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

Table 1 Topology test results.

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

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.

ISSN: 2730-7182