SMM 2015 (continued)

It’s been an incredible few days here in San Francisco — meeting marine mammal researchers from around the globe and hearing talks on wide-ranging topics, some familiar and some very new.

I’ve learned there’s a “whale temple” in Thailand where fishermen bring the remains of stranded cetaceans for worship (Long Vu, Vietnam Marine Mammal Network).

We’ve heard experts discuss climate change’s effects on the Jet Stream (Jennifer Francis, Rutgers University) and the implications for marine mammal populations (Dr. Sue Moore, NOAA).

There was an entire session dedicated to sea otter research led by Dr. Tim Tinker (UCSC) and Dr. Jim Estes (UCSC), with presentations on a huge array of topics including diving behaviors (Joseph Tomoleoni, USGS), variance in reproductive success (Max Tarjan, UCSC), tactile sensing abilities (Sarah Macay Strobel, USGS/UCSC), and more!

I’ve learned about the genetics of scent in fur seals (Martin Stoffel, Bielefeld University) and the difficulties of SNP detection in the fur seal draft genome (Emily Humble, Bielefeld University).

I’ve had fantastic talks with otter researchers about the uses of isotopes from ancient otter bones for understanding changes in diet over time (Emma Elliott Smith, UNM) and gotten amazing advice about how to use ancient otter samples in my own genomic research (Dr. Shawn Larson, Seattle Aquarium).

My own talk on the whale gut microbiome was a blast — I got insightful questions and talked to interested researchers extensively afterward. Tomorrow, I’m looking forward to a last wander through the posters, more genetics talks, and a big Society for Marine Mammalogy “Birthday Bash” at SF City Hall!

 

Society for Marine Mammalogy Conference

This week I am attending the Society for Marine Mammalogy biennial conference in San Francisco. Around 3,000 marine mammal researchers have descended on the city for a week of workshops, talks, posters and get-togethers. I’ll be speaking on Thursday about our work on the whale gut microbiome.

Today I saw a variety of fascinating talks ranging from ancient whale dietary transitions (Robert Gooddall), to the use of DNA sequencing to determine prey biomass in pinniped feces (Austen Thomas), to the impacts of the Deepwater Horizon oil spill on bottlenose dolphin population dynamics and immune function (Lori Schwacke; Teri Rowles; Sylvain De Guise), to the use of gene expression data in understanding factors affecting population decline in sea otters (Elizabeth Bowen).

More updates to come during the week.

The Baleen Whale Gut Microbiome

Next-generation sequencing has allowed us to characterize cetacean gut microbial communities and discover surprising similarities to the microbiomes of terrestrial herbivores and carnivores.

I am thrilled to announce the publication of our paper on the whale gut microbiome in Nature Communications.

By sequencing the bacterial genomes contained in whale fecal samples, we explore the gut community of baleen whales and its functional potential. We find a remarkable ‘fusion’ microbiome that, while highly diverged overall from that of terrestrial mammals, contains functional elements characteristic of both terrestrial carnivore and terrestrial herbivore gut microbiomes. We find evidence to support the hypothesis that whales (which are descended from herbivorous terrestrial mammals, but are carnivores, eating small crustaceans and small fish) may use foregut fermentation to break down their food, much as ruminants do. In particular, the need to break down recalcitrant chitin in the exoskeletons of krill and copepods seems to have led the whale gut community to evolve the ability to bind and degrade chitin in the exoskeletons of krill and copepods.

This paper represents over four years of work carried out by Jon Sanders, myself, Joe Roman, Jarrod Scott, David Emerson, James McCarthy and Peter Girguis.

The study started as my senior thesis as an undergraduate at Harvard. In 2011, Dr. Roman and Dr. McCarthy were planning to collect right whale fecal samples in the Bay of Fundy to determine whales’ role as a ‘nutrient pump’ (bringing nitrogen up from the deep water where they feed, to the surface where they defecate), and I was eager to carry out marine fieldwork on a system that had always fascinated me. Given my interest in genetics, I wanted to add a molecular component to the research. Guided by Dr. McCarthy and Dr. Roman, we thought about exploring the whale gut microbiome. We teamed up with Dr. Girguis and Jon Sanders and worked together to conceive the microbiome study.

Dr. Roman, our colleague John Nevins and I traveled to Grand Manan in New Brunswick, Canada to carry out the fieldwork. We worked with Drs. Heather Koopman and Andrew Westgate at the Grand Manan Whale and Seabird Research Station to collect the fecal samples from right whales using fine mesh nets. We would stay on the water all day to search for “surface active groups” of right whales, then wait nearby until we smelled or saw the whale poop float to the surface in large brown clumps. We would then scoop it up and freeze a portion for genetic analysis.

I extracted DNA from the fecal samples and carried out an initial survey of the gut community using high throughput DNA sequencing. Jon Sanders and Peter Girguis advised me as I carried out initial analyses and found that the whale gut community is highly diverged from that of terrestrial mammals. We were excited by this result, and after I gradated from Harvard, Jon expanded the dataset to include metagenomic data and he and I worked with Dr. Emerson and Dr. Scott on the analyses to characterize the microbial community and its functionality.

Working with this amazing team of researchers to conceive such an exciting study was an unforgettable experience as an undergraduate and young researcher.

 

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!

 

Characterizing Dolphin Gene Expression with RNA-Seq

In order to examine the effects of chronic exposure to pollutants on the dolphin transcriptome, I am working to characterize the skin transcriptome of long-beaked common dolphins (Delphinus capensis) in the Southern California Bight using high throughput sequencing of RNA (RNA-Seq). I am seeking to understand seasonal variation in gene expression and to determine how accumulated heavy metals influence expression patterns. RNA is extracted from dart biopsies provided by Dr. Nicholas Kellar (NOAA Fisheries, Southwest Fisheries Science Center), converted to cDNA and sequenced on an Illumina Hi-Seq sequencer. Concentrations of RNA are quantified at UC Davis’ CAHFS.

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The Cetacean Gut Microbiome

Collecting whale poop in the Bay of FundyNext-generation sequencing has allowed us to characterize cetacean gut microbial communities and discover surprising similarities to the microbiomes of terrestrial herbivores and carnivores.

With colleagues at Harvard, I am extending my senior thesis research on the right whale gut microbiome. We have added gut microbiome data from IMG_5950many other cetaceans, terrestrial carnivores, omnivores and herbivores and insectivores to our dataset and Jon Sanders (Harvard) has carried out metagenomic analyses to determine which functional pathways are enriched in the cetacean gut microbiome. We have discovered exciting convergence between cetacean microbial pathways and those found in terrestrial herbivores. Preliminary results were presented by Jon at the General Meeting of the American Society for Microbiology. [Manuscript in final preparation]

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Human Demography

We are using the site frequency spectrum to model the demographic histories of European and Asian populations.

With Dr. Kirk Lohmueller (UCLA), I am estimating demographic parameters for European and Asian populations, based on a two-dimensional site Carnacfrequency spectrum (SFS) from 564 Danish and Han Chinese individuals. I am using a maximum-likelihood coalescent approach in the program fastsimcoal2 (Excoffier et al. 2013) to estimate parameters for the divergence time between the two populations, historical population sizes,bottlenecks and the timing and rates of growth.

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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.

GL_GRID

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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SCaLE Genetics & Genomics Meeting

I visited UC Riverside’s beautiful campus this Saturday (4/11) for the Southern California Evolutionary Genetics & Genomics meeting. It was a fantastic venue for graduate students, post-docs and faculty to chat informally and to hear some fascinating talks from across evolutionary genetics. I heartily recommend this (free!) meeting to any evolutionary geneticists in SoCal.

UC Riverside

I was particularly interested in Dr. Melissa Sayres talk about a dip in male Y chromosomal diversity around the time agriculture was introduced into different human populations, which could possibly be explained by an increase in variance of male reproductive success due to a more stratified society.