Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes.

Determining how plasticity of developmental traits responds to environmental conditions is a challenge that must combine evolutionary sciences, ecology, and developmental biology. During metamorphosis, fish alter their morphology and color pattern according to environmental cues. We observed that juvenile clownfish (Amphiprion percula) modulate the developmental timing of their adult white bar formation during metamorphosis depending on the sea anemone species in which they are recruited. We observed an earlier formation of white bars when clownfish developed with Stichodactyla gigantea (Sg) than with Heteractis magnifica (Hm). As these bars, composed of iridophores, form during metamorphosis, we hypothesized that timing of their development may be thyroid hormone (TH) dependent. We treated clownfish larvae with TH and found that white bars developed earlier than in control fish. We further observed higher TH levels, associated with rapid white bar formation, in juveniles recruited in Sg than in Hm, explaining the faster white bar formation. Transcriptomic analysis of Sg recruits revealed higher expression of duox, a dual oxidase implicated in TH production as compared to Hm recruits. Finally, we showed that duox is an essential regulator of iridophore pattern timing in zebrafish. Taken together, our results suggest that TH controls the timing of adult color pattern formation and that shifts in duox expression and TH levels are associated with ecological differences resulting in divergent ontogenetic trajectories in color pattern development.

Spatial and temporal analysis of juvenile blacktip reef shark (Carcharhinus melanopterus) demographies identifies critical habitats.

Reef shark species have undergone sharp declines in recent decades, as they inhabit coastal areas, making them an easy target in fisheries (i.e., sharks are exploited globally for their fins, meat, and liver oil) and exposing them to other threats (e.g., being part of by-catch, pollution, and climate change). Reef sharks play a critical role in coral reef ecosystems, where they control populations of smaller predators and herbivorous fishes either directly via predation or indirectly via behavior, thus protecting biodiversity and preventing potential overgrazing of corals. The urgent need to conserve reef shark populations necessitates a multifaceted approach to policy at local, federal, and global levels. However, monitoring programmes to evaluate the efficiency of such policies are lacking due to the difficulty in repeatedly sampling free-ranging, wild shark populations. Over nine consecutive years, we monitored juveniles of the blacktip reef shark (Carcharhinus melanopterus) population around Moorea, French Polynesia, and within the largest shark sanctuary globally, to date. We investigated the roles of spatial (i.e., sampling sites) and temporal variables (i.e., sampling year, season, and month), water temperature, and interspecific competition on shark density across 10 coastal nursery areas. Juvenile C. melanopterus density was found to be stable over 9 years, which may highlight the effectiveness of local and likely federal policies. Two of the 10 nursery areas exhibited higher juvenile shark densities over time, which may have been related to changes in female reproductive behavior or changes in habitat type and resources. Water temperatures did not affect juvenile shark density over time as extreme temperatures proven lethal (i.e., 33°C) in juvenile C. melanopterus might have been tempered by daily variation. The proven efficiency of time-series datasets for reef sharks to identify critical habitats (having the highest juvenile shark densities over time) should be extended to other populations to significantly contribute to the conservation of reef shark species.

Abiotic drivers of the space use and activity of gray reef sharks Carcharhinus amblyrhynchos in a dynamic tidal environment.

Predators display rhythms in behavior and habitat use, often with the goal of maximizing foraging success. The underlying mechanisms behind these rhythms are generally linked to abiotic conditions related to diel, lunar, or seasonal cycles. To understand their effects on the space use, activity, and swimming depth of gray reef sharks (Carcharhinus amblyrhynchos), we tagged 38 individuals with depth and accelerometer sensors in a French Polynesian atoll channel exposed to strong tidal flow, and monitored them over a year. C. amblyrhynchos used a larger space during nighttime and were more active at night and during outgoing currents. Shark activity also peaked during the full and new moons. The swimming depth of sharks was mostly influenced by diel cycles, with sharks swimming deeper during the day compared to nighttime. The dynamic energyscape may promote the emergence of discrete behavioral strategies in reef sharks that use the south channel of Fakarava for resting and foraging purposes. Turbulence imposed by outgoing tides induces additional foraging cost on sharks, shifting their hunting areas to the southern part of the channel, where turbulence is less pronounced. Understanding when and where sharks are active and foraging is important for our understanding of predator-prey dynamics and ecosystem dynamics. This study highlights how abiotic rhythms in a highly dynamic environment likely generate spatiotemporal heterogeneity in the distribution of predation pressure.

Macroalgae exhibit diverse responses to human disturbances on coral reefs.

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.

Characterization of 25 new microsatellite markers for the green turtle (Chelonia mydas) and cross-species amplification in other marine turtle species.

BACKGROUND: The green sea turtle, Chelonia mydas, is a migratory species with a strong natal homing behavior leading to a complex population structure worldwide. The species has suffered severe declines in local populations; it is therefore crucial to understand its population dynamics and genetic structure to adopt appropriate management policies. Here, we describe the development of 25 new microsatellite markers specific to C. mydas and suitable for these analyses. METHODS AND RESULTS: They were tested on 107 specimens from French Polynesia. An average allelic diversity of 8 alleles per locus was reported and observed heterozygosity ranged from 0.187 to 0.860. Ten loci were significantly deviant from the Hardy-Weinberg equilibrium, and 16 loci showed a moderate to high level of linkage disequilibrium (4-22%). The overall Fis was positive (0.034, p-value < 0.001), and sibship analysis revealed 12 half- or full-sibling dyads, suggesting possible inbreeding in this population. Cross-amplification tests were performed on two other marine turtle species, Caretta caretta and Eretmochelys imbricata. All loci successfully amplified on these two species, though 1 to 5 loci were monomorphic. CONCLUSION: These new markers will not only be relevant for further analyses on the population structure of the green turtle and the two other species, but they will also be invaluable for parentage studies, for which a high number of polymorphic loci are necessary. This can provide important insight into male reproductive behavior and migration, an aspect of sea turtle biology that is of critical importance for the conservation of the species.

Characterization of 35 new microsatellite markers for the blacktip reef shark (Carcharhinus melanopterus) and cross-species amplification in eight other shark species.

BACKGROUND: Shark species are overfished at a global scale, as they are poached for the finning industry or are caught as bycatch. Efficient conservation measures require fine-scale spatial and temporal studies to characterize shark habitat use, infer migratory habits, analyze relatedness, and detect population genetic differentiation. Gathering these types of data is costly and time-consuming, especially when it requires collection of shark tissue samples. METHODS AND RESULTS: Genetic tools, such as microsatellite markers, are the most economical sampling method for collecting genetic data, as they enable the estimation of genetic diversity, population structure and parentage relationships and are thus an efficient way to inform conservation strategies. Here, a set of 45 microsatellite loci was tested on three blacktip reef shark (Carcharhinus melanopterus) populations from three Polynesian islands: Moorea, Morane and Tenararo. The set was composed of 10 previously published microsatellite markers and 35 microsatellite markers that were developed specifically for C. melanopterus as part of the present study. The 35 novel and 10 existing loci were cross-amplified on eight additional shark species (Carcharhinus amblyrhynchos, C. longimanus, C. sorrah, Galeocerdo cuvier, Negaprion acutidens, Prionacea glauca, Rhincodon typus and Sphyrna lewini). These species had an average of 69% of successful amplification, considered if at least 50% of the individual samples being successfully amplified per species and per locus. CONCLUSIONS: This novel microsatellite marker set will help address numerous knowledge gaps that remain, concerning genetic stock identification, shark behavior and reproduction via parentage analysis.

Elucidating the role of competition in driving spatial and trophic niche patterns in sympatric juvenile sharks.

The coexistence of ecologically and morphologically similar species is often facilitated by the partitioning of ecological niches. While subordinate species can reduce competition with dominant competitors through spatial and/or trophic segregation, empirical support from wild settings, particularly those involving large-bodied taxa in marine ecosystems, are rare. Shark nursery areas provide an opportunity to investigate the mechanisms of coexistence. We used experimental and field studies of sympatric juvenile sharks (blacktip reef shark, Carcharhinus melanopterus; sicklefin lemon shark, Negaprion acutidens) to investigate how competitive ability influenced realized niches at St. Joseph Atoll, Seychelles. Captive trials revealed that sicklefin lemon sharks were dominant over blacktip reef sharks, consistently taking food rewards. In the field, blacktip reef sharks were captured over a broader area than sicklefin lemon sharks, but daily space use of actively tracked sharks showed a high degree of overlap across microhabitats. While stomach contents analysis revealed that blacktip reef shark diets included a broader range of prey items, stable isotope analysis demonstrated significantly higher mean δ13C values for sicklefin lemon sharks, suggesting diverging dietary preferences. Overall, our results matched theoretical predictions of subordinate competitors using a greater range of habitats and displaying broader feeding niches than competitively dominant species. While separating the realized and fundamental niche of marine predators is complicated, we provide evidence that resource partitioning is at least partially driven by interspecific competition.

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.

Escape response kinematics in two species of tropical shark: short escape latencies and high turning performance.

Accelerative manoeuvres, such as fast-starts, are crucial for fish to avoid predation. Escape responses are fast-starts that include fundamental survival traits for prey that experience high predation pressure. However, no previous study has assessed escape performance in neonate tropical sharks. We quantitatively evaluated vulnerability traits of neonate tropical sharks by testing predictions on their fast-start escape performance. We predicted (1) high manoeuvrability, given their high flexibility, but (2) low propulsive locomotion owing to the drag costs associated with pectoral fin extension during escape responses. Further, based on previous work on dogfish, Squalus suckleyi, we predicted (3) long reaction times (as latencies longer than teleosts, >20 ms). We used two-dimensional, high-speed videography analysis of mechano-acoustically stimulated neonate blacktip reef shark, Carcharhinus melanopterus (n=12), and sicklefin lemon shark, Negaprion acutidens (n=8). Both species performed a characteristic C-start double-bend response (i.e. two body bends), but single-bend responses were only observed in N. acutidens. As predicted, neonate sharks showed high manoeuvrability with high turning rates and tight turning radii (3-11% of body length) but low propulsive performance (i.e. speed, acceleration and velocity) when compared with similar-sized teleosts and S. suckleyi. Contrary to expectations, escape latencies were <20 ms in both species, suggesting that the neurophysiological system of sharks when reacting to a predatory attack may not be limited to long response times. These results provide a quantitative assessment of survival traits in neonate tropical sharks that will be crucial for future studies that consider the vulnerability of these sharks to predation.

Global tropical reef fish richness could decline by around half if corals are lost.

Reef fishes are a treasured part of marine biodiversity, and also provide needed protein for many millions of people. Although most reef fishes might survive projected increases in ocean temperatures, corals are less tolerant. A few fish species strictly depend on corals for food and shelter, suggesting that coral extinctions could lead to some secondary fish extinctions. However, secondary extinctions could extend far beyond those few coral-dependent species. Furthermore, it is yet unknown how such fish declines might vary around the world. Current coral mass mortalities led us to ask how fish communities would respond to coral loss within and across oceans. We mapped 6964 coral-reef-fish species and 119 coral genera, and then regressed reef-fish species richness against coral generic richness at the 1° scale (after controlling for biogeographic factors that drive species diversification). Consistent with small-scale studies, statistical extrapolations suggested that local fish richness across the globe would be around half its current value in a hypothetical world without coral, leading to more areas with low or intermediate fish species richness and fewer fish diversity hotspots.

Sharks surf the slope: Current updrafts reduce energy expenditure for aggregating marine predators.

An animal's energy landscape considers the power requirements associated with residing in or moving through habitats. Within marine environments, these landscapes can be dynamic as water currents will influence animal power requirements and can change rapidly over diel and tidal cycles. In channels and along slopes with strong currents, updraft zones may reduce energy expenditure of negatively buoyant fishes that are also obligate swimmers. Despite marine predators often residing within high-current area, no study has investigated the potential role of the energetic landscape in driving such habitat selectivity. Over 500 grey reef sharks Carcharhinus amblyrhynchos reside in the southern channel of Fakarava Atoll, French Polynesia. We used diver observations, acoustic telemetry and biologging to show that sharks use regions of predicted updrafts and switch their core area of space use based on tidal state (incoming versus outgoing). During incoming tides, sharks form tight groups and display shuttling behaviour (moving to the front of the group and letting the current move them to the back) to maintain themselves in these potential updraft zones. During outgoing tides, group dispersion increases, swimming depths decrease and shuttling behaviours cease. These changes are likely due to shifts in the nature and location of the updraft zones, as well as turbulence during outgoing tides. Using a biomechanical model, we estimate that routine metabolic rates for sharks may be reduced by 10%-15% when in updraft zones. Grey reef sharks save energy using predicted updraft zones in channels and 'surfing the slope'. Analogous to birds using wind-driven updraft zones, negatively buoyant marine animals may use current-induced updraft zones to reduce energy expenditure. Updrafts should be incorporated into dynamic energy landscapes and may partially explain the distribution, behaviour and potentially abundance of marine predators.

Natural hybridization between pen shell species: Pinna rudis and the critically endangered Pinna nobilis may explain parasite resistance in P. nobilis.

Recently, Pinna nobilis pen shells population in Mediterranean Sea has plummeted due to a Mass Mortality Event caused by an haplosporidian parasite. In consequence, this bivalve species has been included in the IUCN Red List as "Critically Endangered". In the current scenario, several works are in progress to protect P. nobilis from extinction, being identification of hybrids (P. nobilis x P. rudis) among survivors extremely important for the conservation of the species.Morphological characteristics and molecular analyses were used to identify putative hybrids. A total of 10 individuals of each species (P. nobilis and P. rudis) and 3 doubtful individuals were considered in this study. The putative hybrids showed shell morphology and mantle coloration intermingled exhibiting both P. nobilis and P. rudis traits. Moreover, the analyses of 1150 bp of the 28S gene showed 9 diagnostic sites between P. rudis and P. nobilis, whereas hybrids showed both parental diagnostic alleles at the diagnostic loci. Regarding the multilocus genotypes from the 8 microsatellite markers, the segregation of two Pinna species was clearly detected on the PCoA plot and the 3 hybrids showed intermediate positions.This is the first study evidencing the existence of hybrids P. nobilis x P. rudis, providing molecular methodology for a proper identification of new hybrids. Further studies testing systematically all parasite-resisting isolated P. nobilis should be undertaken to determine if the resistance is resulting from introgression of P. rudis into P. nobilis genome and identifying aspects related to resistance.

Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population.

The relative contributions of environmental, maternal and additive genetic factors to the Lifetime reproductive success (LRS) determine whether species can adapt to rapid environmental change. Yet to date, studies quantifying LRS across multiple generations in marine species in the wild are non-existent. Here we used 10-year pedigrees resolved for a wild orange clownfish population from Kimbe Island (PNG) and a quantitative genetic linear mixed model approach to quantify the additive genetic, maternal and environmental contributions to variation in LRS for the self-recruiting portion of the population. We found that the habitat of the breeder, including the anemone species and geographic location, made the greatest contribution to LRS. There were low to negligible contributions of genetic and maternal factors equating with low heritability and evolvability. Our findings imply that our population will be susceptible to short-term, small-scale changes in habitat structure and may have limited capacity to adapt to these changes.

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate.

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m2 of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.

Thermal tolerance and hypoxia tolerance are associated in blacktip reef shark (Carcharhinus melanopterus) neonates.

Thermal dependence of growth and metabolism can influence thermal preference and tolerance in marine ectotherms, including threatened and data-deficient species. Here, we quantified the thermal dependence of physiological performance in neonates of a tropical shark species (blacktip reef shark, Carcharhinus melanopterus) from shallow, nearshore habitats. We measured minimum and maximum oxygen uptake rates (MO2 ), calculated aerobic scope, excess post-exercise oxygen consumption and recovery from exercise, and measured critical thermal maxima (CTmax), thermal safety margins, hypoxia tolerance, specific growth rates, body condition and food conversion efficiencies at two ecologically relevant acclimation temperatures (28 and 31°C). Owing to high post-exercise mortality, a third acclimation temperature (33°C) was not investigated further. Acclimation temperature did not affect MO2  or growth, but CTmax and hypoxia tolerance were greatest at 31°C and positively associated. We also quantified in vitro temperature (25, 30 and 35°C) and pH effects on haemoglobin-oxygen (Hb-O2) affinity of wild-caught, non-acclimated sharks. As expected, Hb-O2 affinity decreased with increasing temperatures, but pH effects observed at 30°C were absent at 25 and 35°C. Finally, we logged body temperatures of free-ranging sharks and determined that C. melanopterus neonates avoided 31°C in situ We conclude that C. melanopterus neonates demonstrate minimal thermal dependence of whole-organism physiological performance across a seasonal temperature range and may use behaviour to avoid unfavourable environmental temperatures. The association between thermal tolerance and hypoxia tolerance suggests a common mechanism warranting further investigation. Future research should explore the consequences of ocean warming, especially in nearshore, tropical species.

New microsatellite DNA markers to resolve population structure of the convict surgeonfish, Acanthurus triostegus, and cross-species amplifications on thirteen other Acanthuridae.

Microsatellites are widely used to investigate connectivity and parentage in marine organisms. Despite surgeonfish (Acanthuridae) being dominant members of most reef fish assemblages and having an ecological key role in coral reef ecosystems, there is limited information describing the scale at which populations are connected and very few microsatellite markers have been screened. Here, we developed fourteen microsatellite markers for the convict surgeonfish Acanthurus triostegus with the aim to infer its genetic connectivity throughout its distribution range. Genetic diversity and variability was tested over 152 fishes sampled from four locations across the Indo-Pacific: Mayotte (Western Indian Ocean), Papua New Guinea and New Caledonia (Southwestern Pacific Ocean), and Moorea (French Polynesia). Over all locations, the number of alleles per locus varied from 5 to 24 per locus, and expected heterozygosities ranged from 0.468 to 0.941. Significant deviations from Hardy-Weinberg equilibrium were detected for two loci in two to three locations and were attributed to the presence of null alleles. These markers revealed for the first time a strong and significant distinctiveness between Indian Ocean and Pacific Ocean A. triostegus populations. We further conducted cross-species amplification tests in 13 Pacific congener species to investigate the possible use of these microsatellites in other Acanthuridae species. The phylogenetic placement of A. triostegus branching off from the clade containing nearly all Acanthurus + Ctenochaetus species likely explain the rather good transferability of these microsatellite markers towards other Acanthuridae species. This suggests that this fourteen new microsatellite loci will be helpful tools not only for inferring population structure of various surgeonfish but also to clarify systematic relationships among Acanthuridae.

Development of 26 highly polymorphic microsatellite markers for the highly endangered fan mussel Pinna nobilis and cross-species amplification.

The fan mussel, Pinna nobilis is a highly endangered bivalve species endemic to the Mediterranean Sea. During the last few decades, populations have been greatly reduced due to anthropic impacts and they are now under strict protection in most Mediterranean countries. Today, the species is facing a major crisis following the introduction of an haplosporidan parasite which is driving mass mortality in almost all P. nobilis populations throughout the Mediterranean Sea. Gathering additional knowledge regarding dynamics and connectivity patterns of P. nobilis populations is now more than ever critical. Here, we describe the development of 26 highly polymorphic microsatellite markers. Average allelic diversity of 10.9 alleles per locus was reported and heterozygosity ranged from 0.0294 to 0.9737. We tested cross-species amplification in four Pinna species for the new markers together with 10 already published markers, and analysed its success according to the genetic distances among species. Cross-species transferability success ranged from 3 to 38% and had a negative relationship with the genetic distance between the target species and the tested species. The establishment of this new set of high-resolution markers provides a useful tool to understand processes driving gene flow and genetic diversity in P. nobilis populations and the closest congeneric species.

Characterization of 25 new microsatellite markers for the fin whale (Balaenoptera physalus) and cross-species amplification in other cetaceans.

Cetaceans are large mammals widely distributed on Earth. The fin whale, Balaenoptera physalus, is the second largest living animal. In the 20th century, commercial whaling reduced its global population by 70%, and in the Mediterranean Sea not only was their overall population depleted but the migration between the Mediterranean Sea and the Atlantic Ocean was reduced. Previous genetic studies identified isolation between these two regions, with a limited gene-flow between these adjacent populations based on nuclear and mitochondrial markers. However, only limited information exists for the Mediterranean population as genetic diversity and abundance trends are still unknown. In this study, 39 highly polymorphic microsatellite markers were tested, including 25 markers developed de novo together with 14 markers previously published. An average allelic diversity of 8.3 alleles per locus was reported, ranging from 3 to 15 alleles per locus, for B. physalus. Expected heterozygosity was variable among loci and ranged from 0.34 to 0.91. Only two markers in the new set were significantly deviant from the Hardy Weinberg equilibrium. Cross-species amplification was tested in four other cetacean species. A total of 27 markers were successfully amplified in the four species (Balaenoptera acutorostrata, Megaptera novaeangliae, Physeter macrocephalus and Globicephala melas). A multivariate analysis on the multilocus genotypes successfully discriminated the five species. This new set of microsatellite markers will not only provide a useful tool to identify and understand the genetic diversity and the evolution of the B. physalus population, but it will also be relevant for other cetacean species, and will allow further parentage analyses. Eventually, this new set of microsatellite markers will provide critical data that will shed light on important biological data within a conservation perspective.

Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus).

The evolutionary history of species is a dynamic process as they modify, expand, and contract their spatial distributions over time. Range expansions (REs) occur through a series of founder events that are followed by migration among neighboring demes. The process usually results in structured metapopulations and leaves a distinct signature in the genetic variability of species. Explicitly modeling the consequences of complex demographic events such as REs is computationally very intensive. Here we propose an an alternative approach that requires less computational effort than a comprehensive RE model, but that can recover the demography of species undergoing a RE, by combining spatially explicit modelling with simplified but realistic metapopulation models. We examine the demographic and colonization history of Carcharhinus melanopterus, an abundant reef-associated shark, as a test case. We first used a population genomics approach to statistically confirm the occurrence of a RE in C. melanopterus, and identify its origin in the Indo-Australian Archipelago. Spatial genetic modelling identified two waves of stepping-stone colonization: an eastward wave moving through the Pacific and a westward one moving through the Indian Ocean. We show that metapopulation models best describe the demographic history of this species and that not accounting for this may lead to incorrectly interpreting the observed genetic variation as signals of widespread population bottlenecks. Our study highlights insights that can be gained about demography by coupling metapopulation models with spatial modeling and underscores the need for cautious interpretation of population genetic data when advancing conservation priorities.

First genealogy for a wild marine fish population reveals multigenerational philopatry.

Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.