View article

Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within a set of homologous sequences is a difficult question. Here we develop a new statistic, Φ_w, that can be used to test for recombination. We show through simulation that our test can discriminate effectively between the presence and absence of recombination, even in diverse situations such as exponential growth (star-like topologies) and patterns of substitution rate correlation. A number of other tests, Max χ², NSS, a coalescent-based likelihood permutation test (from LDHat), and correlation of linkage disequilibrium (both r² and |D′|) with distance, all tend to underestimate the presence of recombination under strong population growth. Moreover, both Max χ² and NSS falsely infer the presence of recombination …