DOI: 10.5061/dryad.tx95x6b6k
title: Adaptive radiation despite conserved modularity patterns in San Salvador Island Cyprinodon pupfishes and their hybrids

description: Adaptive radiations are striking examples of rapid speciation along
 ecological lines. In adaptive radiations, fast rates of lineage
 diversification often pair with rapid rates of morphological
 diversification. Such diversification has often been documented through
 the lens of ecological drivers, overlooking the intrinsic structural
 constraints that may also have a key role in configuring patterns of trait
 diversification. Covariation within and between traits has been
 hypothesized to govern the axes of trait evolution, either by increasing
 the degree of covariation between traits (i.e., integration), which
 promotes morphological coordination, or by strengthening the degree of
 covariation within traits (i.e., modularity), which allows organisms to
 explore novel trait combinations and different regions of morphospace.
 Here, we study the modularity of the skull within an adaptive radiation of
 pupfishes that is endemic to San Salvador Island, Bahamas. This radiation
 exhibits divergent craniofacial morphologies, including generalist,
 snail-eating specialist, and scale-eating specialist species. We assessed
 morphological disparity, integration strength, and modularity patterns
 across the sympatric San Salvador Island pupfish radiation, lab-reared
 hybrids, and closely related outgroup species. Our findings revealed an
 unexpected uniformity in the pattern of modularity across diverse species,
 supporting a five-module functional hypothesis comprising the oral jaw,
 pharyngeal jaw, neurocranium, hyoid apparatus, and hyomandibula. Despite
 this conserved modularity pattern, all species exhibited weak but
 significantly varying strengths of overall between-module integration and
 significant disparity across all cranial regions. Our results suggest
 rapid morphological diversification can occur even with conserved patterns
 of modularity. We propose that broadscale patterns of modularity are more
 conserved while between-module associations are more evolvable between
 species.
description: Adaptive radiation despite conserved modularity patterns in San Salvador
 Island Cyprinodon pupfishes and their hybrids
 [https://doi.org/10.5061/dryad.tx95x6b6k](https://doi.org/10.5061/dryad.tx95x6b6k) This dataset includes an R script and 3D landmark data used to analyze the integration and modularity in the skull of pupfish species from adaptive radiation on San Salvador Island, Bahamas. The study investigates conserved modularity patterns and varying integration strengths in different cranial regions across species. Description of file and data structure Files: 1. **R Script (`158Gloco.R`)**: Contains code for loading and processing landmark data, defining hypotheses for skull modularity, running integration tests, testing morphological disparity, and plotting figures. 2. **3D Landmark Data (`landmark.zip`)**: Contains the original checkpoint file with digitized 3D cranial landmarks used to assess skull morphology. Can be viewed as a .txt file. The digitized landmarks are located under the [Landmarks] section. File Descriptions * **1. `158Gloco.R`**: **Sections**: 1. **Local superimposition**: This part includes code for the superimposition of landmarks by bones 2. **Model Hypotheses**: This section categorizes landmarks into various hypotheses related to skull patterns of modularity (oral jaw, neurocranium, pharyngeal jaw, etc.). We further test these hypotheses with covariance ratio (CR) and graphical modeling. 3. **Integration Tests**: We assessed integration between and within different cranial bones using integration.test and integration.Vrel. 4. **Network plot**: We visualized the patterns of integration using a custom network plot function. * **2. Landmark Data** * **Landmarks**: 3D coordinates (x, y, z) for each cranial landmark. * **Units**: Landmark coordinates are scaled to 0.0001mm per unit. * **Bones**: The list of landmarks can be referred to in the main text or from the R code. The landmark set focuses on the oral jaw, pharyngeal jaw, neurocranium, ceratohyal, urohyal, and hyomandibula. * **Species Labels**: Each .ckpt file is labeled by species name (e.g., *Cyprinodon variegatus*, *Cyprinodon desquamator*).