Ancestral State Estimation with Phylogenetic Ridge Regression

Silvia Castiglione; Carmela Serio; Alessandro Mondanaro; Marina Melchionna; Francesco Carotenuto; Mirko Di Febbraro; Antonio Profico; Davide Tamagnini; Pasquale Raia

doi:10.1007/s11692-020-09505-x

Ancestral State Estimation with Phylogenetic Ridge Regression

Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Francesco Carotenuto, Mirko Di Febbraro, Antonio Profico, Davide Tamagnini, Pasquale Raia^*

^*Corresponding author for this work

Archaeology

Research output: Contribution to journal › Article › peer-review

Abstract

The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications. We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values. We tested the new implementation, named RRphylo-noder (which is available as part of the RRphylo R package) on tree and data generated according to evolutionary processes of differing complexity and under variable sampling conditions. We compared RRphylo-noder performance to other available methods for ancestral state estimation, including Bayesian approaches and methods allowing rate variation between the tree branches. We additionally applied RRphylo-noder to two real cases studies, the evolution of body size in baleen whales and in caniform carnivores. Variable-rate methods proved to be more accurate than single-rate methods in estimating ancestral states when the pattern of phenotypic evolution changes across the tree. RRphylo-noder proved to be slightly more accurate and sensibly faster than Bayesian approaches, and the least sensitive to the kind of phenotypic pattern simulated. The use of fossil phenotypes as ancestral character values noticeably increases the probability to find a phenotypic trend through time when it applies to either the entire tree or just to specific clades within it. We found Cope’s rule to apply to both mysticete cetaceans and caniform carnivores. The RRphylo-noder implementation is particularly appropriate to study phenotypic evolution in the presence of complex phenotypes generated by different processes acting in different parts the tree, and when suitable information about fossil phenotypes is at hand.

Original language	English
Pages (from-to)	220-232
Number of pages	13
Journal	Evolutionary Biology
Volume	47
Early online date	17 Jun 2020
DOIs	https://doi.org/10.1007/s11692-020-09505-x
Publication status	Published - 1 Sept 2020

Keywords

Ancestral states estimation
Fossil phylogenies
Phenotypic evolution
Phylogenetic comparative methods
Rrphylo

Access to Document

10.1007/s11692-020-09505-x

Cite this

@article{c3a4cb2e291e4ba5947f5ff6140aafae,

title = "Ancestral State Estimation with Phylogenetic Ridge Regression",

abstract = "The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications. We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values. We tested the new implementation, named RRphylo-noder (which is available as part of the RRphylo R package) on tree and data generated according to evolutionary processes of differing complexity and under variable sampling conditions. We compared RRphylo-noder performance to other available methods for ancestral state estimation, including Bayesian approaches and methods allowing rate variation between the tree branches. We additionally applied RRphylo-noder to two real cases studies, the evolution of body size in baleen whales and in caniform carnivores. Variable-rate methods proved to be more accurate than single-rate methods in estimating ancestral states when the pattern of phenotypic evolution changes across the tree. RRphylo-noder proved to be slightly more accurate and sensibly faster than Bayesian approaches, and the least sensitive to the kind of phenotypic pattern simulated. The use of fossil phenotypes as ancestral character values noticeably increases the probability to find a phenotypic trend through time when it applies to either the entire tree or just to specific clades within it. We found Cope{\textquoteright}s rule to apply to both mysticete cetaceans and caniform carnivores. The RRphylo-noder implementation is particularly appropriate to study phenotypic evolution in the presence of complex phenotypes generated by different processes acting in different parts the tree, and when suitable information about fossil phenotypes is at hand.",

keywords = "Ancestral states estimation, Fossil phylogenies, Phenotypic evolution, Phylogenetic comparative methods, Rrphylo",

author = "Silvia Castiglione and Carmela Serio and Alessandro Mondanaro and Marina Melchionna and Francesco Carotenuto and {Di Febbraro}, Mirko and Antonio Profico and Davide Tamagnini and Pasquale Raia",

year = "2020",

month = sep,

day = "1",

doi = "10.1007/s11692-020-09505-x",

language = "English",

volume = "47",

pages = "220--232",

journal = "Evolutionary Biology",

issn = "0071-3260",

publisher = "Springer",

}

TY - JOUR

T1 - Ancestral State Estimation with Phylogenetic Ridge Regression

AU - Castiglione, Silvia

AU - Serio, Carmela

AU - Mondanaro, Alessandro

AU - Melchionna, Marina

AU - Carotenuto, Francesco

AU - Di Febbraro, Mirko

AU - Profico, Antonio

AU - Tamagnini, Davide

AU - Raia, Pasquale

PY - 2020/9/1

Y1 - 2020/9/1

N2 - The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications. We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values. We tested the new implementation, named RRphylo-noder (which is available as part of the RRphylo R package) on tree and data generated according to evolutionary processes of differing complexity and under variable sampling conditions. We compared RRphylo-noder performance to other available methods for ancestral state estimation, including Bayesian approaches and methods allowing rate variation between the tree branches. We additionally applied RRphylo-noder to two real cases studies, the evolution of body size in baleen whales and in caniform carnivores. Variable-rate methods proved to be more accurate than single-rate methods in estimating ancestral states when the pattern of phenotypic evolution changes across the tree. RRphylo-noder proved to be slightly more accurate and sensibly faster than Bayesian approaches, and the least sensitive to the kind of phenotypic pattern simulated. The use of fossil phenotypes as ancestral character values noticeably increases the probability to find a phenotypic trend through time when it applies to either the entire tree or just to specific clades within it. We found Cope’s rule to apply to both mysticete cetaceans and caniform carnivores. The RRphylo-noder implementation is particularly appropriate to study phenotypic evolution in the presence of complex phenotypes generated by different processes acting in different parts the tree, and when suitable information about fossil phenotypes is at hand.

AB - The inclusion of fossil phenotypes as ancestral character values at nodes in phylogenetic trees is known to increase both the power and reliability of phylogenetic comparative methods (PCMs) applications. We implemented the R function RRphylo as to integrate fossil phenotypic information as ancestral character values. We tested the new implementation, named RRphylo-noder (which is available as part of the RRphylo R package) on tree and data generated according to evolutionary processes of differing complexity and under variable sampling conditions. We compared RRphylo-noder performance to other available methods for ancestral state estimation, including Bayesian approaches and methods allowing rate variation between the tree branches. We additionally applied RRphylo-noder to two real cases studies, the evolution of body size in baleen whales and in caniform carnivores. Variable-rate methods proved to be more accurate than single-rate methods in estimating ancestral states when the pattern of phenotypic evolution changes across the tree. RRphylo-noder proved to be slightly more accurate and sensibly faster than Bayesian approaches, and the least sensitive to the kind of phenotypic pattern simulated. The use of fossil phenotypes as ancestral character values noticeably increases the probability to find a phenotypic trend through time when it applies to either the entire tree or just to specific clades within it. We found Cope’s rule to apply to both mysticete cetaceans and caniform carnivores. The RRphylo-noder implementation is particularly appropriate to study phenotypic evolution in the presence of complex phenotypes generated by different processes acting in different parts the tree, and when suitable information about fossil phenotypes is at hand.

KW - Ancestral states estimation

KW - Fossil phylogenies

KW - Phenotypic evolution

KW - Phylogenetic comparative methods

KW - Rrphylo

UR - http://www.scopus.com/inward/record.url?scp=85087055950&partnerID=8YFLogxK

U2 - 10.1007/s11692-020-09505-x

DO - 10.1007/s11692-020-09505-x

M3 - Article

AN - SCOPUS:85087055950

SN - 0071-3260

VL - 47

SP - 220

EP - 232

JO - Evolutionary Biology

JF - Evolutionary Biology

ER -

Ancestral State Estimation with Phylogenetic Ridge Regression

Abstract

Keywords

Access to Document

Other files and links

Cite this