Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes—actually a collection of traits—that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.

Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.

How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.

Abstract

Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.

Abstract

Egg trading—whereby simultaneous hermaphrodites exchange each other’s eggs for fertilization—constitutes one of the few rigorously documented and most widely cited examples of direct reciprocity among unrelated individuals. Yet how egg trading may initially invade a population of nontrading simultaneous hermaphrodites is still unresolved. Here, we address this question with an analytical model that considers mate encounter rates and costs of egg production in a population that may include traders (who provide eggs for fertilization only if their partners also have eggs to reciprocate), providers (who provide eggs regardless of whether their partners have eggs to reciprocate), and withholders (cheaters who mate only in the male role and just use their eggs to elicit egg release from traders). Our results indicate that a combination of intermediate mate encounter rates, sufficiently high costs of egg production, and a sufficiently high probability that traders detect withholders (in which case eggs are not provided) is conducive to the evolution of egg trading. Under these conditions, traders can invade—and resist invasion from—providers and withholders alike. The prediction that egg trading evolves only under these specific conditions is consistent with the rare occurrence of this mating system among simultaneous hermaphrodites.

Abstract

Abstract

Associations between resembling species have been noted long ago by naturalists and have been traditionally interpreted in terms of mimicry, whereby a mimetic species is naturally selected to resemble a model (Batesian and aggressive mimicry) or a co-mimic (Müllerian mimicry). Recently, it has been proposed that resemblances among reef fishes might be coincidental and that associations between them may result from social-traps, i.e., out-of-normal-context responses toward similar-looking individuals. The social-trap hypothesis is stimulating and calls for an in-depth reassessment of putative cases of mimicry in reef fishes. Nevertheless, an explicit field-based evaluation of these two hypotheses has yet to be conducted. Here, we test five specific predictions derived from the two hypotheses in the association between the butter hamlet (Hypoplectrus unicolor, Serranidae) and the foureye butterflyfish (Chaetodon capistratus, Chaetodontidae), which was one of the associations considered to develop the social-trap hypothesis. We present the results from 117 h of behavioral observation, 21 transect surveys covering 8400 m2 of reef, stomach content analysis of 107 fish, morphometric analysis of 165 fish and size measurements of 386 fish from Bocas del Toro, Panama. These data indicate that (i) C. capistratus is 14 times more abundant than H. unicolor at our study site, (ii) the association with C. capistratus represents only 4% of H. unicolor’s time, (iii) the association targets Coryphopterus gobies in particular and deceives this prey, (iv) H. unicolor departs from sympatric hamlets not only in terms of color pattern but also behavior, diet, size and body shape, and (v) H. unicolor spends only 0.66% of its time with conspecifics out of mating contexts. We conclude that the association between H. unicolor and C. capistratus in Bocas del Toro is a true mimetic relationship, but do not rule out the possibility that a social-trap might have contributed to its evolution.

Abstract

Stocking can be an effective management and conservation tool, but it also carries the danger of eroding natural population structure, introducing non-native strains and reducing genetic diversity. Sea trout, the anadromous form of the brown trout (Salmo trutta), is a highly targeted species that is often managed by stocking. Here, we assess the present-day population genetic structure of sea trout in a backdrop of 125 years of stocking in Northern Germany. The study area is characterized by short distances between the Baltic and North Sea river watersheds, historic use of fish from both watersheds for stocking, and the creation of a potential migration corridor between the Baltic and North Sea with the opening of the Kiel Canal 120 years ago. A survey of 24 river systems with 180 SNPs indicates that moderate but highly significant population genetic structure has persisted both within and between the Baltic and North Sea. This genetic structure is characterized by (i) heterogeneous patterns of admixture between the Baltic and North Sea that do not correlate with distance from the Kiel Canal and are therefore likely due to historic stocking practises, (ii) genetic isolation by distance in the Baltic Sea at a spatial scale of < 200 km that is consistent with the homing behaviour of sea trout, and (iii) at least one genetically distinct Baltic Sea river system. In light of these results, we recommend keeping fish of North Sea and Baltic Sea origin separate for stocking, and restricting Baltic Sea translocations to neighbouring river systems.

Abstract

When there is no recombination (achiamsy) in one sex, it is in the heterogametic one. This observation is so consistent that it constitutes one of the few patterns in biology that may be regarded as a ‘rule’ and Haldane proposed that it might be driven by selection against recombination in the sex chromosomes. Yet differences in recombination rate between the sexes (heterochiasmy) have also been reported in hermaphroditic species that lack sex chromosomes. In plants—the vast majority of which are hermaphroditic—selection at the haploid stage has been proposed to drive heterochiasmy. Yet few data are available for hermaphroditic animals, and barely any for hermaphroditic vertebrates. Here, we leverage reciprocal crosses between two black hamlets (Hypoplectrus nigricans, Serranidae), simultaneously hermaphroditic reef fishes from the wider Caribbean, to generate high-density egg- and sperm-specific linkage maps for each parent. We find globally higher recombination rates in the eggs, with dramatically pronounced heterochiasmy at the chromosome peripheries. We suggest that this pattern may be due to female meiotic drive, and that this process may be an important source of heterochiasmy in animals. We also identify a large non-recombining region that may play a role in speciation and local adaptation in Hypoplectrus.

Abstract
Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly coloredreef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (Fst estimate = 0.0042) and sympatric species (Fst estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (Fst estimate
0), a very small proportion of Fst outlier loci (0.05–0.07%), and remarkably few repeated outliers (1–3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation.

Abstract
Because the vast majority of species are well diverged, relatively little is known about the genomic architecture of speciation during the early stages of divergence. Species within recent evolutionary radiations are often minimally diverged from a genomic perspective, and therefore provide rare opportunities to address this question. Here, we leverage the hamlet radiation (Hypoplectrus spp., brightly coloured reef fishes from the tropical western Atlantic) to characterize genomic divergence during the early stages of speciation. Transect surveys and spawning observations in Belize, Honduras and Panama confirm that sympatric barred (H. puella), black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically distinct and reproductively isolated, although hybrid spawnings and individuals with intermediate phenotypes are seen on rare occasions. A survey of approximately 100 000 restriction site-associated SNPs in 126 samples from the three species across the three replicate populations reveals extremely slight genomewide divergence among species (FST = 0.0038), indicating that ecomorphological differences and functional reproductive isolation are maintained in sympatry in a backdrop of extraordinary genomic similarity. Nonetheless, a very small proportion of SNPs (0.05% on average) are identified as FST outliers among sympatric species. Remarkably, a single SNP is identified as an outlier in repeated populations for the same species pair. A minicontig assembled de novo around this SNP falls into the genomic region containing the HoxCa10 and HoxCa11 genes in 10 teleost species, suggesting an important role for Hox gene evolution in this radiation. This finding, if confirmed, would provide a better understanding of the links between micro- and macroevolutionary processes.

Abstract

Whether sexual selection alone can drive the evolution of assortative mating in the presence of gene flow is a long-standing question in evolutionary biology. Here, we report a role for pairing dynamics of individuals when mate choice is mutual, which is sufficient for the evolution of assortative mating by sexual selection alone in the presence of gene flow. Through behavioural observation, individual-based simulation and population genetic analysis, we evaluate the pairing dynamics of coral reef fish in the genus Hypoplectrus (Serranidae), and the role these dynamics can play for the evolution of assortative mating. When mate choice is mutual and the stability of mating pairs is critical for reproductive success, the evolution of assortative mating in the presence of gene flow is not only possible, but is also a robust evolutionary outcome.

Abstract
Marine biologists have gone through a paradigm shift, from the assumption that marinepopulations are largely ‘open’ owing to extensive larval dispersal to the realization that marine dispersal is ‘more restricted than previously thought’. Yet, population genetic studies often reveal low levels of genetic structure across large geographic areas. On the other side, more direct approaches such as mark-recapture provide evidence of localized dispersal. To what extent can direct and indirect studies of marine dispersal be reconciled? One approach consists in applying genetic methods that have been validated with direct estimates of dispersal. Here, we use such an approach—genetic isolation by distance between individuals in continuous populations—to estimate the spatial scale of dispersal in five species of coral reef fish presenting low levels of genetic structure across the Caribbean. Individuals were sampled continuously along a 220-km transect following the Mesoamerican Barrier Reef, population densities were estimated from surveys covering 17 200 m2 of reef, and samples were genotyped at a total of 58 microsatellite loci. A small but positive isolation-by-distance slope was observed in the five species, providing mean parent-offspring dispersal estimates ranging between 7 and 42 km (CI 1–113 km) and suggesting that there might be a correlation between minimum/maximum pelagic larval duration and dispersal in coral reef fishes. Coalescent-based simulations indicate that these results are robust to a variety of dispersal distributions and sampling designs. We conclude that low levels of genetic structure across large geographic areas are not necessarily indicative of extensive dispersal at ecological timescales.

Abstract

Matching was developed in the 1960s to match such entities as residents and hospitals, colleges and students, or employers and employees. This approach is based on ‘‘preference lists,’’ whereby each participant ranks potential partners according to his/her preferences and tries to match with the highest-ranking partner available. Here, we discuss the implications of matching for the study of mate choice and speciation. Matching differs from classic approaches in several respects, most notably because under this theoretical framework, the formation of mating pairs is context-dependant (i.e., it depends on the configuration of pairings in the entire population), because the stability of mating pairs is considered explicitly, and because mate choice is mutual. The use of matching to study mate choice and speciation is not merely a theoretical curiosity; its application can generate counter-intuitive predictions and lead to conclusions that differ fundamentally from classic theories about sexual selection and speciation. For example, it predicts that when mate choice is mutual and the stability of mating pairs is critical for successful reproduction, sympatric speciation is a robust evolutionary outcome. Yet the application of matching to the study of mate choice and speciation has been largely dominated by theoretical studies. We present the hamlets, a group of brightly colored Caribbean coral reef fishes in the genus Hypoplectrus (Serranidae), as a particularly apt system to test empirically specific predictions generated by the application of matching to mate choice and speciation.

Abstract

The spatial scale of dispersal in coral reef fishes eludes ecologists despite the importance of this parameter for understanding the dynamics of ecological and evolutionary processes. Genetic isolation by distance (IBD) has been used to estimate dispersal in coral reef fishes, but its application in marine systems has been limited by insufficient sampling at different spatial scales and a lack of information regarding population density. Here, we present an analysis of IBD in the barred hamlet (Hypoplectrus puella, Serranidae) at spatial scales ranging from 10 to 3200 km complemented with SCUBA surveys of population densities covering 94 000 m2 of reef. We used 10 hypervariable DNA markers to genotype 854 fish from 15 locations, and our results establish that IBD in H. puella emerges at a spatial scale of 175 km and is preserved up to the regional scale (3200 km). Assuming a normal or a Laplace dispersal function, our data are consistent with mean dispersal distances in H. puella that range between 2 and 14 km. Such small mean dispersal distances is a surprising result given the three-week pelagic larval duration of H. puella and the low level of genetic structure at the Caribbean scale (Wright’s fixation index, FST, estimate=0.005). Our data reinforce the importance of considering population density when estimating dispersal from IBD and underscore the relevance of sampling at local scales, even when genetic structure is weak at the regional scale.

Abstract

Absolute barriers to dispersal are not common in marine systems, and the prevalence of planktonic larvae in marine taxa provides potential for gene flow across large geographic distances. These observations raise the fundamental question in marine evolutionary biology as to whether geographic and oceanographic barriers alone can account for the high levels of species diversity observed in marine environments such as coral reefs, or whether marine speciation also operates in the presence of gene flow between diverging populations. In this respect, the ecological hypothesis of speciation, in which reproductive isolation results from divergent or disruptive natural selection, is of particular interest because it may operate in the presence of gene flow. Although important insights into the process of ecological speciation in aquatic environments have been provided by the study of freshwater fishes, comparatively little is known about the possibility of ecological speciation in marine teleosts. In this study, the evidence consistent with different aspects of the ecological hypothesis of speciation is evaluated in marine fishes. Molecular approaches have played a critical role in the development of speciation hypotheses in marine fishes, with a role of ecology suggested by the occurrence of sister clades separated by ecological factors, rapid cladogenesis or the persistence of genetically and ecologically differentiated species in the presence of gene flow. Yet, ecological speciation research in marine fishes is still largely at an exploratory stage. Cases where the major ingredients of ecological speciation, namely a source of natural divergent or disruptive selection, a mechanism of reproductive isolation and a link between the two have been explicitly documented are few. Even in these cases, specific predictions of the ecological hypothesis of speciation remain largely untested. Recent developments in the study of freshwater fishes illustrate the potential for molecular approaches to address specific questions related to the ecological hypothesis of speciation such as the nature of the genes underlying key ecological traits, the magnitude of their effect on phenotype and the mechanisms underlying their differential expression in different ecological contexts. The potential provided by molecular studies is fully realized when they are complemented with alternative (e.g. ecological, theoretical) approaches.

Abstract
Large-scale, spatially explicit models of adaptive radiation suggest that the spatial genetic structure within a species sampled early in the evolutionary history of an adaptive radiation might be higher than the genetic differentiation between different species formed during the same radiation over all locations. Here we test this hypothesis with a spatial population genetic analysis of Hypoplectrus coral reef fishes (Serranidae), one of the few potential cases of a recent adaptive radiation documented in the marine realm. Microsatellite analyses of Hypoplectrus puella (barred hamlet) and Hypoplectrus nigricans (black hamlet) from Belize, Panama and Barbados validate the population genetic predictions at the regional scale for H. nigricans despite the potential for high levels of gene flow between populations resulting from the 3-week planktonic larval phase of Hypoplectrus. The results are different for H. puella, which is characterized by significantly lower levels of spatial genetic structure than H. nigricans. An extensive field survey of Hypoplectrus population densities complemented by individual-based simulations shows that the higher abundance and more continuous distribution of H. puella could account for the reduced spatial genetic structure within this species. The genetic and demographic data are also consistent with the hypothesis that H. puella might represent the ancestral form of the Hypoplectrus radiation, and that H. nigricans might have evolved repeatedly from H. puella through ecological speciation. Altogether, spatial genetic analysis within and between Hypoplectrus species indicate that local processes can operate at a regional scale within recent marine adaptive radiations.

Abstract

Theory shows that speciation in the presence of gene flow occurs only under narrow conditions. One of the most favourable scenarios for speciation with gene flow is established when a single trait is both under disruptive natural selection and used to cue assortative mating. Here, we demonstrate the potential for a single trait, colour pattern, to drive incipient speciation in the genus Hypoplectrus (Serranidae), coral reef fishes known for their striking colour polymorphism. We provide data demonstrating that sympatric Hypoplectrus colour morphs mate assortatively and are genetically distinct. Furthermore, we identify ecological conditions conducive to disruptive selection on colour pattern by presenting behavioural evidence of aggressive mimicry, whereby predatory Hypoplectrus colour morphs mimic the colour patterns of non-predatory reef fish species to increase their success approaching and attacking prey. We propose that colour-based assortative mating, combined with disruptive selection on colour pattern, is driving speciation in Hypoplectrus coral reef fishes.