sequencing

Kyle L. Gunther, Sula Vanderplank, Jon P. Rebman, Andres Orduño Cruz, & Lluvia Flores-Rentería, San Diego State University, San Diego Natural History Museum, San Diego Zoo Global, Centro de Investigaciones Biológicas del Noroeste

California and the Baja peninsula are home to high levels of floral abundance, diversity, and endemism. Much of this region is part of a biodiversity hotspot and therefore a conservation priority. The Mission Manzanita (Xylococcus bicolor) is endemic to this area, an ecologically and ethnobotanically important shrub, and the sole member of a monotypic genus within Ericaceae. Xylococcus bicolor is narrowly distributed from the middle of Baja California to the Los Angeles area, and has been predicted to experience up to 88% habitat loss due to climate change and development. However, little is known about its population structure, demographics, and genetic diversity, which may be useful information for conservation purposes. In order to fill this gap in knowledge, we are studying these aspects from a genetic perspective. Using a genome skimming technique to reveal thousands of single nucleotide polymorphisms, we are analyzing the population structure, genetic diversity, gene flow, and effective population sizes across the X. bicolor distribution. Preliminary results suggest the presence of intraspecific divergence and population structure, while niche models show loss of suitable habitat using climate change scenarios. We hope our study will provide useful information for land management and conservation decisions.

Date Recorded: 
Wednesday, September 11, 2019

Dr. Aryn Wilder, Institute for Conservation Research, San Diego Zoo Global

Human activity has left species worldwide on the brink of extinction, where they are susceptible to the loss of genetic diversity and the accumulation of deleterious mutations that reduce adaptive potential and increase extinction risk. The application of modern genomic tools allows us to more accurately assess the conservation status of populations and examine the genetic factors that contribute to extinction. I will present case studies from animal populations where we are applying genomics as a conservation tool. First, we compared genomic characteristics of two closely related white rhino subspecies, the northern white rhino (NWR) which has been driven effectively to extinction, and the southern white rhino which has mounted a remarkable recovery, to provide insight into the potential for restoration of NWR. Second, we are currently generating low-coverage, whole genome sequence data from hundreds of wild and captive Pacific pocket mice. Combined with imputation, low coverage sequencing provides a cost-effective way to infer genotypes across the genome for a large number of individuals, providing statistical power needed to measure the genetic basis of fitness-related traits. The advancement and increasing cost-effectiveness of genomic technologies will continue to provide valuable insights applicable to conservation across taxa.

Date Recorded: 
Tuesday, September 10, 2019