Shifting patterns of selection on matK.

Likelihood Ratio Tests indicate shifts in pattern of selection on Cuscuta nitida (Convolvulaceae) and Epifagus virginiana (Orobanchaceae) matK genes following loss of all but one (3′rps12 in Cuscuta nitida) or two (3′rps12 and rpl2 in Epifagus virginiana) group IIA introns from the plastid genome. Models and parameters are described in text. Models with significantly improved likelihoods relative to null hypothesis are shown in boldface. Clade and branch descriptions refer to relationships depicted in Figure 1.*Models M0, M1a, M2a, and M3 are described in text with branchXsites (bXs) models for M3 and M1a.§Null model 2 for positive selection is BranchXSites model constraining foreground ω2 to neutrality (ω2 = 1.0).