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Gaps: an elusive source of phylogenetic information
journal contribution
posted on 2023-05-17, 11:42 authored by Saurabh, K, Barbara HollandBarbara Holland, Gibb, GC, Penny, DIn 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.
Funding
Australian Research Council
History
Publication title
Systematic BiologyVolume
61Issue
6Pagination
1075-1082ISSN
1063-5157Department/School
School of Natural SciencesPublisher
Taylor & Francis IncPlace of publication
325 Chestnut St, Suite 800, Philadelphia, USA, Pa, 19106Rights statement
Copyright 2012 The AuthorsRepository Status
- Restricted