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.

The mutation spectrum of wild populations. As an NIH T32 “Biological Mechanisms of Healthy Aging” postdoctoral trainee in Dr. Kelley Harris’ lab at the University of Washington, I am working on characterizing the mutation spectrum of wild populations, including bears and whales. We are aiming to better understand mutational processes in these species, particularly how introgression may affect the mutation spectrum in bear and whether we can identify genomic stability in the spectrum of large-bodied and long-lived whales.

Selection in Bottlenecked Sea Otter Populations: 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. We carried out a project to assess the impact of the fur trade using sea otter genomic data from across the species’ range (Beichman et al, in revision).
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Aquatic Adaptation and Depleted Diversity in Otter Genomes: We have sequenced, assembled and annotated the de novo sea otter genome and compared it to the giant otter genome sequenced by the Broad Institute. We found intriguing patterns of genetic changes associated with aquatic adaptation and extremely low genetic diversity in the sea otter that may be related to multiple periods of population decline (Beichman et al (2019), MBE).
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Comparison of Demographic Inference Methods: We demonstrated that popular demographic inference methods often don’t recapitulate other summaries of the data, casting doubt on their literal interpretation (Beichman et al., 2017, G3). We have also written a review meant to help people who, like me, study non-model organisms get started with demographic inference from genomic data (Beichman et al, 2018, Annual Reviews). Back to top


The CetaceaIMG_5950n Microbiome:  With colleagues at Harvard, I extended 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 (Sanders, Beichman, et al. 2015, Nature Communications).
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