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An algorithm for morphological phylogenetic analysis with inapplicable data

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Title: An algorithm for morphological phylogenetic analysis with inapplicable data
Authors: Brazeau, MD
Guillerme, T
Smith, MR
Item Type: Journal Article
Abstract: Morphological data play a key role in the inference of biological relationships and evolutionary history and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used “reductive coding” approach treats taxa in which a character is inapplicable as though the character’s state is simply missing (unknown). This approach has long been known to create spurious tree length estimates on certain topologies, potentially leading to erroneous results in phylogenetic searches—but pratical solutions have yet to be proposed and implemented. Here, we present a single-character algorithm for reconstructing ancestral states in reductively coded data sets, following the theoretical guideline of minimizing homoplasy over all characters. Our algorithm uses up to three traversals to score a tree, and a fourth to fully resolve final states at each node within the tree. We use explicit criteria to resolve ambiguity in applicable/inapplicable dichotomies, and to optimize missing data. So that it can be applied to single characters, the algorithm employs local optimization; as such, the method provides a fast but approximate inference of ancestral states and tree score. The application of our method to published morphological data sets indicates that, compared to traditional methods, it identifies different trees as “optimal.” As such, the use of our algorithm to handle inapplicable data may significantly alter the outcome of tree searches, modifying the inferred placement of living and fossil taxa and potentially leading to major differences in reconstructions of evolutionary history.
Issue Date: 1-Jul-2019
Date of Acceptance: 3-Nov-2018
URI: http://hdl.handle.net/10044/1/79869
DOI: 10.1093/sysbio/syy083
ISSN: 1063-5157
Publisher: Oxford University Press (OUP)
Start Page: 619
End Page: 631
Journal / Book Title: Systematic Biology
Volume: 68
Issue: 4
Copyright Statement: © The Author(s) 2018. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor/Funder: Commission of the European Communities
Funder's Grant Number: 311092
Keywords: Science & Technology
Life Sciences & Biomedicine
Evolutionary Biology
Character independence
character optimization
cladistic analysis
inapplicable data
phylogenetic tree search
SEQUENCE ALIGNMENT
MISSING ENTRIES
LOGICAL BASIS
OPTIMIZATION
CHARACTERS
TREES
Character independence
character optimization
cladistic analysis
inapplicable data
phylogenetic tree search
Algorithms
Classification
Fossils
Phylogeny
Phylogeny
Algorithms
Fossils
Classification
Science & Technology
Life Sciences & Biomedicine
Evolutionary Biology
Character independence
character optimization
cladistic analysis
inapplicable data
phylogenetic tree search
SEQUENCE ALIGNMENT
MISSING ENTRIES
LOGICAL BASIS
OPTIMIZATION
CHARACTERS
TREES
0603 Evolutionary Biology
0604 Genetics
Evolutionary Biology
Publication Status: Published
Open Access location: https://academic.oup.com/sysbio/article/68/4/619/5238046
Online Publication Date: 2018-12-11
Appears in Collections:Faculty of Natural Sciences