User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/07/08

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Evolutionary Regime Shift examples

Time to get more data and examples to start testing methods, particularly for cases in where regime shifts are hypothesized by painting a tree. Starting a Mendeley public collection for the literature in Web of Science that actually applies either the OUCH or Brownie framework to identify shifts in rates of continuous trait evolution.

<html> <div style="padding:0;margin:0;text-align:left"><iframe src="http://www.mendeley.com/research-papers/collections/embed/3304441/A70805/" style="height:300px;width:450px;border:none;"></iframe><hr style="border:1px solid #E0E0E0;margin:0px 0px 5px 0px;padding:0;width:450px;"/><span style="color:#666666;font-size:11px;"><a style="color:#A70805" href="http://www.mendeley.com">Research</a> collected using Mendeley</span></div> </html>


now I'll have to see how hard it is to obtain both the trees and trait data...


  • Web of Science has 77 papers citing Butler and King 2004, of 21 promising-looking ones 13 actually applied (or came close enough) to applying a regime-based method (some of these actually used Brownie but make mention of the ouch approach. Smith Sa, Beaulieu JM. 2009 actually comments about no method existing to vary alpha across trees. 47 cite O'Meara et al. 2006, with considerable overlap.
  • Edwards & Smith evaluate a fantastically large data set painted with C3 and C4 plants looking at temperature analysis.
  • Andrew Hipp's datasets on chromosome evolution in sedges might be a good place to start. Data is included in his maticce R package (built on ouch).