Phylogeography of Japanese water crowfoot based on chloroplast DNA haplotypes

Water crowfoot, Ranunculus subgenus Batrachium, are submerged macrophytes in the Ranunculaceae. We aimed to infer the Quaternary history of these aquatic macrophytes in the Japanese archipelago. We studied 212 individuals of three perennial and one annual species from 46 populations covering the entire geographic range and found eight haplotypes based on approximately 1800 bp of four spacers in chloroplast DNA. The relationships among haplotypes were resolved using maximum parsimony and parsimony network analyses. To identify the zones of clear genetic boundaries, Monmonier's algorithm was used. The eight haplotypes were distinguished from adjacent haplotypes by one substitution or indel. Each of the 46 populations was fixed for a single haplotype. Inconsistency between cpDNA haplotypes and Batrachium taxa was found, except in one annual species. The distribution of the haplotypes in perennial species was highly geographically structured. An abrupt genetic change was detected between the Tohoku region and more southerly regions. Since the perennial Batrachium are cold-adapted, this genetic differentiation may be due to historical changes in their distributions caused by Quaternary climatic oscillations: interglacial retreats in colder refugia and glacial range expansions. The single haplotype composition of each population may have been shaped by founder effects during colonization and/or by genetic drift. The interglacial refugial populations must have been small enough to deplete haplotype diversity. Inconsistency between cpDNA haplotypes and Batrachium taxa may be due to incomplete lineage sorting of ancestral polymorphic haplotypes.