Collection of Morphological Data
We measured morphological traits to compare the phenotypes and P matrices of pupfish across species and populations. We measured 18 craniofacial traits detailed in Martin et al. (2016) (Figure 2). We specifically focused on craniofacial traits for this study because jaw diversity is the primary axis of diversification in this system and is hypothesized to be adaptive for each specialist’s unique ecological niches (Martin et al., 2017; Hernandez et al., 2018). We measured traits using the program DLTdv8a (Hedrick, 2008), which outputs X and Y coordinates for each landmark and subsequently calculated linear distances from these coordinates. We standardized each cranial trait measurement by performing a linear model with each trait measurement as the response variable and log-transformed standard length as the predictor variable using the lme4 package in R 4.1.1 (Bates et al. 2014, R Core Team, 2021). We extracted the residuals for each individual and used these values in all further analyses.