Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets

Mark W Coulson, H Dawn Marshall, Pierre Pepin, Steven M Carr

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

Phylogenetic analysis of 13 substantially complete mitochondrial DNA genome sequences (14,036 bp) from 10 taxa of gadine codfishes and pollock provides highly corroborated resolution of outstanding questions on their biogeographic evolution. Of 6 resolvable nodes among species, 4 were supported by >95% of bootstrap replications in parsimony, distance, likelihood, and similarly high posterior probabilities in bayesian analyses, one by 85%-95% according to the method of analysis, and one by 99% by one method and a majority of the other two. The endemic Pacific species, walleye pollock (Theragra chalcogramma), is more closely related to the endemic Atlantic species, Atlantic cod (Gadus macrocephalus), than either is to a second Pacific endemic, Pacific cod (Gadus macrocephalus). The walleye pollock should thus be referred to the genus Gadus as originally described (Gadus chalcogrammus Pallas 1811). Arcto-Atlantic Greenland cod, previously regarded as a distinct species (G. ogac), are a genomically distinguishable subspecies within pan-Pacific G. macrocephalus. Of the 2 endemic Arctic Ocean genera, Polar cod (Boreogadus) as the outgroup to Arctic cod (Arctogadus) and Gadus sensu lato is more strongly supported than a pairing of Boreogadus and Arctogadus as sister taxa. Taking into consideration historical patterns of hydrogeography, we outline a hypothesis of the origin of the 2 endemic Pacific species as independent but simultaneous invasions through the Bering Strait from an Arcto-Atlantic ancestral lineage. In contrast to the genome data, the complete proteome sequence (3830 amino acids) resolved only 3 nodes with >95% confidence, and placed Alaska pollock outside the Gadus clade owing to reversal mutations in the ND5 locus that restore ancestral, non-Gadus, amino acid residues in that species.

Original languageEnglish
Pages (from-to)1115-30
Number of pages16
JournalGenome Biology
Volume49
Issue number9
DOIs
Publication statusPublished - Sep 2006

Keywords

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • DNA, Mitochondrial
  • Gadiformes
  • Genomics
  • Geography
  • Molecular Sequence Data
  • Oceans and Seas
  • Phylogeny
  • Proteomics
  • Sequence Alignment
  • Journal Article
  • Research Support, Non-U.S. Gov't

Fingerprint Dive into the research topics of 'Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets'. Together they form a unique fingerprint.

  • Cite this