Sicyopterus lagocephalus post-larvae migrating in Mascarene Archipelago rivers, La Réunion Island, provide an important food source to local populations and fishing activity has a socioeconomic impact. Improved knowledge of the life traits and the characterisation of post-larval stages should enable a better understanding of physiological changes triggering migratory behaviour. It would also help to explain the recruitment processes to managers and to implement conservation measures for stock management. Sicyopterus lagocephalus is an amphidromous fish: adults live in rivers, but larvae are carried to the sea after hatching. The present study characterised the metamorphosis and post-larval stages of Sicyopterus lagocephalus during river recolonisation on La Réunion Island. The results show that cranium reorganisation and pectoral fins transformation are part of the first and major transformations and are completed less than 2 weeks after freshwater colonisation (post-larval stages PL1 and PL2). These transformations, mobilising all the available calcium, seem to be critical for survival in their new environment. Individuals then progressively acquire pigmentation, complete scalation and the fork at the end of the caudal fin disappears (juvenile stages J1 and J2). The end of the recruitment phase takes place 21 to 28 days after entering the river mouth, when territorial behaviour appears.

Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing.

ABSTRACT.Aim The global biodiversity crisis requires identifying regions with high evolutionary potential, i.e. Evolutionary Hotspots (Evospots). We created an analytical framework based on comparative phylogeography and coalescent methods to assess the dynamics of diversification and population persistence in the reef ecosystem of a little studied region: the Southwestern Indian Ocean (SWIO).Location Coral reefs of the SWIO, with comparative data from the Pacific Ocean.Methods We generated sequences of mitochondrial DNA for 10 widespread brittle-stars (345 specimens) from 21 localities (8 in the SWIO). We analysed them by combining comparative phylogeography approaches, coalescent-based methods, molecular clock and the concept of Evolutionary Significant Units to draw conclusions about the drivers of biodiversity in the region.Results Cryptic diversity was prevalent, increasing lineage diversity within the 10 nominal species by 70% within the SWIO and by 200% across the Indo-west Pacific. All seven new SWIO lineages meet the 1 criteria for evolutionary significant units (ESUs) and at least six are biological species. We detected likely intraregional diversifications dating to the Plio-Pleistocene, supporting the SWIO as a generator of biodiversity. Geographic restriction of ESUs, long coalescent times (>80 ka) and old (>1 Ma) in situ diversification point to persistence of populations over multiple glacio-eustatic cycles. We provide data suggesting demographic expansion during sea-level high stands. Regional connectivity was lower, and cryptic differentiation higher in lecithotrophs than planktotrophs. Main conclusionsThe analytical framework based on a biodiversity survey makes it possible to identify Evospots by assessing the potential of a region to maintain and generate biodiversity and evaluating the evolutionary processes and potential drivers at play.

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The 2 amphidromous gobiids Sicyopterus lagocephalus and Cotylopus acutipinnis from La Réunion Island (Mascarene archipelago, south-western Indian Ocean) are heavily exploited by traditional fisheries during their river colonisation. Traits of their oceanic larval life were investigated to better understand the complex life cycle of these fishes. Age estimates were established using otolith increment counts and an alizarin complexon validation method. Larval duration was longer for the widespread S. lagocephalus (133 to 266 d; mean 199 ± 33 d) than for the endemic C. acutipinnis (78 to 150 d; mean 101 ± 14 d), which reflects their distributional ranges. For both species, no correlation was established between age and size, suggesting a decrease in growth during the larval phase. From the back-calculated birth dates, all S. lagocephalus of a major colonisation episode (December 2002) were hatched during the cool season. All results are discussed in terms of the recruitment origins of S. lagocephalus and C. acutipinnis within the Mascarenes. Recognition of the differences in larval life traits is essential for proposing both management and conservation measures for each species.

The molecular clock hypothesis is fundamental in evolutionary biology as by assuming constancy of the molecular rate it provides a timeframe for evolution. However, increasing evidence shows time dependence of inferred molecular rates with inflated values obtained using recent calibrations. As recent demographic calibrations are virtually non-existent in most species, older phylogenetic calibration points (>1 Ma) are commonly used, which overestimate demographic parameters. To obtain more reliable rates of molecular evolution for population studies, I propose the calibration of demographic transition (CDT) method, which uses the timing of climatic changes over the late glacial warming period to calibrate expansions in various species. Simulation approaches and empirical data sets from a diversity of species (from mollusk to humans) confirm that, when compared with other genealogy-based calibration methods, the CDT provides a robust and broadly applicable clock for population genetics. The resulting CDT rates of molecular evolution also confirm rate heterogeneity over time and among taxa. Comparisons of expansion dates with ecological evidence confirm the inaccuracy of phylogenetically derived divergence rates when dating population-level events. The CDT method opens opportunities for addressing issues such as demographic responses to past climate change and the origin of rate heterogeneity related to taxa, genes, time, and genetic information content.

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In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large‐scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005–0.064) and mean interspecific genetic distances within genera (0.056–0.316) were concordant with previous echinoderm studies. This study revealed that brittle‐star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo‐West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.