DOI: 10.5061/dryad.3j9kd51g8
title: Relationships of song structure to phylogenetic history, habitat, and morphology in the vireos, greenlets, and allies (Passeriformes: Vireonidae)

description: Acoustic signals show immense variation among passerines, and several
 hypotheses have been proposed to explain this diversity. In this study, we
 tested, for the first time, the relationships of song structure to
 phylogeny, habitat type, and morphology in the vireos and allies
 (Vireonidae). Every measure of song structure considered in this study had
 moderate and significant phylogenetic signal. Furthermore, two
 song-constraining morphological traits, bill shape and body mass, also
 exhibited significant phylogenetic signal. Song length showed the largest
 within-clade similarity; longer songs were highly conserved in part of the
 greenlet (Hylophilus) clade, whereas shorter songs characterized the
 remaining seven genera. We found no differences in song structure among
 vireonids living in different habitat types. However, vireonids with
 shorter, stouter bills and larger bodies sang songs with lower minimum and
 maximum peak frequency, compared with species with longer, thinner bills
 and smaller bodies. We conclude that Vireonidae song evolution is driven
 partially by phylogenetically conserved morphological traits. Our findings
 support the phylogenetic signal and morphological constraints hypotheses
 explaining structural diversity in avian acoustic signals.
description: This data was collected as part of the main author’s PhD thesis,
 Miguel Mejias. We collected vireonid songs from two song libraries:
 (1) the Macaulay Library and (2) xeno-canto; songs from the former were
 emailed via request while the latter database was readily downloadable
 from their main website. Morphology data was obtained from Vert-Net and
 the personal dataset belonging to one of our coauthors, Dr. Tyler Imfeld.
 Habitat information for each species obtained from the Vireonidae chapter
 in the Handbook of Birds of the World. Lastly, the ND2 Vireonidae
 alignment data was obtained from Dr. J. Klicka and Dr. D. Slager; this
 alignment can also be found on GeneBank. All of the specifics in how the
 songs were processed and measured, as well as how the ND2 was used to
 created a Vireonidae phylogenetic tree(s) can be found in great detail
 under the METHODS section of the relevant publication, "Relationships
 of song structure to phylogenetic history, habitat, and morphology in the
 vireos, greenlets, and allies (Passeriformes: Vireonidae)." Readers
 who cannot gain access to this paper can request it by contacting the
 primary author at mmejias@mun.ca.
description: The database contains all of the excel datafiles and R files that
 were used to produce the results/findings of this publication. Our
 co-authors, Dr. Tyler Imfeld and Sander Boisson, were primairly
 responsible for contructing this R code.
 1. Mejias_Workflow.R. - The primary R script which has all the
 code. All lines are annotated so that the code can be readily
 re-run.  2. Chapter 1 Functions. -  Contains functions
 needed to run phylogenetic analyses  3. Chapter 1
 Functions_V2. - Contains additional phylogenetic functions. 
 4. Chapter 1 Functions._V3. - Contains additional phylogenetic
 functions.  5. All Vireonid Measurements_V2. - An excel
 file with all song measurements, morphology measurements, and habitat
 type, per species.  6. VireoND2-taxaset-MCC.tree - The
 Maximum Credibility or "Consensus Tree" for the Vireonidae
 family, based on the ND2 sequence. 
 7. VireoND2-taxaset-MCC.trees - The 100 "best"
 Vireonidae trees based on posterior probabilities.  8.
 ImfeldVireoData - An excel file with Dr. Tyler Imfeld's Vireo data
 which contains the bill measurements used in analyses.
 9. AllVireoData - An excel file that is automatically created by
 following lines of code in "Mejias_WorkflowV2," which simply
 produces a single summary excel file pertaining to all variables for all
 study vireonids. 10. BeastOutputforR_2 - This is a text
 file which has the poster probabilities of multiple Vireonid trees, used
 to obtain the "best" 100 trees.  11.
 AllVireoData_LessSpecies_PGLS1 - A csv file with some species dropped (due
 to non-normality; see methods for more detail) to run the first
 phylogenetic generalized least square model.  12. 11.
 AllVireoData_LessSpecies_PGLS5 - A csv file with some species dropped (due
 to non-normality; see methods for more detail) to run the fifth
 phylogenetic generalized least square model. 13.
 AllVireoData_LessSpecies_PGLS7 - A csv file with some species dropped (due
 to non-normality; see methods for more detail) to run the seventh
 phylogenetic generalized least square model.   14.
 VireoNamesTable - An excel file with the latin vireonid names that match
 those that appear on tip branches; needed to make phylogenetic tree
 analyses run properly.