DOI: 10.5061/dryad.hx3ffbggp
title: Dataset for: The radiation continuum and the evolution of frog diversity

description: Most of life’s vast diversity of species and phenotypes is often
 attributed to adaptive radiation. Yet its contribution to species and
 phenotypic diversity of a major group has not been examined. Two key
 questions remain unresolved. First, what proportion of clades show
 macroevolutionary dynamics similar to adaptive radiations? Second, what
 proportion of overall species richness and phenotypic diversity do these
 adaptive-radiation-like clades contain? We address these questions with
 phylogenetic and morphological data for 1,226 frog species across 43
 families (which represent &gt;99% of all species). Less than half of
 frog families resembled adaptive radiations (with rapid diversification
 and morphological evolution). Yet, these adaptive-radiation-like clades
 encompassed ~75% of both morphological and species diversity, despite
 rapid rates in other clades (e.g., non-adaptive radiations). Overall, we
 support the importance of adaptive-radiation-like evolution for explaining
 diversity patterns and provide a framework for characterizing
 macroevolutionary dynamics and diversity patterns in other groups.
description: # This Dryad data package contains the data, computer code and document
 files for the article: "The radiation continuum and the evolution of
 frog diversity", published by Gen Morinaga, John J. Wiens, and Daniel
 S. Moen in *Nature Communications.* ## Data files included are:
 "Supplementary Data 1 Morphometrics Anura 4628 specimens": The
 full intraspecific phenotypic dataset. The vast majority of these data are
 raw measurements. The infrequent values with more than three digits were
 estimated based on intraspecific scaling relationships, due to
 unavailability of photos. We provide both MS Excel and '.CSV'
 files, the former with a tab of metadata. "Supplementary Data 2 Anura
 species means sd se n": Interspecific species means, standard
 deviations, standard errors calculated per species, and standard errors
 calculated with a pooled estimate of measurement variance from Ives *et
 al.* (2007). All values were rounded to three digits; wherever fewer
 digits occur, these values rounded to end in one or more zeros. We provide
 both MS Excel and '.CSV' files, the former with a tab of
 metadata. "Supplementary Data 3 new microhabitat data.xlsx":
 Full documentation of our microhabitat classifications for taxa new to
 this study (i.e., not coming from Moen and Wiens [2017]). The file
 includes a data tab with short reference information and a reference tab
 with the full references. "Supplementary Data 4 family rates
 raw": ages, species diversity, and raw rates of morphological
 evolution and net diversification estimated for each family in this paper.
 These are the rates most amenable to comparison with other studies. We
 provide both MS Excel and '.CSV' files, the former with a tab of
 metadata. "Supplementary Data 5 family rates scaled": ages,
 species diversity, and transformed (logged, centered, and scaled) rates of
 morphological evolution and net diversification estimated for each family
 in this paper. These were the rates we used for most analyses. We provide
 both MS Excel and '.CSV' files, the former with a tab of
 metadata. "frog\_hypervolumes.RData": We include this R data
 file for completeness, though it not used directly in our R Markdown
 tutorial in Supplementary Code 1. We explain it within the tutorial. ##
 Data analysis documentation, zipped as Supplementary Code 1 and deposited
 on Zenodo: "amph\_shl\_new\_Consensus\_7238.tre": Consensus of
 10,000 fully-sampled trees from the posterior distribution of Jetz and
 Pyron (2018), containing species with genetic data (4,061) and imputed
 taxa (3,177). We used this tree for estimating species diversity of
 time-sliced clades. "aw.latest.csv": A file from AmphibiaWeb
 (2021) that we used to calculate current species diversity of each anuran
 family. This was the diversity on AmphibiaWeb on the date of our accession
 for these analyses, 7 December 2021.
 "JP\_NatEE\_2018\_3349tax\_ultra.nex": A nexus file of the
 ultrametric maximum-clade credibility tree of the anuran taxa for which
 Jetz and Pyron (2018) had genetic data. This tree was the basis for most
 of our analyses.
 "Moen\_etal\_2021\_SuppInfoS9.diversification.data.csv": We used
 this file from Moen *et al.* (2021) to extract birth-death net
 diversification-rate estimates for anuran families.
 "Morphometrics\_anura\_4628\_specimens.csv": The full
 intraspecific phenotypic dataset. This file is the same as Supplementary
 Data 4 (see above for details) but renamed here for using in the analysis.
 "Radiation\_continuum\_essential\_objects.RData": This R data
 file is loaded for facilitating data analysis in our R Markdown document.
 "Radiation\_continuum": An R Markdown tutorial that walks
 readers through our analyses. We provide the optimal viewing format (HTML
 file), in addition to the raw R Markdown (.Rmd) and just the R code (.R).
 The latter two files facilitate quick analysis and review of code. ##
 References: AmphibiaWeb. AmphibiaWeb: Information on amphibian biology and
 conservation, http://amphibiaweb.org (2021). Accessed 7 December 2021.
 Ives, A. R., P. E. Midford, & T. Garland, Jr. Within-species
 variation and measurement error in phylogenetic comparative methods.
 *Syst. Biol.* 56, 252–270 (2007). Jetz, W. & Pyron, R. A. The
 interplay of past diversification and evolutionary isolation with present
 imperilment across the amphibian tree of life. *Nat. Ecol. Evol.* 2,
 850–858 (2018). Moen, D. S., & J. J. Wiens. Microhabitat and
 climatic niche change explain patterns of diversification among frog
 families. *Am. Nat.* 190, 29–44 (2017). Moen, D. S., Ravelojaona, R. N.,
 Hutter, C. R. & Wiens, J. J. Testing for adaptive radiation: A new
 approach applied to Madagascar frogs. *Evolution* 75, 3008–3025 (2021).