Annabel Beichman
Ph.D., UCLA
Postdoctoral researcher
Harris Lab
Department of Genome Sciences
University of Washington, Seattle, WA
EDUCATION
Ph.D. in Biology (2020), University of California, Los Angeles, CA
Co-advised by Dr. Robert Wayne and Dr. Kirk Lohmueller
Harvard University, Cambridge, MA
A.B., summa cum laude, Organismic & Evolutionary Biology (2012)
Secondary Field: Celtic Languages & Literatures
PUBLICATIONS
Beichman, A. C., Robinson, J., Lin, M., Moreno-Estrada, A., Nigenda-Morales, S., Harris, K. (in revision). “Evolution of the mutation spectrum across a mammalian phylogeny.”
Beichman, Annabel C, Emilia Huerta-Sanchez, Kirk E. Lohmueller. 2018. “Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms.” Annual Review of Ecology, Evolution, and Systematics: 49:433-56. [Complimentary one-time access to our Annual Reviews article is available 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/]
GRANTS, AWARDS & FELLOWSHIPS
Science Teaching Experience Program: Working in Science Education Fellow (2022-2023)
NIH T32 “Biological Mechanisms of Healthy Aging” Traineeship (2020-2023)
Society for Molecular Biology and Evolution Best Student Paper Award, Honorable Mention (2020)
Scherbaum Award for excellence in graduate research, UCLA Ecology & Evolutionary Biology Department (2020)
Fitch Award Finalist, SMBE (2019)
National Science Foundation Graduate Research Fellowship (NSF GRFP) (2015)
NIH Genomic Analysis Training Program Training Grant (2014-2015;2015-2016)
UCLA Pauley Fellowship (2013)
Henry Russell Shaw Summer Fellowship (2012)
Junior 24 Phi Beta Kappa (2011)
Museum of Comparative Zoology Grant for Undergraduate Research (2011)
Alex G. Booth ’30 Fund Fellowship (2011)
Herchel-Smith Summer Undergraduate Research Fellowship (2010)
Detur Book Prize (2009)
John Harvard Scholar (2009, 2010)
SERVICE & OUTREACH
Extensive mentorship experience. I mentored two undergraduates at UCLA (Amber deVries and Pooneh Kalhori), which included training in advanced laboratory, computational, and population genetics analyses, collaboration on publications, attending academic conferences, and help applying to graduate research programs. Mentoring graduate students at the University of Washington, Genome Sciences (Lincoln Harris, Gabrielle Ferra, Candice Young), and undergraduates (Quinn Bellamy) in projects related to population genetics, simulations, bear evolution, and the mutation spectrum.
Co-organizer, SMBE Satellite Meeting “Molecular Evolution of Small Populations,” Princeton, NJ (June 2023)
Reviewer for Nature Genetics, Nature Ecology & Evolution, Molecular Biology & Evolution, Conservation Genetics, Genome Biology and Evolution, Evolution, Molecular Ecology, Marine Mammal Science, Marine Ecology Progress Series, Antonie van Leeuwenhoek Journal of Microbiology
Graduate student member of population genetics faculty search committee (UCLA, 2017)
Organizing workshops for middle school children to learn about natural history and evolution
Training graduate students in demographic inference at the La Kretz Conservation Genomics Workshop
Co-facilitator Empowering Prevention and Inclusive Communities workshop (UW, 2021)
Speaking to middle school classrooms about careers in science via the “Skype a Scientist” program (2020-21)
Facilitator, Girls Who Code club to introduce female and non-binary high school students to coding (2021)
Postdoc representative on the University of Washington Genome Sciences Department’s Diversity, Equity, and Inclusion (DEI) committee (2022-present)
Other outreach including radio interviews (“Quirks and Quarks)”, public blog posts for the Monterey Bay Aquarium, designing infographics for California State Parks, and giving public lectures (Cabrillo Aquarium)
Facilitator for Wednesdays at the Genome: DNA Ice Cream Social, a public science outreach event (2022)
Co-organizer, “Bacteremon Battles” a Genome Sciences outreach event (2023)
PRESENTATIONS
Society for Molecular Biology and Evolution, Satellite Meeting: “Evolution in Small Populations”) (Princeton University, Princeton), “Global opportunities and challenges in small populations research” [led panel discussion; organized conference], June 30th, 2023.
University of Oregon Departmental Seminar (Eugene, OR), “Non-model organism genomics:
from aquatic adaptation in the sea otter to the evolution of mutagenesis” [1-hour departmental seminar], June 9th, 2023.
Western Washington University Departmental Seminar (Bellingham, WA), “Non-model organism genomics:
from aquatic adaptation in the sea otter to the evolution of mutagenesis” [1-hour departmental seminar], May 10, 2023.
SciencePlus (Vancouver, CA), “How genomes of endangered marine mammals provide insights into their (and our) evolution and survival,” [invited 2-hour public seminar and discussion], March 28, 2023.
Plant and Animal Genomes Conference (San Diego, CA), “Characterizing mutation spectrum variation across a mammalian phylogeny” [invited 25-minute oral presentation], January 15, 2023.
Genome Sciences 20th Anniversary Symposium (Seattle, WA), “Does DNA mutate in the same way across species?” [lightning talk], November 9-10, 2022.
University of Washington Nathan Shock Center Annual Geroscience Symposium (Seattle WA), “Characterizing mutation spectrum variation across a mammalian phylogeny” [invited 20-minute oral presentation], October 28, 2022
NIA Workshop on Genetic Variation in Aging (Seattle, WA), “Characterizing mutation spectrum variation across a mammalian phylogeny” [poster], July 10, 2022
Genomics Salon (Seattle, WA), “Conservation Biology in the Genomics Era: The Case of the Vaquita” [public lecture and facilitated discussion], May 26, 2022.
Plant and Animal Genomes Conference (San Diego, CA), “Characterizing mutation spectrum variation across a mammalian phylogeny” [invited 25-minute oral presentation], January 9, 2022. *Cancelled due to COVID*
Probabilistic Modeling in Genomics (Cold Spring Harbor Laboratories) [virtual], “Disentangling biased gene conversion from the mutation spectrum,” [poster], April 14-16, 2021
Genomes of Animals and Plants Virtual Conference, “Genomic analyses reveal range-wide devastation of sea otter populations,” [Invited 30 minute oral presentation via Zoom], January 12th, 2021
Genomics Working Group Seminar (Smithsonian-Mason School of Conservation), “Genomic analyses reveal range-wide devastation of sea otter populations,’ [Invited 45-minute oral presentation via Zoom], December 17th, 2020
Sea Otter Research and Conservation Symposium [virtual], “Range-wide Genomic Sampling Illuminates Sea Otter Population Structure and Consequences of Fur Trade Exploitation,” [oral presentation], April 1-2, 2021.
Demographic Inference Tutorial (UCLA), “What you otter know about demographic inference from the site frequency spectrum: a tutorial,” [two-day Zoom workshop], April 7-8, 2020
Marine Mammal Genomics Workshop, World Marine Mammal Conference (Barcelona, Spain), “Aquatic adaptation and fur trade devastation: a deep dive into the genomes of the sea otter and giant otter,” [invited 25 min oral presentation via Skype], December 8, 2019
Genome Analysis Workshop (Trinity College Dublin, Ireland), “What you otter know about demographic inference: Methods comparison and the decline of the sea otter,” [60 min oral presentation], November 7, 2019
PopGenLunch Seminar (University of Washington, Seattle), “What you otter know about demographic inference: comparing inference methods and applying to non-model organisms,” [60 min oral presentation], October 17, 2019
Genome 10K & Vertebrate Genome Project Annual Meeting (Rockefeller University, NY), “Aquatic adaptation and fur trade devastation: a deep dive into the genomes of the sea otter and giant otter,” [invited 20 min oral presentation], August 28, 2019
Speaking at the Fitch Symposium at SMBE 2019
Society for Molecular Biology & Evolution (SMBE) Meeting (Manchester, UK), Fitch Symposium, “Aquatic adaptation and fur trade devastation: a deep dive into the genomes of the sea otter and giant otter,” [15 min oral presentation], July 23, 2019
Plant and Animal Genome (PAG) Conference XXVII, “Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter,” [20 min oral presentation], San Diego, CA, January 12, 2019
UC Conservation Genomics Consortium Workshop, “Sea otter demographic history, diversity and deleterious variation,” [20 min oral presentation], Asilomar, CA, November 9, 2018
La Kretz Conservation Genomics Workshop, Annabel Beichman & Kirk Lohmueller, “Whole-genome vs. SFS based demographic inference methods: choices, comparisons and caveats,” [60 min oral presentation], Los Angeles, CA, March 26, 2018
Southern Sea Otter Research Update Meeting (Santa Cruz, CA), “Sea Otter Genomics: First Findings & Project Progress,” [20 min. talk], March 2018
UC Conservation Genomics Consortium PI Meeting & Workshop, “Sea Otter Genomics,” San Jose, CA, August 15-18, 2017.
La Kretz Conservation Genomics Workshop, Annabel Beichman & Kirk Lohmueller, “Comparison of single genome and allele frequency data reveals discordant demographic histories,” Los Angeles, CA, March 25-29, 2017, oral presentation
Global Biodiversity Genomics Conference, “Comparison of single genome and allele frequency data reveals discordant demographic histories,” Washington D.C., February 21-23, 2017, oral presentation
Southern California Academy of Sciences 2016 Annual Meeting, “The Paradox of the Whale Gut Microbiome: Baleen Whales Host a Unique Bacterial Community with Similarities to both Carnivores and Herbivores,” May 2016.
BWF-CHIP, GATP, & SIB Research Symposium (UCLA), “The Potential Impacts of Exploitation on Modern Sea Otter Genomes” [Poster], Winner — Best Poster, April 2016
2016 NHGRI Annual Meeting (Bethesda, MD), “The Paradox of the Whale Gut Microbiome” [Poster], April 2016
American Cetacean Society, Los Angeles Chapter, Monthly Seminar (San Pedro, CA), “The Paradox of the Whale Gut Microbiome” [1 hour public talk], March 2016
Southern Sea Otter Research Update Meeting (Santa Cruz, CA), “The Potential Impacts of Exploitation on Modern Sea Otter Genomes,” February 2016
Ecology & Evolutionary Biology Pub Seminar Series (UCLA), “The Paradox of the Whale Gut Microbime,” January 2016
21st Biennial Society for Marine Mammalogy Conference (San Francisco, CA) “The whale gut microbiome digests a carnivorous diet using pathways common in terrestrial herbivores,” December 2015
Monterey Bay Aquarium Brown Bag Seminar Series (Monterey, CA) “Sea Otter Genomics: Impacts of Exploitation on Marine Mammal Genomes,” September 2015
BWF-CHIP, GATP, & SIB Research Symposium (UCLA) “The whale gut microbiome digests a carnivorous diet using pathways common in terrestrial herbivores,” May 2015
UC Santa Cruz, “Insights into the Whale Gut Microbiome,” March 2013
PAST RESEARCH
Senior Thesis 2011 – 2012
Harvard University, Girguis & McCarthy Labs
“Gut Flora of the North Atlantic Right Whale: the 0.2 micron inhabitants of a 17 meter Leviathan.”
Advisers: James McCarthy & Peter Girguis (Harvard) and Joe Roman (Gund Institute for Ecological Economics)
Thesis Readers: Colleen Cavanaugh, Christopher Marx, Peter Girguis, James McCarthy
Thesis Description: I collected cetacean fecal samples for genetic and chemical analysis, extracted genomic DNA from the feces and pyrosequenced the microbial 16S region to characterize the bacteria expelled from the gut. I worked with Dr. Girguis’ student Jon Sanders to analyze the resulting data in the program QIIME and carried out principal components analyses to compare the whale gut microbial community to those of terrestrial mammals, discovering that baleen whales have unique and highly diverged gut microbial communities. I have continued to work on these questions with my Harvard colleagues after graduation, adding metagenomic fecal data from many other cetaceans and a range of terrestrial animals to expand our dataset. We theorize that the need to digest large amounts of chitin (in the exoskeletons of krill and copepods) may the driving force behind the divergence in the gut flora of baleen whales.
Summer Research Internship Summer 2010
Stanford University, Hopkins Marine Station, Palumbi Lab
Advisers: Steve Palumbi & Melissa Pespeni
Projects: I participated in two projects, the first on corals sampled from American Samoa and the second on genome-wide signatures of selection in purple sea urchins along the west coast. I used PCR to amplify genes with known markers to discover that certain corals were new recruits to a reef in a marine sanctuary, demonstrating gene flow between the marine reserve and other reefs. The second project was more extensive; Dr. Melissa Pespeni had used a Restriction Site Tiling Analysis (RSTA) array to identify sites in urchin genomes that differ between Boiler Bay, OR and San Diego, CA populations. I looked for patterns of adaptive variation by expanding her dataset to encompass four additional sites on the west coast. I carried out sample collection in local intertidal zones, extracted genomic DNA from spine samples, amplified the genes of interest using PCR and edited the sequences in the program Sequencher. In the process, I trained a high school student in laboratory and analysis techniques. As published in Pespeni & Palumbi (2013, Molecular Ecology), our study found signatures of selection across the urchins’ range in patterns suggestive of ongoing balancing selection, possibly acting on the urchins’ larval form.
Undergraduate Lab Assistant 2009 – 2011
Harvard University, Edwards Lab
Advisers: Scott Edwards & Miguel Alcaide
Project: I studied the genetic variation of zebra finch song learning genes for my first laboratory research experiences at Harvard. We sequenced song learning genes from finches sampled on the Australian mainland and a nearby island to look for single nucleotide polymorphisms (SNPs) between the populations. The presence of such polymorphisms would demonstrate divergence in highly conserved song-learning genes between the parent and island populations, hinting at the evolution of different song ‘dialects’ as a possible factor in speciation. Our sample size was too small for significant results, but we did identify a few polymorphisms which may indicate that some divergence is occurring.