Open Access Research article

Evolution by selection, recombination, and gene duplication in MHC class I genes of two Rhacophoridae species

Mian Zhao, Yongzhen Wang, Hang Shen, Chenliang Li, Cheng Chen, Zhenhua Luo and Hua Wu*

Author Affiliations

Molecular and Behavioural Ecology Research Group, College of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China

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BMC Evolutionary Biology 2013, 13:113  doi:10.1186/1471-2148-13-113

Published: 5 June 2013

Additional files

Additional file 1:

Goodness of fit for different codon evolution models and estimated parameter values. Notes: P refers to the number of parameters in the x distribution; x is the selection parameter. pn is the proportion of sites falling within the xn site class. For models M7 and M8, p and q denote the shape parameters of the b function. Positively selected sites were identified in models M2a and M8 using the Bayes empirical Bayes procedure [67]. Sites inferred to be undergoing positive selection at the 95% and 99% confidence interval level are marked with * and **, respectively.

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Additional file 2:

Summary of the test statistics for the likelihood ratio test of codon evolution. Notes: df refers to degrees of freedom. Test statistics were computed using formula 2 (Lb - La); La and Lb are log-likelihood values for each of the nested models being compared.

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Additional file 3:

Sites undergoing positive selection detected using the FEL program. Note: Numbering of the three domains differs from that shown in Additional file 1. Rather, the sites positions of domains α2 and α3 are counted from the first amino acids of domain α1. Only those sites with a significance level <0.05 are shown. aNormalized dN-dS refers to dN-dS divided by the total length of the appropriate tree.

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Additional file 4:

Sites undergoing positive selection detected using the MEME program. Note: The numbering strategy is described in Additional file 3. This summary table reports the distribution of synonymous (α) and non-synonymous (β) substitution rates for sites inferred using the MEME model. Sites with a significance level <0.01 are shown.

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