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
Geneticsjournal_title
Geneticsauthors
Thornton KRdoi
10.1534/genetics.107.074948subject
Has Abstractpub_date
2007-10-01 00:00:00pages
987-1000issue
2eissn
0016-6731issn
1943-2631pii
genetics.107.074948journal_volume
177pub_type
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