Beyond SNPs: how to detect selection on transposable element insertions

Summary Identifying the genomic basis of adaptive evolution is a growing field of research. The number of statistics and methodologies aimed at identifying adaptive loci continues to increase. Moreover, the availability of whole-genome sequences allows us to make inferences of selection on a diverse set of species. However, detecting footprints of selection has mostly been restricted to one type of genomic variation: single-nucleotide polymorphisms (SNPs). Other genomic variants such as transposable element (TE) insertions that are likely to contribute to adaptive evolution have been largely ignored. Here, we present an overview of different approaches that can be used to infer selection acting on TE insertions. We focused on five main approaches: (i) DNA sequence conservation analysis; (ii) selection on linked polymorphisms; (iii) environmental association analyses; (iv) estimation of allele age; and (v) functional assays to identify the molecular and fitness effects. For each of these five approaches, we focus on the latest developments and illustrate them with recent examples from the literature. We also identify the data requirements and the limitations associated with the different methodologies. We conclude that the availability of third-generation sequencing technologies should allow for a systematic analysis of TE insertions as sources of adaptive mutations. Incorporating the knowledge of the role of TE insertions in adaptive evolution will allow us to get a more complete picture of the adaptive process.