradient consistent with Bergmann's rule on the modest spatial scale of ca. 600 km.     

Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci

We describe the genetic population structure of65 bull trout (Salvelinus confluentus)populations from the northwestern United Statesusing four microsatellite loci. Thedistribution of genetic variation as measuredby microsatellites is consistent with previousallozyme and mitochondrial DNA analysis. Thereis relatively little genetic variation withinpopulations (H ^S = 0.000 – 0.404,average H ^S = 0.186, but substantialdivergence between populations (F ^ST = 0.659). In addition, those populations that had low genetic variation forallozymes also tended to have low geneticvariation at microsatellite loci. Microsatellite analysis supports the existenceof at least three major geneticallydifferentiated groups of bull trout: (1)``Coastal' bull trout populations, (2) ``SnakeRiver' populations, which also include the JohnDay, Umatilla, and Walla Walla Rivers and, (3)populations from the upper Columbia River,primarily from the Clark Fork basin. Withinthe major assemblages, populations are furthersubdivided, primarily at the river basin level. Most of the genetic similarities we havedetected probably reflect patterns of historicisolation and gene flow. However, in somecases, genetic drift and low levels ofvariation appear to have influenced therelationships inferred from these data. Finally, we suggest using a hierarchicalapproach to direct management actions inspecies such as bull trout for which most ofthe genetic variation exists among populationsand local populations in close proximitytypically are genetically distinct.