A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
Lloyd, Graeme; Slater, Graham (2021), A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses, Dryad, Dataset, https://doi.org/10.5061/dryad.vq83bk3qf
Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species--rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the $\sim 90$ extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.
Morphological character taxon matrices were collected via literature review. The molecular dataset was obtained from the supplementary information of McGowen 2009 and supplemented with sequence data from genbank. Fossil taxon ages were obtained from the paleobiology database and supplemented with published dates obtained via literature review.
All data processing was done via custom R scripts.