PT  - JOURNAL ARTICLE
AU  - Hirzi Luqman
AU  - Alex Widmer
AU  - Simone Fior
AU  - Daniel Wegmann
TI  - Identifying loci under selection via explicit demographic models
AID  - 10.1101/2020.07.20.211581
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.07.20.211581
4099  - http://biorxiv.org/content/early/2020/07/21/2020.07.20.211581.short
4100  - http://biorxiv.org/content/early/2020/07/21/2020.07.20.211581.full
AB  - Adaptive genetic variation is a function of both selective and neutral forces. In order to accurately identify adaptive loci, it is hence critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that the genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify Loci under Selection via explicit Demographic models (LSD). Under this framework, signatures of selection are inferred by demographic parameters, rather than through isolated summary statistics, and demographic history is accounted for explicitly. Given that demographic models can incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in dissecting the genomics of local adaptation, by characterising genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via Approximate Bayesian Computation and demonstrate, via simulations, that LSD has high power to identify selected loci across a large range of demographic-selection regimes, including complex demographies, and that the directionality of selection can be inferred accurately for identified candidates. Using the same simulations, we further characterise the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we apply LSD to the detection and characterisation of loci underlying floral guides in Antirrhinum majus, and find consistent results with previous studies.Competing Interest StatementThe authors have declared no competing interest.