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203 results for “Fish Evolution”
Fluvial geomorphic evolution and stream fish community trajectories in the Bayou Pierre, Mississippi
<p>Changing environments place stresses on ecosystems, and are contributing to widespread losses of biodiversity and ecosystem function. Comparisons of historical and contemporary data offer considerable utility in understanding how ecosystems respond to, adapt to, or recover from changing environments. Stream fishes offer a particularly interesting study system for this topic, as streams are naturally dynamic environments and human needs have placed increasing pressure on aquatic systems. The effects of fine sediments on stream fishes and aquatic ecosystems more broadly have been well studied. Yet studies from fluvial geomorphology have resulted in models of watershed morphological evolution which encompass far broader processes and changes to aquatic systems. Our dataset integrates a fluvial geomorphic approach to characterize stream channel and habitat evolution over a four decade period in the Bayou Pierre, Mississippi, an ecological approach to study related change in stream fish communities in the same watershed, and analyses linking the two. Fluvial geomorphic processes were characterized both from remote sensing data sources for historic and contemporary time periods, and local fish habitat data for contemporary time periods. Historical fish community data were extracted from museum records, and contemporary fish community data were collected via sampling for fishes at the same localities as historic efforts using similar methods.</p>
Figure 1 in Hard tissues in fish evolution: history and current issues
Figure 1. – Appearance of elasmoid scales within osteichthyans shown on an interrelationship scheme of Osteichthyes after Long et al. (2015), Schultze (2015), and King et al. (2017) for the lower part and after Giles et al. (2017) for the actinopterygians above Ligulalepis. Node A = Osteichthyes: de, dentine, i, isopedine, r, rhomboid scale; node B = de, dentine, en, enamel, i, isopedine, r, rhomboid; node C = Sarcopterygii: el, elasmoid; node C' = r, rhomboid, co, cosmine (dipnoi are represented by Diabolepis and their elasmoid scale by that of Neoceratodus); node D = Actinopterygii: ga?, questionable for basal taxa, r, rhomboid; canal system of Andreolepis typical for lower actinopterygians and osteichthyans; node D' = a, acrodine in Ligulalepis (after Schultze, 2015: fig.13) and higher actinopterygians, ga, ganoine, r, rhomboid (only branches with elasmoid scale are named in lower actinopterygians). Scales of Lophosteus superbus after Gross (1968, fig. 1A), of Actinistia after Smith (1940: fig. 70, Latimeria chalumnae), Onychodontida after Andrews et al. (2006: fig. 60b, Onychodus jandemarrai), of Dipnoi after Kerr (1955: fig. 4B, Neoceratodus), of Rhizodontida after Long (1989: fig. 13, Barameda decipiens), of Tristichopterida after Jarvik (1980: fig. 138 B3, Eusthenopteron foordi), of Holoptychiidae after Ørvig (1957: fig. 13A, Holoptychius sp.), of Sphaerolepis after Fritsch (1893: pl. 109, fig. 5), of Polypteridae after Rauther (1929: fig. 136, Erpetoichthys calabricus), of Coccolepis combination after Agassiz (1843: vol. 2, pl. 26, fig. 7) and Schultze (1996: fig. 4), of Eurycormus (original), of Leptolepis coryphaenoides (original), and of an amiid after Grande and Bemis (1998: fig. 201, Cyclurus macrocephalus).
Fluvial geomorphic evolution and stream fish community trajectories in the Bayou Pierre, Mississippi
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Evolution of size-fecundity relationship in medaka fish from different latitudes
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Data for Predation and resource availability interact to drive life-history evolution in an adaptive radiation of livebearing fish
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Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization
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Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
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Data from: Recurrent evolution of small body size and loss of the sword ornament in Northern swordtail fish
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The impact of paleoclimatic changes on body size evolution in marine fishes
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Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs
<p>Evidence of contemporary evolution across ecological time scales stimulated research on the eco-evolutionary dynamics of natural populations. Aquatic systems provide a good setting to study eco-evolutionary dynamics owing to a wealth of long-term monitoring data and the detected trends in fish life-history traits across intensively harvested marine and freshwater systems. In the present study, we focus on modelling approaches to simulate eco-evolutionary dynamics of fishes and their ecosystems. Firstly, we review the development of modelling from single-species to multispecies approaches. Secondly, we advance the current state-of-the-art methodology by implementing evolution of life-history traits of a top predator into the context of complex food web dynamics as described by the allometric trophic network (ATN) framework. The functioning of our newly developed eco-evolutionary ATNE framework is illustrated using a well-studied lake food web. Our simulations show how both natural selection arising from feeding interactions and size-selective fishing cause evolutionary changes in the top predator and how those feed back to its prey species and further cascade down to lower trophic levels. Finally, we discuss future directions, particularly the need to integrate genomic discoveries into eco-evolutionary projections.</p>
Data from: Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes
<p>The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The <em>Oryzias latipes</em> species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The <em>O. javanicus</em> species group has similar numbers of chromosomes to the <em>O. latipes</em> species group, but smaller arm numbers, with most chromosomes being acrocentric. The <em>O. celebensis</em> species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of <em>O. latipes</em>, <em>O. javanicus</em>, and <em>O. celebensis</em>, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.</p>
Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes
<p>Active electroreception — the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs) — has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that produces diverse EODs. Neofunctionalization of a voltage-gated sodium channel accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein with biogeographic data and EOD recordings. We test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the absence of predators, which likely selected for reduced EOD complexity, exhibited increased scn4aa evolutionary rates. We model mutations in the protein that may underlie changes in protein function and discuss our findings in the context of gymnotiform signalling ecology. Together, this work sheds light on the selective forces underpinning major evolutionary transitions in electric signal production.</p>
Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika
<p><span>The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in the virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the achromatic environment with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth-related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability, and 11 sites that may be functionally important on the basis of their </span><span>physicochemical properties. Among the strongest candidate sites for deep-water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is th first compralehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.</span></p>
Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish
<p class="MsoNormal"><span>Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. S</span><span>everal ricefishes</span><span> (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females </span><span>carry externally fertilized eggs until hatching using their pelvic fins.</span><span> Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus </span><span>mapping using a cross between a pelvic-fin brooder</span><span> <em>Oryzias eversi</em> and</span><span> a non-brooding </span><em><span>O. dopingdopingensis</span></em><span> reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes</span><span>. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders</span><span>, indicating that </span><span>introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding</span><span>. </span><span>These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.</span></p>
Data from: Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes
<p><span><span><span><span>Brain region size generally scales allometrically with total brain size, but mosaic shifts in brain region size independent of brain size have been found in several lineages and may be related to the evolution of behavioral novelty. African weakly electric fishes (Mormyroidea) evolved a mosaically enlarged cerebellum and hindbrain, yet the relationship to their behaviorally novel electrosensory system remains unclear. We addressed this by studying South American weakly electric fishes (Gymnotiformes) and weakly electric catfishes (<em>Synodontis</em> spp.), which evolved varying aspects of electrosensory systems, independent of mormyroids. If the mormyroid mosaic increases are related to evolving an electrosensory system, we should find similar mosaic shifts in gymnotiforms and <em>Synodontis</em>. Using micro-computed tomography scans, we quantified brain region scaling for multiple electrogenic, electroreceptive, and non-electrosensing species. We found mosaic increases in cerebellum in all three electrogenic lineages relative to non-electric lineages and mosaic increases in torus semicircularis and hindbrain associated with the evolution of electrogenesis and electroreceptor type. These results show that evolving novel electrosensory systems is repeatedly and independently associated with changes in the sizes of individual brain regions independent of brain size, which suggests that selection can impact structural brain composition to favor specific regions involved in novel behaviors.</span></span></span></span></p>
Data from: Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish
<p>Recent work has revealed the importance of contemporary evolution for shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically-important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead / resident rainbow trout (<em>Oncorhynchus mykiss</em>). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size-structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident <em>O. mykiss</em> populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.</p>
A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
Background <p>Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species-poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus <em>Campylomormyrus</em> is mostly endemic to the Congo Basin. <em>Campylomormyrus</em> serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorph fish in general and of electric fish in particular.</p> Results <p>A high-quality weakly electric fish (<em>C. compressirostris</em>) genome was produced from a single individual with a genome size of 862Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of <em>Paramormyrops</em> <em>kingsleyae</em> and <em>Scleropages</em> <em>formosus</em>. A CAFE5 analysis of gene family evolution comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (<em>Cyprinus</em> <em>carpio</em> and <em>Oncorhynchus</em> <em>mykiss</em>). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of <em>C</em>. <em>compressirostris</em>.</p> Conclusions <p>We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appears to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among <em>Campylomormyrus</em> species.</p>
Data from "The evolution of fast-growing coral reef fishes"
<p>Datasets and scripts generated during and/or analysed in the paper '<strong>The evolution of fast-growing coral reef fishes</strong>', published in <em>Nature</em>. More details can be found in the README file.</p>
Data from 'On the evolution of fish-coral interactions'
<p>Datasets and scripts generated during and/or analysed in the paper '<strong>On the evolution of fish-coral interactions</strong>', published in <em>Ecology Letters</em>. More details can be found in the README file.</p>
Divergent processes drive parallel evolution in marine and freshwater fishes
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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