Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks

Koichiro Tamura, Sankar Subramanian, Sudhir Kumar

Research output: Contribution to journalArticle

418 Citations (Scopus)

Abstract

Drosophila melanogaster has been a canonical model organism to study genetics, development, behavior, physiology, evolution, and population genetics for nearly a century. Despite this emphasis and the completion of its nuclear genome sequence, the timing of major speciation events leading to the origin of this fruit fly remain elusive because of the paucity of extensive fossil records and biogeographic data. Use of molecular clocks as an alternative has been fraught with nonclock-like accumulation of nucleotide and amino-acid substitutions. Here we present a novel methodology in which genomic mutation distances are used to overcome these limitations and to make use of all available gene sequence data for constructing a fruit fly molecular time scale. Our analysis of 2977 pairwise sequence comparisons from 176 nuclear genes reveals a long-term fruit fly mutation clock ticking at a rate of 11.1 mutations per kilobase pair per Myr. Genomic mutation clock-based timings of the landmark speciation events leading to the evolution of D. melanogaster show that it shared most recent common ancestry 5.4 MYA with D. simulans, 12.6 MYA with D. erecta+D. orena, 12.8 MYA with D. yakuba+D. teisseri, 35.6 MYA with the takahashii subgroup, 41.3 MYA with the montium subgroup, 44.2 MYA with the ananassae subgroup, 54.9 MYA with the obscura group, 62.2 MYA with the willistoni group, and 62.9 MYA with the subgenus Drosophila. These and other estimates are compatible with those known from limited biogeographic and fossil records. The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic.

Original languageEnglish (US)
Pages (from-to)36-44
Number of pages9
JournalMolecular Biology and Evolution
Volume21
Issue number1
DOIs
StatePublished - Jan 2004

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fruit flies
Fruits
Drosophila
Clocks
mutation
Fruit
fruit
Diptera
Mutation
Genes
Drosophila melanogaster
fossil record
genomics
fossils
gene
Physiology
Population Genetics
amino acid substitution
common ancestry
habitat fragmentation

Keywords

  • Drosophila
  • Evolutionary distance estimation
  • Molecular clock
  • Molecular evolution
  • Mutation rate
  • Speciation

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks. / Tamura, Koichiro; Subramanian, Sankar; Kumar, Sudhir.

In: Molecular Biology and Evolution, Vol. 21, No. 1, 01.2004, p. 36-44.

Research output: Contribution to journalArticle

Tamura, Koichiro ; Subramanian, Sankar ; Kumar, Sudhir. / Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks. In: Molecular Biology and Evolution. 2004 ; Vol. 21, No. 1. pp. 36-44.
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