TY  - JOUR
A1  - Burleigh, J. Gordon
A1  - Bansal, Mukul S.
A1  - Eulenstein, Oliver
A1  - Hartmann, Stefanie
A1  - Wehe, Andre
A1  - Vision, Todd J.
T1  - Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees
JF  - Systematic biology
N2  - 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.
KW  - Gene tree-species tree reconciliation
KW  - gene tree parsimony
KW  - plant phylogeny
KW  - phylogenomics
Y1  - 2011
U6  - https://doi.org/10.1093/sysbio/syq072
SN  - 1063-5157
VL  - 60
IS  - 2
SP  - 117
EP  - 125
PB  - Oxford Univ. Press
CY  - Oxford
ER  -