Using genomic data and novel analytical tools to understand Mountain Lion demographic history and enhance management of extant populations.

Campus: UCSC, UCB

PI(s): Shapiro, Wilmers

Student researcher: Nedda Saremi

Background: Mountain lions are affected by habitat fragmentation and other impacts of human population growth, including rodenticide use, hunting, and competition for resources. We propose a conservation genomics approach to address the following questions:

• How has habitat fragmentation affected gene flow? Are some barriers to gene flow more or less permeable than others? How should we devise and implement plans to protect corridors, and where should those corridors be?
• What is the genomic influence of rodenticide? Is there evidence of selection in resistance genes in high (LA) versus low (SC/Monterey) rodenticide exposure areas?
• What are the genomic consequences of long-term inbreeding and small Ne in more isolated (LA) compared to large and connected (SC/Monterey) populations? [in addition to the within-California analysis, we propose to compare the LA population to a genome sequenced from the FL population prior to introduction of panthers from TX]

Approach: We will finish the mountain lion genome during the next several months, after which we will focus on generating the data required to describe the connectivity between populations across the state. Next, we will assess high-level genomic consequences of inbreeding, by sequencing a transcriptome to annotate the genome, which will make it feasible to identify genes under selection due to different environmental challenges, including rodenticides. We will extract DNA and prepare libraries for 120 modern and 15-20 historic (from collections at MVZ Berkeley). We will sequence low-coverage (1-2X) genomes from 120 individuals representing populations across the state and from 20 historic specimens in the collection at the MVZ, Berkeley.

Resources:

• We have sequenced and assembled the genome of one mountain lion from the Santa Cruz Mountains (36M) using Dovetail Genomics technology, and have a high quality, (unannotated) genome to use as a reference.
• We have long-term data about spatial dynamics and structure of the mountain lion populations in Santa Cruz Mountains and surrounding habitats via the long-term radiotracking project (Wilmers), and historic samples of mountain lions from these populations at MVZ (Berkeley) dating to the last ~100 years.
• We have small funding from the Moore Foundation to cover the cost of low-coverage sequence data from 10 additional individuals in SC mountains (Wilmers)
• We have collaborations with F&G across the state, as well as with SI, which will provide samples from across California and the US.