Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

  title={Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution},
  author={Richard E. Broughton and Ricardo Betancur-R and Chenhong Li and Gloria Arratia and Guillermo Ort{\'i}},
  journal={PLoS Currents},
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various… 
Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages
It is estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major o tocephalan lineages were hypothesized.
The early evolution of ray‐finned fishes
Some major outlines of actinopterygian diversification seem reasonably clear from the fossil record: low richness and disparity in the Devonian; elevated morphological variety, linked to increases in taxonomic dominance, in the early Carboniferous; and further gains inTaxonomic dominance in the Early Triassic associated with earliest appearance of trophically diverse crown neopterygians.
The Tree of Life and a New Classification of Bony Fishes
A comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages and the order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny.
Ray-finned fishes (Actinopterygii) constitute approximately half of all living vertebrate species. A stable hypothesis of relationships among major modern lineages has emerged over the past decade,
Molecular cytogenetics of selected actinopterygian fishes: insight from repetitive sequences to whole genome analyses
The outcomes of this Thesis reveal the dynamic nature and the complexity of the fish genome, as well as the importance of cytogenetic and cytogenomic methodologies in the age of the next generation sequencing.
Combined phylogeny of ray‐finned fishes (Actinopterygii) and the use of morphological characters in large‐scale analyses
  • J. M. Mirande
  • Biology
    Cladistics : the international journal of the Willi Hennig Society
  • 2017
This study evaluates the phylogeny of ray‐finned fishes (Actinopterygii) combining most available information (44 markers from nuclear and mitochondrial DNA and 274 morphological characters) to obtain synapomorphies and diagnoses for most clades.
Multigene phylogeny of cyprinodontiform fishes suggests continental radiations and a rogue taxon position of Pantanodon
The phylogeny matched more closely continent-scale distribution than current classification, suggesting that the delimitation of the families Cyprinodontidae, Poeciliidae, and Valenciidae is in need of revision.
Using information from the fossil record and time calibrated molecular phylogenies, this work investigates the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray‐finned fishes (Actinopterygii), and demonstrates polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years.
The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects
Actinopterygii are the most speciose living vertebrate clade, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest


Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)
Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians are obtained, representing 17 out of 44 orders within the class Actinoperygii.
Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish
Individual gene trees for these three genes and a concatenated dataset support the hypothesis that the fish-specific genome duplication event took place after the split of the Acipenseriformes and the Semionotiformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes.
Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates
This tree confirms that chondrichthyans are basal to all living gnathostomes, that lungfishes (Dipnoi) are the closest living relatives of tetrapods, and that bichirs are the living members of the most ancient family of ray-finned fishes.
Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes
Cartilaginous fishes have been inferred to be basal to other jawed vertebrates, which is consistent with the generally accepted view and the bichir has been shown to be the basal ray-finned fish.
Molecular phylogeny and divergence times of deuterostome animals.
It is found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils and that several lineages had originated before periods of global glaciation in the Precambrian.
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
A practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny is presented and is an improvement over traditional approaches because it uses genomic information and automates the process to identify large numbers of candidate makers.
Resolution of ray-finned fish phylogeny and timing of diversification
  • T. Near, R. Eytan, W. Smith
  • Biology, Environmental Science
    Proceedings of the National Academy of Sciences
  • 2012
Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for
A phylogeny of the families of fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent
The new phylogenetic hypothesis, together with stratigraphic and biogeographical data, is used to discuss scenarios of the origin and evolution of the major clades of the tetraodontiform order.
A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms.
In maximum parsimony trees, nodes congruent with those of the morphologically based cladogram were found to be robust (chondrichthyans, neopterygians, euteleosteans), but some expected monophyletic groups were not finding to be so (lissamphibians, tetrapods, osteichthyans).
A new time-scale for ray-finned fish evolution
New palaeontological evidence is presented that the neopterygian crown radiation is a Palaeozoic event, and it is demonstrated that conflicts between molecular and morphological data for the age of the Neopterygii result, in part, from missing fossil data.