Widespread gene flow from Betula tianshanica and Betula pendula to Betula microphylla: a rare species from Northwest China

Understanding the genomic composition of endangered species across its populations is important for conservation and management. Betula microphylla, an endangered species in Northwest China, grows in close proximity to B. tianshanica and B. pendula. However, whether populations of B. microphylla are genetically distinct or introgressed from B. tianshanica and B. pendula remains less clear. Here, we included restriction-site associated DNA (RAD) data for 135 individuals of B. microphylla, B. tianshanica, and B. pendula with RAD data of 87 individuals generated in this study. PCA results identify three genetic clusters, corresponding to B. pendula, B. tianshanica, and B. microphylla. ADMIXTURE analyses show two admixed populations of B. microphylla from B. tianshanica and one admixed population from B. pendula. ABBA-BABA test indicates that the genetic admixture in B. microphylla reflects significant signals of introgression from B. tianshanica and B. pendula. Furthermore, we identified 378 functional genes within the introgressed regions with eight genes related to environmental stress. Conservation strategies to protect genetically distinct populations of B. microphylla from genetic swamping by B. pendula need to be implemented. In addition, ex situ conservation of B. microphylla and conservation efforts towards B. tianshanica should be taken into consideration as the two may represent sister taxa or different subspecies.