A new paper (not free):
Iker Irisarri, Denis Baurain, Henner Brinkmann, Frédéric Delsuc, Jean-Yves Sire, Alexander Kupfer, Jörn Petersen, Michael Jarek, Axel Meyer, Miguel Vences & Hervé Philippe (2017)
Phylotranscriptomic consolidation of the jawed vertebrate timetree.
Nature Ecology & Evolution (2017)
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
"The new tree of jawed vertebrates resolves several key relationships that have remained controversial despite decades of research, including the identification of lungfishes as the closest living relatives of land vertebrates, the close association of turtles with crocodilians and birds (the Archosaurs), or the relationships among amphibian groups (salamanders, frogs, caecilians) (supporting the Batrachia hypothesis). The phylogenetic tree was time-calibrated using fossils as anchors, which allowed testing of temporal relationship of diversification with major geological events. For example, two major groups of birds and mammals had been hypothesised to have diversified as a consequence of the extinction of dinosaurs (67 million years ago). The new study invalidates this hypothesis by showing that both groups are in fact much older."