Genomic fingerprinting versus nuclear gene sequences: A comparative approach for studying the Lupinus montanus (Fabaceae) species complex

- Lupinus montanus is a widespread species complex of Mexico and Central America.
- ISSR and COS & ETS were tested for clarifying taxon delimitation.
- The tree topologies were congruent for both ISSR and nuclear gene sequence analysis.
- ISSR were more variable than nuclear gene sequences.

The taxonomy and systematics of Mexican Lupinus are lacking in resolution, because the taxa are distinguished using a few minor and inconsistent morphological characters. The use of molecular markers can contribute to resolving such issues. In this study, we focused on two varieties of the Lupinus montanus complex (Fabaceae) in Mexico, L. montanus subsp. montanus var. montanus and L. montanus subsp. montanus var. nelsonii, and aimed to determine the most suitable genetic markers for clarifying taxon delimitation based on morphology. We compared hypervariable Inter Simple Sequence Repeats (ISSR) to gene sequences (External Transcribed Spacer (ETS) and Conserved Orthologous Sets (COS)).Distance analysis (ISSR) and maximum likelihood (ETS + COS) generated congruent results but with much more variability and resolution for ISSR. These data confirm the potential of ISSR for working at low taxonomic level and their reliability compared to that of gene sequences.