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

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

Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits

Wild plant species develop their own way of living to adapt to the specific environment of their habitats. Their life-history traits strongly affect the genetic structure of the population. The wild species Oryza glumaepatula Steud. growing in the Amazon basin seems to have characteristic life-history traits suited for the flood condition. At the vegetative growth stage, the culms frequently break at internodes. With no roots anchoring on the ground, plant bodies floating in the water move downriver by water current and wind. To examine the association between the life-history traits and genetic population structure of Amazonian O. glumaepatula , we analysed allozyme variability at 29 loci of 16 enzymes using 37 populations from five regions. Allozymes were not so variable (total gene diversity H _E = 0.044) compared with Asian wild rice, O. rufipogon Griff. The bottleneck effect and rare opportunity of interspecies gene flow may prevent the development of allozyme variability. Population genotypes tended to be differentiated among geographically isolated regions. Observed heterozygosities were much lower than expected heterozygosities, or gene diversity ( H _O = 0.003 for whole population) and F _IS over polymorphic loci was 0.931, indicating that O. glumaepatula has developed an inbreeding system. But, the intrapopulation gene diversity ( H _S) was higher than interpopulation gene diversity ( D _ST), as generally observed in outbreeding populations. The migration ability of O. glumaepatula makes long-distance seed dispersal possible. This might have led to frequent gene flow among populations.     

Population genetic structure of the butterfly Melitaea didyma (Nymphalidae) along a northern distribution range border

The population genetic structure of the butterfly Melitaea didyma was studied along the northern distribution range border in Central Germany by means of allozyme electrophoresis. Individuals were sampled from a total of 21 habitat patches from four regions, and two provinces. Sampling was designed to estimate local vs. regional differentiation. High levels of variability were found, H _e= 0.14–0.21. The mean expected sample heterozygosity from one region, Mosel, was significantly lower than from the Hammelburg region, H _e= 0.17 and 0.19, respectively. Two hierarchical levels of genetic differentiation were found. Within regions individuals sampled from different patches behaved as belonging to one population with high levels of gene flow (Hammelburg F _ST= 0.015, Mosel F _ST= 0.044), though local isolation barriers did create a substructuring of these populations. The inbreeding coefficients, F _IS, were constant over all sample levels, suggesting a similar distribution of habitat patches within regions. Between regions gene flow was limited. An isolation by distance analysis indicated that the hierarchical structure, at the provincial level, may be breaking down due to isolation of regional populations. A more general observation was that the sampling design may greatly have influenced the estimation of genetic differentiation. Depending on which samples were included, overall F _ST estimates ranged from 0.059–0.090.     

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

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

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.     

Understanding population structure and historical demography in a conservation context: population genetics of an endangered fern

The construction of the world's largest hydroelectric scheme across the Yangtze River, the Three Gorges Dams (TGD), in the centre of a southern-central Chinese biodiversity hot spot, the Three Gorges Reservoir Area (TGRA), has attracted international concern and conservation action. To examine whether landscape changes to date have impacted regional flora, and to establish long-term monitoring baselines, we assessed the distribution and dynamics of an endangered and TGRA endemic fern, Adiantum reniforme var. sinense . For eight nuclear microsatellites, high levels of genetic diversity ( H _E = 0.653–0.781) and slightly elevated inbreeding ( F _IS = 0.077–0.197) were found across 13 surveyed populations. The population history of this fern is characterized by a balance of gene flow and genetic drift, where historical dispersal, inferred from coalescent ( F =  0.129) and genetic differentiation ( F _ST = 0.094 and R _ST = 0.180) approaches, is moderate, reflecting an isolation by distance relationship. Importantly, most populations exhibited mutation-drift disequilibrium, suggesting a recent population decline, which is congruent with the known demographic history of the species following dam-related activities. Based on these results, populations of A. reniforme var. sinense are expected to lose genetic diversity and increase genetic structure as dam-related activities decrease size and increase genetic isolation of remnants.     

Indo-West Pacific patterns of genetic differentiation in the high-dispersal starfish Linckia laevigata

Genetic variation in four natural populations of the starfish Linckia laevigata from the Indo-West Pacific was examined using restriction fragment analysis of a portion of the mtDNA including the control region. Digestion with seven restriction enzymes identified 47 haplotypes in a sample of 326 individuals. Samples collected from reef sites within each location were not significantly differentiated based on Φ_ST or spatial distribution of haplotypes, indicating that dispersal is high over short to moderate distances. Evidence of gene flow is further supported by the low divergence among haplotypes and the lack of any clear geographical structuring among different haplotypes in the gene phylogeny. However, analysis of molecular variance ( AMOVA ), Φ_ST and contingency χ² analyses of the spatial distribution of haplotypes demonstrate the presence of significant broad scale population genetic structure among the four widespread locations examined. RFLP data are consistent with high gene flow between the Philippines and Western Australia and moderate gene flow between the Great Barrier Reef (GBR) and Fiji, but only limited gene flow between either the Philippines or Western Australia and either the GBR or Fiji. The presence of mtDNA structure contrasts with previous allozyme data which suggest that dispersal among widely separated locations is equivalent to dispersal among populations within the highly connected GBR studies. This discordance between patterns of gene flow inferred from these two markers cannot be fully accounted for by differences in effective population size for mtDNA. This might suggest that while mtDNA variation may represent contemporary patterns of gene flow, allozyme variation among populations is yet to reach equilibrium between drift and migration over the range surveyed.     

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

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

Genetic structure of populations of the threatened eastern massasauga rattlesnake, Sistrurus c. catenatus: evidence from microsatellite DNA markers

Throughout its distribution in North America, the threatened eastern massasauga rattlesnake ( Sistrurus c. catenatus ) persists in a series of habitat-isolated disjunct populations of varying size. Here, we use six microsatellite DNA loci to generate information on the degree of genetic differentiation between, and the levels of inbreeding within populations to understand how evolutionary processes operate in these populations and aid the development of conservation plans for this species. Samples were collected from 199 individuals from five populations in Ontario, New York and Ohio. Our results show that all sampled populations: (i) differ significantly in allele frequencies even though some populations are < 50 km apart, and may contain genetically distinct subpopulations < 2 km apart; (ii) have an average of 23% of alleles that are population specific; and (iii) have significant F _IS values (mean overall F _IS= 0.194) probably due to a combination of Wahlund effects resulting from fine-scale genetic differentiation within populations and the presence of null alleles. Our results imply that massasauga populations may be genetically structured on an extremely fine scale even within continuous populations, possibly due to limited dispersal. Additional information is needed to determine if dispersal and mating behaviour within populations can account for this structure and whether the observed differentiation is due to random processes such as drift or to local adaptation. From a conservation perspective, our results imply that these massasauga populations should be managed as demographically independent units and that each has high conservation value in terms of containing unique genetic variation.     

Population genetic patterns suggest a behavioural change in wild common frogs (Rana temporaria) following disease outbreaks (Ranavirus)

We use 14 microsatellite loci to investigate the impact of a viral disease ( Ranavirus ) on the population genetic structure of wild common frogs ( Rana temporaria ). Populations with a history of Ranavirus mortalities (and 83% declines in the number of frogs) were compared with populations with no history of infection. Infected ponds showed significantly elevated F _IS (homozygote excess), significantly reduced relatedness, and no detectable effect on allelic richness. We hypothesize that the elevated F _IS and reduced relatedness are consequences of assortative mating, and that allelic richness is maintained by immigration from nearby populations. Simulations indicate that the elevated F _IS cannot be explained by population size reductions, but can indeed be explained by assortative mating (even if a mate choice locus is unlinked to the genetic markers). While the majority of studies consider demographic outcomes following disease outbreaks, our results indicate that emerging infectious diseases could also result in behavioural changes.     

Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)

Study of adaptive evolutionary changes in populations of invasive species can be advanced through the joint application of quantitative and population genetic methods. Using purple loosestrife as a model system, we investigated the relative roles of natural selection, genetic drift and gene flow in the invasive process by contrasting phenotypical and neutral genetic differentiation among native European and invasive North American populations ( Q _ST −  F _ST analysis). Our results indicate that invasive and native populations harbour comparable levels of amplified fragment length polymorphism variation, a pattern consistent with multiple independent introductions from a diverse European gene pool. However, it was observed that the genetic variation reduced during subsequent invasion, perhaps by founder effects and genetic drift. Comparison of genetically based quantitative trait differentiation ( Q _ST) with its expectation under neutrality ( F _ST) revealed no evidence of disruptive selection ( Q _ST >  F _ST) or stabilizing selection ( Q _ST <  F _ST). One exception was found for only one trait (the number of stems) showing significant sign of stabilizing selection across all populations. This suggests that there are difficulties in distinguishing the effects of nonadaptive population processes and natural selection. Multiple introductions of purple loosestrife may have created a genetic mixture from diverse source populations and increased population genetic diversity, but its link to the adaptive differentiation of invasive North American populations needs further research.     

The patterns of genetic diversity in Carpentaria acuminata (Arecaceae), and rainforest history in northern Australia

Carpentaria acuminata occurs in monsoon rainforest and is endemic to the Northern Territory, Australia. The genetic diversity of C. acuminata populations was surveyed across the geographical range of the species using isozyme analysis. Genetic diversity within C. acuminata populations ( H _E = 0.143) was typical of rainforest species and woody angiosperms generally. Genetic diversity was not correlated with rainforest patch size. However, there was significant heterogeneity among populations ( F _ST = 0.379), with infrequent effective gene flow among populations ( Nm = 0.39). Genetic diversity was negatively correlated with increasing distance between neighbouring C. acuminata populations, but geographical distance was not a good predictor of genetic similarity. C. acuminata is a favoured food of mobile frugivores such as Torres Strait pigeons and flying foxes. The decreased diversity with decreasing density of populations indicated that seed dispersal by frugivores has been important for the maintenance of diversity in this species. Populations known to have originated on relatively young, Holocene landforms were not necessarily genetically depauperate. Gene flow by pollen is apparently limited because C. acuminata populations are significantly inbred regardless of genetic diversity ( F = 0.641). The distribution and diversity of rare alleles, i.e. those occurring in few populations, is consistent with the theory of rainforest contraction during the Pleistocene.     

Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

Habitat fragmentation is one of the greatest threats to biodiversity. Despite their importance for conservation, the genetic consequences of small-scale habitat fragmentation for bat populations are largely unknown. In this study, we linked genetic with ecological and demographic data to assess the effects of habitat fragmentation on two species of phyllostomid bats ( Uroderma bilobatum and Carollia perspicillata ) that differ in their dispersal abilities and demographic response to fragmentation. We hypothesized that population differentiation and the effect of habitat fragmentation on levels of genetic diversity will be a function of the species' mobility. We sequenced mtDNA from 232 bats caught on 11 islands in Gatún Lake, Panamá, isolated from the mainland for ca 90 yr, and in adjacent, continuous forest on the mainland. Populations of both species showed significant genetic differentiation ( F _ST). Consistent with our prediction, population subdivision was lower in the highly mobile U. bilobatum ( F _ST= 0.01) compared to the less vagile C. perspicillata ( F _ST= 0.06), and only the latter species showed a pattern indicative of isolation by distance and, in addition, an effect of fragmentation. Genetic erosion as a result of fragmentation was also only detectable in the less mobile species, C. perspicillata , where haplotype diversity was lower in island compared to mainland populations. Our results suggest that some Neotropical bat species are prone to loss of genetic variation in response to anthropogenic small-scale habitat fragmentation. In this context, our findings point toward mobility as a good predictor of a species' vulnerability to fragmentation and altered population genetic structure.     

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

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

Microsatellite data reveals weak population substructuring in Copadichromis sp.'virginalis kajose', a demersal cichlid from Lake Malawi, Africa

Small but significant differences were found in allele frequencies among five populations (overall F _ST estimate (θ)=0·004, P=0·006; overall R _ST estimate (RHO)=0·019, P <0·00001) of the demersal cichlid Copadichromis sp.'virginalis kajose', collected from five locations in Lake Malawi. Pairwise F _ST estimates revealed significant differences between the most southerly population (Cape Maclear), and the three most northerly populations (Mbamba Bay, Metangula and Chilola). Pairwise R _ST estimates also revealed significant differences between some populations, but no geographical pattern was discernible. There was no evidence of isolation by distance using either the shortest straight-line distance between samples, or the distance around the shoreline following a 50 m depth contour. F _ST estimates were considerably lower than found in previous studies on the mbuna (rock-dwelling species), but higher than those found in a study of three pelagic cichlid species from Lake Malawi. Substructuring in C. sp.'virginalis kajose' appears to be on a similar scale to the Atlantic cod.     

Q ST MEETS THE G MATRIX: THE DIMENSIONALITY OF ADAPTIVE DIVERGENCE IN MULTIPLE CORRELATED QUANTITATIVE TRAITS

The Q _ST– F _ST comparison has become an increasingly common method for inferring adaptive quantitative trait divergence among populations. For cases in which there is divergence in multiple traits, most studies have applied the method by performing multiple univariate Q _ST– F _ST comparisons. However, because traits are often genetically correlated, such univariate analyses are likely to paint a simplified picture of adaptive divergence. Here we show how the multivariate analogue of Q _ST, F_STq, which accounts for genetic correlations among traits, can be used to supply a more detailed picture of multitrait divergence. We apply the method to naturally occurring genetic variation for a suite of sexually selected display traits in Drosophila serrata . The analyses suggest the operation of divergent multivariate selection that has influenced multiple independent axes of genetic variance in a sex-specific manner. Finally, we show how a comparison of the components of F_STq, the average within and among population genetic variance–covariance matrices, G_W and G_B, can be used as an additional test of the null expectation of neutral divergence, and allows for an investigation of whether natural populations have diverged along major or minor axes of genetic variance.     

Allozyme Diversity in Populations of Cymbidium goeringii (Orchidaceae)

Abstract: Using 14 allozyme loci, we investigated levels of genetic diversity within populations, and degree of genetic divergence among 24 populations of Cymbidium goeringii (Orchidaceae) in Korea and Japan. Cymbidium goeringii maintains high levels of genetic diversity both at population (mean expected heterozygosity, H _e = 0.238) and species levels (0.260). Means of H _e found in 24 populations were not significantly different from each other. About 90 % of the total variation in the species is common to all populations (mean G _ST = 0.108). No unique allele was found in any population. The indirect estimate of gene flow based on the mean G _ST was high ( Nm = 2.06). Nei's genetic identities for pairs of populations had high values (mean = 0.974 [SD = 0.013]). The Mantel-Z test showed a significant correlation between genetic distance and geographic distance. However, the mean G _ST value between 17 populations in Korea and seven Japanese populations was relatively low (0.029), even though the land connection between the southern Korean peninsula and southern Japanese archipelagos has not existed since the middle Pleistocene. Large numbers of small seeds of C. goeringii might travel long distances by wind from populations to populations both in Korea and Japan, increasing genetic diversity within populations and maintaining low genetic differentiation among populations.     

Genetic variability in the European bison (Bison bonasus) population from Białowieża forest over 50 years

The aim of this study was to assess potential post-bottleneck temporal genetic differentiation following the reintroduction of the species into the Białowieża Forest. Variability of 12 polymorphic microsatellite markers was analysed for 178 individuals born between 1955 and 2005, divided by birth year into five temporal groups. Low overall allelic richness (AR) per locus (AR = 2.0) and a low overall expected heterozygosity (H_E = 0.28) were observed. The overall F _IS was not significantly different from zero. The mean F _IS values were, however, significantly different from zero for individuals born between 1955 and 1965 ( F _IS = 0.19). A Bayesian computation was used to estimate effective population size (N_e) for each temporal group. We observed relatively small values of N_e ranging from 7.9 to 28.4. The low N_e values confirm that, despite a rapid growth of the bison population following the founder event, N_e increased only slowly.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 801–809.     

Isolated in an ocean of grass: low levels of gene flow between termite subpopulations

Habitat fragmentation is one of the most important causes of biodiversity loss, but many species are distributed in naturally patchy habitats. Such species are often organized in highly dynamic metapopulations or in patchy populations with high gene flow between subpopulations. Yet, there are also species that exist in stable patchy habitats with small subpopulations and presumably low dispersal rates. Here, we present population genetic data for the ‘magnetic’ termite Amitermes meridionalis, which show that short distances between subpopulations do not hinder exceptionally strong genetic differentiation (F_ST: 0.339; R_ST: 0.636). Despite the strong genetic differentiation between subpopulations, we did not find evidence for genetic impoverishment. We propose that loss of genetic diversity might be counteracted by a long colony life with low colony turnover. Indeed, we found evidence for the inheritance of colonies by so‐called ‘replacement reproductives’. Inhabiting a mound for several generations might result in loss of gene diversity within a colony but maintenance of gene diversity at the subpopulation level.     

Clinal genetic variation and isolation by distance in the European eel Anguilla anguilla (L.)

The genetic variability and structure of the European eel ( Anguilla anguilla L.) in populations throughout Europe was reassessed using 15 allozymic loci, seven of which were polymorphic. Seven sites were sampled on a latitudinal gradient across the natural continental range, extending from southern France to southern Norway. Heterozygosity ( H _e = 0.05) and level of polymorphism (P = 0.43) were comparable to other marine fish. Populations were poorly differentiated ( G _ST = 0.014, F _ST = 0.002), which is not surprising considering the high dispersal capability of the European eel. However, a significant geographical cline was detected at two alleles ( IDH-1 * 100 and GPI-1 * 110 ), and genetic distances ( D _CE) were concordant with geographical coastal distances. Mantel tests, pairwise F _ST's and multidimensional scaling analyses identify three distinct groups: Northern Europe, Western Europe and the Mediterranean Sea. We propose that the clinal genetic structure in the European eel may be due to (1) isolation by distance (as recently detected with microsatellites), (2) temporal reproductive separation, (3) post-larval selective forces, (4) contact between formerly separated groups or (5) some combination thereof.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 509–521