Dataset for: The radiation continuum and the evolution of frog diversity
Data files
Nov 07, 2023 version files 670.87 MB
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frog_hypervolumes.RData
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README.md
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Supplementary_Data_1_Morphometrics_Anura_4628_specimens.csv
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Supplementary_Data_1_Morphometrics_Anura_4628_specimens.xlsx
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Supplementary_Data_2_Anura_species_means_sd_se_n.csv
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Supplementary_Data_2_Anura_species_means_sd_se_n.xlsx
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Supplementary_Data_3_new_microhabitat_data.xlsx
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Supplementary_Data_4_family_rates_raw.csv
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Supplementary_Data_4_family_rates_raw.xlsx
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Supplementary_Data_5_family_rates_scaled.csv
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Supplementary_Data_5_family_rates_scaled.xlsx
Abstract
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 >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.
README: 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).