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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals
Biology, Volume 2, No. 1, Year 2013
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Description
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. © 2013 by the authors; licensee MDPI, Basel, Switzerland.
Authors & Co-Authors
Yuri, Tamaki
United States, Gainesville
University of Florida
United States, Norman
The University of Oklahoma
Kimball, Rebecca T.
United States, Gainesville
University of Florida
Harshman, John
Unknown Affiliation
Bowie, Rauri C. K.
United States, Berkeley
University of California, Berkeley
Braun, Michael J.
United States, Washington, D.c.
Smithsonian Institution
United States, College Park
University of Maryland, College Park
Chojnowski, Jena L.
United States, Gainesville
University of Florida
Han, Kin Lan
United States, Gainesville
University of Florida
Hackett, Shannon J.
United States, Chicago
Field Museum of Natural History
Huddleston, Christopher J.
United States, Washington, D.c.
Smithsonian Institution
Moore, William Samuel
United States, Detroit
Wayne State University
Reddy, Sushma
United States, Chicago
Loyola University Chicago
Sheldon, Frederick H.
United States, Baton Rouge
Louisiana State University
Steadman, David W.
United States, Gainesville
University of Florida
Witt, Christopher C.
United States, Albuquerque
The University of new Mexico
Braun, Edward L.
United States, Gainesville
University of Florida
Statistics
Citations: 81
Authors: 15
Affiliations: 10
Identifiers
Doi:
10.3390/biology2010419
ISSN:
20797737
Research Areas
Cancer