Patterns Of Population Differentiation Research Articles

Bathymetric and geographic population structure in the pan‐Atlantic deep‐sea bivalve Deminucula atacellana (Schenck, 1939)

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Extent and Distribution of Genetic Variation in U.S. Maize: Historically Important Lines and Their Open‐Pollinated Dent and Flint Progenitors

Ancestral open‐pollinated populations of U.S. maize (Zea mays L.) are a resource to broaden the genetic base of modern maize and to ensure long‐term gains in maize breeding. We report the extent and distribution of simple sequence repeat (SSR) variation in a comprehensive study of Northern Flints (NFs), Southern Dents (SDs), Corn Belt Dents (CBDs), and historically important inbred lines, and address their implications for maize improvement and conservation. We found that the loss of rare alleles in open‐pollinated cultivars from elite gene pools resulted in the divergence of inbred lines as a distinct group apart from their progenitor races. In contrast, the Corn Belt Dent cultivars retained high levels of genetic variation that approximated or exceeded that found in their NF and SD progenitors. Within open‐pollinated varieties, the absence of any clear pattern of population differentiation indicates frequent admixture, a relatively recent time of divergence, or poor correlation between the degree of divergence at neutral marker loci and quantitative trait variation. This research suggests that the inbred lines currently used by breeders as the primary genetic resource for line improvement do not represent the genetic variation available in the temperate races from which they are derived: only 56% of the alleles found in the Corn Belt Dents were displayed in a diverse set of inbred lines. Extensive sampling targeted at a limited number of Corn Belt Dent cultivars is a promising approach toward the identification and introgression of rare alleles that were lost during early inbred development or the maintenance of open‐pollinated populations.

POPULATION DIFFERENTIATION DECREASES WITH DEPTH IN DEEP-SEA BIVALVES

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by phiST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530-3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864-4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.

The Genetic Structure of Australian Populations of Mycosphaerella musicola Suggests Restricted Gene Flow at the Continental Scale

ABSTRACT Mycosphaerella musicola causes Sigatoka disease of banana and is endemic to Australia. The population genetic structure of M. musicola in Australia was examined by applying single-copy restriction fragment length polymorphism probes to hierarchically sampled populations collected along the Australian east coast. The 363 isolates studied were from 16 plantations at 12 sites in four different regions, and comprised 11 populations. These populations displayed moderate levels of gene diversity (H = 0.142 to 0.369) and similar levels of genotypic richness and evenness. Populations were dominated by unique genotypes, but isolates sharing the same genotype (putative clones) were detected. Genotype distribution was highly localized within each population, and the majority of putative clones were detected for isolates sampled from different sporodochia in the same lesion or different lesions on a plant. Multilocus gametic disequilibrium tests provided further evidence of a degree of clonality within the populations at the plant scale. A complex pattern of population differentiation was detected for M. musicola in Australia. Populations sampled from plantations outside the two major production areas were genetically very different to all other populations. Differentiation was much lower between populations of the two major production areas, despite their geographic separation of over 1,000 km. These results suggest low gene flow at the continental scale due to limited spore dispersal and the movement of infected plant material.

POPULATION DIFFERENTIATION DECREASES WITH DEPTH IN DEEP-SEA BIVALVES

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by ΦST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530–3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864–4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.

Analysis of the Angiotensinogen Gene T174M Polymorphism in Populations of the Volga–Ural Region

The method of polymerase chain reaction was used to analyze T174M polymorphism at the angiotensinogen (AGT) gene in a number of populations of the Volga-Ural region, belonging to Finno-Ugric (Komi-Permyaks, Maris, Mordovians, and Udmurts), Turkic (Chuvashes, Tatars, and Bashkirs), and Eastern-Slavic (Russians) ethnic groups. Population-specific patterns of the polymorphic alleles and genotypes frequency distribution were established. Comparison of the results with the literature data on the AGT gene polymorphism in different world populations provided identification of specific trends in the changes of genotype frequency of the AGT gene depending on the ethnicity of the populations.

Microsatellite Variation and its Comparison with Allozyme and RAPD Variation in Elymus Fibrosus (Schrenk) Tzvel. (Poaceae)

Genetic variation of ten Elymus fibrosus populations was analyzed using six microsatellite loci. The mean number of alleles per locus (A) was 1.8, ranging from 1.3 to 2.3, the mean percent of polymorphic loci (P) was 53.3%, ranging from 16.7% to 83.3%, and the mean gene diversity (HT) was 0.252, varying from 0.063 to 0.444. The total microsatellite variation for the species was HT=0.548. When partitioned (GST), 54% of the total variation was found among populations. Specific alleles were observed for different populations and geographical areas. In comparison with the genetic variation detected by allozymes and RAPDs, microsatellite loci always showed higher levels of genetic variation. For instance, the gene diversity (He) found at microsatellite loci was approximately 30 and 3 times higher than that at allozyme and RAPD loci (He= 0.008 and He= 0.097, respectively). In general, different pictures of the amount of the genetic variation were given by isozyme, RAPD and microsatellites but agreement was found regarding how this genetic variation is distributed among populations. In addition, a geographical pattern of population differentiation, where the Finnish and Russian populations were clearly separated from each other, was revealed by both the cluster and principal coordinates analyses when using both RAPDs and microsatellites.

Distribution of the HLA-DRB1 Specificities in Populations of the Volga–Ural Region

Polymorphism at the HLA-DRB1 locus in six Turkic (Bashkirs, Tatars, and Chuvashes) and Finno-Ugric (Udmurts, Maris, and Komis) populations of the Volga–Ural region was studied by PCR. A total of 12 DRB1 specificities displaying population-specific frequency distribution patterns were described. The most frequently observed specificities in Bashkirs and Udmurts were DRB1*07 (25 and 34%, respectively) and *15 (by 15%). In Tatars the prevalence of *04 (18%), *01 (17%), *07 (16%), and *15 (13%) specificities was observed, while in Chuvashes these were *04 (28%), *11 (18%), *01 (16%), and *07 (16%). High frequencies of *11 (21%),*04 (17%), *01 (13%), and *07 (13%) specificities were characteristic of Komis, whereas Maris were distinguished by high frequencies of *01 (23%), *11 (14%), *07 (13%), and *04 (11%). In general, the pattern of DRB1 allelic polymorphism in populations of the Volga–Ural region, occupying the intermediate position between the Caucasoid- and Mongoloid-specific allelic frequency distribution patterns, was consistent with their anthropological type rather than with their linguistic affiliation.

Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.

REPRODUCTIVE CHARACTER DISPLACEMENT AND THE GENETICS OF GAMETE RECOGNITION IN TROPICAL SEA URCHINS

Reproductive character displacement occurs when sympatric and allopatric populations of a species differ in traits crucial to reproduction, and it is commonly thought of as a signal of selection acting to limit hybridization. Most documented cases of reproductive character displacement involve characters that are poorly understood at the genetic level, and rejecting alternative hypotheses for biogeographic shifts in reproductive traits is often very difficult. In sea urchins, the gamete recognition protein bindin evolves under positive selection when species are broadly sympatric, suggesting character displacement may be operating in this system. We sampled sympatric and allopatric populations of two species in the sea urchin genus Echinometra for variation in bindin and for the mitochondrial cytochrome oxidase I to examine patterns of population differentiation and molecular evolution at a reproductive gene. We found a major shift in bindin alleles between central Pacific (allopatric) and western Pacific (sympatric) populations of E. oblonga. Allopatric populations of E. oblonga are polyphyletic with E. sp. C at bindin, whereas sympatric populations of the two species are reciprocally monophyletic. There is a strong signal of positive selection (P(N)/P(S) = 4.5) in the variable region of the first exon of bindin, which is associated with alleles found in sympatric populations of E. oblonga. These results indicate that there is a strong pattern of reproductive character displacement between E. oblonga and E. sp. C and that the divergence is driven by selection. There is much higher population structure in sympatric populations at the bindin locus than at the neutral mitochondrial locus, but this difference is not seen in allopatric populations. These data suggest a pattern of speciation driven by selection for local gamete coevolution as a result of interactions between sympatric species. Although this pattern is highly suggestive of speciation by reinforcement, further research into hybrid fitness and egg-sperm interactions is required to address this potential mechanism for character displacement.

Hierarchical genetic structure in fragmented populations of the Little Pocket Mouse (Perognathus longimembris) in Southern California

The geographic genetic structure, based onsequence variation of an 810 base pair fragmentof the mitochondrial cytochrome b gene,is described for populations of five subspeciesof the Little Pocket Mouse, Perognathuslongimembris, from Southern California. Oneof these, P. l. pacificus (Pacific PocketMouse), is listed as Endangered by the U.S.Federal Government. Sixty-two uniquehaplotypes were recovered from 99 individualssampled. Phylogenetic analyses of thesevariants do not identify regionallyreciprocally monophyletic lineages concordantwith the current subspecies designations, butmost haplotypes group by subspecies in networksgenerated by either statistical parsimony ormolecular variance parsimony. Moreover, asubstantial proportion of the total pool ofhaplotype variation is attributed to thesesubspecies, or to local populations withingeographic segments of each, indicating theirrelative evolutionary independence. The pooledextant populations of the endangered PacificPocket Mouse exhibit the same levels ofnucleotide and haplotype diversity as other,presumptively less-impacted populations ofadjacent subspecies, although the sample fromDana Point, Orange County, has markedly lowhaplotype diversity in comparison to allothers. These populations also show a geneticsignature of population expansion rather thanone of decline. Both pieces of evidence are atodds with current empirical populationestimates, which reinforces the fact thatpresent-day patterns of genetic diversity arethe product of coalescent history and will notnecessarily reflect recent anthropogenic, orother, perturbations. Comparison of haplotypevariation within and among extant populationsof the Pacific Pocket Mouse with those obtainedfrom museum samples collected more than 70years ago suggests that the pattern ofpopulation differentiation and diversity was inplace before the post-World War II exponentialurbanization of Southern California.

REPRODUCTIVE CHARACTER DISPLACEMENT AND THE GENETICS OF GAMETE RECOGNITION IN TROPICAL SEA URCHINS

Reproductive character displacement occurs when sympatric and allopatric populations of a species differ in traits crucial to reproduction, and it is commonly thought of as a signal of selection acting to limit hybridization. Most documented cases of reproductive character displacement involve characters that are poorly understood at the genetic level, and rejecting alternative hypotheses for biogeographic shifts in reproductive traits is often very difficult. In sea urchins, the gamete recognition protein bindin evolves under positive selection when species are broadly sympatric, suggesting character displacement may be operating in this system. We sampled sympatric and allopatric populations of two species in the sea urchin genus Echinometra for variation in bindin and for the mitochondrial cytochrome oxidase I to examine patterns of population differentiation and molecular evolution at a reproductive gene. We found a major shift in bindin alleles between central Pacific (allopatric) and western Pacific (sympatric) populations of E. oblonga. Allopatric populations of E. oblonga are polyphyletic with E. sp. C at bindin, whereas sympatric populations of the two species are reciprocally monophyletic. There is a strong signal of positive selection (PN/PS = 4.5) in the variable region of the first exon of bindin, which is associated with alleles found in sympatric populations of E. oblonga. These results indicate that there is a strong pattern of reproductive character displacement between E. oblonga and E. sp. C and that the divergence is driven by selection. There is much higher population structure in sympatric populations at the bindin locus than at the neutral mitochondrial locus, but this difference is not seen in allopatric populations. These data suggest a pattern of speciation driven by selection for local gamete coevolution as a result of interactions between sympatric species. Although this pattern is highly suggestive of speciation by reinforcement, further research into hybrid fitness and egg-sperm interactions is required to address this potential mechanism for character displacement.

Natural selection at linked sites in humans

Theoretical and empirical work indicates that patterns of neutral polymorphism can be affected by linked, selected mutations. Under background selection, deleterious mutations removed from a population by purifying selection cause a reduction in linked neutral diversity. Under genetic hitchhiking, the rise in frequency and fixation of beneficial mutations also reduces the level of linked neutral polymorphism. Here we review the evidence that levels of neutral polymorphism in humans are affected by selection at linked sites. We then discuss four approaches for distinguishing between background selection and genetic hitchhiking based on (i) the relationship between polymorphism level and recombination rate for neutral loci with high mutation rates, (ii) relative levels of variation on the X chromosome and the autosomes, (iii) the frequency distribution of neutral polymorphisms, and (iv) population-specific patterns of genetic variation. Although the evidence for selection at linked sites in humans is clear, current methods and data do not allow us to clearly assess the relative importance of background selection and genetic hitchhiking in humans. These results contrast with those obtained for Drosophila, where the signals of positive selection are stronger.

Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla).

We characterized the pattern and magnitude of phylogeographical variation among breeding populations of a long-distance migratory bird, the Wilson's warbler (Wilsonia pusilla), and used this information to assess the utility of mtDNA markers for assaying demographic connectivity between breeding and overwintering regions. We found a complex pattern of population differentiation in mitochondrial DNA (mtDNA) variation among populations across the breeding range. Individuals from eastern North America were differentiated from western individuals and the eastern haplotypes formed a distinct, well-supported cluster. The more diverse western group contained haplotype clusters with significant geographical structuring, but there was also broad mixing of haplotype groups such that no haplotype groups were population specific and the predominance of rare haplotypes limited the utility of frequency-based assignment techniques. Nonetheless, the existence of geographically diagnosable eastern vs. western haplotypes enabled us to characterize the distribution of these two groups across 14 overwintering locations. Western haplotypes were present at much higher frequencies than eastern haplotypes at most overwintering sites. Application of this mtDNA-based method of linking breeding and overwintering populations on a finer geographical scale was precluded by the absence of population-specific markers and by insufficient haplotype sorting among western breeding populations. Our results suggest that because migratory species such as the Wilson's warbler likely experienced extensive gene flow among regional breeding populations, molecular markers will have the greatest utility for characterizing breeding-overwintering connectivity at a broad geographical scale.

Correlations between observed dispersal capabilities and patterns of genetic differentiation in populations of four aquatic insect species from the Arizona White Mountains, U.S.A.

SUMMARY 1. Dispersal ability is an important ecological factor that can influence population structure. In an attempt to determine the extent that the pattern of genetic differentiation is correlated with dispersal ability in stream‐dwelling aquatic insects, we used the amplified fragment length polymorphism (AFLP) technique to characterise genetic variation in four aquatic insect species: Gumaga griseola (Trichoptera: Sericostomatidae), Helicopsyche mexicana (Trichoptera: Helicopsychidae), Psephenus montanus (Coleoptera: Psephenidae) and Ambrysus thermarum (Hemiptera: Naucoridae). Individuals were sampled from several sites within two adjacent catchments in the Arizona White Mountains. In addition to the genetic analyses, a 20‐week‐long trapping study was used to determine the relative dispersal ability of adults of the four species examined.2. We obtained hierarchical indicators of genetic differentiation for catchments, sites within catchments and sites across the region examined. Overall, average estimators of genetic differentiation (F‐statistics) were consistent with direct observations of organismal movement, although it was our direct observations on adult insect flight that permitted us to interpret our results correctly. This was because of the fact that a lack of genetic differentiation across watersheds can be interpreted in two ways.3. In contrast to F‐statistics, patterns of genetic isolation by distance for each species more clearly reflected dispersal ability, suggesting that such analytical approaches provide less ambiguous information about the importance of gene flow in the hierarchical partitioning of genetic variation in stream organisms.

Genetic structure of populations of Calomys laucha (muridae, sigmodontinae) from central Argentina

The genetic structure of populations of the Sigmodontinae rodent Calomys laucha was studied by means of allozyme electrophoresis. This highly opportunistic species is found preferably in periodically perturbed habitats of crop fields in central Argentina, where it can attain very high densities. A total of 17 enzymatic proteins assayed gave information on 25 loci; only four were monomorphic in the seven populations studied. Levels of genetic variability (H o from 0.144 to 0.171; P 95% from 44% to 56%) were higher than mean values reported for mammals and rodents. These high levels of heterozygosity could be maintained by large populations that do not experience great fluctuations in size, or by a social structure consistent in many small breeding groups that are formed and dissappear every breeding season. Genetic differentiation at a macrogeographical scale (θ=0.018) was low but statistically significant, and showed no correlation with geographic distance between pairs of populations. The pattern of population differentiation found is compatible with a relatively recent range expansion.

Formation and maintenance of discrete wild rabbit (Oryctolagus cuniculus) population systems in arid Australia: Habitat heterogeneity and management implications

Abstract The wild rabbit (Oryctolagus cuniculus L.) is a significant pest in arid and semi‐arid Australia, where erratic rainfall and irregular pasture growth cause population sizes to oscillate, increasing virtually without limit and then crashing during drought conditions. Vacant habitat patches can be rapidly recolonized from nearby patches in high rainfall years. Using two adjoining rabbit population systems in arid and semi‐arid south‐west Queensland, this study evaluates patterns of population differentiation and proposes a mechanism that may lead to the formation of multiple rabbit population systems in the same locality. Using the combined haplotype frequency data from both a local and regional study, estimates of genetic exchange among local populations are considered in conjunction with ecological data to evaluate the significance of habitat attributes (and their spatial distribution) on the local distribution of rabbit populations, both within and between two adjacent population systems. A tentative model is proposed to explain the observed differences in population structure between the two adjoining systems. Under this model, population structure at specific locations is determined primarily by the availability of areas suitable for prolonged colonization and the quality of the intervening habitat that dictates the degree of isolation between locations and therefore the probability of recolonization following local extinctions. It is also suggested that the current rabbit distribution may be a function of the flexibility of behavioural responses in rabbits to the level of spatial heterogeneity of favourable habitats within the two regions.

Optimal drug therapy and therapeutic drug monitoring after spinal cord injury: a population-specific approach.

Study of the clinical pharmacology of SCI has revealed population-specific patterns of drug metabolism and disposition. PD/PK profiles reflect the changed physiology associated with SCI and correlate well with the neurologic or anatomic level and the magnitude and completeness of the injury. The greatest value of SCI PK/PD profiles lies in their use in developing criteria and strategies for the optimal prescribing of drugs and in therapeutic drug monitoring. Patients with SCI, acute or long-standing, comprise a therapeutically unique and distinct population. Rational, efficacious, and cost-effective approaches to drug development and pharmacotherapy in spinal cord-injured patients can only come about when population-specific PK/PD behavior is incorporated early into the drug development process and used to develop safe, effective therapeutic guidelines.

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar).

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.

Genetic Diversity of Everglades Sawgrass,Cladium jamaicense(Cyperaceae)

Genetic diversity studies of wetland plants are scarce, but estimates of genetic diversity are useful for learning about plant biology or developing appropriate management strategies. We used allozymes to examine patterns of genetic diversity in Cladium jamaicense, the dominant plant species of the Florida Everglades. We sampled 18 populations (a total of 818 plants) in a replicated grid pattern. Because C. jamaicense can reproduce asexually, we compared estimates of genetic diversity calculated using all sampled ramets to those using only genets within populations. Fewer than half of the 13 loci studied were polymorphic ($$P_{\mathrm{s}\,}=46.2\% $$), with just under two alleles per locus on average ($$A_{\mathrm{s}\,}=1.9$$). Heterozygosity was also low and was lower for ramet‐level estimates (ramets: $$H_{\mathrm{es}\,}=0.069$$, $$H_{\mathrm{ep}\,}=0.051$$; genets: $$H_{\mathrm{es}\,}=0.094$$, $$H_{\mathrm{ep}\,}=0.067$$). Ramet‐level estimates indicated heterozygote excess in eight populations and heterozygote deficiencies in four populations, but genet‐level estimates indicated inbreeding in only one population. Ramet‐level estimates indicated significant population differentiation ($$F_{\mathrm{ST}\,}=0.268$$), but genet‐level estimates did not ($$F_{\mathrm{ST}\,}=0.035$$). Similarly, mean genetic distance between populations was higher based on ramet‐level estimates ($$\overline{D}=0.024$$) than genet‐level estimates ($$\overline{D}=0.016$$), and we found a weak correlation between genetic and geographic distance based on ramet‐level estimates ($$r=0.15$$, $$P=0.02$$) but not genet‐level estimates ($$r=0.04$$, $$P=0.2$$). Thus, clonal reproduction resulted in effective genetic differentiation among populations. Observed patterns of population differentiation may reflect high levels of gene flow among populations or patterns established during colonization that persist through long‐lived clones. Genetic diversity of Everglades C. jamaicense was low compared to other sedges or other species with similar life histories (ramets: $$H_{\mathrm{T}\,}=0.150$$; genets: $$H_{\mathrm{T}\,}=0.203$$). This low genetic diversity may reflect a relatively recent origin of C. jamaicense populations in south Florida.