Publication: Patchy-tachy leads to false positives for recombination.

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Title Patchy-tachy leads to false positives for recombination.
Authors/Editors* S.Sun, B.J.Evans, G.B. Golding
Where published* Molecular Biology Evolution
How published* Journal
Year* 2011
Volume in press
Publisher Oxford Univ Press
Keywords recombination, false positives, mitochondrial DNA, heterotachy, substitution rate heterogeneity, animal mtDNA
Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call ``patchy-tachy'', where different partitions of sequences evolve at different rates, that leads to an excess of false positives for recombination inferred by indirect tests. To explore this phenomena, we characterized the false positive rates of six widely used indirect tests for recombination using simulations of general models for mtDNA evolution with patchy-tachy but without recombination. All tests produced 30-99\% false positives for recombination, although the conditions that produced the maximal level of false positives differed between the tests. To evaluate the degree to which conditions that exacerbate false positives are found in published sequence data, we turned to twenty animal mtDNA datasets in which recombination is suggested by indirect tests. Using a model where different regions of the sequences were free to evolve at different rates in different lineages, we demonstrated that patchy-tachy is prevalent in many datasets in which recombination was previously inferred using indirect tests. Taken together, our results argue that patchy-tachy without recombination is a viable alternative explanation for detection of widespread recombination in animal mtDNA using indirect tests.
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