New substitution models for rooting phylogenetic trees.
The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made.
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK tom.williams2@ncl.ac.uk.
Tom A
TA
Williams
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
Sarah E
SE
Heaps
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
Svetlana
S
Cherlin
School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
Tom M W
TM
Nye
School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
Richard J
RJ
Boys
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
T Martin
TM
Embley
D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D003198:Computer Simulation; D014644:Genetic Variation; D008957:Models, Genetic; D010802:Phylogeny
phylogenetics; substitution models; tree of life