Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral

Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is subdivided into three genetically distinct regions in the Atlantic: Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern Tropical Atlantic (West Africa). Within each region, populations have similar allele frequencies and levels of genetic diversity; indeed, no significant differentiation was found between populations separated by as much as 3000 km, suggesting that this coral species has the ability to disperse over large distances. Gene flow within regions does not, however, translate into connectivity across the entire Atlantic. Instead, substantial differences in allele frequencies across regions suggest that genetic exchange is infrequent between the Caribbean, Brazil and West Africa. Furthermore, markedly lower levels of genetic diversity are observed in the Brazilian and West African populations. Genetic diversity and connectivity may contribute to the resilience of a coral population to disturbance. Isolated peripheral populations may be more vulnerable to human impacts, disease or climate change relative to those in the genetically diverse Caribbean-North Atlantic region.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios

The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish ( Amphiprion polymnus ) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2–6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population ( F _ST = 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.     

Population structure and connectivity of the mountainous star coral,Orbicella faveolata,throughout the wider Caribbean region

As coral reefs continue to decline worldwide, it becomes ever more necessary to understand the connectivity between coral populations to develop efficient management strategies facilitating survival and adaptation of coral reefs in the future. Orbicella faveolata is one of the most important reef‐building corals in the Caribbean and has recently experienced severe population reductions. Here, we utilize a panel of nine microsatellite loci to evaluate the genetic structure of O. faveolata and to infer connectivity across ten sites spanning the wider Caribbean region. Populations are generally well‐mixed throughout the basin (F_ST = 0.038), although notable patterns of substructure arise at local and regional scales. Eastern and western populations appear segregated with a genetic break around the Mona Passage in the north, as has been shown previously in other species; however, we find evidence for significant connectivity between Curaçao and Mexico, suggesting that the southern margin of this barrier is permeable to dispersal. Our results also identify a strong genetic break within the Mesoamerican Barrier Reef System associated with complex oceanographic patterns that promote larval retention in southern Belize. Additionally, the diverse genetic signature at Flower Garden Banks suggests its possible function as a downstream genetic sink. The findings reported here are relevant to the ongoing conservation efforts for this important and threatened species, and contribute to the growing understanding of large‐scale coral reef connectivity throughout the wider Caribbean.     

Landscape features impact connectivity between soil populations: a comparative study of gene flow in earthworms

Landscape features are known to alter the spatial genetic variation of aboveground organisms. Here, we tested the hypothesis that the genetic structure of belowground organisms also responds to landscape structure. Microsatellite markers were used to carry out a landscape genetic study of two endogeic earthworm species, Allolobophora chlorotica (N = 440, eight microsatellites) and Aporrectodea icterica (N = 519, seven microsatellites), in an agricultural landscape in the North of France, where landscape features were characterized with high accuracy. We found that habitat fragmentation impacted genetic variation of earthworm populations at the local scale. A significant relationship was observed between genetic diversity (H_e, A_r) and several landscape features in A. icterica populations and A. chlorotica. Moreover, a strong genetic differentiation between sites was observed in both species, with a low degree of genetic admixture and high F_st values. The landscape connectivity analysis at the regional scale, including isolation by distance, least‐cost path and cost‐weighted distance approaches, showed that genetic distances were linked to landscape connectivity in A. chlorotica. This indicates that the fragmentation of natural habitats has shaped their dispersal patterns and local effective population sizes. Landscape connectivity analysis confirmed that a priori favourable habitats such as grasslands may constitute dispersal corridors for these species.     

Benthic-pelagic coupling on coral reefs: Feeding and growth of Caribbean sponges

Benthic-pelagic coupling and the role of bottom-up versus top-down processes are recognized as having a major impact on the community structure of intertidal and shallow subtidal marine communities. Bottom-up processes, however, are still viewed as principally affecting the outcome of top-down processes. Sponges on coral reefs are important members of the benthic community and provide a crucial coupling between water-column productivity and the benthos. Other than scleractinian corals, sponges dominate many of these habitats where water column productivity is composed of mostly autotrophic and heterotrophic picoplankton that sponges actively filter. While predation upon sponges by invertebrates, fish, and turtles occurs, the sponges Callyspongia vaginalis, Agelas conifera, and Aplysina fistularis from Florida, Belize, and the Bahamas, respectively, exhibit a consistent and significant pattern of greater biomass, rates of growth, and feeding, as does their food supply, with increasing depth. Sponges consume 65-93% of the available particulate food supply and, at all sites, sponges increase in size and growth rate as depth increases, suggesting that food supply and, therefore, bottom-up processes significantly influence the distribution and abundance of sponges in these habitats.     

Seascape analysis reveals regional gene flow patterns among populations of a marine planktonic diatom

We investigated the gene flow of the common marine diatom, Skeletonema marinoi, in Scandinavian waters and tested the null hypothesis of panmixia. Sediment samples were collected from the Danish Straits, Kattegat and Skagerrak. Individual strains were established from germinated resting stages. A total of 350 individuals were genotyped by eight microsatellite markers. Conventional F-statistics showed significant differentiation between the samples. We therefore investigated whether the genetic structure could be explained using genetic models based on isolation by distance (IBD) or by oceanographic connectivity. Patterns of oceanographic circulation are seasonally dependent and therefore we estimated how well local oceanographic connectivity explains gene flow month by month. We found no significant relationship between genetic differentiation and geographical distance. Instead, the genetic structure of this dominant marine primary producer is best explained by local oceanographic connectivity promoting gene flow in a primarily south to north direction throughout the year. Oceanographic data were consistent with the significant F_ST values between several pairs of samples. Because even a small amount of genetic exchange prevents the accumulation of genetic differences in F-statistics, we hypothesize that local retention at each sample site, possibly as resting stages, is an important component in explaining the observed genetic structure.     

Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean

Geographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one-fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long-term biogeographic barrier for Caribbean animals.     

High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin

The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling.     

Modeling the emergence of migratory corridors and foraging hot spots of the green sea turtle

Environmental factors shape the spatial distribution and dynamics of populations. Understanding how these factors interact with movement behavior is critical for efficient conservation, in particular for migratory species. Adult female green sea turtles, Chelonia mydas, migrate between foraging and nesting sites that are generally separated by thousands of kilometers. As an emblematic endangered species, green turtles have been intensively studied, with a focus on nesting, migration, and foraging. Nevertheless, few attempts integrated these behaviors and their trade‐offs by considering the spatial configurations of foraging and nesting grounds as well as environmental heterogeneity like oceanic currents and food distribution. We developed an individual‐based model to investigate the impact of local environmental conditions on emerging migratory corridors and reproductive output and to thereby identify conservation priority sites. The model integrates movement, nesting, and foraging behavior. Despite being largely conceptual, the model captured realistic movement patterns which confirm field studies. The spatial distribution of migratory corridors and foraging hot spots was mostly constrained by features of the regional landscape, such as nesting site locations, distribution of feeding patches, and oceanic currents. These constraints also explained the mixing patterns in regional forager communities. By implementing alternative decision strategies of the turtles, we found that foraging site fidelity and nesting investment, two characteristics of green turtles' biology, are favorable strategies under unpredictable environmental conditions affecting their habitats. Based on our results, we propose specific guidelines for the regional conservation of green turtles as well as future research suggestions advancing spatial ecology of sea turtles. Being implemented in an easy to learn open‐source software, our model can coevolve with the collection and analysis of new data on energy budget and movement into a generic tool for sea turtle research and conservation. Our modeling approach could also be useful for supporting the conservation of other migratory marine animals.     

Development and characterization of microsatellite loci for two Caribbean Heliconia (Heliconiaceae: H. bihai and H. caribaea)

? Premise of the study: Microsatellite loci were developed to characterize genetic variation and population subdivision in Heliconia bihai and H. caribaea from the Caribbean Islands. ? Methods and Results: A total of 13 new microsatellite markers were developed and characterized in the two Caribbean heliconias. Di-, tri-, and tetranucleotide repeats were identified with one to 17 alleles per locus, and the observed heterozygosity ranged from 0.13 to 0.87. Additionally, cross-species amplification was successful in eight out of 13 loci. ? Conclusions: The microsatellite loci developed have discriminatory potential to be used in genetic characterizations of Caribbean Heliconia. Both H. bihai and H. caribaea are known to have adaptive interactions with their hummingbird pollinators, and the characterized microsatellite markers will be used to study mating system, genetic structure, and phylogeographic patterns in Caribbean Heliconia.     

How river structure and biological traits influence gene flow: a population genetic study of two stream invertebrates with differing dispersal abilities

1. Determined by landscape structure as well as dispersal‐related traits of species, connectivity influences various key aspects of population biology, ranging from population persistence to genetic structure and diversity. Here, we investigated differences in small‐scale connectivity in terms of gene flow between populations of two ecologically important invertebrates with contrasting dispersal‐related traits: an amphipod (Gammarus fossarum) with a purely aquatic life cycle and a mayfly (Baetis rhodani) with a terrestrial adult stage. 2. We used highly polymorphic markers to estimate genetic differentiation between populations of both species within a Swiss pre‐alpine catchment and compared these results to the broader‐scale genetic structure within the Rhine drainage. Landscape genetic approaches were used to test for correlations of genetic and geographical structures and in‐stream barrier effects. 3. We found overall very weak genetic structure in populations of B. rhodani. In contrast, G. fossarum showed strong genetic differentiation, even at spatial scales of a few kilometres, and a clear pattern of isolation by distance. Genetic diversity decreased from downstream towards upstream populations of G. fossarum, suggesting asymmetric gene flow. Correlation of genetic structure with landscape topography was more pronounced in the amphipod. Our study also indicates that G. fossarum might be capable of dispersing overland in headwater regions and of crossing small in‐stream barriers. 4. We speculate that differences in dispersal capacity but also habitat specialisation and potentially the extent of local adaptation could be responsible for the differences in genetic differentiation found between the two species. These results highlight the importance of taking into account dispersal‐related traits when planning management and conservation strategies.     

cid: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries

cid is a computational tool developed in the Web environment to process cloned DNA fragments with the objective of masking the vector and adaptor regions, detecting the presence of microsatellites and designing the most appropriate primer pairs for the amplification of the identified repetitive sequences. This entire process is executed by the user in a simple and automated manner with the data input as a Zip file of chromatograms or a multiFASTA file. Thus, it is possible to analyse dozens of sequences at the same time, optimizing data processing and the search for the information of interest. cid is freely available on http://www.shrimp.ufscar.br/cid/index.php.     

How mechanisms of habitat preference evolve and promote divergence with gene flow

Habitat preference may promote adaptive divergence and speciation, yet the conditions under which this is likely are insufficiently explored. We use individual‐based simulations to study the evolution and consequence of habitat preference during divergence with gene flow, considering four different underlying genetically based behavioural mechanisms: natal habitat imprinting, phenotype‐dependent, competition‐dependent and direct genetic habitat preference. We find that the evolution of habitat preference generally requires initially high dispersal, is facilitated by asymmetry in population sizes between habitats, and is hindered by an increasing number of underlying genetic loci. Moreover, the probability of habitat preference to emerge and promote divergence differs greatly among the underlying mechanisms. Natal habitat imprinting evolves most easily and can allow full divergence in parameter ranges where no divergence is possible in the absence of habitat preference. The reason is that imprinting represents a one‐allele mechanism of assortative mating linking dispersal behaviour very effectively to local selection. At the other extreme, direct genetic habitat preference, a two‐allele mechanism, evolves under restricted conditions only, and even then facilitates divergence weakly. Overall, our results indicate that habitat preference can be a strong reproductive barrier promoting divergence with gene flow, but that this is highly contingent on the underlying preference mechanism.     

A simulation-based evaluation of methods for inferring linear barriers to gene flow

Different analytical techniques used on the same data set may lead to different conclusions about the existence and strength of genetic structure. Therefore, reliable interpretation of the results from different methods depends on the efficacy and reliability of different statistical methods. In this paper, we evaluated the performance of multiple analytical methods to detect the presence of a linear barrier dividing populations. We were specifically interested in determining if simulation conditions, such as dispersal ability and genetic equilibrium, affect the power of different analytical methods for detecting barriers. We evaluated two boundary detection methods (Monmonier's algorithm and WOMBLING), two spatial Bayesian clustering methods (TESS and GENELAND), an aspatial clustering approach (STRUCTURE), and two recently developed, non-Bayesian clustering methods [PSMIX and discriminant analysis of principal components (DAPC)]. We found that clustering methods had higher success rates than boundary detection methods and also detected the barrier more quickly. All methods detected the barrier more quickly when dispersal was long distance in comparison to short-distance dispersal scenarios. Bayesian clustering methods performed best overall, both in terms of highest success rates and lowest time to barrier detection, with GENELAND showing the highest power. None of the methods suggested a continuous linear barrier when the data were generated under an isolation-by-distance (IBD) model. However, the clustering methods had higher potential for leading to incorrect barrier inferences under IBD unless strict criteria for successful barrier detection were implemented. Based on our findings and those of previous simulation studies, we discuss the utility of different methods for detecting linear barriers to gene flow.     

The reproductive biology of closely related coral species: gametogenesis in<Emphasis Type="Italic"> Madracis</Emphasis> from the southern Caribbean

Reproductive patterns were studied in closely related coral species of the genus Madracis on Curaçao, Netherlands Antilles. Gonadal development of six sympatric species was examined over a 13-month period. Reproductive differences among Madracis species are small. All species are hermaphroditic brooders and show similar patterns in gamete development. Timing of gamete maturation is positively correlated with seawater temperature in all species. Oocyte development typically begins in June and precedes the development of spermaries. Mature gametes, male and female, are present from August to November when seawater temperatures reach their yearly maximum. Developmental pathways for male and female gametes are identical among species. Interspecific differences exist in the number and size of oocytes. Our data indicates that differences in gametogenic development between closely related, but ecologically different subspecies are small or absent and do not necessarily match with species separations based on morphological criteria.Communicated by Topic Editor D. Barnes     

Marine stepping‐stones: Connectivity of Mytilus edulis populations between offshore energy installations

Recent papers have suggested that epifaunal organisms use artificial structures as stepping‐stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the blue mussel, Mytilus edulis, was expected to follow a pattern predicted by a particle tracking model (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal subpopulations. The fixation coefficient F_ST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping‐stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters.     

The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data

Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck , M-ratio and msvar ), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.     

Complex migration and the development of genetic structure in subdivided populations: an example from Caribbean coral reef ecosystems

A matrix‐based projection model is used in conjunction with the results of a coupled bio‐physical dispersal model to examine the spread of alleles through subdivided populations over time, and the associated development of genetic structural patterns. Applying this approach, it becomes possible to quantitatively evaluate the contribution of spatially explicit migration towards patterns of genetic structure observed in the field. To provide a concrete example, the model was used to examine genetic dispersal between coral reef patches of the Caribbean. Using generic life‐history parameters, the model shows the formation of a strong genetic break between eastern and western patches, as well as the development of a gradient along the length of the Bahamian archipelago, corresponding with evidence previously collected for coral and fish species. The data also suggest that Jamaica and the Cayman Islands are important stepping stones between the reefs of the northern Caribbean (Hispaniola and the Bahamas) and the Mesoamerican Barrier Reef. The model provides an effective means of evaluating regional‐scale genetic connectivity through time and identifying natural clusters of genetic exchange.     

Its all about connections: hubs and invasion in habitat networks

During the early stages of invasion, the interaction between the features of the invaded landscape, notably its spatial structure, and the internal dynamics of an introduced population has a crucial impact on establishment and spread. By approximating introduction areas as networks of patches linked by dispersal, we characterised their spatial structure with specific metrics and tested their impact on two essential steps of the invasion process: establishment and spread. By combining simulations with experimental introductions of Trichogramma chilonis (Hymenoptera: Trichogrammatidae) in artificial laboratory microcosms, we demonstrated that spread was hindered by clusters and accelerated by hubs but was also affected by small‐population mechanisms prevalent for invasions, such as Allee effects. Establishment was also affected by demographic mechanisms, in interaction with network metrics. These results highlight the importance of considering the demography of invaders as well as the structure of the invaded area to predict the outcome of invasions.