Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, 1 but it is becoming increasingly apparent that inferences derived from extant species alone 2 can be highly misleading. Trees incorporating living and extinct taxa are are needed to 3 address fundamental questions about the origins of diversity and disparity but it has 4 proved challenging to generate robust, species-rich phylogenies that include large numbers 5 of fossil taxa. As a result, most studies of diversification dynamics continue to rely on 6 molecular phylogenies. Here, we extend and apply a recently developed meta-analytic 7 approach for synthesizing previously published phylogenetic studies to infer a well-resolved 8 set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans 9 (whales, dolphins and allies). Our trees extend sampling from the ⇠ 90 extant species to 10 over 400 living and extinct species, and therefore allow for more robust inference of 11 macroevolutionary dynamics. While the diversification scenarios we recover are broadly 12 concordant with those inferred from molecular phylogenies they di↵er in critical ways, 13 most notably in the relative contributions of extinction and speciation rate shifts in driving 14 rapid radiations. Supertrees are often viewed as poor substitute for phylogenies inferred 15 directly from character data but the metatree pipeline overcomes many of the past 16 2 LLOYD AND SLATER criticisms leveled at these approaches. Meta-analytic phylogenies provide the most 17 immediate route for integrating fossils into macroevolutionary analyses, the results of 18 which range from untrustworthy to nonsensical without them.
19It is now widely accepted that a phylogenetic framework is essential for addressing 23 questions regarding diversification dynamics, phenotypic evolution, and historical 24 biogeography. The covariances between species that are imposed by the hierarchical 25 structure of a phylogenetic tree mean that any attempt to understand the processes 26 responsible for generating observed patterns of diversity must take the tree and its 27 associated branch lengths into account (Felsenstein, 1985; Harvey and Pagel, 1991; Foote, 28 1996; O'Meara et al., 2006; Ree and Smith, 2008). As a consequence of this phylogenetic 29 dependence, the development of new tools for inferring macroevolutionary dynamics has 30 been paralleled by innovations in the field of phylogenetic inference, and it is now possible 31 to infer time-scaled trees using complex models of molecular evolution applied to 32 genome-scale data.
33The need for a well-resolved, time-calibrated phylogeny places substantial 34 constraints on the kinds of clades that are accessible to most biologists for testing 35 macroevolutionary hypotheses. Some authors have noted that clades are often selected for 36 study due to their tractability rather than because they are suitable candidates for testing 37 a particular hypothesis, resulting in a form of empirical ascertainment bias (Beaul...