Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus

The mummichog, Fundulus heteroclitus, exhibits extensive latitudinal clinal variation in a number of physiological and biochemical traits, coupled with phylogeographical patterns at mitochondrial and nuclear DNA loci that suggest a complicated history of spatially variable selection and secondary intergradation. This species continues to serve as a model for understanding local and regional adaptation to variable environments. Resolving the influences of historical processes on the distribution of genetic variation within and among extant populations of F. heteroclitus is crucial to a better understanding of how populations evolve in the context of contemporary environments. In this study, we analysed geographical patterns of genetic variation at eight microsatellite loci among 15 populations of F. heteroclitus distributed throughout the North American range of the species from Nova Scotia to Georgia. Genetic variation in Northern populations was lower than in Southern populations and was strongly correlated with latitude throughout the species range. The most common Northern alleles at all eight loci exhibited concordant latitudinal clinal patterns, and the existence of an abrupt transition zone in allele frequencies between Northern and Southern populations was similar to that observed for mitochondrial DNA and allozyme loci. A significant pattern of isolation by distance was observed both within and between northern and southern regions. This pattern was unexpected, particularly for northern populations, given the recent colonization history of post-Pleistocene habitats, and was inconsistent with either a recent northward population expansion or a geographically restricted northern Pleistocene refugium. The data provided no evidence for recent population bottlenecks, and estimates of historical effective population sizes suggest that post-Pleistocene populations have been large throughout the species distribution. These results suggest that F. heteroclitus was broadly distributed throughout most of its current range during the last glacial event and that the abrupt transition in allele frequencies that separate Northern and Southern populations may reflect regional disequilibrium conditions associated with the post-Pleistocene colonization history of habitats in that region.     

Similarity of contemporary and historical gene flow among highly fragmented populations of an endangered rattlesnake

Populations of endangered taxa in recently fragmented habitats often show high levels of genetic structure, but the role that contemporary versus historical processes play in generating this pattern is unclear. The eastern massasauga rattlesnake (Sistrurus c. catenatus) is an endangered snake that presently occurs throughout central and eastern North America in a series of populations that are isolated because of habitat fragmentation and destruction. Here, we use data from 19 species-specific microsatellite DNA loci to assess the levels of genetic differentiation, genetic effective population size, and contemporary and historical levels of gene flow for 19 populations sampled across the range of this snake. Eastern massasaugas display high levels of genetic differentiation (overall θ(Fst) = 0.21) and a Bayesian clustering method indicates that each population represents a unique genetic cluster even at regional spatial scales. There is a twofold variation in genetically effective population sizes but little genetic evidence that populations have undergone recent or historical declines in size. Finally, both contemporary and historical migration rates among populations were low and similar in magnitude even for populations located <7 km apart. A test of alternate models of population history strongly favours a model of long-term drift-migration equilibrium over a recent isolation drift-only model. These results suggest that recent habitat fragmentation has had little effect on the genetic characteristics of these snakes, but rather that this species has historically existed in small isolated populations that may be resistant to the long-term negative effects of inbreeding.     

Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish

Interpreting patterns of population structure in nature is often challenging, especially in dynamic landscapes where population genetic connectivity evolves over time. In this study, we document the absence of migration-drift equilibrium in a stream-dwelling euryhaline fish resulting from past fine-scale drainage rearrangements and evaluate the relative contribution of past and current hydrological landscapes on observed population structure. Based on allelic variation at nine microsatellite loci, genetic relationships among 12 populations of brook charr, Salvelinus fontinalis, from Gros Morne National Park of Canada (GMNP, Newfoundland, Canada) did not reflect current stream hierarchical structure. In addition, we observed no correlation between population differentiation and contemporary landscape features (waterway distance and sums of altitudinal differences). Instead, population relationships were consistent with historical hydrological structure predicted a priori based on geomorphological and biogeographical evidences. Also, population differentiation was strongly correlated with inferred historical landscape features. Contemporary barriers have apparently preserved the signature of past genetic connectivity by constraining gene flow. Based on the relationships between population differentiation and current and past landscape features at various spatial scales, we suggest that brook charr genetic diversity in GMNP is mostly the result of small distance migrations at the time of colonization and subsequent differentiation through drift. This study highlights the potential of approaching landscapes from a combination of contemporary and historical perspectives when interpreting nonequilibrium population structures resulting from landscape rearrangement.     

Hierarchical population structure and genetic diversity of lake trout (Salvelinus namaycush) in a dendritic system in Northern Labrador

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Phylogeography of the banded killifish (Fundulus diaphanus): glacial races and secondary contact

Spatial patterns of morphological and genetic polymorphisms between the two banded killifish sub-species ( Fundulus diaphanus diaphanus and F. d. menona ) provide evidence that these sub-species represent distinct evolutionary lineages corresponding to glacial races of Atlantic and Mississippian origins. Individuals with intermediate phenotypes in Lake Ontario and the upper St Lawrence River probably result from secondary contacts between these races. The hybrid zone unexpectedly extends to Lake Erie and involves the introgression of the F. d. diaphanus mitochondrial genome into fish with morphology like that of F. d. menona .     

Genetic structure in a tropical lek-breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest

Determining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek-mating blue manakin (Chiroxiphia caudata), sampled along a 414-km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations. F(ST) values varied from 0.0 to 0.023 (overall F(ST)=0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration-drift equilibrium. N(e)m values estimated using a coalescent-based method were small (相似文献   

Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales

Genetic isolation by distance (IBD) has rarely been described in marine species with high potential for dispersal at both the larval and adult life-history stages. Here, we report significant relationships between inferred levels of gene flow and geographic distance in the Atlantic cod, Gadus morhua, at 10 nuclear restriction-fragment-length-polymorphism (RFLP) loci at small regional scales in the western north Atlantic region (< 1,600 km) that mirror those previously detected over its entire geographic range (up to 7,300 km). Highly significant allele frequency differences were observed among eight northwestern Atlantic populations, although the mean FST for all 10 loci was only 0.014. Despite this weak population structuring, the distance separating populations explained between 54% and 62% of the variation in gene flow depending on whether nine or 10 loci were used to estimate Nm. Across the species' entire geographic range, highly significant differences were observed among six regional populations at nine of the 10 loci (mean FST = 0.068) and seven loci exhibited significant negative relationships between gene flow and distance. At this large geographic scale, natural selection acting in the vicinity of one RFLP locus (GM798) had a significant effect on the correlation between gene flow and distance, and eliminating it from the analysis caused the coefficient of determination to increase from 17% to 62%. The role of vicariance was assessed by sequentially removing populations from the analysis and was found to play a minor role in contributing to the relationship between gene flow and distance at either geographic scale. The correlation between gene flow and distance detected in G. morhua at small and large spatial scales suggests that dispersal distances and effective population sizes are much smaller than predicted for the species and that the recent age of populations, rather than extensive gene flow, may be responsible for its weak population structure. Our results suggest that interpreting limited genetic differences among populations as reflecting high levels of ongoing gene flow should be made with caution.     

Reduced Genetic Diversity and Effective Population Size in an Endangered Atlantic Salmon (Salmo Salar) Population from Maine, USA

Atlantic salmon (Salmo salar) populations in Maine, USA, are listed as a Distinct Population Segment under the U.S. Endangered Species Act due to reduced spawning runs and juvenile densities. Whenever possible, optimal conservation strategies for endangered populations should incorporate both present and historical knowledge of genetic variation. We assayed genetic diversity at seven microsatellite loci and at the mitochondrial ND1 gene in an endangered wild population of Atlantic salmon captured from the Dennys River from 1963 to 2001 using DNA’s extracted from archival scale and tissue samples. We examined temporal trends of genetic diversity, population structure, and effective population size (Ne). Overall temporal trends of diversity and Ne show significant reductions from 1963 to 2001 raising the possibility that current restoration efforts may be impacted by historical loss of diversity potentially critical to adaptation. Although our results suggest genetic stability in this population from 1963 to 1981, significant differentiation was observed for both the 1995 and 2001 samples compared with all other temporal samples. The presence of an ND1 mtDNA haplotype in this population, historically observed only in European and Newfoundland stocks, may represent previously unrecognized local wild diversity or, alternatively, may represent introgression from non-native fish.     

Short‐term temporal instability in fine‐scale genetic structure of masu salmon

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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.     

Analysis of microsatellite variation in Pinus radiata reveals effects of genetic drift but no recent bottlenecks

Most conifer species occur in large continuous populations, but radiata pine, Pinus radiata, occurs only in five disjunctive natural populations in California and Mexico. The Mexican island populations were presumably colonized from the mainland millions of years ago. According to Axelrod (1981), the mainland populations are relicts of an earlier much wider distribution, reduced some 8,000 years ago, whereas according to Millar (1997, 2000), the patchy metapopulation-like structure is typical of the long-term population demography of the species. We used 19 highly polymorphic microsatellite loci to describe population structure and to search for signs of the dynamics of population demography over space and time. Frequencies of null alleles at microsatellite loci were estimated using an approach based on the probability of identity by descent. Microsatellite genetic diversities were high in all populations [expected heterozygosity (H(e)) = 0.68-0.77], but the island populations had significantly lower estimates. Variation between loci in genetic differentiation (F(ST)) was high, but no locus deviated statistically significantly from the rest at an experiment wide level of 0.05. Thus, all loci were included in subsequent analysis. The average differentiation was measured as F(ST) = 0.14 (SD 0.012), comparable with earlier allozyme results. The island populations were more diverged from the other populations and from an inferred common ancestral gene pool than the mainland ones. All populations showed a deficiency of expected heterozygosity given the number of alleles, the mainland populations more so than the island ones. The results thus do not support a recent important contraction in the mainland range of radiata pine.     

Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small,peripheral Atlantic salmon populations

Small populations may be expected to harbour less genetic variation than large populations, but the relation between census size (N), effective population size (N _e), and genetic diversity is not well understood. We compared microsatellite variation in four small peripheral Atlantic salmon populations from the Iberian peninsula and three larger populations from Scotland to test whether genetic diversity was related to population size. We also examined the historical decline of one Iberian population over a 50-year period using archival scales in order to test whether a marked reduction in abundance was accompanied by a decrease in genetic diversity. Estimates of effective population size (N _e) calculated by three temporal methods were consistently low in Iberian populations, ranging from 12 to 31 individuals per generation considering migration, and from 38 to 175 individuals per generation if they were regarded as closed populations. Corresponding N _e/N ratios varied from 0.02 to 0.04 assuming migration (mean=0.03) and from 0.04 to 0.18 (mean=0.10) assuming closed populations. Population bottlenecks, inferred from the excess of heterozygosity in relation to allelic diversity, were detected in all four Iberian populations, particularly in those year classes derived from a smaller number of returning adults. However, despite their small size and declining status, Iberian populations continue to display relatively high levels of heterozygosity and allelic richness, similar to those found in larger Scottish populations. Furthermore, in the R. Asón no evidence was found for a historical loss of genetic diversity despite a marked decline in abundance during the last five decades. Thus, our results point to two familiar paradigms in salmonid conservation: (1)␣endangered populations can maintain relatively high levels of genetic variation despite their small size, and (2) marked population declines may not necessarily result in a significant loss of genetic diversity. Although there are several explanations for such results, microsatellite data and physical tagging suggest that high levels of dispersal and asymmetric gene flow have probably helped to maintain genetic diversity in these peripheral populations, and thus to avoid the negative consequences of inbreeding.     

Gene flow among native bush rat,Rattus fuscipes (Rodentia: Muridae), populations in the fragmented subtropical forests of south‐east Queensland

Abstract Many natural populations in areas of continuous habitat exhibit some form of local genetic structure. Anthropogenic habitat fragmentation can also strongly influence the dynamics of gene flow between populations. We used eight microsatellite markers to investigate the population genetic structure of an abundant forest species, the Australian bush rat (Rattus fuscipes), in the subtropical forests of south‐east Queensland. Five sites were sampled, allowing pairwise comparisons within continuous habitat and across clearings. Weak, but significant population differentiation and a significant pattern of isolation by distance was detected over the small scale (<10 km) of this study. Fine‐scale analysis at a single site (<1 km) showed a significant correlation between individual female genetic distance and geographical distance, but no similar pattern among male individuals. There was no evidence of increased population differentiation across clearings relative to comparisons within continuous forest. This was attributed to dispersal within corridors of remnant and revegetated habitat between the forested areas. We concluded that an inherently restricted dispersal ability, female philopatry and natural habitat heterogeneity play an important part in the development of genetic structure among populations of R. fuscipes. It is important to understand the relationship between landscape features and the pattern of gene flow among continuous populations, as this allows us to predict the impact of fragmentation on natural populations.     

Phylogeography of a specialist insect, Adelges cooleyi: historical and contemporary processes shape the distribution of population genetic variation

Adelges cooleyi is a host-alternating, gall-making insect native to the Rocky Mountains and Cascade Mountains in western North America. The insect's primary hosts are Picea (spruce) species, and its secondary host is Pseudotsuga menziesii , Douglas fir. To determine whether there are large-scale patterns of genetic variation in this specialist insect, we created molecular phylogenies of geographically separate samples of A. cooleyi using sequence data from two mitochondrial (mtDNA) genes and amplified fragment length polymorphisms (AFLPs). Three divergent mtDNA lineages were identified. Analysis of mtDNA and AFLP genetic variation revealed that samples from southeastern Arizona are genetically isolated from all other samples. AFLP data identified possible gene flow between individuals from divergent mtDNA lineages in an area in the central Rocky Mountains. Factors that likely affected divergence within A. cooleyi were identified by comparing our conclusions with well-known changes in the distribution of vegetation in response to glaciations and previous phylogeographical work conducted on this specialist insect's host-plants. In addition to documenting previously unknown patterns of genetic variation in A. cooleyi , our work provides the basis for a testable hypothesis regarding the extent to which the distribution of variation in Picea and Pseudotsuga hosts mediates the distribution of genetic variation for this specialist insect.     

Genetic differentiation associated with commercial traffic in the Polynesian mosquito, Aedes polynesiensis Marks 1951

The population structure of the Polynesian mosquito Aedes polynesiensis was investigated using electrophoretic data from two polymorphic protein loci. Considerable differentiation was observed both within and between islands in different archipelagos (Society, Tuamotu, Austral). Gene flow evaluated by F_st estimates was independent of geographic distance between islands but related to commercial traffic intensity. The results are discussed in view of recent findings on the variability of susceptibility to insecticides and of suitability as a vector for the nematode Wuchereria bancrofti.     

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.     

Higher genetic diversity on mountain tops: the role of historical and contemporary processes in shaping genetic variation in the bank vole

Glacial phases during the Pleistocene caused remarkable changes in species range distributions, with inevitable genetic consequences. Specifically, during interglacial phases, when the ice melted and new habitats became suitable again, species could recolonize regions that were previously covered by ice, such as high latitudes and elevations. Based on theoretical models and empirical data, a decrease in genetic variation is predicted along recolonization routes as a result of the consecutive founder effects that characterize the recolonization process. In the present study, we assessed the relative importance of historical and contemporary processes in shaping genetic diversity and differentiation of bank vole (Myodes glareolus) populations at different elevations in the Swiss Alps. By contrast to expectations, we found that genetic variation increased with elevation. Estimates of recent migration rates and a contrasting pattern of genetic differentiation observed at the mitochondrial cytochrome b gene and nuclear microsatellites support the hypothesis that higher genetic diversity at high elevation results from contemporary gene flow. Although historical recolonization processes can have marked effects on the genetic structure of populations, the present study provides an example where contemporary processes along an environmental gradient can reverse predicted patterns of genetic variation.     

Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source–sink metapopulation structure,founder events and population bottlenecks

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.     

Founder effects, inbreeding and effective sizes in the Southern cattle tick: the effect of transmission dynamics and implications for pest management

Since its immigration in the Pacific island of New Caledonia in 1942 (i.e. about 240 tick-generations ago), the cattle tick Boophilus microplus has experienced a remarkable adaptive diversification there. In order to better understand the population factors involved, we have investigated the B. microplus population structure on that main host-species, Bos taurus. This study was based microsatellite loci and confirmed that the island colonization came along with a significant bottleneck. Knowledge on B. microplus biology led us to expect B. microplus populations to be composed of highly inbred lineages irregularly dispatched among the individual hosts belonging to the same herds. Instead, this study evidenced a weak inbreeding level and an absence of genetic differentiation within herds. Complementarily, a significant signal of isolation by distance exhibited that human-traffic of cattle does not promote high tick dispersal within the island. Finally, the tick density was found to be about a few hundreds of reproducing adults per squared kilometre, for a gene dispersal range of about a few hundred metres per tick generation. Results are discussed with regard to the evolution of new adaptive changes.