Low genetic differentiation among morphologically distinct cycas species informs the delineation of conservation management units

BACKGROUND AND AIMS: Cycads are the most threatened group of seed plants, with isolation and habitat fragmentation among the primary drivers of species decline. Understanding how genetic diversity is distributed across populations is crucial for informing conservation management and identifying genetically vulnerable populations that require conservation attention. METHODS: Here we investigated the genetic diversity and structure of two endemic Australian species of significant conservation concern, Cycas armstrongii and C. maconochiei subsp. maconochiei. Two hundred and thirty-six individuals were sampled from 26 populations across their native ranges, including a presumed putative hybrid population (C. armstrongii × maconochiei), utilizing next-generation sequencing in the form of restriction site-associated DNA sequencing (RADseq). KEY RESULTS: Our results suggested low levels of genetic diversity in both taxa (C. armstrongii, He ≤ 0.038; C. maconochiei subsp. maconochiei, He ≤ 0.061) and no evidence for inbreeding (mean GIS -0.143 and -0.153, respectively). Analysis of molecular variance indicated minimal genetic differentiation between populations (2.41 %) and between taxa (1.81 %). However, pairwise FST values and the Mantel test revealed significant isolation by distance (r = 0.606, P < 0.0001). Discriminant analysis of principal components and popuatlion STRUCTURE analysis indicated admixture, between populations. Morphological traits, principal component and environmental analysis based on seven traits found significant differentiation in five characters, four of which were environmentally linked. The results showed no clear signal of interspecific hybridization for either taxon. CONCLUSIONS: These findings indicate C. armstrongii and C. maconochiei subsp. maconochiei likely represent a morphologically variable species. In addition to updating the threat assessment, we recommend: (1) formally recognizing genetically depauperate or geographically isolated populations (e.g. Tiwi Islands) as conservation management units (CMUs); (2) establishing new ex situ assurance collections for at-risk CMUs; and (3) implementing assisted gene flow among genetically compatible populations to enhance adaptive potential. These actions will ensure conservation strategies are tailored to evolutionary and ecological units.