Estimating Species Trees

The first book devoted exclusively to methodology for estimating species trees

Estimating Species Trees provides a comprehensive treatment of the methods now available to estimate species-level evolutionary histories using data from multiple genes. In addition to discussing the development of models that explicitly incorporate the links between gene and species trees, each method is described in detail, with attention to its strengths, weaknesses, implementation, and availability to the community.

Empirical examples are interspersed with theoretical results, so the reader can examine concrete applications of the described methodology. Recent improvements in DNA sequencing technology have created new opportunities for estimating evolutionary relationships based on multilocus data, driving new development in molecular systematics?the direct estimation of species trees, as opposed to relying on gene trees for phylogenetic inference.

Historically, interest has centered on the problem of estimating the evolutionary relationships among present-day organisms, and early methodologies developed to address this question made the assumption that the evolutionary relationships within a single gene mirrored those that actually occurred in the formation of species. However, it is now widely acknowledged that such direct correspondence between the evolutionary history of genes and of species divergence does not necessarily exist. In cases of rapid speciation, for example, it may actually be more common for gene histories to disagree with one another than to match.

Estimating Species Trees brings together knowledge from multiple fields, with the goal of bridging the gap between the population-genetic principles upon which these new phylogenetic methods are based and the backgrounds of those interested in applying these procedures, to enable researchers to make informed decisions as they delve into this exciting new area of phylogenetic study.

Excellent as a supplemental or graduate seminar text, its diversity of information will speak to people with varying levels of familiarity on the topic of species-tree estimation, and it is essential reading for professionals in evolutionary biology and genetics who are interested in exploring these new phylogenetic methodologies. The text provides access to a molecular phylogenetic perspective that, unlike the vast majority of phylogenetic methods that focus on the estimation of gene trees, places the focus on the primary target of interest?the species tree?and provides a look to the future of phylogenetic inference in modern molecular systematics.