On the spatial scale of dispersal in coral reef fishes

Marine biologists have gone through a paradigm shift, from the assumption that marine populations are largely ‘open’ owing to extensive larval dispersal to the realization that marine dispersal is ‘more restricted than previously thought’. Yet, population genetic studies often reveal low levels of genetic structure across large geographic areas. On the other side, more direct approaches such as mark‐recapture provide evidence of localized dispersal. To what extent can direct and indirect studies of marine dispersal be reconciled? One approach consists in applying genetic methods that have been validated with direct estimates of dispersal. Here, we use such an approach—genetic isolation by distance between individuals in continuous populations—to estimate the spatial scale of dispersal in five species of coral reef fish presenting low levels of genetic structure across the Caribbean. Individuals were sampled continuously along a 220‐km transect following the Mesoamerican Barrier Reef, population densities were estimated from surveys covering 17 200 m² of reef, and samples were genotyped at a total of 58 microsatellite loci. A small but positive isolation‐by‐distance slope was observed in the five species, providing mean parent‐offspring dispersal estimates ranging between 7 and 42 km (CI 1–113 km) and suggesting that there might be a correlation between minimum/maximum pelagic larval duration and dispersal in coral reef fishes. Coalescent‐based simulations indicate that these results are robust to a variety of dispersal distributions and sampling designs. We conclude that low levels of genetic structure across large geographic areas are not necessarily indicative of extensive dispersal at ecological timescales.     

Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex

Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (10(4) km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average F(ST) = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (F(ST) = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.     

Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae)

The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self-seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self-recruitment rather than passive dispersal.     

Genetic population structure of the endemic fourline wrasse (Larabicus quadrilineatus) suggests limited larval dispersal distances in the Red Sea

The connectivity among marine populations is determined by the dispersal capabilities of adults as well as their eggs and larvae. Dispersal distances and directions have a profound effect on gene flow and genetic differentiation within species. Genetic homogeneity over large areas is a common feature of coral reef fishes and can reflect high dispersal capability resulting in high levels of gene flow. If fish larvae return to their parental reef, gene flow would be restricted and genetic differentiation could occur. Larabicus quadrilineatus (Labridae) is considered as an endemic fish species of the Red Sea and Gulf of Aden. The juveniles of this species are cleaner fish that feed on ectoparasites of other fishes. Here, we investigated the genetic population structure and gene flow in L. quadrilineatus among five locations in the Red Sea to infer connectivity among them. To estimate genetic diversity, we analysed 369 bp of 237 mitochondrial DNA control region sequences. Haplotype and nucleotide diversities were higher in the southern than in the northern Red Sea. Analysis of molecular variance (amova) detected the highest significant genetic variation between northern and central/southern populations (Phi(CT) = 0.01; P < 0.001). Migration analysis revealed a several fold higher northward than southward migration, which could be explained by oceanographic conditions and spawning season. Even though the Phi(ST) value of 0.01 is rather low and implies a long larval dispersal distance, estimates based on the isolation-by-distance model show a very low mean larval dispersal distance (0.44-5.1 km) compared to other studies. In order to enable a sustainable ornamental fishery on the fourline wrasse, the results of this study suggest that populations in the northern and southern Red Sea should be managed separately as two different stocks. The rather low larval dispersal distance of about 5 km needs to be considered in the design of marine protected areas to enable connectivity and self-seeding.     

Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newt Calotriton asper (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA

Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt ( Calotriton asper ) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F _ST values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper . The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

Spatial genetic structuring in a vagile species, the European wood mouse

We examined the genetic structure of natural populations of the European wood mouse Apodemus sylvaticus at the microgeographic (<3 km) and macrogeographic (>30 km) scales. Ecological and behavioural studies indicate that this species exhibits considerable dispersal relative to its home-range size. Thus, there is potential for high gene flow over larger geographic areas. As levels of population genetic structure are related to gene flow, we hypothesized that population genetic structuring at the microgeographic level should be negligible, increasing only with geographic distance. To test this, four sites were sampled within a microgeographic scale with two additional samples at the macrogeographic level. Individuals ( n =415) were screened and analysed for seven polymorphic microsatellite loci. Contrary to our hypothesis, significant levels of population structuring were detected at both scales. Comparing genetic differentiation with geographic distance suggests increasing genetic isolation with distance. However, this distance effect was non-significant being confounded by surprisingly high levels of differentiation among microgeographic samples. We attribute this pattern of genetic differentiation to the effect of habitat fragmentation, splitting large populations into components with small effective population sizes resulting in enhanced genetic drift. Our results indicate that it is incorrect to assume genetic homogeneity among populations even where there is no evidence of physical barriers and dispersal can occur freely. In the case of A. sylvaticus , it is not clear whether dispersal does not occur across habitat barriers or behavioural dispersal occurs without consequent gene flow.     

Genetic structure of natural populations of the California black abalone (Haliotis cracherodii Leach, 1814), a candidate for endangered species status

The black abalone (Haliotis cracherodii) has been severely depleted across much of its historic range by a combination of overexploitation and disease. Natural recovery of extirpated populations along the southern California coast will depend on the extent to which remnant populations can serve as larval sources to geographic locations formerly supporting abalone populations. Population genetic analyses of mitochondrial cytochrome oxidase subunit one (COI) DNA sequences, four nuclear microsatellites, and 142 amplified fragment length polymorphisms (AFLPs) were used to evaluate connectivity among populations of H. cracherodii sampled from the central California coast and four islands in the Southern California Bight. Global divergence among populations was significant at COI and the AFLP loci. The Hka28 microsatellite locus and AFLP data showed significant divergence in multiple pairwise population comparisons and exhibited a signal of isolation by distance. Although estimates of gene flow based on genetic analyses must be interpreted with caution, the observed level of interpopulation genetic divergence suggests that larval dispersal is restricted, and natural recovery of decimated H. cracherodii populations along the coast of California is unlikely to occur in the near future.     

Contrasting phylogeography in three endemic Hawaiian limpets (Cellana spp.) with similar life histories

The marine environment offers few obvious barriers to dispersal for broadcast-spawning species, yet population genetic structure can occur on a scale much smaller than the theoretical limits of larval dispersal. Comparative phylogeographical studies of sympatric sister species can illuminate how differences in life history, behaviour, and habitat affinity influence population partitioning. Here we use a mitochondrial DNA marker (612 bp of cytochrome c oxidase subunit I) to investigate population structure of three endemic Hawaiian broadcast-spawning limpets (Cellana spp.) with planktonic larvae that are competent to settle within 4 days. All three species exhibit significant population structure and isolation by distance, but the spatial scales of partitioning differ among the species. Cellana talcosa (n = 105) exhibits strong population structure between Kauai and the other main Hawaiian Islands (MHI) where the maximum channel width is 117 km, and no shared haplotypes were observed (Phi(CT) = 0.30, P < 0.001). In contrast, populations of Cellana exarata (n = 149) and Cellana sandwicensis (n = 109) exhibit weaker population structure within the MHI (Phi(ST) = 0.03-0.04, P < 0.05), and between the MHI and the Northwestern Hawaiian Islands (Phi(ST) = 0.03-0.09, P < 0.01), where the maximum channel width is 260 km. Biogeographical range and microhabitat use were correlated with estimates of dispersal, while phylogenetic affiliation and minimum pelagic larval duration were poor predictors of population partitioning. Despite similar life histories, these closely related limpets have contrasting patterns of population structure, illustrating the danger of relying on model species in management initiatives to predict population structure and dispersal in the context of marine protected area delineation.     

Isolation by distance and gene flow in the Eurasian badger (Meles meles) at both a local and broad scale

Eurasian badgers, Meles meles, have been shown to possess limited genetic population structure within Europe; however, field studies have detected high levels of philopatry, which are expected to increase population structure. Population structure will be a consequence of both contemporary dispersal and historical processes, each of which is expected to be evident at a different scale. Therefore, to gain a greater understanding of gene flow in the badger, we examined microsatellite diversity both among and within badger populations, focusing on populations from the British Isles and western Europe. We found that while populations differed in their allelic diversity, the British Isles displayed a similar degree of diversity to the rest of western Europe. The lower genetic diversity occurring in Ireland, Norway and Scotland was more likely to have resulted from founder effects rather than contemporary population density. While there was significant population structure (F ST = 0.19), divergence among populations was generally well explained by geographic distance (P < 0.0001) across the entire range studied of more than 3000 km. Transient effects from the Pleistocene appear to have been replaced by a strong pattern of genetic isolation by distance across western Europe, suggestive of colonization from a single refugium. Analysis of individuals within British populations through Mantel tests and spatial autocorrelation demonstrated that there was significant local population structure across 3-30 km, confirming that dispersal is indeed restricted. The isolation by distance observed among badger populations across western Europe is likely to be a consequence of this restricted local dispersal.     

NONSTATIONARY PATTERNS OF ISOLATION‐BY‐DISTANCE: INFERRING MEASURES OF LOCAL GENETIC DIFFERENTIATION WITH BAYESIAN KRIGING

Patterns of isolation‐by‐distance (IBD) arise when population differentiation increases with increasing geographic distances. Patterns of IBD are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate nonstationary patterns of IBD where the rate at which genetic differentiation accumulates varies across space. To characterize nonstationary patterns of IBD, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with two datasets: single nucleotide polymorphisms from human Swedish populations and dominant markers for alpine plant species.     

Partitioning the effects of isolation by distance,environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation‐by‐distance (IBD) and isolation‐by‐environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently developed population genetic software (BEDASSLE) to analyze partial genomic data from three lake‐stream clines on Vancouver Island. We find support for IBD within each of three outlet streams (unlike prior studies of lake‐stream stickleback). In addition, we find evidence for IBE (controlling for geographic distance): the genetic effect of habitat is equivalent to geographic separation of ～1.9 km of IBD. Remarkably, of our three lake‐stream pairs, IBE is strongest where migration between habitats is easiest. Such microgeographic genetic divergence would require exceptionally strong divergent selection, which multiple experiments have failed to detect. Instead, we propose that nonrandom dispersal (e.g., habitat choice) contributes to IBE. Supporting this conclusion, we show that the few migrants between habitats are a nonrandom subset of the phenotype distribution of the source population.     

DEPENDENCE OF GENE FLOW ON GEOGRAPHIC DISTANCE IN TWO SOLITARY CORALS WITH DIFFERENT LARVAL DISPERSAL CAPABILITIES

When the level of gene flow among populations depends upon the geographic distance separating them, genetic differentiation is relatively enhanced. Although the larval dispersal capabilities of marine organisms generally correlate with inferred levels of average gene flow, the effect of different modes of larval development on the association between gene flow and geographic distance remains unknown. In this paper, I examined the relationship between gene flow and distance in two co-occurring solitary corals. Balanophyllia elegans broods large, nonfeeding planulae that generally crawl only short distances from their place of birth before settling. In contrast, Paracyathus stearnsii free-spawns and produces small planktonic larvae presumably capable of broad dispersal by oceanic currents. I calculated F-statistics using genetic variation at six (P. stearnsii) or seven (B. elegans) polymorphic allozyme loci revealed by starch gel electrophoresis, and used these F-statistics to infer levels of gene flow. Average levels of gene flow among twelve Californian localities agreed with previous studies: the species with planktonic, feeding larvae was less genetically subdivided than the brooding species. In addition, geographic isolation between populations appeared to affect gene flow between populations in very different ways in the two species. In the brooding B. elegans, gene flow declined with increasing separation, and distance explained 31% of the variation in gene flow. In the planktonically dispersed P. stearnsii distance of separation between populations at the scale studied (10–1000 km) explained only 1% of the variation in gene flow between populations. The mechanisms generating geographic genetic differentiation in species with different modes of larval development should vary fundamentally as a result of these qualitative differences in the dependence of gene flow on distance.     

Evaluating connectivity in the brooding brittle star Astrotoma agassizii across the drake passage in the Southern Ocean

Studies examining population structure and genetic diversity of benthic marine invertebrates in the Southern Ocean have emerged in recent years. However, many taxonomic groups remain largely unstudied, echinoderms being one conspicuous example. The brittle star Astrotoma agassizii is distributed widely throughout Antarctica and southern South America. This species is a brooding echinoderm and therefore may have limited dispersal capacity. In order to determine the effect of hypothesized isolating barriers in the Southern Ocean, such as depth, geographic distance, and the polar front, 2 mitochondrial DNA markers were used to compare populations from the South American and Antarctic continental shelves. Astrotoma agassizii was shown to be genetically discontinuous across the polar front. In fact, populations previously assumed to be panmictic instead represent 3 separate lineages that lack morphological distinction. However, within lineages, genetic continuity was displayed across a large geographic range (>500 km). Therefore, despite lacking a pelagic larval stage, A. agassizii can disperse across substantial geographic distance within continental shelf regions. These results indicate that geographic distance alone may not be a barrier to dispersal, but rather the combined effects of distance, depth, and the polar front act to prevent gene flow between A. agassizii populations in the Southern Ocean.     

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.     

Genetic structure in the coral-reef-associated Banggai cardinalfish, Pterapogon kauderni

In this study, we used 11 polymorphic microsatellite loci to show that oceanic distances as small as 2-5 km are sufficient to produce high levels of population genetic structure (multilocus F(ST) as high as 0.22) in the Banggai cardinalfish (Pterapogon kauderni), a heavily exploited reef fish lacking a pelagic larval dispersal phase. Global F(ST) among all populations, separated by a maximum distance of 203 km, was 0.18 (R(ST) = 0.35). Moreover, two lines of evidence suggest that estimates of F(ST) may actually underestimate the true level of genetic structure. First, within-locus F(ST) values were consistently close to the theoretical maximum set by the average within-population heterozygosity. Second, the allele size permutation test showed that R(ST) values were significantly larger than F(ST) values, indicating that populations have been isolated long enough for mutation to have played a role in generating allelic variation among populations. The high level of microspatial structure observed in this marine fish indicates that life history traits such as lack of pelagic larval phase and a good homing ability do indeed play a role in shaping population genetic structure in the marine realm.     

Evidence for isolation by time in the European eel (Anguilla anguilla L.)

Life history traits of highly vagile marine species, such as adult reproductive success and larval dispersal, are strongly determined by oceanographic and climatic forces. Nevertheless, marine organisms may show restricted dispersal in time and space. Patterns of isolation by distance (IBD) have been repeatedly observed in marine species. If spawning time is a function of geographical location, temporal and spatial isolation, can easily be confounded or misinterpreted. In this study, we aimed at discriminating between various forces shaping the genetic composition of recruiting juveniles of the European eel (Anguilla anguilla L.). By controlling for geographical variation, we assessed temporal variation and tested for possible isolation by time (IBT) between recruitment waves within and between years. Using 12 polymorphic allozyme and six variable microsatellite loci, we show that genetic differentiation was low (F(ST) = 0.01-0.002) and significant between temporal samples. Regression analysis between genetic and temporal distance, was consistent with a subtle interannual pattern of IBT. Our data suggest that the population dynamics of the European eel may be governed by a double pattern of temporal variance in genetic composition: (i) a broad-scale IBT of spawning cohorts, possibly as a consequence of the large migration loop in anguillids and strong variance in annual adult reproductive contribution; and (ii) a smaller-scale variance in reproductive success (genetic patchiness) within cohorts among seasonally separated spawning groups, most likely originating from fluctuating oceanic and climatic forces. The consistency of both mechanisms remains to be verified with fine-scale analyses of both spawning/migrating aged adults and their offspring to confirm the stochastic/deterministic nature of the IBT pattern in eel.     

Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans

Outcomes of host-pathogen coevolution are influenced by migration rates of the interacting species. Reduced gene flow with increasing spatial distance between populations leads to spatial genetic structure, as predicted by the isolation by distance (IBD) model. In wind-dispersed plant-pathogenic fungi, a significant spatial genetic structure is theoretically expected if local spore dispersal is more frequent than long-distance dispersal, but this remains to be documented by empirical data. For 29 populations of the oilseed rape fungus Leptosphaeria maculans sampled from two French regions, genetic structure was determined using eight minisatellite markers. Gene diversity (H = 0.62-0.70) and haplotypic richness (R = 0.96-1) were high in all populations. No linkage disequilibrium was detected between loci, suggesting the prevalence of panmictic sexual reproduction. Analysis of molecular variance showed that > 97% of genetic diversity was observed within populations. Genetic differentiation was low among populations (F(st) < 0.05). Although direct methods previously revealed short-distance dispersal for L. maculans, our findings of no correlation between genetic and geographic distances among populations illustrate that the IBD model does not account for dispersal of the fungus at the spatial scale we examined. These results indicate high gene flow among French populations of L. maculans, suggesting high dispersal rates and/or large effective population sizes, two characteristics giving the pathogen high evolutionary potential against the deployment of resistant oilseed rape cultivars.     

What constitutes a population for the plant parasitic nematode Globodera pallida in its native area (Peru)?

Although numerous species are distributed in discrete populations easily recognised by geographical barriers, continuous populations are a common feature of plants or marine organisms. This is particularly true for soil organisms as their habitat is continuous and their range cannot easily be assessed as they are buried below ground. In the case of organisms for which standard methods such as Capture/Mark/Recapture cannot be used, population genetics provide a straightforward approach to delimitate populations. In this study, we have pursued this topic with a soil-dwelling nematode (Globodera pallida), which parasitises potato roots and is indigenous to South America. Potential barriers to gene flow were identified using the analysis of the F(ST)/(1-F(ST)) ratio against geographical distance and spatial autocorrelation combined with model-based clustering algorithm. Inside regions, neither genetic differentiation nor isolation by distance (IBD) occur among fields less than 50 km distant. We hypothesise that the large amount of gene flow revealed by the absence of genetic structure of this organism could be due to large passive dispersion inside an agronomic area where G. pallida has a continuous distribution and is found at high density. The first evidence of genetic differentiation appeared when a field was separated from others by an area free of farms (where G. pallida is absent or rare). Among regions, a high genetic structure coupled with an IBD pattern occurs as the consequences of the limitations of passive dispersal across deep valleys or high mountains. To our knowledge, this is the first study identifying the spatial limit of a population for a plant nematode parasite.     

USING ISOLATION BY DISTANCE AND EFFECTIVE DENSITY TO ESTIMATE DISPERSAL SCALES IN ANEMONEFISH

Robust estimates of dispersal are critical for understanding population dynamics and local adaptation, as well as for successful spatial management. Genetic isolation by distance patterns hold clues to dispersal, but understanding these patterns quantitatively has been complicated by uncertainty in effective density. In this study, we genotyped populations of a coral reef fish (Amphiprion clarkii) at 13 microsatellite loci to uncover fine‐scale isolation by distance patterns in two replicate transects. Temporal changes in allele frequencies between generations suggested that effective densities in these populations are 4–21 adults/km. A separate estimate from census densities suggested that effective densities may be as high as 82–178 adults/km. Applying these effective densities with isolation by distance theory suggested that larval dispersal kernels in A. clarkii had a spread near 11 km (4–27 km). These kernels predicted low fractions of self‐recruitment in continuous habitats, but the same kernels were consistent with previously reported, high self‐recruitment fractions (40–60%) when realistic levels of habitat patchiness were considered. Our results suggested that ecologically relevant larval dispersal can be estimated with widely available genetic methods when effective density is measured carefully through cohort sampling and ecological censuses, and that self‐recruitment studies should be interpreted in light of habitat patchiness.