NOTE: PLEASE ALSO SEE Kotrc B, Knoll AH (2015) A morphospace of planktonic marine diatoms. II. Sampling standardization and spatial disparity partitioning. Paleobiology 41(1): 68-88. http://dx.doi.org/10.1017/pab.2014.5. Both molecular clocks and the first appearances of major groups in the fossil record suggest that most of the range of diatom morphologies observed today had evolved by the end of the Cretaceous Period. Despite this, a canonical reading of the Cenozoic fossil record suggests a dramatic rise in taxonomic diversity that can be interpreted as an explosion of morphological variety. We investigated this apparent discrepancy by using a discrete-character-based, empirical diatom morphospace, resolved by molecular phylogeny and by fossil occurrences through time. The morphospace shows little correspondence to phylogeny and little Cenozoic change in disparity as measured by mean pairwise distance. There is, however, an increase in the total volume of morphospace occupied. Although the increase in occupied volume through time ostensibly supports a conclusion of increasing morphological variety, sampling biases and other data suggest an underlying stationary pattern more consistent with molecular clock data.
KotrcKnoll2015Data
This .zip archive contains the data and software necessary to carry out the analyses and produce the figures in two publications by Kotrc, B. and Knoll, A.H. published side by side in the Journal Paleobiology in 2015. .R files are functions and scripts in the R programming language (www.r-project.org). The file Morphospace.R contains an R script to clean the data, carry out the analyses, and produce the figures. It makes calls to functions in the files MorphospaceFunctions.R, MorphoPlotFunctions.R, and DiversityFunctions.R. The file Matrix.txt is a comma-delimited value (.csv) file which contains the morphological data matrix. The first row contains the names of the morphological characters (X1, X2, etc). Subsequent rows contain the name of the genus and then the state of each character. The file MatrixDescriptionOfCharacters.txt contains a description of the morphological characters in that matrix, and a description of what each character state (0, 1, 2, etc) represents. The file SourcesForMorphologicalData.txt lists the literature sources consulted to compile this data. A table relating which specific references were consulted for each genus is provided in B. Kotrc’s PhD thesis, freely available at http://dash.harvard.edu/handle/1/11051218. The file NeptuneGenNamesCorrCret.txt is a download of the diatom entries Neptune database of microfossil occurrences with genus names corrected and Cretaceous occurrences from three publications added. The file NeptuneProcessed.txt is the same, but further processed to remove errors. The files ulf.aln and ulf.nwk contain RNA sequence data and a phylogenetic tree based on that data, and were supplied by Ulf Sorhannus; they are used to compare phylogenetic distance to distance in morphospace. Finally, divdisp-ow.pdf and divdisp-uw.pdf are supplemental plots (also generated by the code in this archive) pertaining to the second of the companion papers to which this archive belongs.
KotrcKnollData.zip
