Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable

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Varon-Gonzalez, CeferinoUniv Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England. (author)

Estimating Phylogenies from Shape and Similar Multidimensional Data : Why It Is Not Reliable

Article/chapterEnglish2020

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2020-01-27
Oxford University Press (OUP),2020
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LIBRIS-ID:oai:DiVA.org:uu-430588
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-430588URI
https://doi.org/10.1093/sysbio/syaa003DOI

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Language:English
Summary in:English

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In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared-change parsimony performed similarly well as maximum likelihood, and both methods outperformed Wagner and Euclidean parsimony, neighbor-joining and UPGMA. Under an evolutionary model of isotropic Brownian motion, phylogeny can be estimated reliably if dimensionality is high, even with relatively unfavorable combinations of branch lengths. By contrast, if there is phenotypic integration such that most variation is concentrated in one or a few dimensions, the reliability of phylogenetic estimates is severely reduced. Evolutionary models with stabilizing selection also produce highly unreliable estimates, which are little better than picking a phylogenetic tree at random. To examine how these results apply to phylogenies with more than four taxa, we conducted further simulations with up to eight taxa, which indicated that the effects of dimensionality and phenotypic integration extend to more than four taxa, and that convergence among internal nodes may produce additional complications specifically for greater numbers of taxa. Overall, the simulations suggest that multidimensional data, under evolutionary models that are plausible for biological data, do not produce reliable estimates of phylogeny.

Subject headings and genre

NATURVETENSKAP Biologi Evolutionsbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Evolutionary Biology hsv//eng
NATURVETENSKAP Biologi Biologisk systematik hsv//swe
NATURAL SCIENCES Biological Sciences Biological Systematics hsv//eng
Brownian motion
gene expression data
geometric morphometrics
morphological integration
squared-change parsimony
phylogeny
shape
stabilizing selection

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Whelan, SimonUppsala universitet,Evolutionsbiologi,Univ Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England.(Swepub:uu)simwh294 (author)
Klingenberg, Christian PeterUniv Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England. (author)
Univ Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England.Evolutionsbiologi (creator_code:org_t)

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In:Systematic Biology: Oxford University Press (OUP)69:5, s. 863-8831063-51571076-836X

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