Review
Intraspecific gene genealogies: trees grafting into networks

https://doi.org/10.1016/S0169-5347(00)02026-7Get rights and content

Abstract

Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena.

Section snippets

Gene genealogies

Given a sample of genes, the relationships among them can be traced back in time to a common ancestral gene. The genealogical pathways interconnecting the current sample to the common ancestor constitute a gene tree or gene genealogy. A gene tree is the pedigree of a set of genes and exists independently of potential mutations. The only portion of a gene tree that can generally be estimated with genetic data is that portion marked by the (potential) mutational events that define the different

Solution: network methods

Phylogenetic methods that allow for persistent ancestral nodes, multifurcations and reticulations are needed to take these population phenomena into account. The advantage of networks over strictly bifurcating trees for estimating within-species relationships now becomes obvious. Networks can account effectively for processes acting at the species level and they might be able to incorporate predictions from population genetics theory (Box 2). In addition, networks provide a way of representing

Strengths and weaknesses of network methods

The comparison of different networking strategies is not straightforward. Comprehensive simulation studies are needed to evaluate the accuracy and robustness of different methods. In general, distance methods might imply a loss of information by summarizing the difference between haplotypes with one value. Optimality criterion methods (likelihood and least squares) offer a reliable statistical assessment, hypotheses testing and, in some cases, parameter estimation. Most of these methods are

Rooting intraspecific phylogenies

In many cases, the problem of biological interest requires a root, or at least some knowledge of the relative ages of haplotypes 22. Rooting networks is especially difficult because outgroups are often separated from the ingroup by many mutational steps and because individuals within a species are similar to each other. This leads to a lack of power to decide where the rooting should take place. However, predictions from coalescent theory can be applied in intraspecific phylogeny reconstruction

Conclusions and future directions

Traditional methods for estimating phylogenies were not designed and might not be adequate for within-species phylogeny. Network approaches can incorporate population processes in the construction or refinement of haplotype relationships. Moreover, networks allow a more detailed display of populational information than strictly bifurcating trees. Although we have focused on the application of networks to sequence data, most methods described here can be applied to proteins or

Acknowledgements

Comments by Chris Simon and François-Joseph Lapointe improved this review. We thank M. Coulthart, A. Whiting, M. Porter and J.W. Sites Jr for helpful suggestions. Our work was supported by NSF-DEB 0073154, the Alfred P. Sloan Foundation and NIH R01-HD34350.

Glossary

Additive tree
a tree on which the pairwise distances between haplotypes are equal to the sum of the lengths of the branches on the path between the members of each pair.
Coalescent event
The time inverse of a DNA replication event; that is, the event leading to the common ancestor of two sequences looking back in time.
Gene
a segment of DNA.
Gene tree
The representation of the evolutionary history of a group of genes.
Haplotype or allele
a unique combination of genetic markers present in a sample.

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