Data from: Diversification rates have declined in the Malagasy herpetofauna

 

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Title MCC and Posterior Trees - output from BEAST
Downloaded 22 times
Description This compressed file contains the posterior distribution of trees as well as the MCC tree (with mean node heights) for each clade.
Download rawtrees.zip (43.71 Mb)
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Title Trees pruned of extraneous taxa for diversification analyses
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Description These are the MCC and posterior trees of each clade that have been pruned of inappropriate taxa for the diversification analyses. Pruned tips are not from Madagascar, are intraspecific samples, and/or are not valid species.
Download droptip_trees.zip (11.64 Mb)
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Title Model fitting results and summaries
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Description This file contains the results of the HMM model fits for each clade. Each clade was analyzed at two levels of taxonomic sampling completeness - 100% and 50%. Thus, the files that include "_1_Complete" or "_0.5_Complete" refer to 100% or 50% complete respectively. The files with "AnalyzedTrees" in their names are the randomly selected trees from the posterior distributions that were analyzed. Note that in producing these lists, the MCC tree was placed on top of all posterior trees. Thus, the first row in all refers to the MCC tree (1), and the remaining 49 rows are the number of the randomly selected posterior tree plus 1.
Download modelstats.zip (263.8 Kb)
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Title R code and functions to run this analysis
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Description This contains relevant functions and the code I used to collect these data. See the README within for more details.
Download Rcode.zip (5.49 Kb)
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When using this data, please cite the original publication:

Scantlebury DP (2013) Diversification rates have declined in the Malagasy herpetofauna. Proceedings of the Royal Society B 280(1766): 20131109. http://dx.doi.org/10.1098/rspb.2013.1109

Additionally, please cite the Dryad data package:

Scantlebury DP (2013) Data from: Diversification rates have declined in the Malagasy herpetofauna. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r1hk5
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