Evolutionary Origin and Early Biogeography of Otophysan Fishes (Ostariophysi: Teleostei)

Chen, Wei‐Jen; Lavoué, Sébastien; Mayden, Richard L.

doi:10.1111/evo.12104

Cited by 92 publications

(114 citation statements)

References 107 publications

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101

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“…Our phylogenetic reconstruction confirms the monophyly of Siluriformes and Gymnotiformes, but indicates that Characiformes are non-monophyletic and are divided into Characoidei and Citharinoidei, as seen in other molecular studies (Nakatani et al 2011;Chen et al 2013), and in contrast to morphological evidence (see summary in Chen et al 2013). Within Gymnotiformes, patterns of relationships largely match expectations based on taxonomy and prior phylogenetic studies.…”

supporting

confidence: 80%

Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes)

Elbassiouny

Schott

Waddell

et al. 2016

Mitochondrial DNA Part B

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Three complete mitochondrial genomes of South American electric fishes (Gymnotiformes), derived from high-throughput RNA sequencing (RNA-Seq), are reported herein. We report the complete mitochondrial genome of the bluntnose knifefish Brachyhypopomus n.sp. VERD, determined from newly sequenced data. We also provide the complete mitochondrial genomes for Sternopygus arenatus and the electric eel Electrophorus electricus , assembled from previously published transcriptome data. The mitochondrial genomes of Brachyhypopomus n.sp. VERD , Sternopygus arenatus and Electrophorus electricus have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs and 22 transfer RNAs, and are 16,547, 16,667 and 16,906 bp in length, respectively. Phylogenetic analysis of the eight available mitochondrial genomes of gymnotiform fishes shows Apteronotus to be the sister lineage of other gymnotiformes, contradicting the “Sinusoidea” hypothesis that Apteronotidae and Sternopygidae are sister taxa.

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supporting

confidence: 80%

Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes)

Elbassiouny

Schott

Waddell

et al. 2016

Mitochondrial DNA Part B

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“…Placement of these families has varied across different studies [1, 4, 7, 69, 70] and here we obtain sister relationships between Acheilognathidae + Gobionidae and Tanichthyidae + Leuciscidae, with Xenocyprididae sister to all four of these families (Fig. 2).…”

Section: Discussionsupporting

confidence: 58%

Resolving Cypriniformes relationships using an anchored enrichment approach

et al. 2016

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BackgroundCypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp).ResultsConcatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae.ConclusionsMost major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0819-5) contains supplementary material, which is available to authorized users.

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“…Despite having some characteristics of a redundant gene duplicate, this classification is usually attributed to genes resulting from relatively recent gene duplication events, with the vast majority of gene duplicates being silenced within a few million years (Lynch et al, 2001). However, unlike a more recent rhodopsin gene duplication, which may generate species-specific duplicates (Lim et al, 1997), our analyses suggest a much more ancient origin for the rh1-2 gene, within the rh1 gene family of a major group of bony fishes, which would place the duplication leading to the birth of rh1-2 somewhere between 153 and 248 million years ago (Nakatani et al, 2011;Chen et al, 2013). PAML analyses also suggest the potential for increased evolutionary rates at a variety of sites along the branch leading to the rh1-2 clade, followed by strong selective constraint characteristic of rh1 genes within the rh1-2 clade.…”

Section: Discussionmentioning

confidence: 56%

A second visual rhodopsin gene,rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes

Morrow

Lazic

Fox

et al. 2016

Journal of Experimental Biology

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Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1. We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1. These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.

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Evolutionary Origin and Early Biogeography of Otophysan Fishes (Ostariophysi: Teleostei)

Cited by 92 publications

References 107 publications

Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes)

Mitochondrial genomes of the South American electric knifefishes (Order Gymnotiformes)

Resolving Cypriniformes relationships using an anchored enrichment approach

A second visual rhodopsin gene,rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes

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