Phenotypic plasticity drives local adaptation by disrupting a genetically integrated jaw apparatus in Trinidadian guppies

Consistently across clades researchers find a high degree of covariation in the shape of disparate elements within the same individual, a pattern known as morphological integration. Although integration can help to maintain functionality of multi-component systems, it can also constrain long-term evolution. On shorter time scales, morphology is often shaped by plastic environmental responses, however, it remains an open question whether plasticity is constrained by the patterns of morphological integration that emerge over longer evolutionary time scales. Here we ask whether an incipient adaptive trophic divergence among Trinidadian guppies displays similar patterns of covariation between benthic and limnetic populations that are either reared in a common lab environment or sampled from wild populations. We perform geometric morphometric analysis (n=83) on the premaxilla, dentary, anguloarticular, and lower pharyngeal jaw, and find that morphology correlates with trophic niche in both l..., , # Data for \"Phenotypic plasticity drives local adaptation by disrupting a genetically integrated jaw apparatus in Trinidadian guppies\"

[Access this dataset on Dryad](https://doi.org/10.5061/dryad.p8cz8wb54)

Our analysis includes four geometric morphometric analyses, as well as an integration analysis. This is reflected in the folder structure, with each of these five analyses having their own folder.

To run any of the codes, you must first install all required packages in R (below). Then you set the working directory as appropriate. After this, the code should run as normal.

## Description of the data and file structure

All data listed below is contained in a single compressed file called \"DataAndCode.zip\"

Each of the four geometric morphometric analysis folders are named after the bone that they examine; Anguloarticular, dentary, lower pharyngeal jaw, and premaxilla. Within each of these folders is an R code that runs the analysis, a .PLY file of the focal bone that is used for v...,