The Rokyta Lab has two major research programs involving snake venoms that address two very different levels of biological organization. The first project focuses on developing transcriptomic, proteomic, and genomic tools for the study of snake venoms and applying these tools to study the roles of gene flow and selection in generating patterns of venom variation within species. The second project takes a broader approach to assess the relationship between venom properties and genetics to the patterns of diversification among species across all venomous snakes. Venom largely defines the ecology of those species possessing it and is a genetically tractable complex trait known to frequently be under strong Darwinian selection. These relatively unique properties of venom allow us to study the effects of strong selection on micro- and macroevolutionary processes and the underlying genetic details of these processes.
Intraspecific snake-venom variation
The Rokyta Lab was awarded a National Science Foundation grant in 2012 (NSF DEB 1145987) with CoPIs Dr. Emily Lemmon in the Department of Biological Science and Dr. Alan Lemmon in the Department of Scientific Computing at Florida State University to study intraspecific variation in venom of snake species native to the southeastern United States (see our species page). As part of this project, we developed transcriptomic and proteomic techniques for the characterization of the genetics of venom systems and population-genomic techniques for studying venom-gene sequence variation. We have been using these techniques to study the roles of selection and gene flow in the intraspecific patterns of venom variation in the eastern diamondback rattlesnake (Crotalus adamanteus), the timber rattlesnake (Crotalus horridus), the pygmy rattlesnake (Sistrurus miliarius), the cottonmouth (Agkistrodon piscivorus), and the eastern coralsnake (Micrurus fulvius). We are particularly interested in the biases introduced in the process of adaptation by the genetic architecture of traits. Now that we have done the work of characterizing patterns of variation, we plan to focus on determining the precise nature of the selective forces favoring this variation and the functional consequences of the observed variation. In particular, we plan to determine whether venoms are diverging among populations in response to differences in prey availability, environments, or just due to independent instances of coevolutionary interactions and why particular venom-gene alleles are favored in particular geographic regions.
Snake venom and species diversity
This project is an international collaboration involving researchers in the U.S. and Brazil and is funded by the National Science Foundation and FAPESP. In addition to the Rokyta Lab, the collaborators include Dr. Lisle Gibbs at Ohio State University, Dr. Christopher Parkinson at the University of Central Florida, Drs. Inácio de Loiola Meirelles Junqueira de Azevedo, Ana Maria Moura da Silva, and Erika Hingst-Zaher at the Instituto Butantan, and Dr. Hassam Zaher at the University of São Paulo. Understanding rapid diversification within evolutionary lineages requires determination of the factors and traits that promoted that diversification. Key innovations can lead to adaptive radiations by rendering new areas of ecological niche space accessible to a lineage and its descendents. The advanced snakes (superfamily Colubroidea) are comprised of more than 2,500 species, account for the majority of extant snake species, and represent one of the most diverse groups of terrestrial vertebrates. This superfamily originated approximately 100 million years ago and includes the front-fanged venomous families Viperidae and Elapidae and a diverse array of rear-fanged venomous species in the family Colubridae. Venom is hypothesized to have been the innovation initiating this radiation by expanding trophic opportunities, and subsequent toxin recruitment and toxin-gene neofunctionalization may have secondarily promoted further diversification. Venom and its coevolutionary interactions with prey provide strong selective pressures necessary to drive rapid evolution as well as natural mechanisms to generate extrinsic pre- and postzygotic isolation through reduced immigrant and hybrid fitnesses. Our goals for this project include determining how secondary key innovations within the venom system contributed to diversification patterns in the advanced snakes and testing for biases in the genetic pathways underlying rapid phenotypic evolution in venoms between closely related species as a means for understanding the process of diversification. An overview of our sampling strategy can be found here.
Viral Experimental Evolution
This project is currently funded by the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health (NIH) and is a collaboration with Dr. Wei Yang in the Department of Chemistry at Florida State University. The goals of this research include testing theoretical predictions about pleiotropy, epistasis, and adaptation in bacteriophages (i.e., viruses that infect bacteria) and identifying the mechanistic bases for these phenomena. The bacteriophages we use are all in the family Microviridae, have small genomes encoding only 11 proteins, and have generation times of approximately 12 minutes under standard laboratory conditions. These short generation times allow us to observe adaptive evolutionary changes in hours or days by applying defined selective pressures to laboratory populations. We use a unique protocol involving rapidly fluctuating selective pressures to induce a two-component fitness based on growth rate and capsid stability. The selection protocol, inspired by the population dynamics experienced by many pathogens, consists of periods of growth within hosts punctuated by strong selection for survival in the absence of hosts. Growth is allowed under normal culturing conditions, but survival selection involves extreme heat or pH, which selects for capsid stability, a simple yet fundamental biophysical property. We are using this protocol to study the pleiotropic effects of beneficial mutations in terms of a reaction rate and protein stability and to determine how this conflict, and pleiotropy in general, affects the genetic variation available for adaptation. By engineering identified beneficial mutations into new genetic contexts, we are measuring the extent to which biophysical properties of mutations are additive across backgrounds. By allowing long-term adaptation, we are determining whether deleterious pleiotropic effects can be overcome through compensatory evolution so that the two traits can be simultaneously maximized. We are also using molecular-dynamics simulation to determine the biophysical bases for the beneficial and epistatic effects of identified mutations.
The newest area of research in the Rokyta Lab is the evolution of scorpion and centipede venoms. This work is currently funded by a planning grant from the Florida State University Council on Research and Creativity. The goals of this project include testing the generality of the snake-venom results and developing a system for which prey-based studies of venom function and coevolution are more feasible. The number of snake species for which dense, range-wide sampling required for population genetics is possible is fairly limited, and venomous snakes represent only a tiny fraction of the diversity of venomous animal species. Centipedes, scorpions, and their prey are much more locally abundant than snakes and far easier to maintain and work with in the lab in large numbers. We are currently focusing on single-animal characterizations of venom composition and genes for scorpion and centipede species native to the U.S. and generating data to measure the extent of genetic and proteomic variation within and between species. See our species page for examples of our focal species.