DNA Barcoding Africa’s Endemic Cycads

Rousseau, Philip; Vorster, P.; Little, Damon P.; Bank, Michelle van der

doi:10.21135/893275389.020

Cited by 1 publication

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“…These individual samples were also unexpectedly clustered with their other species groups in the dendrograms and network analyses (Figure 6; Figure S3). Although the results suggest that these species are genetically indistinguishable from E. hirsutus, this is unlikely since E. hirsutus is phylogenetically distinct from the E. eugene-maraisii complex [86,103]. The behaviour of these samples may instead reflect missing alleles or numerous spurious bands since samples deemed genetically similar to E. hirsutus samples all possess approximately 50 bands, whereas E. hirsutus samples possessed 83 and 73 bands respectively.…”

Section: Structure Analysismentioning

confidence: 82%

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

Murphy,

Barker,

Frisby

2024

Preprint

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Recent technological advancements in conservation genetics and genomics have resulted in diverse tools for aiding 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. Silica dried cycad leaflets were extracted using the Oktopure robot employing Sbeadex chemistry and amplified with fluorescently tagged ISSR primers. Band presence was scored with an ABI 3130 genetic sequencer under three different fluorescence cut-off values. Phenetic analyses were performed in NTSYS software while Bayesian analysis was performed in STRUCTURE, and haplotype network analysis, AMOVA and Tajima’s D statistic was computed with PopART. Our analyses support 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 demonstrated the suitability of automated ISSR fingerprinting as a method for plant conservation studies, especially in resource-constrained countries.

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Section: Structure Analysismentioning

confidence: 82%