Are populations of coral reef fish open or closed?

A rapid increase in tropical species of grouper (Perciformes: Serranidae) in the temperate waters, the Goto Islands, Japan

Global warming has resulted in rapid poleward shifts in the geographical distributions of many tropical fish species. This study conducted daily market surveys from 2008 to 2013 to investigate catch trends of seven commercially important grouper species in the temperate Goto Islands, Japan. Our results revealed that the catch numbers of tropical grouper species increased rapidly by an average of 5.9-fold (12.3-fold at maximum) within six years, whereas the temperate and subtropical species did not exhibit substantial changes. Based on the findings of several previous studies, the rapid increase in the number of tropical groupers in temperate waters was most likely caused by the successful settlement of larvae transported from tropical waters. Large-scale ocean currents may facilitate larval transport from tropical waters because the Goto Islands face the Tsushima Warm Current, which branches from the Kuroshio Current. Meanwhile, the transition processes of size distribution in tropical groupers suggest a possible hypothesis that adults migrating from tropical waters first settle in temperate waters and then enhance their populations by reproduction. Further studies are required to determine how tropical grouper species settle and how their populations increase in temperate waters.

Broad-scale analysis of fish community data suggests critical need to support regional connectivity of coral reefs

Connectivity is vital for the biodiversity and functioning of marine ecosystems. It is known to be important for coral reefs, but the scales at which connectivity effects matter-and, correspondingly, the scales at which management responses are needed-are poorly understood in marine systems. We used 23 years of fish monitoring data collected from ~50 different coral reefs by the Australian Institute of Marine Science, together with a range of geographic data layers (including the Allen Coral Atlas) and additional network analysis, to explore the balance of local and regional influence on fish communities. Variance partitioning indicated that 42% of the variance in fish community composition could be explained by regional effects or their interaction with coarse-grained local influences (habitat). The variance explained by regional influences was divided evenly between measures that capture location on environmental gradients (e.g., proximity to coastal shelf, latitude) and cross-scale centrality measures of reef location within a broader reef network. A total of 11% of variance could be directly or indirectly attributed to management. Our results provide clear evidence that management and restoration of reefs across the globe must consider both local and regional influences on reef-associated organisms and highlight the potential benefits of improving connectivity in human-dominated coastal seascapes.

Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery

Dispersal of eggs and larvae from spawning sites is critical to the population dynamics and conservation of marine fishes. For overfished species like critically endangered Nassau grouper (Epinephelus striatus), recovery depends on the fate of eggs spawned at the few remaining aggregation sites. Biophysical models can predict larval dispersal, yet these rely on assumed values of key parameters, such as diffusion and mortality rates, which have historically been difficult or impossible to estimate. We used in situ imaging to record three-dimensional positions of individual eggs and larvae in proximity to oceanographic drifters released into egg plumes from the largest known Nassau grouper spawning aggregation. We then estimated a diffusion-mortality model and applied it to previous years' drifter tracks to evaluate the possibility of retention versus export to nearby sites within 5 days of spawning. Results indicate that larvae were retained locally in 2011 and 2017, with 2011 recruitment being a substantial driver of population recovery on Little Cayman. Export to a nearby island with a depleted population occurred in 2016. After two decades of protection, the population appears to be self-replenishing but also capable of seeding recruitment in the region, supporting calls to incorporate spawning aggregation protections into fisheries management.

Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific

The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the Φ_ST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.

A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific

Coupled with geological and geographical history, climatic oscillations during the Pleistocene period had remarkable effects on species biodiversity and distribution along the northwestern Pacific. To detect the population structure and demographic history of Odontamblyopuslacepedii, 547-bp fragments of the mitochondrial DNA control region were sequenced. A low level of nucleotide diversity (0.0065 ± 0.0037) and a high level of haplotype diversity (0.98 ± 0.01) was observed. The Maximum Likelihood (ML) and Bayesian Inference phylogenetic trees showed no significant genealogical structure corresponding to sampling locations. The results of AMOVA and pairwise F_ST values revealed some significant genetic differentiation among populations, and the isolation by distance (IBD) analysis supported that the genetic differentiation was associated with the geographic distances. The demographic history of O.lacepedii examined by neutrality tests, mismatch distribution analysis, and Bayesian Skyline Plots (BSP) analysis suggested a sudden population expansion, and the expansion time was estimated to be around the Pleistocene. We hypothesize that the climate changes during the Pleistocene, ocean currents, and larval dispersal capabilities have played an important role in shaping contemporary phylogeographic pattern and population structure of O.lacepedii.

Local connections and the larval competency strongly influence marine metapopulation persistence

The relationship between metapopulation stability and connectivity has long been investigated in ecology, however, most of these studies are focused on theoretical species and habitat networks, having limited ability to capture the complexity of real-world metapopulations. Network analysis became more important in modeling connectivity, but it is still uncertain which network metrics are reliable predictors of persistence. Here we quantify the impact of connectivity and larval life history on marine metapopulation persistence across the complex seascape of southeast Australia. Our work coupled network-based approaches and eigenanalysis to efficiently estimate metapopulation-wide persistence and the subpopulation contributions. Larval dispersal models were used to quantify species-specific metapopulation connectivity for five important fisheries species, each summarized as a migration matrix. Eigenanalysis helped to reveal metapopulation persistence and determine the importance of node-level network properties. Across metapopulations, the number of local outgoing connections was found to have the largest impact on metapopulation persistence, implying these hub subpopulations may be the most influential in real-world metapopulations. Results also suggest the length of the pre-competency period may be the most influential parameter on metapopulation persistence. Finally, we identified two major hot spots of local connectivity in southeast Australia, each contributing strongly to multispecies persistence. Managers and ecologists would benefit by employing similar approaches in making more efficient and more ecologically informed decisions and focusing more on local connectivity patterns and larval competency characteristics to better understand and protect real-world metapopulation persistence. Practically this could mean developing more marine protected areas at shorter distances and supporting collaborative research into the early life histories of the species of interest.

Stochastic nature of larval dispersal at sea

The movement of individuals across landscapes remains a fundamental process in population and community ecology. All species have developed a capacity to disperse but this process remains elusive in organisms with complex life-cycles, and none more so than in the marine environment. Here, most organisms have developed a two-phased life-cycle, leaving the risky business of dispersing through the open ocean to their very small and intractable larval offspring. To this day, quantifying dispersal patterns in marine seascapes remains a significant challenge, and yet it is critical to the way we preserve marine ecosystems and the services they provide. In this issue of Molecular Ecology, Catalano et al. (2021) present one of the first longitudinal studies to demonstrate the stochastic nature of larval dispersal. Their work challenges some of our current ideas about marine population connectivity and provides new methodological insights to study its temporal dimension.

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only 1 year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects population genetics. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

Reconciling seascape genetics and fisheries science in three codistributed flatfishes

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits.

Diversity patterns of reef fish along the Brazilian tropical coast

Causal mechanisms for broad-scale reef fish diversity patterns are poorly understood and current knowledge is limited to trends of species richness. This work compared the effects of ecological drivers on components of fish diversity across reefs spanning over 2.000 km of the tropical Brazilian coastline. A quarter of communities' diversity is accountable to common and dominant species, while remaining species are rare. Low-latitude sites were more diverse in rare species. Communities along the coast share common and dominant species, which display high densities across all reefs, but differ in rare species that show abundance peaks in particular reef morphotypes. The disproportionate distribution of rare species reveals a higher vulnerability of these communities to impacts and stochastic density fluctuations. Uneven conservation efforts directed to these morphotypes pose a threat to the maintenance of a paramount component of the reef fish diversity represented by rare species.

Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region

Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (F_ST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.

Do differences in mating behaviour lead to differences in connectivity patterns of reef fishes? Insights from two sympatric surgeonfish species in the Indian Ocean

Disentangling the contribution of biotic and abiotic factors in the structuring of the genetic diversity of reef species is critical to illuminate the diversification of evolutionary lineages in marine environment. Howevr, previous studies have mainly focused on determining the influence of pelagic larval duration on the connectivity and demographic history of reef fishes, whereas few studies have examined the effects of other biotic factors, such as mating behaviour and habitat preference. Here, we use mitochondrial DNA (ATPase 6/8) and ten microsatellite loci to compare the population genetic structure and demographic history of the spawning aggregating Acanthurus triostegus with the monogamous spawning Acanthurus leucosternon. Pairwise comparisons and discriminant analysis of principal components showed that the genetic structuring patterns of the two species are not consistent with the influence of mating behaviour, suggesting the possible role of other biotic and abiotic factors. However, demographic history estimates revealed that these species may have responded differently to sea level fluctuations during the glacial maxima.

Relationship between swimming capacities and morphological traits of fish larvae at settlement stage: a study of several coastal Mediterranean species

Experimental measurements were made in the laboratory to determine the swimming capacities of settlement-stage fish larvae of several Mediterranean coastal species collected from the nearshore waters of Corsica, France. Critical swimming speed (U_crit , cm s^-1 ) was measured to provide a realistic laboratory estimate of in situ swimming speed. Morphometric traits were measured to assess potential predictors of a species' swimming ability and, when possible, daily otolith increments were used to estimate age. Observed swimming speeds were consistent with other temperate species and demonstrated that the tested species are competent swimmers and not passive components of their environment. Morphological traits varied in their correlation with U_crit across groups and species. Direct measurements of morphological traits were better predictors than calculated ratios. Pelagic larval duration had little relationship with swimming speed among species for which daily otolith increments were counted. In addition to expanding the database on swimming capacities of settlement-stage fish larvae in the Mediterranean Sea, this study also developed methods that simplify the assessment of larval fish swimming ability. Swimming speed data are essential for improving larval dispersal models and for predicting recruitment rates in coastal fish populations.

Life-history characteristics of an exploited bonefish Albula glossodonta population in a remote South Pacific atoll

Bonefishes Albula spp. are important components of subsistence fisheries and lucrative sport fishing industries throughout their circumtropical distribution. In Oceania, however, Albula spp. have historically been overexploited and there is a growing need to balance the demands of competing fishing sectors, making the description of their life history a regional priority. To this aim, we collected biological samples from Albula spp. of Anaa atoll, French Polynesia, to identify the species that compose the stock and estimate their life-history parameters including age, growth, reproduction and natural mortality. Our results indicate that Albula glossodonta is the species of bonefish present, with a maximum age that is below the, 20 year longevity of the genus (8 years in males and 10 years in females). Differential growth patterns existed between the two sexes (L_∞ = 58, 78 cm fork length (L_F ) and K = 0.38, 0.21 for males and females, respectively). Males attained sexual maturity at 43 cm L_F (c. 3 years) whereas females matured at 48 cm L_F (c. 4 years) and oocyte production was significantly related to body mass, with a maximum batch fecundity of 1,133,767 oocytes in a 4406 g (70 cm L_F ) female. The gonado-somatic index of harvested fishes indicated that the spawning season extends from March through September. Based on the observation of a, 20 year bonefish at the proximate Tetiaroa Atoll and several empirical models, estimates of natural mortality ranged from 0.21 to 0.68; however, an estimate of 0.21 was deemed most appropriate. This information facilitated the resurgence of a Rahui (temporary fishing closure) and community-based management to protect A. glossodonta during a critical portion of their spawning season and in this context our results provide an important demographic baseline in evaluating the recovery of this fishery.

A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations

Dispersal is one of the main determining factors of population structure. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal patterns between populations or over time is often associated to geographic distance or changing oceanographic barriers. Consequently, detecting structure and variation in dispersal on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the black-faced blenny across a small-scale (2 km) coastline as well as at a larger-scale area (<50 kms). A total of 178 single nucleotide polymorphism markers were used to evaluate relatedness patterns within this well-connected population. In our clustering models we categorized SHORT-range dispersers to be potential local recruits based on their high relatedness within and low relatedness towards other spatial clusters. Local retention and/or dispersal of this potential local recruitment varied across the 2 km coastline with higher frequency of SHORT-range dispersers towards the southwest of the area for adults. An inverse pattern was found for juveniles, showing an increase of SHORT-range dispersers towards the northeast. As we rule out selective movement and mortality from one year to the next, this pattern reveals a complex but not full genetic mixing, and variability in coastal circulation is most likely the main driver of this fine-scale chaotic genetic patchiness within this otherwise homogeneous population. When focusing on the patterns within one recruitment season, we found large differences in temperatures (from approx. 17 °C to 25 °C) as well as pelagic larval duration (PLD) for juveniles from the beginning of the season and the end of the season. We were able to detect fine-scale differences in LONG-range juvenile dispersers, representing distant migrants, depending on whether they were born at the beginning of the season with a longer PLD, or at the end of the reproductive season. The ability to detect such fine-scale dispersal patchiness will aid in our understanding of the underlying mechanisms of population structuring and chaotic patchiness in a wide range of species even with high potential dispersal abilities.

Evidence of local adaptation in a waterfall-climbing Hawaiian goby fish derived from coupled biophysical modeling of larval dispersal and post-settlement selection

Background

Local adaptation of marine and diadromous species is thought to be a product of larval dispersal, settlement mortality, and differential reproductive success, particularly in heterogeneous post-settlement habitats. We evaluated this premise with an oceanographic passive larval dispersal model coupled with individual-based models of post-settlement selection and reproduction to infer conditions that underlie local adaptation in Sicyopterus stimpsoni, an amphidromous Hawaiian goby known for its ability to climb waterfalls.

Results

Our model results demonstrated that larval dispersal is spatio-temporally asymmetric, with more larvae dispersed from the southeast (the Big Island) to northwest (Kaua‘i) along the archipelago, reflecting prevailing conditions such as El Niño/La Niña oscillations. Yet connectivity is nonetheless sufficient to result in homogenous populations across the archipelago. We also found, however, that ontogenetic shifts in habitat can give rise to adaptive morphological divergence when the strength of predation-driven post-settlement selection crosses a critical threshold. Notably, our simulations showed that larval dispersal is not the only factor determining the likelihood of morphological divergence. We found adaptive potential and evolutionary trajectories of S. stimpsoni were greater on islands with stronger environmental gradients and greater variance in larval cohort morphology due to fluctuating immigration.

Conclusions

Contrary to expectation, these findings indicate that immigration can act in concert with selection to favor local adaptation and divergence in species with marine larval dispersal. Further development of model simulations, parameterized to reflect additional empirical estimates of abiotic and biotic factors, will help advance our understanding of the proximate and ultimate mechanisms driving adaptive evolution, population resilience, and speciation in marine-associated species.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1413-4) contains supplementary material, which is available to authorized users.

Long-Distance Benefits of Marine Reserves: Myth or Reality?

Long-distance (>40-km) dispersal from marine reserves is poorly documented; yet, it can provide essential benefits such as seeding fished areas or connecting marine reserves into networks. From a meta-analysis, we suggest that the spatial scale of marine connectivity is underestimated due to the limited geographic extent of sampling designs. We also found that the largest marine reserves (>1000km²) are the most isolated. These findings have important implications for the assessment of evolutionary, ecological, and socio-economic long-distance benefits of marine reserves. We conclude that existing methods to infer dispersal should consider the up-to-date genomic advances and also expand the spatial scale of sampling designs. Incorporating long-distance connectivity in conservation planning will contribute to increase the benefits of marine reserve networks.

Genetic diversity and gene flow of the threatened Brazilian endemic parrotfish Scarus trispinosus (Valenciennes, 1840)

The greenback parrotfish, Scarus trispinosus, is the largest herbivorous fish inhabiting Southwestern Atlantic reefs, and was recently included in the IUCN red list of threatened species as endangered due to the overexploitation of their populations. The aim of this work was to evaluate the existence of structured populations (i.e. genetic unities) along a coast of approximately 2000 km of the NE Brazilian coast. The transferability of 17 primers synthesized for Scarus rubroviolaceus was tested for S. trispinosus and five transferable loci were validated and used. Two localities within the Abrolhos Bank, off the Central Brazilian coast (Corumbau and Caravelas) and in close proximity to the MPA, which encompasses the largest remnants of the S. trispinosus population, exhibited higher levels of genetic richness. Remaining locations, Pernambuco, Porto Seguro and Rio Grande do Norte exhibited lower genetic diversity. We found no genetic differences among sampled localities however, when those samples were gathered into latitudinal groups (northern vs southern) a subtle but significant genetic substructuring was revealed. It is proposed that a combination of high local individual admixture favoured by habitat connectivity drived genetic homogeneity at regional scales while larval dispersal contributed to heterogeneities observed at large scales maintaining gene flow through oceanographic currents.

Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries

Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (∼3 ppt to ∼18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from GenBank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries. Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work. Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population. Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and regional patterns of population connectivity and gene flow.

Collapse, Tipping Points, and Spatial Demographic Structure Arising from the Adopted Migrant Life History

The roles of dispersal and recruitment have long been a focal point in ecology and conservation. The adopted migrant hypothesis proposes a life history in which social learning transmits migratory knowledge between generations of iteroparous fish. Specifically, juveniles disperse from the parental spawning site, encounter and recruit to a local adult population, and learn migration routes between spawning and foraging habitats by following older, experienced fish. Although the adopted migrant life history may apply to many species of pelagic marine fishes, there is scant theoretical or empirical work on the consequent population dynamics. We developed and analyzed a mathematical model of this life history in which the recruitment of juveniles depends on the relative abundance of the local populations and recruitment overlap, which measures the ease with which juveniles are recruited by a nonparental population. We demonstrate that the adopted migrant life history can maintain spatial demographic structure among local populations, that it can also predispose local populations to collapse when a tipping point is crossed, and that recovery after collapse is impaired by reduced recruitment at small local population sizes.

Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar-cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids, identifying 124 interspecific hybrids from a collection of 2,991 coral trout sampled in inshore and mid-shelf reefs of the southern Great Barrier Reef. Hybrids were ubiquitous among reefs, fertile and spanned multiple generations suggesting both ecological and evolutionary processes are acting to maintain species barriers. We elaborate on these finding to investigate the extent of genomic introgression and admixture from 2,271 SNP loci recovered from a ddRAD library of pure and hybrid individuals. An analysis of genomic clines on recovered loci indicates that 261 SNP loci deviate from a model of neutral introgression, of which 132 indicate a pattern of introgression consistent with selection favouring both hybrid and parental genotypes. Our findings indicate genome-wide, bidirectional introgression between two sympatric species of coral reef fishes and provide further support to a growing body of evidence for the role of hybridization in the evolution of coral reef fishes.

Independent estimates of marine population connectivity are more concordant when accounting for uncertainties in larval origins

Marine larval dispersal is a complex biophysical process that depends on the effects of species biology and oceanography, leading to logistical difficulties in estimating connectivity among populations of marine animals with biphasic life cycles. To address this challenge, the application of multiple methodological approaches has been advocated, in order to increase confidence in estimates of population connectivity. However, studies seldom account for sources of uncertainty associated with each method, which undermines a direct comparative approach. In the present study we explicitly account for the statistical uncertainty in observed connectivity matrices derived from elemental chemistry of larval mussel shells, and compare these to predictions from a biophysical model of dispersal. To do this we manipulate the observed connectivity matrix by applying different confidence levels to the assignment of recruits to source populations, while concurrently modelling the intrinsic misclassification rate of larvae to known sources. We demonstrate that the correlation between the observed and modelled matrices increases as the number of observed recruits classified as unknowns approximates the observed larval misclassification rate. Using this approach, we show that unprecedented levels of concordance in connectivity estimates (r = 0.96) can be achieved, and at spatial scales (20-40 km) that are ecologically relevant.

Insight into the population structure of hardhead silverside, Atherinomorus stipes (Teleostei: Atherinidae), in Belize and the Florida Keys using nd2

Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.

Seascape and life-history traits do not predict self-recruitment in a coral reef fish

The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4-0.5% at 0.15 km(2)) and the lagoon scale (0.6-0.8% at approx. 700 km(2)). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.

Life-history predicts past and present population connectivity in two sympatric sea stars

Life‐history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic‐developing sea star, Parvulastra exigua, has lower levels of within‐ and among‐population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima (LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic‐developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic‐developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post‐Pleistocene introgression.

Reconstructing larval growth and habitat use in an amphidromous goby using otolith increments and microchemistry

High-resolution analysis of growth increments, trace element chemistry and oxygen isotope ratios (δ¹⁸ O) in otoliths were combined to assess larval and post-larval habitat use and growth of Awaous stamineus, an amphidromous goby native to Hawai'i. Otolith increment widths indicate that all individuals experience a brief period of rapid growth during early life as larvae and that the duration of this growth anomaly is negatively correlated with larval duration. A protracted high-growth period early in larval life is associated with a lower ratio of Sr:Ca, which may reflect low salinity conditions in nearshore habitats. A distinct shift in δ¹⁸ O (range: 4-5‰) is closely associated with the metamorphic mark in otoliths, indicating that larval metamorphosis occurs promptly upon return to fresh water. Strontium and other trace elements are not as tightly coupled to the metamorphosis mark, but confirm the marine-to-freshwater transition. Integration of microstructural and microchemical approaches reveals that larvae vary substantially in growth rate, possibly in association with habitat differences. Although time and financial costs make it difficult to achieve large sample sizes, present results show that examining even a small number of individuals can lead to novel inferences about early life history in diadromous fishes and illustrates the value of integrating analyses.

Modeled Population Connectivity across the Hawaiian Archipelago

We present the first comprehensive estimate of connectivity of passive pelagic particles released from coral reef habitat throughout the Hawaiian Archipelago. Potential connectivity is calculated using a Lagrangian particle transport model coupled offline with currents generated by an oceanographic circulation model, MITgcm. The connectivity matrices show a surprising degree of self-recruitment and directional dispersal towards the northwest, from the Main Hawaiian Islands (MHI) to the northwestern Hawaiian Islands (NWHI). We identify three predicted connectivity breaks in the archipelago, that is, areas in the mid and northern part of the archipelago that have limited connections with surrounding islands and reefs. Predicted regions of limited connectivity generally match observed patterns of genetic structure reported for coral reef species in the uninhabited NWHI, but multiple genetic breaks observed in the inhabited MHI are not explained by passive dispersal. The better congruence in our modeling results based on physical transport of passive particles in the low-lying atolls of the uninhabited NWHI, but not in the anthropogenically impacted high islands of the MHI begs the question: what ultimately controls connectivity in this system?

Genetic diversity and population structure of Hyporhamphus sajori (Beloniformes: Hemiramphidae) inferred from mtDNA control region and msDNA markers

This paper presents preliminary data on the genetic diversity and population structure of Hyporhamphus sajori by analysing a 510 bp sequence in the mitochondrial DNA (mtDNA) control region and eight polymorphic microsatellite DNA loci. The H. sajori individuals from different locations were indistinguishable from one another based on mtDNA variation, as demonstrated with a neighbour-joining tree and minimum spanning network analysis. Low level of genetic diversity and the absence of population structure in H. sajori from the north-west Pacific Ocean, combined with negative indices for neutral evolution in these populations, suggest that H. sajori underwent a population expansion after a recent bottleneck. The Structure analysis, discriminant analysis of principal components (DAPC) and the pair-wise Φ_ST values after Bonferroni correction using eight microsatellite loci provided no clear inference on the genetic differentiation and thus no evidence of population structure of H. sajori. The genetic connectivity among locations might be due to fairly high gene flow via transport of eggs and larvae by the Kuroshio and Tsushima warm current. This study revealed low levels of genetic diversity and suggested high level of contemporary gene flow among populations of H. sajori in the East (Japan) Sea and the Pacific Ocean.

Near-bottom circulation and dispersion of sediment containing Alexandrium fundyense cysts in the Gulf of Maine during 2010-2011

The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010-May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s^-1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment are small compared to the inventory of cysts in the upper few centimeters of sediment.

Interspecific, spatial and temporal variability of self-recruitment in anemonefishes

Polymorphic microsatellite DNA parentage analysis was used to investigate the spatio-temporal variability of self-recruitment in populations of two anemonefishes: Amphiprion ocellaris and A. perideraion. Tissue samples of A. ocellaris (n = 364) and A. perideraion (n = 105) were collected from fringing reefs around two small islands (Barrang Lompo and Samalona) in Spermonde Archipelago, Indonesia. Specimens were genotyped based on seven microsatellite loci for A. ocellaris and five microsatellite loci for A. perideraion, and parentage assignment as well as site fidelity were calculated. Both species showed high levels of self-recruitment: 65.2% of juvenile A. ocellaris in Samalona were the progeny of parents from the same island, while on Barrang Lompo 47.4% of A. ocellaris and 46.9% of A. perideraion juveniles had parents from that island. Self-recruitment of A. ocellaris in Barrang Lompo varied from 44% to 52% between the two sampling periods. The site fidelity of A. ocellaris juveniles that returned to their reef site in Barang Lompo was up to 44%, while for A. perideraion up to 19%. In Samalona, the percentage of juveniles that returned to their natal reef site ranged from 8% to 11%. Exchange of progeny between the two study islands, located 7.5 km apart, was also detected via parentage assignments. The larger Samalona adult population of A. ocellaris was identified as the parents of 21% of Barrang Lompo juveniles, while the smaller adult population on Barrang Lompo were the parents of only 4% of Samalona juveniles. High self-recruitment and recruitment to nearby island reefs have important implications for management and conservation of anemonefishes. Small MPAs, preferably on every island/reef, should ensure that a part of the population is protected to enable replenishment by the highly localised recruitment behaviour observed in these species.

Fishery management priorities vary with self‐recruitment in sedentary marine populations

Fisheries science often uses population models that assume no external recruitment, but nearshore marine populations harvested on small scales of <200 km often exhibit an unknown mix of self-recruitment and recruitment from external sources. Since empirical determination of self-recruitment vs. external recruitment is difficult, we used a modeling approach to examine the sensitivity of fishery management priorities to recruitment assumptions (self [closed], external [open]) in a local population of harvested giant clams (Tridacna maxima) on Mo'orea, French Polynesia. From 2006 to 2010, we measured growth, fecundity, recruitment, and survival (resulting from natural and fishing mortality). We used these data to parameterize both a closed (complete self-recruitment) and an open (no self-recruitment) integral projection model (IPM), and then calculated elasticities of demographic rates (growth, survival, recruitment) to future population abundance in 20 years. The models' lowest projected abundance was 93.4% (95% CI, [86.5%, 101.8%]) of present abundance, if the local population is entirely open and the present level of fishing mortality persists. The population will exhibit self-sustaining dynamics (1 ≤ λ ≤ 1.07) as for a closed population if the ratio of self-recruits per gram of dry gonad is >0.775 (equivalent to 52.85% self-recruitment under present conditions). Elasticity analysis of demographic parameters indicated that future abundance can most effectively be influenced by increasing survival of mid-sized clams (∼80–120 mm) if the population is self-sustaining, and by increasing survival of juvenile clams (∼40–70 mm) if the population is non-self-sustaining (as for an open population). Our results illustrate that management priorities can vary depending on the amount of self-recruitment in a local population.

Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops)

Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in each country or between the two countries. We used isolation-by-distance theory to estimate the scale of dispersal from microsatellite data in the black rockfish, Sebastes melanops, and compared this estimate with the distance between RCAs that would protect this species. Within each country, we found that the distance between RCAs was generally within the confidence intervals of mean dispersal per generation. The distance between these two RCA networks, however, was greater than the average dispersal per generation. The data were also consistent with a genetic break between southern Oregon and central Oregon. We discuss whether additional nearshore RCAs in southern Oregon and Washington would help promote connectivity between RCA's for shallow-water rockfishes.

The effects of mysid grazing on kelp zoospore survival and settlement

Recent studies have indicated that long-distance dispersal by kelp zoospores may play an important role in the colonization of newly exposed rocky habitats and in the recovery of recently disturbed kelp forests. This may be facilitated by the vertical transport of zoospores into the shallower portions of the water column where they are exposed to greater alongshore currents that increase their dispersal potential. However, this vertical transport can also expose them to elevated irradiances and enhanced grazing by zooplankton, both of which negatively impact zoospore survival and settlement. In this study, we used plankton tows to show that zooplankton (mysids) were at least seven times more abundant in the surface waters than near the benthos along the edge of a large kelp forest at the time of our spring sampling. We then used feeding experiments and epifluorescence microscopy to verify that these mysids grazed on kelp zoospores. Finally, we conducted laboratory experiments to show that grazing by these mysids over a 12 h period reduced kelp zoospore settlement by at least 50% relative to treatments without grazing. Together with previous studies that have revealed the impacts of high irradiance on zoospore survival and settlement, our study indicates that the vertical transport of kelp zoospores into the shallower portions of the water can also expose them to significantly increased mortality from mysid grazing. Thus, if these patterns are consistent over broader temporal and geographic scales, vertical transport may not be a viable method for sustained long-distance zoospore dispersal.

Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

Limited contemporary gene flow and high self-replenishment drives peripheral isolation in an endemic coral reef fish

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long-term persistence of these species following local extinction. This study explored population connectivity in the ecologically-specialized endemic three-striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self-replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self-replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self-replenishment (95%), and low contemporary abundance.

Nonsignificant isolation by distance implies limited dispersal

Understanding the scale of dispersal is an important consideration in the conservation and management of many species. However, in species in which the high-dispersal stage is characterized by tiny gametes or offspring, it may be difficult to estimate dispersal directly. This is the case for many marine species, whose pelagic larvae are dispersed by ocean currents by several days or weeks before beginning a benthic, more sedentary, adult stage. As consequence of the high-dispersal larval stage, many marine species have low genetic structure on large spatial scales (Waples 1998; Hellberg 2007). Despite the high capacity for dispersal, some tagging studies have found that a surprising number of larvae recruit into the population they were released from (self-recruitment). However, estimates of self-recruitment are not informative about mean dispersal between subpopulations. To what extent are limited dispersal estimates from tagging studies compatible with high potential for dispersal and low genetic structure? In this issue, a study on five species of coral reef fish used isolation by distance (IBD) between individuals to estimate mean dispersal distances (Puebla et al. 2012). They found that mean dispersal was unexpectedly small (<50 km), given relatively low IBD slopes and long pelagic durations. This study demonstrates how low genetic structure is compatible with limited dispersal in marine species. A comprehensive understanding of dispersal in marine species will involve integrating methods that estimate dispersal over different spatial and temporal scales. Genomic data may increase power to resolve these issues but must be applied carefully to this question.

Evidence of stable genetic structure across a remote island archipelago through self-recruitment in a widely dispersed coral reef fish

We used microsatellite markers to assess the population genetic structure of the scribbled rabbitfish Siganus spinus in the western Pacific. This species is a culturally important food fish in the Mariana Archipelago and subject to high fishing pressure. Our primary hypothesis was to test whether the individuals resident in the southern Mariana Island chain were genetically distinct and hence should be managed as discrete stocks. In addition to spatial sampling of adults, newly-settled individuals were sampled on Guam over four recruitment events to assess the temporal stability of the observed spatial patterns, and evidence of self-recruitment. We found significant genetic structure in S. spinus across the western Pacific, with Bayesian analyses revealing three genetically distinct clusters: the southern Mariana Islands, east Micronesia, and the west Pacific; with the southern Mariana Islands being more strongly differentiated from the rest of the region. Analyses of temporal samples from Guam indicated the southern Mariana cluster was stable over time, with no genetic differentiation between adults versus recruits, or between samples collected across four separate recruitment events spanning 11 months. Subsequent assignment tests indicated seven recruits had self-recruited from within the Southern Mariana Islands population. Our results confirm the relative isolation of the southern Mariana Islands population and highlight how local processes can act to isolate populations that, by virtue of their broad-scale distribution, have been subject to traditionally high gene flows. Our results add to a growing consensus that self-recruitment is a highly significant influence on the population dynamics of tropical reef fish.

Assessing dispersal patterns of fish propagules from an effective mediterranean marine protected area

Successfully enforced marine protected areas (MPAs) have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called ‘recruitment subsidy’, the augmented production of propagules (i.e. eggs and larvae) due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea) using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1) spatial distribution patterns of individuals (post-settlers and adults) assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2) Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration) and 3) a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward) from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices), suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings provide crucial information for the design of MPAs and MPA networks effective to replenish fish stocks and enhance fisheries in unprotected areas.

Global-scale relationships between colonization ability and range size in marine and freshwater fish

Although fish range sizes are expected to be associated with species dispersal ability, several studies failed to find a clear relationship between range size and duration of larval stage as a measure of dispersal potential. We investigated how six characteristics of the adult phase of fishes (maximum body length, growth rate, age at first maturity, life span, trophic level and frequency of occurrence) possibly associated with colonization ability correlate with range size in both freshwater and marine species at global scale. We used more than 12 million point records to estimate range size of 1829 freshwater species and 10068 marine species. As measures of range size we used both area of occupancy and extent of occurrence. Relationships between range size and species traits were assessed using Canonical Correlation Analysis. We found that frequency of occurrence and maximum body length had a strong influence on range size measures, which is consistent with patterns previously found (at smaller scales) in several other taxa. Freshwater and marine fishes showed striking similarities, suggesting the existence of common mechanisms regulating fish biogeography in the marine and freshwater realms.