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Eight ORF clusters (Table 2) showed significant evidence of positive selection, after a sequential Bonferroni correction for multiple comparisons (eight clusters by site tests, and two clusters by branch-site tests).
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However, positive selection can be difficult to detect, even for relatively more powerful branch-site tests and BEB analyses (Zhang et al. 2005).
In total, 50 null hypothesis tests to identify positive selection, as described above, were carried out, representing 38 site-model tests (19 M7 vs M8 and 19 M8 vs M8a), six branch-site tests and six two-ratio tests.
Thus whilst evidence for rapid diversifying selection exists in the evolution of the hsp-90 gene (as evidenced by the significance of the branch-site tests) and most likely occurred early in nematode divergence, we have been unable to prove with confidence that the selection seen correlates with a change in the GA-binding function of Hsp-90.
While it has been shown that high recombination rates can lead to false positives in overall analysis using PAML, such as the TO test [ 86], no studies have evaluated the effect of recombination on the branch-site tests and it is unclear how recombination affects this analysis.
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