Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites

Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis.

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F_IS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise F_ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

Evolutionary dynamics in the southwest Indian ocean marine biodiversity hotspot: a perspective from the rocky shore gastropod genus Nerita

The Southwest Indian Ocean (SWIO) is a striking marine biodiversity hotspot. Coral reefs in this region host a high proportion of endemics compared to total species richness and they are particularly threatened by human activities. The island archipelagos with their diverse marine habitats constitute a natural laboratory for studying diversification processes. Rocky shores in the SWIO region have remained understudied. This habitat presents a high diversity of molluscs, in particular gastropods. To explore the role of climatic and geological factors in lineage diversification within the genus Nerita, we constructed a new phylogeny with an associated chronogram from two mitochondrial genes [cytochrome oxidase sub-unit 1 and 16S rRNA], combining previously published and new data from eight species sampled throughout the region. All species from the SWIO originated less than 20 Ma ago, their closest extant relatives living in the Indo-Australian Archipelago (IAA). Furthermore, the SWIO clades within species with Indo-Pacific distribution ranges are quite recent, less than 5 Ma. These results suggest that the regional diversification of Nerita is closely linked to tectonic events in the SWIO region. The Reunion mantle plume head reached Earth's surface 67 Ma and has been stable and active since then, generating island archipelagos, some of which are partly below sea level today. Since the Miocene, sea-level fluctuations have intermittently created new rocky shore habitats. These represent ephemeral stepping-stones, which have likely facilitated repeated colonization by intertidal gastropods, like Nerita populations from the IAA, leading to allopatric speciation. This highlights the importance of taking into account past climatic and geological factors when studying diversification of highly dispersive tropical marine species. It also underlines the unique history of the marine biodiversity of the SWIO region.

One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan

Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive F_IS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise F_ST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.

Modern alongside traditional taxonomy-Integrative systematics of the genera Gymnangium Hincks, 1874 and Taxella Allman, 1874 (Hydrozoa, Aglaopheniidae)

We studied the diversity within the former genus Gymnangium in the South West Indian Ocean by using an integrative approach of both traditional (morphology-based) and modern molecular taxonomy. Nine species were recorded in the material collected. A total of 97 16S mitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differences in the studied Gymnangium species that make it necessary to split the genus. It is proposed to revalidate the genus Taxella which is currently regarded as a synonym of Gymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until now regarded as distinct species based on morphological characteristics, cluster together in one phylogenetic clade. Possible explanations are discussed. Two species from Madagascar new to science are herein described and rare species from the Indian Ocean islands are re-described.

Phylogeography and population genetics of the cryptic bonnethead shark Sphyrna aff. tiburo in Brazil and the Caribbean inferred from mtDNA markers

Resolving the identity, phylogeny and distribution of cryptic species within species complexes is an essential precursor to management. The bonnethead shark, Sphyrna tiburo, is a small coastal shark distributed in the Western Atlantic from North Carolina (U.S.A.) to southern Brazil. Genetic analyses based on mitochondrial markers revealed that bonnethead sharks comprise a species complex with at least two lineages in the Northwestern Atlantic and the Caribbean (S. tiburo and Sphyrna aff. tiburo, respectively). The phylogeographic and phylogenetic analysis of two mitochondrial markers [control region (mtCR) and cytochrome oxidase I (COI)] showed that bonnethead sharks from southeastern Brazil correspond to S. aff. tiburo, extending the distribution of this cryptic species >5000 km. Bonnethead shark populations are only managed in the U.S.A. and in the 2000s were considered to be regionally extinct or collapsed in southeast Brazil. The results indicate that there is significant genetic differentiation between S. aff. tiburo from Brazil and other populations from the Caribbean (Φ_ST  = 0.9053, P < 0.000), which means that collapsed populations in the former are unlikely to be replenished from Caribbean immigration. The species identity of bonnethead sharks in the Southwest Atlantic and their relationship to North Atlantic and Caribbean populations still remains unresolved. Taxonomic revision and further sampling are required to reevaluate the status of the bonnethead shark complex through its distribution range.

Sphyrna alleni sp. nov., a new hammerhead shark (Carcharhiniformes, Sphyrnidae) from the Caribbean and the Southwest Atlantic

Hammerhead sharks (Family Sphyrnidae) comprise a monophyletic Miocene radiation of carcharhiniform sharks characterized by their laterally expanded and dorsoventrally compressed head ('cephalofoil'). The bonnethead shark (Sphyrna tiburo) is currently described as a single amphi-American hammerhead species composed of the subspecies Sphyrna tiburo tiburo in the Western Atlantic Ocean (WA) and S. tiburo vespertina in the Eastern Pacific Ocean (EP). Variation in mitochondrial DNA and cephalofoil shape suggest a species complex, with S. tiburo occurring in the U.S., Mexico, and Bahamas; S. aff. tiburo occurring from Belize to Brazil; and S. vespertina occurring in the EP. Morphometric, meristic, and genetic variation was used to resolve the bonnethead shark complex in the Western Atlantic. Twenty-three specimens (12 S. aff. tiburo from Belize and 11 S. tiburo from U.S.) were subject to sixty-one morphometric measurements and three meristic characters (counts of the number of precaudal vertebrae, lower and upper rows of functional teeth). An allometric formula was used to standardize any effect caused by differences in size of the individuals and data were analyzed with univariate and multivariate statistics. Sphyrna aff. tiburo and S. tiburo have non-overlapping vertebral counts (80-83 and 71-74 respectively) but no morphometric differences were detected. Although not captured in morphometric analysis, the cephalofoil of S. aff. tiburo has a more pointed anterior margin than S. tiburo that together with lobule shaped posterior margins gives the cephalofoil a distinctive shovel-shaped appearance. Concatenated mitochondrial sequences and 12 nuclear microsatellite markers clearly separated S. aff. tiburo and S. tiburo. We conclude that this complex comprises two species in the Western Atlantic, S. tiburo and S. alleni sp. nov., and we provide a description of the latter, which is distinguished by precaudal vertebral counts (80-83), a shovel-shaped cephalofoil with rounded posterior margins, and robust differences in mitochondrial and nuclear genetic markers. We suggest nuclear genetic and meristic examination of EP bonnetheads is needed to update the taxonomical status and redescribe S. vespertina.