ajdmarques/Pcultripes_v0.1.0: Pcultripes_Release

Marques, A.J.D., Hanson, J.O., Camacho-Sanchez, M. et al. Range-wide genomic scans and tests for selection identify non-neutral spatial patterns of genetic variation in a non-model amphibian species (Pelobates cultripes). Conserv Genet (2022). https://doi.org/10.1007/s10592-021-01425-3

Adaptive genetic diversity is a key factor in conservation planning as it relates to the evolutionary potential of populations and their responses to environmental change. Developments in landscape genomics have fostered a proliferation of tests for selection that aim to identify candidate adaptive markers in natural populations. However, these tests rely on different assumptions and may produce contrasting results. Here we applied six tests for selection in a range-wide genomic scan of an Iberian amphibian, Pelobates cultripes, which shows spatially structured genetic variation across its range, encompassing different bioclimatic zones. As a cursory scan for selection, one test identified candidate markers that describe a pattern of putatively adaptive genetic variation, highlighting coastal Atlantic localities as exhibiting putatively non-neutral patterns of genetic variation. While generalized genomic scans for selection in non-model species have limitations, exploratory searches can highlight areas to guide subsequent hypothesis-driven studies and conservation efforts.

Code for analysis and figures is available in code. Raw data with DarTseq genotypes and sample metadata are available in data/raw. Intermediate results from scripts are stored in data/intermediate. Final outputs and figures are saved in data/final.

This version includes the raw data and initial scripts used in analysis originally completed in late 2018. Ongoing revisions will be added as of 2022 to ensure that the scripts are compatible with updated R packages and software.