DOI: 10.5061/dryad.ttdz08m8q
title: Tempo and mode of evolution across multiple traits in an adaptive radiation of birds (Vangidae)

description: An ongoing challenge in macroevolutionary research is identifying common
 drivers of diversification amid the complex interplay of many potentially
 relevant traits, ecological contexts, and intrinsic characteristics of
 clades. In this study, we used geometric morphometric and phylogenetic
 comparative methods to evaluate the tempo and mode of morphological
 evolution in an adaptive radiation of Malagasy birds, the vangas, and
 their mainland relatives (Aves: Vangidae). To characterize the
 morphological diversity of the clade we used both landmarks and
 semilandmark curves from the bill and neurocranium, and linear
 measurements of pedal bones, all collected from microCT scans of museum
 specimens. The Malagasy radiation is more diverse in both skull and foot
 shape. However, rather than following the classic "early burst"
 of diversification, trait evolution accelerated well after their arrival
 in Madagascar, likely driven by the evolution of new modes of foraging and
 especially of a few species with highly divergent morphologies. Anatomical
 regions showed differing evolutionary patterns, and the presence of
 morphological outliers impacted the results of some analyses, particularly
 of trait integration and modularity. Our results demonstrate that the
 adaptive radiation of Malagasy vangas has evolved exceptional
 ecomorphological diversity along multiple, independent trait axes, mainly
 driven by a late expansion in niche space due to key innovations. Our
 findings highlight the evolution of extreme forms as an overlooked feature
 of adaptive radiation warranting further study.
description: # Tempo and mode of evolution across multiple traits in an adaptive
 radiation of birds (Vangidae) Dataset DOI:
 [10.5061/dryad.ttdz08m8q](10.5061/dryad.ttdz08m8q) ## Description of the
 data These data and scripts were used in analyses of of morphological
 evolution in the adaptive radiation of Malagasy vangas. ### Data files ###
 RAW DATA FOR MORPHOMETRIC ANALYSES IN R raw_coordinates.csv - a csv file
 containing the raw (compiled) landmark data for the cranium and upper bill
 * Column 1 is the unique specimen identifier
 (e.g. Artamella_viridis_100859)  * The other 408 columns are the x,y,z
 coordinates for each of the 136 landmarks in the cranium and upper bill.
 These are ordered the same as in landmark_names.csv
 raw_coordinates_lower.csv - a csv file containing the raw (compiled)
 landmark data for the cranium and upper bill * Column 1 is the unique
 specimen identifier (e.g. Artamella_viridis_100859)  * The other 234
 columns are the x,y,z coordinates for each of the 78 landmarks in the
 lower bill. These are ordered the same as in landmark_names_lower.csv
 foot_data_raw.csv - a csv file containing the raw linear measurements of
 pedal bones * *Specimen ID-* An extended specimen id,
 e.g. *calicalicus_madagascariensis_feet_fluid_352874*. Indicates species,
 body part, preservation type (fluid or [round] skin), and museum accession
 number. See table S1 for detailed specimen info, including the museum each
 specimen is from. * *Species-* The currently recognized species scientific
 name * *Genus-* The genus that species belongs to * *Vanga*- Binary
 identifier of whether or not the species is a Malagasy vanga; 1 =
 Malagasy, 0 = non-Malagasy. * * tmt-d4p4 (12 columns)-* Measurements of
 each pedal bone. See Table S2 for descriptions of each measurement. *
 *Mass-* Body mass in grams * *Foraging-* Classification of foraging
 behavior (gleaning, probing, or sallying) foot_data_logshape.csv - a csv
 file containing the size-corrected foot measurements (log-shape variables)
 * Column 1- Species name * tmt-d4p4 (12 columns)- the mean size-corrected
 measurement for each bone for that species. See Table S2 for descriptions
 of each measurement. landmark_names.csv - a csv file containing the names
 of each landmark. Used in data_subsetting_clean.R to define sliding
 landmarks and modules. * *number*- the landmark number (1-136) * *name-*
 the name of the landmark. Landmarks 1-10 are type 1 landmarks with unique
 names describing their location. All others are semilandmark curves. Each
 curve has a unique name (e.g. maxilla_midline), which is followed by a
 number for that curve (.1 through .6) and then each landmark in that curve
 is numbered (e.g. .01 - .22). See Table S2 for a definition of each
 landmark and semilandmark curve. landmark_names_lower.csv - a csv file
 containing the names of each landmark in the lower bill. Used in
 data_subsetting_clean.R to define sliding landmarks and modules. *
 *number-* the landmark number (1-78) * *name-* the name of the landmark.
 Landmarks 1-3 are type 1 landmarks with unique names describing their
 location. All others are semilandmark curves. Each curve has a unique name
 (e.g. lower_tomium), which is followed by a number for that curve (.1
 through .3) and then each landmark in that curve is numbered (e.g. .01 -
 .25). See Table S2 for a definition of each landmark and semilandmark
 curve. ### PHYLOGENIES vanga_timetree_10_8_24 - a tree file in nexus
 format, containing the time-calibrated phylogeny used in all analyses
 foot_timetree_10_8_24 - a tree file in nexus format, the same phylogeny
 but pruned to the taxa represented in the foot dataset ### BAYESTRAITS
 & DTT vangas_foot.txt; vangas_mass.txt; vangas_pc9_bill.txt;
 vangas_pc13_all.txt; vangas_posthoc.txt - text files containing the PC
 scores for axes summarizing 95% of variance for each dataset. Used as
 input for Bayestraits & dtt analyses. bayestraits_commfiles.zip - a
 zipped folder of files used to run Bayestraits analyses. Contains: 17
 individual command files, setting up the bayestraits parameters for each
 model. These are the versions for the full skull dataset; the only
 differences for the other datasets are the name of the Log file and in
 some cases the number of iterations. commands_list_all - the line of code
 used to actually run each model for the full skull dataset; this is set up
 for submitting as a batch to a supercomputer, but each can be run
 individually very easily on a laptop. output_files.zip - a zipped folder
 containing all output files from every replicate for every model and every
 dataset. Organized as a separate subfolder for each dataset: out_all,
 out_bill, out_feet, out_mass, and out_posthoc.See main text for
 descriptions of these datasets. each individual analysis produces 3 (BM)
 to 5 (rj) output files, resulting in 345 files total per subfolder. These
 are: the Log file (.Log.txt), Schedule file (.Schedule.txt), results of
 the stepping stone sampler (.Stones.txt), .Output.trees (for all models
 but BM) the rescaled trees in nexus format, and .VarRates.txt (for rj
 models) which summarizes the modeling results. reduced_output.zip - a
 zipped folder containing files from just one replicate of the
 best-supported models for the skull and foot datasets. Sufficient to
 replicate the figures and get a sense of how the full analyses work.
 Contains 10 files, one of each of the above for the reversible-jump delta
 transform for the feet, and the reversible-jump branch transform for the
 full skull landmark dataset. ## Code Most analyses were performed in R
 (see session_info.txt file for all version details).  Bayestraits analyses
 were performed using Bayestraits V4.0. Stationarity and convergence (from
 the .Log files) were assessed with Tracer. ## Code files
 data_subsetting_clean.R - an R file that organizes the landmark data, does
 mirroring, procrustes superimposition, and creates data and tree subsets.
 MUST BE RUN prior to other morphometrics analyses; saves an Rdata file at
 the end. Not required to run Bayestraits or foot analyses. ``` \--INPUT:
 raw_coordinates, raw_coordinates_lower, landmark_names,
 landmark_names_lower, and vanga_timetree ``` feet_code_clean.Rmd - an R
 Markdown file that formats the raw foot measurement data and runs most
 foot morphometric analyses: PCA, ANOVA and MANOVAs, morphological
 disparity, phylogenetic signal, net evolutionary rate, and integration
 (eigenvalue dispersion). Written primarily by Euan Lim with contributions
 from Anya. ``` \--INPUT foot_data_raw or foot_data_logshape and
 foot_timetree \--OUTPUT: \--Figure 2, Figures S2 & S3 \--Tables 1
 & 3, Tables S3, S4, S5, S6 ``` morphometric_analyses_clean.R - an R
 file that performs many of the morphometric analyses on the skull landmark
 dataset. Requires Rdata file produced by data_subsetting_clean.R as input.
 Generates PCAs and runs analyses of phylogenetic signal, morphological
 disparity, MANOVAs, and net evolutionary rate. ``` \--OUTPUT: \--Figure 2,
 Figures S1, & S2 \--Tables 1 & 3, Tables S4, S5, and S12 ```
 hypervolumes_clean.R - an R script that calculates and plots the
 morphospace hypervolumes and associated statistics for both skull and foot
 datasets. Requires Rdata file produced by data_subsetting_clean.R as
 input. ``` \--OUTPUT: \--Figure 3, Figure S4 \--Table 1 ```
 integration_clean.R - an R script that runs all analyses of integration
 (eigenvalue dispersion and PLS). Requires Rdata file produced by
 data_subsetting_clean.R as input. Calculates and compares eigenvalue
 dispersion, phylogenetic 2-block partial least squares, and PLS of foot
 and skull. Makes PLS plots. ``` \--OUTPUT: \--Figure 4 \--Tables S6, S7,
 S8 ``` modularity_clean.R - calculates and compares skull modularity
 (covariance ratio) and plots null covariance ratio distributions. Requires
 Rdata file produced by data_subsetting_clean.R as input. ``` \--OUTPUT:
 \--Figure S5 \--Table 2 ``` bayestraits_dtt_clean.R - creates the
 morphometric data files for these analyses and analyzes output. For
 Bayestraits: calculates Bayes factors, summarizes output files, and plots
 the phylogenies. For dtt: performs dtt analysis, plots results. ```
 \--INPUT: \--Bayestraits: output_files (or reduced_output) and both
 phylogenies as input \--dtt: PC score .txt files and phylogenies as input
 \--OUTPUT: \--Figure 5, Figures S6 & S7 \--Tables S9, S10, S11 ```