Computational protocol: Nucleotide sequence and results of test of adaptive evolution in the α-globin gene of octodontoid rodents

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[…] We selected 10 caviomorph rodent species, including two independent subterranean lineages (Ctenomys and Spalacopus cyanus), three fossorial but non-subterranean relatives (Aconaemys fuscus, Octodon degus and Tympanoctomys barrerae), a non-fossorial spiny rat (Proechimys longicaudatus), and two species of Cavia (C. porcellus and C. aperea) used as outgroup. We chose a sample of 3 species from Ctenomys in an attempt to capture the diversity of lifestyles, molecular differentiation and habitat features .Total DNA extractions were made from liver preserved in 95% ethyl-alcohol . PCR amplification were carried out with two pair of primers specially designed for this study . PCR products were purified and automatic sequencing from both ends was done by Macrogen. Inc. (http://www.macrogen.com), under BigDyeTM terminator cycling conditions in an ABI 3730xl Sequencer. The intron-exon structure and inspections of the lack of stop codons and in/dels that generate frameshift were checked. Aligned CDS are shown in .Codon sites with evidence of have evolved under positive selection by different methods has been shown and summarized in . Here we show additional results obtained with MEME implemented in Datamonkey web server (http://www.datamonkey.org/, ) and TreeSAAP software. MEME evaluates variation in dN/dS along branches, and then assess which sites contribute to variation in dN/dS, and the level for significance was 0.05 for the site and, conditional upon that, an Empirical Bayes Factor (EBF) greater than 20 for the branch or branches. TreeSAAP compares physicochemical properties of the amino acid changes observed. Nonsynonymous changes were considered to be the result of positive, destabilizing selection (from now on, “radical changes”) only if they met two stringent criteria: a) they were assigned to the most extreme categories of structural or functional changes (categories 6, 7 and 8 of ); and b) they were significant at the p<0.001. We ran ModelGenerator to select a substitution model for each gene and reconstruct ancestral sequences in Baseml , and the model selected was REV . The phylogeny considered for this study is shown in and and was obtained by pruning the comprehensive tree of octodontoid genera in , and . […]

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