INVESTIGATING THE GENETIC BASIS OF CAVEFISH EVOLUTION

We use the Mexican tetra, Astyanax mexicanus, to study genetic changes that underlie morphological and physiological evolution

Cave-dwelling populations of Astyanax mexicanus have adapted to a dramatically different environment than their river-dwelling ancestors. Over 200,000 years ago, these fish colonized the perpetual darkness of underground limestone caves in northeastern Mexico. With food sources scarce, they evolved to survive on bat droppings and seasonal flood debris, while their surface relatives thrived on a diet rich in plants and insects.

Cavefish look strikingly different from their surface-dwelling relatives, despite being the same species. The most noticeable differences are their lack of eyes and reduced pigmentation. They have also evolved an insatiable appetite and a unique metabolism that allows them to store more fat than surface fish—an advantage in their food-scarce environment. Interestingly, some of their adaptations, like insulin resistance, are harmful in humans but help cavefish survive. There are multiple independent cavefish populations that can be utilized as natural replicates in the study of evolution.

The Mexican tetra has become an important model system due to the increasing availability of tools for studying gene function. Our research uses quantitative trait loci (QTL) mapping to identify genomic regions associated with metabolic changes. To pinpoint the genetic changes driving cavefish adaptations, we integrate comparative genomics, transcriptomics, and gene editing techniques.

Current projects are aimed at uncovering how evolution has modified:

Carotenoid and Vitamin A metabolism
Host-microbiome interactions
Gastrointestinal homeostasis
Development and function of the enteric nervous system

A complete publication list can be viewed on Google Scholar

Our Team

We are a group of scientists from diverse backgrounds, united by a shared passion for advancing our understanding of the natural world. Our lab's mission is to conduct research that makes a lasting impact on our knowledge of life, and create an environment where members can learn, grow, and build a strong community.

Lab members

Misty Riddle PhD

Principle Investigator

Misty earned her bachelor's degree from Westminster College, studying the brine shrimp microbiome, and her Ph.D. from UC Santa Barbara, researching cell fate determination in C. elegans. Driven by an interest in natural variation and development, she joined Clifford Tabin's lab at Harvard Medical School, where she established her research on Eco-Evo-Devo in the Mexican tetra. She is now an assistant professor in the Biology Department.

email: mistyriddle@unr.edu

Pavani Perera Ponnimbaduge

PhD candidate in Molecular Biosciences

Pavani is an international student. She earned her B.Sc (hon) in Zoology with a first class at the University of Colombo, Sri Lanka. As an undergraduate, Pavani became passionate about studying cave ecosystems and the adaptive plasticity of vertebrates in extreme environments. Now, as a graduate student in the Riddle Lab, Pavani studies the evolution and development of the vertebrate gastrointestinal tract using the unique model system, Mexican cavefish (Astyanax mexicanus).

Email: pponnimbadugeperera@unr.edu

Website: https://pavanidperera.faculty.bio

Bethany Ponte

PhD candidate in Integrative Neuroscience

Bethany has a BS degree in Psychology with an Emphasis in Biology from UC Davis. She joined the integrative neuroscience program to learn more about neuroscience and conduct laboratory research. In Dr. Riddle’s lab, she is investigating the evolution of oocyte maturation in A. mexicanus with an emphasis on the role of the neuronal network that surrounds the ovaries.

Email: bethanyponte@nevada.unr.edu

Maeve Nave

PhD candidate in Molecular Biosciences

Maeve received her BS in Biology from University of California, Santa Cruz in 2020, and continued as a research assistant in the COVID Molecular Diagnostic Lab there at UCSC post grad. She then went on to working for the Miura lab at UNR studying 3’UTR effects on glutamatergic neurons differentiation. In the Riddle lab, she investigates the genetic basis of microbiome composition in A. mexicanus with a keen interest in understanding how host-microbiome interactions influence physiology, metabolism, and evolution.

Email: mnave@nevada.unr.edu

Halleluyah Kola-Adebayo

Graduate Student in Ecology, Evolution, and Conservation Biology

Halleluyah is an international graduate student from Nigeria. She earned her B.Tech. in Fisheries and Aquaculture Technology with a First-Class degree from Federal University of Technology Akure, Nigeria. During her undergraduate studies, she developed a strong interest in fish biology and physiology, which later evolved into a broader curiosity about evolutionary processes in aquatic organisms. In the Riddle Lab, Halleluyah is interested in exploring differences in carotenoid metabolism between A. mexicanus populations and how these variations contribute to adaptation in extreme environments.

Email: hkolaadebayo@unr.edu

LinkedIN: Halleluyah Kola-Adebayo

Dasha Yu

Undergraduate

Dasha is an undergraduate student majoring in biology and minoring in psychology at the University of Nevada, Reno. She is interested in studying the evolution of vertebrate GI tract. In Riddle lab, she assists in understanding the evolution of gut anatomy/morphology using Mexican tetra.

Kaitlyn Webster PhD

Postdoc at Harvard Medical School

Kaitlyn collaborates closely with the Riddle lab. She is a postdoctoral fellow with experience in germ cells and models of male infertility. Kaitlyn is interested in understanding the developmental biology and genetics of gonadal sex differentiation in teleosts, particularly zebrafish and Astyanax mexicanus.

Email: kaitlyn_webster@hms.harvard.edu

Zack Johnson

Fish Facility Manager

Zack earned his undergraduate degree at the University of Puget Sound with a Biology major and a Neuroscience minor. He spent his undergrad studying the serotonergic control of oxygen-seeking behaviors exhibited in anoxic environments by embryonic pond snails (H. trivolvis). He joined the lab in December 2025 as the fish facility manager and ensures the fish are healthy and happy.

Join Us!

Graduate Research Assistant Position

Evolutionary Genetics of Host–Microbiome Interactions

Spring 2027 Start

We are recruiting a Ph.D. student to participate in a funded NSF CAREER project investigating the genetic basis of host–microbiome interactions during evolution. The successful applicant will investigate how host genetic variation shapes microbiome composition and how microbiome evolution contributes to adaptation in extreme environments. Students will receive interdisciplinary training at the interface of evolutionary biology, genetics, microbiology, and genomics.

Projects may include:

Microbiome profiling
Host transcriptomics and gene expression analysis
Quantitative trait locus (QTL) mapping
Evolutionary genomics and population genetics
CRISPR-based functional genetics
Germ-free and microbiome manipulation experiments
Bioinformatics

Applicants should have:

A B.S. or M.S. in biology, microbiology, genetics, ecology, bioinformatics, or a related field
Strong interest in evolutionary biology and host–microbe interactions
Experience in molecular biology, microbiology, genomics, aquatic husbandry, or computational biology is desirable but not required

Funding

The position includes a graduate stipend, tuition support, health insurance, and funding for conference travel.

Prospective students should contact Dr. Misty Riddle (mistyriddle@unr.edu) directly and include:

CV
Unofficial transcripts
Brief statement of research interests

The lab is located in the University of Nevada, Reno within the Department of Biology, an integrative department that spans molecular biology, physiology, ecology, and evolution. Reno sits at the base of the Sierra Nevada mountains and offers immediate access to outdoor recreation, including Lake Tahoe, hiking, skiing, and mountain biking.