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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

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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 bird classification; avian phylogeny; nucleotide sequence alignment; total evidence; Columbiformes; Coraciiformes; Galliformes
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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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