ddRADseq

Kristen Hasenstab-Lehman, C. Matt Guilliams, Santa Barbara Botanic Gardens

Dithyrea maritima (Davidson), or beach spectaclepod, is a dune specialist endemic to coastal dunes from central California, United States, to northwestern Baja California, Mexico. Individuals of this perennial herb spread by rhizomes, forming a diffuse colony of ramets, each terminating in rosette of 1 to several fleshy leaves, and a two-chambered fruit (silicle). It is listed on the California Native Plant Society Rare and Endangered Plant Inventory on list 1B.1 and was listed as Threatened under the California Endangered Species Act. Studied occurrences of the self-incompatible D. maritima have low seed set, though manual outcrosses boost seed production. Knowledge of the distribution of genotypes on the landscape is be a critical first step toward any number of recovery actions. In this study, we sample from approximately 30 individuals from each of eleven samplinglocations spanning the range of the taxon from Morro Bay, CA, USA to San Quintín, Baja CA, MX. We used double digestion RADseq to prepare libraries for high-throughput sequencing, assemble the dataset in ipyrad producing 5092 SNPs, and analyze population genomics of the species. We place the observed population genomic patterns into the context of regional biogeography, and conclude with recommendations for managing the species.

Date Recorded: 
Wednesday, September 11, 2019

Cynthia Steiner, Aryn Wilder, Debra Shier and Natalie Calatayud, San Diego Zoo Institute of Conservation Research

Among the main roles of conservation management is to mitigate the negative effect of anthropogenic activities in nature by ensuring the persistence of biodiversity and species in the wild. Conservation geneticists have recently developed a new toolbox of genomic methods to address the management of species in-situ and ex-situ. Among these approaches, the reduce representation or ddRADseq method allows to sample a fraction of the genome-wide genetic variation to estimate population summary statistics and individuals’ relationships for breeding management. The study of the southern mountain yellow-legged frog, an endemic and critically endangered amphibian species from southern California provides importance lessons about the use of ddRADseq in species with large genome size, in terms of quality/quantity of DNA samples required for generating genomic libraries, quality control of restriction enzymes chosen, optimization of parameters in the STACK pipeline for data analysis and selection of criteria for filtering genetic variants.

Date Recorded: 
Tuesday, September 10, 2019