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Phylogenies in EcologyA Guide to Concepts and Methods$
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Marc W. Cadotte and T. Jonathan Davies

Print publication date: 2016

Print ISBN-13: 9780691157689

Published to Princeton Scholarship Online: January 2018

DOI: 10.23943/princeton/9780691157689.001.0001

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Building and Using Phylogenies

Building and Using Phylogenies

(p.10) Chapter 2 Building and Using Phylogenies
Phylogenies in Ecology

Marc W. Cadotte

T. Jonathan Davies

Princeton University Press

This chapter explains how to build a phylogeny for a certain set of species. A phylogenetic tree is a representation of species interrelatedness and conveys information about which taxa share recent common ancestors, which evolutionary groups (clades) species belong to, and the distances (time, genetic, or character differences) separating species. The chapter first considers two R packages called ape and picante for use in analysis of the R phylogenetic object (referred to as a phylo object type), along with a few other packages, before discussing the steps in reconstructing phylogenetic relationships. It also evaluates some tree-building approaches that are easily implemented in R, including distance-based methods and maximum likelihood methods. Finally, it describes ways of finding and adapting available phylogenetic trees, together with tree scaling and rate smoothing.

Keywords:   phylogeny, phylogenetic tree, species interrelatedness, R package, R phylogenetic object, phylogenetic relationships, distance-based methods, maximum likelihood, tree scaling, rate smoothing

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