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39 results for “ray-finned fishes”
iNaturalist data on South American ray-finned fish
<p>Cleaned dataset of South American ray-finned fish from iNaturalist platform with classified observations based on the status of the fish (live/dead), characteristics of the species (taxonomy and habitat) and the circumstances of the observation (e.g., fishing or diving). Species attributes compiled from fishbase are also provided for each observation. Two appendices are available with summarized data by species and maps with distribution of observations by orders.</p>
Fig. 2 in Application of genomic markers generated for ray-finned fishes in chondrichthyan Phylogenomics
Fig. 2 Phylogenomic relationship of investigated 26 jawed fish species based on single-copy orthologous exon markers. Bootstrap values are shown in each node
Fig. 1 in Application of genomic markers generated for ray-finned fishes in chondrichthyan Phylogenomics
Fig. 1 Phylogenomic relationships of investigated chondrichthyans based on two approaches in this study. Branches with inconsistency in phylogenomic inferences between BUSCO and exon approaches were denoted with red stars. Colors highlighted orders of Chondrichthyes
Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
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The oldest Devonian circumpolar ray-finned fish?
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Data from: Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes
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Data from: An exceptionally preserved Late Devonian actinopterygian provides a new model for primitive cranial anatomy in ray-finned fishes
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Data from: The oldest actinopterygian highlights the cryptic early history of the hyperdiverse ray-finned fishes
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Data from: Molecular evolution of the neural crest regulatory network in ray-finned fish
Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of non-synonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits – suggesting an important role for NC network architecture during the diversification in vertebrates.
Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results: We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions: Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
Data from: Virtual reconstruction of endocast anatomy in early ray-finned fishes (Osteichthyes: Actinopterygii)
Cranial endocasts, infillings of the skeletal void that once contained the brain and associated soft tissues, represent detailed anatomical structures that have long been the focus of paleontological investigation. We applied computed tomographics (CTs) in order to generate endocast models for the Paleozoic actinopterygian fishes Mimipiscis and Kentuckia, which serve as key representatives of anatomically primitive, early ray fins in analyses of early vertebrate relationships. The resultant endocranial models generally corroborate existing accounts of endocranial anatomy in these genera, drawn from descriptions of the inner face of the brain cavity. However, the endocasts also provide new anatomical details, the most significant of which are the presence in Mimipiscis of widely divergent olfactory tracts, small optic lobes, and anterior and posterior semicircular canals that extend dorsal to the roof of the endocranial chamber. By contrast, Kentuckia possesses a single, straight olfactory tract, wide optic lobes, and anterior and posterior semicircular canals that do not reach the dorsal surface of the endocast. In each of these features, Kentuckia resembles stratigraphically younger actinopterygians such as Lawrenciella and Kansasiella, whereas Mimipiscis more closely resembles sarcopterygians and other outgroups. This character distribution provides further support for earlier phylogenetic interpretations of these genera.
Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
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Data from: Virtual reconstruction of endocast anatomy in early ray-finned fishes (Osteichthyes: Actinopterygii)
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Data from: Molecular evolution of the neural crest regulatory network in ray-finned fish
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Data from: Endoskeletal structure in Cheirolepis (Osteichthyes, Actinopterygii), an early ray-finned fish
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Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)
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Data from: DNA barcodes of the native ray-finned fishes in Taiwan
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Data on mitochondrial genome rearrangement patterns, annotation resources, and phylogenetic visualization in Actinopteri (ray-finned fishes)
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International Brain Laboratory public data
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OpenNeuro
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