High mutation rates in the mitochondrial genomes of Daphnia pulex

Sen Xu, Sarah Schaack, Amanda Seyfert, Eunjin Choi, Michael Lynch, Melania E. Cristescu

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10 -7 and 1.73 × 10 -7 per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.

Original languageEnglish (US)
Pages (from-to)763-769
Number of pages7
JournalMolecular biology and evolution
Issue number2
StatePublished - Feb 2012
Externally publishedYes


  • asexuality
  • mitochondria effective population size
  • mitochondrial DNA
  • mitochondrial evolution
  • mutation hotspots
  • mutation-accumulation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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