Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.
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.
Department of Biology, University of Florida, Gainesville, FL 32611, USA. tyuri@ou.edu.
Tamaki
T
Yuri
Department of Biology, University of Florida, Gainesville, FL 32611, USA. rkimball@ufl.edu.
Rebecca T
RT
Kimball
Pepperwood Way, San Jose, CA 95124, USA. jharshman@pacbell.net.
John
J
Harshman
Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. bowie@berkeley.edu.
Rauri C K
RC
Bowie
Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA. braunm@si.edu.
Michael J
MJ
Braun
Department of Biology, University of Florida, Gainesville, FL 32611, USA. kixs4@uga.edu.
Jena L
JL
Chojnowski
Department of Biology, University of Florida, Gainesville, FL 32611, USA. hankin@ufl.edu.
Kin-Lan
KL
Han
Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA. shackett@fieldmuseum.org.
Shannon J
SJ
Hackett
Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA. huddlestonc@si.edu.
Christopher J
CJ
Huddleston
Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA. wmoore1415@gmail.com.
William S
WS
Moore
Biology Department, Loyola University Chicago, Chicago, IL 60660, USA. sreddy6@luc.edu.
Sushma
S
Reddy
Department of Biology, University of Florida, Gainesville, FL 32611, USA.
Frederick H
FH
Sheldon
Department of Biology, University of Florida, Gainesville, FL 32611, USA.
David W
DW
Steadman
Department of Biology, University of Florida, Gainesville, FL 32611, USA.
Christopher C
CC
Witt
Department of Biology, University of Florida, Gainesville, FL 32611, USA. ebraun68@ufl.edu.
Edward L
EL
Braun