Current & Past Projects

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.

Selection in Bottlenecked Sea Otter Populations: We are setting out to sequence the de novo sea otter genome. 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 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.
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The CetaceaIMG_5950n Microbiome:  With colleagues at Harvard, I am extending my senior thesis research on the right whale gut microbiome. We have added gut microbiome data from many 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 Departially collapsed tumulusmography: With Dr. Kirk Lohmueller (UCLA), I am estimating demographic parameters for European and Asian populations, based on a two-dimensional site frequency 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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Dolphin GeDolphin_Bunburyne Expression: 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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