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In this paper, we use an example shorebird data set to explore three related questions regarding the interplay between alignment and phylogeny estimation: 1) can gap-rich alignments be used for reasonably accurate and unbiased phylogenetic inference? 2) How much phylogenetic information is contained in gap characters as compared with the nucleotides alone? 3) Are models of the insertion/deletion process advantageous and if so at what level of phylogenetic divergence? We report that there is considerable information created by the indel (insertion/deletion) process that is potentially available for phylogenetic inference. Ideally, we should be able to independently obtain the same tree from both nucleotide characters and from gap characters; however, there is still considerable variability in the alignments produced by different programs.We predict that better and more computationally tractable models of the indel process will be required before the information in gaps can be fully exploited for phylogenetic inference.

Item Type:	Refereed Article
Research Division:	Mathematical Sciences
Research Group:	Applied mathematics
Research Field:	Biological mathematics
Objective Division:	Expanding Knowledge
Objective Group:	Expanding knowledge
Objective Field:	Expanding knowledge in the mathematical sciences
UTAS Author:	Holland, BR (Professor Barbara Holland)
ID Code:	77705
Year Published:	2012
Funding Support:	Australian Research Council (FT100100031)
Web of Science® Times Cited:	12
Deposited By:	Mathematics and Physics
Deposited On:	2012-05-18
Last Modified:	2017-11-15
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