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Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
Pepperwood Way, San Jose, CA 95124, USA
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA
Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
Biology Department, Loyola University Chicago, Chicago, IL 60660, USA
Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
* Author to whom correspondence should be addressed.
Received: 28 December 2012; in revised form: 21 February 2013 / Accepted: 22 February 2013 / Published: 13 March 2013
Abstract: 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.
Keywords: bird classification; avian phylogeny; nucleotide sequence alignment; total evidence; Columbiformes; Coraciiformes; Galliformes
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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.
Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han K-L, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals. Biology. 2013; 2(1):419-444.
Yuri, Tamaki; Kimball, Rebecca T.; Harshman, John; Bowie, Rauri C.K.; Braun, Michael J.; Chojnowski, Jena L.; Han, Kin-Lan; Hackett, Shannon J.; Huddleston, Christopher J.; Moore, William S.; Reddy, Sushma; Sheldon, Frederick H.; Steadman, David W.; Witt, Christopher C.; Braun, Edward L. 2013. "Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals." Biology 2, no. 1: 419-444.