First genealogy for a wild marine fish population reveals multigenerational philopatry

Anemonefishes: A model system for evolutionary genomics

Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.

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.

Evaluating new species for aquaculture: A genomic dissection of growth in the New Zealand silver trevally (Pseudocaranx georgianus)

Aquaculture is the fastest-growing food production sector worldwide, yet industry has been slow to implement genomic techniques as routine tools. Applying genomics to new breeding programmes can provide important information about pedigree structure and genetic diversity; key parameters for a successful long-term breeding programme. It can also provide insights on potential gains for commercially important, yet complex, quantitative traits such as growth rate. Here we investigated a population of 1100 captive-bred F1 silver trevally (Pseudocaranx georgianus), a promising new species for New Zealand aquaculture. We used whole-genome information, coupled with image-based phenotypic data collected over two years, to build the pedigree of the population, assess its genetic diversity, describe growth patterns of ten growth traits and estimate their genetic parameters. Successful parentage assignment of 664 F1 individuals showed that the pedigree consisted of a complex mixture of full- and half-sib individuals, with skewed reproductive success among parents, especially in females. Growth patterns showed seasonal fluctuations (average increase across all traits of 27.3% in summer and only 7% in winter) and strong inter-family differences. Heritability values for growth traits ranged from 0.27 to 0.76. Genetic and phenotypic correlations between traits were high and positive, ranging from 0.57 to 0.94 and 0.50 to 1.00 respectively. The implications of these findings are threefold: first, the best on-growing conditions are in warmer months, where highest growth peaks can be achieved; second, size- and family-based selection can be used as early selection criterion if pedigree structure and inbreeding risks are closely monitored; third, selection for body length results in concomitant increases in height and weight, traits of paramount importance for aquaculture. It is concluded that there is substantial potential for genetic improvement of economically important traits, suggesting that silver trevally is a promising species for selective breeding for enhanced growth.

Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis

Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, Pinna nobilis, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, Haplosporidium pinnae. In this context, we focused on a single population (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in 2011, 2015, and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (H o) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011-2015 and 2015-2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9% of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that P. nobilis exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by H. pinnae, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.

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.

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact

BACKGROUND

One of the most charismatic, and yet not completely resolved example of mutualistic interaction is the partnership of clownfish and its symbiotic sea anemone. The mechanism explaining this tolerance currently relies on the molecular mimicry of clownfish epithelial mucus, which could serve as camouflage, preventing the anemone's nematocysts' discharge. Resident bacteria are known as key drivers of epithelial mucus chemical signature in vertebrates. A recent study has proposed a restructuration of the skin microbiota in a generalist clown fish when first contacting its symbiotic anemone. We explored a novel hypothesis by testing the effect of remote interaction on epithelial microbiota restructuration in both partners.

METHODS

With metataxonomics, we investigated the epithelial microbiota dynamic of 18 pairs of percula clownfish (Amphiprion percula) and their symbiotic anemone Heteractis magnifica in remote interaction, physical interaction and control groups for both partners during a 4-week trial.

RESULTS

The Physical and Remote Interaction groups' results evidence gradual epithelial microbiota convergence between both partners when fish and anemone were placed in the same water system. This convergence occurred preceding any physical contact between partners, and was maintained during the 2-week interaction period in both contact groups. After the interaction period, community structure of both fish and anemone's epthelial community structures maintained the interaction signature 2 weeks after fish-anemone pairs' separation. Furthermore, the interaction signature persistence was observed both in the Physical and Remote Interaction groups, thus suggesting that water-mediated chemical communication between symbiotic partners was strong enough to shift the skin microbiota durably, even after the separation of fish-anemone pairs. Finally, our results suggest that fish-anemone convergent microbiota restructuration was increasingly associated with the parallel recruitment of three Flavobacteriaceae strains closely related to a tyrosinase-producing Cellulophaga tyrosinoxydans.

CONCLUSIONS

Our study shows that bacterial community restructuration, in the acclimation process, does not only rely on direct physical contact. Furthermore, our results challenge, for the first time, the traditional unidirectional chemical camouflage hypothesis, as we argue that convergence of the epithelial microbiota of both partners may play essential roles in establishing mutual acceptance. Video abstract Fish-anemone symbiotic relationship.

Anemonefish, a model for Eco-Evo-Devo

Anemonefish, are a group of about 30 species of damselfish (Pomacentridae) that have long aroused the interest of coral reef fish ecologists. Combining a series of original biological traits and practical features in their breeding that are described in this paper, anemonefish are now emerging as an experimental system of interest for developmental biology, ecology and evolutionary sciences. They are small sized and relatively easy to breed in specific husbandries, unlike the large-sized marine fish used for aquaculture. Because they live in highly structured social groups in sea anemones, anemonefish allow addressing a series of relevant scientific questions such as the social control of growth and sex change, the mechanisms controlling symbiosis, the establishment and variation of complex color patterns, and the regulation of aging. Combined with the use of behavioral experiments, that can be performed in the lab or directly in the wild, as well as functional genetics and genomics, anemonefish provide an attractive experimental system for Eco-Evo-Devo.

Natal philopatry increases relatedness within groups of coral reef cardinalfish

A central issue in evolutionary ecology is how patterns of dispersal influence patterns of relatedness in populations. In terrestrial organisms, limited dispersal of offspring leads to groups of related individuals. By contrast, for most marine organisms, larval dispersal in open waters is thought to minimize kin associations within populations. However, recent molecular evidence and theoretical approaches have shown that limited dispersal, sibling cohesion and/or differential reproductive success can lead to kin association and elevated relatedness. Here, we tested the hypothesis that limited dispersal explains small-scale patterns of relatedness in the pajama cardinalfish Sphaeramia nematoptera. We used 19 microsatellite markers to assess parentage of 233 juveniles and pairwise relatedness among 527 individuals from 41 groups in Kimbe Bay, Papua New Guinea. Our findings support three predictions of the limited dispersal hypothesis: (i) elevated relatedness within groups, compared with among groups and elevated relatedness within reefs compared with among reefs; (ii) a weak negative correlation of relatedness with distance; (iii) more juveniles than would be expected by chance in the same group and the same reef as their parents. We provide the first example for natal philopatry at the group level causing small-scale patterns of genetic relatedness in a marine fish.

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.

Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning

How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. Integrating meta-analysis, field data, and population modeling, we show that the ocean’s smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs.

Clownfishes evolution below and above the species level

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

Development of a site fidelity index based on population capture-recapture data

Background

Site fidelity is considered as an animal’s tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal’s life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies.

Methods

This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson’s dolphins (Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability (p). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case.

Results

Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index—SSFI).

Discussion

The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons.