READING LIST
A workshop on the relationship between trait evolution and species diversification, with a
focus on the R package ‘diversitree’
29–31 October 2014
Instituto de Biología, UNAM
General
diversitree R manual: http://www.zoology.ubc.ca/prog/diversitree/doc/diversitreemanual.pdf
diversitree tutorial: http://www.zoology.ubc.ca/prog/diversitree/doc/diversitreetutorial.pdf
Maddison WP. 2006. Confounding asymmetries in evolutionary diversification and character
change. Evolution 60:1743–1746. (Introduces the general difficulty in relating
diversification to character evolution.)
Maddison WP, Midford PE, Otto SP. 2007. Estimating a binary character's effect on
speciation and extinction. Syst Biol 56:701–710. (Introduces the main method to
simultaneously examining diversification and character evolution.)
Jablonski D. 2008. Species selection: theory and data. Ann Rev Ecol Evol Syst 39:501–524. (A
key conceptual paper that reviews the biological theory behind differences in
diversification rates among clades and what factors might cause such variation.)
BiSSE
Maddison WP, Midford PE, Otto SP. 2007. Estimating a binary character's effect on
speciation and extinction. Syst Biol 56:701–710.
FitzJohn RG, Maddison WP, Otto SP. 2009. Estimating trait-dependent speciation and
extinction rates from incompletely resolved phylogenies. Syst Biol 58:595–611.
Other variations on the basic state-dependent diversification
FitzJohn RG. 2012. Diversitree: comparative phylogenetic analyses of diversification in R.
Method Ecol Evol 3:1084–1092. (MuSSE)
FitzJohn RG. 2010. Quantitative traits and diversification. Syst Biol 59:619–633. (QuaSSE)
Magnuson-Ford K, Otto SP. 2012. Linking the investigations of character evolution and
species diversification. Am Nat 180:225–245. (BiSSE-ness)
Goldberg EE, Igic B. 2012. Tempo and mode in plant breeding system evolution. Evolution
66:3701–3709. (ClaSSE)
Goldberg EE, Lancaster LT, Ree RH. 2011. Phylogenetic inference of reciprocal effects
between geographic range evolution and diversification. Syst Biol 60:451–465.
(GeoSSE)
Correlation between rates of phenotypic evolution and diversification rates
Adams DC, Berns CM, Kozak KH, Wiens JJ. 2009. Are rates of species diversification
correlated with rates of morphological evolution? Proc R Soc B 276:2729–2738.
Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas BL, et al. 2013. Rates of speciation
and morphological evolution are correlated across the largest vertebrate radiation.
Nature Comm 4:1958.
Rabosky DL. 2014. Automatic detection of key innovations, rate shifts, and diversitydependence on phylogenetic trees. PLoS One 9:e89543.
Rabosky DL, Grundler M, Anderson C, Title P, Shi JJ, et al. 2014. BAMMtools: an R package
for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol Evol
5:701–707.
The future
Davis M, Midford PE, Maddison WP. 2013. Exploring power and parameter estimation of the
BiSSE method for analyzing species diversification. BMC Evol Biol 13:38. (statistical
properties of state-dependent methods)
Maddison WP, FitzJohn RG. 2014. The unsolved challenge to phylogenetic correlation tests
for categorical characters. Syst Biol Early View. (problems with correlation)
Some nice empirical papers that use diversitree
(1) See full list at http://www.zoology.ubc.ca/prog/diversitree/studies.html
(2) Pyron RA, Wiens JJ. 2013. Large-scale phylogenetic analyses reveal the causes of high
tropical amphibian diversity. Proc R Soc B 280:20131622. (QuaSSE)
(3) Maia R, Rubenstein DR, Shawkey MD. 2013. Key ornamental innovations facilitate
diversification in an avian radiation. Proc Nat Acad Sci USA 110:10687–10692.
(MuSSE with rates changing over time)
(4) Rolland J, Condamine FL, Jiguet F, Morlon H. 2014. Faster speciation and reduced
extinction in the tropics contribute to the mammalian latitudinal diversity gradient.
PLoS Biology 12:e1001775. (BiSSE with rates changing over time)
(5) Rolland J, Jiguet F, Jonsson KA, Condamine FL, Morlon H. 2014. Settling down of seasonal
migrants promotes bird diversification. Proc R Soc B 281:20140473. (ClaSSE)