Computational protocol: Interacting Proteins on Human Spermatozoa: Adaptive Evolution of the Binding of Semenogelin I to EPPIN

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Protocol publication

[…] We aligned nucleotides sequences of EPPIN and SEMG1 from Homo sapiens, Pan troglodytes, Gorilla gorilla gorilla, Pongo abelii, Nomascus leucogenys, Macaca mulatta, Papio anubis, and Saimiri boliviensis boliviensis (GenBank accession numbers in ) with ClustalW. We used MEGA5 molecular evolutionary genetic analysis software package (version 5.1) [] to obtain phylogenetic trees using the Maximum Likelihood method based on the Tamura-Nei model [] and to perform the test of homogeneity of substitution patterns between sequences for EPPIN and SEMG1 using the neighbor-joining method []. Codon positions included were 1st+2nd+3rd. All positions containing gaps and missing data were eliminated. For technical details of these tests, please refer to their original descriptions [-]. We chose the phylogenetic trees with the highest log likelihood (EPPIN) -926.2396 or (SEMG1) -2108.0861 and used them for further analysis. We investigated evidence of positive selection codon-by-codon in the primate phylogenetic tree of EPPIN and SEMG1 using the CodeML software in the PAML 4 package [,]. In this case, we compared the likelihood of a nearly-neutral model M1a with that of a selection model M2a. Next, we compared the likelihood of a neutral model M7 with that of a selection model M8. In both cases we used a Likelihood Ratio Test (LRT) to determine if the selection model was a better fit to the data than the neutral model by comparing the (-2[Log(neutral) – Log(positive)]) value between the two models with the χ2-distribution [,]. When the calculations suggested positive selection, we used the BEB method to calculate the probability that each codon experienced positive selection under models M2a and M8 []. […]

Pipeline specifications

Software tools Clustal W, MEGA, PAML
Application Phylogenetics
Organisms Homo sapiens
Diseases Musculoskeletal Abnormalities
Chemicals Amino Acids, Glycine