University of Tasmania
Browse
Article_Holland_2013_Reconstruct_Past_Chang_Recomb_Rates.pdf (706.75 kB)

Reconstructing past changes in locus-specific recombination rates

Download (706.75 kB)
journal contribution
posted on 2023-05-17, 17:39 authored by Cox, MP, Barbara HollandBarbara Holland, Wilkins, MC, Schmid, J

Background: Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existing inferential methods, predominantly based on linkage disequilibrium patterns, return a long-term average estimate of past recombination rates. Such estimates can be misleading, but no analytical framework to infer recombination rates that have changed over time is currently available.

Results: We apply coalescent modeling in conjunction with a suite of summary statistics to show that the recombination history of a locus can be reconstructed from a time series of genetic samples. More usefully, we describe a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point. This subsampling strategy can correctly assign simulated loci to constant, increasing and decreasing recombination models with an accuracy of 84%.

Conclusions: While providing an important stepping-stone to determining past recombination rates, n-tuple subsampling still exhibits a moderate error rate. Theoretical limitations indicated by coalescent theory suggest that highly accurate inference of past recombination rates will remain challenging. Nevertheless, we show for the first time that reconstructing historic recombination rates is possible in principle.

Funding

Australian Research Council

History

Publication title

BMC Genetics

Volume

14

Article number

11

Number

11

Pagination

1-11

ISSN

1471-2156

Department/School

School of Natural Sciences

Publisher

Biomed Central Ltd

Place of publication

United Kingdom

Rights statement

Licensed under Creative Commons Attribution 2.0 Generic (CC BY 2.0) http://creativecommons.org/licenses/by/2.0/

Repository Status

  • Open

Socio-economic Objectives

Expanding knowledge in the mathematical sciences

Usage metrics

    University Of Tasmania

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC