Evidence for a population expansion in the West Nile virus vector Culex tarsalis

Population genetic structure of the West Nile Virus vector Culex tarsalis was investigated in 5 states in the western United States using 5 microsatellite loci and a fragment of the mitochondrial reduced form of nicotinamide adenine dinucleotide dehydrogenase 4 (ND4) gene. ND4 sequence analysis revealed a lack of isolation by distance, panmixia across all populations, an excess of rare haplotypes, and a star-like phylogeny. Microsatellites revealed moderate genetic differentiation and isolation by distance, with the largest genetic distance occurring between populations in southern California and New Mexico (F(ST) = 0.146). Clustering analysis and analysis of molecular variance on microsatellite data indicated the presence of 3 broad population clusters. Mismatch distributions and site-frequency spectra derived from mitochondrial ND4 sequences displayed pattern's characteristic of population expansion. Fu and Li's D* and F*, Fu's F(S), and Tajima's D statistics performed on ND4 sequences all revealed significant, negative deviations from mutation-drift equilibrium. Microsatellite-based multilocus heterozygosity tests showed evidence of range expansion in the majority of populations. Our results suggest that C. tarsalis underwent a range expansion across the western United States within the last 375,000-560,000 years, which may have been associated with Pleistocene glaciation events that occurred in the midwestern and western United States between 350,000 and 1 MYA.     

Geographic differentiation in the house fly estimated by microsatellite and mitochondrial variation

Gene flow over very large geographic scales has been investigated in few species. Examples include Drosophila melanogaster, Drosophila subobscura, Drosophila simulans, and the Mediterranean fruit fly (Ceratitis capitata). The cosmopolitan house fly, a highly vagile, fecund, colonizing species offers an additional exemplar. Genotypes at seven microsatellite loci were scored in 14 widely separated natural house fly populations from the Nearctic, neotropics, Afrotropics, Palearctic, and Asia. Allelic diversities and heterozygosities differed significantly among populations. Averaged over all populations, Weir and Cockerham's theta = 0.13 and RST = 0.20. Pairwise genetic distance measures were uncorrelated with geographic distance. Microsatellite frequencies were compared with mitochondrial data from 13 of the same populations in which theta = 0.35 and Nei's GST = 0.72. Mitochondrial variation indicated up to threefold greater indices of genetic differentiation than the microsatellites. We were unable to draw any biogeographical inferences from these results or from tree or network topologies constructed from the genetic data. It is likely that high microsatellite diversities, mutation rates, and homoplasy greatly compromised their usefulness in estimating gene flow. House fly colonization dynamics include a large number of primary and secondary colonizations coupled with substantial genetic drift, but no detectable bottlenecks.     

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.     

栓皮栎天然群体SSR遗传多样性研究

利用微卫星(SSR)标记对我国4个省内的5个栓皮栎（Quercus variabilis Bl.）天然群体的遗传多样性进行了研究。16对SSR标记揭示了栓皮栎丰富的遗传多样性：等位基因数（A）平均8.4375个,有效等位基因数(Ne)平均为5.9512个,平均期望杂合度(He)0.8059,Nei多样性指数(h)为0.8041。栓皮栎自然分布区中心地带的群体具有较高的遗传多样性,而人为对森林的破坏将降低林木群体的遗传多样性。栓皮栎群体的变异主要来源于群体内,群体间分化较小,遗传分化系数仅为0.0455。此外,栓皮栎群体间的遗传距离与地理距离之间存在显著的正相关。这些遗传信息为栓皮栎遗传多样性的保护和利用提供了一定依据。Abstract: Genetic diversity of five Quercus variabilis natural populations in four provinces of China was studied with microsatellite (SSR) markers. A relatively high level of genetic diversity was detected in Q. variabilis species with 16 polymorphic microsatellite loci. Average number of alleles (A) and effective number of alleles (Ne) were 8.4375 and 5.9512 respectively. The mean expected heterozygosity (He) was 0.8059 and Nei diversity index (h) was 0.8041. Higher diversity was found with the populations from the central range of the species in contrast to those from peripheral areas and human activities might decrease the genetic diversity of populations. The majority of genetic variation occurred within populations, which could be concluded from the low coefficient of genetic differentiation (Fst=0.0455). In addition, significant correlation was found between geographical distance and genetic distance. All these results present a basis to the conservation and utilization of genetic diversity of Quercus variabilis.     

Hierarchical Genetic Analysis of German Cockroach (Blattella germanica) Populations from within Buildings to across Continents

Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species.     

Fine‐scale Spatial Genetic Structure of Ten Dipterocarp Tree Species in a Bornean Rain Forest

Fine‐scale spatial genetic structure is increasingly recognized as an important factor in the studies of tropical forest trees as it influences genetic diversity of local populations. The biologic mechanisms that generate fine‐scale spatial genetic structure are not fully understood. We studied fine‐scale spatial genetic structure in ten coexisting dipterocarp tree species in a Bornean rain forest using microsatellite markers. Six of the ten species showed statistically significant fine‐scale spatial genetic structure. Fine‐scale spatial genetic structure was stronger at smaller spatial scales (≤ 100 m) than at larger spatial scales (> 100 m) for each species. Multiple regression analysis suggested that seed dispersal distance was important at the smaller spatial scale. At the larger scale (> 100 m) and over the entire sample range (0–1000 m), pollinators and spatial distribution of adult trees were more important determinants of fine‐scale spatial genetic structure. Fine‐scale spatial genetic structure was stronger in species pollinated by less mobile small beetles than in species pollinated by the more mobile giant honeybee (Apis dorsata). It was also stronger in species where adult tree distributions were more clumped. The hypothesized mechanisms underlying the negative correlation between clump size and fine‐scale spatial genetic structure were a large overlap among seed shadows and genetic drift within clumped species.     

Microsatellite analysis of population structure in Canadian polar bears

Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait - Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long-distance seasonal movements undertaken by polar bears.     

The genetic effects of forest fragmentation on five species of Amazonian birds

Restriction fragment length polymorphisms of mtDNA were used to assess genetic structure at two geographic scales for five species of Neotropical forest‐understory birds. At the local scale (in northeastern Bolivia), I studied populations of each species from six sites within 200 km of one another. At this scale, I studied the effects of forest fragmentation on mtDNA genetic structure: three sites were in natural forest fragments separated by cerrado (savanna), and three sites were in continuous forest. Genetic variation did not appear to have been lost in the forest fragment populations of any species. However, for three antbirds (Thamnophilidae), patterns of haplotype distributions suggest fragmentation affected genetic structure in an unusual way. For these species, numerically dominant haplotypes in forest fragments did not occur in continuous forest, whereas predominant haplotypes in continuous forest are widespread (occurring in fragments and continuous forest). These results suggest that forest fragmentation on a local geographic scale can affect genetic differentiation even in birds, a group that is considered to disperse well. The two other taxa studied were a woodcreeper (Dendrocolaptidae) and a tyrant‐flycatcher (Tyrannidae). These two taxa did not show genetic effects of forest fragmentation, but they possessed notably different numbers of haplotypes per total individuals surveyed. The woodcreeper had few haplotypes (5 in 58 individuals), whereas the flycatcher had many (31 in 34 individuals). The numbers of haplotypes per individuals surveyed for the three antbirds were intermediate. Such variable levels of polymorphism can greatly influence analyses of genetic structure. At the regional geographic scale (across southwestern Amazonia), the flycatcher exhibited lower levels of differentiation than the other taxa. Levels of estimated sequence divergence within the other four taxa are similar to levels of differentiation between species from other avian studies, suggesting that genetic diversity is underestimated by current species‐level taxonomy in these birds.     

Hierarchical population structure and habitat differences in a highly mobile marine species: the Atlantic spotted dolphin

Recent molecular studies have shown that highly mobile species with continuous distributions can exhibit fine‐scale population structure. In this context, we assessed genetic structure within a marine species with high dispersal potential, the Atlantic spotted dolphin (Stenella frontalis). Using 19 microsatellite loci and mitochondrial control region sequences, population structure was investigated in the western North Atlantic, the Gulf of Mexico and the Azores Islands. Analyses of the microsatellite data identified four distinct genetic clusters, which were supported by the control region sequences. The highest level of divergence was seen between two clusters corresponding to previously described morphotypes that inhabit oceanic and shelf waters. The combined morphological and genetic evidence suggests these two lineages are on distinct evolutionary trajectories and could be considered distinct subspecies despite their parapatry. Further analysis of the continental shelf cluster resulted in three groups: animals inhabiting shelf waters in the western North Atlantic, the eastern Gulf of Mexico and the western Gulf of Mexico. Analyses of environmental data indicate the four genetic clusters inhabit distinct habitats in terms of depth and sea surface temperature. Contemporary dispersal rate estimates suggest all of these populations should be considered as distinct management units. Conversely, no significant genetic differentiation was observed between S. frontalis from offshore waters of the western North Atlantic and the Azores, which are separated by approximately 4500 km. Overall, the hierarchical structure observed within the Atlantic spotted dolphin shows that the biogeography of the species is complex because it is not shaped solely by geographic distance.     

Predicted range shifts in North American boreal forest birds and the effect of climate change on genetic diversity in blackpoll warblers (Setophaga striata)

As North American species’ ranges shift northward in response to climate change, populations isolated in high-elevation habitat “islands” at the southern edge of distributions are predicted to decrease in size or be extirpated. Levels of genetic structure and gene flow and the number of private alleles held within these peripheral populations can be used as a measure of the potential loss of genetic diversity due to climate change. We use GIS-based climate niche models to project geographic distributions of 15 boreal forest bird species for the year 2080 under two carbon emissions scenarios to predict the extent to which ranges will shift, leading to the extirpation of isolated populations at the southern periphery of the boreal forest. Breeding distributions of nearly all boreal bird species are predicted to expand as they shift northward, but will dramatically decrease or be completely lost from mountain populations in New York, Vermont, and New Hampshire by 2080. To examine the effect of these shifts on gene pools of migratory bird species we genotyped 178 blackpoll warblers (Setophaga striata) at nine microsatellite loci, sampling four imperiled high-elevation populations and four northern populations. In S. striata 10.4 % of microsatellite alleles were confined to populations expected to be lost due to climate change. However, these accounted for a nonsignificant percent of the genetic structure, and loss of these alleles would not significantly erode species heterozygosity or allelic richness. Our results indicate that isolated southern populations of S. striata, and possibly other migratory species with high gene flow, do not represent genetically isolated, independently evolving units. Efforts to mitigate the effect of climate change on boreal forest birds should focus on species in which peripheral populations harbor significant genetic diversity.     

Genetic differentiation on multiple spatial scales in an ecotype-forming marine snail with limited dispersal: Littorina saxatilis

The population genetic structure of marine species lacking free-swimming larvae is expected to be strongly affected by random genetic drift among populations, resulting in genetic isolation by geographical distance. At the same time, ecological separation over microhabitats followed by direct selection on those parts of the genome that affect adaptation might also be strong. Here, we address the question of how the relative importance of stochastic vs. selective structuring forces varies at different geographical scales. We use microsatellite DNA and allozyme data from samples of the marine rocky shore snail Littorina saxatilis over distance scales ranging from metres to 1000 km, and we show that genetic drift is the most important structuring evolutionary force at distances > 1 km. On smaller geographical scales (< 1 km), divergent selection between contrasting habitats affects population genetic structure by impeding gene flow over microhabitat borders (microsatellite structure), or by directly favouring specific alleles of selected loci (allozyme structure). The results suggest that evolutionary drivers of population genetic structure cannot a priori be assumed to be equally important at different geographical scales. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 31–40.     

Microsatellite analysis of genetic structure in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae)

The level of genetic variation throughout the entire worldwide range of the mangrove species Avicennia marina (Forsk.) Vierh. was examined using microsatellite markers. Three microsatellite loci detected high levels of allelic diversity (70 alleles in total), essential for an accurate estimation of population genetic parameters. The informativeness of the microsatellite loci tended to increase with increasing average number of repeats. The levels of heterozygosity detected for each population, over all loci, ranged from 0.0 to 0.8, with an average of 0.407, indicating that some populations had little or no genetic variation, whereas others had a large amount. Populations at the extremes of the distribution range showed reduced levels of heterozygosity, and significant levels of inbreeding. This is not unexpected as these populations may be subject to founder effects and environmental constraints. The presence of genetic structure was tested in A. marina populations using three models: (i) a single panmictic model; (ii) the discrete subpopulation model; and (iii) the isolation by distance model. The discrete subpopulations model was supported by the overall measures of population differentiation based on the infinite alleles model (F-statistics), and the stepwise mutation model (R statistics). In addition, an analysis of molecular variance (AMOVA), using both theoretical models, found that most of the variation was between populations (41-71%), and within individuals in the total population (31-49%). There was little variation among individuals within populations (0-10%). There was no significant isolation by distance. The high levels of genetic differentiation observed among populations of A. marina may be due to environmental and ecological factors, particularly past sea level and climatic changes.     

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.     

Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens

Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations.     

Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

Evolutionary relationships among populations of chamois (Rupicapra spp.) across their current range from the Caucasus to the Cantabrian Mountains were investigated. The allelic variation in 23 microsatellite loci was assessed in eight geographical populations, recognised as subspecies of the two closely related species R. pyrenaica and R. rupicapra. Analysis of variance in allele frequencies (Fst, statistics) and in repeat numbers (Rst, statistics) showed these data to be highly structured. Two genetic distances between pairs of populations, Ds and (deltamu)(2), were computed and phylogenetic trees were constructed. Similar patterns were produced by the different statistics. All trees indicate a deep divergence between the two recognised species, which is compatible with archaeological data that place their split in the Riss-Würm interglacial period. Genetic distances between pairs of populations are highly correlated with geographical distance. This suggests that the history of the genus during Pleistocene glacial-interglacial periods was dominated by expansions and contractions within limited geographic regions, leading to alternate contact and isolation of contiguous populations. In addition, the alpine barrier has played a substantial role in West-East differentiation.     

Molecular evidence for limited dispersal of vegetative propagules in the epiphytic lichen Lobaria pulmonaria

Propagation, whether sexual or asexual, is a fundamental step in the life cycle of every organism. In lichenized fungi, a great variety of vegetative propagules have evolved in order for the symbiotic partners to disperse simultaneously. For lichens with the ability of sexual and asexual reproduction, the relative contribution of vegetative dispersal is unknown but could, nonetheless, be inferred by studying genotype distribution. The genetic structure of three Lobaria pulmonaria (Lobariaceae) populations from Switzerland was investigated based on the observed variation at six microsatellite loci. All three populations had a clustered distribution of identical genotypes at small spatial scales. The maximum distance between identical genotypes was 230 m. At a distance of 350 m from a source tree, seemingly suitable habitat patches were too far apart to be colonized. Some multilocus genotypes were frequent within local populations but no genotypes were shared among populations. The restricted occurrences of common genotypes as well as the clustered distributions are evidence for a limited dispersal of vegetative propagules in L. pulmonaria. Gene flow among isolated populations will ultimately depend on the capacity of long-distance dispersal and thus probably depend on sexual reproduction.     

Weak large‐scale population genetic structure in a philopatric seabird,the European Shag Phalacrocorax aristotelis

Quantifying population genetic structure is fundamental to testing hypotheses regarding gene flow, population divergence and dynamics across large spatial scales. In species with highly mobile life‐history stages, where it is unclear whether such movements translate into effective dispersal among discrete philopatric breeding populations, this approach can be particularly effective. We used seven nuclear microsatellite loci and mitochondrial DNA (ND2) markers to quantify population genetic structure and variation across 20 populations (447 individuals) of one such species, the European Shag, spanning a large geographical range. Despite high breeding philopatry, rare cross‐sea movements and recognized subspecies, population genetic structure was weak across both microsatellites and mitochondrial markers. Furthermore, although isolation‐by‐distance was detected, microsatellite variation provided no evidence that open sea formed a complete barrier to effective dispersal. These data suggest that occasional long‐distance, cross‐sea movements translate into gene flow across a large spatial scale. Historical factors may also have shaped contemporary genetic structure: cluster analyses of microsatellite data identified three groups, comprising colonies at southern, mid‐ and northern latitudes, and similar structure was observed at mitochondrial loci. Only one private mitochondrial haplotype was found among subspecies, suggesting that this current taxonomic subdivision may not be mirrored by genetic isolation.     

The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon

The effect of natural selection on the _mMEP-2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F_ST) averaged over loci when data on the _mMEP-2 * locus were either included or excluded. The level of F_ST among populations at various geographic scales was estimated from allele frequencies at up to four loci (_s AAT-4 *, IDDH-1 *, IDHP-3 *, and _mMEP-2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in _mMEP-2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in _mMEP-2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the _mMEP-2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini- and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F _ST estimates which include data on the _mMEP-2 * locus should be viewed with caution.     

Population structure in a common Caribbean coral-reef fish: implications for larval dispersal and early life-history traits

Genetic population structure throughout the Caribbean Basin for one of the most common and widespread reef fish species, the bicolour damselfish Stegastes partitus was examined using microsatellite DNA markers. Spatial autocorrelation analysis showed a significant positive correlation between genetic and geographic distance (isolation by distance) over distances <1000 km, suggesting that populations are connected genetically but probably not demographically, i.e. over shorter time scales. A difference in spatial patterns of populations in the eastern v. the western Caribbean also raises the probability of an important role for meso-scale oceanographic features and landscape complexity within the same species. A comparison of S. partitus population structure and life-history traits with those of two other species of Caribbean reef fish studied earlier showed the findings to be concordant with a common hypothesis that shorter pelagic larval dispersal periods are associated with smaller larval dispersal scales.