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

Biology

Tamaki Yuri⁸  Rebecca T. Kimball⁸  John Harshman¹⁰  Rauri C. K. Bowie⁶  Michael J. Braun³  Jena L. Chojnowski⁸  Kin-Lan Han⁸  Shannon J. Hackett⁴  Christopher J. Huddleston³  William S. Moore⁵  Sushma Reddy⁹  Frederick H. Sheldon¹  David W. Steadman²  Christopher C. Witt^7,8 

[1] Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:;Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:;Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails:;Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:;Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:;Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:;Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:;Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails:;Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:;4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:

关键词: bird classification;    avian phylogeny;    nucleotide sequence alignment;    total evidence;    Columbiformes;    Coraciiformes;    Galliformes;   

DOI  :  10.3390/biology2010419

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2013 by the authors; licensee MDPI, Basel, Switzerland.