A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species

Hawkins, John A.; Kaczmarek, Maria E.; Müller, Marcel A.; Drosten, Christian; Press, William H.; Sawyer, Sara L.

Phylogenetic Analysis. Phylogenetic trees were constructed from these multiple sequence alignments, using multiple strategies and software packages. First, using the 1,107 genes found in all species, we constructed the species tree with a partitioned nucleotide analysis in Mr. Bayes (48) , which fits for one species tree while allowing the model parameters to vary for each gene. Next, using the same genes, we constructed the species tree with concatenated data using RAxML (49) . This we did for the full coding sequence (CDS), the amino acid sequence, and each codon position separately. We additionally fit the phylogenetic tree using RAxML with the CDS sequence of the longest 100 alignments after subjecting the corresponding amino acid alignments to manual inspection. The full length of all 100 alignments looked highly credible to manual inspection. Finally, we constructed the 1,107 gene trees with all species using Mr. Bayes and determined the species tree via coalescent analysis as implemented in AS-TRAL (50) . This was done for the full CDS sequence and each codon position separately.