Author: Clayton M. Carey; Sarah E. Apple; Zoe A. Hilbert; Michael S. Kay; Nels C. Elde
Title: Conflicts with diarrheal pathogens trigger rapid evolution of an intestinal signaling axis Document date: 2020_3_30
ID: ju826pao_15
Snippet: Evolutionary analysis GC-C and NPR1-3 nucleotide sequences were retrieved from NCBI GenBank for each species. Prior to analysis, sequences for each gene within each clade were first aligned using clustalW. In each analysis, a generally agreed upon phylogeny was used for each clade. Evidence for gene-wide positive selection was obtained using the branch-site models implemented in PAML and BUSTED software. In PAML, alignments were fitted to a F3x4 .....
Document: Evolutionary analysis GC-C and NPR1-3 nucleotide sequences were retrieved from NCBI GenBank for each species. Prior to analysis, sequences for each gene within each clade were first aligned using clustalW. In each analysis, a generally agreed upon phylogeny was used for each clade. Evidence for gene-wide positive selection was obtained using the branch-site models implemented in PAML and BUSTED software. In PAML, alignments were fitted to a F3x4 codon model and likelihood ratio tests were performed based on comparisons of NSsites model 2 to model 1 and model 8 to model 7. BUSTED analysis was performed on all branches of a user-specified tree using an online webserver with default parameters (https://www.datamonkey.org/busted). Gene trees based on the amino acid sequence of GC-C and NPR2 were generated by first aligning amino acid sequences with clustalW in each clade. Trees were generated using the PhyML plugin implemented in Geneious software using the Le Gascuel substitution model.
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