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opencc-zeroDec 2015View details →

Data from: Repeated evolution of amphibious behavior in fish and its implications for the colonization of novel environments

We know little about on how frequently transitions into new habitats occur, especially the colonization of novel environments that are the most likely to instigate adaptive evolution. One of the most extreme ecological transitions has been the shift in habitat associated with the move from water to land by amphibious fish. We provide the first phylogenetic investigation of these transitions for living fish. Thirty-three families have species reported to be amphibious and these are likely independent evolutionary origins of fish emerging onto land. Phylogenetic reconstructions of closely related taxa within one of these families, the Blenniidae, inferred as many as seven convergences on a highly amphibious lifestyle. Taken together, there appear to be few constraints on fish emerging onto land given amphibious behavior has evolved repeatedly many times across ecologically diverse families. The colonization of novel habitats by other taxa resulting in less dramatic changes in environment should be equally, if not, more frequent in nature, providing an important prerequisite for subsequent adaptive differentiation.

opencc-zeroMar 2020View details →

Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits

Cichlid fishes' famous diversity in body coloration is accompanied by a highly diverse and complex visual system. Although cichlids possess an unusually high number of seven cone opsin genes, they express only a subset of these during their ontogeny, accounting for their astonishing interspecific variation in visual sensitivities. Much of this diversity is thought to have been shaped by natural selection as cichlids inhabit a variety of habitats with distinct light environments. Also, sexual selection might have contributed to the observed visual diversity, and sexual dimorphism in coloration potentially co-evolved with sexual dimorphism in opsin expression. We investigated sex-specific opsin expression of several cichlids from Africa and the Neotropics and collected and integrated datasets on sex-specific body coloration, species-specific visual sensitivities, lens transmission and habitat light properties for some of them. We comparatively analyzed this wide range of molecular and ecological data, illustrating how integrative approaches can address specific questions on the factors and mechanisms driving diversification, and the evolution of cichlid vision in particular. We found that both sexes expressed opsins at the same levels - even in sexually dimorphic cichlid species – which argues against coevolution of sexual dichromatism and differences in sex-specific visual sensitivity. Rather, a combination of environmental light properties and body coloration shaped the diversity in spectral sensitivities among cichlids. We conclude that although cichlids are particularly colorful and diverse and often sexually dimorphic, it would appear that natural rather than sexual selection is a more powerful force driving visual diversity in this hyper-diverse lineage.

opencc-zeroDec 2014View details →

Data from: How predation shaped fish: the impact of fin spines on body form evolution across teleosts

It is well known that predators can induce morphological changes in some fish: individuals exposed to predation cues increase body depth and the length of spines. We hypothesize that these structures may evolve synergistically, as together, these traits will further enlarge the body dimensions of the fish that gape-limited predators must overcome. We therefore expect that the orientation of the spines will predict which body dimension increases in the presence of predators. Using phylogenetic comparative methods, we tested this prediction on the macroevolutionary scale across 347 teleost families, which display considerable variation in fin spines, body depth and width. Consistent with our predictions, we demonstrate that fin spines on the vertical plane (dorsal and anal fins) are associated with a deeper-bodied optimum. Lineages with spines on the horizontal plane (pectoral fins) are associated with a wider-bodied optimum. Optimal body dimensions across lineages without spines paralleling the body dimension match the allometric expectation. Additionally, lineages with longer spines have deeper and wider body dimensions. This evolutionary relationship between fin spines and body dimensions across teleosts reveals functional synergy between these two traits and a potential macroevolutionary signature of predation on the evolutionary dynamics of body shape.

opencc-zeroDec 2014View details →

Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes

Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental conditions, implying that speciation was driven by repeated adaption to temperate environments. Location: Northern Hemisphere Arctic and subarctic oceans. Methods: Fifty-five new sequences of four genes from 23 tissue samples were combined with 10 GenBank sequences to generate a time-calibrated phylogenetic hypothesis. Combining the phylogeny with information on species' ecological niche tolerances inferred from correlational models, I reconstructed ancestral environmental tolerances of each of the focal clades. These results were combined with Bayesian area-based biogeographical analysis and regional palaeoclimatic history to develop a holistic biogeographical history of Gadinae. Results: Of 18 environmental variables describing species' tolerances to salinity, temperature, sea ice concentration, and mixed layer depth, only mean, maximum and minimum sea bottom temperature, and mean and minimum sea surface temperature showed phylogenetic signal across Gadinae. Both ecological niche and geographical distributions of gadine fishes are largely conservative, but two clades contain both Pacific and Atlantic species. Focal clade divergence time estimates suggest a Pliocene origin for both, with further Pleistocene divergence. Main conclusions: Reconstructed ancestral environmental tolerances of crown cods and tomcods support a temperate origin of both groups. The timing of diversification of these two clades and the intolerance of temperate species to sea ice suggest that cyclical Arctic ice formation drove divergence. Future sea ice reduction may have dramatic consequences for distributions and persistence of commercially important species when currently allopatric temperate species come into secondary contact.

opencc-zeroDec 2011View details →

Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.

opencc-zeroMay 2020View details →

Extreme genomic volatility characterises the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes

The evolution of the adaptive immune system has provided vertebrates with a uniquely sophisticated immune toolkit, enabling them to mount precise immune responses against a staggeringly diverse range of antigens. Like other vertebrates, teleost fishes possess a complex and functional adaptive immune system; however, our knowledge of the complex antigen-receptor genes underlying its functionality has been restricted to a small number of experimental and agricultural species, preventing a systematic investigation of how these crucial gene loci evolve. Here, we analyse the genomic structure of the immunoglobulin heavy chain (IGH) gene loci in the cyprinodontiforms, a diverse and important group of teleosts present in many different habitats across the world. We reconstruct the complete IGH loci of the turquoise killifish (Nothobranchius furzeri) and the southern platyfish (Xiphophorus maculatus) and analyse their in vivo gene expression, revealing the presence of species-specific splice isoforms of transmembrane IGHM. We further characterise the IGH constant regions of ten additional cyprinodontiform species, including guppy, amazon molly, mummichog and mangrove killifish. Phylogenetic analysis of these constant regions suggests multiple independent rounds of duplication and deletion of the teleost-specific antibody class IGHZ in the cyprinodontiform lineage, demonstrating the extreme volatility of IGH evolution. Focusing on the cyprinodontiforms as a model taxon for comparative evolutionary immunology, this work provides novel genomic resources for studying adaptive immunity and sheds light on the evolutionary history of the adaptive immune system.

opencc-zeroDec 2015View details →

Data from: Evolution of the immune system influences speciation rates in teleost fishes

Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.

opencc-zeroAug 2021View details →

Data from: The little fishes that could: smaller fishes demonstrate slow body size evolution but faster speciation in the family Percidae

<p>Body size impacts numerous aspects of organismal biology and many factors have been invoked to explain body size distributions in a macroecological and macroevolutionary context. Body size in the freshwater fish family Percidae is strongly right-skewed (i.e, dominated by small sizes), with small body size potentially being associated with fast water habitats. We constructed a new species-level, multi-locus, time-calibrated phylogeny of Percidae, and used it to test for changes in the rate and pattern of maximum body size evolution. We also tested whether speciation rates varied as a function of body size. We found that Etheostomatinae evolved towards a smaller adaptive optimum in body size compared to the other subfamilies of Percidae, and that this shift was associated with a reduction in the rate of body size evolution. Speciation rates were associated with body size across percids, showing a peak around small to medium body size. Small body size appears to partially, but not fully, explain the diversity of small percids, as many darters fall well below the "optimum" body size. Reinforcement of selection for small body size via selection for novel morphologies or via sexual selection may help to fully explain the remarkable diversity of the darter radiation.</p>

Figure 27 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 27. Hypopygus neblinae, nontype, head, and lateral and dorsal views of body. UF 148540 (WC49.150304), female, 78 mm: Venezuela, Caño Viejita, on road from San Fernando de Atabapo to Santa Bárbara, 16.5 km and 142° from San Fernando de Atabapo town centre, Río Orinoco drainage. Scale bars = 5 mm.

Figure 17 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 17. Electric organ discharges (EODs) of Hypopygus as time-voltage waveforms recorded in the far-field. The EODs were in all cases taken from immature specimens or females with adult morphology, and are representative of most individuals of each species (small juveniles and sexually mature males present EODs that in some cases differ from those of larger juveniles, immature adults, and females). A, Hypopygus cryptogenes, INPA uncatalogued, 80 mm (poor signal recording quality). B, Hypopygus isbruckeri, UF 148537 (WC38.150304), immature, 76 mm. C, Hypopygus lepturus, UF 176883 (WC21.090307), female, 92 mm. D, Hypopygus minissimus, UF 148533 (WC41.120304), female, 42 mm. E, Hypopygus neblinae, UF 148540 (WC36.150304), female, 77 mm. F, Hypopygus nijsseni MCP 44740 (WC01.070703), immature, 70 mm. G, Hypopygus ortegai, MUSM 35305, holotype (WC02.160104), female, 107 mm. Scale bars = 1 ms. Dashed horizontal line = 0 volts. Note that all species generate EODs with a similar four- or five-phase structure, with minimal interspecific variation in duration (except in H. neblinae where the EOD is clearly longer).

Figure 11 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 11. Pectoral girdle of Hypopygus ortegai, UF 148540 (WC04.160104), 130 mm; left side, medial view, anterior to left, inverted figure.

Figure 15 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 15. Postpectoral accessory electric organ and associated dorsal and ventral grooves of Hypopygus nijsseni MCP 44737, 75 mm; left side, lateral view, anterior to left.

Figure 10 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 10. Pectoral girdle of Hypopygus cryptogenes MZUSP 30088, 147 mm; left side, medial view, anterior to left, inverted figure. Note the extension of the posteroventral portion of the coracoid.

Figure 6 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 6. Lower jaw of Hypopygus isbruckeri, UF 148539, 90 mm; left side, medial view, anterior to left. Note the posterodorsal margin of the dentary is straight.

Figure 14 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 14. Ventral portion of the gill arches of Hypopygus hoedemani, MZUSP 81488, 47.7 mm TL; dorsal view, anterior to left. Abbreviations: bb, basibranchial; bh, basihyal; cb, ceratobranchial; eb, epibranchial; hb, hypobranchial; ib, infrapharyngobranchial; up, upper pharyngeal tooth-plate. Note the posterior portion of the dorsal surface of the basihyal does not bear a ridge and the lack of ossification of the second to fifth basibranchial. Note also the well-developed pharyngeal teeth on cb5. Right dorsal portion of the gill arches not illustrated.

Figure 18 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 18. Map of northern South America showing collection records of Hypopygus cryptogenes. Some symbols represent more than one nearby collecting locality.

Figure 3 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 3. Head of adult Hypopygus ortegai, UF 176879, 101 mm; left side, lateral view, anterior to left. Cephalic sensory canal elements, and the outline of an unidentified bone (located under the antorbital), are highlighted grey. Abbreviations: dpoc, dorsal branch of the preopercular canal; esc, extrascapular canal; io, infraorbital canal; mc, mandibular canal; nc, nasal laterosensory canal; pac, parietal canal; pocl, postotic canal of the lateral line; ptoc, pterotic canal; soc, supraorbital canal; uib, unidentified bone; vpoc, ventral branch of the preopercular canal.

Figure 9 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 9. Posterior portion of endopterygoid and quadrate, metapterygoid (with anterodorsally directed process), symplectic, and adjoining bones in Hypopygus neblinae UF 1480540 (WC12.130304), female, 75 mm; left side, lateral view, anterior to left; larger stippling represents cartilage.

Figure 4 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 4. Head of adult Hypopygus minissimus, UF 148533 (WC 41.120304), female, 43 mm; left side, lateral view, anterior to left. Cephalic sensory canal elements, and the outline of an unidentified bone (located under the antorbital), are highlighted grey. Abbreviations: esc, extrascapular canal; mc, mandibular canal; ptoc, pterotic canal; soc, supraorbital canal; uib, unidentified bone.

Figure 2 in Phylogenetic interrelationships, taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei, Ostariophysi, Gymnotiformes)

Figure 2. Cleared and stained head of juvenile Brachyhypopomus sp. indet, MCP uncatalogued, 74 mm; left side, lateral view, anterior to left. Upper image shows unmanipulated digital photograph. Lower image is presented as a 'negative', for contrast, with cephalic sensory canal elements highlighted (red) and labeled, and the outline of an unidentified bone, located underneath the antorbital, highlighted (yellow), with no labels. Some of the elements highlighted (red and yellow) are outside the focal plane of the upper image. Abbreviations: aoc, antorbital canal; esc, extrascapular; ioc, infraorbital canal; mc, mandibular canal; nc, nasal laterosensory canal; pac, parietal canal; pasoc, parietal branch of supraorbital canal; poc, preopercular canal; pocl, postotic canal of the lateral line; ptoc, pterotic canal; soc, supraorbital canal. See Zoological Journal of the Linnean Society online for the colour version of this Figure.