Biology 2013, 2(1), 419-444; doi:10.3390/biology2010419
Article

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

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.
Received: 28 December 2012; in revised form: 21 February 2013 / Accepted: 22 February 2013 / Published: 13 March 2013
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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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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.

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