Incomplete lineage sorting and secondary admixture results in the paraphyly of Lecanorchis cerina, L. suginoana, and L. thalassica (Orchidaceae) in Taiwan

Inferring the evolutionary history of a group of closely related species can be challenging. Genetic diversity, structure, and multilocus phylogeny were studied to shed light on the evolutionary processes that shapes diversity in three closely related Lecanorchis species (L. cerina, L. suginoana, and L. thalassica). In this study, we surveyed nucleotide and genetic variation, respectively, using nuclear internal transcribed spacer 1 (nrITS1) and amplified fragment length polymorphism (AFLP) in individuals of Lecanorchis species. Both nrITS1 parsimonious and AFLP neighbor-joining trees showed paraphyly indicated that lineage sorting for these species may be incomplete. ITS1 haplotype sharing was found within L. cerina, within L. suginoana, and between L. suginoana and L. thalassica. Higher AFLP diversity was observed in L. cerina than that in L. suginoana and in L. thalassica, indicating larger population size in L. cerina. Two contrasting patterns of AFLP genetic differentiation between geographic neighbors relative to geographic distant populations were observed. Two major AFLP genetic components were found in individuals of Lecanorchis species examined. Individuals of L. cerina and of L. thalassica were classified into either component with high probabilities. Most individuals of L. suginoana were classified into one of these components, but two individuals showed apparent admixture of these components. The evidence of paraphyly, haplotype sharing, higher L. cerina diversity, sharing and admixture of genetic components, and the contrasting patterns of genetic differentiation suggest that both incomplete lineage sorting and secondary gene flow could have occurred in these closely related species, though at different temporal scale.