Format

Send to:

Choose Destination
See comment in PubMed Commons below
Genome Res. 2008 Jul;18(7):1020-9. doi: 10.1101/gr.074187.107. Epub 2008 Apr 14.

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.

Author information

  • 1Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA. inesh@berkeley.edu

Abstract

We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show that the elevated diversity in telomeric regions is mainly due to elevated mutation rates and not due to decreased levels of background selection. However, we find indications that telomeres as well as centromeres experience greater impact from natural selection than intrachromosomal regions. Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate.

PMID:
18411405
[PubMed - indexed for MEDLINE]
PMCID:
PMC2493391
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 ...
    Write to the Help Desk