Joanna L. Kelley, PhD, Principal Investigator

Joanna is currently an Associate Professor in the Department of Ecology and Evolutionary Biology at University of California Santa Cruz. She was previously in the School of Biological Sciences at Washington State University. Her research focuses on the genomic basis of adaptation, with a special emphasis on extreme environments. She is a member of the Society for Molecular Biology and Evolution (SMBE).

She received her AB in Mathematics and Biology from Brown University. She received her PhD in Genome Sciences from University of Washington with advisor Willie Swanson and held postdoctoral positions at University of Chicago in Human Genetics and at Stanford University in the Department of Genetics.

email: jokelley-at-ucsc-dot-edu

Google scholar
profile at GenomeWeb
NSF Biosketch

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Muh-Ching Yee, PhD, Lab Manager

Muh-ching (M.C.) has worked as a laboratory researcher at Stanford University in the departments of Genetics, Chemical and Systems Biology, Biology, and the Carnegie Institution for Science. M.C.’s childhood passion for solving the New York Times crossword has led to her current work playing with the letters of the genetic code in genomics and synthetic biology in human, animal and plant systems. M.C. received an SB in Chemistry at MIT, and a PhD in Chemistry at UC Berkeley, CA.

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Isabel Kline, Lab Technician

Isabel is a science enthusiast. She is a UCSC graduate with a BS in Biochemistry and Molecular Biology. Her work til now has spanned a couple different aspects of the life sciences domain including tissue culture of strawberry plants, assorted industry work and a CDC Foundation position funded by a TikTok grant.

 

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Blair Perry, PhD, Postdoctoral Researcher

Blair completed his PhD in Todd Castoe’s lab at the University of Texas at Arlington in April 2021. For his dissertation, he used functional genomics to understand the molecular basis and evolution of adaptations in non-traditional model systems. This included comparative transcriptomic studies of post-feeding regenerative organ growth in multiple snake species and functional genomic studies focused on understanding the regulation and evolution of snake venom systems. Broadly, Blair is interested in understanding how complex adaptations evolve through the integration of functional, population, and comparative genomics data. In the Kelley Lab, Blair is funded by an NSF Office of Polar Programs Postdoctoral Research Fellowship to study the genomic basis and evolution of Arctic adaptations in the polar bear. Additionally, Blair will be contributing to ongoing efforts to understand the genomic mechanisms of hibernation in brown bears.

Website: blairperry.net

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Ellie Armstrong, PhD, Postdoctoral Researcher

Ellie completed her PhD at Stanford University with Dmitri Petrov and Liz Hadly, where she investigated the diversity patterns of large carnivores across their range and assembled genomes from a variety of species. Specifically, she built large range-wide datasets for the lion and tiger, to serve as both a conservation resource and to gain insights into the patterns that have shaped present diversity. She is very interested in understanding how we can better use genomics as a conservation tool and what patterns in the genome can help us understand population health. In the Kelley lab, Ellie will work on brown bears (and other carnivores!) to build range-wide genomic databases for the populations in North America and better understand their population dynamics. She is also building SNP panels that can be used as a monitoring tool in close collaboration with the USFWS.

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Rishi De-Kayne, PhD, Postdoctoral Researcher

Rishi is interested in the ecological and evolutionary processes that shape complex patterns of diversity. Prior to joining UCSC as a postdoc, Rishi was awarded an SNSF postdoctoral fellowship to study the origin and maintenance of structural variation in the African monarch butterfly at the University of Edinburgh, UK. In 2020 Rishi completed his PhD on the genomic basis of adaptation and speciation in Alpine whitefish adaptive radiation at the University of Bern and Eawag, Switzerland, under the supervision of Ole Seehausen and Philine Feulner. He also holds an MRes in Tropical Forest Ecology and a BSc in Biology from Imperial College London where his work highlighted the role of the microbiome in facilitating speciation in Howea palm trees. In the Kelley lab, Rishi hopes to help elucidate the evolutionary history of adaptation to extreme environments in poeciliid fishes.

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Sam Bogan, PhD, Postdoctoral Researcher

Sam is an evolutionary ecologist who integrates genomics and physiology to study environmental adaptation, primarily in marine systems. He is interested in ecological and evolutionary mechanisms that drive or limit environmental adaptation and how that adaptation affects eco-evolutionary processes. Sam recently received his PhD from UC Santa Barbara where he studied the evolution and regulation of plastic responses to global change in populations of marine invertebrates. He also completed a MSc at Sonoma State University where he studied the regulatory evolution of adaptation to extreme cold in Antarctic fishes. As a postdoc in the Kelley Lab, Sam is returning to the spectacular world of polar biology where he will research molecular evolution in Zoarcid eelpouts during their convergent adaptation to both poles. He is interested in connecting this research to speciation at the poles and developing new methods for genomic studies of thermal adaptation.

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Paul Wheeler, Fish Guru

Paul graduated from Washington State with a BS in Animal Science in 1984 and has lived in Pullman ever since. After two year stays in a cell biology lab at Washington State and the Fisheries Department at the University of Idaho, Paul was fortunate enough to land in the salmonid fish genetics lab directed by Gary Thorgaard at Washington State where he has worked since 1988. Paul’s core responsibility has been to develop and propagate homozygous clonal lines of rainbow trout (Oncorhynchus mykiss) for use as biomedical and aquacultural models. More recently he has also had the opportunity to learn how to raise and breed the aquatic frog species Xenopus tropicalis in association with Erica Crespi. Paul currently helps the Kelley lab develop breeding colonies of the live-bearing fish Poecilia mexicana. Paul originally developed his interest in biology and natural history as a child growing up in Kenya and now spends as much time as he can fishing and hiking in the wilderness.

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Tait Algayer, Masters Graduate Student (started August 2021)

Tait graduated from The College of New Jersey (TCNJ) with a BS in Biology in 2021. At TCNJ, she worked under the guidance of Gary Dickinson studying the effects of ocean acidification on exoskeletal properties in Alaskan snow crabs. At Washington State University, Tait’s research examines the regulatory mediation of seasonal run-time variation in Chinook salmon. She has also worked with the Cooperative Institute for Great Lakes Research (CIGLR) and NOAA Great Lakes to develop genetic methods for monitoring larval fish abundance in the Great Lakes. Tait is broadly interested in exploring genomic mechanisms underlying novel and adaptive traits in exploited aquatic species.

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Tina Cai, PhD Graduate Student (started September 2023)

Tina graduated from Middlebury College with a BA in Conservation Biology in 2023. At Middlebury, Tina worked in the Evolutionary Ecosystem Ecology (E3) Lab under the guidance of Eric Moody. Tina has spent most of her undergraduate thinking about stoichiometric constraints in aquatic macroinvertebrates. Tina also completed an honors senior thesis studying the morphological changes associated with diel vertical migration patterns in lanternfishes using micro-CT scan. Tina is currently an NSF GRFP fellow in the Kelley lab and is interested in studying climate change (mal)adaptation in polar fishes. Tina is also always learning about environmental justice.

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Abby Lehmann, Undergraduate Researcher (Fall 2022 – Spring 2024)
Abby Lehmann is an undergraduate student at Washington State University majoring in biology and minoring in economics. She is currently investigating sex specific gene expression in grizzly bears. More specifically, looking at sex-specific relationships between gene expression and hibernation. She has always been interested in biology and loves to learn about anything and everything in the field. She plans to pursue epidemiology or infectious disease in graduate school.

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Alumni

 
Anne Nakamoto
Position: PhD rotation student (Fall 2023)
Research focus: Comparative transcriptomics of mammalian hibernation
Current position: PhD student in the Corbett-Detig Lab

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Kerry McGowan
Position: PhD student (2017-2023)
Research focus: Functional genomics of hydrogen sulfide adaptation in Poeciliid fish
Current position: Data Scientist at A-Alpha Bio

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Marc Palmada Flores
Position: Visiting PhD Student (Spring 2023)
Research focus: Comparative genomics of vertebrates.

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Xiaomeng Tian
Position: SMBE Virtual Lab Meeting Training Program participant, PhD Student at University of Konstanz (Fall 2022 – Spring 2023)
Research focus: Genomic mechanisms of phenotypic variation and adaptation.

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Małgorzata Gazda (Gosia)
Position: SMBE Virtual Lab Meeting Training Program participant, Postdoctoral Researcher at Institut Pasteur (Fall 2022 – Spring 2023)
Research focus: Molecular evolution of menstruation.

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Jake Landers
Position: Undergraduate Researcher (2019-2022)
Research focus: Bioinformatics.

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Scott Hotaling
Position: Postdoctoral Researcher (2017-2022)
Research focus: Adaptation to cold and high-altitude environments
Current position: Assistant Professor at Utah State University

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Alexandra Fraik
Position: PhD student (2015-2021)
Research focus: Conservation genomics of Tasmanian devils and salmonids
Current position: Research biologist at the Rocky Mountain Research Station

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Michael Saxton
Position: PhD student (2014-2021, co-advised with Dr. Charles Robbins)
Research focus: Genomic mechanisms of hibernation physiology in brown bears
Current position: Wildlife biologist at Katmai National Park

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Anthony Brown
Position: PhD student (2014-2019)
Research focus: Genomics of hydrogen sulfide adaptation in Poeciliid fish
Current position: Bioinformatics programmer at UC Davis

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Corey Quackenbush
Position: Lab Manager (2013-2017)

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Luana Lins
Position: Postdoctoral Researcher (2016-2018)
Research focus: genome variation in Kryptolebias marmoratus
Current position: Post-doctoral scholar at CSIRO in Australia
Website: https://www.drluanalins.com/

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Laura Helou
Position: Intern and Master’s Student in Montpellier, France (April 2017 – August 2017)
Research focus: Comparative genomics, impacts of structural variation on evolution.
Current position: PhD student in at the INRA of Tours, France.

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Shawn Trojahn
Position: Masters student (Jan 2017 – Nov 2020)
Research focus: genetic causes of coloration variation in Rainbow Trout.

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Alexia Gee
Position: Masters student (Aug 2019 – Dec 2020)
Research focus: Gene expression in hibernating bears.

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Graduate Students / Visiting Scientists:
John Coffin, PhD student at KSU (Summer 2018)
Annabelle Vesterman, visiting veterinary student (Summer 2017)
Ryan Greenway, PhD student at KSU (Summer 2015)
Kyle Taylor, Non-thesis Master’s (Fall 2014-Fall 2015)
Luca Giordani, Volunteer (Spring 2014)

Undergraduates:
Breeana Barnes, WSU Undergraduate (Spring 2015)
Julian Bennett Ponsford, WSU Undergraduate (2013-2015), Now graduate student at University of Wyoming with Cynthia Weinig
Connor Carrillo, School of Molecular Biosciences STARS student (Fall 2014)
Emma Cordray, WSU Undergraduate (2017)
Kayla Cribbin, WSU Undergraduate (2013-2016), Now studying with the Seattle Children’s Research Institute
Chris Cornelius, University of Alabama Tuscaloosa Undergraduate (Summer 2014)
Jarod Herrera, WSU Undergraduate (Spring 2018 – Fall 2018)
Samantha Kallinen, WSU Undergraduate (Spring 2017 – Spring 2018)
Nicholas Kelly, WSU Undergraduate (Summer 2018 – Fall 2018)
Allegra Sundstrom, WSU Undergraduate (Fall 2015 – Summer 2017)
Samantha Varrelman, WSU Undergraduate (2013-2014), Now a Registered Nurse at Mid-Valley Hospital
Bineeta Veach, WSU Undergraduate (2015-2016), Now a Manufacturing Associate at Infectious Disease Research Institute
Charlotte Walker, WSU Undergraduate (Fall 2017)
Courtney Jensen, WSU Undergraduate (2017-2019)
Anna McDonald, WSU Undergraduate (2019-2020)
Caitlyn Patel, WSU Undergraduate (2019-2020)
Maddi Bibby, WSU Undergraduate (2019-2020)
Lili Bahrami, WSU Undergraduate & Lab Technician (2019-2020)
Keegan Paras, WSU Undergraduate (2019-2020)
Kiersey Nielsen, Undergraduate (2020)