Last updated: 2022-04-11
Checks: 2 0
Knit directory: Code/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version e47dde2. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: Flexibility Comparisons.nb.html
Ignored: Main.nb.html
Ignored: PGLS.FullData.nb.html
Ignored: PGLSforeachMeasFeature.nb.html
Ignored: PGLSwithPCA_Dims.nb.html
Ignored: PreppedVertMeas.nb.html
Ignored: ProcessCymatogasterFiles.nb.html
Ignored: ProcessFCSVfiles.nb.html
Ignored: TestingHabitatwithFriedmanData.nb.html
Ignored: Trilok_tree.nb.html
Ignored: VertLM.nb.html
Ignored: VertMeasLDA_Attempt.nb.html
Ignored: VertPGLS.nb.html
Ignored: VertPairs.nb.html
Ignored: analysis/.DS_Store
Ignored: analysis/10-VertLM.nb.html
Ignored: analysis/20-plot_phylogeny.nb.html
Ignored: analysis/21-plot_fits_and_summary.nb.html
Ignored: analysis/CheckSpeciesMatch.nb.html
Ignored: caper_test.nb.html
Ignored: data/.DS_Store
Ignored: ggtree_attempt.nb.html
Ignored: plot_example_data.nb.html
Ignored: plot_fits_and_summary.nb.html
Ignored: plot_phylogeny.nb.html
Ignored: renv/library/
Ignored: renv/staging/
Ignored: summarize_vert_meas.nb.html
Ignored: test_phylogeny.nb.html
Ignored: test_vertebraspace.nb.html
Ignored: vert_evol.Rproj
Untracked files:
Untracked: Main.html
Untracked: ProcessFCSVfiles.Rmd
Untracked: VertPGLS.html
Untracked: gg_saver.R
Untracked: output/BodyDistribution.pdf
Untracked: output/MasterVert_Measurements.csv
Untracked: output/mean_d_alphaPos_CBL.pdf
Untracked: output/pair_plot.pdf
Untracked: output/plot_example_data_figure.pdf
Untracked: output/stats_table.rtf
Untracked: plot_fits_and_summary.Rmd
Untracked: summarize_vert_meas.html
Untracked: testtree.csv
Untracked: vert_tree.csv
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 7983950 | Eric Tytell | 2022-04-11 | wflow_git_commit(c(“analysis/about.Rmd”, “analysis/index.Rmd”, |
| Rmd | b9f4976 | Eric Tytell | 2021-12-30 | Start workflowr project. |
Dana Baxter\(^1\) | Karly E. Cohen\(^3\) | Cassandra M. Donatelli\(^2\) | Eric D. Tytell\(^1\)
\(^1\)Tufts University, Department of Biology \(^2\)University of Ottawa, Department of Biology \(^3\)University of Washington, Friday Harbor Labs
Submitted to Ecology and Evolution April 12, 2022.
Fishes have repeatedly evolved characteristic body shapes depending on how close they live to the substrate. Pelagic fishes live and feed in open water and typically have narrow, streamlined body shapes; benthic and demersal fishes live in close association with the substrate and often have deeper bodies. These shape differences are often associated with behavioral differences: pelagic fishes swim nearly constantly, demersal fishes tend to maneuver near the substrate, and fully benthic fishes often lie in wait on the substrate. We hypothesized that these morphological and behavioral differences would be reflected in the mechanical properties of the vertebral column, with pelagic fishes having stiffer vertebral columns than the others. The vertebrae of bony fishes are composed of two cones connected by a foramen, which is filled by the notochord. Since the notochord is much more flexible than the bony vertebral centra, we predicted that pelagic fishes would have narrower foramina or shallower cones, which would reduce the amount of flexible notochord, and should cause them to have stiffer vertebral columns to support continuous swimming behavior. To test this hypothesis, we examined differences in vertebral morphology in 55 species from the three habitat categories by measuring vertebrae along the length of the body of each fish based on micro-computed tomography scans. From these scans, six vertebral features were measured: notochordal foramen diameter, centrum body length, and the cone angles and diameters for the anterior and posterior vertebral cones. Using a phylogenetic generalized least squares (PGLS) analysis to control for phylogeny, we found that notochordal foramen diameter and posterior cone angle differed significantly among species from benthic, demersal, and pelagic habitats. Benthic species had significantly larger posterior cone angles than other fishes, while pelagic species had significantly smaller notochordal foramen diameters. Thus, morphological differences in the internal shape of the vertebrae of fishes are consistent with a stiffer vertebral column in pelagic fishes, which could support the behavioral differences across benthic, demersal, and pelagic species.