Find research datasets worth reusing

Data from: Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution

Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.

opencc-zeroDec 2015View details →

Data from: Seasonal population and individual niche dynamics in a tetra fish in the Pantanal wetlands

In seasonal tropical regions, rainfall and/or temporary floods during the wet season generally increase the abundance and diversity of food resources to many consumers as compared to the dry season. Therefore, seasonality can affect intraspecific competition and ecological opportunity, which are two important ecological mechanisms underlying population and individual niche variations. Here, we took advantage of the strong seasonality in the Pantanal wetlands to investigate how within- and between-individual diet variations relate to seasonal population niche dynamics of the tetra fish Astyanax lacustris. We quantified dietary niche using gut contents and stable isotopes. Tetras had higher gut fullness and better body condition in the wet season, suggesting that competition is more intense in the dry season. The population niche was broader in the wet season due to an increase in diet divergence between individuals, in spite of potential stronger competition in the dry season. We posit that low ecological opportunity in the dry season limits the diversifying effect of intraspecific competition, constraining population niche expansion. Our results add new insights on how seasonality affects population and individual diets, indicating that intraspecific competition and ecological opportunity interact to determine temporal niche variations in seasonal environments.

Data from: Meteorological conditions influence short-term survival and dispersal in a reinforced bird population.

A high immediate mortality rate of released animals is an important cause of translocation failure ("release cost"). Post-release dispersal (i.e. the movements from the release site to the first breeding site) has recently been identified as another source of local translocation failure. In spite of their potential effects on conservation program outcomes, little is known about the quantitative effects of these two sources of translocation failure and their interactions with environmental factors and management designs. Based on long-term monitoring data of captive-bred North African houbara bustards Chlamydotis undulata undulata (hereafter, houbara) over large spatial scales, we investigated the relative effects of release (e.g. release group size, period of release), individual (e.g. sex and body condition) and meteorological (e.g. temperature and rainfall) conditions on post-release survival (N = 957 individuals) and dispersal (N = 436 individuals). We found that (i) rainfall and ambient air temperature had, respectively, a negative and a positive effect on houbara post-release dispersal distance, (ii) in interaction with the release period, harsh meteorological conditions had negative impact on the survival of houbara, (iii) density-dependent processes influenced the pattern of departure from the release site and (iv) post-release dispersal distance was male-biased, as natal dispersal of wild birds (although the dispersal patterns and movements may be influenced by different processes in captive-bred and in wild birds). Synthesis and applications. Our results demonstrate that post-release dispersal and mortality costs in translocated species may be mediated by meteorological factors, which in turn can be buffered by the release method. As the consequences of translocation programs on population dynamics depend primarily upon release costs and colonisation process, we suggest that their potential interactions with meteorological conditions must be carefully addressed in future programs (i) through monitoring of short-term post-release mortality to understand its link with environmental conditions; (ii) by carefully choosing the season of release to minimize exposition of inexperienced individuals to harsh conditions and (iii) generalising the use of long-term weather forecast to adapt release effort and staggering releases over several years to buffer meteorological effects.

Data from: Rapid adaptation in large populations with very rare sex: scalings and spontaneous oscillations

Genetic exchange in microbes and other facultative sexuals can be rare enough that evolution is almost entirely asexual and populations almost clonal. But the benefits of genetic exchange depend crucially on the diversity of genotypes in a population. How very rare recombination together with the accumulation of new mutations shapes the diversity of large populations and gives rise to faster adaptation is still poorly understood. This paper analyzes a particularly simple model: organisms with two asexual chromosomes that can reassort during rare matings that occur at a rate r. The speed of adaptation for large population sizes, N, is found to depend on the ratio ∼ log(Nr)/log(N). For larger populations, the r needed to yield the same speed deceases as a power of N. Remarkably, the population undergoes spontaneous oscillations alternating between phases when the fittest individuals are created by mutation and when they are created by reassortment, which—in contrast to conventional regimes—decreases the diversity. Between the two phases, the mean fitness jumps rapidly. The oscillatory dynamics and the strong fluctuations this induces have implications for the diversity and coalescent statistics. The results are potentially applicable to large microbial populations, especially viruses that have a small number of chromosomes. Some of the key features may be more broadly applicable for large populations with other types of rare genetic exchange.

Data from: Can collective memories shape fish distributions? A test, linking space-time occurrence models and population demographics

Social learning can be fundamental to cohesive group living, and schooling fishes have proven ideal test subjects for recent work in this field. For many species, both demographic factors, and inter- (and intra-) generational information exchange are considered vital ingredients in how movement decisions are reached. Yet key information is often missing on the spatial outcomes of such decisions, and questions concerning how migratory traditions are influenced by collective memory, density-dependent and density-independent processes remain open. To explore these issues, we focused on Atlantic herring (Clupea harengus), a long-lived, dense-schooling species of high commercial importance, noted for its unpredictable shifts in winter distribution, and developed a series of Bayesian space-time occurrence models to investigate wintering dynamics over 23 years, using point-referenced fishery and survey records from Icelandic waters. We included covariates reflecting local-scale environmental factors, temporally-lagged prey biomass and recent fishing activity, and through an index capturing distributional persistence over time, derived two proxies for spatial memory of past wintering sites. The previous winter's occurrence pattern was a strong predictor of the present pattern, its influence increasing with adult population size. Although the mechanistic underpinnings of this result remain uncertain, we suggest that a 'wisdom of the crowd' dynamic may be at play, by which navigational accuracy towards traditional wintering sites improves in larger and/or denser, better synchronized schools. Wintering herring also preferred warmer, fresher, moderately stratified waters of lower velocity, close to hotspots of summer zooplankton biomass, our results indicative of heightened environmental sensitivity in younger cohorts. Incorporating spatiotemporal correlation structure and time-varying regression coefficients improved model performance, and validation tests on independent observations one-year ahead illustrate the potential of uniting demographic information and non-stationary models to quantify both the strength of collective memory in animal groups and its relevance for the spatial management of populations.

opencc-zeroDec 2012View details →

Data from: Association of polyandry and sex-ratio drive prevalence in natural populations of Drosophila neotestacea

Selfish genetic elements bias their own transmission to the next generation, even at the expense of the fitness of their carrier. Sex-ratio (SR) meiotic drive occurs when an X-chromosome causes Y-bearing sperm to die during male spermatogenesis, so that it is passed on to all of the male's offspring, which are all daughters. How SR is maintained as a stable polymorphism in the absence of genetic suppressors of drive is unknown. Here, we investigate the potential for the female remating rate to affect SR dynamics in natural populations, using the fly Drosophila neotestacea. In controlled laboratory conditions, females from populations where SR is rare mate more often than females from populations where SR is common. Furthermore, only when males mate multiply does the average fertility of SR males relative to wild-type males decrease to a level that can prevent SR from spreading. Our results suggest that differences in the female mating rate among populations may contribute to SR dynamics in the wild, and thus also affect the outcome of this intragenomic conflict. In line with this, we also present evidence of a localized population crash due to SR that may have resulted from habitat fragmentation along with a reduced mating rate.

opencc-zeroDec 2018View details →

Data from: Quantifying niche availability, niche overlap and competition for recruitment sites in plant populations without explicit knowledge of niche axes.

1. Niche availability, niche overlap and competitive ability are key determinants of the distribution and abundance of species. However, quantifying each of these components is difficult because it is not always possible to identify or measure relevant environmental gradients (niche axes) along which species might partition or compete for niche space. 2. We describe a method that uses seed addition experiments to quantify the number of 'safe-sites' (microsites suitable for a species to recruit from seed) at a location and show how this method can be used to quantify niche availability, niche overlap and competitive ability. We illustrate our approach using two seed addition experiments in grassland. 3. In the first experiment, we added seeds of one native and two exotic grass species, alone and in mixture, to plots that were arrayed along a gradient of soil moisture availability. We show that the three species partitioned safe-sites, implying that all three species could locally co-occur through niche partitioning, in part due to different responses to moisture availability. 4. In the second experiment, we added seeds of three commonly co-occurring native grass species, alone and in mixture, to plots with no obvious environmental gradients. One species outcompeted two others for site occupancy, allowing us to quantify both the degree of niche overlap and the relative ability of each species to compete for safe-site occupancy without a priori knowledge of the niche axes. Results from both experiments demonstrate the fine-scales at which species can partition niches to facilitate co-occurrence. 5. Synthesis. By conceptualising a plot of ground as containing a limited number of microsites that are safe for the recruitment of a given species, and using seed addition experiments to measure both the number of safe-sites and degree of safe-site overlap among species, we show how niche availability, niche overlap and competitive ability can be quantified at fine-scales without a priori knowledge of niche axes. Our approach allows questions about niche availability and competition for shared niche space to be empirically tested, and to examine how these processes vary along environmental gradients to shape species distributions and patterns of co-occurrence.

opencc-zeroDec 2008View details →

Data from: Temporally variable multivariate sexual selection on sexually dimorphic traits in a wild insect population

A widely held view is that the strength and form of natural selection varies in time and space in response to varying ecological forces; however, adequate quantitative evaluations of this are relatively scarce. In this study, we measured the strength and form of sexual selection acting on a suite of male morphological traits in a wild ambush bug (Phymata americana) population at 10 sampling dates over 2 years. We tested the prediction that the strength and direction of sexual selection would be associated with one or more important ecological variables. We found that patterns of multivariate selection varied considerably over time, and even within a season. Yet, for this population, a sexually dimorphic color pattern trait was consistently a target of directional selection. The strength of sexual selection on this trait was related to both sex ratio and density, which is consistent with the idea that ecological factors can play an important role in generating patterns of sexual selection. We also demonstrate that the median strength of linear selection obtained from replicated cross‐sectional methods was qualitatively similar to the estimates obtained from longitudinal methods, providing multiple lines of evidence that the evolution of sexual color dimorphism in this species is attributable to sexual selection.

Data from: Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches

Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.

Data from: Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides

A population's potential for rapid evolutionary adaptation can be estimated from the amount of genetic variation in fitness-related traits. Inshore populations of the mustard hill coral (Porites astreoides) have been shown to be more tolerant to thermal stress than offshore populations, but it is unclear whether this difference is due to long-term physiological acclimatization or genetic adaptation. Here, we evaluated variation in growth rate and survival among 38 families of juvenile recruits of P. astreoides spawned by colonies originating from inshore and offshore locations. Recruits were reared in a common garden for 5 weeks and then subjected to two thermal treatments (28 and 31 °C) for 2.5 weeks. The most significant effects were detected during the first 5 weeks, before thermal stress was applied: 27–30% of variance in growth and 94% of variance in recruit survival was attributable to parental effects. Genotyping of eight microsatellite loci indicated that the high early mortality of some of the recruit families was not due to higher inbreeding. Post treatment, parental effects diminished such that only 10–15% of variance in growth rate was explained, which most likely reflects the dissipation of maternal effects. However, offshore-origin recruits still grew significantly less under elevated temperature compared with inshore-origin recruits. These differences observed in naive juvenile corals suggest that population-level variation in fitness in response to different thermal environments has a genetic basis and could represent raw material for natural selection in times of climate change.

opencc-zeroDec 2011View details →

Data from: Stochastic population dynamics and life-history variation in marine fish species

We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.

Data from: Evolution of sociality in spiders leads to depleted genomic diversity at both population and species level

Across several animal taxa, the evolution of sociality involves a suite of characteristics, a 'social syndrome', that includes cooperative breeding, reproductive skew, primary female biased sex-ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genome-wide diversity in spider species that differ in level of sociality, reproductive skew, and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within population diversity were 6-10 fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genome-wide diversity, likely to limit their evolutionary potential.

opencc-zeroDec 2017View details →

Data from: High genotypic diversity and strong spatial structure in populations of Trifolium alpestre with low seed production

The studies on clonal plant populations indicate that the proportion between clonal and sexual reproduction may be highly variable, depending on the biological characteristics of species and the ecological conditions of habitats. We focused on the genotypic diversity of Trifolium alpestre populations in Estonia. We assayed the genetic diversity, spatial genotypic structure and diversity with the use of allozyme markers. Populations revealed high levels of genotypic diversity and showed strong spatial structure of MLGs. The values of genetic diversity were moderately high. Spatially aggregated, identical genotypes spread up to 15 meters along the linear transects and in 4 m2 plots indicate extensive clonal propagation in populations. However, numerous unique and small-sized clones in transects and quadrates reflect significant contribution from the sexual reproduction. The spatially and temporarily stochastic soil disturbances have evidently opened new opportunities for the successful sexual reproduction from the permanent soil seed bank and have thus avoided the losses of genotypic and genetic diversity. The seed production in all populations during the three study years was low, in average up to 1.5-2.4 seeds per shoot. The almost total lack of seed set from all 57 bagged flower heads of genets grown in a common garden indicates that T. alpestre needs pollinators for the seed production.

Data from: Genetic resources of teak (Tectona grandis Linn. f.) – strong genetic structure among natural populations

Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern of genetic diversity supports the hypothesis that teak has its centre of origin in India, from where it spread eastwards. The analysis of molecular variance (AMOVA) gave an overall highly significant F st value of 0.227—population pairwise F st values were in the range 0.01–0.48. Applying the G″st differentiation parameter, the estimated overall differentiation was 0.632, implying a strong genetic structure among populations. A neighbour-joining (NJ) tree, using the pairwise population matrix of G″st values as input, contained three distinct groups: (1) the eight provenances from Thailand and Laos, (2) the Indian provenances from the dry interior and the moist west coast and (3) the provenances from northern Myanmar. The provenances from southern Myanmar were placed close to the root of the tree together with the three provenances from the semi-moist east coast of India. A Bayesian cluster analysis using the STRUCTURE software gave very similar results, with three main clusters, each containing two sub-clusters, while Bayesian cluster analysis in the Geneland software, exploiting the spatial coordinates of the provenances, resulted in five clusters in accordance with the former results. The implications of the findings for conservation and use of genetic resources of the species are discussed.

Data from: Noninvasive physiological markers demonstrate link between habitat quality, adult sex ratio and poor population growth rate in a vulnerable species, the Cape mountain zebra

Effective conservation and species management requires an understanding of the causes of poor population growth. Conservation physiology uses biomarkers to identify factors that contribute to low individual fitness and population declines. Building on this, macrophysiology can use the same markers to assess how individual physiology varies with different ecological or demographic factors over large temporal and spatial scales. Here, we use a macrophysiological approach to identify the ecological and demographic correlates of poor population growth rates in the Cape mountain zebra metapopulation. We use two non-invasive biomarkers: faecal glucocorticoids as a measure of chronic stress, and faecal androgens as an indicator of male physiological status. We found that faecal glucocorticoid concentrations were highest in the spring prior to summer rainfall, and were elevated in individuals from populations associated with low quality habitat (lower grass abundance). In addition, faecal androgen concentrations were higher in populations with a high proportion of non-breeding stallions (where male:female adult sex ratios exceed 2:1) suggesting sex ratio imbalances may intensify male competition. Finally, population growth rate was negatively associated with faecal glucocorticoid concentrations and female fecundity was negatively associated with faecal androgens, indicating a relationship between hormone profiles and fitness. Together, our results provide cross population evidence for how poor population growth rates in Cape mountain zebra can be linked to individual physiological biomarkers. More broadly, we advocate physiological biomarkers as indicators of population viability, and as a way to evaluate the impact of variable ecological and demographic factors. In addition, conservation physiology can be used to assess the efficacy of management interventions for this subspecies, and this approach could inform models of species' responses to future environmental change.

opencc-zeroDec 2018View details →

Data from: Botfly infections impair the aerobic performance and survival of montane populations of deer mice, Peromyscus maniculatus rufinus

1. Elevations >2000 m represent consistently harsh environments for small endotherms because of abiotic stressors such as cold temperatures and hypoxia. 2. These environmental stressors may limit the ability of populations living at these elevations to respond to biotic selection pressures — such as parasites or pathogens — that in other environmental contexts would impose only minimal energetic- and fitness-related costs. 3. We studied deer mice (Peromyscus maniculatus rufinus) living along two elevational transects (2300 – 4400 m) in the Colorado Rockies and found that infection prevalence by botfly larvae (Cuterebridae) declined at higher elevations. We found no evidence of infections at elevations > 2400 m, but that 33.6% of all deer mice, and 52.2% of adults, were infected at elevations < 2400 m. 4. Botfly infections were associated with reductions in hematocrit levels of 23%, hemoglobin concentrations of 27%, and cold-induced VO2max measures of 19% compared to uninfected individuals. In turn, these reductions in aerobic performance appeared to influence fitness, as infected individuals suffered 19-34% higher overwinter mortality. 5. In contrast to studies at lower elevations, we found evidence indicating that botfly infections influence the aerobic capabilities and fitness of deer mice living at elevations between 2000 – 2400 m. Our results therefore suggest that the interaction between botflies and small rodents is likely highly context-dependent and that, more generally, high-elevation populations may be susceptible to additional biotic selection pressures.

Data from: Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

Data from: Influence of mortality factors and host resistance on the population dynamics of emerald ash borer (Coleoptera: Buprestidae) in urban forests

The success of emerald ash borer (Agrilus planipennis Fairmaire) in North America is hypothesized to be due to both the lack of significant natural enemies permitting easy establishment and a population of trees that lack the ability to defend themselves, which allows populations to grow unchecked. Since its discovery in 2002, a number of studies have examined mortality factors of the insect in forests, but none have examined the role of natural enemies and other mortality agents in the urban forest. This is significant because it is in the urban forest where the emerald ash borer has had the most significant economic impacts. We studied populations in urban forests in three municipalities in Ontario, Canada, between 2010 and 2012 using life tables and stage-specific survivorship to analyze data from a split-rearing manipulative experiment. We found that there was little overall mortality caused by natural enemies; most mortality we did observe was caused by disease. Stage-specific survivorship was lowest in small and large larvae, supporting previous observations of high mortality in these two stages. We also used our data to test the hypothesis that mortality and density in emerald ash borer are linked. Our results support the prediction of a negative relationship between mortality and density. However, the relationship varies between insects developing in the crown and those in the trunk of the tree. This relationship was significant because when incorporated with previous findings, it suggests a mechanism and hypothesis to explain the outbreak dynamics of the emerald ash borer.

Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Harnessing the power of genomic scans, we test the debated 'species pump' hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches, we infer a stepping-stone colonization model and high levels of genetic differentiation across the Virgin Islands, which have been periodically inter-connected until 8 ka. Estimates of divergence times from models based on the site frequency spectrum coincide with a period of repeated connection and fragmentation of the islands at 75–130 ka. These results are consistent with a role of island connectivity cycles in promoting genomic divergence and indicate that the genetic distinctiveness of island populations has persisted despite subsequent and extended interisland connections identified from bathymetric data. We discuss these findings in the broader context of Caribbean biogeography, and more specifically why high levels of genomic divergence across the Virgin Islands associated with repeated connectivity cycles do not actually translate into species diversification.