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R markdown for reproducible workflow
R markdown file containing the fully reproducible workflow of the study.
Revell-etal-2018.MEE.Rmd
Built reproducible workflow
Built reproducible workflow containing all analyses of the study including (low quality versions of) all figures & tables.
Revell-etal-2018.MEE.html
Phenotypic data
Phenotypic data file used for empirical example of study. Data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers A\u00d8 (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660p
iguanids.csv
Phylogeny of lizard tribe Liolaemini
File containing phylogeny of lizard tribe Liolaemini. Phylogeny data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers A\u00d8 (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660p
liolaeminipl.phy
Phylogeny of lizard subfamily Phrynosomatinae
File containing phylogeny of lizard subfamily Phrynosomatinae. Phylogeny data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers A\u00d8 (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660p
phrynosomatpl.phy

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1350474

", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "Del Rosario University" } ], "person_or_org": { "family_name": "Revell", "given_name": "Liam J.", "name": "Revell, Liam J.", "type": "personal" } }, { "affiliations": [ { "name": "Departamento de Ciencias Biol\u00f3gicasUniversidad de los Andes Bogot\u00e1 Colombia*" } ], "person_or_org": { "family_name": "Gonz\u00e1lez-Valenzuela", "given_name": "Laura E.", "name": "Gonz\u00e1lez-Valenzuela, Laura E.", "type": "personal" } }, { "affiliations": [ { "name": "Departamento de Ciencias Biol\u00f3gicasUniversidad de los Andes Bogot\u00e1 Colombia*" } ], "person_or_org": { "family_name": "Alfonso", "given_name": "Alejandro", "name": "Alfonso, Alejandro", "type": "personal" } }, { "affiliations": [ { "name": "Departamento de Ciencias Biol\u00f3gicasUniversidad de los Andes Bogot\u00e1 Colombia*" } ], "person_or_org": { "family_name": "Castellanos-Garc\u00eda", "given_name": "Luisa A.", "name": "Castellanos-Garc\u00eda, Luisa A.", "type": "personal" } }, { "affiliations": [ { "name": "Departamento de Ciencias Biol\u00f3gicasUniversidad de los Andes Bogot\u00e1 Colombia*" } ], "person_or_org": { "family_name": "Guarnizo", "given_name": "Carlos E.", "name": "Guarnizo, Carlos E.", "type": "personal" } }, { "affiliations": [ { "name": "Departamento de Ciencias Biol\u00f3gicasUniversidad de los Andes Bogot\u00e1 Colombia*" } ], "person_or_org": { "family_name": "Crawford", "given_name": "Andrew J.", "name": "Crawford, Andrew J.", "type": "personal" } } ], "description": "1. The tempo of evolutionary change through time is among the most heavily studied dimensions of macroevolution using phylogenies. 2. Here, we present a simple, likelihood-based method for comparing the rate of phenotypic evolution for continuous characters between trees. Our method is derived from a previous approach published by Brian O'Meara and colleagues in 2006. 3. We examine the statistical performance of the method and find that it suffers from the typical downward bias expected for maximum likelihood estimates of the variance, but only for very small trees. We find that evolutionary rates are estimated with minimal bias for trees of even relatively modest size. 4. We also find that type I error rates based on a likelihood-ratio test are minimally elevated above the nominal level, even for small phylogenies. The type I error rate can be reduced to a level at or below its nominal value by substituting a test-statistic distribution obtained via simulation under the null hypothesis of no difference in evolutionary rate among trees. 5. We discuss the consequences of failing to account for uncertainty in the estimation of species means or in the phylogeny, and describe strategies for taking this uncertainty into consideration during estimation. We also identify how our approach is related to previous methods for comparing the rate of evolution among different clades of a single tree or between different phenotypic traits. Finally, we describe how the method can be applied to different evolutionary models and to discrete characters \u2013 options that are already implemented in software. 6. Evolutionary biologists continue to be intrigued by changes in the tempo of phenotypic evolution across the tree of life. The method described herein should be useful for contexts in which changes in the evolutionary rate or process between two or more clades of distant or unknown relationship are of interest.", "publication_date": "2019-01-23", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1111/2041-210x.12977", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "Phrynosomatinae" }, { "subject": "Liolaemini" } ], "title": "Data from: Comparing evolutionary rates between trees, clades, & traits" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "

The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.

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