Population genetics and ecological niche modelling shed light on species boundaries and evolutionary history of Aconitum pendulum and A. flavum

As species are fundamental units of evolutionary biology research, accurate species delimitation plays a crucial role in current biodiversity management. The Qinghai-Tibet Plateau (QTP) comprises one of the global biodiversity hotspots, and plant speciation and its evolutionary history in this region still need much research. Aconitum pendulum and A. flavum (Ranuculaceae) are mainly distributed in the QTP and its adjacent regions. The two species have extremely similar morphological characteristics, and their evolutionary relationship is still controversial. In this study, we collected 244 individuals in 14 populations from the main distribution areas of the two species. Genome-wide single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS) of A. pendulum and A. flavum were obtained to decipher the taxonomic delimitation and explore the evolutionary history. We performed neighbor-joining (NJ), PCA, structure, and niche overlap analyses. None of them support that A. pendulum and A. flavum can be considered as two separate species. In addition, the genetic difference between species is less than that among populations. We propose merging the two species into one. We also found that the genetic difference between the two species was not associated with morphological species or geographic distance. Gene flow and genetic drift may play a crucial role in weakening the correlation between genetic distance and geographical distance. A bottleneck effect occurred in the two species during the last glacial maximum. Based on the Maxent and Stairway Plot results, we inferred that A. pendulum and A. flavum still had large survival ranges during the LGM, similar to other cold-tolerant species. Furthermore, human activity, such as overexploitation causing habitat fragmentation, might be one of the factors that threat to the survival of A. pendulum and A. flavum in the current period.