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The scleractinian coral Pocillopora damicornis type β is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type β populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P. damicornis type β determined a posteriori from their mtDNA haplotype (a 840 bp sequenced fragment of the Open Reading Frame). Overall, 47% of all the sampled colonies presented the same multi-locus genotype (MLG), a superclone, suggesting that asexual propagation is extremely important in Reunion Island. Within each site, numerous MLGs were shared by several colonies, suggesting local clonal propagation through fragmentation. Moreover, some of these MLGs were found to be shared among several sites located 40 km apart. While asexual reproduction by fragmentation seems unlikely over long distances, our results suggest a production of parthenogenetic larvae. Despite shared MLGs, two differentiated clusters were enclosed among populations of the west coast of Reunion Island, revealing the necessity to set up appropriate managing strategies at a local scale.

Aim: The unique biodiversity in the Red Sea is the result of complex ecological and evolutionary processes driven by Pleistocene climatic change. Here we investigate the species diversity, phylogenetic relationships and phylogeographical patterns of giant clams in the Western Indian Ocean (WIO) and the Red Sea to explore scenarios of marine speciation in this under-studied region. Location: Mozambique Channel, Madagascar, and the Mascarene Islands (WIO); the Farasan Islands (Red Sea). Taxon: Giant clams of the genus Tridacna (Cardiidae: Tridacninae). Methods: Giant clams were sampled as complete organisms or through underwater biopsies. Nuclear (28S) and mitochondrial (16S and COI) DNA sequences were subjected to Bayesian and maximum likelihood analyses to generate a phylogenetic hypothesis for all known species within the genus Tridacna. Bayesian inference with molecular and fossil calibration was used to infer their colonization history. Results: From the 10 genetically distinct clades recovered from the analyses of 253 sequenced specimens, five distinct Tridacna lineages were sampled, three of which were endemics of the WIO and the Red Sea. Each lineage corresponded to a distinct species, except one grouping the two formerly known WIO endemics, T. lorenzi and T. rosewateri. This lineage clustered with two other well-supported lineages: the Red Sea endemic T. squamosina, and a previously unrecognized lineage, restricted to the WIO, for which we resurrect the long-forgotten name T. elongatissima Bianconi, 1856. For the two other species sampled (T. maxima and T. squamosa), contrasting phylogeographical patterns were observed. Main conclusions: Our data confirm the validity of the species T. rosewateri, a WIO endemic genetically indistinguishable from T. lorenzi, which should be considered a junior synonym. The phylogenetic placement of the newly resurrected T. elongatissima provides insights into the probable origin of T. squamosina, which split from its sister species no later than 2 Ma, likely during Middle Pleistocene glacial periods. Two | 1087 FAUVELOT ET AL.

Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt‐Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi‐locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.

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Aim Convergence, stasis and plasticity can frequently confound our understanding of species distributions in the seas. Yet delimiting species and understanding population connectivity across marine environments is mandatory for establishing appropriate management of coral reefs, which are experiencing critical declines. We test whether morphospecies from Pocillopora corals found on outer reef slopes are unique species or species complexes, in order to correctly define their respective distributions and consequently to accurately assess their population connectivity. Location Archipelagos and islands of the Western Indian Ocean and the Southern Pacific (New Caledonia, Tonga, French Polynesia). Taxon Pocillopora eydouxi/meandrina and Pocillopora verrucosa morphospecies (Scleractinia). Methods We analysed the 13‐microsatellite genotypes of 4837 colonies from six understudied ecoregions in the southern part of the genus distribution, to first explore the genetic partitioning within morphospecies. We then characterized the spatial distribution of each delimited species and analysed patterns of genetic diversity and connectivity for each species separately. Results Both morphospecies are complexes of species, each found almost exclusively in the Indian or the Pacific Oceans. Moreover, some of these cryptic species are found in sympatry over their whole distribution, which sometimes was very restricted. However, within each species, genetic diversity and connectivity were relatively high, although some populations were found differentiated for some species, while not for others. Main conclusions A weak connectivity was found between the Indian and Pacific Oceans, but high connectivity within both oceans, supporting the existence of a barrier impeding gene flow between both ocean basins in Pocillopora. Although constrained by the same geography and current patterns, some sympatric species present different connectivity patterns, demonstrating the importance of multi‐species connectivity models to set up appropriate management plans.

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 FIS 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 FST 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.