Deciphering the taxonomical controversies of Rhizophora hybrids using AFLP, plastid and nuclear markers

•15 years of taxonomical controversy between Rhizophora hybrid species was resolved.•AFLP, chloroplast and nuclear markers revealed R. × annamalayana and R. × lamarckii as two separate hybrids.•A low level of genetic diversity was observed among Rhizophora genotypes.•R. apiculata was found to be the maternal species of R. × annamalayana.

Natural hybridization is ubiquitous in flowering plants and it plays a crucial role in plant evolution and diversification. Among mangroves, the tribe Rhizophoreae (Rhizophoraceae) includes the largest taxonomic congregation exclusively of mangroves. However, the systemic distinction between two hybrids Rhizophora × annamalayana and Rhizophora × lamarckii remains imprecise, and their parental species are still uncertain. In the present study, AFLP analysis of Rhizophora genotypes namely Rhizophora apiculata, Rhizophora mucronata, Rhizophora stylosa, R. × lamarckii and R. × annamalayana revealed 46.65% polymorphic bands. Jaccard similarity coefficient, Nei’s genetic diversity analysis (0.1851 ± 0.19) and Shannon’s diversity index (0.2790 ± 0.27) revealed low levels of genetic diversity among Rhizophora individuals. The cluster and phylogenetic analyses of AFLP and DNA sequence data evidently untangled the taxonomical controversy between R. × annamalayana and R. × lamarckii and demonstrated that the hybrids are simple F1s and there is no trace of backcrossing or introgression with their parental species. R. apiculata was found to be the maternal species of R. × annamalayana. Chloroplast (matK, rbcL) and nuclear (ITS) markers further substantiated the results of AFLP analysis.