Genomic data support Betula halophila and Betula microphylla as one species and reveal unidirectional introgression from Betula pendula to Betula microphylla

Conservation of rare species faces challenges arising from uncertainties in species recognition, interspecific gene flow and global climate change. Betula microphylla and Betula halophila are endangered species in Xinjiang province, Northwest China, where they occur with the abundant Betula pendula. The species status of B. halophila remains dubious. The extent of gene flow between B. microphylla and B. pendula remain unexplored. Here, we first resolve the identity of B. halophila and then assess the extent of gene flow between B. microphylla and B. pendula using restriction-site associated DNA sequencing (RADseq). We sequenced 40 B. pendula individuals, 40 B. microphylla individuals, one B. halophila individual and seven B. tianshanica individuals. Our molecular analyses show that B. halophila and B. microphylla refer to the same species. STRUCTURE analyses show unidirectional genetic admixture from B. pendula to B. microphylla. The ABBA-BABA test indicates that the genetic admixture reflects introgression rather than incomplete lineage sorting. Furthermore, we identified 233 functional genes within the introgressed regions with eight genes related to salt-tolerance, suggesting the possibility of potential adaptive introgression. Our study shows an urgent need to conserve the genetically pure populations of B. microphylla and to shift conservation efforts from B. halophila to B. microphylla. In addition, ex-situ conservation of B. microphylla and conservation strategies to avoid genetic swamping by B. pendula and B. tianshanica should be implemented.