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Assembling the Tree of Life: Orchidaceae ONCIDIINAE (ORCHIDACEAE) University of Florida Herbarium Home

This study expands our previous work on subtribes Maxillariinae, Oncidiinae, Zygopetalinae, and Stanhopeinae.


DATABASES

The *.nex files can be downloaded for you to examine on your computer. These files are available for viewing by downloading them (search for Oncidiinae) from the Dryad digital repository site (or just click on the file name below, but the files you download from here will not be aligned) and will work only on a late model computer with lots of RAM. If you are using a MAC, then you can examine the matrices using color fonts, but you need to first extract or expand the Colorfonts.sea.bin file and then put it in your SYSTEM folder in the FONTS folder on your MAC. You need the latest version of PAUP* (- available from Sinaeur Associates - ) to examine or run these files, but this is the only good way for you to see our data matrices. We assume you know something about cladistics and molecular systematics, as well as how to execute a NEXUS file and run PAUP* analyses.

The file Oncid7gene.nex is a combined large data matrix of 736 samples (representing approximately 600 species) and 8,020 characters. This will allow you to generate a cladogram based on nrITS, trnH-psbA, 5'ycf1, 3'ycf1, and matK.

The file Oncid_COMB.nex is a matrix of ITS, trnH-psbA, 3'ycf1, 5'ycf1, matK, rbcL, and psaB for 122 taxa and 10,023 characters. It is set up so you can analyze for any one region, or all of them combined. This smaller, restricted taxon analysis included several relatively conserved plastid genes (rbcL, psaB) with the goal of providing increased resolution and support for the spine of the tree.

The file Colorfonts.sea.bin contains the color font file you will need to really work with the data matrix and see what's going on.


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Page developed and maintained by Norris H. Williams.
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Page last updated: 5 May 2014