Genetics and Genomics Commons^™

Parsimony And Model-Based Analyses Of Indels In Avian Nuclear Genes Reveal Congruent And Incongruent Phylogenetic Signals, Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri C.K. Bowie, Michael J. Braun, Jena L. Chojnowski, Kin-Lan Han, Shannon J. Hackett, Christopher J. Huddleston, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt, Edward L. Braun

Faculty Publications

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven …