Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics.
As systematists grapple with assembling the Tree of Life, recent studies have encouraged a genomic-scale approach, obtaining DNA sequence data for entire nuclear, plastid or mitochondrial genomes for a few exemplar taxa. Some have proclaimed that this comparative genomic strategy heralds the end of incongruence in phylogeny reconstruction. Although we applaud the use of many genes to resolve phylogenetic patterns, there is a significant caveat. In spite of, or even because of, the abundant data per taxon, whole-genome sequencing for a few exemplars can provide completely resolved and strongly supported, but incorrect, evolutionary reconstructions. We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor.
Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA. dsoltis@botany.ufl.edu
Douglas E
DE
Soltis
Victor A
VA
Albert
Vincent
V
Savolainen
Khidir
K
Hilu
Yin-Long
YL
Qiu
Mark W
MW
Chase
James S
JS
Farris
Sasa
S
Stefanović
Danny W
DW
Rice
Jeffrey D
JD
Palmer
Pamela S
PS
Soltis
D003062:Codon / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D015203:Reproducibility of Results
D003062:Codon; D004272:DNA, Mitochondrial; D018744:DNA, Plant