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Table 1 Topology test results.

From: Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome coxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection

Parsimony-based tests:    Test   
Tree Length Difference KH Templeton Winning sites   
Unconstrained 2832 Best      
Taxa with 3 helices constrained 2987 155 p < 0.0001 p < 0.0001 p < 0.0001   
Taxa with 4 helices constrained 3251 419 p < 0.0001 p < 0.0001 p < 0.0001   
Taxa with 5 helices constrained 3175 343 p < 0.0001 p < 0.0001 p < 0.0001   
All taxa constrained 3418 586 p < 0.0001 p < 0.0001 p < 0.0001   
Likelihood-based tests:    Test
Tree -ln L Difference AU KH SH WKH WSH
Unconstrained - 13059.96460 Best      
Taxa with 3 helices constrained - 13286.28131 226.31671 p = 7e-10 p = 0 p = 0 p = 0 p = 0
Taxa with 4 helices constrained - 14055.57046 995.60586 p = 1e-08 p = 0 p = 0 p = 0 p = 0
Taxa with 5 helices constrained - 13764.70315 704.73856 p = 2e-05 p = 0 p = 0 p = 0 p = 0
All taxa constrained - 14218.22053 1158.25593 p = 6e-44 p = 0 p = 0 p = 0 p = 0
  1. Results of the parsimony-based Kishino-Hasegawa (KH), Templeton (Wilcoxon signed-ranks) and winning sites (sign) tests calculated using PAUP*, and the likelihood-based approximately unbiased (AU), Kishino-Hasegawa (KH), Shimodiara-Hasegawa (SH), weighted Kishino-Hasegawa (WKH), and weighted Shimodiara-Hasegawa (WSH) tests calculated using CONSEL. The phylogenetic trees compared were the best topology from the unconstrained Bayesian analysis versus analyses where the species with 3, 4, and 5 helices were individually constrained to be monophyletic, and an analysis where all species with equal numbers of helices were simultaneously constrained to be monophyletic.