DOI: 10.5061/dryad.m37pvmd7w
title: Data from: The neck as a keystone structure in avian macroevolution and mosaicism

description: BackgroundThe origin of birds from non-avian theropod dinosaur ancestors
 required a comprehensive restructuring of the body plan to enable the
 evolution of powered flight. One of the proposed key mechanisms that
 allowed birds to acquire flight and modify the associated anatomical
 structures into diverse forms is mosaic evolution, which describes the
 parcelization of phenotypic traits into separate modules that evolve with
 heterogeneous tempo and mode. Avian mosaicism has been investigated with a
 focus on the cranial and appendicular skeleton, and as such we don’t
 understand the role of the axial column in avian macroevolution. The long,
 flexible neck of extant birds lies between the cranial and pectoral
 modules and represents an opportunity to study the contribution of the
 axial skeleton to avian mosaicism. ResultsHere we use 3D geometric
 morphometrics in tandem with phylogenetic comparative methods to provide,
 to our knowledge, the first integrative analysis of avian neck evolution
 in context with the head and wing and to interrogate how the interactions
 between these anatomical systems have influenced macroevolutionary trends
 across a broad sample of extant birds. We find that the neck is integrated
 with both the head and the forelimb. These patterns of integration are
 variable across clades and only specific ecological groups exhibit either
 head-neck or neck-forelimb integration. Finally, we find that ecological
 groups that display head-neck and neck-forelimb integration tend to
 display significant shifts in the rate of neck morphological evolution.
 ConclusionsCombined, these results suggest that the interaction between
 trophic ecology and head-neck-forelimb mosaicism influences the
 evolutionary variance of the avian neck. By linking together the
 biomechanical functions of these distinct anatomical systems, the cervical
 vertebral column serves as a keystone structure in avian mosaicism and
 macroevolution.
description: This README file was generated on 05-03-2024 by Ryan Marek. GENERAL
 INFORMATION 1. Title of Dataset: The neck as a keystone structure in avian
 macroevolution and mosaicism 2. Author Information A. Corresponding Author
 Name: Ryan D. Marek Institution: University College London Email:
 [r.marek@ucl.ac.uk](mailto:r.marek@ucl.ac.uk) Twitter/X: @ryndmrk B.
 Associate or Co-Investigator Name: Ryan N. Felice Institution: University
 College London Email:
 [ryan.felice@ucl.ac.uk](mailto:ryan.felice@ucl.ac.uk) 3. Date of data
 collection (approximate): 2021-2023 4. Funding sources that supported the
 collection of this project: Leverhulme Trust Research Project Grant, award
 number 182676 SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed
 on the data: This work is licensed under a CC0 1.0 Universal (CC0 1.0)
 Public Domain Dedication license. 2. Links to publication that cites this
 data: Marek, R. D., & Felice, R. N. (2023). The neck as a keystone
 structure in avian macroevolution and mosaicism. BMC Biology, 21(1), 216.
 DATA & FILE OVERVIEW 1. File list: A) 'pts' folder B)
 marekfelice2023_Rcode.R C) PCscores.csv D) pcscorescategories.csv E)
 shapedata.csv F) svp2022data.csv G) svp2022data_v2.csv H) output.nex I)
 tiplabels.csv J) tree_1_BTraits_lambda_a.rds DATA-SPECIFIC INFORMATION
 FOR: 'pts' folder 1. Structure of folder: 567 .pts files 2. File
 naming convention: vertebrae_genus.pts, e.g. C2_acanthisitta.pts 3. Other
 relevant information: Each .pts folder (e.g. C2_acanthisitta.pts) contains
 the 3D coordinates (x, y and z) for each individual landmark placed on
 that specific vertebrae DATA-SPECIFIC INFORMATION FOR: marekfelice_Rcode.R
 1. Other relevant information: R code used to process data contained
 within this data repository. Follow comments within file to reproduce
 results from Marek, R. D., & Felice, R. N. (2023). The neck as a
 keystone structure in avian macroevolution and mosaicism. BMC Biology,
 21(1), 216. DATA-SPECIFIC INFORMATION FOR: PCscores.csv 1. Number of
 variables: 565 2. Number of cases/rows: 560 3. Variable list: * Specimen:
 vertebrae of interest (naming convention follows naming convention
 outlined in description for 'pts' folder) * Comp1-Comp564:
 Principal component (PC) scores for PC1-564 4. Missing data codes: NA
 (data not applicable) DATA-SPECIFIC INFORMATION FOR:
 pcscorescategories.csv 1. Number of variables: 20 2. Number of cases/rows:
 560 3. Variable list: * vertspecies: specimen information, follows the
 naming convention outlined in description for 'pts' folder *
 vertebrae: vertebral identity (C2 - second cervical vertebrae, C25% -
 vertebrae that is 25% along the length of the cervical column, C50% -
 vertebrae that is 50% along the length of the cervical column, C75% -
 vertebrae that is 75% along the length of the cervical column, last - last
 cervical vertebrae) * genus_species: scientific name (genus and species)
 of the bird * diet: dietary guild of that specific bird (taken from AVONET
 database) * foraging: foraging guild of that specific bird (taken from
 AVONET database) * IOCOrder: taxonomic order of bird * Superorder:
 taxonomic superorder of bird * Comp1: PC scores for the first principal
 component * Comp2: PC scores for the second principal component * Comp3:
 PC scores for the third principal component * Comp4: PC scores for the
 fourth principal component * Habitat: habitat data taken from AVONET
 database * Flesh: binary character dependent on if the bird eats
 vertebrate flesh or not * Water: binary character dependent on if the bird
 spends a significant portion of the time in water * headmass: head mass of
 the bird (kg) * pheadmass: head mass as a percentage of total body mass
 (%) * BI: brachial index of forelimb measurements * proxdist: ratio of the
 length of proximal (coracoid, scapula, humerus) to distal (radius, ulna,
 carpometacarpus) forelimb elements 4. Missing data codes: NA (not
 applicable) DATA-SPECIFIC INFORMATION FOR: shapedata.csv 1. Number of
 variables: 1232 2. Number of cases/rows: 560 3. Variable list: * specimen:
 specimen information, follows the naming convention outlined in
 description for 'pts' folder * genus_species: scientific name
 (genus and species) of the bird * 1.X: X coordinates for landmark 1
 (repeats for X coordinates of landmarks 2-410) * 1.Y: Y coordinate for
 landmark 1 (repeats for Y coordinates of landmarks 2-410) * 1.Z: Z
 coordinates for landmark 1 (repeats for Z coordiantes of landmarks 2-410)
 4. Missing data codes: NA (not applicable) DATA-SPECIFIC INFORMATION FOR:
 svp2022data.csv 1. Number of variables: 49 2. Number of cases/rows: 112 3.
 Variable list: * species: binomial name (in the format genus_species) for
 each bird * Diet: dietary guild of that specific bird (taken from AVONET
 database) * Foraging: foraging guild of that specific bird (taken from
 AVONET database) * Habitat: habitat data taken from the AVONET database *
 Flesh: binary character dependent on if the bird eats vertebrate flesh or
 not * Water: binary character dependent on if the bird spends a
 significant portion of the time in water * LogBodyMass: body mass data
 (log transformed), taken from the AVONET database * Coracoid: measured
 length of the coracoid in m * Scapula: measured length of the scapula in m
 * Humerus: measured length of the humerus in m * Radius: measured length
 of the radius in m * Ulna: measured length of the ulna in m * CMC:
 measured length of the carpometacarpus in m * HeadVol: calculated volume
 of the head (mm^3) * HeadMass: calculated mass of the head (kg) * BI:
 calculated brachial index of the forelimb * ForelimbLength: summed length
 of the forelimb (coracoid + scapula + humerus + ulna + carpometacarpus) *
 HAF: length of the humeral articulation facet (mm) * lnBMHAF: log
 transformed BMHAFg values * BMHAFg: body mass (in grams) calculated from
 the length of the humeral articular facet (with scaling equations from
 Field, D. J., Lynner, C., Brown, C., & Darroch, S. A. (2013). Skeletal
 correlates for body mass estimation in modern and fossil flying birds.
 PLOS one, 8(11), e82000.) * avgBMg: raw body mass values (in grams) taken
 from the AVONET database * BMHAFkg: body mass (in KG) calculated fom the
 length of the humeral articulation facet * bmCoracoid: body mass adjusted
 coracoid length (using BMHAFkg as the body mass) * bmScapula: body mass
 adjusted scapula length (using BMHAFkg as the body mass) * bmHumerus: body
 mass adjusted humerus length (using BMHAFkg as the body mass) * bmRadius:
 body mass adjusted radius length (using BMHAFkg as the body mass) *
 bmUlna: body mass adjusted ulna length (using BMHAFkg as the body mass) *
 bmCMC: body mass adjusted carpometacarpus length (using BMHAFkg as the
 body mass) * avgBMkg: avgBMg converted to kg * abmCoracoid: body mass
 adjusted coracoid length (using avgBMkg as the body mass) * abmScapula:
 body mass adjusted scapula length (using avgBMkg as the body mass) *
 abmHumerus: body mass adjusted humerus length (using avgBMkg as the body
 mass) * abmRadius: body mass adjusted radius length (using avgBMkg as the
 body mass) * abmUlna: body mass adjusted ulna length (using avgBMkg as the
 body mass) * abmCMC: body mass adjusted carpometacarpus length (using
 avgBMkg as the body mass) * bmForelimb: forelimb length adjusted for body
 mass (using BMHAFkg as the body mass) * abmForelimb: forelimb length
 adjusted for body mass (using avgBMkg as the body mass) * pHeadMass: head
 mass as a percentage of total body mass (%) * cervcount: count of the
 total number of cervical vertebrae * c2preza: prezygapophysis joint angle
 for the C2 vertebra * c2posta: postzygapophysis joint angle for the C2
 vertebra * p25preza: prezygapophysis joint angle for the C25% vertebra *
 p25postza: postzygapophysis joint angle for the C25% vertebra * p50preza:
 prezygapophysis joint angle for the C50% vertebra * p50postza:
 postzygapophysis joint angle for the C50% vertbra * p75preza:
 prezygapophysis joint angle for the C75% vertebra * p75postza:
 postzygapophysis joint angle for the C75% vertebra * lastpreza:
 prezygapophysis joint angle for the last cervical vertebra * lastpostza:
 postzygapophysis joint angle for the last cervical vertebra 4. Missing
 data codes: NA (not applicable) DATA-SPECIFIC INFORMATION FOR:
 svpdata2022_v2.csv Copy of svp2022data.csv, formatted for specific use in
 BayesTraits analysis (marekfelice2023_Rcode.R line 1045) DATA-SPECIFIC
 INFORMATION FOR: output.nex 1. Number of variables: 9993 2. File summary:
 .nex file containing all relevant information to build phylogenetic trees
 of bird relationships within marekfelice2023_Rcode.R DATA-SPECIFIC
 INFORMATION FOR: tiplabels.csv 1. Number of variables: 4 2. Number of
 cases/rows: 112 3. Variable list: * TipLabel: binomial name of bird
 species from dataset that matches with the tip labels found within
 output.nex * IOCFamily: taxonomic family of bird * IOCORder: taxonomic
 order of bird * Superorder: taxonomic superorder of bird 4. Missing data
 codes: NA (not applicable) DATA SPECIFIC INFORMATION FOR:
 tree_1_BTraits_lambda_a.rds Data outputted from BayesTraits, needed to
 calculate evolutionary rates of vertebral evolution. Used in lines
 1043-1176 of marekfelice2023_Rcode.R