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

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

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

Whelan, Simon (author): Uppsala universitet,Evolutionsbiologi,Univ Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England.

Klingenberg, Christian Peter (author): Univ Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England.

Univ Manchester, Sch Biol Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England Evolutionsbiologi (creator_code:org_t)

2020-01-27
2020
English.
In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 69:5, s. 863-883

Related links:: https://www.research...; show more...; https://urn.kb.se/re...; https://doi.org/10.1...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

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

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)

Keyword

Brownian motion
gene expression data
geometric morphometrics
morphological integration
squared-change parsimony
phylogeny
shape
stabilizing selection

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Evolutionary Bio ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biological Syste ...

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By the university: Uppsala University

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