Darin Rokyta

Darin Rokyta
Florida State University | FSU · Department of Biological Science

Ph.D.

About

128
Publications
15,401
Reads
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2,681
Citations
Citations since 2016
56 Research Items
1885 Citations
20162017201820192020202120220100200300
20162017201820192020202120220100200300
20162017201820192020202120220100200300
20162017201820192020202120220100200300
Additional affiliations
August 2014 - present
Florida State University
Position
  • Professor (Associate)
July 2008 - August 2014
Florida State University
Position
  • Professor (Assistant)
May 2006 - July 2008
University of Idaho
Position
  • PostDoc Position
Education
August 2000 - May 2006
University of Idaho
Field of study
  • Bioinformatics and Computational Biology
August 1995 - December 1999
University of Texas at Austin
Field of study
  • Zoology

Publications

Publications (128)
Article
Traits for prey acquisition form the phenotypic interface of predator–prey interactions. In venomous predators, morphological variation in venom delivery apparatus like fangs and stingers may be optimized for dispatching prey. Here, we determine how a single dimension of venom injection systems evolves in response to variation in the size, climatic...
Article
On 17 June 2019, we collected a unique juvenile rattlesnake from a wildlife response call on Jekyll Island State Park, GA. The snake exhibited intermediate color patterns and gross anatomical features suggesting potential hybridization between Crotalus horridus (Canebrake/Timber Rattlesnake) and Crotalus adamanteus (Eastern Diamond-back Rattlesnake...
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Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in east Asia and belongs to a monotypic subfamily, s...
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Understanding the joint roles of amino acid sequences variation of proteins and differential expression during adaptive evolution is a fundamental, yet largely unrealized, goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom gland transcriptome dataset spanning three genera of pitvipers to identify...
Article
As biochemical traits with clear fitness consequences, venoms serve a critical ecological role for the animals that produce them. Understanding how venoms are maintained and regenerated after use will, therefore, provide valuable insight into the ecology of venomous animals. Furthermore, most studies on venomous organisms often require removing ani...
Article
[https://doi.org/10.1016/j.toxicon.2021.11.009] Most traditional research on snake venoms has focused on front-fanged snake families (Viperidae, Elapidae, and Atractaspididae). However, venom is now generally accepted as being a much more broadly possessed trait within snakes, including species traditionally considered harmless. Unfortunately, due...
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Ecologically divergent selection can lead to the evolution of reproductive isolation through the process of ecological speciation, but the balance of responsible evolutionary forces is often obscured by an inadequate assessment of demographic history and the genetics of traits under selection. Snake venoms have emerged as a system for studying the...
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The voltage-gated sodium channel Nav1.8 is linked to neuropathic and inflammatory pain, highlighting the potential to serve as a drug target. However, the biophysical mechanisms that regulate Nav1.8 activation and inactivation gating are not completely understood. Progress has been hindered by a lack of biochemical tools for examining Nav1.8 gating...
Preprint
Full-text available
The voltage-gated sodium channel Nav1.8 is linked to neuropathic and inflammatory pain, high-lighting the potential to serve as a drug target. However, the biophysical mechanisms that regu-late Nav1.8 activation and inactivation gating are not completely understood. Progress has been hindered by a lack of biochemical tools for examining Nav1.8 gati...
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Pitviper sensory perception incorporates diverse stimuli through the integration of trichromatic color vision, bifocal heat-sensing, and dual-system chemoperception. Chemoperception, or olfaction, is mediated by chemoreceptors in the olfactory bulb and the vomeronasal organ, but the true genomic complexity of the gene families and their relative co...
Article
Venom is an integral feeding trait in many animal species. Although venom often varies ontogenetically, little is known about the proximate physiological mediators of venom variation within individuals. The glucocorticoid hormone corticosterone can alter transcription and activation of proteins, including homologues of snake venom components such a...
Article
Significance Why biological complexity evolves is a major question in the life sciences, but the specific selection pressures favoring simple or complex traits remain unclear. Using high-resolution measurements of venom complexity in North American pitvipers, we link changes in complexity to natural history via phylogenetic diversity of snake diets...
Article
Motivation Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time...
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The genus Calliophis is the most basal branch of the family Elapidae and several species in it have developed highly elongated venom glands. Recent research has shown that C. bivirgatus has evolved a seemingly unique toxin (calliotoxin) that produces spastic paralysis in their prey by acting on the voltage-gated sodium (NaV) channels. We assembled...
Article
Significance A central question in biology is whether trait differences are the result of variation in gene number, sequence, or regulation. Snake venoms are an excellent system for addressing this question because of their genetic tractability, contributions to fitness, and high evolutionary rates. We sequenced and assembled the genome of the Tige...
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Ontogenetic changes in venom composition have been described in Bothrops snakes, but only a few studies have attempted to identify the targeted paralogues or the molecular mechanisms involved in modifications of gene expression during ontogeny. In this study, we decoded B. jararacussu venom gland transcripts from six specimens of varying sizes and...
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Ontogenetic shifts in venom occur in many snakes but establishing their nature as gradual or discrete processes required additional study. We profiled shifts in venom expression from the neonate to adult sizes of two rattlesnake species, the eastern diamondback and the timber rattlesnake. We used serial sampling and venom chromatographic profiling...
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An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the Eastern Massasauga rattlesnake (Sistrurus catenatus...
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Background: Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a tra...
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Voltage-gated sodium (NaV) channels play a fundamental role in normal neurological function, especially via the initiation and propagation of action potentials. The NaV1.1 subtype is found in inhibitory interneurons of the brain and it is essential for maintaining a balance between excitation and inhibition in neuronal networks. Heterozygous loss-o...
Article
Sexually dimorphic traits are widespread across metazoans and are often the result of sex-specific inheritance or sex-based differences in gene expression. Intersexual differences have even been observed in invertebrate venoms, although the identification of these differences has been limited to the more well-studied groups, such as scorpions and s...
Article
Traits can evolve rapidly through changes in gene expression or protein-coding sequences. However, these forms of genetic variation can be correlated and changes to one can influence the other. As a result,we might expect traits lacking differential expression to preferentially evolve through changes in protein sequences or morphological adaptation...
Article
Many venom proteins have presumably been convergently recruited by taxa from diverse venomous lineages. These toxic proteins have characteristics that allow them to remain stable in solution and have a high propensity for toxic effects on prey and/or potential predators. Despite this well-established convergent toxin recruitment, some toxins seem t...
Article
A longstanding prediction in evolutionary biology is that organisms experience a “cost of complexity” such that an increase in the number of phenotypes under selection results in a decreased rate of adaptation in the population... A long-standing prediction in evolutionary biology is that organisms experience a so-called “cost of complexity” manife...
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Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e.g., trehalose, alter local wate...
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Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage...
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The migration-selection interaction is the strongest determinant of whether a beneficial allele increases in frequency within a population. Results of empirical studies examining the role of gene flow in an adaptive context, however, have largely been equivocal, with examples of opposing outcomes being repeatedly documented (e.g., local adaptation...
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Changes in gene expression can rapidly influence adaptive traits in the early stages of lineage diversification. Venom is an adaptive trait comprised of numerous toxins used for prey capture and defense. Snake venoms can vary widely between conspecific populations, but the influence of lineage diversification on such compositional differences are u...
Preprint
Full-text available
A longstanding prediction in evolutionary biology is that organisms experience a so-called "cost of complexity" manifested as a decreasing rate of adaptation in populations as organisms or selective environments become increasingly complex. This theory assumes the ubiquity of antagonistic pleiotropy, or tradeoffs in fitness, for mutations affecting...
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The Asian genus Boiga (Colubridae) is among the better studied non-front-fanged snake lineages because their bites have minor, but noticeable, effects on humans. Further, B. irregularis has gained worldwide notoriety for successfully invading Guam and other nearby islands with drastic impacts on the local bird populations. One of the factors though...
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Facultative parthenogenesis (FP) is asexual reproduction in plant and animal species that would otherwise reproduce sexually. This process in vertebrates typically results from automictic development (likely terminal fusion) and is phylogenetically widespread. In squamate reptiles and chondrichthyan fishes, FP has been reported to occur in nature a...
Article
The limited number of centipede venom characterizations have revealed a rich diversity of toxins, and recent work has suggested centipede toxins may be more rapidly diversifying than previously considered. Additionally, many identified challenges in venomics research, including assembly and annotation methods, toxin quantification, and the ability...
Article
Sex-biased genes are expressed at higher levels in one sex and contribute to phenotypic differences between males and females, as well as overall phenotypic variation within and among populations. Venom has evolved primarily for predation and defense, making venom expression a highly variable phenotype as a result of local adaptation. Several scorp...
Article
Identifying the environmental correlates of divergence in functional traits between populations can provide insights into the evolutionary mechanisms that generate local adaptation. Here, we assess patterns of population differentiation in expressed venom proteins in Northern Pacific rattlesnakes (Crotalus oreganus) from 13 locations across Califor...
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Venom-gland transcriptomics is a key tool in the study of the evolution, ecology, function, and pharmacology of animal venoms. In particular, gene-expression variation and coding sequences gained through transcriptomics provide key information for explaining functional venom variation over both ecological and evolutionary timescales. The accuracy a...
Article
Significance: Analysis of individual transcripts and venom protein isoforms produced by specimens of a venomous snake (Bothrops atrox), from the Brazilian Amazon rainforest, revealed that transcriptional and translational mechanisms contribute to venom phenotypic variation. Our finding of evidence for high expression of toxin proteins with conserv...
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Phenotypic diversity generated through altered gene expression is a primary mechanism facilitating evolutionary response in natural systems. By linking the phenotype to genotype through transcriptomics, it is possible to determine what changes are occurring at the molecular level. High phenotypic diversity has been documented in rattlesnake venom,...
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Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases (SVMP). Type II venoms are highly neuro...
Article
Of the 14 extant scorpion families, Buthidae has the most thoroughly characterized venoms. Most of this characterization, however, has been limited to species with medically significant stings, including members of the Centruroides genus, which have caused human deaths (e.g., Centruroides sculpturatus). To understand the origin and evolution of hig...
Article
Gene interactions, or epistasis, play a large role in determining evolutionary outcomes. The ruggedness of fitness landscapes, and thus the predictability of evolution and the accessibility of high-fitness genotypes, is determined largely by the pervasiveness of epistasis and the degree of correlation between similar genotypes. We created all possi...
Article
Convergent evolution has been demonstrated across all levels of biological organization, from parallel nucleotide substitutions to convergent evolution of complex phenotypes, but whether instances of convergence are the result of selection repeatedly finding the same optimal solution to a recurring problem or are the product of mutational biases re...
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A trait’s genomic architecture can affect the rate and mechanism of adaptation, and although many ecologically-important traits are polygenic, most studies connecting genotype, phenotype, and fitness in natural populations have focused on traits with relatively simple genetic bases. To understand the genetic basis of polygenic adaptation, we must i...
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Gene duplication is the primary mechanism leading to new genes and phenotypic novelty, but the proximate evolutionary processes underlying gene family origin, maintenance, and expansion are poorly understood. Although sub- and neofunctionalization provide clear long-term advantages, selection does not act with foresight, and unless a redundant gene...
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The same selective forces that give rise to rapid inter-and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. Th...
Article
The order Scorpiones is one of the most ancient and diverse lineages of venomous animals, having originated approximately 430 million years ago and diversified into 14 extant families. Although partial venom characterizations have been described for numerous scorpion species, we provided the first quantitative transcriptome/proteome comparison for...
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Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from mult...
Article
Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can...
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Adaptive evolution progresses as a series of steps toward a multidimensional phenotypic optimum, and organismal or environmental complexity determine the number of phenotypic dimensions, or traits, under selection. Populations evolving in complex environments may experience costs of complexity such that improvement in one or more traits is impeded...
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Protein expression level is one of the strongest predictors of protein sequence evolutionary rate, with high-expression protein sequences evolving at slower rates than low-expression protein sequences, largely because of constraints on protein folding and function. Expression evolutionary rates have also been shown to be negatively correlated with...
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Horizontal gene transfer and recombination occur across many groups of viruses and play key roles in important viral processes such as host-range expansion and immune-system avoidance. To have any predictive power regarding the ability of viruses to readily recombine, we must determine the extent to which epistasis restricts the success of recombin...
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Protein expression is a major link in the genotype-phenotype relationship, and processes affecting protein abundances, such as rates of transcription and translation, could contribute to phenotypic evolution if they generate heritable variation. Recent work has suggested that mRNA abundances do not accurately predict final protein abundances, which...
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Documentamos dos nuevas localidades y confirmamos el establecimiento de una población reproductora del ciempiés no nativo Rhysida longipes longipes (Scolopendromorpha: Scolopendridae: Otostigminae) en el sur de la Florida por primera vez. Los animales se observaron de varias clases de tamaño a través de una gran propiedad en Islamorada, Upper Matec...