Venom Evolution

Snake Venoms

The Rokyta Lab’s primary systems for studying the genetics of adaptation are the venomous snakes, particularly the pitvipers. Animal venoms are powerful systems for studying the adaptive impacts and phenotypic consequences of gene-regulatory variation because of their modest levels of complexity (i.e., 20–200 venom genes), exceptional levels of variation across all evolutionary scales, and, perhaps most importantly, genetic and functional tractability. Discerning the phenotypic and fitness impacts of gene-regulatory variation, however, requires understanding how this variation transmits through gene-regulatory networks to affect phenotypes. Because most traits emerge from poorly characterized developmental pathways where gene-regulatory changes may have effects mediated through complex interaction networks, linking regulatory variation to phenotypic divergence in complex traits remains a challenge. Given that venoms are secretions, changes in toxin-gene expression levels directly alter protein amounts in the venom and thereby directly influence venom efficacy.

Our early efforts in this system focused on transcriptomic and proteomic characterizations of patterns of variation within and between species and has more recently expanded to genomics and epigenomics. We have studied the roles of gene flow and selection in generating patterns of  venom variation within species and have taken a broader approach to assess the relationship between venom properties and genetics to the patterns of diversification among species across all venomous snakes. The 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.

In addition to studying patterns of variation within and between species, we are using epigenomic techniques to understand the control of expression within individuals. For examples, the Eastern Diamondback Rattlesnake (Crotalus adamanteus), like many rattlesnake species, undergoes a change in venom composition with age which mirrors major size-related dietary shifts. We are determining the genetic mechanisms underlying this major expression change and using differences in the ontogenetic change among closely related species as a model for understanding how genes can evolve new regulatory patterns.

Invertebrate Venoms

Convergent evolution is a hallmark of adaptation and provides a means for delineating the roles of genetic and functional constraints in determining evolutionary trajectories. Venoms are one of the most common and convergent functions among animals, with more than 200,000 venomous species from more than 100 venom-origin events, and venom function requires recurrent evolution of specialized tissues and gene-regulatory networks to express, process, secrete, and store toxins. Substantial convergence in recruited protein families, tissues of origin, and contributing gene-regulatory networks has been observed, yet venoms are exceptionally variable at all taxonomic levels. Venoms therefore represent a unique opportunity for discerning rules and idiosyncrasies of complex trait origin and subsequent evolution under parallel constraints. The Rokyta Lab has therefore expanded our venom work in snakes to encompass the evolution of scorpion, centipede, and spider venoms.

Centipedes, scorpions, and spiders are much more locally abundant than snakes and far easier to maintain and work with in the lab in large numbers. In addition to developing genomic resources for these major terrestrial lineages, we have also begun to use diet metabarcoding approaches to characterize the diets of local venomous species such as the Hentz Striped Scorpion (Centruroides hentzi) and several species of wolf spiders in the genus Hogna. The goal of this work is to assess the relationship between diet complexity and venom complexity. Much of this work is being undertaken by the excellent undergraduate researchers in the lab. See our species page for examples of our focal species.

Venom Resistance

Model Prey

Venomous animals and interacting species represent powerful systems for studying the genetics of coevolution because venoms function solely following injection into another organism, resulting in direct species interactions. The extensive variation in venoms is typically attributed to coevolution with particular interacting species, but the full genetic basis of venom resistance is almost entirely unknown. Previous work has focused largely on single toxin-gene/resistance-gene interactions. Venoms, hoever, are cocktails of numerous proteins and peptides; the multifarious activities of its components make resistance far more complex than a single-locus arms race. Therefore, a systems-level analysis of venom and resistance is needed to determine how the relative genetic complexities of interacting traits affect coevolutionary dynamics

Although none of our local venomous invertebrate species likely preys on fruit flies (Drosophila melanogaster), all are primarily insectivorous and at least some consume dipterans. Additionally, venoms generally target basic physiological systems that are likely to be evolutionarily conserved. By using D. melanogaster as model prey, we gain access to genetic tools, resources, and knowledge that are unparalleled in any other animal system, including collections of sequenced inbred lines, pre-constructed RNAi knockdown lines, and comprehensive databases of genetic information. These resources substantially increase our power to detect, confirm, and understand loci contributing to venom resistance and, therefore, directly link venom genes to the genomes of venom recipients.

We are currently using two primary approaches to studying the genetics of venom resistance in fruit flies. We are using experimental evolution to directly observe the evolution of resistance by using direct venom injection as a selective pressure over many generations, and we are using the response to single venom-based selective events in an extreme quantitative trait loci (XQTL) mapping framework. Our goal is to apply these approaches to a diverse array of venoms from scorpions, centipedes, and spiders to assess relationships between venom and resistance complexities, determine the generality of resistance mechanisms across venoms, and assess the extent to which venoms from closely related species differ in the selective pressures they engender in prey.

Natural Prey

To assess the generality of our results from model prey (Drosophila melanogaster), we are actively developing several native prey species of our local venom invertebrates for use in mapping the genes contributing to variation in venom resistance. These include the Sand Field Cricket (Gryllus firmus), the Ambitious Ground Cricket (Pictonemobius ambitiosus), and the Florida Woods Cockroach (Eurycotis floridana). All of these species are locally abundant and easy to maintain and breed in a lab setting, and all should be readily amenable to XQTL analysis of resistance.

Viral Experimental Evolution

Although research efforts in the lab have shifted toward venom evolution for the last several years, experimental evolution is still a core interest of the lab. 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 also use molecular-dynamics simulation to determine the biophysical bases for the beneficial and epistatic effects of identified mutations.