10.5061/DRYAD.5HR25NV
Title, Pascal O.
University of Michigan-Ann Arbor
Rabosky, Daniel L.
University of Michigan-Ann Arbor
Data from: Tip rates, phylogenies, and diversification: what are we
estimating, and how good are the estimates?
Dryad
dataset
2019
2019-02-05T19:32:09Z
2019-02-05T19:32:09Z
en
https://doi.org/10.1111/2041-210x.13153
3905386069 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
1. 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. 2. 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 (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. 3.
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. 4. 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.
tipRatesDataScriptsR scripts and data files needed to reproduce all
analyses and figures.tipRates_dryad.tar.gztreesForTipRatesDirectory of all
phylogenies used to evaluate tip rate metrics.