| bioproject id |
PRJNA357627
to NCBI
|
| key word |
baseline;PLACENTAL MAMMAL PHYLOGENY;MOLECULAR CLOCK;MITOCHONDRIAL GENOMES;SQUAMATE TREE;DIVERSIFICATION;ORIGIN;ROOT;TURTLES;DIVERSITY;EVOLUTION |
| experiment type |
baseline |
| publication |
Irisarri, I. , et al. "Phylotranscriptomic consolidation of the jawed vertebrate timetree." Nature Ecology & Evolution (2017). |
| description |
Transcriptomes of developing jaws of vertebrates, sequenced for develelopmental study and phylotranscriptomic assessment of the vertebrate tree of life |
| abstract |
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on 'standards' for data selection, curation and tree inference. We use jawedvertebrates (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 oflarge, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates. |
Gene
RNA