Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.

Citation data:

Biology, ISSN: 2079-7737, Vol: 2, Issue: 1, Page: 419-44

Publication Year:
2013
Usage 6
Abstract Views 5
Link-outs 1
Captures 88
Readers 88
Mentions 31
References 31
Social Media 1
Tweets 1
Citations 41
Citation Indexes 41
Repository URL:
https://ecommons.luc.edu/biology_facpubs/41; https://scholarcommons.sc.edu/beaufort_naturalsciences_facpub/12
PMID:
24832669
DOI:
10.3390/biology2010419
PMCID:
PMC4009869
Author(s):
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. Show More Hide
Publisher(s):
MDPI AG
Tags:
Immunology and Microbiology; Biochemistry, Genetics and Molecular Biology; Agricultural and Biological Sciences; bird classification; avian phylogeny; nucleotide sequence alignment; total evidence; Columbiformes; Coraciiformes; Galliformes; Biology; Genetics and Genomics; Poultry or Avian Science; Zoology
Most Recent Tweet View All Tweets
article 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.