BAMM at the court of false equivalency: A response to Meyer and Wiens

The software program BAMM has been widely used to study rates of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model‐based clustering algorithm to identify clades that share common macroevolutionary rate dynamics and to estimate parameters. A recent simulation study by Meyer and Wiens (M&W) argued that (1) a simple inference framework (MS) performs much better than BAMM, and (2) evolutionary rates inferred with BAMM are poorly correlated with true rates. I address two statistical concerns with their assessment that affect the generality of their conclusions. These considerations are not specific to BAMM and apply to other methods for estimating parameters from empirical data where the true grouping structure of the data is unknown. M&W constrain roughly half of the parameters in their MS analyses to their true values, but BAMM is given no such information and must estimate all parameters from the data. This information disparity results in a substantial degrees of freedom advantage for the MS estimators. When both methods are given equivalent information, BAMM outperforms the MS estimators.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146370/1/evo13566.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146370/2/evo13566_am.pd

Unlinked Mendelian inheritance of red and black pigmentation in snakes: Implications for Batesian mimicry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/1/evo12902_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135324/2/evo12902.pd

Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?

Species‐specific diversification rates, or ‘tip rates’, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait‐dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model‐free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model‐based approach (Bayesian analysis of macroevolutionary mixtures [BAMM]). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model‐free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non‐model‐based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait‐dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/1/mee313153-sup-0001-FigS1-S10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/2/mee313153.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149536/3/mee313153_am.pd

Continuous traits and speciation rates: Alternatives to state‐dependent diversification models

Many quantitative traits, for example body size, have been hypothesized to influence the diversification dynamics of lineages over macroevolutionary time‐scales. The Quantitative State Speciation‐Extinction (QuaSSE) model and related methods provide an elegant framework for jointly modelling the relationship between change in continuous traits and diversification. However, model misspecification and phylogenetic pseudoreplication can result in elevated false discovery rates in this and other state‐dependent speciation‐extinction models.Here, we evaluate alternative trait‐dependent diversification methods that do not formally model the relationship between traits and diversification, but instead test for correlations between summary statistics of phylogenetic branching patterns and trait variation at the tips of a phylogenetic tree (hereafter tip‐rate correlations or TRCs). We compare alternative branching pattern statistics and significance tests, and we evaluate their performance relative to QuaSSE under a range of evolutionary scenarios.We found that a simple statistic derived from branch lengths (inverse equal splits) can detect trait‐associated rate variation, and that a simulation‐based method performs better than phylogenetic generalized least squares for testing the significance of trait‐rate correlations. This test (ES‐sim) had better power to detect trait‐dependent diversification than other TRCs. By testing the approach across a diverse set of simulation scenarios, we found that ES‐sim is similar to QuaSSE in statistical power. However, the approach rarely led to false inferences of trait‐dependent diversification, even under conditions that are problematic for formal state‐dependent models. We illustrate the application of ES‐sim to real data by re‐assessing the relationship between dispersal ability and diversification in Furnariid birds.We conclude that simple, semi‐parametric tests like ES‐sim represent a promising approach for trait‐dependent diversification analyses in groups with heterogeneous diversification histories and provide a useful alternative or complement to formal state‐dependent speciation‐extinction models.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143736/1/mee312949.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/143736/2/mee312949_am.pd

Speciation dynamics during the global radiation of extant bats

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/1/evo12681-sup-0008-FIGURE7.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/2/evo12681-sup-0003-FIGURE2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/3/evo12681.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/4/evo12681-sup-0002-FIGURE1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/5/evo12681-sup-0009-FIGURE8.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/6/evo12681-sup-0007-FIGURE6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/7/evo12681-sup-0006-FIGURE5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/8/evo12681-sup-0004-FIGURE3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111917/9/evo12681-sup-0005-FIGURE4.pd

World Heritage lizard: population genetics and species status of the range-restricted Hamelin skink, Ctenotus zastictus

The Shark Bay World Heritage region in western Australia is home to a number of species of substantial conservation concern. Among these is a small scincid lizard, Ctenotus zastictus, which represents one of the most geographically-restricted vertebrates on the Australian mainland. The long-term persistence of Ctenotus zastictus is threatened due to the small size of its range, isolation from suitable habitat patches elsewhere, and potential impacts from climate change and mining. Accordingly, conservation efforts in Australia have targeted C. zastictus as the focus of protection. But this attention might be unwarranted – the species might not be evolutionarily unique. Previous genetic assessments have suggested limited differentiation between C. zastictus and its putative sister taxon, and the taxonomic status of C. zastictus has never been formally evaluated. Here, we use population genomic, phylogenetic, and ecoclimatic analyses to characterize the species status of C. zastictus in context of its closely-related congeners. In doing so, we explore the practical and conceptual challenges of revising species boundaries in threatened species, many of which are also rare and range-restricted. We demonstrate that C. zastictus is a coherent evolutionary unit that has been isolated from its putative sister species for at least two million years. Based on these results, we recommend that C. zastictus should retain its taxonomic status