Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae

Drosophila ananassae is a cosmopolitan species with a geographic range throughout most of the tropical and subtropical regions of the world. Previous studies of DNA sequence polymorphism in three genes has shown evidence of selection affecting broad expanses of the genome in regions with low rates of recombination in geographically local populations in and around India. The studies suggest that extensive physical and genetic maps based on molecular markers, and detailed studies of population structure may provide insight into the degree to which natural selection affects DNA sequence polymorphism across broad regions of chromosomes. We have isolated 85 dinucleotide repeat microsatellite sequences and developed assay conditions for genotyping using PCR. The dinucleotide repeats we isolated are shorter, on average, than those isolated in many other Drosophila species. Levels of genetic variation are high, comparable to Drosophila melanogaster. The levels of variation indicate the effective population size of an Indonesian population of D. ananassae is 58,692 (infinite allele model) and 217,284 (stepwise mutation model), similar to estimates of effective population size for D. melanogaster calculated using dinucleotide repeat microsatellites. The data also show that the Indonesian population is in a rapid expansion phase. Cross-species amplification of the microsatellites in 11 species from the Ananassae, Elegans, Eugracilis and Ficusphila subgroups indicates that the loci may be useful for studies of the sister species, D. pallidosa, but will have limited use for more distantly related species.     

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.     

Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.)

The resolution of taxonomic classifications for delphinid cetaceans has been problematic, especially for species in the genera Delphinus, Tursiops and Stenella. The frequent lack of correspondence between morphological and genetic differentiation in these species raises questions about the mechanisms responsible for their evolution. In this study we focus on the genus Delphinus, and use molecular markers to address questions about speciation and the evolution of population structure. Delphinus species have a worldwide distribution and show a high degree of morphological variation. Two distinct morphotypes, long-beaked and short-beaked, have been considered different species named D. capensis and D. delphis, respectively. However, genetic differentiation between these two forms has only been demonstrated in the Pacific. We analysed samples from eight different geographical regions, including two morphologically defined long-beaked form populations, and compared these with the eastern North Pacific populations. We found high differentiation among the populations described as long-beaked instead of the expected monophyly, suggesting that these populations may have evolved from independent events converging on the same morphotype. We observed low genetic differentiation among the short-beaked populations across a large geographical scale. We interpret these phylogeographical patterns in the context of life history and population structure in related species.     

SPECIATION AND POPULATION GENETIC STRUCTURE IN TROPICAL PACIFIC SEA URCHINS

Unlike populations of many terrestrial species, marine populations often are not separated by obvious, permanent barriers to gene flow. When species have high dispersal potential and few barriers to gene flow, allopatric divergence is slow. Nevertheless, many marine species are of recent origin, even in taxa with high dispersal potential. To understand the relationship between genetic structure and recent species formation in high dispersal taxa, we examined population genetic structure among four species of sea urchins in the tropical Indo-West Pacific that have speciated within the past one to three million years. Despite high potential for gene flow, mtDNA sequence variation among 200 individuals of four species in the urchin genus Echinometra shows a signal of strong geographic effects. These effects include (1) substantial population heterogeneity; (2) lower genetic variation in peripheral populations; and (3) isolation by distance. These geographic patterns are especially strong across scales of 5000-10,000 km, and are weaker over scales of 2500-5000 km. As a result, strong geographic patterns would not have been readily visible except over the wide expanse of the tropical Pacific. Surface currents in the Pacific do not explain patterns of gene flow any better than do patterns of simple spatial proximity. Finally, populations of each species tend to group into large mtDNA regions with similar mtDNA haplotypes, but these regional boundaries are not concordant in different species. These results show that all four species have accumulated mtDNA differences over similar spatial and temporal scales but that the precise geographic pattern of genetic differentiation varies for each species. These geographic patterns appear much less deterministic than in other well-known coastal marine systems and may be driven by chance and historical accident.     

Inferring the population structure and demography of Drosophila ananassae from multilocus data

Inferring the origin, population structure, and demographic history of a species is a major objective of population genetics. Although many organisms have been analyzed, the genetic structures of subdivided populations are not well understood. Here we analyze Drosophila ananassae, a highly substructured, cosmopolitan, and human-commensal species distributed in the tropical, subtropical, and mildly temperate regions of the world. We adopt a multilocus approach (with 10 neutral loci) using 16 population samples covering almost the entire species range (Asia, Australia, and America). Analyzed with our recently developed Bayesian method, 5 populations in Southeast Asia are found to be central, while the other 11 are peripheral. These 5 central populations were sampled from localities that belonged to a single landmass ("Sundaland") during the late Pleistocene ( approximately 18,000 years ago), when sea level was approximately 120 m below the present level. The inferred migration routes of D. ananassae out of Sundaland seem to parallel those of humans in this region. Strong evidence for a population size expansion is seen particularly in the ancestral populations.     

Behavioral genetics of Drosophila ananassae

Drosophila ananassae has a unique status among Drosophila species because of certain peculiarities in its genetic behavior. The most unusual feature of this species is its relatively high frequency of spontaneous male recombination. The results of studies on non-sexual behavior, such as phototactic responses, eclosion rhythm, and preferences for oviposition and pupation sites, lead us to suggest that this behavior is under polygenic control, with a substantial amount of additive genetic variation. Sexual isolation has been reported in D. ananassae with the degree of such isolation being stronger in isofemale lines than in natural populations. The significant variations seen in the mating propensity of several isofemale strains, inversion karyotypes and wild type strains, the diminishing effects of certain mutations on the sexual activity of males, and the positive responses to selection for high and low mating propensity point to a genetic control of sexual behavior in D. ananassae. Males contribute more to variation and thus are more subject to intrasexual selection than females. There is a positive correlation between sternopleural bristle number, mating propensity and fertility in D. ananassae. This correlation between morphometric traits and mating success suggests that larger flies are more successful in mating than smaller ones. There is also evidence for adaptive plasticity and a trade-off between longevity and productivity in D. ananassae. Rare, specific courtship song parameters that provide males with a mating advantage have also been reported in different geographic strains of D. ananassae. The remating behavior of males and females, sperm displacement, and the bi-directional selection for female remating speed indicate that post-mating behavior in this species may also be under genetic control. The occurrence of size assortative mating further indicates that there is size-dependent sexual selection in D. ananassae.     

Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island,China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long‐lived trees. Dracaena cambodiana is an endangered, long‐lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter‐simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat‐private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.     

The influence of ecology and genetics on behavioral variation in salamander populations across the Eastern Continental Divide

Understanding the unique contributions of ecology and history to the distribution of species within communities requires an integrative approach. The Eastern Continental Divide in southwestern Virginia separates river drainages that differ in species composition: the more aquatic, predatory Desmognathus quadramaculatus is present only in the New River drainage (which drains to the Gulf of Mexico), while Desmognathus monticola is present in both the New River drainage and the James River drainage (which drains to the Atlantic Ocean). We investigated natural distributions, behavioral variation in experimental mesocosms, population genetic, and phylogenetic implications of community structure. The presence of D. quadramaculatus increased the terrestriality of D. monticola in natural and experimental situations but to different degrees in allopatric and sympatric populations. Our ecological data suggest that the degree of terrestriality in D. monticola is a result of a balance between the optimal aquatic habitat and risks of predation. Our genetic analyses suggest that D. monticola has experienced a recent range expansion and has only a recent history of association with D. quadramaculatus in Virginia. This is surprising given the strong behavioral variation that exists in populations experiencing unique community compositions over a scale of meters. This study demonstrates the need to combine both ecology and genetics toward an understanding of the factors affecting species distributions, behavioral variation between populations, and patterns of genetic variation across a landscape.     

The effects of contemporary processes in maintaining the genetic structure of western song sparrows (Melospiza melodia)

Historic events and contemporary processes work in concert to create and maintain geographically partitioned variation and are instrumental in the generation of biodiversity. We sought to gain a better understanding of how contemporary processes such as movement and isolation influence the genetic structure of widely distributed vagile species such as birds. Song sparrows (Melospiza melodia) in western North America provide a natural system for examining the genetics of populations that have different patterns of geographic isolation and migratory behavior. We examined the population genetics of 576 song sparrows from 23 populations using seven microsatellite loci to assess genetic differentiation among populations and to estimate the effects of drift and immigration (gene flow) on each population. Sedentary, isolated populations were characterized by low levels of immigration and high levels of genetic drift, whereas those populations less isolated displayed signals of high gene flow and little differentiation from other populations. Contemporary dispersal rates from migratory populations, estimated by assignment test, were higher and occurred over larger distances than dispersal from sedentary populations but were also probably too low to counter the effects of drift in most populations. We suggest that geographic isolation and limited gene flow facilitated by migratory behavior are responsible for maintaining observed levels of differentiation among Pacific coastal song sparrow populations.     

Which evolutionary processes influence natural genetic variation for phenotypic traits?

Although many studies provide examples of evolutionary processes such as adaptive evolution, balancing selection, deleterious variation and genetic drift, the relative importance of these selective and stochastic processes for phenotypic variation within and among populations is unclear. Theoretical and empirical studies from humans as well as natural animal and plant populations have made progress in examining the role of these evolutionary forces within species. Tentative generalizations about evolutionary processes across species are beginning to emerge, as well as contrasting patterns that characterize different groups of organisms. Furthermore, recent technical advances now allow the combination of ecological measurements of selection in natural environments with population genetic analysis of cloned QTLs, promising advances in identifying the evolutionary processes that influence natural genetic variation.     

Population genetic consequences of geographic disjunction: a prairie plant isolated on Great Lakes alvars

Species may often exhibit geographic variation in population genetic structure due to contemporary and historical variation in population size and gene flow. Here, we test the predictions that populations on the margins of a species' distribution contain less genetic variation and are more differentiated than populations towards the core of the range by comparing patterns of genetic variation at five microsatellite loci between disjunct and core populations of the perennial, allohexaploid herb Geum triflorum. We sampled nine populations isolated on alvar habitat within the eastern Great Lakes region in North America, habitats that include disjunct populations of several plant species, and compared these to 16 populations sampled from prairie habitat throughout the core of the species' distribution in midwestern Canada and the USA. Alvar populations exhibited much lower within-population diversity and contained only a subset of alleles found in prairie populations. We detected isolation by distance across the species' range and within alvar and prairie regions separately. As predicted, genetic differentiation was higher among alvar populations than among prairie populations, even after controlling for the geographic distance between sampled populations. Low diversity and high differentiation can be accounted for by the greater contemporary spatial isolation of alvar populations. However, the genetic structure of alvar populations may also have been influenced by postglacial range expansion and contraction. Our results are consistent with alvar populations being founded during an expansion of prairie habitat during the warmer, hypsithermal period approximately 5000 bp and subsequently becoming stranded on isolated alvar habitat as the climate grew cooler and wetter.     

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.     

Standing variation boosted by multiple sources of introduction contributes to the success of the introduced species, Lotus corniculatus

Although ecological differences between native and introduced ranges have been considered to drive rapid expansion of invasive species, recent studies suggest that rapid evolutionary responses of invasive species to local environments may also be common. Such expansion across heterogeneous environments by adaptation to local habitats requires genetic variation. In this study, we investigated the source and role of standing variation in successful invasion of heterogeneous abiotic environments in a self-incompatible species, Lotus corniculatus. We compared phenotypic and genetic variation among cultivars, natives, and introduced genotypes, and found substantial genetic variation within both native and introduced populations. Introduced populations possessed genotypes derived from both cultivars and native populations, and had lower population differentiation, indicating multiple sources of introduction and population admixture among the sources in the introduced range. Both cultivars and introduced populations had similarly outperforming phenotypes on average, with increased biomass and earlier flowering compared with native populations, but those phenotypes were within the range of the variation in phenotypes of the native populations. In addition, clinal variation within introduced populations was detected along a climatic gradient. Multiple introductions from different sources, including cultivars, may have contributed to pre-adaptive standing variation in the current introduced populations. We conclude that both introduction of cultivar genotypes and natural selection in local environments contributed to current patterns of genetic and phenotypic variation observed in the introduced populations.     

Population genetic structure of three freshwater mussel (Unionidae) species within a small stream system: significant variation at local spatial scales

1. Unionid mussels are highly threatened, but little is known about genetic structure in populations of these organisms. We used allozyme electrophoresis to examine partitioning of genetic variation in three locally abundant and widely distributed species of mussels from a catchment in Ohio. 2. Within‐population variation was similar to that previously reported for freshwater mussels, but genotype frequencies exhibited heterozygote deficiencies in many instances. All three species exhibited significant among‐population variation. Evidence of isolation‐by‐distance was found in Elliptio dilatata and Ptychobranchus fasciolaris, while Lampsilis siliquoidea showed no geographical pattern of among‐population variation. 3. Our results suggest that the isolating effects of genetic drift were greater in L. siliquoidea than in the other species. Differentiation of populations occurred at a much smaller spatial scale than has previously been found in freshwater mussels. Differences among species may reflect differences in the dispersal abilities of fishes that serve as hosts for the glochidia larvae of mussels. 4. Based on our results, we hypothesise that species of mussels that are common to large rivers exhibit relatively large amounts of within‐population genetic variation and little differentiation over large geographical distances. Conversely, species typical of small streams show lower within‐population genetic variation and populations will be more isolated. If this hypothesis can be supported, it may prove useful in the design of conservation strategies that maintain the genetic structure of target species.     

Preliminary insights into the phylogeography of the yellow-bellied sea snake, Pelamis platurus

The yellow-bellied sea snake, Pelamis platurus (Elapidae, Hydrophiinae), has the largest distribution of any snake species, and patterns related to its distribution and regional color variation suggest there is population structuring in this species. Here, we use mitochondrial (ND4, Cyt-b) and nuclear (RAG-1) DNA to (1) test whether genetic variation is associated with local variation in color pattern, and (2) assess whether large-scale patterns of genetic variation are correlated with geographic distribution across the Pacific Ocean. We found low levels of genetic variation and shallow population structure that are correlated with local variation in color pattern and with geographic distribution. The low levels of genetic divergence indicate a relatively high rate of gene flow throughout the Pacific region and/or a recent expansion of range, both of which could be attributable to the passive drifting of these snakes on oceanic surface currents. The mtDNA data conform closely to a model of past exponential population growth, and this may have been associated with the species' large eastward and westward expansion of range. The pattern of low nucleotide and high haplotype diversity suggests that this population growth occurred in the relatively recent past. Data from drifting buoys can potentially act as informative models for predicting patterns of drifting in Pelamis and for generating additional testable hypotheses relating to its population structure and biogeography. Future studies should employ nuclear microsatellite markers to investigate population structure in this species at a finer scale. The exploitation of oceanic currents as a novel and highly efficient dispersal mechanism has likely facilitated gene flow throughout the Pacific Ocean in this uniquely pelagic species of sea snake, resulting in a distribution spanning over half of the earth's circumference.     

Evolution of mating isolation between populations of Drosophila ananassae

Prezygotic mating isolation has been a major interest of evolutionary biologists during the past several decades because it is likely to represent one of the first stages in the transition from populations to species. Mate discrimination is one of the most commonly measured forms of prezygotic isolation and appears to be relatively common among closely related species. In some cases, it has been used as a measure to distinguish populations from subspecies, races, and sister species, yet the influences of various evolutionary mechanisms that may generate mate discrimination are largely unknown. In this study, we measured the level and pattern of mate discrimination among 18 populations of a cosmopolitan drosophilid species, Drosophila ananassae , from throughout its geographical range and its sister species, Drosophila pallidosa, which has a restricted geographical distribution in the South Pacific Islands. In addition, we measured genetic differentiation between all 18 populations using mitochondrial DNA polymorphism data. Mate discrimination varies considerably throughout the species range, being higher among populations outside the ancestral Indonesian range, and highest in the South Pacific. Our results suggest that colonization and genetic differentiation may have an influence on the evolutionary origin of mate discrimination. Our phylogeographical approach clarifies the ancestral relationships of several populations from the South Pacific that show particularly strong mate discrimination and suggests that they may be in the early stages of speciation. Furthermore, both the genetic and behavioral results cast doubt on the status of D. pallidosa as a good species.     

Genetic similarity of disjunct populations of the giant sea bass Stereolepis gigas

Sequence variation in nuclear and mitochondrial genes of the giant sea bass Stereolepis gigas collected from the Pacific coast and the northern Sea of Cortez was examined. Restriction fragment length polymorphism analysis and direct sequencing showed extremely low mtDNA sequence diversity (13 closely related haplotypes with no evidence of geographical population subdivision). The mitochondrial haplotype mismatch distribution is consistent with a population expansion following the Last Pleistocene glaciation. Differences in single nucleotide polymorphism frequencies between Pacific and Sea of Cortez populations were detected at two of four nuclear loci, which may reflect natural selection or genetic drift in populations with low effective numbers of males. Although Pacific coast and Sea of Cortez populations of giant sea bass do not exhibit the mitochondrial phylogenetic break characteristic of many species with disjunct Pacific and Gulf populations, the possibility of genetic differentiation at nuclear loci suggests that a cautious approach to broodstock selection for captive breeding and restoration programmes be exercised.     

Global phylogeography of the band-rumped storm-petrel (Oceanodroma castro; Procellariiformes: Hydrobatidae)

Factors shaping population differentiation in low latitude seabirds are not well-understood. In this study, we examined global patterns of DNA sequence variation in the mitochondrial control region of the band-rumped storm-petrel (Oceanodroma castro), a highly pelagic seabird distributed across the sub-tropical and tropical Atlantic and Pacific Oceans. Despite previous classification as a single, monotypic species, fixed haplotype differences occurred between Atlantic and Pacific populations, and among all Pacific populations. In addition, Cape Verde and Galapagos birds formed distinct clades, estimated to have diverged from all other populations at least 150,000years ago. Azores hot season populations were also genetically distinct, lending support to previous phenotypic evidence that they be recognized as a separate species. Seasonal populations in Madeira probably represent separate genetic management units. The phylogeography of the band-rumped storm-petrel appears to have been shaped by both nonphysical barriers to gene flow and Pleistocene oceanographic conditions. Ancestral populations likely expanded through contiguous range expansion and infrequent long-distance colonization into their current breeding range. These findings suggest several possible revisions to the taxonomy of the band-rumped storm-petrel.     

Population subdivision and genetic diversity in two narrow endemics of Antirrhinum L

Genetic diversity and its partition within and among populations and families of two species of Antirrhinum L., A. charidemi Lange and A. valentinum F.Q., have been studied. Both species are narrow-range endemics, self-incompatible, ecologically specialized and form small isolated populations. Despite these similarities, the species differ markedly in the distribution of genetic diversity. In A. valentinum, 61.64% of the total variation was distributed among populations, whereas in A. charidemi it was only 8.55%. A. charidemi showed little population divergence (GST = 0.0542) relative to A. valentinum (GST = 0.4805). In neither species was within-population genetic diversity correlated with population size, nor were there significant correlations between genetic and geographical distances. These results are discussed in relation to differences in flowering time and habitat continuity. They suggest that caution should be taken when making generalizations about levels of genetic variation and patterns of plant reproduction, life history and geographical distribution.     

Inter‐oceanic variation in patterns of host‐associated divergence in a seabird ectoparasite

Aim Parasites with global distributions and wide host spectra provide excellent models for exploring the factors that drive parasite diversification. Here, we tested the relative force of host and geography in shaping population structure of a widely distributed and common ectoparasite of colonial seabirds, the tick Ixodes uriae. Location Two natural geographic replicates of the system: numerous seabird colonies of the North Pacific and North Atlantic Ocean basins. Methods Using eight microsatellite markers and tick samples from a suite of multi‐specific seabird colonies, we examined tick population structure in the North Pacific and compare patterns of diversity and structure to those in the Atlantic basin. Analyses included population genetic estimations of diversity and population differentiation, exploratory multivariate analyses, and Bayesian clustering approaches. These different analyses explicitly took into account both the geographic distance among colonies and host use by the tick. Results Overall, little geographic structure was observed among Pacific tick populations. However, host‐related genetic differentiation was evident, but was variable among host types and lower than in the North Atlantic. Main conclusions Tick population structure is concordant with the genetic structure observed in seabird host species within each ocean basin, where seabird populations tend to be less structured in the North Pacific than in the North Atlantic. Reduced tick genetic structure in the North Pacific suggests that host movement among colonies, and thus tick dispersal, is higher in this region. In addition to information on parasite diversity and gene flow, our findings raise interesting questions about the subtle ways that host behaviour, distribution and phylogeographic history shape the genetics of associated parasites across geographic landscapes.