An Introduction to Supertree Construction (and Partitioned Phylogenetic Analyses) with a View Toward the Distinction Between Gene Trees and Species Trees

Abstract

The dominant approach to the analysis of phylogenomic data is the concatenation of the individual gene data sets into a giant supermatrix that is analyzed en masse. Nevertheless, there remain compelling arguments for a partitioned approach in which individual partitions (usually genes) are instead analyzed separately and the resulting trees are combined to yield the final phylogeny. For instance, it has been argued that this supertree framework, which remains controversial, can better account for natural evolutionary processes like horizontal gene transfer and incomplete lineage sorting that can cause the gene trees, although accurate for the evolutionary history of the genes, to differ from the species tree. In this chapter, I review the different methods of supertree construction (broadly defined), including newer model-based methods based on a multispecies coalescent model. In so doing, I elaborate on some of their strengths and weaknesses relative to one another as well as provide a rough guide to performing a supertree analysis before addressing criticisms of the supertree approach in general. In the end, however, rather than dogmatically advocating supertree construction and partitioned analyses in general, I instead argue that a combined, “global congruence” approach in which data sets are analyzed under both a supermatrix (unpartitioned) and supertree (partitioned) framework represents the best strategy in our attempts to uncover the Tree of Life.

Glossary

Hidden support (AKA signal enhancement)

The phenomenon whereby consistent secondary signals among a set of data partitions can overrule their conflicting primary signals to yield a novel solution not to be found among any of the individual data sets. As a simplified example, take the case of two separate gene data sets, each with an aligned length of 1000 nucleotides. In the first data set, 60 % of the positions support a sister-group relationship between A and B (primary signal), whereas 40 % support the clustering of B and C (secondary signal). In the second data set, 60 % support A and C, whereas 40 % support B and C.

Separate analyses of each data set will yield conflicting results (AB vs. AC); however, when the data sets are combined, each of these solutions is now only supported by 30 % of the data. By contrast, the secondary signals supporting BC are now present among 40 % of the combined data and now form the primary signal. In other words, each separate data set possessed hidden support for BC that could combine and determine the overall solution upon the concatenation of the data sets. Because supertree analyses work with trees as their primary data source, these secondary signals in the raw character data are normally invisible and cannot be accounted for.

Long-branch attraction

An artifact in the phylogenetic analysis of DNA sequence data that was first exposed by Felsenstein (1978) and is a result of saturation in such data. Felsenstein observed that taxa at the ends of very long branches that themselves were separated by a short intervening branch often clustered to form sister taxa in a maximum parsimony analysis. Optimization criteria that used an explicit model of evolution like maximum likelihood were more immune to this problem.

This artifactual attraction of the long branches arises because the taxa are characterized by high rates of molecular evolution (as indicated by the long branches) and concomitant large number of shared convergent changes that, through their high number, are falsely interpreted as evidence for shared common ancestry. It is now known that long-branch attraction is a general problem (i.e., it can affect nonmolecular data, although is far less likely to do so) and can occur even if the branches occur on distant parts of the tree (see Bergsten 2005).

Matrix representation

A long-standing mathematical principle (Ponstein 1966) showing that there is a one-to-one correspondence between a tree (a “directed acyclic graph”) and its encoding as a binary matrix. Whereas additive binary coding (Farris et al. 1970) of the tree will derive the matrix, the tree can be recreated from the matrix via analysis of the latter using virtually any optimization criterion (see Fig. 3.2).

NP-complete

A class of nondeterministic polynomial (NP) time methods for which no efficient solution is known and for which the running time increases tremendously with the size of the problem. As such, heuristic rather than exact algorithms must be used beyond a certain problem size, meaning that there is no guarantee that the optimal solution has been found. In phylogenetics, classic examples of NP-complete algorithms include maximum parsimony and maximum likelihood.

Polynomial time

Polynomial time algorithms are said to be “fast” in the sense that they have an efficient solution that scales “reasonably” with the size of the problem. A cogent example here is neighbor joining (NJ), the running time of which scales no worse than the cube of the number of taxa (i.e., O(n ³)). This is in stark contrast to the NP-complete maximum parsimony and maximum-likelihood methods, where the running times scale super-exponentially with respect to the problem size.

Saturation

A phenomenon attributed primarily to DNA sequence data and which arises because of the limited character state space for such data (i.e., the four nucleotides A, C, G, and T). As such, the potential for homoplasy in the form of either convergence or back mutation is high (e.g., two completely random DNA sequences are expected to be 25 % similar). Saturation, however, can also occur, but is less likely, for both amino-acid and morphological character data.

In practice, saturation is visualized by the degree of divergence between two sequences leveling off or plateauing with time since their divergence because faster evolving sites have experienced multiple substitutions (“multiple hits”) with the increased potential for homoplastic similarity. Another method is to examine for deviations from an expected transition: transversion ratio of 1:2 in neutral/silent sites, given the faster rate of evolution for transitions compared to transversions and, again, greater opportunity for multiple hits.