DOI: 10.5061/dryad.9qd51
title: Data from: Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution

description: A long-standing hypothesis in adaptive radiation theory is that ecological
 opportunity constrains rates of phenotypic evolution, generating a burst
 of morphological disparity early in clade history. Empirical support for
 the early burst model is rare in comparative data, however. One possible
 reason for this lack of support is that most phylogenetic tests have
 focused on extant clades, neglecting information from fossil taxa. Here, I
 test for the expected signature of adaptive radiation using the
 outstanding 40-My fossil record of North American canids. Models implying
 time- and diversity-dependent rates of morphological evolution are
 strongly rejected for two ecologically important traits, body size and
 grinding area of the molar teeth. Instead, Ornstein–Uhlenbeck processes
 implying repeated, and sometimes rapid, attraction to distinct dietary
 adaptive peaks receive substantial support. Diversity-dependent rates of
 morphological evolution seem uncommon in clades, such as canids, that
 exhibit a pattern of replicated adaptive radiation. Instead, these clades
 might best be thought of as deterministic radiations in constrained
 Simpsonian subzones of a major adaptive zone. Support for adaptive peak
 models may be diagnostic of subzonal radiations. It remains to be seen
 whether early burst or ecological opportunity models can explain broader
 adaptive radiations, such as the evolution of higher taxa.
description: canidae_topology_MCCTMaximum clade credibility tree from topology-only Bayesian analysis of canid morphological datacanidae_dated_MCCTMaximum clade credibility tree from Bayesian tip-dating analysis of canid morphological data. Branch lengths are in units of millions of yearscanid_tree_dataAn R data object containing p and t files, as well as the tree with the highest Likelihood, from the Bayesian tip dating analysis of canid morphological data. Note that branch lengths for trees in the t files are not in units of millions of years; to obtain time scaled branch lengths, one needs to divide lengths by the corresponding clock rate from the p filesextant_ratiosa csv file containing ecomorphological data for extant canids and select non-canid caniforms. Data used in discriminant analyses for classifying fossil canids to dietary regimes.fossil.ratiosa .csv file containing mean ecomorphological trait values for fossil canids. used in discriminant function analyses and in subsequent macroevolutionary analysesall.final.dataCSV file containing Ln(body mass), relative grinding areas and dietary classifications for fossil and extant North American canids used in macroevolutionary analysesdiscriminant_analysisAn R script used to perform discriminant analyses for classifying fossil canids to dietary regimesdiscrete trait analysesAn R script for performing analyses of dietary evolution under Markov models. The script fits models and estimates rates to the best tree and a sample of 500 trees from the posterior distribution (see posteriorSample.csv)continuous trait analysesAn R script for performing analyses of body size and relative grinding area evolution. The script fits models to a sample of trees drawn from the posterior distribtion (see posteriorSample.csv)posteriorSampleCSV file containing a single column - these are the trees sampled from the posterior distribution when accounting for phylogenetic uncertainty in macroevolutionary model fitting.canidae_final_datingA nexus data file containing 123 characters coded for 133 living and fossil canids. The MrBayes block contains blocks to perform both topology-only and tip-dating analyses. Comments are provided showing which blocks to uncomment to perform specific analyses.canidae.nex