A Bayesian framework to estimate diversification rates and their variation through time and space

Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
BMC Evolutionary Biology (Impact Factor: 3.37). 10/2011; 11(1):311. DOI: 10.1186/1471-2148-11-311
Source: PubMed


Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification.
We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification.
Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling.

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Available from: Daniele Silvestro
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    • "Finally, all the aspects outlined above are integrated in a joint Bayesian framework to estimate the model parameters while incorporating several sources of uncertainty. The resulting posterior distributions of the parameters are therefore comparable to those obtained by the standard (Bayesian) phylogenetic methods for molecular dating (Thorne et al. 1998; Drummond et al. 2006; Ronquist, Teslenko et al. 2012) and estimation of diversification rates (Ryberg et al. 2011; Silvestro et al. 2011; Stadler et al. 2013). We evaluate the robustness of the joint estimation of the times of speciation and extinction of individual species and rates of speciation and extinction using simulations that reflect commonly observed diversity dynamics. "
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    ABSTRACT: The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
    Full-text · Article · Feb 2014 · Systematic Biology
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    • "This is particularly true for Asia, for which the pattern was derived from only eight species. Because sensitivity and statistical power of methods for detection of shifts in diversification rates may correlate positively with the number of species in the clade (Silvestro et al., 2011), rate shifts in clades with a small number of species (as in Asia for Manilkara s.s.) may not have been detected by the methods used here (a potential type two error). A simulation study would be required to examine the impact of taxon number on type two error rates in these analyses. "

    Full-text · Article · Jan 2014 · Frontiers in Genetics
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    • "Several phylogeny-based approaches have been developed to estimate rates of diversification and test hypotheses of key innovations based on the symmetry of the trees (Chan and Moore 2002; Heard and Mooers 2002; Paradis 2011) or on the patterns of branching times (Rabosky 2006; Alfaro et al. 2009; Rabosky and Glor 2010; Morlon et al. 2011; Silvestro et al. 2011; Stadler 2011; Etienne et al. 2012). Although these approaches can estimate changes of speciation and extinction rates through time and between clades, they do not explicitly link such changes to the evolution of a trait, for example a key innovation. "
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    ABSTRACT: The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water-impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank-forming lineages compared to tank-less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.
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