I have sequenced, assembled and annotated the de novo sea otter genome, and compared it to the giant otter genome to discover genetic changes associated with aquatic adaptation and the impact of the extreme fur trade bottleneck on genetic diversity. I am now using a custom sequence capture to study demographic history and genetic load in modern sea otter populations using modern and ancient DNA. I have also compared methods of demographic inference from genomic data to determine which methods, if any, are able to recapitulate multiple summaries of the data, and written a review of popular demographic inference methods and their applications to non-model organisms. In the past I have worked on forward-in-time simulations to assess the impacts of the 18th-19th fur trade on sea otter genomic diversity and genetic load, characterized the cetacean gut microbiome with high-throughput sequencing data, and modeled human demography using the site frequency spectrum.
Harvard University, Cambridge, MA
A.B., summa cum laude, Organismic & Evolutionary Biology (2012)
Secondary Field: Celtic Languages & Literatures
Junior 24 Phi Beta Kappa
Chaves, J. A., Martinez-Torres, P. J., Depino, E. A., Espinoza-Ulloa, S., García-Loor, J., Beichman, A.C., & Stervander, M. 2020. “Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples.” Diversity.
Barr, K., Beichman, A. C., Kalhori, P., Rajbhandary, J., Bay, R. A., Ruegg, K., & Smith, T. B. 2020. “Persistent Panmixia Despite Extreme Habitat Loss and Population Decline in the Threatened Tricolored Blackbird (Agelaius tricolor).” Evolutionary Applications.
Sura, Shayna A., Lauren L. Smith, Monique R. Ambrose, C. Eduardo Guerra Amorim, Annabel C. Beichman, Ana CR Gomez, Mark Juhn et al. 2019. “Ten simple rules for giving an effective academic job talk.” PLoS computational biology 15, no. 7.
Annabel C Beichman, Klaus-Peter Koepfli, Gang Li, William Murphy, Pasha Dobrynin, Sergei Kliver, Martin T Tinker, Michael J Murray, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K Karlsson, Kirk E Lohmueller, Robert K Wayne. 2019. “Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter.” Molecular Biology and Evolution: msz101
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/]
Beichman, Annabel C, Tanya Phung, Kirk E. Lohmueller. 2017. “Comparison of single genome and allele frequency data reveals discordant demographic histories.” G3: Genes | Genomes | Genetics. doi.org/10.1534/g3.117.300259
Sanders, Jon G, Annabel C Beichman, Joe Roman, Jarrod J Scott, David Emerson, James J McCarthy, and Peter R Girguis. 2015. “Baleen Whales Host a Unique Gut Microbiome with Similarities to Both Carnivores and Herbivores.” Nature Communications 6 (September): 8285. doi:10.1038/ncomms9285.
GRANTS AND AWARDS
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)
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
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
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
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.