A basic total evidence matrix for basal angiosperms — combining Soltis et al. (2011) with Doyle & Endress (2010)

2018-03-18T12:35:21Z (GMT) by Guido Grimm
This fileset includes a curated, reduced version of the matrix used by Soltis et al. (2011) that I generated in 2012 for a colleague at the Swedish Museum of Natural History, who was looking for plant matrices that can be used for total-evidence dating. The experiment failed, and the project was abondoned (see Footnote 7 of the linked post).<br><br>The taxon set was reduced to match the set used in Sareela et al. (2007), respectively Doyle & Endress (2010).<br><br>The final matrix combines data from placeholder-genera and well-covered gene regions (nuclear-encoded 18S rDNA, 25S rDNA; mitochondrial <i>atp1</i>, <i>matR, nad5; </i>plastid <i>atpB, matK, ndhF, psbB...psbH, rbcL, rpoC2) </i>and corresponding morphological data as extra partition<i>.<br> <br></i><b>Content<br></b>— An 7z-archive (http://www.7-zip.org/) including the matrices, a fully annotated version generated with and optimised for Mesquite (http://mesquiteproject.wikispaces.com/) and a simple-NEXUS version for MrBayes.<br>— Several draft graphs as PDF: a ML tree inferred from the matrix (bootstrap support annotated) with RAxML (00all.ML...); a Bayesian total evidence generated with MrBayes by my colleague (01b.withFossils....); a neighbour-net based on morphological distance inferred from the morphological partition in the combined matrix.<br>— A tabulation of the checked data, with some curating information, in two formats: CSV (for general compatibility), and xlsx (for further functionality, includes summarising Pivot-table)<br><br>Cited literature (make sure to include as <b>addititional</b> reference when re-using the data provided here)<br>Sareela JM, Rai HS, Doyle JA, ... , Briggs BG, Graham SW. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446:312–315. — no data from this study has been used for generating the matrix.<br>Soltis DE, Smith SA, Cellinese N, ..., Donoghue MJ, Soltis PS. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98:704–730 — this is the main source, but not exclusive source, for the genetic data (some data has been updated, and blanks filled)<br>Doyle JA, Endress PK. 2010. Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots. Journal of Systematics and Evolution 48:1–35. — this is the source of the morphological data<br><b></b><br><br><br><br><br>