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

Research output: Contribution to journalArticlepeer-review

75 Scopus citations


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 difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

Original languageEnglish (US)
Pages (from-to)419-444
Number of pages26
Issue number1
StatePublished - Mar 13 2013
Externally publishedYes


  • Avian phylogeny
  • Bird classification
  • Columbiformes
  • Coraciiformes
  • Galliformes
  • Nucleotide sequence alignment
  • Total evidence


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