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495 results for “Reef Fishes”
Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes
Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. While both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25-times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fishes.
Data from: Seascape and life-history traits do not predict self-recruitment in a coral reef fish
The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4–0.5% at 0.15 km2) and the lagoon scale (0.6–0.8% at approx. 700 km2). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.
Data from: Biogeography of functional trait diversity in the Taiwanese reef fish fauna
The richness of Taiwanese reef fish species is inversely correlated to latitude as a direct consequence of the abiotic environment and its effects on benthic habitats. However, to date, no studies have investigated the variations in the diversity of traits (FD) linked with the role of these fishes in the ecosystem. FD is usually considered more sensitive than species richness in detecting early changes in response to disturbances, and therefore could serve as an indicator of ecological resilience to environmental changes. Here, we aim to characterize FD in the Taiwanese reef fish fauna and to document its regional variations. Six traits were used to categorize the 1,484 reef fish species occurring in four environmentally contrasted regions around Taiwan. The number of unique trait combinations (FEs), their richness (FRic), their redundancy (FR), their over-redundancy (FOR), and their vulnerability (FV) were compared among these regions. Overall, 416 FEs were identified. Their number decreased from south to north in step with regional species richness but FRic remained similar among regions. FR and FOR were higher to the south. At the local scale, variations in FEs and FRic are in concordance with the worldwide pattern of FD. High-latitude, impoverished fish assemblages, offer a range of trait combinations similar to diversified tropical assemblages. Increasing diversity in the latter mainly contributes to raising FR and supports already over-redundant entities. High vulnerability makes many combinations highly sensitive to species loss, and was higher at intermediate latitudes when using a fine resolution in trait categories. It suggests that the loss of FEs may first be characterized by an increase in their vulnerability, a pattern that could have been overlooked in previous global scale analyses. Overall, this study provides new insights into reef fish trait biogeography with potential ramifications for ecosystem functioning.
Data from: Incomplete datasets obscure associations between traits affecting dispersal ability and geographic range size of reef fishes in the Tropical Eastern Pacific
Dispersal is thought to be an important process determining range size, especially for species in highly spatially structured habitats, such as tropical reef fishes. Despite intensive research efforts, there is conflicting evidence about the role of dispersal on determining range size. We hypothesize that traits related to dispersal drive range sizes, but that complete and comprehensive datasets are essential for detecting relationships between species' dispersal ability and range size. We investigate the roles of six traits affecting several stages of dispersal (adult mobility, spawning mode, pelagic larval duration (PLD), body size, aggregation behaviour and circadian activity), in explaining range size variation of reef fishes in the Tropical Eastern Pacific (TEP). All traits, except for PLD (148 species), had data for all 497 species in the region. Using a series of models, we investigated which traits were associated with large range sizes, when analysing all TEP species or only species with PLD data. Furthermore, using null models, we analysed whether the PLD-subset is representative of the regional species pool. Several traits affecting dispersal ability were strongly associated with range size, although these relationships could not be detected when using the PLD-data subset. Pelagic spawners (allowing for passive egg dispersal) had on average 56% larger range sizes than non-pelagic spawners. Species with medium or high adult mobility had on average a 25% or 33% larger range, respectively, than species with low mobility. Null models showed that the PLD-subset was non-representative of the regional species pool, explaining why model outcomes using the PLD-subset differed from the ones based on the complete dataset. Our results show that in the TEP, traits affecting dispersal ability are important in explaining range size variation. Using a regionally complete dataset was crucial for detecting the theoretically expected, but so far empirically unresolved, relationship between dispersal and range size.
Data from: Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success
Many marine organisms can be transported hundreds of kilometers during their pelagic larval stage, yet little is known about spatial and temporal patterns of larval dispersal. Although traditional population-genetic tools can be applied to infer movement of larvae on an evolutionary time scale, large effective population sizes and high rates of gene-flow present serious challenges to documenting dispersal patterns over shorter, ecologically-relevant, time scales. Here, we address these challenges by combining direct parentage analysis and indirect genetic analyses over a four-year period to document spatial and temporal patterns of larval dispersal in a common coral-reef fish: the bicolor damselfish (Stegastes partitus). At four island locations surrounding Exuma Sound, Bahamas, including a long-established marine reserve, we collected 3,278 individuals and genotyped them at 10 microsatellite loci. Using Bayesian parentage analysis, we identified eight parent-offspring pairs, thereby directly documenting dispersal distances ranging from 0 km (i.e., self-recruitment) to 129 km (i.e., larval connectivity). Despite documenting substantial dispersal and gene-flow between islands, we observed more self-recruitment events than expected if the larvae were drawn from a common, well-mixed pool (i.e., a completely open population). Additionally, we detected both spatial and temporal variation in signatures of sweepstakes and Wahlund effects. The high variance in reproductive success (i.e., "sweepstakes") we observed may be influenced by seasonal mesoscale gyres present in the Exuma Sound, which play a prominent role in shaping local oceanographic patterns. This study documents the complex nature of larval dispersal in a coral-reef fish, and highlights the importance of sampling multiple cohorts and coupling both direct and indirect genetic methods in order disentangle patterns of dispersal, gene-flow, and variable reproductive success.
Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific
The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co-occurrence between sister-species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister-taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial context beyond regression curves. Mapping this relationship across spatial grids, however, may unravel how speciation processes have shaped current biodiversity patterns through space and time. This can be particularly relevant for coral reef fishes of the Indo-Pacific since the origin of the exceptional concentration of biodiversity in the Indo-Australian Archipelago (IAA) has been actively debated, with several alternative hypotheses involving species diversification and dispersal. We reconstructed the phylogenetic relationships between three species-rich families of coral reef fish (Chaetodontidae, Labridae, Pomacentridae) and calculated co-occurrence metrics between closely related lineages of those families. We demonstrated that repeated biogeographic processes can be identified in present-day species distribution by projecting co-occurrence metrics between related lineages in a geographical context. Our study also evidence that sister-species do not co-occur randomly across the Indo-Pacific, but tend to overlap their range within the IAA. We identified the imprint of two important biogeographic processes that caused this pattern in 48% of the sister-taxa considered: speciation events within the IAA and repeated divergence between the Indian and Pacific Ocean, with subsequent secondary contact in the IAA.
Data from: 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' due 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 PLD 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.
Data from: Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea
Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.
Data from: Increased behavioural lateralization in parasitized coral reef fish
Preferential use of one side of the body for cognitive or behavioural tasks (lateralization) is common in many animals, including humans. However, few studies have demonstrated whether lateralization is phenotypically plastic, and varies depending on the ecological context. We studied lateralization (measured as a turning preference) in the bridled monocle bream (Scolopsis bilineatus). This coral reef fish is commonly infected by a large, ectoparasitic isopod (Anilocra nemipteri) that attaches to the left or right side of its host's head. Fish that were parasitized showed no turning bias with respect to the side on which the parasite had attached. On average, however, parasitised fish were significantly more lateralized (i.e. had a strong side bias) than unparasitized fish. The extent of lateralization declined significantly when we experimentally removed the parasite. Our results indicate that lateralization can vary with the ecological context. One possible explanation is that lateralization shortens the response time until fish flee after encountering a predator. A stronger side bias might be advantageous for parasitized individuals to overcome their recently documented lower maximum swimming speed.
Data from: Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp, Serranidae)
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 colored 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 genome-wide 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 mini-contig 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.
Figure 1 in Wolves in sheep's clothing: three new cases of aggressive mimicry in Red Sea coral reef fishes
Figure 1. New records of mimicry in the Red Sea: (a) juvenile Diploprion drachi, a mimic of (b) Meiacanthus nigrolineatus; (c) juvenile Epinephelus leucogrammicus, a mimic of (d) Larabicus quadrilineatus; (e) juvenile Plectropomus marisrubri, a mimic of (f) Cheilinus quinquecinctus. (Photos: Luiz A. Rocha).
Figure 2. A in Wolves in sheep's clothing: three new cases of aggressive mimicry in Red Sea coral reef fishes
Figure 2. A juvenile Epinephelus leucogrammicus embedded in a cleaning station with Larabicus quadrilineatus. (Photo: Luiz A. Rocha).
FIGURE 1 in Huffmanela spp. (Nematoda, Trichosomoididae) parasites in coral reef fishes off New Caledonia, with descriptions of H. balista n. sp. and H. longa n. sp.
FIGURE 1. Outer surface of the swimbladder of Abalistes stellatus (fish JNC2163). Dark zones are accumulations of eggs of Huffmanela balista n. sp.
FIGURE 5 in Huffmanela spp. (Nematoda, Trichosomoididae) parasites in coral reef fishes off New Caledonia, with descriptions of H. balista n. sp. and H. longa n. sp.
FIGURE 5. Histogram of egg length of the two Huffmanela species parasitic in Gymnocranius grandoculis. JNC892: eggs from the gills, syntypes of H. filamentosa Justine, 2004. JNC1726, JNC 2166, JNC2174, eggs of H. lata n. sp. JNC1726: eggs from the mesentery. JNC2166 and JNC2174: eggs from the swimbladder.
FIGURE 7. X in Huffmanela spp. (Nematoda, Trichosomoididae) parasites in coral reef fishes off New Caledonia, with descriptions of H. balista n. sp. and H. longa n. sp.
FIGURE 7. X-ray photographs of the spinal cord in two Bodianus perditio. A. Specimen not parasitized by Huffmanela ossicola. B. Specimen heavily parasitized by Huffmanela ossicola. Negative prints.
FIGURE 3 in Huffmanela spp. (Nematoda, Trichosomoididae) parasites in coral reef fishes off New Caledonia, with descriptions of H. balista n. sp. and H. longa n. sp.
FIGURE 3. Eggs and larvae of Huffmanela balista n. sp. from Abalistes stellatus. A–J. Eggs. A–B, C–D. Optical section and surface views of same eggs. F, G. Eggs with hatching larvae (note that hatching occurs in both clear and dark eggs). H. Dark-brown egg. I. Black egg, larva present but not visible. J. Black egg, larva present but not visible, envelope visible. K. L1 larva, spontaneously hatched.
FIGURE 6. A in Huffmanela spp. (Nematoda, Trichosomoididae) parasites in coral reef fishes off New Caledonia, with descriptions of H. balista n. sp. and H. longa n. sp.
FIGURE 6. A. Egg of Huffmanela mexicana Moravec et Fajer-Avila, 2000, for comparison with other species. B–D. Hatching eggs and larvae of Huffmanela ossicola Justine, 2004 from the gills of Bodianus perditio.
FIGURE 5. Flagellotrema reburrus n in Revision of Flagellotrema Ozaki, 1936 (Digenea, Gyliauchenidae Fukui, 1929), including the description of two species from acanthuroid fishes from the Great Barrier Reef, Queensland, Australia
FIGURE 5. Flagellotrema reburrus n. sp. from Siganus corallinus, Lizard Island, Great Barrier Reef, Australia. A, paratype. B, paratype, detail of egg forming complex. Scale bars: A = 500 µm, B = 250µm.
FIGURE 2. Flagellotrema convolutum Ozaki, 1936 in Revision of Flagellotrema Ozaki, 1936 (Digenea, Gyliauchenidae Fukui, 1929), including the description of two species from acanthuroid fishes from the Great Barrier Reef, Queensland, Australia
FIGURE 2. Flagellotrema convolutum Ozaki, 1936 from Prionurus scalprum, presumably from Japan. Detail of male terminal genitalia; composite sketch based on paratypes (sections). Scale bar =250 µm.
FIGURE 10 in Revision of Flagellotrema Ozaki, 1936 (Digenea, Gyliauchenidae Fukui, 1929), including the description of two species from acanthuroid fishes from the Great Barrier Reef, Queensland, Australia
FIGURE 10. Scatterplot of the area of the oesophageal bulb length (length × width) against body length for specimens of Flagellotrema amphitrite n. sp. and F. re b u r r u s n. sp. Measurements from laterally mounted specimens only are used in the analysis.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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