I am so pleased to announce that I have finished my Ph.D. at UCLA and have moved up to Seattle to start a postdoc with Kelley Harris at UW Genome Sciences! It’s been a whirlwind finishing and moving during the pandemic. I’m finally settled in and ready to start tackling research on the mutation spectrum in non-model organisms ranging from bears to fin whales!
Author: ab08028
A deep dive into the sea otter and giant otter genomes
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!
Demographic Inference from Genomic Data
My favorite aspect of population genetics is inference of population history from genetic data. Whether you are thinking about human history or the history of your favorite non-model organism, inferring demographic history is not just interesting for its own sake, but is also a critical step for any study of selection.
I have worked on a variety of demographic inference projects and am particularly interested in comparing different methods and making the subject more accessible to all of us who study non-model organisms.
You can check out our paper that demonstrates that popular methods of demographic inference don’t always predict other summaries of the data, and so shouldn’t be taken too literally, and our review paper detailing different inference methods and their application to non-model organisms. Use our flow chart to find the method that’s right for your data and questions!
[ Note: I am happy to be able to offer complimentary one-time access to my Annual Reviews article as a PDF file, for your own personal use. Any further/multiple distribution, publication, or commercial usage of this copyrighted material requires submission of a permission request addressed to the Copyright Clearance Center (http://www.copyright.com/) ]
Otter Genomics
Aquatic adaptation and depleted diversity in the sea otter and giant otter genomes.
I have sequenced, assembled and annotated the de novo southern sea otter genome, and annotated the giant otter genome that was assembled by the Broad Institute. We are comparing these two highly divergent otter species to understand the genetic changes that underlie their recent aquatic adaptation and to get a first look at the potential impacts of the extreme fur trade bottleneck on the sea otter’s genome.
Stay tuned for more discussion of our results soon!
Guide to demographic inference in non-model organisms
Have you ever wanted to infer the population history of your study species, had genomic data, but not known where to start? Check out our review of popular demographic inference techniques and their application to non-model organisms! We describe each method’s theoretical underpinnings, how each has been applied to non-model organisms, and explain some important caveats. My favorite part is the flow-chart I made to help guide researchers to different techniques that will work for their data and questions.
Demographic inference is my favorite part of population genetics, and I hope this helps it feel doable!
You can access the paper here with complimentary one-time access, for your own personal use. (Any further/multiple distribution, publication, or commercial usage of this copyrighted material requires submission of a permission request addressed to the Copyright Clearance Center (http://www.copyright.com/)
New Blog Post from the Monterey Bay Aquarium!
I got to collaborate with the great folks at the Monterey Bay Aquarium on the latest update on the sea otter genome project! Check it out here:
Blood, bone and brainpower: A deep dive into sea otter DNA
New pre-print: Comparison of single genome and allele frequency data reveals discordant demographic histories
Our new pre-print has caused a small flurry on Twitter!
In it, we compare published demographic histories of human populations based on three popular methods, and find that the models don’t always predict other summaries of the data. It is currently in press at G3: Genes | Genomes | Genetics.
Quirks & Quarks
An interview on the whale microbiome that I did for Quirks & Quarks with Bob McDonald on CBC radio has been released! I was very happy that I happened to be in Canada at the time, and so could be told I was on the radio by my Canadian family! Check it out!
Southern California Academy of Sciences Annual Meeting
I will be giving a talk on the whale gut microbiome today at the SCAS 2016 Annual Meeting at USC. Come learn about whale poop!
Come see a public lecture at the Cabrillo Aquarium!
I will be giving a public lecture at the Cabrillo Aquarium in San Pedro, CA as part of the monthly meeting of the American Cetacean Society, Los Angeles Chapter. Come hear about whale evolution, the search for whale poop, and our remarkable findings about the bacteria that live in the whale gut!
Information here