Physical barriers and corridors in urban habitats affect colonisation and parasitism rates of a specialist leaf miner

1. Urban environments are fragmented habitats characterised by the presence of physical barriers, which may negatively affect dispersal and colonisation by insect herbivores and their natural enemies. Conversely, plants growing along pavements may function as dispersal corridors, helping to moderate the harmful effects of resource patch isolation on organism movement and population persistence. 2. We experimentally tested the effects of walls as physical barriers to the dispersal of the leaf miner Liriomyza commelinae Frost and colonisation of its host plant, Commelina erecta L., in urban habitats. We also evaluated whether plants along pavements could act as corridors for this species. 3. We exposed experimental host plants to the leaf miner in houses with front gardens and back yards, the latter being completely surrounded by walls. The front gardens had walls but none separating them from the pavement. Previously mined plants were also exposed to parasitoids in the yards to determine parasitoid attack. 4. Liriomyza commelinae took longer to colonise back yards with higher walls, and the abundance of mined plants along pavements reduced the colonisation time. Leaf‐miner abundance was marginally affected by the yard type, and was lower in back yards. Cumulative parasitism rates decreased with increasing distance at which mined plants were placed from pavements. 5. Constructions act as physical barriers, having a negative impact on colonisation of host plants by leaf miners. The function of pavements as corridors seems to depend on the abundance of mined plants. Parasitism may be affected by distance from the corridor rather than physical barriers or other potential hosts.     

Contrasting demographic and genetic estimates of dispersal in the endangered Coahuilan box turtle: a contemporary approach to conservation

The evolutionary viability of an endangered species depends upon gene flow among subpopulations and the degree of habitat patch connectivity. Contrasting population connectivity over ecological and evolutionary timescales may provide novel insight into what maintains genetic diversity within threatened species. We employed this integrative approach to evaluating dispersal in the critically endangered Coahuilan box turtle (Terrapene coahuila) that inhabits isolated wetlands in the desert‐spring ecosystem of Cuatro Ciénegas, Mexico. Recent wetland habitat loss has altered the spatial distribution and connectivity of habitat patches; and we therefore predicted that T. coahuila would exhibit limited movement relative to estimates of historic gene flow. To evaluate contemporary dispersal patterns, we employed mark–recapture techniques at both local (wetland complex) and regional (intercomplex) spatial scales. Gene flow estimates were obtained by surveying genetic variation at nine microsatellite loci in seven subpopulations located across the species’ geographical range. The mark–recapture results at the local spatial scale reveal frequent movement among wetlands that was unaffected by interwetland distance. At the regional spatial scale, dispersal events were relatively less frequent between wetland complexes. The complementary analysis of population genetic substructure indicates strong historic gene flow (global F_ST = 0.01). However, a relationship of genetic isolation by distance across the geographical range suggests that dispersal limitation exists at the regional scale. Our approach of contrasting direct and indirect estimates of dispersal at multiple spatial scales in T. coahuila conveys a sustainable evolutionary trajectory of the species pending preservation of threatened wetland habitats and a range‐wide network of corridors.     

Modelling the spread of Fagus sylvatica and Picea abies in southern Scandinavia during the late Holocene

Aim To test the hypothesis that dispersal characteristics alone can explain the past migration patterns of Fagus sylvatica and Picea abies observed in southern Scandinavia. Location Scandinavia, Europe. Methods The spreading dynamics of both species were analysed using a quantitative data–model comparison approach. Pollen data recording the arrival of the two species at 24 small forest‐hollow sites distributed across the study area were compared with simulated arrival times. The simulations were based on diffusive spread combined with long‐distance dispersal events. By systematically applying different parameter combinations yielding the desired colonization speeds we could identify values for the long‐distance dispersal component that minimized deviations from the observed arrival times. Results According to the minimization process, the optimal spreading rates were 100 m year^?1 for F. sylvatica and 250 m year^?1 for P. abies. Simulated dispersal alone could adequately explain the wave‐like spread of P. abies but failed to explain the scattered establishment pattern observed for F. sylvatica in Scandinavia. At the fine scale of stand establishment, local microclimatic conditions or site disturbance might be more important. The estimated spreading rates are high because the species colonized Scandinavia from different geographic directions and the rates slowed when their ranges overlapped. We present new estimates for the distance and frequency of long‐distance dispersal events for our modelled species. Main conclusions Our analyses suggest that the late Holocene spread of P. abies in Scandinavia was fairly rapid and was limited only by biological processes of dispersal, while that of F. sylvatica was limited by other factors probably controlled by site properties. Picea abies has maintained a rapid and constant rate of spread throughout at least the last 4000 years, despite significant changes in climate. There is uncertainty about the precise relationship between P. abies and climate in Scandinavia, so future distributions are not easy to forecast. For F. sylvatica in Scandinavia, site quality appears to have been a limiting factor, so future land use is likely to dictate its future distribution dynamics in combination with climatic factors.     

Neither connectivity nor genetic diversity matter in the conservation of a rare fern and a moss on insular erratic boulders

Erratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern Asplenium septentrionale, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of A. septentrionale and the moss Hedwigia ciliata on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid A. septentrionale, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of A. septentrionale mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of H. ciliata were identified, and populations consisting of a single multilocus genotype were less common than in A. septentrionale. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of A. septentrionale seems to be rare, while colonisation by H. ciliata appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.

     

Dispersal distance and the pool of taxa,but not barriers,determine the colonisation of restored river reaches by benthic invertebrates

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Recolonisation by diffusion can generate increasing rates of spread

Diffusion is one of the most frequently used assumptions to explain dispersal. Diffusion models and in particular reaction-diffusion equations usually lead to solutions moving at constant speeds, too slow compared to observations. As early as 1899, Reid had found that the rate of spread of tree species migrating to northern environments at the beginning of the Holocene was too fast to be explained by diffusive dispersal. Rapid spreading is generally explained using long distance dispersal events, modelled through integro-differential equations (IDEs) with exponentially unbounded (EU) kernels, i.e. decaying slower than any exponential. We show here that classical reaction-diffusion models of the Fisher-Kolmogorov-Petrovsky-Piskunov type can produce patterns of colonisation very similar to those of IDEs, if the initial population is EU at the beginning of the considered colonisation event. Many similarities between reaction-diffusion models with EU initial data and IDEs with EU kernels are found; in particular comparable accelerating rates of spread and flattening of the solutions. There was previously no systematic mathematical theory for such reaction-diffusion models with EU initial data. Yet, EU initial data can easily be understood as consequences of colonisation-retraction events and lead to fast spreading and accelerating rates of spread without the long distance hypothesis.     

Route,speed and mode of oak postglacial colonisation across the British Isles: Integrating molecular ecology,palaeoecology and modelling approaches

Summary

This paper describes the route, speed and mode of colonisation of oaks by integrating a number of independent analyses using molecular ecology, palaeoecology and simulation modelling approaches. Using a synthetic map of the contemporary distribution of chloroplast DNA (integrating several published and unpublished data sets and describing variation in 1468 trees from 313 autochthonous stands of Q. robur and Q. petraea from Britain and Ireland), and considering the postglacial topographic landscape, the most likely routes of postglacial colonisation across the British Isles are suggested. The overall pattern of these directions agrees with previous interpretations, but several routes, particularly those into Ireland, differ from previous interpretations and benefit here from using a single synthesised data set. Interestingly, the Atlantic oakwoods appear to have been colonised by individuals bearing a single haplotype (type 12). Two palaeoecology data sets, published separately for Britain and Ireland, are synthesised here and used to infer the timing of first arrival of oaks across the British Isles (between 9500 and 6000 years before present). The maximum observed colonisation speed within the British Isles is approximately 500 m year^-1 in central and southern England. Outputs from a simulation model, which mimics postglacial colonisation processes, and which has been parameterised for the colonisation rate observed from the pollen core record and contemporary cpDNA structure, predict that the rapid colonisation rate observed, for at least the southern portion of the British Isles, can only be achieved via very rare (an approximate frequency 0.01%), very long distance seed dispersal events (up to 100 km). Potential agents of such dispersal events are birdsor major meteorological disturbances, e.g. hurricanes. Additional simulation modelling and genetic analysis of latitudinally stratified populations indicate that non-synchronous colonisation fronts, topographic barriers and temperature related survival may also have had an effect on the speed of migration and resulting genetic structure. Finally, in an attempt to record predicted long distance seed dispersal events, a novel curve fitting technique is applied to molecular parentage assignment data for field established seedlings from a contemporary population. A notable discrepancy is recorded between contemporary field estimates (just over 1 km) and those predicted by simulation modelling, and is discussed in detail. A concluding section describes future research priorities.     

Genetic differentiation between individuals

I describe a method of analysis of genetic differentiation which is suitable for the comparison of genetic and demographic estimates of the ‘neighborhood size’– more precisely the product of density and second moment of dispersal distance σ²– in continuous populations sampled at the smallest scale. This method is based on results of models of isolation by distance common to a wide variety of dispersal distances. The performance of this method is tested by simulation for some highly leptokurtic dispersal distributions, and it is applied to a previous study of a kangaroo‐rat (Dipodomys spectabilis) population. In this case, genetic and demographic estimates are within a factor of two from each other. Thus, in line with some previous examples, this study shows that a better agreement may be attained than is usually recognized between genetic and demographic estimates.     

Maintenance of high pollen dispersal in Eucalyptus wandoo, a dominant tree of the fragmented agricultural region in Western Australia

Pollen dispersal was investigated in five remnant populations of Eucalyptus wandoo, a dominant insect-pollinated tree in the fragmented agricultural region of southern Western Australia. Paternity analysis using six microsatellite loci identified a pollen source for 45% of seedlings, and the remainder were assumed to have arisen from pollen sources outside the stands. Outcrossing was variable, ranging from 52 to 89%, and long distance pollen dispersal was observed in all populations with up to 65% of pollen sourced from outside the populations over distances of at least 1 km. Modelling dispersal functions for pollination events within the two larger populations showed little difference between the four two-parameter models tested and indicated a fat-tailed dispersal curve. Similarity of direct and indirect historical estimates of gene flow indicates maintenance of gene flow at levels experienced prior to fragmentation. The study revealed extensive long distance pollen dispersal in remnant patches of trees within a fragmented agricultural landscape in the southern temperate region and highlighted the role of remnant patches in maintaining genetic connectivity at the landscape scale.     

Contributions of long‐distance dispersal to population growth in colonising Pinus ponderosa populations

Long‐distance dispersal is an integral part of plant species migration and population development. We aged and genotyped 1125 individuals in four disjunct populations of Pinus ponderosa that were initially established by long‐distance dispersal in the 16th and 17th centuries. Parentage analysis was used to determine if individuals were the product of local reproductive events (two parents present), long‐distance pollen dispersal (one parent present) or long‐distance seed dispersal (no parents present). All individuals established in the first century at each site were the result of long‐distance dispersal. Individuals reproduced at younger ages with increasing age of the overall population. These results suggest Allee effects, where populations were initially unable to expand on their own, and were dependent on long‐distance dispersal to overcome a minimum‐size threshold. Our results demonstrate that long‐distance dispersal was not only necessary for initial colonisation but also to sustain subsequent population growth during early phases of expansion.     

Relative importance of different dispersal vectors for small aquatic invertebrates in a rock pool metacommunity

The extent and frequency of passive overland dispersal of freshwater invertebrates as well as the relative importance of different dispersal vectors is not well documented. Although anecdotal evidence subscribing the feasibility of individual vectors in various aquatic systems is abundant, dispersal rates have rarely been quantified for different vectors in one study system. Earlier studies also usually investigated dispersal potential rather than actual dispersal rates. In this study we have estimated passive dispersal rates of invertebrate propagules within a cluster of temporary rock pools via water, wind and amphibians in a direct way. Overflows after heavy rains mediated dispersal of a large number of propagules through eroded channels between pools, which were collected in overflow traps. Taking into account model based predictions of overflow frequency, this corresponds with average dispersal rates of 4088 propagules/channel yr^?1. Wind dispersal rates as measured by numbers of propagules collected on sticky traps mounted between pool basins were very high (average dispersal rate: 649 propagules m^?2 in one month) and were positively related to the proximity of source populations. Finally, invertebrate propagules were also isolated from the faeces of African clawed frogs Xenopus laevis caught from the pools (on average 368 propagules/frog). The combination of short distance wind and overflow dispersal rates likely explain the dominant species sorting and mass effect patterns observed in the metacommunity in a previous study. Amphibian mediated dispersal was much less important as the Xenopus laevis population was small and migrations very rare. Based on our own results and available literature we conclude that both vector and propagule properties determine local passive dispersal dynamics of freshwater invertebrates. Accurate knowledge on rates and vectors of dispersal in natural systems are a prerequisite to increase our understanding of the impact of dispersal on ecology (colonisation, community assembly, coexistence) and evolution (gene flow, local adaptation) in fragmented environments.     

Mobility and metapopulation structure of Geocrinia alba and Geocrinia vitellina,two endangered frog species from southwestern Australia

Abstract Dispersal rates can have an important impact on many population processes. Dispersal can lead to population regulation and regional stability in the face of local instability through the formation of a metapopulation. This may be particularly true for frogs because they often have patchy distributions. In this paper I investigate dispersal by male Geocrinia alba and Geocrinia vitellina, using a mark-recapture study. Pit traps were used to determine whether frogs move out of their breeding habitat. I found that both species were very philopatric. Between the 1993 and 1994 breeding seasons, 76–86% of individuals were displaced less than 10m and 90–97% were displaced less than 20m. Dispersal was even lower within each breeding season, with 92–95% of individuals being displaced less than 5 m. Pit trapping indicated that some individuals of both species move out of the swamps in late autumn and return at the beginning of the breeding season, in late winter and early spring. Therefore, although displacement may be very restricted, the frogs are likely to move greater distances. The extreme breeding-site philopatry exhibited by G. alba and G. vitellina suggests that movement between disjunct populations is unlikely and that populations in continuous habitat may be relatively isolated from one another by distance alone. This is consistent with previous predictions based on genetic studies, which suggested there was very little migration between populations. These data support the contention that neither species is likely to exist as a metapopulation because recolonization of vacant habitat is improbable.     

How to define nativeness in vagile organisms: lessons from the cosmopolitan moss Bryum argenteum on the island of Tenerife (Canary Islands)

The distinction between native and introduced biotas presents unique challenges that culminate in organisms with high long‐distance dispersal capacities in a rapidly changing world. Bryophytes, in particular, exhibit large distribution ranges, and some species can truly be qualified as cosmopolitan. Cosmopolitan species, however, typically occur in disturbed environments, raising the question of their nativeness throughout their range. Here, we employ genetic data to address the question of the origin of the cosmopolitan, weedy moss Bryum argenteum on the island of Tenerife. The genetic diversity of B. argenteum on Tenerife was comparable to that found in continental areas due to recurrent colonisation events, erasing any signature of a bottleneck that would be expected in the case of a recent colonisation event. The molecular dating analyses indicated that the first colonisation of the island took place more than 100,000 years ago, i.e. well before the first human settlements. Furthermore, the significant signal for isolation‐by‐distance found in B. argenteum within Tenerife points to the substantial role of genetic drift in establishing the observed patterns of genetic variation. Together, the results support the hypothesis that B. argenteum is native on Tenerife; although the existence of haplotypes shared between Tenerife and continental areas suggests that more recent, potentially man‐mediated introduction also took place. While defining nativeness in organisms that are not deliberately introduced, and wherein the fossil record is extremely scarce, is an exceedingly challenging task, our results suggest that population genetic analyses can represent a useful tool to help distinguish native from alien populations.     

Gene dispersal inference across forest patches in an endangered medicinal tree: comparison of model‐based approaches

Propagule dispersal in plants is a fundamental mechanism for colonizing new sites and adapting to changing climates, as well as for maintaining genetic diversity. Contrasting past and current gene dispersal can provide useful insights to gauge the extent of recent human disturbances and guide management strategies. However, research on gene dispersal of plants is not yet exhaustive because evolutionary or environmental impacts are often species‐specific and most existing studies have focused on analysis of dispersal at a single site, which may not be helpful for landscape‐level inferences and management interventions. In the present study, we assessed whether current gene or propagule dispersal would be more restricted than past gene dispersal at multiple patches of the endangered medicinal tree, Prunus africana. We employed eight highly polymorphic microsatellite markers in conjunction with isolation‐by‐distance, spatial genetic structure (SGS), and parentage assignment models to estimate gene dispersal distance in a spatial extent of approximately 400 km². There was no significant difference between gene dispersal distances across the different models (Friedman chi‐squared = 7.286, d.f. = 5, P = 0.2002). Estimates of current gene dispersal distance were comparable to dispersal in the last few generations. However, gene dispersal distance was much shorter in smaller than bigger forest patches. Further, significant (P < 0.05) SGS was detected in most forest patches, with the extent of SGS among adults being stronger in the smaller than bigger patches. These results suggest the need for practicing enrichment plantings in most forest patches, particularly in the smaller ones, to assist gene exchange among individuals and patches. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 887–904.     

Rapid recovery of an insect–plant interaction following habitat loss and experimental wetland restoration

This study examined the impact of wetland habitat loss and isolation on an insect–plant interaction, and the subsequent rate of recovery of the interaction following experimental habitat restoration. We compared herbivore colonisation rates and herbivory damage by ‘Batrachedra’ sp. (Lepidoptera: Coleophoridae) on experimentally placed potted Sporadanthus ferrugineus (Restionaceae) plants at increasing distances (up to 800 m) from an intact habitat (the source population). These tests showed that even a moderate degree of isolation (i.e. greater than 400 m) from the intact wetland habitat caused an almost complete collapse of the insect–plant interaction, at least in the short term. The number of eggs and larvae of colonising ‘Batrachedra’ sp., as well as average larval size and the proportion of S. ferrugineus stems damaged, all decreased logarithmically with increasing distance from the intact habitat, presumably due to dispersal limitation of the herbivore. Subsequently, to test whether the interaction can recover following habitat restoration, we surveyed herbivore colonisation rates and herbivory damage on naturally regenerated S. ferrugineus plants on experimentally restored ‘islands’ at increasing distances (up to 800 m) from an intact habitat. The rate of recovery of the interaction was surprisingly rapid (i.e. between 196 and 308 weeks). The degree of difference in the density of eggs and larvae, and in the proportion of stems damaged with increasing isolation from the intact wetland, gradually diminished over 196 weeks. After 308 weeks there was no significant difference in the insect–plant interaction between the intact wetland sites and any of the experimentally restored sites up to 800 m away. These results suggest that some insect–plant interactions can recover rapidly from habitat loss with restoration management.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Apparent widespread gene flow in the predominantly flightless planthopper Tumidagena minuta

1. To determine whether dispersal biology can predict the pattern of population‐genetic variation among insect populations accurately, allozyme variation was assayed for populations of a saltmarsh planthopper, Tumidagena minuta, in which > 99% of the adults are flightless. 2. The pattern of genetic isolation by distance in T. minuta was compared with that in other insects, to determine whether it was similar to isolation by distance in other sedentary insects. 3. In contrast to predictions, the pattern of isolation by distance in T. minuta was most similar to that seen in the most mobile insects in a recent review of population‐genetic variation in insects. Furthermore, population‐genetic subdivision over a spatial scale of > 400 km was weak. 4. Possible causes of the apparent contradiction between dispersal biology and population‐genetic structure in this species are discussed. The results for T. minuta highlight the fact that although mobility is generally correlated with gene flow in insects, studies of population‐genetic variation must be combined with direct studies of dispersal to understand fully the degree to which populations exchange individuals.     

Spatial connectivity in an adult‐sedentary reef fish with extended pelagic larval phase

Understanding the spatial scale of demographic connectivity in marine reef fishes dispersing pelagic larvae is a challenging task because of the technical difficulties associated with tagging and monitoring the movements of progeny at early life stages. Several studies highlighted a strong importance of local retention with levels of dispersal of ecological significance restricted to short distances. To date little information is available in species where pelagic dispersal lasts for long periods of time. In this work, population structure and connectivity were studied in the grey triggerfish, Balistes capriscus. Grey triggerfish larvae and juveniles remain associated with floating Sargassum sp. beds for an estimated period of 4–7 months before settling on benthic habitats where they remain sedentary as adults. Analysis of genetic variation among populations along the continental shelf of the northern Gulf of Mexico and U.S. east coast, encompassing over 3,100 km of coastline, revealed homogeneous allele frequencies and a weak isolation‐by‐distance pattern. Moment and maximum‐likelihood estimates of dispersal parameters both indicated occurrence of large neighbourhoods with estimates of the dispersal distribution parameter σ of 914 and 780 km, respectively. Simulated distributions of dispersal distances using several distribution functions all featured substantial fractions of long‐distance dispersal events with the 90% percentiles of travel distance prior to settlement averaging 1,809 km. These results suggest a high dependency of local recruitment on the output of nonlocal spawning stocks located hundreds of kilometres away and a reduced role of local retention in this species.     

Modelling the impact of colonisation on genetic diversity and differentiation of forest trees: interaction of life cycle,pollen flow and seed long-distance dispersal

It was shown previously that the long lifespan and juvenile phase of trees strongly attenuate founder effects during colonisation in a diffusive dispersal model. However, this model yielded too slow a colonisation rate in comparison with palynological data for temperate forest trees. Since rare long-distance dispersal events have been shown to increase considerably colonisation rates in population dynamics models, we investigate here the impact of long-distance dispersal on within-population diversity (H(S)) and among-population differentiation (F(ST)) during the colonisation process. We use a stochastic approach and compare several dispersal strategies, ranging from very rare dispersal events of large amplitude to more frequent events of smaller amplitude. Using a simulation approach, which takes into account tree life-history traits, we show that long-distance dispersal events increase colonisation speed, and yield much larger founder effects in comparison with the diffusive model. The two models that include intermediate- and long-distance dispersal events show stronger deviations from experimental F(ST) values during and at the end of the colonisation process than the model with more frequent events of smaller dispersal variance. Furthermore, the introduction of a high level of pollen flow has a much more limited impact on models that include long-distance dispersal than on a diffusive dispersal model. The relatively high H(S) values that were obtained in all models are discussed according to the assumed mutation rate and effective population size. This study is an example of how observed genetic data can provide additional evidence on the best demographic model for a given species or group of species.     

Host habitat patchiness and the distance decay of similarity among gastro-intestinal nematode communities in two species of <Emphasis Type="Italic">Mastomys</Emphasis> (southeastern Senegal)

Beta-diversity, or how species composition changes with geographical distance, has seldom been studied for different habitats. We present here quantitative estimates of the relationship between geographic distance and similarity of parasitic nematode communities in two closely related rodent host species that live in habitats with very different spatial configurations. In southeastern Senegal Mastomys natalensis lives exclusively inside human villages whereas M. erythroleucus is continuously distributed outside villages. Both host species and their gastro-intestinal nematodes were sampled on the same spatial scale. Beta-diversity was found to be higher in parasite communities of M. erythroleucus than in those of M. natalensis, and significantly related to geographic distance in this first species. Even on the local spatial scale studied, host dispersal limitation, and stochastic events, may affect species turnover in nematode communities of M. erythroleucus. In M. natalensis, no relationship was found between geographic distance and nematode community similarity, however, suggesting low host dispersal rates between habitat patches. Together with previous population genetic results, this study illustrates the need for different approaches with regard to dispersal in natural populations and its effect on biodiversity.     

Dispersal and population genetic structure of Telmatherina antoniae,an endemic freshwater Sailfin silverside from Sulawesi,Indonesia

Population genetic structure in the presence of substantial dispersal provides a unique perspective on the evolution of reproductive isolation. We sampled Telmatherina antoniae, an endemic fish species, at 10 sites in Lake Matano, Indonesia. Significant genetic structure (F_ST = 0.03) was found, despite a migration rate of 10.2% and a mean dispersal distance of 13.6 km, estimated by genotype assignment. Neither dispersal distance nor direction differed from random expectations, indicative of no dispersal barrier in Lake Matano. However, Bayesian genotype cluster assignment identified a population structure consisting of four to six clusters that did not coincide with sample site distribution, but explained two to three times more genetic variance than sample site. The mechanism for continued isolation of those genetic clusters is unknown, but assortative mating and temporal isolation are obvious candidates. Our results resolve the apparent paradox of population genetic structure coupled with frequent dispersal, and highlight the importance of considering cryptic genetic structure.