DOI: 10.5061/dryad.np5hqc00h
title: Empirical data for: Extending phylogenetic regression models for comparing within-species patterns across the Tree of Life

description: Biologists use phylogenetic comparative methods to characterize
 macroevolutionary trends of phenotypic change across species.
 Within-species variation can complicate such investigations, and
 procedures incorporating nonstructured (random) intraspecific variation
 have been developed. However, intraspecific variation can also be
 structured (sex-specific differences, allometric trends), and biologists
 often wish to compare such intraspecific patterns across taxa.
 Unfortunately, current analytical approaches cannot interrogate
 within-species patterns while simultaneously accounting for phylogenetic
 nonindependence. Thus, deciphering how intraspecific trends evolve remains
 a challenge. We introduce an extended phylogenetic generalized least
 squares (E-PGLS) procedure which facilitates comparisons of within-species
 patterns across species while accounting for phylogenetic nonindependence.
 Our method uses an expanded phylogenetic covariance matrix, a hierarchical
 linear model, and permutation methods to obtain empirical sampling
 distributions and effect sizes for model effects that can evaluate
 differences in intraspecific trends across species for both univariate and
 multivariate data while conditioning them on the phylogeny. The method has
 appropriate statistical properties and obtains evolutionary covariance
 estimates that reflect those from existing approaches for nonstructured
 (random) intraspecific variation. Additionally, E-PGLS can detect
 differences in structured intraspecific patterns across species when such
 trends are present. Thus, E-PGLS extends the reach of phylogenetic
 comparative methods into the intraspecific comparative realm, by providing
 the ability to evaluate within-species trends across species while
 simultaneously accounting for shared evolutionary history.
description: Specimens were obtained from museum collections (from the
 University of Michigan Museum of Zoology and the Museum of Southwestern
 Biology) containing a large number of males and females for each species.
 A total of 969 individuals representing both males and females from each
 of the seven species were used in this example.  The sample sizes ranged
 from 75 to 239 individuals per species (with a mean of 138 individuals per
 species).  An average of 69 individuals for each Species X Sex combination
 were measured (range: 35 - 122).  All specimens were
 imaged using either a Nikon D90 digital camera (MSB) or a Panasonic
 DC-GX850 digital camera (UMMZ), and from each, the locations of 12
 landmarks and 74 semilandmarks were then digitized using the digitizing
 software for `R`, `Steromorph`, version 1.6.5. The 74 semilandmarks were
 sampled from Bézier curves digitized on images, rather than points.
  Geometric morphometric methods were then used to obtain body shape
 information. Specifically, generalized Procrustes analysis was performed
 to eliminate non-shape variation, where semilandmarks were slid based on
 minimizing bending energy. Next, the resulting Procrustes residuals were
 subjected to a principal components analysis, and the first 40 PCs (which
 together represented 99.4% of the total shape variation), were retained,
 and treated as a set of shape variables for all subsequent statistical
 analyses. All digitizing and data analysis was
 performed in R, using the packages: geomorph, RRPP, and Stereomorph. The
 fish phylogeny was obtained from the R-package Fishtree.
description: # Data from: Extended phylogenetic regression models for comparing
 within-species patterns across the Tree of Life ## General Information 1.
 Author Information Corresponding Investigator Name: Dean C. Adams
 Institution: Iowa State University, Ames, Iowa Co-investigator 1 Name:
 Michael L. Collyer Institution: Chatham University, Pittsburgh,
 Pennsylvania 2. Recommended citation for this dataset: Adams and Collyer
 (2024), Data from: Extended phylogenetic regression models for comparing
 within-species patterns across the tree of life. Dryad Digital
 Repository.  ## DATA & FILE OVERVIEW 1. Description of dataset A total
 of 12 landmarks and 74 semilandmarks were digitized from lateral images of
 adult pupfish and were digitized using the digitizing software for `R`,
 `Steromorph`, version 1.6.5. The 74 semilandmarks were sampled from Bzier
 curves digitized on images, rather than points. 1. File List: File 1 Name:
 pupfishGM.filtered.Rdata File 1 Description: Rdata file containing all
 landmark data and specimen information File 2 Name: PupFishExample-DRYAD.R
 (hosted on Zenodo) File 2 R script for obtaining phylogeny from Fishtree,
 and performing all analyses. ## DATA-SPECIFIC INFORMATION FOR:
 pupfishGM.filtered.Rdata The file contains a list 'gdf2' with
 the following components: * coords: Procrustes-aligned landmark
 coordinates for 969 specimens (12 landmarks + 74 semilandmarks optimized
 using minimum bending energy) * Csize: the centroid size for each specimen
 * Sex: a factor designating the sex of each specimen * Species: a factor
 designating the species to which each specimen belongs * Population: a
 factor designating the population from which each specimen was obtained *
 Sample: a factor designating the sample for each specimen