Format

Send to

Choose Destination
See comment in PubMed Commons below
Genetics. 2009 Apr;181(4):1567-78. doi: 10.1534/genetics.108.100032. Epub 2009 Feb 9.

Detecting selective sweeps: a new approach based on hidden markov models.

Author information

1
Institute of Statistics and Decision Support Systems, University of Vienna, Vienna, Austria. simon.boitard@toulouse.inra.fr

Abstract

Detecting and localizing selective sweeps on the basis of SNP data has recently received considerable attention. Here we introduce the use of hidden Markov models (HMMs) for the detection of selective sweeps in DNA sequences. Like previously published methods, our HMMs use the site frequency spectrum, and the spatial pattern of diversity along the sequence, to identify selection. In contrast to earlier approaches, our HMMs explicitly model the correlation structure between linked sites. The detection power of our methods, and their accuracy for estimating the selected site location, is similar to that of competing methods for constant size populations. In the case of population bottlenecks, however, our methods frequently showed fewer false positives.

PMID:
19204373
PMCID:
PMC2666521
DOI:
10.1534/genetics.108.100032
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center