Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 7-Day Trial for You or Your Team.

Learn More →

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? The advent and maturation of algorithms for estimating species trees—phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes—represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Evolution Oxford University Press

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

Edwards, Scott V.
Evolution , Volume 63 (1): 19 – Jan 1, 2009
Download PDF
19 pages

Loading next page...
 
/lp/oxford-university-press/is-a-new-and-general-theory-of-molecular-systematics-emerging-11kagzE8gT

References (155)

Copyright
© 2009, Society for the Study of Evolution
ISSN
0014-3820
eISSN
1558-5646
DOI
10.1111/j.1558-5646.2008.00549.x
Publisher site
See Article on Publisher Site

Abstract

The advent and maturation of algorithms for estimating species trees—phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes—represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a “local optimum” for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term “phylogeny” for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.

Journal

Evolution – Oxford University Press

Published: Jan 1, 2009

Keywords: Fossil; genome; macroevolution; Neanderthal; phylogeography; polytomy

There are no references for this article.