Genetics, Vol. 162, 1805-1810, December 2002, Copyright © 2002

The Evolution of Isochores: Evidence From SNP Frequency Distributions

Martin J. Lerchera, Nick G. C. Smithb, Adam Eyre-Walkerc, and Laurence D. Hursta
a Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom,
b Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
c Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom

Corresponding author: Martin J. Lercher, University of Bath, Claverton Down, Bath, Somerset BA2 7AY, UK., m.j.lercher{at}bath.ac.uk (E-mail)

Communicating editor: J. HEY

The large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.




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