8 files

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

posted on 17.10.2019, 13:43 by Guido GrimmGuido 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).

The taxon set was reduced to match the set used in Sareela et al. (2007), respectively Doyle & Endress (2010).

The final matrix combines data from placeholder-genera and well-covered gene regions (nuclear-encoded 18S rDNA, 25S rDNA; mitochondrial atp1, matR, nad5; plastid atpB, matK, ndhF, psbB...psbH, rbcL, rpoC2) and corresponding morphological data as extra partition.

— 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.
— 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.
— 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)
— Additional figures (v. 2) shown in blogposts using this matrix or subsets of it (see provided links)

Cited literature (make sure to include as addititional reference when re-using the data provided here)
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.
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)
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


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