51
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Rautsaw RM, Hofmann EP, Margres MJ, Holding ML, Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes ( Crotalus cerastes). Proc Biol Sci 2019; 286:20190810. [PMID: 31266424 DOI: 10.1098/rspb.2019.0810] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
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. Given the lack of differential expression across the distribution of sidewinder rattlesnakes ( Crotalus cerastes), we tested this hypothesis by comparing the coding regions of genes expressed in the venom gland transcriptomes and fang morphology. We calculated Tajima's D and FST across four populations comparing toxin and nontoxin loci. Overall, we found little evidence of directional selection or differentiation between populations, suggesting that changes to protein sequences do not underlie the evolution of sidewinder venom or that toxins are under extremely variant selection pressures. Although low-expression toxins do not have higher sequence divergence between populations, they do have more standing variation on which selection can act. Additionally, we found significant differences in fang length among populations. The lack of differential expression and sequence divergence suggests sidewinders-given their generalist diet, moderate gene flow and environmental variation-are under stabilizing selection which functions to maintain a generalist phenotype. Overall, we demonstrate the importance of examining the relationship between gene expression and protein-coding changes to understand the evolution of complex traits.
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Affiliation(s)
- Rhett M Rautsaw
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA
| | - Erich P Hofmann
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA
| | - Mark J Margres
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA
| | - Matthew L Holding
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA.,3 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Jason L Strickland
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA
| | - Andrew J Mason
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA
| | - Darin R Rokyta
- 3 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Christopher L Parkinson
- 1 Department of Biological Sciences, Clemson University , Clemson, SC 29634 , USA.,2 Department of Forestry and Environmental Conservation, Clemson University , Clemson, SC 29634 , USA
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52
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Margres MJ, Patton A, Wray KP, Hassinger ATB, Ward MJ, Lemmon EM, Lemmon AR, Rokyta DR. Tipping the Scales: The Migration-Selection Balance Leans toward Selection in Snake Venoms. Mol Biol Evol 2019; 36:271-282. [PMID: 30395254 DOI: 10.1093/molbev/msy207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
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 with high levels of gene flow vs. gene swamping). We compared neutral genomic and venom expression divergence for three sympatric pit vipers with differing ecologies to determine if and how migration-selection disequilibria result in local adaptation. We specifically tested whether neutral differentiation predicted phenotypic differentiation within an isolation-by-distance framework. The decoupling of neutral and phenotypic differentiation would indicate selection led to adaptive divergence irrespective of migration, whereas a significant relationship between neutral and venom expression differentiation would provide evidence in favor of the constraining force of gene flow. Neutral differentiation and geographic distance predicted phenotypic differentiation only in the generalist species, indicating that selection was the predominant mechanism in the migration-selection balance underlying adaptive venom evolution in both specialists. Dispersal is thought to be a stronger influence on genetic differentiation than specialization, but our results suggest the opposite. Greater specialization may lead to greater diversification rates, and extreme spatial and temporal variation in selective pressures can favor generalist phenotypes evolving under strong stabilizing selection. Our results are consistent with these expectations, suggesting that the equivocal findings of studies examining the role of gene flow in an adaptive context may be explained by ecological specialization theory.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL.,School of Biological Sciences, Washington State University, Pullman, WA.,Department of Biological Sciences, Clemson University, Clemson, SC
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Alyssa T B Hassinger
- Department of Biological Science, Florida State University, Tallahassee, FL.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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53
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Mathé-Hubert H, Kremmer L, Colinet D, Gatti JL, Van Baaren J, Delava É, Poirié M. Variation in the Venom of Parasitic Wasps, Drift, or Selection? Insights From a Multivariate QST Analysis. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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54
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Goetz SM, Piccolomini S, Hoffman M, Bogan J, Holding ML, Mendonça MT, Steen DA. Serum-based inhibition of pitviper venom by eastern indigo snakes ( Drymarchon couperi). Biol Open 2019; 8:bio.040964. [PMID: 30824421 PMCID: PMC6451346 DOI: 10.1242/bio.040964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
When organisms possess chemical defenses, their predators may eventually evolve resistance to their toxins. Eastern indigo snakes (Drymarchon couperi; EIS) prey on pitvipers and are suspected to possess physiological resistance to their venom. In this study, we formally investigated this hypothesis using microassays that measured the ability of EIS blood sera to inhibit (A) hemolytic and (B) snake venom metalloproteinase (SVMP) activity of copperhead (Agkistrodon contortrix) venom. To serve as controls, we also tested the inhibitory ability of sera from house mice (Mus musculus) and checkered gartersnakes (Thamnophis marcianus), a snake that does not feed on pitvipers. Sera from both EIS and gartersnakes inhibited over 60% of SVMP activity, while only EIS sera also inhibited venom hemolytic activity (78%). Our results demonstrate that EIS serum is indeed capable of inhibiting two of the primary classes of toxins found in copperhead venom, providing the first empirical evidence suggesting that EIS possess physiological resistance to venom upon injection. Because we documented resistance to hemolytic components of pitviper venom within EIS but not gartersnakes, we speculate this resistance may be driven by selection from feeding on pitvipers while resistance to SVMP may be relatively widespread among snakes. Summary: We confirm eastern indigo snakes possess a physiological resistance to pitviper venom and speculate that venom resistance in snakes may be a product of antagonistic interactions and phylogenetically conserved traits.
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Affiliation(s)
- Scott M Goetz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Sara Piccolomini
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Michelle Hoffman
- Orianne Center for Indigo Conservation, Central Florida Zoo & Botanical Gardens, Eustis, FL 32736, USA
| | - James Bogan
- Orianne Center for Indigo Conservation, Central Florida Zoo & Botanical Gardens, Eustis, FL 32736, USA
| | - Matthew L Holding
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32304, USA
| | - Mary T Mendonça
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - David A Steen
- Georgia Sea Turtle Center, Jekyll Island Authority, Jekyll Island, GA 31527, USA
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55
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Harris RJ, Jenner RA. Evolutionary Ecology of Fish Venom: Adaptations and Consequences of Evolving a Venom System. Toxins (Basel) 2019; 11:E60. [PMID: 30678265 PMCID: PMC6409815 DOI: 10.3390/toxins11020060] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 01/21/2023] Open
Abstract
Research on venomous animals has mainly focused on the molecular, biochemical, and pharmacological aspects of venom toxins. However, it is the relatively neglected broader study of evolutionary ecology that is crucial for understanding the biological relevance of venom systems. As fish have convergently evolved venom systems multiple times, it makes them ideal organisms to investigate the evolutionary ecology of venom on a broader scale. This review outlines what is known about how fish venom systems evolved as a result of natural enemy interactions and about the ecological consequences of evolving a venom system. This review will show how research on the evolutionary ecology of venom in fish can aid in understanding the evolutionary ecology of animal venoms more generally. Further, understanding these broad ecological questions can shed more light on the other areas of toxinology, with applications across multiple disciplinary fields.
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Affiliation(s)
- Richard J Harris
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
| | - Ronald A Jenner
- Department of Life Sciences, the Natural History Museum, Cromwell Road, SW7 5BD London, UK.
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56
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Healy K, Carbone C, Jackson AL. Snake venom potency and yield are associated with prey-evolution, predator metabolism and habitat structure. Ecol Lett 2019; 22:527-537. [PMID: 30616302 DOI: 10.1111/ele.13216] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/15/2018] [Accepted: 12/01/2018] [Indexed: 01/17/2023]
Abstract
Snake venom is well known for its ability to incapacitate and kill prey. Yet, potency and the amount of venom available varies greatly across species, ranging from the seemingly harmless to those capable of killing vast numbers of potential prey. This variation is poorly understood, with comparative approaches confounded by the use of atypical prey species as models to measure venom potency. Here, we account for such confounding issues by incorporating the phylogenetic similarity between a snake's diet and the species used to measure its potency. In a comparative analysis of 102 species we show that snake venom potency is generally prey-specific. We also show that venom yields are lower in species occupying three dimensional environments and increases with body size corresponding to metabolic rate, but faster than predicted from increases in prey size. These results underline the importance of physiological and environmental factors in the evolution of predator traits.
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Affiliation(s)
- Kevin Healy
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland.,School of Biology, University of St Andrews, St Andrews, KY16 9TH, UK.,School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Chris Carbone
- Institute of Zoology, Zoological Society of London, London, UK
| | - Andrew L Jackson
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
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57
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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58
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O’Brien AM, Sawers RJH, Ross-Ibarra J, Strauss SY. Evolutionary Responses to Conditionality in Species Interactions across Environmental Gradients. Am Nat 2018; 192:715-730. [DOI: 10.1086/700118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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59
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Hofmann EP, Rautsaw RM, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation. Sci Rep 2018; 8:15534. [PMID: 30341342 PMCID: PMC6195556 DOI: 10.1038/s41598-018-33943-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
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 unknown. To explore venom differentiation in the early stages of lineage diversification, we used RNA-seq and mass spectrometry to characterize Sidewinder Rattlesnake (Crotalus cerastes) venom. We generated the first venom-gland transcriptomes and complementary venom proteomes for eight individuals collected across the United States and tested for expression differences across life history traits and between subspecific, mitochondrial, and phylotranscriptomic hypotheses. Sidewinder venom was comprised primarily of hemorrhagic toxins, with few cases of differential expression attributable to life history or lineage hypotheses. However, phylotranscriptomic lineage comparisons more than doubled instances of significant expression differences compared to all other factors. Nevertheless, only 6.4% of toxins were differentially expressed overall, suggesting that shallow divergence has not led to major changes in Sidewinder venom composition. Our results demonstrate the need for consensus venom-gland transcriptomes based on multiple individuals and highlight the potential for discrepancies in differential expression between different phylogenetic hypotheses.
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Affiliation(s)
- Erich P Hofmann
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Rhett M Rautsaw
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Jason L Strickland
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- University of Central Florida, Department of Biology, Orlando, FL, 32816, USA
| | - Matthew L Holding
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Michael P Hogan
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Andrew J Mason
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Florida State University, Department of Biological Science, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Clemson University, Department of Biological Sciences, Clemson, SC, 29634, USA.
- Clemson University, Department of Forestry and Environmental Conservation, Clemson, SC, 29634, USA.
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60
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Pekár S, Bočánek O, Michálek O, Petráková L, Haddad CR, Šedo O, Zdráhal Z. Venom gland size and venom complexity-essential trophic adaptations of venomous predators: A case study using spiders. Mol Ecol 2018; 27:4257-4269. [DOI: 10.1111/mec.14859] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Stano Pekár
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Ondřej Bočánek
- Central European Institute of Technology; Masaryk University; Brno Czech Republic
- National Centre for Biomolecular Research; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Ondřej Michálek
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Lenka Petráková
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Charles R. Haddad
- Department of Zoology & Entomology; University of the Free State; Bloemfontein South Africa
| | - Ondrej Šedo
- Central European Institute of Technology; Masaryk University; Brno Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology; Masaryk University; Brno Czech Republic
- National Centre for Biomolecular Research; Faculty of Science; Masaryk University; Brno Czech Republic
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61
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Holding ML, Margres MJ, Rokyta DR, Gibbs HL. Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (
Crotalus oreganus
). J Evol Biol 2018; 31:1513-1528. [DOI: 10.1111/jeb.13347] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/23/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Matthew L. Holding
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University Columbus OH USA
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - Mark J. Margres
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - Darin R. Rokyta
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - H. Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University Columbus OH USA
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62
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Margres MJ, Wray KP, Hassinger ATB, Ward MJ, McGivern JJ, Moriarty Lemmon E, Lemmon AR, Rokyta DR. Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation. Mol Biol Evol 2018; 34:3099-3110. [PMID: 28962003 DOI: 10.1093/molbev/msx231] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
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 integrate genomics, phenotypic data, ecology, and fitness effects for a genetically tractable, polygenic trait; snake venoms provide such a system for studying polygenic adaptation because of their genetic tractability and vital ecological role in feeding and defense. We used a venom transcriptome-proteome map, quantitative proteomics, genomics, and fitness assays in sympatric prey to construct a genotype-phenotype-fitness map for the venoms of an island-mainland pair of rattlesnake populations. Reciprocal fitness experiments demonstrated that each population was locally adapted to sympatric prey. We identified significant expression differentiation with little to no coding-sequence variation across populations, demonstrating that expression differentiation was exclusively the genetic basis of polygenic adaptation. Previous research on the genetics of adaptation, however, has largely been biased toward investigating protein-coding regions because of the complexity of gene regulation. Our results showed that biases at the molecular level can be in the opposite direction, highlighting the need for more systematic comparisons of different molecular mechanisms underlying rapid, adaptive evolution in polygenic traits.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - James J McGivern
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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63
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Aird SD, Arora J, Barua A, Qiu L, Terada K, Mikheyev AS. Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry. Genome Biol Evol 2018; 9:2640-2649. [PMID: 29048530 PMCID: PMC5737360 DOI: 10.1093/gbe/evx199] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 12/24/2022] Open
Abstract
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested. Using a combination of de novo genome sequencing, population genomics, transcriptomics, and proteomics, we compare the two modes of evolution in the pitviper, Protobothrops mucrosquamatus. By partitioning selective constraints and adaptive evolution in a McDonald–Kreitman-type framework, we find support for both hypotheses: venom proteins indeed experience both stronger positive selection, and lower selective constraint than other genes in the genome. Furthermore, the strength of selection may be modulated by expression level, with more abundant proteins experiencing weaker selective constraint, leading to the accumulation of more deleterious mutations. These findings show that snake venoms evolve by a combination of adaptive and neutral mechanisms, both of which explain their extraordinarily high rates of molecular evolution. In addition to positive selection, which optimizes efficacy of the venom in the short term, relaxed selective constraints for deleterious mutations can lead to more rapid turnover of individual proteins, and potentially to exploration of a larger venom phenotypic space.
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Affiliation(s)
- Steven D Aird
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Jigyasa Arora
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Lijun Qiu
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
| | - Kouki Terada
- Okinawa Prefectural Institute of Health and the Environment, Biology and Ecology Group, Nanjo-shi, Okinawa, Japan
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa-ken, Japan
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64
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Pekár S, Petráková L, Šedo O, Korenko S, Zdráhal Z. Trophic niche, capture efficiency and venom profiles of six sympatric ant-eating spider species (Araneae: Zodariidae). Mol Ecol 2018; 27:1053-1064. [DOI: 10.1111/mec.14485] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/22/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Stano Pekár
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Lenka Petráková
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Ondrej Šedo
- Research Group Proteomics, CEITEC - Central European Institute of Technology; Masaryk University; Brno Czech Republic
- National Centre for Biomolecular Research; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Stanislav Korenko
- Department of Agroecology and Biometeorology; Faculty of Agrobiology, Food and Natural Resources; Czech University of Life Sciences; Prague Czech Republic
| | - Zbyněk Zdráhal
- Research Group Proteomics, CEITEC - Central European Institute of Technology; Masaryk University; Brno Czech Republic
- National Centre for Biomolecular Research; Faculty of Science; Masaryk University; Brno Czech Republic
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65
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Coevolution takes the sting out of it: Evolutionary biology and mechanisms of toxin resistance in animals. Toxicon 2017; 140:118-131. [DOI: 10.1016/j.toxicon.2017.10.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/06/2017] [Accepted: 10/23/2017] [Indexed: 01/09/2023]
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66
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Melani RD, Nogueira FCS, Domont GB. It is time for top-down venomics. J Venom Anim Toxins Incl Trop Dis 2017; 23:44. [PMID: 29075288 PMCID: PMC5648493 DOI: 10.1186/s40409-017-0135-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
The protein composition of animal venoms is usually determined by peptide-centric proteomics approaches (bottom-up proteomics). However, this technique cannot, in most cases, distinguish among toxin proteoforms, herein called toxiforms, because of the protein inference problem. Top-down proteomics (TDP) analyzes intact proteins without digestion and provides high quality data to identify and characterize toxiforms. Denaturing top-down proteomics is the most disseminated subarea of TDP, which performs qualitative and quantitative analyzes of proteoforms up to ~30 kDa in high-throughput and automated fashion. On the other hand, native top-down proteomics provides access to information on large proteins (> 50 kDA) and protein interactions preserving non-covalent bonds and physiological complex stoichiometry. The use of native and denaturing top-down venomics introduced novel and useful techniques to toxinology, allowing an unprecedented characterization of venom proteins and protein complexes at the toxiform level. The collected data contribute to a deep understanding of venom natural history, open new possibilities to study the toxin evolution, and help in the development of better biotherapeutics.
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Affiliation(s)
- Rafael D. Melani
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Fabio C. S. Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, 149, CT A-542, Cidade Universitária, Rio de Janeiro, RJ CEP 21941-909 Brazil
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Lemos-Costa P, Martins AB, Thompson JN, de Aguiar MAM. Gene flow and metacommunity arrangement affects coevolutionary dynamics at the mutualism-antagonism interface. J R Soc Interface 2017; 14:rsif.2016.0989. [PMID: 28566509 DOI: 10.1098/rsif.2016.0989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/08/2017] [Indexed: 11/12/2022] Open
Abstract
Interspecific interactions are affected by community context and, as a consequence, show spatial variation in magnitude and sign. The selective forces imposed by interactions at the mutualism-antagonism interface are a consequence of the traits involved and their matching between species. If mutualistic and antagonistic communities are linked by gene flow, coevolution between a pair of interacting species is influenced by how selection varies in space. Here we investigate the effects of metacommunity arrangement, i.e. patterns of connection between communities and the number of communities, on the coevolutionary dynamics between two species for which the sign and magnitude of the interaction varies across the landscape. We quantify coevolutionary outcome as an index that can be decomposed into the contribution of intraspecific genetic diversity and interspecific interaction. We show that polymorphisms and mismatches are an expected outcome, which is influenced by spatial structure, interaction strength and the degree of gene flow. The index describes how variation is distributed within and between species, and provides information on the directionality of the mismatches and polymorphisms. Finally, we argue that depending on metacommunity arrangement, some communities have disproportionate roles in maintaining genetic diversity, with implications for the coevolution of interacting species in a fragmented landscape.
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Affiliation(s)
- Paula Lemos-Costa
- Programa de pós-graduação em Ecologia-Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-865, Campinas/SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas/SP, Brazil.,Department of Fish Ecology and Evolution, Center of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - John N Thompson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-859, Campinas/SP, Brazil
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68
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Zancolli G, Sanz L, Calvete JJ, Wüster W. Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics. Toxins (Basel) 2017; 9:toxins9060179. [PMID: 28555029 PMCID: PMC5488029 DOI: 10.3390/toxins9060179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 12/30/2022] Open
Abstract
Venom research has attracted an increasing interest in disparate fields, from drug development and pharmacology, to evolutionary biology and ecology, and rational antivenom production. Advances in “-omics” technologies have allowed the characterization of an increasing number of animal venoms, but the methodology currently available is suboptimal for large-scale comparisons of venom profiles. Here, we describe a fast, reproducible and semi-automated protocol for investigating snake venom variability, especially at the intraspecific level, using the Agilent Bioanalyzer on-chip technology. Our protocol generated a phenotype matrix which can be used for robust statistical analysis and correlations of venom variation with ecological correlates, or other extrinsic factors. We also demonstrate the ease and utility of combining on-chip technology with previously fractionated venoms for detection of specific individual toxin proteins. Our study describes a novel strategy for rapid venom discrimination and analysis of compositional variation at multiple taxonomic levels, allowing researchers to tackle evolutionary questions and unveiling the drivers of the incredible biodiversity of venoms.
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Affiliation(s)
- Giulia Zancolli
- Molecular Ecology and Fisheries Genetics Lab, School of Biological Sciences, Bangor University, Bangor LL57 2UW, UK.
| | - Libia Sanz
- Venomics and Structural Proteomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Jaume Roig 11, Valencia 46010, Spain.
| | - Juan J Calvete
- Venomics and Structural Proteomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Jaume Roig 11, Valencia 46010, Spain.
| | - Wolfgang Wüster
- Molecular Ecology and Fisheries Genetics Lab, School of Biological Sciences, Bangor University, Bangor LL57 2UW, UK.
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69
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Smiley-Walters SA, Farrell TM, Gibbs HL. Evaluating local adaptation of a complex phenotype: reciprocal tests of pigmy rattlesnake venoms on treefrog prey. Oecologia 2017; 184:739-748. [DOI: 10.1007/s00442-017-3882-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 05/08/2017] [Indexed: 11/24/2022]
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70
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Putman BJ, Clark RW. Behavioral thermal tolerances of free-ranging rattlesnakes ( Crotalus oreganus ) during the summer foraging season. J Therm Biol 2017; 65:8-15. [DOI: 10.1016/j.jtherbio.2017.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 11/26/2022]
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71
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Gorson J, Holford M. Small Packages, Big Returns: Uncovering the Venom Diversity of Small Invertebrate Conoidean Snails. Integr Comp Biol 2016; 56:962-972. [PMID: 27371389 PMCID: PMC6058754 DOI: 10.1093/icb/icw063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Venomous organisms used in research were historically chosen based on size and availability. This opportunity-driven strategy created a species bias in which snakes, scorpions, and spiders became the primary subjects of venom research. Increasing technological advancements have enabled interdisciplinary studies using genomics, transcriptomics, and proteomics to expand venom investigation to animals that produce small amounts of venom or lack traditional venom producing organs. One group of non-traditional venomous organisms that have benefitted from the rise of -omic technologies is the Conoideans. The Conoidean superfamily of venomous marine snails includes, the Terebridae, Turridae (s.l), and Conidae. Conoidea venom is used for both predation and defense, and therefore under strong selection pressures. The need for conoidean venom peptides to be potent and specific to their molecular targets has made them important tools for investigating cellular physiology and bioactive compounds that are beneficial to improving human health. A convincing case for the potential of Conoidean venom is made with the first commercially available conoidean venom peptide drug Ziconotide (Prialt®), an analgesic derived from Conus magus venom that is used to treat chronic pain in HIV and cancer patients. Investigation of conoidean venom using -omics technology provides significant insights into predator-driven diversification in biodiversity and identifies novel compounds for manipulating cellular communication, especially as it pertains to disease and disorders.
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Affiliation(s)
- J Gorson
- *Department of Chemistry, Hunter College, The City University of New York, Belfer Research Building, NY, 10021 USA
- Departments of Biology, Chemistry, and Biochemistry, The Graduate City, The City University of New York, NY, 10016 USA
- Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, 10024 USA
| | - M Holford
- *Department of Chemistry, Hunter College, The City University of New York, Belfer Research Building, NY, 10021 USA
- Departments of Biology, Chemistry, and Biochemistry, The Graduate City, The City University of New York, NY, 10016 USA
- Invertebrate Zoology, Sackler Institute of Comparative Genomics, American Museum of Natural History, NY, 10024 USA
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72
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Rapid Radiations and the Race to Redundancy: An Investigation of the Evolution of Australian Elapid Snake Venoms. Toxins (Basel) 2016; 8:toxins8110309. [PMID: 27792190 PMCID: PMC5127106 DOI: 10.3390/toxins8110309] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/06/2023] Open
Abstract
Australia is the stronghold of the front-fanged venomous snake family Elapidae. The Australasian elapid snake radiation, which includes approximately 100 terrestrial species in Australia, as well as Melanesian species and all the world's sea snakes, is less than 12 million years old. The incredible phenotypic and ecological diversity of the clade is matched by considerable diversity in venom composition. The clade's evolutionary youth and dynamic evolution should make it of particular interest to toxinologists, however, the majority of species, which are small, typically inoffensive, and seldom encountered by non-herpetologists, have been almost completely neglected by researchers. The present study investigates the venom composition of 28 species proteomically, revealing several interesting trends in venom composition, and reports, for the first time in elapid snakes, the existence of an ontogenetic shift in the venom composition and activity of brown snakes (Pseudonaja sp.). Trends in venom composition are compared to the snakes' feeding ecology and the paper concludes with an extended discussion of the selection pressures shaping the evolution of snake venom.
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73
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Rodríguez de la Vega RC, Giraud T. Intragenome Diversity of Gene Families Encoding Toxin-like Proteins in Venomous Animals. Integr Comp Biol 2016; 56:938-949. [PMID: 27543626 DOI: 10.1093/icb/icw097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolution of venoms is the story of how toxins arise and of the processes that generate and maintain their diversity. For animal venoms these processes include recruitment for expression in the venom gland, neofunctionalization, paralogous expansions, and functional divergence. The systematic study of these processes requires the reliable identification of the venom components involved in antagonistic interactions. High-throughput sequencing has the potential of uncovering the entire set of toxins in a given organism, yet the existence of non-venom toxin paralogs and the misleading effects of partial census of the molecular diversity of toxins make necessary to collect complementary evidence to distinguish true toxins from their non-venom paralogs. Here, we analyzed the whole genomes of two scorpions, one spider and one snake, aiming at the identification of the full repertoires of genes encoding toxin-like proteins. We classified the entire set of protein-coding genes into paralogous groups and monotypic genes, identified genes encoding toxin-like proteins based on known toxin families, and quantified their expression in both venom-glands and pooled tissues. Our results confirm that genes encoding toxin-like proteins are part of multigene families, and that these families arise by recruitment events from non-toxin genes followed by limited expansions of the toxin-like protein coding genes. We also show that failing to account for sequence similarity with non-toxin proteins has a considerable misleading effect that can be greatly reduced by comparative transcriptomics. Our study overall contributes to the understanding of the evolutionary dynamics of proteins involved in antagonistic interactions.
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Affiliation(s)
- Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, UMR8079, CNRS, Univ. of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, UMR8079, CNRS, Univ. of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
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74
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No safety in the trees: Local and species-level adaptation of an arboreal squirrel to the venom of sympatric rattlesnakes. Toxicon 2016; 118:149-55. [DOI: 10.1016/j.toxicon.2016.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/03/2016] [Accepted: 05/04/2016] [Indexed: 11/29/2022]
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75
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Miller DW, Jones AD, Goldston JS, Rowe MP, Rowe AH. Sex Differences in Defensive Behavior and Venom of The Striped Bark Scorpion Centruroides vittatus (Scorpiones: Buthidae). Integr Comp Biol 2016; 56:1022-1031. [PMID: 27471227 DOI: 10.1093/icb/icw098] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Studies of venom variability have advanced from describing the mechanisms of action and relative potency of medically important toxins to understanding the ecological and evolutionary causes of the variability itself. While most studies have focused on differences in venoms among taxa, populations, or age-classes, there may be intersexual effects as well. Striped bark scorpions (Centruroides vittatus) provide a good model for examining sex differences in venom composition and efficacy, as this species exhibits dramatic sexual dimorphism in both size and defensive behavior; when threatened by an enemy, larger, slower females stand and fight while smaller, fleeter males prefer to run. We here add evidence suggesting that male and female C. vittatus indeed have different defensive propensities; when threatened via an electrical stimulus, females were more likely to sting than were males. We reasoned that intersexual differences in defensive phenotypes would select for venoms with different functions in the two sexes; female venoms should be effective at predator deterrence, whereas male venoms, less utilized defensively, might be better suited to capturing prey or courting females. This rationale led to our predictions that females would inject more venom and/or possess more painful venom than males. We were wrong. While females do inject more venom than males in a defensive sting, females are also larger; when adjusted for body size, male and female C. vittatus commit equal masses of venom in a sting to a potential enemy. Additionally, house mice (Mus musculus) find an injection of male venom more irritating than an equal amount of female venom, likely because male venom contains more of the toxins that induce pain. Taken together, our results suggest that identifying the ultimate causes of venom variability will, as we move beyond adaptive storytelling, be hard-won.
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Affiliation(s)
- D W Miller
- *Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
| | - A D Jones
- Department of Biochemistry and Molecular Biology, Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - J S Goldston
- *Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
| | - M P Rowe
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - A H Rowe
- Neuroscience Program and Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
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76
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Holding ML, Drabeck DH, Jansa SA, Gibbs HL. Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations. Integr Comp Biol 2016; 56:1032-1043. [PMID: 27444525 DOI: 10.1093/icb/icw082] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
SynopsisVenom and venom resistance are molecular phenotypes widely considered to have diversified through coevolution between predators and prey. However, while evolutionary and functional studies on venom have been extensive, little is known about the molecular basis, variation, and complexity of venom resistance. We review known mechanisms of venom resistance and relate these mechanisms to their predicted impact on coevolutionary dynamics with venomous enemies. We then describe two conceptual approaches which can be used to examine venom/resistance systems. At the intraspecific level, tests of local adaptation in venom and resistance phenotypes can identify the functional mechanisms governing the outcomes of coevolution. At deeper evolutionary timescales, the combination of phylogenetically informed analyses of protein evolution coupled with studies of protein function promise to elucidate the mode and tempo of evolutionary change on potentially coevolving genes. We highlight case studies that use each approach to extend our knowledge of these systems as well as address larger questions about coevolutionary dynamics. We argue that resistance and venom are phenotypic traits which hold exceptional promise for investigating the mechanisms, dynamics, and outcomes of coevolution at the molecular level. Furthermore, extending the understanding of single gene-for-gene interactions to the whole resistance and venom phenotypes may provide a model system for examining the molecular and evolutionary dynamics of complex multi-gene interactions.
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Affiliation(s)
- Matthew L Holding
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,*Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Danielle H Drabeck
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.,J. F. Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.,J. F. Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
| | - H Lisle Gibbs
- *Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.,Ohio Biodiversity Conservation Partnership, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
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