From morphometrics to SNPs: reconstructing phylogenetic relationships in Calligonum junceum and Calligonum zakirovii under aridification

We assess whether Calligonum zakirovii and C. junceum—two representative taxa of Central Asian Calligonum—constitute separate species or a single polymorphic lineage. To do so, we integrated fruit morphometrics, nuclear ITS and six plastid loci (psbA-trnH, psbM-ycf6, rpl32-trnL, trnL-F, rbcL, and matK), 17 SSR markers, and genome-wide SNPs. SSR markers partitioned most variation within populations, whereas Sanger-sequenced loci and whole-genome SNP data recovered all samples as a single lineage. Molecular clock dating of the ITS dataset estimates the most recent common ancestor of the two taxa at ~ 2.96 Ma (95% HPD: 1.28–4.59 Ma). Together, morphological and multilocus genomic evidence indicates that C. zakirovii and C. junceum form a genetically cohesive, polymorphic complex that may represent divergent populations within a single species rather than two fully distinct taxa. This result is consistent with Pliocene–Pleistocene aridification and repeated habitat fragmentation in Central Asia, which can preserve ancestral variation and slow lineage separation.