Landscape genomics reveals signals of climate adaptation and a cryptic lineage in Arthropodium fimbriatum

Habitat loss and fragmentation are critical threats to biodiversity. Consequent decreases in population size and connectivity can impact genetic diversity and, thus, future adaptability and resilience to environmental change. Understanding landscape patterns of genetic diversity, including patterns of adaptive variation, can assist in developing conservation strategies that maximise population persistence and adaptability in the face of environmental change. Using a reduced-representation genomic approach, we investigated genetic diversity, structure, and adaptive variation across an aridity gradient in the woodland forb Arthropodium fimbriatum. Moderate levels of genetic diversity (HS = 0.14 – 0.23) were found in all 13 sampled provenances. Inbreeding varied among provenances (FIS = 0.08 – 0.42) but was not associated with estimated population size. Four genetic clusters were identified, including one highly differentiated cluster. Higher pairwise FST (0.23 – 0.42) between the three provenances of this cluster and the remaining 10 provenances (pairwise FST between 10 provenances 0.02 – 0.32) suggested two highly divergent lineages or potentially a cryptic species. After excluding the three highly differentiated populations, outlier and genotype-environment association analysis identified 275 putatively adaptive loci suggesting genomic signatures of adaptation in A. fimbriatum is primarily associated with changes in aridity. Combined, these results suggest that all provenances have conservation value, contributing to the maintenance of genetic diversity and adaptive variation in this species. The uncovering of a potential cryptic taxon highlights the power of genomics approaches in conservation genetics and the importance of understanding the role of landscape variation shaping genetic variation to effectively define conservation management units in an era of rapid biodiversity decline.