Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity

Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.     

Extinction vulnerability of coral reef fishes

With rapidly increasing rates of contemporary extinction, predicting extinction vulnerability and identifying how multiple stressors drive non-random species loss have become key challenges in ecology. These assessments are crucial for avoiding the loss of key functional groups that sustain ecosystem processes and services. We developed a novel predictive framework of species extinction vulnerability and applied it to coral reef fishes. Although relatively few coral reef fishes are at risk of global extinction from climate disturbances, a negative convex relationship between fish species locally vulnerable to climate change vs. fisheries exploitation indicates that the entire community is vulnerable on the many reefs where both stressors co-occur. Fishes involved in maintaining key ecosystem functions are more at risk from fishing than climate disturbances. This finding is encouraging as local and regional commitment to fisheries management action can maintain reef ecosystem functions pending progress towards the more complex global problem of stabilizing the climate.     

Early survivorship of juvenile coral reef fishes

Data on early survivorship of newly settled reef fish were collected by monitoring individuals which recruited to 30 small lagoonal patch reefs over three summers. Preliminary survivorship curves spanning the first 45 days after settlement were derived for 17 species. Most species showed greatest rates of mortality in the first 1–2 weeks in the reef environment however there were substantial differences among species in the extent and the temporal pattern of this. In six species, 75% of individuals survived the 45 days, while in 5 others, 20% or fewer survived that long. In eight species, mortality was negligible after the first 14 days. In the other 9, significant mortality occurred in subsequent weeks. Patterns of survivorship did not appear to differ substantially among years in five of the six species for which data were adequate. In particular, survivorship did not appear to be different among years even when levels of recruitment varied greatly.     

The stability of P in coral reef fishes

The constancy of phenotypic variation and covariation is an assumption that underlies most recent investigations of past selective regimes and attempts to predict future responses to selection. Few studies have tested this assumption of constancy despite good reasons to expect that the pattern of phenotypic variation and covariation may vary in space and time. We compared phenotypic variance-covariance matrices (P) estimated for populations of six species of distantly related coral reef fishes sampled at two locations on Australia's Great Barrier Reef separated by more than 1000 km. The intraspecific similarity between these matrices was estimated using two methods: matrix correlation and common principal component analysis. Although there was no evidence of equality between pairs of P, both statistical approaches indicated a high degree of similarity in morphology between the two populations for each species. In general, the hierarchical decomposition of the variance-covariance structure of these populations indicated that all principal components of phenotypic variance-covariance were shared but that they differed in the degree of variation associated with each of these components. The consistency of this pattern is remarkable given the diversity of morphologies and life histories encompassed by these species. Although some phenotypic instability was indicated, these results were consistent with a generally conserved pattern of multivariate selection between populations.     

Predation on juvenile coral reef fishes: an exclusion experiment

The densities of recruits on caged and uncaged areas were compared in an experiment done to show the extent of predation on recently metamorphosed coral reef fishes. The design was unlike typical caging experiments, however, in that areas were caged only for short periods of 20–30 days and several independent trials, testing the same null hypothesis, were run. This was done to avoid confounding the effects of excluding herbivorous fishes with the effects of excluding piscivorous fishes. A third treatment, partially-meshed cages, revealed that the experiment was complicated by several other factors. Some prey species were attracted to the high relief offered by the experimental structures. Others responded to the differences in shelter from predators by redispersing themselves among the treatments shortly after settlement. There was also at least one significant edge effect caused by fishes preferring to settle near the boundaries of all treatments. In spite of these difficulties, observations on known individuals revealed that rates of mortality were age-dependent and decreased rapidly after metamorphosis. More than 25% of such fishes disappeared during their first five days in the benthic habitat compared with >10% of fishes aged 6–10 days and no losses of fishes aged 11–15 days. These early losses are the greatest instantaneous rates of mortality yet documented for recruited reef fishes. The experiment also suggested different rates of early mortality for various groupings of species: individuals of solitary, sedentary species disappeared approximately half as fast as individuals of the more mobile, and the more gregarious, species. This is probably a true reflection of the different vulnerability of these groups to predation and it may be caused by the different ways in which these fishes use the coral substratum. Our experience suggests that caging artifacts can have major impacts on the results obtained from this type of experiment and they must be controlled for adequately. We conclude that studies of predation on reef fishes may be done more easily using other methods.     

Phylogeography and the conservation of coral reef fishes

Here we present a review of how the study of the geographic distribution of genetic lineages (phylogeography) has helped identify management units, evolutionary significant units, cryptic species, and areas of endemism, and how this information can help efforts to achieve effective conservation of coral reefs. These studies have confirmed the major biogeographic barriers that were originally identified by tropical species distributions. Ancient separations, identified primarily with mtDNA sequence comparisons, became apparent between populations on each side of the barriers. The general lack of correlation between pelagic larval duration and genetic connectivity across barriers indicates that life history and ecology can be as influential as oceanography and geography in shaping evolutionary partitions within ocean basins. Hence, conservation strategies require a recognition of ecological hotspots, those areas where habitat heterogeneity promotes speciation, in addition to more traditional approaches based on biogeography. Finally, the emerging field of genomics will add a new dimension to phylogeography, allowing the study of genes that are pertinent to recent and ongoing differentiation, and ultimately providing higher resolution to detect evolutionary significant units that have diverged in an ecological time scale.     

Community assembly and diversification in Indo-Pacific coral reef fishes

Theories of species coexistence have played a central role in ecology and evolutionary studies of the origin and maintenance of biodiversity in highly diverse communities. The concept of niche and associated theories predict that competition for available ecological space leads to a ceiling in species richness that influences further diversification patterns. By contrast, the neutral theory supports that speciation is stochastic and diversity independent. We examined the phylogenetic community structure and diversification rates in three families and 14 sites within coral reef fish communities from the Indian and Pacific oceans. Using the phylogenetic relationships among 157 species estimated with 2300 bp of mitochondrial DNA, we tested predictions in terms of species coexistence from the neutral and niche theories. At the regional scale, our findings suggest that phylogenetic community structure shifts during community assembly to a pattern of dispersion as a consequence of allopatric speciation in recent times but overall, variations in diversification rates did not relate with sea level changes. At the local scale, the phylogenetic community structure is consistent with a neutral model of community assembly since no departure from a random sorting of species was observed. The present results support a neutral model of community assembly as a consequence of the stochastic and unpredictable nature of coral reefs favoring generalist and sedentary species competing for living space rather than trophic resources. As a consequence, the observed decrease in diversification rates may be seen as the result of a limited supply of living space as expected in a finite island model.     

Importance of live coral habitat for reef fishes

Live corals are the key habitat forming organisms on coral reefs, contributing to both biological and physical structure. Understanding the importance of corals for reef fishes is, however, restricted to a few key families of fishes, whereas it is likely that a vast number of fish species will be adversely affected by the loss of live corals. This study used data from published literature together with independent field based surveys to quantify the range of reef fish species that use live coral habitats. A total of 320 species from 39 families use live coral habitats, accounting for approximately 8 % of all reef fishes. Many of the fishes reported to use live corals are from the families Pomacentridae (68 spp.) and Gobiidae (44 spp.) and most (66 %) are either planktivores or omnivores. 126 species of fish associate with corals as juveniles, although many of these fishes have no apparent affiliation with coral as adults, suggesting an ontogenetic shift in coral reliance. Collectively, reef fishes have been reported to use at least 93 species of coral, mainly from the genus Acropora and Porities and associate predominantly with branching growth forms. Some fish associate with a single coral species, whilst others can be found on more than 20 different species of coral indicating there is considerable variation in habitat specialisation among coral associated fish species. The large number of fishes that rely on coral highlights that habitat degradation and coral loss will have significant consequences for biodiversity and productivity of reef fish assemblages.     

Auditory sensitivity in settlement-stage larvae of coral reef fishes

The larval phase of most species of coral reef fishes is spent away from the reef in the pelagic environment. At the time of settlement, these larvae need to locate a reef, and recent research indicates that sound emanating from reefs may act as a cue to guide them. Here, the auditory abilities of settlement-stage larvae of four species of coral reef fishes (families Pomacentridae, Lutjanidae and Serranidae) and similar-sized individuals of two pelagic species (Carangidae) were tested using an electrophysiological technique, auditory brainstem response (ABR). Five of the six species heard frequencies in the 100–2,000 Hz range, whilst one carangid species did not detect frequencies higher than 800 Hz. The audiograms of the six species were of similar shape, with best hearing at lower frequencies between 100 and 300 Hz. Strong within-species differences were found in hearing sensitivity both among the coral reef species and among the pelagic species. Larvae of the coral reef species had significantly more sensitive hearing than the larvae of the pelagic species. The results suggest that settlement-stage larval reef fishes may be able to detect reef sounds at distances of a few 100 m. If true hearing thresholds are lower than ABR estimates, as indicated in some comparisons of ABR and behavioural methods, the detection distances would be much larger.     

Hypoxia tolerance in two juvenile estuary-dependent fishes

Hypoxia events, or low dissolved oxygen (DO) conditions, occur frequently in North Carolina estuaries during the summer. These events may have harmful effects on important fish stocks, including spot (Leiostomus xanthurus) and Atlantic menhaden (Brevoortia tyrannus), but their consequences are not well understood. We investigated direct mortality due to hypoxia in juvenile spot and Atlantic menhaden to determine how the extent of mortality varies with the severity of hypoxia and the duration of exposure, and to explore how vulnerability to hypoxia changes across species, fish size, and temperature.Atlantic menhaden and spot were tested at two temperatures, 25 and 30 °C, and three dissolved oxygen concentrations, 0.6, 0.9, and 1.2 ppm. Survival analyses were performed on the data relating survival rate of each species to dissolved oxygen concentration, duration of exposure, fish size, and temperature. The data were analyzed using an LC₅₀ approach for comparative purposes, and 12-h LC₅₀ estimates ranged from 0.9 to 1.1 ppm O₂. Spot and menhaden exposed to 1.2 ppm O₂ showed no mortality in 24 h at 25 °C, and only 30-40% mortality at 30 °C. In contrast, both species experienced 100% mortality in 2-6 h at 0.6 ppm O₂. There was an effect of size on hypoxia tolerance, with small spot being less tolerant than large spot, while the converse size effect was observed for menhaden. Spot were consistently less tolerant to hypoxia than menhaden and both species were less tolerant to hypoxia at 30 °C than at 25 °C. Preliminary experiments showed a 24-h acclimation to sublethal levels of hypoxia significantly reduced mortality upon subsequent exposure to lethal hypoxia concentrations.Our results indicate that direct mortality due to hypoxia will vary with species, size, and temperature, but will likely only be substantial when these species are exposed to oxygen concentrations less than about 1 ppm O₂. Given the severity of hypoxia necessary to cause mortality and the ability of fish to behaviorally avoid hypoxia, direct mortality due to hypoxia may have limited impacts on fish population dynamics. Therefore, the greatest effects due to hypoxia may be caused by the stress imposed by sublethal hypoxic conditions alone or in concert with other stressors, or by indirect effects incurred by avoiding hypoxic areas.     

From record performance to hypoxia tolerance: respiratory transition in damselfish larvae settling on a coral reef

The fastest swimming fishes in relation to size are found among coral reef fish larvae on their way to settle on reefs. By testing two damselfishes, Chromis atripectoralis and Pomacentrus amboinensis, we show that the high swimming speeds of the pre-settlement larvae are accompanied by the highest rates of oxygen uptake ever recorded in ectothermic vertebrates. As expected, these high rates of oxygen uptake occur at the cost of poor hypoxia tolerance. However, hypoxia tolerance is needed when coral reef fishes seek nocturnal shelter from predators within coral colonies, which can become severely hypoxic microhabitats at night. When the larvae settle on the reef, we found that they go through a striking respiratory transformation, i.e. the capacity for rapid oxygen uptake falls, while the ability for high-affinity oxygen uptake at low oxygen levels is increased. This transition to hypoxia tolerance is needed when they settle on the reef; this was strengthened by our finding that small resident larvae of Acanthochromis polyacanthus, a damselfish lacking a planktonic larval stage, do not display such a transition, being well adapted to hypoxia and showing relatively low maximum rates of oxygen uptake that change little with age.     

The effect of coral morphology on shelter selection by coral reef fishes

While the loss of structural complexity causes declines in coral reef fish diversity, the processes leading to this decline are largely unexplained. To explore the role of coral morphology in providing shelter for fishes, tabular, branching and massive corals were filmed with video cameras and their usage by large reef fishes compared. Tabular corals were utilised more than the other two morphologies, with at least triple the abundance, biomass and residence times of large fishes. The preference of coral reef fishes for specific structural traits of tabular corals was also examined using artificial structural units. This experimental component showed that large reef fishes preferred opaque rather than translucent canopies. It appears that large fishes cue to tabular corals because of the concealment and/or shade provided. It is suggested that a loss of tabular corals as a result of climate change would have significant ecological impacts for the coral reef fishes that use these structures for shelter.     

Determinants of community structure for coral reef fishes in isolated coral heads at lagoonal and reef slope sites

Summary Ten small isolated corals were selected as units, of habitat in each of two nearby reef sites-a lagoon and a reef slope. On six occasions over two years we collected all fishes resident in each of these corals. Collections yielded 827 fishes of 64 species from the lagoon and 525 fishes of 66 species from the slope, but at each site 12 common species comprised over 80% of the fishes collected. We examined the distribution of species of fishes among units of habitat to assess the extent to which partitioning of habitat was being carried out. Results are compared with others previously reported from a reef flat site. Species discriminated among different types of habitat offered, but to a different degree in each site. Discrimination was most pronounced at the slope site where 7 of the 12 commonest species did not occur in all three types of habitat offered, and least at the lagoon site where no common species failed to occupy both types of habitat offered. No temporal partitioning of habitat could be demonstrated. Fish did not distribute themselves among units of habitat of one type by means of precise microhabitat discrimination. No pair of species in either site could be shown to mutually avoid, or exclude one another from habitat units. At all three sites, chance patterns of recruitment and loss overwhelmingly determined species composition of the groups of fishes coexisting in single habitat units. The significance of these results for our understanding of the ecology of coral reef fishes is discussed.     

The ontogeny of home ranges: evidence from coral reef fishes

The concept of home ranges is fundamental to ecology. Numerous studies have quantified how home ranges scale with body size across taxa. However, these relationships are not always applicable intraspecifically. Here, we describe how the home range of an important group of reef fish, the parrotfishes, scales with body mass. With masses spanning five orders of magnitude, from the early postsettlement stage through to adulthood, we find no evidence of a response to predation risk, dietary shifts or sex change on home range expansion rates. Instead, we document a distinct ontogenetic shift in home range expansion with sexual maturity. Juvenile parrotfishes displayed rapid home range growth until reaching approximately 100–150 mm length. Thereafter, the relationship between home range and mass broke down. This shift reflected changes in colour patterns, social status and reproductive behaviour associated with the transition to adult stages. While there is a clear relationship between body mass and home ranges among adult individuals of different species, it does not appear to be applicable to size changes within species. Ontogenetic changes in parrotfishes do not follow expected mass–area scaling relationships.     

The adaptive significance of larval dispersal in coral reef fishes

Synopsis Coral reef fishes almost universally disperse over relatively great distances during a pelagic larval phase. Barlow (1981) suggested that this dispersal is adaptive because adult fishes inhabit a patchy, uncertain environment. This reiterated an older idea that the random extinction of local populations necessarily favours dispersal, since ultimately all populations of non-dispersers will disappear. Whereas this view is based on adult survival, we emphasize a less frequent view that substantial larval dispersal may be adaptive when offspring experience patchy and unpredictable survival in the pelagic habitat. We do not address the question of why these animals ‘broadcast’ rather than ‘brood’, but suggest that species committed to pelagic offspring will be under selection to disperse siblings to spread the risk of failure among members of a cohort. Our arguments are supported by a heuristic computer simulation.     

Behavioural acclimation to cameras and observers in coral reef fishes

Observer presence can bias behavioural studies of animals in both the wild and the laboratory. Despite existing evidence for significant observer effects across several taxa, little is known about the minimum periods of acclimation that should precede behavioural observations. To date, most studies either do not report any acclimation periods or include a non‐specific period without empirically quantifying its appropriateness. Here, we conducted in situ behavioural observations of two species of demersal coral reef fishes using cameras and/or observers to examine the biases associated with either approach. For both treatments, we generated 25 min time series of a number of vigilance‐associated behaviours (i.e., distance from shelter and mate, time out of shelter, swimming activity) and estimated the point of acclimation using changepoint analysis. In the camera trials, acclimation in both species appeared to occur between 2 and 7 min for different behaviours. When an observer was present, however, no apparent acclimation occurred until the observer left the area. Overall, our findings demonstrate that (i) behavioural studies of wild fishes conducted by an observer may be biased due to permanent observer effects, and (ii) when using video equipment, a species‐ and behaviour‐specific acclimation period should precede behavioural scoring.     

On the spatial scale of dispersal in coral reef fishes

Marine biologists have gone through a paradigm shift, from the assumption that marine populations 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.     

Modelling larval dispersal and behaviour of coral reef fishes

Coral reef fish spend their first few weeks developing in the open ocean, where eggs and larvae appear merciless to tides and currents, before attempting to leave the pelagic zone and settle on a suitable reef. This pelagic dispersal phase is the process that determines population connectivity and allows replenishment of harvested populations across multiple coral reef habitats. Until recently this pelagic larval dispersal phase has been poorly understood and has often been referred to as the ‘black-box’ in the life-history of coral reef fishes. In this perspective article we highlight three areas where mathematical and computational approaches have been used to aid our understanding of this important ecological process. We discuss models that provide insights into the evolution of the pelagic larval phase in coral reef fish, an unresolved question which lends itself well to a modelling approach due to the difficulty in obtaining empirical data on this life history strategy. We describe how studies of fish hearing and physical sound propagation models can be used to predict the detection distance of reefs for settling larval fish, and the potential impact of anthropogenic noise. We explain how random walk models can be used to explore individual- and group-level behaviour in larval fish during the dispersal and settlement stage of their life-history. Finally, we discuss the mutual benefits that mathematical and computational approaches have brought to and gained from the field of larval behaviour and dispersal of reef fishes.     

Choice of microhabitats by coral reef fishes at settlement

A set of small lagoonal patch reefs was searched every 1 to 3 days during the peak recruitment seasons of three summers and newly settled juvenile fishes were located. The majority of species remain rather sedentary during the first few days in the demersal environment, and we assumed that the site occupied was the site chosen at settlement. A series of characteristics of the occupied site were recorded, including percent cover of different types of substratum, and attributes related to the site's position on the patch reef. A set of null sites was randomly located on the same reefs for comparison with those selected by the fish. Sites chosen by individuals of eight common species were compared with these null sites, and sites chosen by fourteen species (including the eight) were compared with each other. Multiple discriminant analysis was used to assess the degree to which each species selected a unique type of site, and, for the eight species, the degree to which sites chosen by fish could be discriminated from randomly selected sites on the same patch reefs. Chosen sites were readily discriminated from null sites in seven of eight species, however the procedure was poor at discriminating among sites chosen by different species, and 8 pairs of species among the 14 chose sites which on average did not differ in the attributes measured. Attributes most important in discriminating sites chosen by each species are considered. Overall, the results indicate that while juvenile fish do not settle indiscriminantly onto lagoonal patch reefs, sites chosen by different species are often not very different from one another.