Resolving Cypriniformes relationships using an anchored enrichment approach.

Carla C Stout,Alan R Lemmon,Emily Moriarty Lemmon,Jonathan W Armbruster,Milton Tan

doi:10.1186/s12862-016-0819-5

Carla C Stout, Alan R Lemmon + Show 3 more

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https://doi.org/10.1186/s12862-016-0819-5

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Abstract

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.

Highlights

Cypriniformes is the largest group of freshwater fishes in the world (~4300 described species)
A total of 315,288 base pairs spanning 219 loci were obtained for use in estimating the phylogenetic relationships
The Cypriniformes is among the most important clades of freshwater fishes and among the most studied with phylogenetic inference. This great deal of work makes them a key group in understanding the various pit-falls of phylogenetic studies, and they exemplify the phylogenetic conflicts from the varying analyses of morphological, mitochondrial, and nuclear data

Summary

Introduction

Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world. To place the Cypriniformes into perspective, about one third of freshwater fish species is a cypriniform and about 6 % of all vertebrate species is a cyprinform [2]. Species of Cypriniformes are distributed in freshwater habitats across Asia, Europe, Africa, and North America [4]. Example representatives include the zebrafish (Danio rerio), a model organism used in genomic and developmental biology, important aquaculture species like the common carp (Cyprinus carpio), major invasive species to North America such as Hypophthalmichthys

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