Speciation, Connectivity and Self-Recruitment Among Mollusc Populations from Isolated Oceanic Islands

The conventional view that marine populations are demographically ‘open’ and exchange migrants (juveniles or adults, but mostly larvae) has been challenged by recent genetic studies and the discovery of significant genetic subdivision among populations on small geographic scales. Despite the numerous publications on the matter, the extent to which some/all marine populations rely on self-recruitment and whether this reliance is stable in time and space currently remains unanswered. This is particularly true for populations from isolated oceanic archipelagos, such as the New Zealand (NZ) subantarctic islands and the Kermadec Islands. The specific objectives of this thesis were to: 1) assess the genetic diversity, phylogeography and contemporary levels of dispersal and self-recruitment in populations of the Cellana strigilis limpet complex, endemic to the NZ subantarctic islands; 2) conduct a morphometric analysis of the C. strigilis complex to complement its molecular investigation; 3) develop and optimize specific microsatellite markers for Nerita melanotragus, a marine gastropod of the Kermadec Islands and New Zealand North Island rocky shores; 4) assess the genetic structuring and levels of connectivity of N. melanotragus populations within the Kermadec Islands, within NZ North Island, and between the Kermadec Islands and NZ; and 5) compare the genetic structuring of N. melanotragus at the Kermadec Islands to that of NZ North Island populations, to test for any “island effect” on connectivity levels, and test for possible gene flow between the two groups. Genetic investigation of the C. strigilis complex confirmed the presence of two distinct lineages, separated by their sister species Cellana denticulata. Morphometric analyses were congruent with molecular analyses, and were used to provide a new taxonomic description of the C. strigilis limpet complex: two species were recognized, Cellana strigilis and Cellana oliveri. The role of the subantarctic islands during the last glacial maximum was highlighted, and the colonisation history of the islands by the two Cellana species was explained. Contemporary levels of connectivity (gene flow) among the different populations of the two lineages were low, or non-existant, revealing their high reliability on self-recruitment. However, the analysis detected a recent migration event in one of the two lineages. Considering the geographical distance of the islands and the life history of the Cellana species, the use of mediated dispersal means (e.g., rafting on a natural substrate such as kelp) seems very likely. Ten novel polymorphic microsatellite loci were developed for N. melanotragus, and seven of those were used to investigate the levels of connectivity and self-recruitment in six populations from the Kermadec Islands, and nine populations from the east coast of NZ North Island. According to what can be expected for a species with a long pelagic larval duration (PLD), genetic homogeneity was recorded for the Kermadec Islands populations. A lack of genetic structuring was also found for the nine populations on the NZ North Island, which is congruent with the literature in this geographic area. However, what was surprising was the high level of genetic homogeneity found between the Kermadec Islands and the NZ North Island, meaning that the two groups are effectively exchanging individuals. Hence, the Kermadec archipelago can be considered “open” at the scale of the South Pacific, for N. melanotragus populations. This Ph.D. highlights the importance of having the correct taxonomy for conservation and connectivity studies, and gives a better understanding of the historical and contemporary patterns of genetic connectivity in the NZ offshore islands. It illustrated how historical events, such as the last glacial maximum, can shape local genetic diversity, and how this historical pattern can be maintained because of limited contemporary gene exchange. Also, this thesis demonstrated that remote populations could be strongly connected to mainland populations, contributing to the resilience of both systems and confirming the necessity of integrating remote oceanic habitats in the creation of effective Marine Protected Areas (MPA) networks to protect the marine environment

Correlation between pelagic larval duration and realised dispersal: long-distance genetic connectivity between northern New Zealand and the Kermadec Islands archipelago

The extent to which marine populations are “open” (panmixia) or “closed” (self- recruitment) remains a matter of much debate, with recent reports of high levels of genetic differentiation and self-recruitment among populations of numerous species separated by short geographic. However, the interpretation of patterns of gene flow (connectivity) is often based on a stepping stone model of dispersal that can genetically homogenise even distant populations and blur genetic patterns that may better reflect realised dispersal. One way in which realised long-distance dispersal can be accurately determined is by examination of gene flow of taxa between isolated archipelagos and a mainland where there is no possible stepping stone dispersal across the open ocean. We investigated the genetic structuring of populations of the intertidal gastropod Nerita melanotragus from the subtropical Kermadec Islands and temperate New Zealand’s North Island (the mainland), separated by 750 km of open ocean and characterised by contrasting environmental conditions. Analyses of seven microsatellite markers revealed an absence of genetic structuring with low F ST and Jost’s D values (from 0.000 to 0.007 and from 0.000 to 0.015, respectively) over large geographic distances and no evidence of isolation by distance among all populations. These results indicate that the realised dispersal of N. melanotragus is of at least 750 km, this species exhibits a very “open” form of connectivity and its larvae exhibit sufficient phenotypic plasticity to settle successfully in different environmental conditions, ranging from subtropical to cool temperate

Identification of general patterns of sex-biased expression in Daphnia, a genus with environmental sex determination

Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna. This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia

Overview and progress of consortium research related to the biology, ecology and aquaculture of rabbitfish

editorial reviewedCoastal habitats support global fisheries by ensuring the survival of juvenile fishes. These habitats constitute one of the fishing areas targeted by small-scale fishermen in the least developed countries, including Madagascar. The accessibility of these habitats at low tides makes it an ideal fishing area for mosquito seine nets as observed for instance in SW Madagascar and beach seining in Kenya. However, this practice negatively impacts fisheries production due to catches of high numbers of juveniles, in Madagascar and Kenya mostly composed of shoemaker spinefoot rabbitfish (Siganus sutor). Despite Malagasy laws that forbid the deployment of mosquito seine nets, fishermen continue with their use. In Kenya, the beach seines have been outlawed but enforcement remains a challenge. This context highlights the need for management measures and alternative sources of income for a sustainable use of marine resources and for improving the fishermen livelihood. The ongoing consortium research entitled “Fish juvenile recruitment in coastal habitats of western Indian Ocean” was funded by MASMA program administered by WIOMSA. It is an interdisciplinary research program intending to understand recruitment patterns of shoemaker spinefoot rabbitfish (Siganus sutor) in coastal habitats of Kenya and Madagascar. It explores evidence-based solutions for improving the welfare of coastal communities and sustainable use of marine resources. Research activities were divided into four work packages. In WP1, Siganus sutor recruitment patterns in coastal habitats were targeted to identify the nursery ground and recruitment periods. It is based on juvenile fish sampling at four coastal habitats (mangroves, seagrass meadows, intermediate areas and seagrass associated with the coral reef) in Madagascar during twelve months. In WP2, sampling for the analysis of the population connectivity of S. sutor for detecting the sources of juveniles in the coastal habitats at five sites along the western coast of Madagascar was completed. In WP3, ecological models for predicting the arrival of newly settled S. sutor will be based on historical and newly collected data (WP1) using the random forests algorithm. Predictors are composed of remotely sensed oceanic conditions and a post-larval supply index calculated from post-larval sampling in the coastal habitats using light-traps. Like juvenile sampling, post-larval sampling was performed three nights per month which will cover all the juvenile sampling periods. In WP4, fish feeding behavior is studied and experiments on capture-based juvenile fish grow-out are ongoing at the Belaza aquaculture facilities (Toliara, Madagascar). Eight fish grow-out treatments focusing on three stocking densities, three fish diets, and pond dimensions are being tested. In WP1, about 5,720 juvenile individuals were obtained from 120 juvenile fish samples. The standard length of each of these individuals were measured for analyzing the spatial distribution of S. sutor. The nursery ground and recruitment seasons for S. sutor emerged from our research. The findings will be presented orally by PhD student Helga Berjulie Ravelohasina during the symposium. In addition, about 360 epifaunal community samples were obtained between July 2021 and April 2022. The spatial distribution of abundance, diversity and richness of epifauna associated with seagrass will be presented in a poster by MSc student Mory Justino. In WP2, at each location, 45 individuals were sampled, for a total of 225 adults for Madagascar and 180 from Kenya. Genotyping is in progress. In WP3, monitoring of the newly settled fish, in parallel with post-larval sampling, is in progress and should be completed by June 2022. In meantime, the extraction of remotely sensed oceanic conditions covering the sampling periods is being processed with R programming for the period. In WP4, preliminary results on fish grow-out identified the best fish diet and the most optimal stocking density at the smallest size (about 2 cm of standard length). More details related to these findings will be presented in a poster by master student Nandrianina Maminantenaina. In addition, the gut content and stage isotopes of three ontogenetic stages (i.e. post-larvae, juvenile, and adult) of S. sutor were analysed the natural trophodynamics. The findings are based on 1160 gut contents and muscle tissue samples collected during the warm (October 2021 to February 2022) and cool season (May to August 2022). The potential nursery areas and the main recruitment seasons of Siganus sutor were identified. The oral presentation entitled “The potential nursery areas and recruitment season of S. sutor in Madagascar” by Helga Berjulie Ravelohasina will provide further details of our findings. The variability of food availability related to epifauna concentration will be known in the poster on Mory Justino. The most optimal fish diet as well as the optimal stocking density will be presented in a separate poster entitled “Density and fish diet effect on rabbitfish growth in controlled systems” presented by Nandrianina Maminantenaina.Biology, ecology and aquaculture of rabbitfish14. Life below water2. Zero hunger11. Sustainable cities and communitie

COI-16S Phylogenetic alignment

Complete phylogenetic alignment of COI and 16S concatenated fragments. Base pair 1-425:COI; base pair 426-852:16S

ATPS Phylogeography alignment

Complete alignment used for the nuclear haplotype network

COI-16S Phylogeography alignment

Complete alignment used for the haplotype network. Base pair 1-425:COI, base pair 426-891:16S

RAPD primers

File containing the primer names for the RPD study, as well as their loci and the size of the product scored in the analysis