Genetic structure of Heliofungia actiniformis (Scleractinia: Fungiidae) populations in the Indo-Malay Archipelago: implications for live coral trade management efforts

The fungiid Heliofungia actiniformis is one of the most popular scleractinian coral species in the growing live aquarium trade, with the majority of specimens originating in Indonesia. Details on population connectivity may potentially provide important information with regards to harvest management efforts. Genetic structure was examined, using ribosomal ITS1, 5.8S and partial ITS2 sequences on a small scale among populations in the Spermonde Archipelago, South Sulawesi (up to 65 km distance, Φ_st = 0.09), and on a large scale throughout the Indo-Malay Archipelago (up to 2,900 km distance, Φ_st = 0.26). Significant genetic structuring was found at both scales. Within the Spermonde Archipelago isolation by distance as well as local oceanographic features shaped patterns of genetic connectivity. On the large scale, the data revealed genetically distinct populations in Tomini Bay, New Guinea and the Thousand Islands near Jakarta, and a lack of genetic differentiation among populations lying close to or directly in the path of the Indonesian throughflow: from the central Visayas to the Flores Sea (Φ_ct = 0.32). Whilst the influence of both historical and present day processes on genetic structuring of H. actiniformis populations was revealed, large scale results further emphasised the importance of oceanographic dynamics on larval dispersal patterns in this species. Potential for larval input from surrounding populations, and the increased vulnerability of upstream as well as isolated populations should be taken into consideration when setting future harvest quotas.     

No gene flow across the Eastern Pacific Barrier in the reef‐building coral Porites lobata

The expanse of deep water between the central Pacific islands and the continental shelf of the Eastern Tropical Pacific is regarded as the world's most potent marine biogeographic barrier. During recurrent climatic fluctuations (ENSO, El Niño Southern Oscillation), however, changes in water temperature and the speed and direction of currents become favourable for trans‐oceanic dispersal of larvae from central Pacific to marginal eastern Pacific reefs. Here, we investigate the population connectivity of the reef‐building coral Porites lobata across the Eastern Pacific Barrier (EPB). Patterns of recent gene flow in samples (n = 1173) from the central Pacific and the Eastern Tropical Pacific (ETP) were analysed with 12 microsatellite loci. Results indicated that P. lobata from the ETP are strongly isolated from those in the central Pacific and Hawaii (  = 0.509; P < 0.001). However, samples from Clipperton Atoll, an oceanic island on the eastern side of the EPB, grouped with the central Pacific. Within the central Pacific, Hawaiian populations were strongly isolated from three co‐occurring clusters found throughout the remainder of the central Pacific. No further substructure was evident in the ETP. Changes in oceanographic conditions during ENSO over the past several thousand years thus appear insufficient to support larval deliveries from the central Pacific to the ETP or strong postsettlement selection acts on ETP settlers from the central Pacific. Recovery of P. lobata populations in the frequently disturbed ETP thus must depend on local larval sources.     

Large‐scale connectivity,cryptic population structure,and relatedness in Eastern Pacific Olive ridley sea turtles (Lepidochelys olivacea)

Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial control region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (F_ST = 0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and preexisting microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (F_ST = 0.08, p < .001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (F_ST = 0.103, p < .001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p < .001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin‐wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life history, particularly in light of the natal‐homing paradigm.     

Small-scale genetic connectivity of bicolor damselfish (Stegastes partitus) recruits in Mexican Caribbean reefs

The analysis of genetic similarities among marine populations is a key method for use in connectivity studies intended to provide information for management strategies. The present study aimed at assessing the connectivity levels of subpopulations of bicolor damselfish (Stegastes partitus) recruits at a small scale (~200 km) among four reefs in the Mexican Caribbean. Samples were collected from 13 sites nested in two Marine Parks (Cozumel and Xcalak), one Biosphere Reserve (Chinchorro Bank) and one unprotected area (Mahahual). A total of 713 samples were genetically characterized by means of seven microsatellite DNA markers and were analyzed on a hierarchical basis. A strong genetic structure was detected among sites with a weak but significant genetic structure among reefs, the combination of which has not been reported in previous studies. These results appear to be related to a “sweepstake-chance effect” combined with oceanographic factors. An isolation by distance test, in addition to a hierarchical Bayesian method, revealed that neither distance among sites and reefs nor any of 10 environmental factors tested could be used to explain the genetic differences observed. The results suggest that conservation strategies for S. partitus based on local scales are likely to be effective.     

Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape

Here, we explore the historical and contemporaneous patterns of connectivity among Encholirium horridum populations located on granitic inselbergs in an Ocbil landscape within the Brazilian Atlantic Forest, using both nuclear and chloroplast microsatellite markers. Beyond to assess the E. horridum population genetic structure, we built species distribution models across four periods (current conditions, mid‐Holocene, Last Glacial Maximum [LGM], and Last Interglacial) and inferred putative dispersal corridors using a least‐cost path analysis to elucidate biogeographic patterns. Overall, high and significant genetic divergence was estimated among populations for both nuclear and plastid DNA (Φ_ST(n) = 0.463 and Φ_ST(plastid) = 0.961, respectively, p < .001). For nuclear genome, almost total absence of genetic admixture among populations and very low migration rates were evident, corroborating with the very low estimates of immigration and emigration rates observed among E. horridum populations. Based on the cpDNA results, putative dispersal routes in Sugar Loaf Land across cycles of climatic fluctuations in the Quaternary period revealed that the populations’ connectivity changed little during those events. Genetic analyses highlighted the low genetic connectivity and long‐term persistence of populations, and the founder effect and genetic drift seemed to have been very important processes that shaped the current diversity and genetic structure observed in both genomes. The genetic singularity of each population clearly shows the need for in situ conservation of all of them.     

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.     

From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal

Defining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here, we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia), a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica), sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum‐difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity, which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths, which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species, which is exposed to various threats.     

Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish,Amphiprion perideraion,in the Indo‐Malay Archipelago: inferences from a mitochondrial and microsatellite loci

To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo‐Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker‐derived results. Both marker systems detected a strong overall genetic structure (Φ_ST = 0.096, P < 0.0001; mean D_est = 0.17; F_ST = 0.015, P < 0.0001) and best supported regional groupings (Φ_CT = 0.199 P < 0.0001; F_CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker‐specific results have important implications for conservation efforts concerning this and similar species.     

Range limits and geographic patterns of abundance of the rocky intertidal owl limpet,Lottia gigantea

Aim We evaluate the stability of the range limits of the rocky intertidal limpet, Lottia gigantea, over the last c. 140 years, test the validity of the abundant centre hypothesis, and test indirectly the roles played by recruitment limitation and habitat availability in controlling the range limits. Because this species is size‐selectively harvested, our results also allow us to assess conservation implications. Location The Pacific coast of North America, from northern California to southern Baja California (41.74° N–23.37° N), encompassing the entire range of L. gigantea. Methods The historical and modern distributions of L. gigantea were established using museum data and field observations. Overall and juvenile abundances of local populations were estimated at 25 field sites. The spatial distribution of abundance was evaluated statistically against the predictions of five hypothetical models. The availability of habitat was estimated by measuring the percentage of unavailable sandy beach within cumulative bins of coast across the range of L. gigantea. Results The northern limit of L. gigantea has contracted by c. 2.4° of latitude over recent decades (after 1963), while the southern limit has remained stable. The highest abundances of L. gigantea occur in the centre of its geographic range. Habitat availability is ample in the centre and northern portions of its range, but is generally lacking in the southern range. The northern range is only sparsely populated by adults, with sharp declines occurring north of Monterey Bay (36.80° N). In the southern range, abundance drops precipitously south of Punta Eugenia (27.82° N), coinciding with the region where suitable habitat becomes sparse. Main conclusions Support for the abundant centre hypothesis was found for L. gigantea. Northern populations are characterized as being recruitment‐limited, demographically unstable and prone to local extinctions, while southern populations are suggested to be habitat‐limited. The abundant centre is suggested to result partly from a combination of the indirect effects of human harvesting, generating denser populations of smaller individuals, and larval recruitment from well‐protected offshore rocky islands primarily found in the range centre.     

Phylogeography and genetic connectivity of the marine macro‐alga Sargassum ilicifolium (Phaeophyceae,Ochrophyta) in the northwestern Pacific1

The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise F_ST) and among populations grouped by geographical proximity (Φ_CT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S. ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S. ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.     

Biophysical connectivity explains population genetic structure in a highly dispersive marine species

Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster (Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F _ST of 0.0016 (P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus (P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation (P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

     

Large‐scale,multidirectional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no‐take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of larval connectivity across larger seascapes remain unknown. Here, we apply genetic parentage analysis to investigate larval dispersal patterns for two exploited coral reef groupers (Plectropomus maculatus and Plectropomus leopardus) within and among three clusters of reefs separated by 60–220 km within the Great Barrier Reef Marine Park, Australia. A total of 69 juvenile P. maculatus and 17 juvenile P. leopardus (representing 6% and 9% of the total juveniles sampled, respectively) were genetically assigned to parent individuals on reefs within the study area. We identified both short‐distance larval dispersal within regions (200 m to 50 km) and long‐distance, multidirectional dispersal of up to ~250 km among regions. Dispersal strength declined significantly with distance, with best‐fit dispersal kernels estimating median dispersal distances of ~110 km for P. maculatus and ~190 km for P. leopardus. Larval exchange among reefs demonstrates that established reserves form a highly connected network and contribute larvae for the replenishment of fished reefs at multiple spatial scales. Our findings highlight the potential for long‐distance dispersal in an important group of reef fishes, and provide further evidence that effectively protected reserves can yield recruitment and sustainability benefits for exploited fish populations.     

Population divergences despite long pelagic larval stages: lessons from crocodile icefishes (Channichthyidae)

Dispersal via pelagic larval stages plays a key role in population connectivity of many marine species. The degree of connectivity is often correlated with the time that larvae spend in the water column. The Antarctic notothenioid fishes develop through an unusually long pelagic larval phase often exceeding 1 year. Notothenioids thus represent a prime model system for studying the influence of prolonged larval phases on population structure in otherwise demersal species. Here, we compare the population genetic structure and demographic history of two sub‐Antarctic crocodile icefish species (Chaenocephalus aceratus and Champsocephalus gunnari) from the Scotia Arc and Bouvet Island in the Atlantic sector of the Southern Ocean to delineate the relative importance of species‐specific, oceanographic and paleoclimatic factors to gene flow. Based on 7 (C. aceratus) and 8 (C. gunnari) microsatellites, as well as two mitochondrial DNA markers (cytochrome b, D‐loop), we detect pronounced population genetic structure in both species (amova FSTs range from 0.04 to 0.53). High genetic similarities were found concordantly in the populations sampled at the Southern Scotia Arc between Elephant Island and South Orkney Islands, whereas the populations from Bouvet Island, which is located far to the east of the Scotia Arc, are substantially differentiated from those of the Scotia Arc region. Nonetheless, haplotype genealogies and Bayesian cluster analyses suggest occasional gene flow over thousands of kilometres. Higher divergences between populations of C. gunnari as compared to C. aceratus are probably caused by lower dispersal capabilities and demographic effects. Bayesian skyline plots reveal population size reductions during past glacial events in both species with an estimated onset of population expansions about 25 000 years ago.     

Highly restricted gene flow and deep evolutionary lineages in the giant clam <Emphasis Type="Italic">Tridacna maxima</Emphasis>

The tropical Indo-West Pacific is the biogeographic region with the highest diversity of marine shallow water species, with its centre in the Indo-Malay Archipelago. However, due to its high endemism, the Red Sea is also considered as an important centre of evolution. Currently, not much is known about exchange among the Red Sea, Indian Ocean and West Pacific, as well as connectivity within the Indo-Malay Archipelago, even though such information is important to illuminate ecological and evolutionary processes that shape marine biodiversity in these regions. In addition, the inference of connectivity among populations is important for conservation. This study aims to test the hypothesis that the Indo-Malay Archipelago and the Red Sea are important centres of evolution by studying the genetic population structure of the giant clam Tridacna maxima. This study is based on a 484-bp fragment of the cytochrome c oxidase I gene from 211 individuals collected at 14 localities in the Indo-West Pacific to infer lineage diversification and gene flow as a measure for connectivity. The analysis showed a significant genetic differentiation among sample sites in the Indo-West Pacific (Φ_st = 0.74, P < 0.001) and across the Indo-Malay Archipelago (Φ_st = 0.72, P < 0.001), indicating restricted gene flow. Hierarchical AMOVA revealed the highest fixation index (Φ_ct = 0.8, P < 0.001) when sample sites were assigned to the following regions: (1) Red Sea, (2) Indian Ocean and Java Sea, (3) Indonesian throughflow and seas in the East of Sulawesi, and (4) Western Pacific. Geological history as well as oceanography are important factors that shape the genetic structure of T. maxima in the Indo-Malay Archipelago and Red Sea. The observed deep evolutionary lineages might include cryptic species and this result supports the notion that the Indo-Malay Archipelago and the Red Sea are important centres of evolution. Communicated by Biology Editor Dr. Ruth Gates     

Asymmetric oceanographic processes mediate connectivity and population genetic structure,as revealed by RADseq,in a highly dispersive marine invertebrate (Parastichopus californicus)

Marine populations are typically characterized by weak genetic differentiation due to the potential for long‐distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation by distance (IBD: genetic structure is explained by geographic distance) and (ii) isolation by resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (F_ST = 0.002, p = .001). After modelling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R² = .49) than geographic distance (IBD) (R² = .18), and directional processes played an important role in shaping fine‐scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.     

Local retention,dispersal and fluctuating connectivity among populations of a coral reef fish

The persistence and resilience of marine populations in the face of disturbances is directly affected by connectivity among populations. Thus, understanding the magnitude and pattern of connections among populations and the temporal variation in these patterns is critical for the effective management and conservation of marine species. Despite recent advances in our understanding of marine connectivity, few empirical studies have directly measured the magnitude or pattern of connections among populations of marine fishes, and none have explicitly investigated temporal variation in demographic connectivity. We use genetic assignment tests to track the dispersal of 456 individual larval fishes to quantify the extent of connectivity, dispersal, self-recruitment and local retention within and among seven populations of a coral reef fish (Stegastes partitus) over a three-year period. We found that some larvae do disperse long distances (~200 km); however, self-recruitment was a regular phenomenon. Importantly, we found that dispersal distances, self-recruitment, local retention and the pattern of connectivity varied significantly among years. Our data highlight the unpredictable nature of connectivity, and underscore the need for more, temporally replicated, empirical measures of connectivity to inform management decisions.     

Patterns and persistence of larval retention and connectivity in a marine fish metapopulation

Connectivity, the demographic linking of local populations through the dispersal of individuals, is one of the most poorly understood processes in population dynamics, yet has profound implications for conservation and harvest strategies. For marine species with pelagic larvae, direct estimation of connectivity remains logistically challenging and has mostly been limited to single snapshots in time. Here, we document seasonal and interannual patterns of larval dispersal in a metapopulation of the coral reef fish Amphiprion polymnus. A 3‐year record of larval trajectories within and among nine discrete local populations from an area of approximately 35 km was established by determining the natal origin of settled juveniles through DNA parentage analysis. We found that spatial patterns of both self‐recruitment and connectivity were remarkably consistent over time, with a low level of self‐recruitment at the scale of individual sites. Connectivity among sites was common and multidirectional in all years and was not significantly influenced by seasonal variability of predominant surface current directions. However, approximately 75% of the sampled juveniles could not be assigned to parents within the study area, indicating high levels of immigrations from sources outside the study area. The data support predictions that the magnitude and temporal stability of larval connectivity decreases significantly with increasing distance between subpopulations, but increases with the size of subpopulations. Given the considerable effort needed to directly measure larval exchange, the consistent patterns suggest snapshot parentage analyses can provide useful dispersal estimates to inform spatial management decisions.     

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long‐distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic–Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b‐RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic–Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic–Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic–Ionian locations indicates species‐specific differences in genetic connectivity patterns and warns against generalizing single‐species results to the entire community of rocky shore habitats.     

Life history,larval dispersal,and connectivity in coral reef fish among the Scattered Islands of the Mozambique Channel

The Western Indian Ocean harbors one of the world’s most diverse marine biota yet is threatened by exploitation with few conservation measures in place. Primary candidates for conservation in the region are the Scattered Islands (Îles Éparses), a group of relatively pristine and uninhabited islands in the Mozambique Channel. However, while optimal conservation strategies depend on the degree of population connectivity among spatially isolated habitats, very few studies have been conducted in the area. Here, we use highly variable microsatellite markers from two damselfishes (Amphiprion akallopisos and Dascyllus trimaculatus) with differing life history traits [pelagic larval duration (PLD), adult habitat] to compare genetic structure and connectivity among these islands using classic population structure indices as well as Bayesian clustering methods. All classical fixation indexes F _ST, R _ST, G′_ST, and Jost’s D show stronger genetic differentiation among islands for A. akallopisos compared to D. trimaculatus, consistent with the former species’ shorter PLD and stronger adult site attachment, which may restrict larval dispersal potential. In agreement with these results, the Bayesian analysis revealed clear genetic differentiation among the islands in A. akallopisos, separating the southern group (Bassas da India and Europa) from the center (Juan de Nova) and northern (Îles Glorieuses) islands, but not for D. trimaculatus. Local oceanographic patterns such as eddies that occur along the Mozambique Channel appear to parallel the results reported for A. akallopisos, but such features seem to have little effect on the genetic differentiation of D. trimaculatus. The contrasting patterns of genetic differentiation between species within the same family highlight the importance of accounting for diverse life history traits when assessing community-wide connectivity, an increasingly common consideration in conservation planning.

     

Population structure and conservation genetics of the Oregon spotted frog, <Emphasis Type="Italic">Rana pretiosa</Emphasis>

The Oregon spotted frog (Rana pretiosa) is one of the most threatened amphibians in the Pacific Northwest. Here we analyzed data from 13 microsatellite loci and 298 bp of mitochondrial DNA in frogs collected from 23 of the remaining R. pretiosa populations in order to (1) assess levels of genetic diversity within populations of R. pretiosa, (2) identify the major genetic groups in the species, (3) estimate levels of genetic differentiation and gene flow among populations within each major group, and (4) compare the pattern of differentiation among R. pretiosa populations with that among populations of R. cascadae, a non-endangered congener that also occurs in Oregon and Washington. There is a strong, hierarchical genetic structure in R. pretiosa. That structure includes six major genetic groups, one of which is represented by a single remaining population. R. pretiosa populations have low genetic diversity (average H _e = 0.31) compared to R. cascadae (average H _e = 0.54) and to other ranid frogs. Genetic subdivision among populations is much higher in R. pretiosa than in R. cascadae, particularly over the largest geographic distances (hundreds of kilometers). A joint analysis of migration rates among populations and of effective sizes within populations (using MIGRATE) suggests that both species have extremely low migration rates, and that R. pretiosa have slightly smaller effective sizes. However, the slight difference in effective sizes between species appears insufficient to explain the large difference in genetic diversity and in large-scale genetic structure. We therefore hypothesize that low connectivity among the more widely-spaced R. pretiosa populations (owing to their patchier habitat), is the main cause of their lower genetic diversity and higher among-population differentiation. Conservation recommendations for R. pretiosa include maintaining habitat connectivity to facilitate gene flow among populations that are still potentially connected, and either expanding habitat or founding additional ‘backup’ populations to maintain diversity in the isolated populations. We recommend that special consideration be given to conservation of the Camas Prairie population in Northern Oregon. It is the most geographically isolated population, has the lowest genetic diversity (H _e = 0.14) and appears to be the only remaining representative of a major genetic group that is now almost extinct. Finally, because the six major groups within R. pretiosa are strongly differentiated, occupy different habitat types, and are geographically separate, they should be recognized as evolutionarily significant units for purposes of conservation planning.