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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, D
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.

Funding

Australian Research Council

History

Publication title

Systematic Biology

Volume

61

Issue

6

Pagination

1075-1082

ISSN

1063-5157

Department/School

School of Natural Sciences

Publisher

Taylor & Francis Inc

Place of publication

325 Chestnut St, Suite 800, Philadelphia, USA, Pa, 19106

Rights statement

Copyright 2012 The Authors

Repository Status

  • Restricted

Socio-economic Objectives

Expanding knowledge in the mathematical sciences

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