A deep dive into the sea otter and giant otter genomes

Our deep dive into the sea otter and giant otter genomes is out today in Molecular Biology & Evolution (early access)!

We investigated phylogenetics, positive selection, loss of olfactory receptor genes, genetic diversity, demography, and deleterious variation in these remarkable animals.

We couldn’t have learned so much about otter evolution without the help of Gidget the sea otter and our fantastic collaborators at the Monterey Bay Aquarium, Smithsonian, Broad, UCSC, Texas A&M, and beyond!

Check it out, or wait for the fancy typeset version! (I particularly love the beautiful otter drawings by recent UCLA graduate Joann Shih!)

[ Gidget’s portrait courtesy of the Monterey Bay Aquarium ]

Investigating sea otter and giant otter demographic history and burden of deleterious variation in our new paper!

Monterey Bay Aquarium Blog Post

A blog post I wrote about the sea otter genome project has been featured on the Monterey Bay Aquarium Blog! I had a great time working on the post with Ken Peterson, the Aquarium’s Communications Director, and absolutely love the sweet infographic on the bottleneck designed by Tiffany Enriquez (courtesy of the Monterey Bay Aquarium).




Monterey Bay

I just got back from a wonderful visit to the Monterey Bay Aquarium – one of my favorite places in California. I have been going there since I was young, and this week I was thrilled to give an in-house seminar on the sea otter genomics project. The Aquarium has sent us samples and given great advice as we move forward with the project and it was a pleasure to get to tell them more details about the project and see such enthusiasm for otter genomics from the audience – which ranged from volunteer guides to the Aquarium’s scientists. Thank you to everyone at the Aquarium, but especially Athena Copenhaver who coordinated my whole visit and made me so welcome.

The day before my talk I went out on a whale watch and saw a large group of lunge-feeding humpbacks, dozens of common dolphins, and an ocean sunfish. Things got more intense when a pod of seven killer whales came onto the scene – the humpbacks trumpeted and became very defensive, and the dolphins scattered. One dolphin didn’t make it, and the orca pod efficiently and swiftly attacked it. I have never seen an orca predation event before, and it was as remarkable as it was grisly. They had a calf with them that was being taught to hunt by its mother and grandmother.

On the way back to my hotel, I passed a female otter and her pup in the harbor by Fisherman’s Wharf – it might have been “Bixby,” a female featured on the BBC/PBS’ Big Blue Live.

Keep an eye out for a longer blog post about my talk here and on the Aquarium blog!


Sea Otter Population Genomics

We will sequence the sea otter genome to assess the effects of the fur trade bottleneck on genomic diversity and genetic load.


Forward-in-time Poisson Random Field simulations demonstrating how sea otter genetic load (decrease in fitness to due harmful alleles) may have increased due to the fur trade population bottleneck.

Sea otters were hunted to near-extinction during the 18th-19th centuries. Only six remnant populations of fewer than 100 individuals survived, many of which have recovered dramatically over the past century. With Bob Wayne (UCLA), Kirk Lohmueller (UCLA), Klaus-Peter Koepfli (Smithsonian Conservation Biology Institute) and James Estes (UC Santa Cruz), I am developing a project to sequence the de novo sea otter genome and combine ancient and modern sea otter genomic data from across the species’ range to assess the effect of this extreme bottleneck on the sea otter genome. I am currently carrying out forward-in-time simulations based on population histories drawn from the literature to model the effect of the fur trade bottleneck on genetic diversity and genetic load (decrease in fitness due to harmful genetic variants) in sea otter populations.

[The featured image is artist John Webber’s “Sea Otter” c. 1780, based on his observations as a member of Captain Cook’s third Pacific voyage.]

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