Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
by
1,2, 1, 3, 4, 5,6, 1, 1, 7, 5, 8, 9, Frederick H. Sheldon 10, David W. Steadman 11, Christopher C. Witt 12 and 1,*
1
Department of Biology, University of Florida, Gainesville, FL 32611, USA
2
Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
3
Pepperwood Way, San Jose, CA 95124, USA
4
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
5
Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
6
Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
7
Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA
8
Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
9
Biology Department, Loyola University Chicago, Chicago, IL 60660, USA
10
Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
11
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
12
Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
*
Author to whom correspondence should be addressed.
Biology 2013, 2(1), 419-444; https://doi.org/10.3390/biology2010419
Received: 28 December 2012 / Revised: 21 February 2013 / Accepted: 22 February 2013 / Published: 13 March 2013
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.
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Keywords:
bird classification; avian phylogeny; nucleotide sequence alignment; total evidence; Columbiformes; Coraciiformes; Galliformes
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This is an open access article distributed under the Creative Commons Attribution License
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Yuri, T.; Kimball, R.T.; Harshman, J.; Bowie, R.C.K.; Braun, M.J.; Chojnowski, J.L.; Han, K.-L.; Hackett, S.J.; Huddleston, C.J.; Moore, W.S.; Reddy, S.; Sheldon, F.H.; Steadman, D.W.; Witt, C.C.; Braun, E.L. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology 2013, 2, 419-444.
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