Roderic D. M. Page

GeneTree: comparing gene and species phylogenies using reconciled trees.

SUMMARY GeneTree is a program for comparing gene and species trees using reconciled trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees. AVAILABILITY The program is free and is available at ((http://taxonomy.zoology.gla.ac. uk/rod/genetree/genetree.html)).

How Should Species Phylogenies Be Inferred from Sequence Data

levels as follows: (1) Separate gene trees are inferred from each linkage partition, and (2) the species phylogeny is then inferred from the set of gene trees. A method (Maddison, 1997; Page and Charleston, 1997a, 1997b; Slowinski et al., 1997) termed gene tree parsimony by Slowinski et al. (1997) is the appropriate method for implementing the second step. Gene tree parsimony operates by finding the species tree or trees that minimizes the number of hypothesized gene tree/ species tree conflict-producing events required to fit each gene tree to the species tree(s). Central to gene tree parsimony is the concept of fitting trees to other trees (Page, 1994a). Gene tree parsimony implements Doyle’s (1992) insightful concept that nucleotides are characters of gene trees, whereas gene trees are characters of species trees. An important caveat relates to the serious question raised by Maddison (1997) of just what a species phylogeny is meant to represent. The search for a species phylogeny assumes that such a diagram has some meaning. This is a difficult issue that we leave to other workers. Below, we briefly discuss the sources of conflict between gene and species trees, identify problems with previous methods for inferring species trees from molecular sequence data, define gene tree parsimony, and then illustrate the application of gene tree parsimony by using the computer program GeneTree (Page, 1998), which is free and available at http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html; it requires Mac OS 7.5 or later running on a PowerMac, or an Intel-based PC running Windows 95/NT 4.0 or later. The issues explored in this article bear directly on the controversial question of whether or not There are two levels of potential error in the inference of species phylogenies from molecular sequence data: (1) A gene tree (herein, we use the term gene for any contiguous block of nucleotides, regardless of whether it codes for a protein or not) for a set of molecular sequences will be incorrectly inferred if there is sufficient random or systematic error (Swofford et al., 1996), and (2) even if a gene tree is correctly inferred, the phenomena of deep coalescence, gene duplication, and horizontal gene transfer can produce a gene tree different from the true species tree (Goodman et al., 1979; Avise et al., 1983; Pamilo and Nei, 1988; Doyle, 1992; Maddison, 1996, 1997). The second level of error would be quite worrisome if all nucleotides of genomes were historically linked (as is generally true with organellar genomes). In this situation, there would only be one gene tree, which might not be the same as the true species tree. But happily, because of intraand interchromosomal recombination, the nuclear genome is composed of many historically linked sets of nucleotides with different histories. We call these linkage partitions (the cgenes of Doyle, 1992, 1997). Sequences sampled from several species and forming a single linkage partition are related by a unique, binary gene tree. Contrary to claims that natural data partitions do not exist (e.g., Kluge and Wolf, 1993; Siddall, 1997), linkage partitions are natural partitions of molecular sequence data and can be considered as independent estimators of the overlying species phylogeny. This strongly suggests that the molecular phylogenetic analysis of species by using 814 SYSTEMATIC BIOLOGY VOL. 48

COMPONENT ANALYSIS: A VALIANT FAILURE?

Abstract— Rerent criticisms of component analysis are based on misunderstandings of the relationship between component analysis, parsimony and consensus methods. These criticisms are rebutted, and the appropriateness of applying the Wagner parsimony criterion to the study of biogcography and co‐speciation is questioned. An alternative parsimony method, previously applied to mapping gene cladograms onto organism cladograms, is developed.

Plant–Insect Interactions: Double-Dating Associated Insect and Plant Lineages Reveals Asynchronous Radiations

An increasing number of plant-insect studies using phylogenetic analysis suggest that cospeciation events are rare in plant-insect systems. Instead, nonrandom patterns of phylogenetic congruence are produced by phylogenetically conserved host switching (to related plants) or tracking of particular resources or traits (e.g., chemical). The dominance of host switching in many phytophagous insect groups may make the detection of genuine cospeciation events difficult. One important test of putative cospeciation events is to verify whether reciprocal speciation is temporally plausible. We explored techniques for double-dating of both plant and insect phylogenies. We use dated molecular phylogenies of a psyllid (Hemiptera)-Genisteae (Fabaceae) system, a predominantly monophagous insect-plant association widespread on the Atlantic Macaronesian islands. Phylogenetic reconciliation analysis suggests high levels of parallel cladogenesis between legumes and psyllids. However, dating using molecular clocks calibrated on known geological ages of the Macaronesian islands revealed that the legume and psyllid radiations were not contemporaneous but sequential. Whereas the main plant radiation occurred some 8 million years ago, the insect radiation occurred about 3 million years ago. We estimated that >60% of the psyllid speciation has resulted from host switching between related hosts. The only evidence for true cospeciation is in the much more recent and localized radiation of genistoid legumes in the Canary Islands, where the psyllid and legume radiations have been partially contemporaneous. The identification of specific cospeciation events over this time period, however, is hindered by the phylogenetic uncertainty in both legume and psyllid phylogenies due to the apparent rapidity of the species radiations.

Visualizing Phylogenetic Trees Using TreeView

TreeView provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE‐PUZZLE, and ClustalX. While some phylogenetic programs (such as the Macintosh version of PAUP*) have excellent tree printing facilities, many programs do not have the ability to generate publication quality trees. TreeView addresses this need. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*.

SEABIRD SUPERTREES: COMBINING PARTIAL ESTIMATES OF PROCELLARIIFORM PHYLOGENY

Abstract The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exist, we need to combine different hypotheses in a way that provides the best estimate of the phylogeny for that group. Here, we combine seven seabird phylogenies (based on behavioral, DNA–DNA hybridization, isozyme, life history, morphological, and sequence data) to generate a comprehensive supertree for the Procellariiformes using matrix representation with parsimony. This phylogeny contains 122 taxa and represents a conservative estimate of combined relationships presented in the original seven source trees. We compared the supertree with results of a combined sequence data supermatrix for 103 seabird taxa. Results of the two approaches are broadly concordant, but matrix representation with parsimony provides a more comprehensive and more conservative estimate of the phylogeny of the group because it is less influenced by the largest of the source studies (which uses a single, relatively quickly evolving gene). Genetic data sets that can be combined in a supermatrix approach are currently less likely to be available than phylogenies that can be combined using some form of supertree approach. Although there are limitations to both of those approaches, both would be simpler if all phylogenetic studies made both their data sets and trees they generate available through databases such as TREEBASE.

RadCon: phylogenetic tree comparison and consensus

SUMMARY RadCon is a Macintosh program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction. AVAILABILITY The program is free and available at http://taxonomy.zoology.gla.ac.uk/ approximately jthorley/radcon/radcon.html.

Modified Mincut Supertrees

A polynomial time supertree algorithm could play a key role in a divide-and-conquer strategy for assembling the tree of life. To date only a single such method capable of accommodate conflicting input trees has been proposed, the MinCutSupertree algorithm of Semple and Steel. This paper describes this algorithm and its implementation, then illustrates some weaknesses of the method. A modification to the algorithm that avoids some of these problems is proposed. The paper concludes by discussing some practical problems in supertree construction.

When Do Parasites Fail to Speciate in Response to Host Speciation

Cospeciation generally increases the similarity between host and parasite phylogenies. Incongruence between host and parasite phylogenies has previously been explained in terms of host switching, sorting, and duplication events. Here, we describe an additional process, failure of the parasite to speciate in response to host speciation, that may be important in some host-parasite systems. Failure to speciate is likely to occur when gene flow among parasite populations is much higher than that of their hosts. We reconstructed trees from mitochondrial and nuclear DNA sequences for pigeons and doves (Aves: Columbiformes) and their feather lice in the genus Columbicola (Insecta: Phthiraptera). Although comparisons of the trees from each group revealed a significant amount of cospeciation, there was also a significant degree of incongruence. Cophylogenetic analyses generally indicated that host switching may be an important process in the history of this host-parasite association. Using terminal sister taxon comparisons, we also identified three apparent cases where the host has speciated but the associated parasite has not. In two of these cases of failure to speciate, these comparisons involve allopatric sister taxa of hosts whose lice also occur on hosts sympatric with both of the allopatric sisters. These additional hosts for generalist lice may promote gene flow with lice on the allopatric sister species. Relative rate comparisons for the mitochondrial cytochrome oxidase I gene indicate that molecular substitution occurs about 11 times faster in lice than in their avian hosts.

Evolutionary informatics: unifying knowledge about the diversity of life

The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwins ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.