Included in this data package are scripts and files to replicate analyses in:
The evolution of a tropical biodiversity hotspot.
Harvey MG, Bravo GA, Claramunt S, Cuervo AM, Derryberry GE, Battilana J, Seeholzer GF, Shearer McKay J, O'Meara BC, Faircloth BC, Edwards SV, Pérez-Emán J, Moyle RG, Sheldon FH, Aleixo A, Smith BT, Chesser RT, Silveira LF, Cracraft J, Brumfield RT, Derryberry EP.
Included are:
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laboratory methods
protocol for toe pad whole DNA extraction -
sequence assembly
new code for sequence assembly/filtering (to supplement phyluce) -
alignments
alignments for the heavily-filtered (HGAPF) and minimally filtered (T400F) datasets -
gene trees
processed gene trees for HGAPF and T400F datasets (nodes with SH-aLRT support <80 collapsed) -
species trees
trees corresponding to all classifications examined, for both HGAPF and T400F datasets (includes raw trees and time-calibrated trees) -
other data
processed range data and climatic data for each species -
diversification analyses
example code used to conduct key analyses of diversification and causes of diversification rate variation