Automated ISSR Fingerprinting Is a Cost-Effective Way to Assess Genetic Diversity and Taxonomic Differentiation—A Case Study on the Encephalartos eugene-maraisii Species Complex

Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding the conservation of species. The precision and resolution of high throughput sequencing technologies provide valuable insights to aid conservation decisions, but these technologies are often financially unfeasible or unavailable in resource constrained countries. Inter-Simple Sequence Repeat (ISSR) markers, when combined with sensitive automated detection systems, provide a simple, cheap means to investigate genetic diversity and discriminate closely related species. Here, we apply this technology to assess genetic diversity and taxonomic delimitation in the Encephalartos eugene-maraisii species complex, a highly threatened, taxonomically dubious group of cycads in South Africa. Our analyses support the taxonomic singularity of E. dyerianus, E. dolomiticus and E. eugene-maraisii. Relationships between E. nubimontanus and E. cupidus remain uncertain. E. middelburgensis samples showed no clustering but had poor amplification success. This study demonstrates the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries, and we make recommendations as to how this methodology can be effectively implemented.