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.

A Primer to Molecular Phylogenetic Analysis in Plants

“…The phylogeny reconstructed using these single copy, nuclear genes in combination, was largely concordant with studies performed using single (Hilu et al, 2003) or multiple (Jansen et al, 2007) plastid genes and work based on the combined use of plastid and nuclear ribosomal DNA targets (Soltis et al, 2000). Using publicly available EST sequences, Burleigh et al (2011) constructed a total of 18,896 gene trees with a variable number of taxa (a minimum of three taxa) represented by each tree. By employing a gene tree parsimony approach that utilized the topology data of the 18,896 trees, a consensus phylogeny was reconstructed that represented all of the 136 species sampled in the gene trees.…”

Phylotranscriptomic analysis of the origin and early diversification of land plants

“…Increasingly, analyses of nuclear genes assembled from publicly available genome or transcriptome databases are being used to assess previously recalcitrant relationships within the green tree of life (27,29,35,(51)(52)(53).…”

Species tree inference in the age of genomics

“…Many phylogenomic studies address hypotheses of deep evolution along the tree of life, [25][26] but questions about species and sub-species relationships are just beginning to be pursued under a phylogenomic framework. 3,19,[27][28][29] The argument of whether increased taxon sampling or increased character sampling will enhance phylogenetic robustness has been a lively debate in the systematic literature for years.…”

“…25,26,35 The importance and effects of missing data on phylogenetic studies has been a point of lively debate for years, but exactly how such missing data affects species tree inference methods discussed below has yet to be studied. 36 Modern phylogenomic studies commonly have missing data, and for this reason an in-depth analysis of how missing data affects species tree inference algorithms should be pursued with vigor.…”