Skip to main content Accessibility help
×
Hostname: page-component-7c8c6479df-7qhmt Total loading time: 0 Render date: 2024-03-29T00:54:28.003Z Has data issue: false hasContentIssue false

7 - Supertrees

from PART I - BASIC TECHNIQUES

Published online by Cambridge University Press:  26 October 2017

Tandy Warnow
Affiliation:
University of Illinois, Urbana-Champaign
Get access

Summary

Introduction

The basic objective of most supertree studies is the assembly of a large species tree from a set of species trees that have been estimated on potentially smaller sets of taxa. Indeed, it is generally believed that construction of the Tree of Life, which will encompass millions of species, will require supertree methods, because no software will be able to deal with the computational challenges involved in such a difficult task. More recently, however, new uses of supertree methods have been discovered, especially in the context of divide-andconquer strategies. This chapter examines both applications of supertree methods.

Traditionally, supertree methods were used to combine trees computed by different researchers that had already been estimated for different taxon sets. In this case, the person constructing the supertree has no control over the inputs, neither how the different subset trees were constructed nor how the taxon sets of the different subset trees overlap. Furthermore, the person constructing the supertree may not have easy access to the data (e.g., sequence alignments) on which the subset trees were constructed.

A modern and more interesting use of supertree methods is in the context of a divideand- conquer strategy to construct a very large tree, or to enable a statistically powerful but computationally intensive method to be applied to a larger dataset. In such a strategy, a large set of taxa is divided into overlapping subsets, trees are estimated (using the desired method) on the subsets, and the estimated subset trees are combined into a tree on the full set of taxa using a supertree method.

Divide-and-conquer techniques for constructing large trees have many desirable features: (1) the subsets can be made small enough that expensive methods can be used to construct trees on them; (2) different methods can be used on each subset, thus making it possible to better address heterogeneity within the full dataset; and (3) the subsets can be created so as to have desirable overlap patterns. The first two of these features tend to increase the accuracy of the estimated subset trees, while the third feature can make it easier to construct an accurate supertree from the subset trees (Wilkinson and Cotton, 2006). We will return to the topic of divide-and-conquer strategies and how to use them to construct large trees under a variety of scenarios in Chapter 11.

Type
Chapter
Information
Computational Phylogenetics
An Introduction to Designing Methods for Phylogeny Estimation
, pp. 121 - 142
Publisher: Cambridge University Press
Print publication year: 2017

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

  • Supertrees
  • Tandy Warnow, University of Illinois, Urbana-Champaign
  • Book: Computational Phylogenetics
  • Online publication: 26 October 2017
  • Chapter DOI: https://doi.org/10.1017/9781316882313.009
Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

  • Supertrees
  • Tandy Warnow, University of Illinois, Urbana-Champaign
  • Book: Computational Phylogenetics
  • Online publication: 26 October 2017
  • Chapter DOI: https://doi.org/10.1017/9781316882313.009
Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

  • Supertrees
  • Tandy Warnow, University of Illinois, Urbana-Champaign
  • Book: Computational Phylogenetics
  • Online publication: 26 October 2017
  • Chapter DOI: https://doi.org/10.1017/9781316882313.009
Available formats
×