Data from: The neck as a keystone structure in avian macroevolution and mosaicism
Data files
Mar 06, 2024 version files 69.10 MB
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output.nex
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PCscores.csv
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pcscorescategories.csv
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pts.zip
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README.md
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shapedata.csv
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svp2022data_v2.csv
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svp2022data.csv
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tiplabels.csv
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tree_1_BTraits_lambda_a.rds
Abstract
Background
The 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.
Results
Here 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.
Conclusions
Combined, 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.
README
This README file was generated on 05-03-2024 by Ryan Marek.
GENERAL INFORMATION
Title of Dataset: The neck as a keystone structure in avian macroevolution and mosaicism
Author Information
A. Corresponding Author
Name: Ryan D. Marek
Institution: University College London
Email: r.marek@ucl.ac.uk
Twitter/X: @ryndmrkB. Associate or Co-Investigator
Name: Ryan N. Felice
Institution: University College London
Email: ryan.felice@ucl.ac.ukDate of data collection (approximate): 2021-2023
Funding sources that supported the collection of this project: Leverhulme Trust Research Project Grant, award number 182676
SHARING/ACCESS INFORMATION
- Licenses/restrictions placed on the data: This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.
- 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
- 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
- Structure of folder: 567 .pts files
- File naming convention: vertebrae_genus.pts, e.g. C2_acanthisitta.pts
- 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
- 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
- Number of variables: 565
- Number of cases/rows: 560
- 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
- Missing data codes: NA (data not applicable)
DATA-SPECIFIC INFORMATION FOR: pcscorescategories.csv
- Number of variables: 20
- Number of cases/rows: 560
- 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
- Missing data codes: NA (not applicable)
DATA-SPECIFIC INFORMATION FOR: shapedata.csv
- Number of variables: 1232
- Number of cases/rows: 560
- 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)
- Missing data codes: NA (not applicable)
DATA-SPECIFIC INFORMATION FOR: svp2022data.csv
- Number of variables: 49
- Number of cases/rows: 112
- 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
- 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
- Number of variables: 9993
- 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
- Number of variables: 4
- Number of cases/rows: 112
- 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
- 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