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39 results for “ray-finned fishes”
Fig. 3 in Feeding convergence among ray-finned fishes: Teeth of the herbivorous actinopterygians from the latest Permian of East European Platform, Russia
Fig. 3. Comparison of teeth of actinopterygian fish Isadia spp. from the Late Permian of Sokovka, Russia with their Recent equivalents. A, B. Isadia aristoviensis. C–E. Labeotropheus fuelleborni (C from Streelman et al. 2003; D, E from Abertson and Kocher 2006). F, G. Isadia suchonensis. H, J. Monotocheirodon kontos (from Menezes et al. 2013). I. Bryconamericus lethostigmus (from Hirschmann et al. 2017). K, L. Isadia arefievi. M–O. Eretmodus cyanosticus (M from Rüber et al. 1999; N, O from Boulenger 1915). Not to scale.
Fig. 2 in Feeding convergence among ray-finned fishes: Teeth of the herbivorous actinopterygians from the latest Permian of East European Platform, Russia
Fig. 2. The isolated teeth of actinopterygian fish Isadia from the Sokovka outcrop, Vyazniki, Russia, late Permian (Upper Vyatkian). A–D. Isadia aristoviensis Minikh, 1990, mandibulary teeth. A. ZPAL V.51/1, lingual view. B. ZPAL V.51/2, labial view. C. ZPAL V.51/3, lingual view. D. ZPAL V.51/4, labial view. E–I. Isadia aristoviensis Minikh, 1990, maxillary teeth. E. ZPAL V.51/6, lingual view. F. ZPAL V.51/7, labial view. G. ZPAL V.51/5, lingual view. H. ZPAL V.51/8, lingual view. I. ZPAL V.51/9, labial view. J. Isadia arefievi Minikh, 2015, ZPAL V.51/10, mandibular tooth,?lingual view. K, L. Isadia suchonensis Minikh, 1986, mandibular teeth. K. ZPAL V.51/11, lingual (K1) and lateral (K2) views. L. ZPAL V.51/12, labial view. M. Isadia suchonensis Minikh, 1986, ZPAL V.51/13, maxillary teeth,?labial view. Scale bars 1 mm (A–I), 0.5 mm (J, K, M), 0.2 mm (L).
Fig. 1 in Feeding convergence among ray-finned fishes: Teeth of the herbivorous actinopterygians from the latest Permian of East European Platform, Russia
Fig. 1. Location of the fish-bearing site and details of the exposed section. A. Map of the Eastern Europe with position of Vyazniki (BY, Belarus, LV, Latvia; EST, Estonia; LT, Lithuania). B. The area around the town of Vyazniki with position of Sokovka site (star). C. Photograph of the Sokovka section from 2013 and exposure of the fish-bearing deposits. D. The simplified section from Sokovka site showing the fish-bearing layers. Modified from Newell et al. 2010, Owocki et al. 2012, and Bajdek et al. 2017.
Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes
<p><span>Migratory animals respond to environmental heterogeneity by predictably moving long distances in their lifetime. Migration has evolved repeatedly in animals, and many adaptations are found across the tree of life that increase migration efficiency. Life history theory predicts that migratory species should evolve a larger body size than non-migratory species and some empirical studies have shown this pattern. A recent study analyzed the evolution of body size between diadromous and non-diadromous </span>shads, herrings, anchovies and allies<span>, finding that species evolved larger body sizes when adapting to a diadromous lifestyle. It remains unknown whether different fish clades adapt to migration similarly. We used an adaptive landscape framework to explore body size evolution for over 4500 migratory and non-migratory species of ray-finned fishes. By fitting models of macroevolution, we show that migratory species are evolving towards a body size that is larger than non-migratory species. Furthermore, we find that migratory lineages evolve towards their optimal body size more rapidly than non-migratory lineages, indicating body size is a key adaption for migratory fishes. Our results show, for the first time, that the largest vertebrate radiation on the planet exhibited strong evolutionary determinism when adapting to a migratory lifestyle.</span></p>
Data from: An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life
1. Comprehensive, time-scaled phylogenies provide a critical resource for many questions in ecology, evolution, and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. 2. We introduce the Fish Tree of Life website and associated R package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations, and diversification rate estimates for the most diverse group of vertebrate organisms, the ray-finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the R package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyze the data. 3. We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the R package. First, we test for the presence of long branch attraction artifacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package. 4. This resource makes a large comparative vertebrate dataset easily accessible via the website, while the R package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other R packages and software for molecular biology and comparative methods.
Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
<p>Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher-order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher-order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. In contrast some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher-order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ~293 million years (Ma), the base of Teleostei at ~211 Ma and the radiation of percomorphs beginning at ~141 Ma (~350 Ma, ~250–283 Ma and ~120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.</p>
Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii)
<p>Classification of the tremendous diversity of ray-finned fishes (Actinopterygii) began with the designation of taxonomic groups based on morphological similarity. Starting in the late 1960s morphological phylogenetics became the basis for the classification of Actinopterygii but failed to resolve many relationships, particularly among lineages within the hyperdiverse Percomorpha. The introduction of molecular phylogenetics led to a dramatic reconfiguration of actinopterygian phylogeny. Refined phylogenetic resolution afforded by molecular studies revealed an uneven diversity among actinopterygian lineages, resulting in a proliferation of redundant group names in Linnean-ranked classifications. Here we provide an unranked phylogenetic classification for actinopterygian fishes based on a summary phylogeny of 830 lineages of ray-finned fishes that includes all currently recognized actinopterygian taxonomic families and 287 fossil taxa. We provide phylogenetic definitions for 90 clade names and review seven previously defined names. For each of the 97 clade names we review the etymology of the clade name, clade species diversity and constituent lineages, clade diagnostic morphological apomorphies, a review of synonyms, and discuss the clade's nomenclatural and systematic history. The new classification is free of redundant group names and includes only one new name among the 97 clade names we review and describe, yielding a comprehensive classification that is based explicitly on the phylogeny of ray-finned fishes that has emerged in the 21st century and rests on the foundation of the previous 200 years of actinopterygian systematic research.</p>
A new Lower Permian ray-finned fish (Actinopterygii) from South Dakota and the use of tree space to find rogue taxa in phylogenetic analysis of morphological data
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Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes
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Data from: An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life
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Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii)
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Data from: A peculiar tooth renewal in a Jurassic ray-finned fish (Lepisosteiformes: †Scheenstia sp.)
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Supplementary information for: From scales to armour: scale losses and trunk bony plate gains in ray-finned fishes
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Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy
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Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
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Data for: Three-dimensional characterization of osteocyte volumes at multiple scales, and its relationship with bone biology and genome evolution in ray-finned fishes
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Data from: The oldest actinopterygian highlights the cryptic early history of the hyperdiverse ray-finned fishes
Osteichthyans comprise two divisions, each containing over 32,000 living species: Sarcopterygii (lobe-finned fishes and tetrapods) and Actinopterygii (ray-finned fishes). Recent discoveries from China highlight the morphological disparity of early sarcopterygians and extend their origin into the late Silurian. By contrast, the oldest unambiguous actinopterygians are roughly 30 million years younger, leaving a long temporal gap populated by fragments and rare body fossils of controversial phylogenetic placement. Here we reinvestigate the enigmatic osteichthyan Meemannia from the Early Devonian (∼415 million years ago) of China, previously identified as an exceptionally primitive lobe-finned fish. Meemannia combines "cosmine"-like tissues taken as evidence of sarcopterygian affinity with actinopterygian-like skull roof and braincase geometry, including endoskeletal enclosure of the spiracle and a lateral cranial canal. We report comparable histological structures in undoubted ray-finned fishes and conclude that they are general osteichthyan features. Phylogenetic analysis places Meemannia as an early-diverging ray-finned fish, resolving it as the sister lineage of Cheirolepis plus all younger actinopterygians. This brings the first appearance of ray-fins more in line with that of lobe-fins and fills a conspicuous faunal gap in the otherwise diverse late Silurian-earliest Devonian vertebrate faunas of the South China Block.
Data from: Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes
Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5–83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils."
Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.
Data from: An exceptionally preserved Late Devonian actinopterygian provides a new model for primitive cranial anatomy in ray-finned fishes
Actinopterygians (ray-finned fishes) are the most diverse living osteichthyan (bony vertebrate) group, with a rich fossil record. However, details of their earliest history during the middle Palaeozoic (Devonian) 'Age of Fishes' remains sketchy. This stems from an uneven understanding of anatomy in early actinopterygians, with a few well-known species dominating perceptions of primitive conditions. Here we present an exceptionally preserved ray-finned fish from the Late Devonian (Middle Frasnian, ca 373 Ma) of Pas-de-Calais, northern France. This new genus is represented by a single, three-dimensionally preserved skull. CT scanning reveals the presence of an almost complete braincase along with near-fully articulated mandibular, hyoid and gill arches. The neurocranium differs from the coeval Mimipiscis in displaying a short aortic canal with a distinct posterior notch, long grooves for the lateral dorsal aortae, large vestibular fontanelles and a broad postorbital process. Identification of similar but previously unrecognized features in other Devonian actinopterygians suggests that aspects of braincase anatomy in Mimipiscis are apomorphic, questioning its ubiquity as stand-in for generalized actinopterygian conditions. However, the gill skeleton of the new form broadly corresponds to that of Mimipiscis, and adds to an emerging picture of primitive branchial architecture in crown gnathostomes. The new genus is recovered in a polytomy with Mimiidae and a subset of Devonian and stratigraphically younger actinopterygians, with no support found for a monophyletic grouping of Moythomasia with Mimiidae.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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