Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Abstract

Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.

FIGURE 1.

Consensus of the 136 taxon NJ/PP GTP supertree bootstrap trees. Numbers represent supertree bootstrap percentages. Asterisk represents branches with at least 50% supertree bootstrap support that are not present in the species tree inferred using ML gene trees. 1

FIGURE 2.

Average quartet similarity for each taxon among bootstrap trees. Each point in the graph represents a single taxon. The x-axis shows the number of gene families trees that have data from the taxon. The y-axis shows the average percentage frequency of quartets (four taxon statements) containing the taxon that are identical between two bootstrap trees. The shaded area in the graph contains all taxa that are present in less than 1300 gene trees.2

FIGURE 3.

Reduced consensus of the GTP supertree bootstrap trees. To build the reduced consensus, 54 taxa that were present in less than 1300 of the gene trees were pruned from the bootstrap tree, and then a consensus was made from the pruned trees. Numbers above the branches are the supertree bootstrap percentages. Asterisk represents branches that are not present in the species tree inferred using ML gene trees.3