RADseq

Manuel Luján, Jian Liu, Nathalie Nagalingum, California Academy of Sciences, Kunming Institute of Botany, Chinese Academy of Sciences

Rare plant species exhibit narrow geographic distribution and are often considered to have smaller populations and lower levels of genetic diversity compared to their more common relatives. The genus Cycas includes about 117 species, 32 of which are native to Australia and 20 occur only in the subtropical and tropical regions of Queensland. Most of the Queensland species of Cycas are known from only a handful of localities and their population characteristics remain to be investigated. Our main objective was to assess genetic diversity and population size of the rare species of Cycas and compare it them the more widely distributed species. We used RADseq to generate genomic data to estimate percentage of polymorphic loci (P), heterozygosity (Ho and He) and nucleotide diversity (π), and footage from unmanned aerial vehicles to estimate populations size. Our preliminary results suggest that rare species (C. terryana) have levels of genetic diversity that are comparable to more common species (C. ophiolitica and C. media). Population size of rare species (e. g. C. tuckeri) tend to be smaller than more common species (C. cairnsiana). Given that Cycas are long-lived plants, rare and small populations constituted by old plants, may be maintaining ancestral allelic variants from previously more widespread and common populations. Further study considering the populations demographic structure are needed to better understand this pattern and inform conservation efforts.

Date Recorded: 
Wednesday, September 11, 2019

Dr. Sally M Chambers, Marie Selby Botanical Gardens

Next generation sequencing technologies have rapidly developed over the past decade, providing new avenues for scientists working on non-model organisms to study patterns at the genome level. Techniques can be used to drastically simplify a complex genome and multiplex samples, which help make these sequencing platforms more cost effective than traditional methods when standardized by the amount of data generated. However, a number of factors need to be taken into account when developing a next-generation sequencing project, including genome size and complexity. Ferns are well known for having large and complex genomes, as many lineages are characterized by reticulate evolution. This produces species complexes that contain multiple hybrid individuals. Based on recent experiences in developing a study to resolve relationships within a species complex of North American Dryopteris, the applicability of double-digest RAD sequencing proved difficult. Lessons learned from this experience will be shared in order to assist others that would like to apply RADseq technologies to taxa with large or complex genomes.

Contributing Author(s): 
Date Recorded: 
Tuesday, September 10, 2019