Moray eels are more common on coral reefs subject to higher human pressure in the greater Caribbean

Proximity and size of the nearest market (‘market gravity’) have been shown to have strong negative effects on coral reef fish communities that can be mitigated by the establishment of closed areas. However, moray eels are functionally unique predators that are generally not subject to targeted fishing and should therefore not directly be affected by these factors. We used baited remote underwater video systems to investigate associations between morays and anthropogenic, habitat, and ecological factors in the Caribbean region. Market gravity had a positive effect on morays, while the opposite pattern was observed in a predator group subject to exploitation (sharks). Environmental DNA analyses corroborated the positive effect of market gravity on morays. We hypothesize that the observed pattern could be the indirect result of the depletion of moray competitors and predators near humans. Environmental science; ecology; biological sciences; zoology; animals; etholog

Connectivité et endémisme d'espèces marines dans le sud-ouest de l'océan Indien : le cas des Aglaopheniidae

Designing biodiversity conservation plans requires knowledge on the biogeographic distribution of taxa but also accurate estimates of species richness and diversification processes. However, measuring the phyletic richness can be biased by the use of inappropriate taxonomical characters, leading to erroneous species delimitation and diversity estimates. This work explores the phyletic richness at several taxonomic levels (generic, specific and intraspecific) of the hydrozoan family Aglaopheniidae (Agassisz, 1862), with a particular focus on the South-Western Indian Ocean. Firstly, using several newly constructed phylogenies based on mitochondrial and nuclear markers, this study reveals that the phyletic diversity of this family is at underestimated by at least 50%: all studied genera are polyphyletic or with doubtful monophyletic status. Then, using several species delimitation methods based on molecular markers, it sheds light on the richness of cryptic diversity of this family, enlightening the potential of using an integrative taxonomic approach on these morphologically simple organisms. Finally, the population genetics of an Aglaopheniidae brooding species shows a high populations structuring with pervasive pattern of isolation by distance at several geographic scales (several to thousands of kilometres), implying a potentially high cryptic diversity existing in this family. The results of this work provide new insights on Aglaopheniidae diversity, underlining the potential influence of reproductive mode on the phyletic diversity and diversification processes of brooding hydrozoan brooders. This thesis further highlights the relevance of using several complementary species delimitation procedures to study the diversity of morphologically simple organisms.La conservation et la gestion sur le long terme de la biodiversité nécessitent une connaissance de la répartition des taxons, mais également une estimation précise de leur diversité spécifique ainsi que des processus de spéciation ayant permis leur formation. Cependant, la mesure de la richesse phylétique peut être biaisée par l'utilisation de caractères taxinomiques ne permettant pas de délimiter les espèces de manière appropriée. Ce travail de thèse propose d'explorer la diversité phylétique à plusieurs niveaux taxinomiques (générique, spécifique et intra-spécifique) des Aglaopheniidae, une famille d'hydrozoaires, notamment présente dans le Sud-Ouest de l'océan Indien. Dans un premier temps, en utilisant des phylogénies basées sur plusieurs marqueurs (mitochondriaux et nucléaires), ce travail démontre que la diversité phylétique de cette famille est, au minimum, sous-estimée de moitié : tous les genres de la famille sont polyphyléthiques ou présentent un statut monophylétique restant à confirmer. Dans un deuxième temps, l'utilisation de méthodes de délimitation d'espèces basées sur des données moléculaires met en évidence la diversité cryptique très élevée des morpho-espèces étudiées, révélant l'intérêt potentiel des protocoles de taxinomie intégrative chez les organismes morphologiquement simples. Enfin, l'étude de génétique des populations d'une espèce incubatrice d'Aglaopheniidae révèle l'importance de la structuration des populations et de l'isolement par la distance chez cette espèce à plusieurs échelles géographiques (de quelques kilomètres à plusieurs milliers), impliquant une potentielle diversité cryptique extrêmement importante chez cette famille. L'ensemble des connaissances acquises lors de ce travail de thèse fournit un nouveau regard sur la diversité de la famille des Aglaopheniidae, soulignant le potentiel impact du cycle de reproduction sur la diversité phylétique et les processus de spéciation des hydrozoaires incubateurs. Cette thèse met en évidence l'importance de l'utilisation de plusieurs procédures complémentaires de délimitation d'espèces pour étudier la diversité des organismes morphologiquement simples

Connectivity and endemic marine species in the southwest Indian Ocean : the case of Aglaopheniidae

La conservation et la gestion sur le long terme de la biodiversité nécessitent une connaissance de la répartition des taxons, mais également une estimation précise de leur diversité spécifique ainsi que des processus de spéciation ayant permis leur formation. Cependant, la mesure de la richesse phylétique peut être biaisée par l'utilisation de caractères taxinomiques ne permettant pas de délimiter les espèces de manière appropriée. Ce travail de thèse propose d'explorer la diversité phylétique à plusieurs niveaux taxinomiques (générique, spécifique et intra-spécifique) des Aglaopheniidae, une famille d'hydrozoaires, notamment présente dans le Sud-Ouest de l'océan Indien. Dans un premier temps, en utilisant des phylogénies basées sur plusieurs marqueurs (mitochondriaux et nucléaires), ce travail démontre que la diversité phylétique de cette famille est, au minimum, sous-estimée de moitié : tous les genres de la famille sont polyphyléthiques ou présentent un statut monophylétique restant à confirmer. Dans un deuxième temps, l'utilisation de méthodes de délimitation d'espèces basées sur des données moléculaires met en évidence la diversité cryptique très élevée des morpho-espèces étudiées, révélant l'intérêt potentiel des protocoles de taxinomie intégrative chez les organismes morphologiquement simples. Enfin, l'étude de génétique des populations d'une espèce incubatrice d'Aglaopheniidae révèle l'importance de la structuration des populations et de l'isolement par la distance chez cette espèce à plusieurs échelles géographiques (de quelques kilomètres à plusieurs milliers), impliquant une potentielle diversité cryptique extrêmement importante chez cette famille. L'ensemble des connaissances acquises lors de ce travail de thèse fournit un nouveau regard sur la diversité de la famille des Aglaopheniidae, soulignant le potentiel impact du cycle de reproduction sur la diversité phylétique et les processus de spéciation des hydrozoaires incubateurs. Cette thèse met en évidence l'importance de l'utilisation de plusieurs procédures complémentaires de délimitation d'espèces pour étudier la diversité des organismes morphologiquement simples.Designing biodiversity conservation plans requires knowledge on the biogeographic distribution of taxa but also accurate estimates of species richness and diversification processes. However, measuring the phyletic richness can be biased by the use of inappropriate taxonomical characters, leading to erroneous species delimitation and diversity estimates. This work explores the phyletic richness at several taxonomic levels (generic, specific and intraspecific) of the hydrozoan family Aglaopheniidae (Agassisz, 1862), with a particular focus on the South-Western Indian Ocean. Firstly, using several newly constructed phylogenies based on mitochondrial and nuclear markers, this study reveals that the phyletic diversity of this family is at underestimated by at least 50%: all studied genera are polyphyletic or with doubtful monophyletic status. Then, using several species delimitation methods based on molecular markers, it sheds light on the richness of cryptic diversity of this family, enlightening the potential of using an integrative taxonomic approach on these morphologically simple organisms. Finally, the population genetics of an Aglaopheniidae brooding species shows a high populations structuring with pervasive pattern of isolation by distance at several geographic scales (several to thousands of kilometres), implying a potentially high cryptic diversity existing in this family. The results of this work provide new insights on Aglaopheniidae diversity, underlining the potential influence of reproductive mode on the phyletic diversity and diversification processes of brooding hydrozoan brooders. This thesis further highlights the relevance of using several complementary species delimitation procedures to study the diversity of morphologically simple organisms

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

Data from: 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 FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (11 000 km distance), with significant pairwise FST 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

Evolutionary Dynamics in the Southwest Indian Ocean Marine Biodiversity Hotspot: A Perspective from the Rocky Shore Gastropod Genus Nerita

International audienceThe 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

Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa)

A comprehensive inventory of global biodiversity would be greatly improved by automating methods for species delimitation. The Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model have been proposed as means of increasing the rate of biodiversity description using single locus data. We applied these methods to explore the diversity within the Aglaopheniidae, a hydrozoan family with many species widely distributed across tropical and temperate oceans. Our analyses revealed widespread cryptic diversity in this family, almost half of the morpho-species presenting several independent evolutionary lineages, as well as support for cases of synonymy. For two common species of this family, Lytocarpia brevirostris and Macrorhynchia phoenicea, we compared the outputs to clustering analyses based on microsatellite data and to nuclear gene phylogenies. For L. brevirostris, microsatellite data were congruent with results of the species delimitation methods, revealing the existence of two cryptic species with Indo-Pacific distribution. For M. phoenicea, all analyses confirmed the presence of two cryptic species within the South-Western Indian Ocean. Our study suggests that the diversity of Aglaopheniidae might be much higher than assumed, likely related to low dispersal capacities. Sequence-based species delimitation methods seem highly valuable to reveal cryptic diversity in hydrozoans; their application in an integrative framework will be very useful in describing the phyletic diversity of these organisms

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

International audienceAssessing 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 (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 (11,000km 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

Sliding-window analysis of the net diversification rate of the genus <i>Nerita</i> through geological periods.

<p>Oligo: Oligocene; P: Pliocene.</p

Database of unique Lytocarpia brevirostris unique MLGs per population

Tab delimited text. On each line is represented a unique MLG, with haplotypes for 10 loci used in all analyses of the publication