Identifying the Degree of Gene Reuse During Repeated Adaptation

The degree or extent of gene reuse during repeated adaptation offers key insights into the genomic constraints on evolution. Although many studies have identified signs of genomic repeatability, a thorough synthesis of methods for detecting gene reuse and estimating its extent is missing. In this review, we first propose a simple framework for studies aimed at identifying gene reuse during repeated adaptation using genomic data. Next, we examine existing approaches to (i) detect gene set overlap, perform significance testing, and perform multivariate dimensionality reduction, (ii) distinguish between gene and allele reuse while emphasising methods for detecting allele reuse, (iii) explore models to identify the mechanisms behind repeated adaptation, and (iv) address issues and potential solutions to differentiate true gene reuse from methodological artifacts. Our review highlights standardised methods developed using genomic data to identify gene reuse. We also note that, although few studies quantify allele reuse, conducting such analyses is essential because it adds a more detailed layer to predicting evolutionary paths. Finally, several strategies can be used to cross-validate signals of gene reuse. These should be applied to confirm true positives, as biological and methodological artifacts can bias predictions. By synthesizing current methods and outlining a robust analytical framework, we provide a roadmap for enhancing the accuracy and reliability of gene reuse detection in adaptive evolution.