Sea Otter

Project Title: Using genomic data and novel analytical tools to understand Sea Otter demographic history and enhance management of extant populations.

Campuses: UCLA & UCSC

PI(s): Wayne, Estes, Shapiro

Background. The sea otter has suffered two historic population declines, one reflecting the effects of the fur trade and a more recent decline across the Aleutian Islands due to killer whale predation. Populations have re-expanded from surviving remnant colonies after the fur trade bottleneck. Several populations have reached historical carrying capacities, but in some areas, such as California, the population has only increased moderately, and has not reached historical levels. The role of deleterious variation and gene flow in the demographic dynamics of extant populations is not known and could benefit management if certain populations are isolated and have high genetic load that could be mitigated by genetic restoration through translocation, increased monitoring, and other measures.

Approach. We propose a four part experimental design. First, de novo sequencing utilizing Dovetail Genomics technology, with annotation enhanced by RNA-seq. Second, low coverage genome sequence for 5-10 individuals from each of six remnant populations and exome capture array sequencing of >300 individuals. Third, demographic simulations to assess the role of drift and selection on levels of variation (Marsden et al. 2015). Finally, DNA from ancient midden sites will be used to compare genetic diversity and genetic load in pre-fur trade populations to those in modern populations in order to ground truth the approach.

Resources. De novo genome sequencing has been initiated with outside support. Samples have been collected previously by project collaborators. We have obtained extensive extramural support for this project, including an NSF small grant, an academic senate grant and a grant from the Monterey Bay Aquarium. An NSF pre-doctoral fellowship award supports Annabel Beichman, a graduate student associated with the project. The project involves 4 catalyst collaborators (Jim Estes, Kirk Lohmueller, Bob Wayne and Beth Shapiro) as well as associated faculty Carlos Garza. [Read more about the project here]