Andrew J. Roger, Laura A.
Hug, Philosophical Transactions of the Royal Society of London
This is a review paper about challenges in eukaryotic phylogenetics published in Philosophical Transactions of the Royal Society. The authors divide the challenges into two categories - recovering tree structure, and dating divergences. Specific topics from the first category include the history of molecular phylogenetics of eukaryotes, efforts to root the eukaryotic tree, difficulties in recovering deep branching structure (namely phylogenetic artefacts and the lack of phylogenetic signal), potential advantages of phylogenomics, and endosymbiosis and lateral gene transfer. As regard to the dating of divergences, the authors briefly introduce molecular clocks, then present a reanalysis of two recently published datasets with particular attention to possible methodological weaknesses. This paper provides a thorough overview of the state of research in this field. There is also a significant bibliography.
