The neutral coalescent process for recent gene duplications and copy-number variants.

Abstract:

:I describe a method for simulating samples from gene families of size two under a neutral coalescent process, for the case where the duplicate gene either has fixed recently in the population or is still segregating. When a duplicate locus has recently fixed by genetic drift, diversity in the new gene is expected to be reduced, and an excess of rare alleles is expected, relative to the predictions of the standard coalescent model. The expected patterns of polymorphism in segregating duplicates ("copy-number variants") depend both on the frequency of the duplicate in the sample and on the rate of crossing over between the two loci. When the crossover rate between the ancestral gene and the copy-number variant is low, the expected pattern of variability in the ancestral gene will be similar to the predictions of models of either balancing or positive selection, if the frequency of the duplicate in the sample is intermediate or high, respectively. Simulations are used to investigate the effect of crossing over between loci, and gene conversion between the duplicate loci, on levels of variability and the site-frequency spectrum.

journal_name

Genetics

journal_title

Genetics

authors

Thornton KR

doi

10.1534/genetics.107.074948

subject

Has Abstract

pub_date

2007-10-01 00:00:00

pages

987-1000

issue

2

eissn

0016-6731

issn

1943-2631

pii

genetics.107.074948

journal_volume

177

pub_type

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