Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes

M. Vincent Hirt, Gloria Arratia, Wei Jen Chen, Richard L. Mayden, Kevin L. Tang, Robert M. Wood, Andrew M Simons

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Gene choice, base compositional heterogeneity and rate heterogeneity are known to influence phylogenetic reconstruction but are often overlooked. Here, we investigate the impact of these factors in reconstructing the phylogenetic relationships and divergence times of cypriniform fishes. We compile a multilocus data set of newly sequenced and previously published nuclear protein-coding genes from species from all major lineages of Cypriniformes. We collect data on the oldest known cypriniform fossils and gather body size information. We demonstrate that body size correlates with rates of molecular evolution and contributes to rate heterogeneity not only in Cypriniformes but also in a number of other fish lineages. We find that miniaturized cypriniforms show exceptionally high rates of molecular evolution that may lead to improper phylogenetic placement of these taxa due to issues associated with branch attraction. We identify and correct for base compositional heterogeneity and find that this has a marked impact on topology and a corresponding impact on the estimation of divergence times within Cypriniformes. Using gene sequences, fossil calibrations and two different methods, we show strong evidence that Catostomidae is sister to all other cypriniform families and the major clades of cypriniform fishes diverged long before their fossil record indicates.

Original languageEnglish (US)
Pages (from-to)319-339
Number of pages21
JournalBiological Journal of the Linnean Society
Volume121
Issue number2
DOIs
StatePublished - Jan 1 2017

Fingerprint

Cypriniformes
fossils
divergence
gene
phylogeny
fish
body size
Catostomidae
phylogenetics
genes
nuclear proteins
fossil
topology
calibration
fossil record
nucleotide sequences
protein
effect
rate
methodology

Keywords

  • Age
  • Body size
  • Catostomidae
  • Fish
  • Miniature
  • Miniaturized
  • Paedocypris
  • Phylogenetics
  • Phylogeny
  • Positive selection

Cite this

Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. / Hirt, M. Vincent; Arratia, Gloria; Chen, Wei Jen; Mayden, Richard L.; Tang, Kevin L.; Wood, Robert M.; Simons, Andrew M.

In: Biological Journal of the Linnean Society, Vol. 121, No. 2, 01.01.2017, p. 319-339.

Research output: Contribution to journalArticle

Hirt, M. Vincent ; Arratia, Gloria ; Chen, Wei Jen ; Mayden, Richard L. ; Tang, Kevin L. ; Wood, Robert M. ; Simons, Andrew M. / Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. In: Biological Journal of the Linnean Society. 2017 ; Vol. 121, No. 2. pp. 319-339.
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