Estimating a binary character’s effect on speciation and extinction. 2002. Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models. Rabosky, DL, M Grundler, C Anderson, JJ Shi, JW Brown, H Huang, JG Larson, et al. Moore, BR, S Höhna, MR May, B Rannala, and JP Huelsenbeck. Given that a more correct solution for computing extinction probabilities is implemented in BAMM, we used that option. To demonstrate the impact of this bug, we compare the results of analyses with (orange) and without (blue) the option on our constant-rate birth-death simulated trees below (Figure 4). In fact, most of the problems that we identify are (predictably) much worse when using the the default ‘combineExtinctionAtNodes = if_different’ option/bug in BAMM. BAMM (Rabosky, 2014) is a popular Bayesian method intended to estimate: (1) the number and location of diversification-rate shifts across branches of a phylogeny, and; (2) the diversification-rate parameters for every branch of the study tree. Steeman, ME, MB Hebsgaard, RE Fordyce, SY Ho, DL Rabosky, R Nielsen, C Rahbek, H Glenner, MV Sørensen, and E Willerslev. 2000. The default option (as of v.2.5) for computing extinction probabilities is the ‘combineExtinctionAtNodes = if_different’ option, which computes extinction probabilities at nodes by taking the product of extinction probabilities of descendant branches if they are different (as described above in the blog post). How important is it to consider lineage diversification heterogeneity in macroevolutionary studies? We present results demonstrating that posterior estimates of the number of diversification-rate shifts are sensitive to the assumed prior on the number of diversification-rate shifts. Contrasting trajectories of morphological diversification on continents and islands in the Afrotropical white‐eye radiation. Huelsenbeck JP, B Larget, and DL Swofford. (2016). Accordingly, Rabosky concluded that posterior estimates of the number of diversification-rate shifts inferred using BAMM are insensitive to the prior assumptions about the expected number of diversification-rate shifts. Systematic Biology, 65:726–736. Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Under the birth-death process model (as also used in BAMM), the fate of a given lineage is independent of other contemporaneous lineages; Maddison et al. In fact, this is exactly what we observe when we summarize the results of our simulation using the same protocol as that used by Rabosky (see the lower row of panels in Figure 2, above). Multiple macroevolutionary routes to becoming a biodiversity hotspot. 2007. Specifically, under the CPP, the observed data may be equally likely to be the outcome of relatively infrequent shifts of large magnitude, or relatively frequent shifts of small magnitude. There is a second curious aspect of the results presented by Rabosky (2014). Sexual Dimorphism and Species Diversity: from Clades to Sites. Maddison W, P Midford, and S Otto. Briefly, speciation rate estimates were inferred using the DR statistic (Jetz, Thomas, Joy, Hartmann, & Mooers, 2012; hereafter, λ DR) and BAMM (λ BAMM). Macroevolutionary convergence connects morphological form to ecological function in birds. estimated speciation rates for all fishes, and these data are available on Dryad (see Data Availability Statement). Is dispersal mode a driver of diversification and geographical distribution in the tropical plant family Melastomataceae?. We may elaborate on these issues in future posts. This is simply because the prior distribution for the number of diversification processes has a mode of one for all values of the prior (see Moore et al., 2016 SI1.3 Joint prior distribution). It is straightforward to assess whether BAMM exhibits prior sensitivity: we simply need to compare the posterior distribution for the estimated number of diversification-rate shifts inferred under a variety of assumed prior distributions for the expected number of diversification-rate shifts. Everything used in this manuscript is available through the r package BAMMtools, available on CRAN: http://cran.r-project.org/web/packages/BAMMtools/index.html. BAMM (www.bamm-project.org) is a program written in C++ that uses reversible‐jump Markov chain Monte Carlo (rjMCMC) to quantify heterogeneous mixtures of dynamic processes on phylogenetic trees. 2009. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model Specification Language. Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades. The impact of Miocene orogeny for the diversification of Caucasian Epeorus (Caucasiron) mayflies (Ephemeroptera: Heptageniidae). In other words, it would make it difficult to interpret the conclusions of our study.