Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach

The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability

Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.

The Eastern Tropical Pacific coral population connectivity and the role of the Eastern Pacific Barrier

Long-distance dispersal is believed to strongly influence coral reef population dynamics across the Tropical Pacific. However, the spatial scale and strength at which populations are potentially connected by dispersal remains uncertain. To determine the patterns in connectivity between the Eastern (ETP) and Central Tropical Pacific (CTP) ecoregions, we used a biophysical model incorporating ocean currents and larval biology to quantify the seascape-wide dispersal potential among all population. We quantified the likelihood and determined the oceanographic conditions that enable the dispersal of coral larvae across the Eastern Pacific Barrier (EP-Barrier) and identified the main connectivity pathways and their conservation value for dominant reef-building corals. Overall, we found that coral assemblages within the CTP and ETP are weakly connected through dispersal. Although the EP-Barrier isolates the ETP from the CTP ecoregion, we found evidence that the EP-Barrier may be breached, in both directions, by rare dispersal events. These rare events could explain the evolutionary genetic similarity among populations of pocilloporids in the ecoregions. Moreover, the ETP may function as a stronger source rather than a destination, providing potential recruits to CTP populations. We also show evidence for a connectivity loop in the ETP, which may positively influence long-term population persistence in the region. Coral conservation and management communities should consider eight-key stepping stone ecoregions when developing strategies to preserve the long-distance connectivity potential across the ETP and CTP.

Evidence of sexual dimorphism in skeletal morphology of a gonochoric reef coral

In the emerald coral Porites panamensis, the rates of elongation and calcification of colonies are higher in males than in females, probably because of the higher energetic demands of the latter in order to cope with the development of the large planulae produced throughout the year. This differing energetic demand could also be reflected in the sexual dimorphism of the calyces; hence, to test this hypothesis, 11 morphological traits of the corallite were assessed from 63 colonies that were collected in the southern Gulf of California, Mexico. Three traits showed statistical differences between sexes, enabling accurate distinction of males from females. Our results confirm for the first time the existence of external sexual dimorphism in a reef-building coral, opening the possibility that sex-related morphological differences may occur generally in gonochoric scleractinians. These findings can be very useful for the correct classification and characterization of recent and fossil records, helping to improve the historical and evolutive understanding of reef-building corals facing threats under environmental changes.

Role of oceanography in shaping the genetic structure in the North Pacific hake Merluccius productus

Determining the relative influence of biotic and abiotic factors on genetic connectivity among populations remains a major challenge in evolutionary biology and in the management and conservation of species. North Pacific hake (Merluccius productus) inhabits upwelling regions in the California Current ecosystem from the Gulf of California to the Gulf of Alaska. In this study, we examined mitochondrial DNA (mtDNA) and microsatellite variation to estimate levels of genetic differentiation of M. productus in relation to the role of oceanographic features as potential barriers to gene flow. Samples were obtained from nine sites spanning a large part of the geographic range of the species, from Puget Sound, Washington to Costa Rica. The microsatellite results revealed three genetically discrete populations: one spanning the eastern Pacific coast, and two apparently resident populations circumscribed to the Puget Sound and the northern Gulf of California (F_ST = 0.032, p = 0.036). Cytochrome b sequence data indicated that isolation between the Puget Sound and northern Gulf of California populations from the coastal Pacific were recent phenomena (18.5 kyr for Puget Sound and 40 kyr for the northern Gulf of California). Oceanographic data obtained from the Gulf of California support the hypothesis that permanent fronts within the region, and strong gradients at the entrance to the Gulf of California act as barriers to gene flow. A seascape genetics approach found significant genetic–environment associations, where the daytime sea surface temperature and chlorophyll concentrations were the best predictive variables for the observed genetic differentiation. Considering the potential causes of genetic isolation among the three populations, e.g. spawning areas in different latitudes associated with upwelling processes, oceanographic barriers, asymmetric migration and specialized diet, oceanographic barriers appear to be a likely mechanism restricting gene flow.

Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity

Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms.

A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

The central-marginal hypothesis (CMH) predicts that population size, genetic diversity and genetic connectivity are highest at the core and decrease near the edges of species' geographic distributions. We provide a test of the CMH using three replicated core-to-edge transects that encompass nearly the entire geographic range of the endemic streamside salamander (Ambystoma barbouri). We confirmed that the mapped core of the distribution was the most suitable habitat using ecological niche modelling (ENM) and via genetic estimates of effective population sizes. As predicted by the CMH, we found statistical support for decreased genetic diversity, effective population size and genetic connectivity from core to edge in western and northern transects, yet not along a southern transect. Based on our niche model, habitat suitability is lower towards the southern range edge, presumably leading to conflicting core-to-edge genetic patterns. These results suggest that multiple processes may influence a species' distribution based on the heterogeneity of habitat across a species' range and that replicated sampling may be needed to accurately test the CMH. Our work also emphasizes the importance of identifying the geographic range core with methods other than using the Euclidean centre on a map, which may help to explain discrepancies among other empirical tests of the CMH. Assessing core-to-edge population genetic patterns across an entire species' range accompanied with ENM can inform our general understanding of the mechanisms leading to species' geographic range limits.

The complete mitochondrial DNA of endemic Eastern Pacific coral (Porites panamensis)

The mitogenome of the endemic coral Porites panamensis (Genbank accession number KJ546638) has a total length of 18,628 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 2 transfer RNA (tRNA) genes. Gene order was equal to other scleractinian coral mitogenomes.