Insights into the aridification history of Central Asian Mountains and international conservation strategy from the endangered wild apple tree

Abstract Aim Evolutionary processes of mountain plants in arid lands remain poorly understood. Here, we investigate population genomics of the endangered wild apple tree to interpret the effects of long‐term aridification on plant diversification and demographical history in Central Asian Mountains. Location The Tianshan Mountains, spanning north‐western China, Kazakhstan, Kyrgyzstan and Tajikistan. Taxon Malus sieversii (Rosaceae) Methods Using genome‐wide single nucleotide polymorphisms, we assessed genetic diversity and genetic structure of 15 populations across the species' range. Demographical history was simulated with approximate Bayesian computation and species distribution modelling. We used a general linear model to identify key environmental factors affecting population genetic diversity and structure. Results We separated the 15 populations into three groups: the eastern group of western Junggar Mountains in China; the central group of the Ili Valley, the Talas Alatau Mountains in Kazakhstan and Kyrgyzstan; and the western group of Tajikistan and the Dzungarian Alatau in Kazakhstan. Central populations had higher genetic diversity and effective population size than eastern and western populations. The three groups split at the late Miocene and subsequently experienced extensive admixture. We detected a significant pattern of isolation by distance, but not isolation by environment, among these populations. Population genetic diversity was significantly associated with longitudinal and current environmental gradients. Main conclusions Long‐term aridification promoted distribution fragmentation and plant lineage divergence of relict broad‐leaved forests in Central Asian Mountains. Both geographical isolation and environmental heterogeneity shaped spatial patterns in genetic variation among M. sieversii populations. To maintain genetic integrity, we propose the establishment of an international network for the conservation of this endangered wild apple tree.