Tarvin Lab @ UC Berkeley

Evolutionary biology of chemically defended animals

An important goal in biology is to link genotype with phenotype for traits that affect fitness. Animals that sequester neurotoxins are a useful model for understanding the genetic underpinnings of simple and complex traits. Further, toxic defenses are common, and resistance and sequestration have evolved repeatedly, providing opportunities to reveal genetic mechanisms underlying convergent traits in diverse organisms.

Our lab leverages complementary approaches in model and non-model systems to understand the molecular mechanisms that animals use to resist and sequester neurotoxins. We aim to understand what the causes and consequences are of acquired chemical defenses from DNA- to ecosystem-level changes. In this way, we study the phenomenon of chemical defenses as a window into adaptation and the evolution of novel traits.

Given that neurotoxins target critical nervous system proteins and interact with several biological pathways targeted by human medicine, our research has translational implications for pharmacology and biology of disease. Further, we work with charismatic animals such as poison frogs, Pacific newts, and Harlequin frogs that can be powerful advocates for promoting conservation and efforts towards understanding the impact of global change.

Click on the links to the right to see more information and videos about our research.

Origins of chemical defense in poison frogs

Over the last 50 million years, poison frogs (family Dendrobatidae) have evolved to sequester alkaloids from diminutive arthropod prey three independent times. Along with origins of chemical defense, these dendrobatids have undergone extensive changes in metabolism, skin morphology, diet, coloration, behavior, and neurophysiology. Thus, poison frogs present an excellent system for identifying mechanisms underlying the origins and diversification of complex novel phenotypes.

Why don't poison frogs poison themselves? Their chemical defenses target a variety of ion channel proteins in nervous systems that govern action potentials and neurotransmitter release. Any organism susceptible to these chemicals would not survive being covered in them. We study evolutionary changes in nervous system proteins and other physiological systems that are targeted by poison frog chemical defenses.

Currently funded by NIH NIGMS R35GM150574

Previously funded by NSF (GRFP, DBI-1556967, DUE-0942345, CHE-1531972, IOS-1556982), National Geographic Society (Young Explorer Grant #9468-14), Society of Systematic Biologists, North Carolina Herpetological Society, Society for the Study of Reptiles and Amphibians, Chicago Herpetological Society, Texas Herpetological Society

PUBLICATIONS

Tarvin et al. 2024. Passive accumulation of alkaloids in putatively non-toxic frogs challenges paradigms of the origins of acquired chemical defenses. bioRxiv DOI: 10.1101/2024.05.13.593697

Tarvin et al. 2017. Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance. Science 357: 1261–1266. PDFhttps://doi.org/10.1126/science.aan5061

Tarvin et al. 2016. Convergent substitutions in sodium channel suggest multiple origins of toxin resistance in poison frogs. Molecular Biology and Evolution 33:1068-1081. PDFhttps://doi.org/10.1093/molbev/msv350

Santos et al. 2016. A review of chemical defense in poison frogs (Dendrobatidae): Ecology, pharmacokinetics and autoresistance. In: Schulte, BA, TE Goodwin, MH Ferkin, editors. Chemical Signals in Vertebrates 13. Switzerland: Springer International Publishing. p. 305-337. PDFlink

Evolution of color and pattern in poison frogs

Coloration plays important ecological roles in animals, including mate choice, thermoregulation, and avoiding predation. However, the understanding of how animals produce coloration is based on only a few species and large gaps in knowledge remain. For example, very little is known about how amphibians, one of the major groups of vertebrate animals, produce their beautiful array of colors and patterns. Using recent advances in genomic and developmental biology, we are working to identify the genes that control color and color patterning in three species of poison frogs that represent some of the most colorful and charismatic vertebrates. The development of poison frogs as a model system for the study of coloration will identify key biological mechanisms that contribute to coloration, and open new avenues of research into genetics of color in other animals.

Among the 300 species of dendrobatid poison frogs, the Epipedobates clade is the youngest group that is both chemically defended and brightly colored, offering a glimpse into incipient origins of aposematism. By studying the extensive phenotypic variation in Epipedobates, we are illuminating the evolutionary pathways, population dynamics, and molecular mechanisms underlying the complex ecological shift to aposematism.

Currently funded by NSF IOS-2319711, a collaborative grant with Rasmus Nielsen, Adam Stuckert, Santiago Ron, Roberto Márquez, Mathieu Chouteau, and Andrés Romero.

Previously funded by NSF (GRFP, DBI-1556967, DUE-0942345, CHE-1531972, IOS-1556982), National Geographic Society (Young Explorer Grant #9468-14), Society of Systematic Biologists, North Carolina Herpetological Society, Society for the Study of Reptiles and Amphibians, Chicago Herpetological Society, Texas Herpetological Society

PUBLICATIONS

Betancourth-Cundar et al. 2024. Honoring the Afro-Colombian musical culture with the naming of Epipedobates [to be revealed] sp. nov. (Anura: Dendrobatidae), a frog from the Pacific rainforests. bioRxiv DOI: https://doi.org/10.1101/2024.03.23.586415

López-Hervas et al. 2024. Deep divergences among inconspicuously colored clades of Epipedobates poison frogs. Molecular Phylogenetics and Evolution 195: 108065. DOI: https://doi.org/10.1016/j.ympev.2024.108065PDF

Tarvin et al. 2017. The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs. ​Molecular Phylogenetics and Evolution 109: 283–295. PDFhttps://doi.org/10.1016/j.ympev.2016.12.035

Evolving toxic flies

Evolutionary transitions underlying large-scale phenotypic change are difficult to study because they often occur over millions of years. However, the fruit fly has a short generation time and a small genome that is well annotated and cheap to sequence. We are using experimental evolution to evolve toxin-sequestering fruit flies. Evolutionary changes in the fruit fly genome, transcriptome, and physiology will generate a model of how chemical defense arises that will inform future studies in poison frogs and other organisms.

Douglas et al. 2022. Trade-offs between cost of ingestion and rate of intake drive defensive toxin use. 2022. Biology Letters 18(2): 20210579. DOI: 10.1098/rsbl.2021.0579PDF

Currently funded by NIH NIGMS R35GM150574

Convergent origins of tetrodotoxin-based defenses in amphibians

Tetrodotoxin is a potent neurotoxin found in many marine organisms. On land, it is known only in amphibians, including the Pacific newts of genus Taricha and Harlequin frogs of genus Atelopus. We study the ecology, evolution, and genetics of both systems to better understand why and how amphibians are able to wield such a dangerous compound.

Currently funded by NIH NIGMS R35GM150574

PUBLICATIONS

Tarvin et al. 2023. The diverse mechanisms animals use to resist toxins. Annual Review of Ecology, Evolution, and Systematics 54: 283-306. https://doi.org/10.1146/annurev-ecolsys-102320-102117PDF

Montana et al. 2023. Are Pacific Chorus Frogs (Pseudacris regilla) resistant to tetrodotoxin (TTX)? Characterizing potential TTX exposure and resistance in an ecological associate of Pacific Newts (Taricha). Journal of Herpetology 57: 220—228. https://doi.org/10.1670/22-002PDF

Pearson and Tarvin. 2022. A review of chemical defense in harlequin toads (Bufonidae; Atelopus). Toxicon: X 13:100092. https://doi.org/10.1016/j.toxcx.2022.100092PDF

Museum, database, and field-based research

Here at the Museum of Vertebrate Zoology, we house nearly 300,000 amphibian and reptile specimens. We care deeply about our collections and their value as a biodiversity library to the scientific community. We work with AmphibiaWeb and the Amphibian Genomics Consortium to connect amphibian researchers, conservationists, and educators. We also work with museum specimens to conduct original research.

PUBLICATIONS

Douglas et al. 2024. Genome size evolution and life history correlates in the poison frog family Dendrobatidae. bioRxiv DOI: 10.1101/2023.06.30.547273

Kosch et al. 2024. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. bioRxiv DOI: https://doi.org/10.1101/2024.06.27.601086

Nachman et al. 2023. Specimen collection is essential for modern science. PLoS Biology 21:e3002318. https://doi.org/10.1371/journal.pbio.3002318PDF

Ramírez Castañeda et al. 2022. A set of principles and practical suggestions for equitable fieldwork in biology. Proceedings of the National Academy of Sciences of the United States of America 119: e2122667119. https://doi.org/10.1073/pnas.2122667119

Womack et al. 2022. State of the Amphibia 2020: Five years of amphibian research, diversity and resources. Journal of Ichthyology and Herpetology 110: 638–661. https://doi.org/10.1643/h2022005PDF

Uetz et al. 2021. A Quarter Century of Reptile and Amphibian Databases. Herpetological Review 52(2): 246-255. PDFlink

Genomics of Kleptocnidy in Nudibranchs

Stolen organelles quite literally fuel much of Earth’s biodiversity. Nudibranch mollusks are small marine invertebrates that inhabit tidal pools around the world; two clades have convergently evolved the ability to acquire nematocysts, the stinging organelles unique to cnidarians. We are working to uncover what mechanisms these nudibranchs use to sequester and mature nematocysts from their food.

Currently seeking funding. This is a collaboration with Jessica Goodheart at the American Museum of Natural History.

Poison frogs resist the effects of their own poisons by tweaking the structure of some proteins that send signals to their brain. But this strategy isn't foolproof, new research shows. Read more: https://www.sciencenews.org/article/way-poison-frogs-keep-poisoning-themselves-complicated Story Laurel Hamers Production Helen Thompson Video & stills Rebecca Tarvin Cecilia Borghese/UCSF Chimera Music "Bouncing" by Blue Dot Sessions http://freemusicarchive.org/music/Blue_Dot_Sessions/Intent/Bouncing (CC BY-NC 4.0) https://creativecommons.org/licenses/by-nc/4.0/ Citation R.