Applications of selective neutrality tests to molecular ecology

Abstract

This paper reviews how statistical tests of neutrality have been used to address questions in molecular ecology are reviewed. The work consists of four major parts: a brief review of the current status of the neutral theory; a review of several particularly interesting examples of how statistical tests of neutrality have led to insight into ecological problems; a brief discussion of the pitfalls of assuming a strictly neutral model if it is false; and a discussion of some of the opportunities and problems that molecular ecologists face when using neutrality tests to study natural selection.

Figure 1

Examples of the identification of codons with high probability of being subject to positive selection. (right) Model of transferrin with sites subject to positive selection in salmonids coloured red and sites contacted by bacterial transferrin‐binding proteins in humans coloured blue (adapted from Ford 2001). (left) Model of class I plant chitinase (A chain only), with positively selected sites coloured red, substrate binding sites coloured blue and catalytic sites coloured green (adapted from Bishop et al. 2000).

Figure 2

Three examples of sliding window analyses showing non‐neutral patterns polymorphism and divergence. (a) Drosophila Adh, showing a peak of intraspecific variation associated with the only amino acid polymorphism in the population (adapted from Hudson & Kreitman 1991; see also Begun et al. 1999). (b) Maize and teosinte tb1, showing reduction of diversity in maize in the 5′ untranslated region of the gene (adapted from Wang et al. 1999). (c) Arabidopsis thaliana Rpm1 region (adapted from Stahl et al. 1999). Dark line shows divergence between A. thaliana resistant (Rpm1 present) and susceptible (Rpm1 deleted) alleles, and the dotted line shows divergence between A. thaliana and A. lyrata. The arrow marks the location of the Rpm1 insertion/deletion.