genomic methods

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