New approaches for the conservation genomics of the genus Cycas L. in Australia
Clugston, James Andrew Ronald
Cycad species exist as small fragmented populations, therefore understanding their genetic variation is imperative for their conservation to ensure their long-term survival. Genetic data plays a fundamental role in identifying genotypes and detecting populations with the highest genetic diversity. This project uses next generation sequencing (NGS) and restriction associated DNA sequencing (RADseq) to identify thousands of genome-wide polymorphisms from populations of selected cycad species from the Northern Territory, Australia, namely: Cycas armstrongii, Cycas calcicola, Cycas maconochiei ssp. maconochiei and the interspecific hybrid C. armstrongii x maconochiei. RADseq was used to determine intra- and interspecific genetic variation in populations, verify the putative hybrid, recognize populations of conservation priority and determine if botanic garden collections currently represent the genetic diversity inherent in the wild. Cycas calcicola showed very low levels of genetic diversity and high inbreeding, and although there was significant geographic partitioning between populations in the Katherine and Litchfield National Park regions, which correlated with genetic differentiation. Additionally, the results showed that C. calcicola was not genetically, well represented in ex-situ collections. The genomic diversity of Cycas armstrongii, C. maconochiei ssp. maconochiei and C. armstrongii x maconochiei differs from that of C. calcicola and shows very low levels of genetic diversity yet generally with lower levels of inbreeding. The results show little genetic distance between Cycas armstrongii and C. maconochiei ssp. maconochiei, the most likely explanation is that they represent morphological extremes of a single species. The results from RADseq have far reaching significance for the conservation of cycads. In the case of C. calcicola, a far more structured acquisition of genetic material will be required if the full genetic diversity of this species is to be preserved in ex-situ collections.