MlRho - A program for estimating the population mutation and recombination rates from shotgunsequenced diploid genomes

Bernhard Haubold, Peter Pfaffelhuber, Michael Lynch

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4N eμ), the sequencing error rate, and the population recombination rate (4Nec). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho.

Original languageEnglish (US)
Pages (from-to)277-284
Number of pages8
JournalMolecular Ecology
Volume19
Issue numberSUPPL. 1
DOIs
StatePublished - Mar 1 2010
Externally publishedYes

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Ciona intestinalis
Daphnia pulex
Population Control
Firearms
Mutation Rate
Diploidy
Genetic Recombination
recombination
mutation
diploidy
Cladocera
genome
Genome
Daphnia
guanine
Guanine
Ecology
Oceans and Seas
Population
sequence analysis

Keywords

  • Bioinformatics/phyloinformatics
  • Evolutionary theory
  • Genomics/proteomics
  • Population genetics - theoretical

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

MlRho - A program for estimating the population mutation and recombination rates from shotgunsequenced diploid genomes. / Haubold, Bernhard; Pfaffelhuber, Peter; Lynch, Michael.

In: Molecular Ecology, Vol. 19, No. SUPPL. 1, 01.03.2010, p. 277-284.

Research output: Contribution to journalArticle

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