Data and scripts for Harvey et al. 2017 (PNAS).
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.gitattributes
100_complete_trees.zip
DR_calculation_lumped.R
DR_calculation_split.R
DR_calculation_time.R
Hackett_lumped_eventsample.rda
Hackett_lumped_justgeneticdata.tre
Hackett_split_eventsample.rda
Hackett_time_eventsample.rda
Hackett_time_justgeneticdata.tre
Main_text_analyses.R
README.md
Supplementary_analyses.R
hackett_split_justgeneticdata.tre
lumped_data_final.txt
mean_rates.py
split_data_final.txt
taxonomy_key.txt

README.md

differentiation_speciation

Included in this data package are scripts and files to replicate analyses in:

Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT. 2017. Positive association between population genetic differentiation and speciation rates in New World birds. Proceedings of the National Academy of Sciences doi:10.1073/pnas.1617397114.

Included are:

  • 100_complete_trees.zip

A file including 100 trees from the pseudo-posterior of Jetz et al. (2012).

  • Hackett_lumped_justgeneticdata.tre
  • Hackett_split_justgeneticdata.tre
  • Hackett_time_justgeneticdata.tre

Maximum clade credibility trees pruned to each taxonomy examined in the paper, containing just species represented by genetic data in Jetz et al. (2012).

  • DR_calculation_lumped
  • DR_calculation_split
  • DR_calculation_time

R scripts calculating the diversification rate (DR) statistic (Jetz et al. 2012) for trees corresponding to the three taxonomies examined in the paper.

  • mean_rates.py

A Python script to calculate the mean DR rate for each species from the DR values from 100 pseudo-posterior samples.

  • Hackett_lumped_eventsample.rda
  • Hackett_split_eventsample.rda
  • Hackett_time_eventsample.rda

Rdata files containing event samples from BAMM analyses of the Jetz et al. (2012) trees pruned to reflect each taxonomy.

  • lumped_data_final.txt
  • split_data_final.txt

Data on population differentiation, species age, sampling, and ecological, environmental, morphological, and biogeographic traits in each species from Smith et al. (2017).

  • taxonomy_key.txt

A key relating species names from the taxonomies examined in our study to those of the taxonomy in Jetz et al. (2012).

  • Main_text_analyses.R
  • Supplementary_analyses.R

Scripts to conduct the analyses used in the main text and supplementary text, respectively.

References:

Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491:444–448.

Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT (2017) A latitudinal phylogeographic diversity gradient in birds. PLoS Biol 15:e2001073.