Evolutionary history of the parrotfishes: biogeography, ecomorphology, and comparative diversity

Ontogenetic shifts in body form in the bull shark Carcharhinus leucas

Recent studies have uncovered mosaic patterns of allometric and isometric growth underlying ontogenetic shifts in the body form of elasmobranch species (shark and rays). It is thought that shifts in trophic and spatial ecology through ontogeny drive these morphological changes; however, additional hypotheses relating to developmental constraints have also been posed. The bull shark (Carcharhinus leucas) is a large-bodied coastal shark that exhibits strong ontogenetic shifts in trophic and spatial ecology. In this study, we utilise a large data set covering a large number of morphological structures to reveal ontogenetic shifts in the body form of C. leucas, stratifying analyses by sex and size classes to provide fine-scale, more ecomorphologically relevant results. Our results indicate shifts in functional demands across the body through ontogeny, driven by selective pressures relating to trophic and spatial ecology driving the evolution of allometry. We also find significant differences in scaling trends between life stages, and between the sexes, highlighting the importance of utilising large, diverse datasets that can be stratified in this way to improve our understanding of elasmobranch morphological evolution. Ultimately, we discuss the implications of these results for existing ecomorphological hypotheses regarding the evolution of specific morphological structures, and pose novel hypotheses where relevant.

Plicidentine in the oral fangs of parrotfish (Scarinae, Labriformes)

Parrotfish play important ecological roles in coral reef and seagrass communities across the globe. Their dentition is a fascinating object of study from an anatomical, functional and evolutionary point of view. Several species maintained non-interlocked dentition and browse on fleshy algae, while others evolved a characteristic beak-like structure made of a mass of coalesced teeth that they use to scrape or excavate food off hard limestone substrates. While parrotfish use their highly specialized marginal teeth to procure their food, they can also develop a series of large fangs that protrude from the upper jaw, and more rarely from the lower jaw. These peculiar fangs do not participate in the marginal dentition and their function remains unclear. Here we describe the morphology of these fangs and their developmental relationship to the rest of the oral dentition in the marbled parrotfish (Leptoscarus vaigiensis), the star-eye parrotfish (Calotomus carolinus), and the palenose parrotfish (Scarus psittacus). Through microtomographic and histological analyses, we show that some of these fangs display loosely folded plicidentine along their bases, a feature that has never been reported in parrotfish. Plicidentine is absent from the marginal teeth and is therefore exclusive to the fangs. Parrotfish fangs develop a particular type of simplexodont plicidentine with a pulpal infilling of alveolar bone at later stages of dental ontogeny. The occurrence of plicidentine and evidence of extensive tooth wear, and even breakage, lead us to conclude that the fangs undergo frequent mechanical stress, despite not being used to acquire food. This strong mechanical stress undergone by fangs could be linked either to forced contact with congeners or with the limestone substrate during feeding. Finally, we hypothesize that the presence of plicidentine in parrotfish is not derived from a labrid ancestor, but is probably a recently evolved trait in some parrotfish taxa, which may even have evolved convergently within this subfamily.

Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes

Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.

Diel vertical movements and feeding behaviour of blue humphead parrotfish Scarus ovifrons in a temperate reef of Japan

The feeding ecology of scarinine parrotfishes on tropical coral reefs has received considerable attention in the past few decades; nonetheless, relatively few studies have been conducted in high-latitude reefs. Among the Indo-Pacific Scarus species, Scarus ovifrons is unique, being largely restricted to the warm temperate waters of Japan. Nonetheless, there is very little information available on the feeding ecology of this species. In this study, the authors used acoustic telemetry to detect the diel vertical movement patterns of S. ovifrons, video survey to detect its feeding depths and substrata and focal follow survey and genetic analysis to identify algae composition on the feeding scars at Kashiwajima Island, southwestern Japan (32° 46' N, 132° 38' E). Acoustic telemetry revealed that S. ovifrons spent most of its time in shallow water (<10 m) during the day and slept in deeper water (10-15 m) at night. Video and focal follow surveys revealed that most fishes of various sizes regularly took bites on epilithic algae and detrital materials on rocky substrata at depths of <10 m, but large fishes (>40 cm total length) sometimes took bites directly on live corals (Acropora solitaryensis) at the 5 m depth zone where live tabular corals dominated the benthos. Molecular phylogenetic analyses revealed that epilithic algae collected from feeding scars were mainly composed of Rhodophyta, and coralline algae were less often targeted. Overall, this study revealed that S. ovifrons feeds mostly at depths <10 m, and the feeding algae substrata of the species are similar to those of tropical coral reef parrotfishes.

A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.

Constraints on the Ecomorphological Convergence of Zooplanktivorous Butterflyfishes

Whether distantly related organisms evolve similar strategies to meet the demands of a shared ecological niche depends on their evolutionary history and the nature of form-function relationships. In fishes, the visual identification and consumption of microscopic zooplankters, selective zooplanktivory, is a distinct type of foraging often associated with a suite of morphological specializations. Previous work has identified inconsistencies in the trajectory and magnitude of morphological change following transitions to selective zooplanktivory, alluding to the diversity and importance of ancestral effects. Here we investigate whether transitions to selective zooplanktivory have influenced the morphological evolution of marine butterflyfishes (family Chaetodontidae), a group of small-prey specialists well known for several types of high-precision benthivory. Using Bayesian ancestral state estimation, we inferred the recent evolution of zooplanktivory among benthivorous ancestors that hunted small invertebrates and browsed by picking or scraping coral polyps. Traits related to the capture of prey appear to be functionally versatile, with little morphological distinction between species with benthivorous and planktivorous foraging modes. In contrast, multiple traits related to prey detection or swimming performance are evolving toward novel, zooplanktivore-specific optima. Despite a relatively short evolutionary history, general morphological indistinctiveness, and evidence of constraint on the evolution of body size, convergent evolution has closed a near significant amount of the morphological distance between zooplanktivorous species. Overall, our findings describe the extent to which the functional demands associated with selective zooplanktivory have led to generalizable morphological features among butterflyfishes and highlight the importance of ancestral effects in shaping patterns of morphological convergence.

Ecomorphological divergence and trophic resource partitioning in 15 syntopic Indo-Pacific parrotfishes (Labridae: Scarini)

Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.

Interspecific variation of prevalence by Scaphanocephalus (Platyhelminthes: Trematoda: Heterophyidae) metacercariae in parrotfishes (Labridae: Scarini) from an Okinawan coral reef

Metacercarial cysts of the parasite Scaphanocephalus (Platyhelminthes: Trematoda: Heterophyidae) are frequently found on the pectoral fins and skin of parrotfishes (Labridae: Scarini) inhabiting Okinawan coral reefs in southern Japan. The prevalence of metacercarial cysts in 30 parrotfish species was investigated and compared through a market survey. Although parasite prevalence differed between parrotfishes, all species examined are considered to be suitable hosts. Prevalence was high in Scarus chameleon (38.5%, n = 13), S. rubroviolaceus (33.4%, 2797), S. ghobban (26.6%, 6441), and several other species that share, in part, common feeding habits. Conversely, prevalence was low in S. prasiognathos (0.4%, 1842), Bolbometopon muricatum (0.4%, 270), and Hipposcarus longiceps (0.1%, 8512) which have different feeding habits. Despite a few exceptions, feeding ecology and other indirect behaviors are considered to affect the prevalence of metacercarial cysts in parrotfishes. Taxonomic affiliation and nocturnal mucous cocoon usage are not considered to affect parasite prevalence.

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Metacercarial cysts prevalence in parrotfishes was investigated.

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All the species seem to be suitable hosts, but prevalence differed among species.

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Feeding ecology is thought to affect the prevalence in parrotfishes.

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Nocturnal mucous cocoon use does not appear to influence parasite prevalence.

Colour dimorphism in labrid fishes as an adaptation to life on coral reefs

Conspicuous coloration displayed by animals that express sexual colour dimorphism is generally explained as an adaptation to sexual selection, yet the interactions and relative effects of selective forces influencing colour dimorphism are largely unknown. Qualitatively, colour dimorphism appears more pronounced in marine fishes that live on coral reefs where traits associated with strong sexual selection are purportedly more common. Using phylogenetic comparative analysis, we show that wrasses and parrotfishes exclusive to coral reefs are the most colour dimorphic, but surprisingly, the effect of habitat is not influenced by traits associated with strong sexual selection. Rather, habitat-specific selective forces, including clear water and structural refuge, promote the evolution of pronounced colour dimorphism that manifests colours less likely to be displayed in other habitats. Our results demonstrate that environmental context ultimately determines the evolution of conspicuous coloration in colour-dimorphic labrid fishes, despite other influential selective forces.

Functional morphogenesis from embryos to adults: Late development shapes trophic niche in coral reef damselfishes

The damselfishes are one of the dominant coral reef fish lineages. Their ecological diversification has involved repeated transitions between pelagic feeding using fast bites and benthic feeding using forceful bites. A highly-integrative approach that combined gene expression assays, shape analyses, and high-speed video analyses was used to examine the development of trophic morphology in embryonic, larval, juvenile, and adult damselfishes. The anatomical characters that distinguish pelagic-feeding and benthic-feeding species do not appear until after larval development. Neither patterns of embryonic jaw morphogenesis, larval skull shapes nor larval bite mechanics significantly distinguished damselfishes from different adult trophic guilds. Analyses of skull shape and feeding performance identified two important transitions in the trophic development of a single species (the orange clownfish; Amphiprion percula): (a) a pronounced transformation in feeding mechanics during metamorphosis; and (b) more protracted cranial remodeling over the course of juvenile development. The results of this study indicate that changes in postlarval morphogenesis have played an important role in damselfish evolution. This is likely to be true for other fish lineages, particularly if they consist of marine species, the majority of which have planktonic larvae with different functional requirements for feeding in comparison to their adult forms.

Age, growth, reproduction and management of Southwestern Atlantic's largest and endangered herbivorous reef fish, Scarus trispinosus Valenciennes, 1840

The Brazilian-endemic greenbeack parrotfish, Scarus trispinosus Valenciennes, 1840, is the largest herbivorous reef fish in the South Atlantic. Following the sharp decline of large carnivorous reef fishes, parrotfishes (Labridae: Scarinae) were progressively targeted by commercial fisheries in Brazil, resulting in a global population decline of 50% for S. trispinosus. Most of its remnant population is concentrated in the Abrolhos Bank, where the present study was conducted. We present novel information on age, growth and the reproductive cycle of S. trispinosus, based on 814 individuals obtained from commercial fisheries’ landings and scientific collections, between 2010 and 2013. Sex ratio was biased toward females (1:8), and spawning occurred year-round with discrete peaks in February-March and June-December. Increment analysis indicated annual deposition of growth rings in otoliths, which presented 1–22 rings. The asymptotic length at which growth is zero (L_∞) was estimated from a Bayesian logistic regression at 85.28 cm, growth rate (K) at 0.14 year⁻¹, and the theoretical age at zero size (t₀) at 0.16. Subregional demographic structuring was detected, with predominance of slower-growing individuals in shallower inshore reefs and predominance of faster-growing and older individuals in deeper offshore sites. We demonstrate that S. trispinosus is highly vulnerable to over-exploitation due to its large size, long live and slow-growth, and review the management measures proposed since its Red List assessment in 2012.

Low connectivity compromises the conservation of reef fishes by marine protected areas in the tropical South Atlantic

The total spatial coverage of Marine Protected Areas (MPAs) within the Brazilian Economic Exclusive Zone (EEZ) has recently achieved the quantitative requirement of the Aichii Biodiversity Target 11. However, the distribution of MPAs in the Brazilian EEZ is still unbalanced regarding the proportion of protected ecosystems, protection goals and management types. Moreover, the demographic connectivity between these MPAs and their effectiveness regarding the maintenance of biodiversity are still not comprehensively understood. An individual-based modeling scheme coupled with a regional hydrodynamic model of the ocean is used to determine the demographic connectivity of reef fishes based on the widespread genus Sparisoma found in the oceanic islands and on the Brazilian continental shelf between 10° N and 23° S. Model results indicate that MPAs are highly isolated due to extremely low demographic connectivity. Consequently, low connectivity and the long distances separating MPAs contribute to their isolation. Therefore, the current MPA design falls short of its goal of maintaining the demographic connectivity of Sparisoma populations living within these areas. In an extreme scenario in which the MPAs rely solely on protected populations for recruits, it is unlikely that they will be able to effectively contribute to the resilience of these populations or other reef fish species sharing the same dispersal abilities. Results also show that recruitment occurs elsewhere along the continental shelf indicating that the protection of areas larger than the current MPAs would enhance the network, maintain connectivity and contribute to the conservation of reef fishes.

Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data

Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources.

Identity of coral reef herbivores drives variation in ecological processes over multiple spatial scales

Overexploitation of key species can negatively impact ecosystem processes, so understanding the ecological roles of individual species is critical for improving ecosystem management. Here, we use coral reefs and the process of herbivory as a model to examine how species identity of consumers influence ecosystem processes to inform management of these consumers. Herbivorous fishes can facilitate the recruitment, growth, and recovery of corals by controlling the fast-growing algae that can outcompete corals for space. However, herbivorous fish guilds are species rich with important differences among species in diet, movement, and habitat preferences. Yet, we lack a general understanding of (1) how these species-specific differences in feeding and behavior scale up to reef-wide rates of ecosystem processes and (2) how species identity and diversity impact these processes. To address these knowledge gaps, we used field observations to derive key species- and size-specific foraging parameters for nine herbivorous parrotfish species on coral reefs in the Florida Keys, USA. We then combined these foraging parameters with fish survey data spanning multiple spatial scales to estimate the rates of three ecosystem processes: area of reef grazed, amount of macroalgae removed, and rate of bioerosion. We found that predicted rates of ecological processes varied dramatically among habitats and among reef zones within habitats, driven primarily by variation in abundance among species with different foraging behaviors. In some cases, assemblages with similar levels of total biomass had different rates of ecological processes, and in others, assemblages with different biomass had similar rates of ecological processes. Importantly, our models of herbivory using species-specific parameters differed from those using genus-level parameters by up to 300% in rates of ecological processes, highlighting the importance of herbivore identity in this system. Our results indicate that there may be little overlap in the roles species play, suggesting that some systems may be vulnerable to loss of ecological function with the reduction or loss of just a few species. This work provides a framework that can be applied across the region to predict how changes in management may affect the ecological impact of these important herbivores.

The evolution of traits and functions in herbivorous coral reef fishes through space and time

Herbivory by fishes has been identified as a key ecological process shaping coral reefs through time. Although taxonomically limited, herbivorous reef fishes display a wide range of traits, which results in varied ecosystem functions on reefs around the world. Yet, we understand little about how these trait combinations and functions in ecosystems changed through time and across biogeographic realms. Here, we used fossils and phylogenies in a functional ecological framework to reveal temporal changes in nominally herbivorous fish assemblages among oceanic basins in both trait space and lineage richness among functions. We show that the trait space occupied by extant herbivorous fishes in the Indo-Pacific resulted from an expansion of traits from the ancestral Tethyan assemblages. By contrast, trait space in the Atlantic is the result of lineage turnover, with relatively recent colonization by lineages that arose in the east Tethys/Indo-Pacific. From an ecosystem function perspective, the Atlantic supports a depauperate fauna, with few extant herbivorous reef fish lineages performing each function. Indo-Pacific fishes support both more functions and more lineages within each function, with a marked Miocene to Pleistocene expansion. These disparities highlight the importance of history in explaining global variation in fish functional composition on coral reefs.

Flickers of speciation: Sympatric colour morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence with gene flow

One of the primary challenges of evolutionary research is to identify ecological factors that favour reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive colour polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few metres apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among colour morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between colour morphs on the same reefs than that between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric colour morphs. Combined with complementary studies of hawkfish ecology and behaviour, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence, the arc-eye hawkfish fulfil theoretical expectations for the earliest phase of speciation with gene flow.

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae)

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary.

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

The adaptive radiation of the seven-spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.

Mitogenomic phylogeny of cone snails endemic to Senegal

Cone snails attain in Senegal one of their highest peaks of species diversity throughout the continental coast of Western Africa. A total of 15 endemic species have been described, all placed in the genus Lautoconus. While there is ample data regarding the morphology of the shell and the radular tooth of these species, virtually nothing is known regarding the genetic diversity and phylogenetic relationships of one of the most endangered groups of cones. In this work, we determined the complete or near-complete (only lacking the control region) mitochondrial (mt) genomes of 17 specimens representing 11 endemic species (Lautoconus belairensis, Lautoconus bruguieresi, Lautoconus cacao, Lautoconus cloveri, Lautoconus cf. echinophilus, Lautoconus guinaicus, Lautoconus hybridus, Lautoconus senegalensis, Lautoconus mercator, Lautoconus taslei, and Lautoconus unifasciatus). We also sequenced the complete mt genome of Lautoconus guanche from the Canary Islands, which has been related to the cones endemic to Senegal. All mt genomes share the same gene arrangement, which conforms to the consensus reported for Conidae, Neogastropoda and Caenogastropoda. Phylogenetic analyses using probabilistic methods recovered three major lineages, whose divergence coincided in time with sea level and ocean current changes as well as temperature fluctuations during the Messinian salinity crisis and the Plio-Pleistocene transition. Furthermore, the three lineages corresponded to distinct types of radular tooth (robust, small, and elongated), suggesting that dietary specialization could be an additional evolutionary driver in the diversification of the cones endemic to Senegal. The reconstructed phylogeny showed several cases of phenotypic convergence (cryptic species) and questions the validity of some species (ecotypes or phenotypic plasticity), both results having important taxonomic and conservation consequences.

Convergent evolution in social swallows (Aves: Hirundinidae)

Behavioral shifts can initiate morphological evolution by pushing lineages into new adaptive zones. This has primarily been examined in ecological behaviors, such as foraging, but social behaviors may also alter morphology. Swallows and martins (Hirundinidae) are aerial insectivores that exhibit a range of social behaviors, from solitary to colonial breeding and foraging. Using a well-resolved phylogenetic tree, a database of social behaviors, and morphological measurements, we ask how shifts from solitary to social breeding and foraging have affected morphological evolution in the Hirundinidae. Using a threshold model of discrete state evolution, we find that shifts in both breeding and foraging social behavior are common across the phylogeny of swallows. Solitary swallows have highly variable morphology, while social swallows show much less absolute variance in all morphological traits. Metrics of convergence based on both the trajectory of social lineages through morphospace and the overall morphological distance between social species scaled by their phylogenetic distance indicate strong convergence in social swallows, especially socially foraging swallows. Smaller physical traits generally observed in social species suggest that social species benefit from a distinctive flight style, likely increasing maneuverability and foraging success and reducing in-flight collisions within large flocks. These results highlight the importance of sociality in species evolution, a link that had previously been examined only in eusocial insects and primates.

Ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae

Parrotfish are fundamental species in controlling algal phase-shifts and ensuring the resilience of coral reefs. Nevertheless, little is known on their ecological role in the south-western Atlantic Ocean. The present study analysed the ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae using behavioural observation and benthic composition analyses. We found a significant negative relationship between fish size and feeding rates for S. zelindae individuals. Thus, terminal phase individuals forage with lower feeding rates compared to juveniles and initial phase individuals. The highest relative foraging frequency of S. zelindae was on epilithic algae matrix (EAM) with similar values for juveniles (86.6%), initial phase (88.1%) and terminal phase (88.6%) individuals. The second preferred benthos for juveniles was sponge (11.6%) compared with initial (4.5%) and terminal life phases (1.3%). Different life phases of S. zelindae foraged on different benthos according to their availability. Based on Ivlev’s electivity index, juveniles selected EAM and sponge, while initial phase and terminal phase individuals only selected EAM. Our findings demonstrate that the foraging frequency of the endemic parrotfish S. zelindae is reduced according to body size and that there is a slight ontogenetic change in feeding selectivity. Therefore, ecological knowledge of ontogenetic variations on resource use is critical for the remaining parrotfish populations which have been dramatically reduced in the Southwestern Atlantic Ocean.

Complete mitochondrial genome of the parrotfish Calotomus japonicus (Osteichthyes: Scaridae) with implications based on the phylogenetic position

The complete mitochondrial genome sequence was determined for a specimen of Calotomus japonicus, a temperate parrotfish endemic to coastal East Asia. It was compared phylogenetically with previously published partial sequences from this species and other parrotfishes. The obtained tree indicated that the three cytb sequences of C. japonicus from a recent molecular study (LC068806-8) probably resulted from introgression through intergeneric hybridization, or possibly from sample confusion. Taking the presently obtained mitogenome as representative of C. japonicus, the species most closely related to this one among congeners is C. zonarchus, which is endemic to the Hawaiian islands.

Formation of the Isthmus of Panama

The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

Spatial distribution of nominally herbivorous fishes across environmental gradients on Brazilian rocky reefs

Assemblages of roving herbivores were consistently different between eastern, warmer, sheltered sites and western, colder, more wave-exposed sites. At eastern sites, detritivorous-herbivorous species dominated while omnivores had the highest biomass and were dominant at western sites. Macroalgivores did not show any trends related to location. These distributional patterns, at relatively small spatial scales of a few kilometres, mirror large-scale latitudinal patterns observed for the studied species along the entire Brazilian coast, where cold water associated species are abundant on south-eastern rocky reefs (analogous to the western sites of this study), and tropical species are dominant on north-eastern coral reefs (analogous to the eastern sites). Species-level analyses demonstrated that depth was an important factor correlated with biomasses of Diplodus argenteus, Sparisoma axillare and Sparisoma tuiupiranga, probably due to resource availability and interspecific competition. Herbivorous fish assemblages in the study area have been historically affected by fishing, and combined with the variation in assemblage structure, this is likely to have important, spatially variable effects on the dynamics of benthic communities.

The evolution of fishes and corals on reefs: form, function and interdependence

Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66-34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34-5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene-Miocene is marked by the appearance of new fish and coral taxa associated with high-turnover fast-growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio-Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.

Testing the stages model in the adaptive radiation of cichlid fishes in East African Lake Tanganyika

Adaptive radiation (AR) is a key process in the origin of organismal diversity. However, the evolution of trait disparity in connection with ecological specialization is still poorly understood. Available models for vertebrate ARs predict that diversification occurs in the form of temporal stages driven by different selective forces. Here, we investigate the AR of cichlid fishes in East African Lake Tanganyika and use macroevolutionary model fitting to evaluate whether diversification happened in temporal stages. Six trait complexes, for which we also provide evidence of their adaptiveness, are analysed with comparative methods: body shape, pharyngeal jaw shape, gill raker traits, gut length, brain weight and body coloration. Overall, we do not find strong evidence for the 'stages model' of AR. However, our results suggest that trophic traits diversify earlier than traits implicated in macrohabitat adaptation and that sexual communication traits (i.e. coloration) diversify late in the radiation.

Modeling sensitive parrotfish (Labridae: Scarini) habitats along the Brazilian coast

In coral reef environments, there is an increasing concern over parrotfish (Labridae: Scarini) due to their rising exploitation by commercial small-scale fisheries, which is leading to significant changes in the reefs' community structure. Three species, Scarus trispinosus (Valenciennes, 1840), Sparisoma frondosum (Agassiz, 1831) and Sparisoma axillare (Steindachner, 1878), currently labeled as threatened, have been intensively targeted in Brazil, mostly on the northeastern coast. Despite their economic importance, ecological interest and worrisome conservation status, not much is known about which variables determine their occurrence. In this study, we adopted a hierarchical Bayesian spatial-temporal approach to map the distribution of these three species along the Brazilian coast, using landing data from three different gears (gillnets, spear guns, and handlines) and environmental variables (bathymetry, shore distance, seabed slope, Sea Surface Temperature and Net Primary Productivity). Our results identify sensitive habitats for parrotfish along the Brazilian coast that would be more suitable to the implementation of spatial-temporal closure measures, which along with the social component fishers could benefit the management and conservation of these species.

Resource partitioning along multiple niche axes drives functional diversity in parrotfishes on Caribbean coral reefs

The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes in the genus Scarus targeted filamentous algal turf assemblages, crustose coralline algae, and endolithic algae and avoided macroalgae, while fishes in the genus Sparisoma preferentially targeted macroalgae. However, species with similar diets were dissimilar in other attributes, including the habitats they frequented, the types of substrate they fed from, and the spatial scale at which they foraged. These differences indicate that species that appear to be functionally redundant when looking at diet alone exhibit high levels of complementarity when we consider multiple functional traits. By identifying key functional differences among parrotfishes, we provide critical information needed to manage parrotfishes to enhance the resilience of coral-dominated reefs and reverse phase shifts on algal-dominated reefs throughout the wider Caribbean. Further, our study provides a framework for predicting the impacts of consumer losses in other species rich ecosystems.

Genetic identification of bucktooth parrotfish Sparisoma radians (Valenciennes, 1840) (Labridae, Scarinae) by chromosomal and molecular markers

Parrotfishes (Labridae, Scarinae) comprise a large marine fish group of difficult identification, particularly during juvenile phase when the typical morphology and coloration of adults are absent. Therefore, the goal of this study was to test cytogenetic markers and DNA barcoding in the identification of bucktooth parrtotfish Sparisoma radians from the northeastern coast of Brazil. Sequencing of cytochrome c oxidase subunit I (COI) confirmed all studied samples as S. radians, and all showed high similarity (99-100%) with Caribbean populations. The karyotype of this species was divergent from most marine Perciformes, being composed of 2n = 46 chromosomes. These consisted of a large number of metacentric and submetacentric pairs with small amounts of heterochromatin and GC-rich single nucleolar organizer regions (NORs) not syntenic to 5S rDNA clusters. These are the first data about DNA barcoding in parrotfish from the Brazilian province and the first refined chromosomal analysis in Scarinae, providing useful data to a reliable genetic identification of S. radians.

Archaeological evidence of validity of fish populations on unexploited reefs as proxy targets for modern populations

Reef-fish management and conservation is hindered by a lack of information on fish populations prior to large-scale contemporary human impacts. As a result, relatively pristine sites are often used as conservation baselines for populations near sites affected by humans. This space-for-time approach can only be validated by sampling assemblages through time. We used archaeological remains to evaluate whether the remote, uninhabited Northwestern Hawaiian Islands (NWHI) might provide a reasonable proxy for a lightly exploited baseline in the Main Hawaiian Islands (MHI). We used molecular and morphological techniques to describe the taxonomic and size composition of the scarine parrotfish catches present in 2 archaeological assemblages from the MHI, compared metrics of these catches with modern estimates of reproductive parameters to evaluate whether catches represented by the archaeological material were consistent with sustainable fishing, and evaluated overlap between size structures represented by the archaeological material and modern survey data from the MHI and the NWHI to assess whether a space-for-time substitution is reasonable. The parrotfish catches represented by archaeological remains were consistent with sustainable fishing because they were dominated by large, mature individuals whose average size remained stable from prehistoric (AD approximately 1400-1700) through historic (AD 1700-1960) periods. The ancient catches were unlike populations in the MHI today. Overlap between the size structure of ancient MHI catches and modern survey data from the NWHI or the MHI was an order of magnitude greater for the NWHI comparison, a result that supports the validity of using the NWHI parrotfish data as a proxy for the MHI before accelerated, heavy human impacts in modern times.

Diet and diversification in the evolution of coral reef fishes

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages.

Individual-based analyses reveal limited functional overlap in a coral reef fish community

Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on coral reefs, as algal removal appears to depend strongly on species-specific microhabitat utilization patterns of herbivores. Furthermore, the results emphasize the capacity of the individual-based analyses to reveal variation in the functional niches of species, even in high-diversity systems such as coral reefs, demonstrating its potential applicability to other high-diversity ecosystems.

Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes)

The clupeoid fishes are distributed worldwide, with marine, freshwater and euryhaline species living in either tropical or temperate environments. Regional endemism is important at the species and genus levels, and the highest species diversity is found in the tropical marine Indo-West Pacific region. The clupeoid distribution follows two general pattern of species richness, the longitudinal and latitudinal gradients. To test historical hypotheses explaining the formation of these two gradients, we have examined the early biogeography of the Clupeoidei in reconstructing the evolution of their habitat preferences along with their ancestral range distributions on a time-calibrated mitogenomic phylogeny. The phylogenetic results support the distinction of nine main lineages within the Clupeoidei, five of them new. We infer several independent transitions from a marine to freshwater environment and from a tropical to temperate environment that occurred after the initial diversification period of the Clupeoidei. These results combined with our ancestral range reconstruction hypothesis suggest that the probable region of origin and diversification of the Clupeoidei during the Cretaceous period was the tropical marine precursor to the present Indo-West Pacific region. Thus, our study favors the hypotheses of “Region of origin” and “Tropical conservatism” to explain the origins of the longitudinal and latitudinal gradients of clupeoid species richness, respectively. Additional geological and paleontological evidence further define the tropical marine paleo-region of origin as the eastern Tethys Sea region. The Cretaceous fossil record of the Clupeoidei is partially incongruent with the results here as it contains taxa found outside this region. We discuss three possible causes of conflict between our biogeographical hypothesis and the distributions of the Cretaceous clupeoid fossils: regional extinction, incomplete taxonomic sampling and incorrect timescale estimation.

Sexual patterns and protogynous sex reversal in the rusty parrotfish, Scarus ferrugineus (Scaridae): histological and physiological studies

Gonadal histology confirmed that Scarus ferrugineus is a diandric protogynous fish. The process of protogynous sex reversal was investigated through histological observations on the gonads of females changing sex to male. This process was divided into three stages on the basis of changes in the structure of the germinal and somatic elements. Ovaries of functional females (stages IV-V) were filled with vitellogenic oocytes during the breeding season but contained no trace of spermatogenic tissue. During post-spawning period, the remaining vitellogenic oocytes began to degenerate and accompanied by a drop in plasma levels of estradiol-17β. At the commencement of sex change, previtellogenic oocytes began to degenerate and stromal cell aggregation was observed in the central region of the lamellae. At mid-reversal stage, steroid-producing cells (Leydig cells) developed at the border of the stromal aggregate and spermatogonial cysts appear at the periphery of lamellae. Finally, sex change to secondary males was considered complete, with the beginning of active spermatogenesis and spermiation. Plasma levels of testosterone remained low throughout the sex change, but II-KT increased rapidly parallel to the increased number of Leydig cells while the level of estradiol-17β decreased. The results indicate also that the sex-changed males had higher level of II-KT than primary males, while primary males had higher level of testosterone. Histological examination revealed that testes of primary and secondary males are almost identical in organization of the spermatogenic cysts, association of sertoli cells, and developing germ cells but differ in clustering and development of Leydig cells.

The likelihood of extinction of iconic and dominant herbivores and detritivores of coral reefs: the parrotfishes and surgeonfishes

Parrotfishes and surgeonfishes perform important functional roles in the dynamics of coral reef systems. This is a consequence of their varied feeding behaviors ranging from targeted consumption of living plant material (primarily surgeonfishes) to feeding on detrital aggregates that are either scraped from the reef surface or excavated from the deeper reef substratum (primarily parrotfishes). Increased fishing pressure and widespread habitat destruction have led to population declines for several species of these two groups. Species-specific data on global distribution, population status, life history characteristics, and major threats were compiled for each of the 179 known species of parrotfishes and surgeonfishes to determine the likelihood of extinction of each species under the Categories and Criteria of the IUCN Red List of Threatened Species. Due in part to the extensive distributions of most species and the life history traits exhibited in these two families, only three (1.7%) of the species are listed at an elevated risk of global extinction. The majority of the parrotfishes and surgeonfishes (86%) are listed as Least Concern, 10% are listed as Data Deficient and 1% are listed as Near Threatened. The risk of localized extinction, however, is higher in some areas, particularly in the Coral Triangle region. The relatively low proportion of species globally listed in threatened Categories is highly encouraging, and some conservation successes are attributed to concentrated conservation efforts. However, with the growing realization of man's profound impact on the planet, conservation actions such as improved marine reserve networks, more stringent fishing regulations, and continued monitoring of the population status at the species and community levels are imperative for the prevention of species loss in these groups of important and iconic coral reef fishes.