Genetic population structure of the catadromous Perciform: Macquaria novemaculeata (Percichthyidae)

Genetic population structure in the catadromous Australian bass Macquaria novemaculeata was investigated using samples from four locations spanning 600 km along the eastern Australian coastline. Both allozymes and mtDNA control region sequences were examined. Population subdivision estimates based on allozymes revealed low levels of population structuring ( G_st =0·043, P <0·05). However, mtDNA indicated moderate levels of geographic population structure ( G_st =0·146, P <0·0l). Phylogenetic analysis of mtDNA control region sequences (mean sequence divergence 1·9%) indicated little phylogeographic structuring. Results suggested that genotypic variation within each river population, while being affected primarily by genetic drift, was also prevented from more significant divergence by homogenizing levels of gene flow—synonymous with a one-dimensional stepping-stone model of population structure. The catadromous life history of Macquaria novemaculeata was considered to be influential on the pattern of population structure displayed. Results were compared to the few population genetic studies involving catadromous fishes, indicating that catadromy alone is unlikely to be a good predictor of population structure. A more comprehensive suite of biological characteristics than simple life-history traits must be considered fully to allow reliable predictive models of population structure to be formulated.     

Morphological variation in the catadromous Australian bass, from seven geographically distinct riverine drainages

The Australian bass Macquaria novemaculeata is a catadromous species restricted to coastal drainages of south-eastern Australia and recently has undergone reductions in population numbers. Morphometric variation among bass from seven distinct drainages was used to test for the presence of stock structuring. Males and females were treated separately. For both male and female bass, significant heterogeneity in morphology among sample locales was revealed by univariate statistics and discriminant function analysis, with morphological variation found to differ in a clinal pattern. The demonstration of population-specific morphological traits among bass from different river drainages may indicate that inter-populational movement is restricted and that each sample locale constitutes a separate stock of bass.     

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata . Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics ( AMOVA ) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (Φ_ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata , culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.     

Population structure of odd-broodline Asian pink salmon and its contrast to the even-broodline structure

Most of the variation (99%) of Asian odd-broodline pink salmon Oncorhynchus gorbuscha , based on data at 32 variable (46 total) allozyme loci from 35 populations, occurred within populations. The remaining interpopulation variation was attributable to: (1) differences between northern (the northern Sea of Okhotsk, eastern Kamchatka Peninsula and western Kamchatka Peninsula) and southern (Hokkaido Island, Kuril Islands and Sakhalin Island) populations; (2) differences between the southern areas; (3) low variation among populations within some areas. The pattern contrasted strongly with that observed for Asian even-broodline populations, which had a strong structure, possibly related to geographic and oceanographic influences. Isolation-by-distance analyses of each of the two broodlines showed a stronger relationship (x 4·8) among even- than odd-broodline populations. Allele frequency differences between even- and odd-broodlines reflected the reproductive isolation of the broodlines. However, there were no fixed frequency differences which, considered with the differing population structures, suggests that migration-drift equilibrium has not yet obtained in one or both broodlines. The structural differences also suggest it is likely that the even- and odd-broodlines are of different ages and that one is derived from the other. Allozyme data do not provide a genealogical basis for identifying the ancestral lineage.     

Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana)

Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (H_O = 0.21, H_E = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant F_ST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.     

Spatial and temporal population genetic structure of the butterfly aglais urticae L. (Lepidoptera, nymphalidae)

The genetic diversity and the temporal and spatial genetic population structure of the butterfly Aglais urticae, a highly mobile species, were studied by allozyme electrophoresis. High levels of allozyme diversity were found. Most of the total genetic diversity occurred at the within-population scale rather than at the between-population scale. This variation could not be accounted for by Wright's model of 'isolation by distance'. No significant temporal variation was observed for those populations that were sampled in different years. A process combining high movement rate between neighbouring patches, long-distance migration and rare extinction/recolonization is suggested to explain the observed genetic structure. This hypothesis is favoured over an island model of population structure because migration in A. urticae is uniform neither with distance nor with time.     

Generalist niche, specialist strategy: the diet of an Australian percichthyid

Dietary analysis revealed that an impoundment population of Australian bass Macquaria novemaculeata holds a generalist niche, but one arising from persistent individual specialization and interindividual variation. This 'individual specialist' strategy appeared adaptive, but the strength of individual specialization was largely independent of variation in diet composition, except during blooms of Daphnia sp. Diet composition and dietary overlap showed only moderate ontogenetic variation, and niche breadth showed no relationship with ontogeny. Macquaria novemaculeata showed an asymmetric predator and prey size distribution, consistent with many aquatic predators, with positive relationships between fish size and average, maximum and minimum prey size. There was no asymmetry in the relative size-based niche breadths of individuals, however, which indicates that the niche is a fixed 'window' of relative prey sizes. The difference in the dietary niche and prey-size relationships of M. novemaculeata at the population and individual levels highlights the necessity of assessing the niche at both these levels.     

Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.     

Population genetic structure in migratory sandhill cranes and the role of Pleistocene glaciations

Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation-by-distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the nonArctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.     

Influence of landscape on the population genetic structure of the alpine butterfly parnassius smintheus (Papilionidae)

Four microsatellite DNA markers were developed which were used to examine the relationship between landscape and population genetic structure among a set of populations of the butterfly Parnassius smintheus located in the foothills of the Canadian Rockies. Detailed information on the dispersal of adult butterflies among this same set of populations was available. Simple and partial Mantel tests were used to examine the relationships between genetic distances, predicted rates of dispersal, and a number of landscape variables, all measured pairwise for 17 sample sites. Nei's standard genetic distance was negatively correlated with predicted dispersal. We observed a significant pattern of isolation by distance at a very small spatial scale. The distance between sites that was through forest was a stronger predictor of genetic distance than the distance through open meadow, indicating a significant effect of landscape on population genetic structure beyond that of simple isolation by distance. Our results suggest that rises in the tree-line in alpine areas, caused by global warming, will lead to reduced gene flow among populations of P. smintheus.     

The names of Spain: a study of the isonymy structure of Spain

In order to estimate the isonymy structure of Spain, we studied surname distribution in 283 Spanish towns based on 3.625 million telephone users selected from 6.328 million users, downloaded from a commercial CD-ROM which contains all 13 million users in the country. Since in Spain the surname is made by the paternal and the maternal surname, it was possible to classify surnames according to parental origin. Two matrices of isonymy distances, one for paternal and one for maternal surnames, were constructed and tested for correlation with geographic distance. For the whole of Spain, Euclidean distance was significantly but weakly correlated with geographic distance both for paternal and maternal surnames, with r = 0.205 +/- 0.013 and r = 0.263 +/- 0.012, respectively. Two dendrograms of the 283 sampled towns were built from the two matrices of Euclidean distance. They are largely colinear. Four main clusters identified by the dendrograms are correlated with geography. Given the surname structure of Spain, we were able to calculate from isonymy and for each town 1). total or expressed inbreeding, 2). random or expected inbreeding, and 3). local inbreeding. Total inbreeding, F(IT), was highest in the North Atlantic regions and lowest along the Mediterranean Coast. The lowest levels were found in Andalusia, Catalunyia, Valencia, and Navarra. Random inbreeding, F(ST), had a similar geographical pattern. Local inbreeding, F(IS), was relatively uniform in the whole of Spain. In towns, random inbreeding dominates over local inbreeding. From the analysis, it emerges that the northwestern area of Spain is the most inbred.     

Spatial population genetic structure and limited dispersal in a Rocky Mountain alpine stream insect

Using the mitochondrial cytochrome oxidase I (COI) gene, we assessed the phylogeographic structure of Prosimulium neomacropyga, a black fly (Simuliidae) whose distribution in the US Southern Rockies ecoregion is limited to alpine tundra streams. Given high habitat specificity, lack of hydrological connection between streams, and a terrestrial environment restrictive to insect flight, we hypothesized limited gene flow. A spatially nested sampling design showed that grouping populations according to high-elevation 'islands' of alpine tundra (which typically include headwater streams of > 1 watershed) explained a significant proportion of genetic variation while grouping streams according to major watershed (across islands) did not. Nested clade analysis and isolation-by-distance (IBD) relationships further implicated limited ongoing gene flow within but not among the isolated alpine islands. IBD was strong among five streams within an individual island using each of four alternative models of pairwise landscape connectivity for flying insects. Results of all landscape models were positively correlated, suggesting that straight-line distance is an acceptable surrogate for presumably more biologically meaningful connectivity measures in this system. IBD was significantly weaker across the entire study area, comprised of three separate islands. Overall, population structure was significant with F(ST) = 0.38, suggesting limited dispersal across a small spatial extent.     

Spatial population genetic structure of a bacterial parasite in close coevolution with its host

Knowledge of a species’ population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here, we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host–parasite interactions and represents an example of coevolution via negative frequency‐dependent selection (aka “Red Queen” dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and western Asia. Using 12 polymorphic variable number tandem repeat loci (VNTR loci), we identified substantial genetic diversity, both within and among localities, that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, although this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host‐specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation by distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

Examining genetic structure in a bogus yucca moth: a sequential approach to phylogeography

Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moth's host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.     

Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama

Populations of the Calafia pearl oyster Pinctada mazatlanica ofthe American Pacific coasts have been considered endangeredbecause of overfishing and/or alteration to coastal areas. Weassessed genetic variability and the pattern of populationstructure among 9 samples collected from Mexico to Panama, usingmtDNA RFLP analysis of two genes: 12S rRNA and subunit one ofCytochrome oxydase (COI). Haplotype diversity varied from 0.000to 0.856. The Panama population appeared to be monomorphic, whilethe other samples exhibited a level of haplotypic variabilitysimilar to those reported in the literature for the same kind ofanalysis on other bivalves species. A test for the impact ofdemographic history on genetic diversity was applied on thesequence data, and the results were congruent with a recentdecline of population sizes. Genetic differentiation was shown tofollow a scheme of isolation by distance, with low levels ofdifferentiation at the scales of ten to one hundred kilometres,whereas stronger and significant genetic structure was detectedat a larger scale. Three significantly distinct groups could thenbe defined, which correspond to Northern Mexico, Southern Mexico,and Panama.     

Population genetic structure across dissolved oxygen regimes in an African cichlid fish

Ecological isolation is a process whereby gene flow between selective environments is reduced due to selection against maladapted dispersers, migrant alleles, or hybrids. Although ecological isolation has been documented in several systems, gene flow can often be high among selective regimes, and more studies are thus needed to better understand the conditions under which ecological gradients or divergent selective regimes should influence population structure. We test for ecological isolation in a system in which high plasticity occurs with respect to traits that are adaptive in alternate forms under different environmental conditions. Pseudocrenilabrus multicolor victoriae is a widespread haplochromine cichlid fish in East Africa that exploits both normoxic (normal oxygen) rivers/lakes and hypoxic (low oxygen) swamps. Here, we examine population structure, using mitochondrial DNA and microsatellites, to determine if genetic divergence is significantly increased between dissolved oxygen regimes relative to within them, while controlling for geographical structure. Our results indicate that geographical separation influences population structure, while no effects of divergent selection with respect to oxygen regimes were detected. Specifically, we document (i) genetic clustering according to geographical region, but no clustering according to oxygen regime; (ii) higher genetic variation among than within regions, but no effect of oxygen regime on genetic variation; (iii) isolation by distance within one region; and (iv) decreasing genetic variability with increasing geographical distance from Lake Victoria. We speculate that plasticity may be facilitating gene flow between oxygen regimes in this system.     

Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae)

Abstract An extensive allozyme survey was conducted within a natural "meta" population of the native North American annual legume, Chamaecrista fasciculata (Leguminosae) to quantify genetic structure at different spatial scales. Gene flow was then estimated by a recently developed indirect method based on a continuous population model, using pairwise kinship coefficients between individuals. The indirect estimates of gene flow, quantified in terms of neighborhood size, with an average value on the order of 150 individuals, were concordant among different spatial scales (subpopulation, population, metapopulation). This gene-flow value lies within the range of direct estimates previously documented from observations of pollen and seed dispersal for the same metapopulation. Monte Carlo simulations using the direct measures of gene flow as parameters further demonstrated that the observed spatial pattern of allozyme variation was congruent with a model of isolation by distance. Combining previously published estimates of pollen dispersal distances with kinship coefficients from this study, we quantified biparental inbreeding relative to either a single subpopulation or the whole metapopulation. At the level of a neighborhood, little biparental inbreeding was observed and most departure from Hardy-Weinberg genotypic proportions was explained by self-fertilization, whereas both selfing and biparental inbreeding contributed to nonrandom mating at the metapopulation level. Gene flow was also estimated from indirect methods based on a discontinuous population structure model. We discuss these results with respect to the effect of a patchy population structure on estimation of gene flow.     

Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping‐stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll‐a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R² = 0.52) and isolation by environment (IBE, R² = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R² = 0.71, MMRR: R² = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure.