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Relationships of song structure to phylogenetic history, habitat, and morphology in the vireos, greenlets, and allies (Passeriformes: Vireonidae)

Citation

Mejias, Miguel (2020), Relationships of song structure to phylogenetic history, habitat, and morphology in the vireos, greenlets, and allies (Passeriformes: Vireonidae), Dryad, Dataset, https://doi.org/10.5061/dryad.3j9kd51g8

Abstract

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.

Methods

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.

Usage Notes

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.