1
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Hogan MP, Holding ML, Nystrom GS, Colston TJ, Bartlett DA, Mason AJ, Ellsworth SA, Rautsaw RM, Lawrence KC, Strickland JL, He B, Fraser P, Margres MJ, Gilbert DM, Gibbs HL, Parkinson CL, Rokyta DR. The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom. Proc Natl Acad Sci U S A 2024; 121:e2313440121. [PMID: 38578985 PMCID: PMC11032440 DOI: 10.1073/pnas.2313440121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/13/2024] [Indexed: 04/07/2024] Open
Abstract
Developmental phenotypic changes can evolve under selection imposed by age- and size-related ecological differences. Many of these changes occur through programmed alterations to gene expression patterns, but the molecular mechanisms and gene-regulatory networks underlying these adaptive changes remain poorly understood. Many venomous snakes, including the eastern diamondback rattlesnake (Crotalus adamanteus), undergo correlated changes in diet and venom expression as snakes grow larger with age, providing models for identifying mechanisms of timed expression changes that underlie adaptive life history traits. By combining a highly contiguous, chromosome-level genome assembly with measures of expression, chromatin accessibility, and histone modifications, we identified cis-regulatory elements and trans-regulatory factors controlling venom ontogeny in the venom glands of C. adamanteus. Ontogenetic expression changes were significantly correlated with epigenomic changes within genes, immediately adjacent to genes (e.g., promoters), and more distant from genes (e.g., enhancers). We identified 37 candidate transcription factors (TFs), with the vast majority being up-regulated in adults. The ontogenetic change is largely driven by an increase in the expression of TFs associated with growth signaling, transcriptional activation, and circadian rhythm/biological timing systems in adults with corresponding epigenomic changes near the differentially expressed venom genes. However, both expression activation and repression contributed to the composition of both adult and juvenile venoms, demonstrating the complexity and potential evolvability of gene regulation for this trait. Overall, given that age-based trait variation is common across the tree of life, we provide a framework for understanding gene-regulatory-network-driven life-history evolution more broadly.
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Affiliation(s)
- Michael P. Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Matthew L. Holding
- Department of Biological Science, Florida State University, Tallahassee, FL32306
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Timothy J. Colston
- Department of Biological Science, Florida State University, Tallahassee, FL32306
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, PR00681
| | - Daniel A. Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH43210
| | - Schyler A. Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
- School of Biological Sciences, Washington State University, Pullman, WA99164
| | - Kylie C. Lawrence
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Biology, University of South Alabama, Mobile, AL36688
| | - Bing He
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL32306
| | - Mark J. Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL33620
| | - David M. Gilbert
- Laboratory of Chromosome Replication and Epigenome Regulation, San Diego Biomedical Research Institute, San Diego, CA92121
| | - H. Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH43210
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC29634
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC29634
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL32306
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2
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Borja M, Neri-Castro E, Gutiérrez-Martínez A, Bledsoe R, Zarzosa V, Rodriguez-López B, Strickland JL, Becerra-López J, Valenzuela-Ceballos S, Parkinson CL, Alagón A, Castañeda-Gaytán G. Ontogenetic change in the venom composition of one Mexican black-tailed rattlesnake (Crotalus molossus nigrescens) from Durango, Mexico. Toxicon 2023; 234:107280. [PMID: 37673344 DOI: 10.1016/j.toxicon.2023.107280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
To corroborate the ontogenetic shift in the venom composition of the Mexican Black-tailed Rattlesnake (Crotalus molossus nigrescens) previously reported through the census approach, we evaluated the shift in the protein profile, lethality, and proteolytic and phospholipase activities of four venom samples obtained in 2015, 2018, 2019, and 2021 from one C. m. nigrescens individual (CMN06) collected in Durango, Mexico. We demonstrated that the venom of C. m. nigrescens changed from a myotoxin-rich venom to a phospholipase A2 and snake venom metalloproteinase-rich venom. Additionally, the proteolytic and phospholipase activities increased with age, but the lethality decreased approximately three times.
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Affiliation(s)
- Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | - Edgar Neri-Castro
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico; Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210, Cuernavaca, Mor., Mexico
| | - Arelí Gutiérrez-Martínez
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | - Richard Bledsoe
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | - Vanessa Zarzosa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210, Cuernavaca, Mor., Mexico
| | - Bruno Rodriguez-López
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | - Jason L Strickland
- Department of Biology, University of South Alabama, 5871 USA Dr. N., Mobile, AL, 36688, USA
| | - Jorge Becerra-López
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | - Sara Valenzuela-Ceballos
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico
| | | | - Alejandro Alagón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210, Cuernavaca, Mor., Mexico
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo., Mexico.
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3
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Peng C, Wu DD, Ren JL, Peng ZL, Ma Z, Wu W, Lv Y, Wang Z, Deng C, Jiang K, Parkinson CL, Qi Y, Zhang ZY, Li JT. Large-scale snake genome analyses provide insights into vertebrate development. Cell 2023; 186:3519. [PMID: 37541200 DOI: 10.1016/j.cell.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
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4
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Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, de la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Castañeda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium. J Mol Evol 2023; 91:514-535. [PMID: 37269364 PMCID: PMC10995822 DOI: 10.1007/s00239-023-10115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.
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Affiliation(s)
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Science Department, Cape Fear Community College, Wilmington, NC, 28401, USA
| | | | - Hector Franz-Chavez
- Herp.mx A.C., Colima, Mexico
- Biodiversa A. C., Chapala, Jalisco, 45900, Mexico
| | | | | | | | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Gamaliel Castañeda-Gaytan
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mahmood Sasa
- Centro Investigaciones en Biodiversidad y Ecología Tropical and Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA.
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5
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Peng C, Wu DD, Ren JL, Peng ZL, Ma Z, Wu W, Lv Y, Wang Z, Deng C, Jiang K, Parkinson CL, Qi Y, Zhang ZY, Li JT. Large-scale snake genome analyses provide insights into vertebrate development. Cell 2023; 186:2959-2976.e22. [PMID: 37339633 DOI: 10.1016/j.cell.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 04/06/2023] [Accepted: 05/19/2023] [Indexed: 06/22/2023]
Abstract
Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of limb loss, an elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations in snakes. We identified some of the genes and regulatory elements that might have shaped the evolution of vision, the skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides insights into the evolution and development of snakes and vertebrates.
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Affiliation(s)
- Changjun Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jin-Long Ren
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhong-Liang Peng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhifei Ma
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunyun Lv
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; College of Life Science, Neijiang Normal University, Neijiang, Sichuan 641100, China
| | - Zeng Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cao Deng
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu 610000, China
| | - Ke Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | | | - Yin Qi
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Zhi-Yi Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar.
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Heptinstall TC, Strickland JL, Rosales-Garcia RA, Rautsaw RM, Simpson CL, Nystrom GS, Ellsworth SA, Hogan MP, Borja M, Fernandes Campos P, Grazziotin FG, Rokyta DR, Junqueira-de-Azevedo ILM, Parkinson CL. Venom phenotype conservation suggests integrated specialization in a lizard-eating snake. Toxicon 2023; 229:107135. [PMID: 37146732 PMCID: PMC11000244 DOI: 10.1016/j.toxicon.2023.107135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
Biological specialization reduces the size of niche space while increasing efficiency in the use of available resources. Specialization often leads to phenotypic changes via natural selection aligning with niche space constraints. Commonly observed changes are in size, shape, behavior, and traits associated with feeding. One often selected trait for dietary specialization is venom, which, in snakes, often shows variation dependent on diet across and within species. The Neotropical Blunt-headed Treesnake (Imantodes cenchoa) is a highly specialized, rear-fanged, arboreal, lizard hunter that displays a long thin body, enlarged eyes, and a large Duvernoy's gland. However, toxin characterization of I. cenchoa has never been completed. Here, we use RNA-seq and mass spectrometry to assemble, annotate, and analyze the venom gland transcriptomes of four I. cenchoa from across their range. We find a lack of significant venom variation at the sequence and expression levels, suggesting venom conservation across the species. We propose this conservation provides evidence of a specialized venom repertoire, adapted to maximize efficiency of capturing and processing lizards. Importantly, this study provides the most complete venom gland transcriptomes of I. cenchoa and evidence of venom specialization in a rear-fanged snake, giving insight into selective pressures of venom across all snake species.
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Affiliation(s)
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA; Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Cassandra L Simpson
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35070, Gómez Palacio, Dgo., Mexico
| | | | - Felipe G Grazziotin
- Laboratório Especial de Colecões Zoológicas, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | | | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, 29634, USA.
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Holding ML, Trevine VC, Zinenko O, Strickland JL, Rautsaw RM, Mason AJ, Hogan MP, Parkinson CL, Grazziotin FG, Santana SE, Davis MA, Rokyta DR. Evolutionary allometry and ecological correlates of fang length evolution in vipers. Proc Biol Sci 2022; 289:20221132. [PMID: 36300520 PMCID: PMC9449470 DOI: 10.1098/rspb.2022.1132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
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 conditions and dietary ecology of viperid snakes. We measured fang length in more than 1900 museum specimens representing 199 viper species (55% of recognized species). We find both phylogenetic signal and within-clade variation in relative fang length across vipers suggesting both general taxonomic trends and potential adaptive divergence in fang length. We recover positive evolutionary allometry and little static allometry in fang length. Proportionally longer fangs have evolved in larger species, which may facilitate venom injection in more voluminous prey. Finally, we leverage climatic and diet data to assess the global correlates of fang length. We find that models of fang length evolution are improved through the inclusion of both temperature and diet, particularly the extent to which diets are mammal-heavy diets. These findings demonstrate how adaptive variation can emerge among components of complex prey capture systems.
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Affiliation(s)
- Matthew L. Holding
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Vivian C. Trevine
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brazil, 1500, 05503-900 São Paulo, SP, Brazil
| | - Oleksandr Zinenko
- V. N. Karazin Kharkiv National University, 4 Svobody square, Kharkiv 61022, Ukraine
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brazil, 1500, 05503-900 São Paulo, SP, Brazil
| | - Sharlene E. Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Mark A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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8
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Manjerovic MB, Hoffman EA, Parkinson CL, Waterman JM. Intraspecific variation in male mating strategies in an African ground squirrel ( Xerus inauris). Ecol Evol 2022; 12:e9208. [PMID: 35991282 PMCID: PMC9379349 DOI: 10.1002/ece3.9208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 06/20/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Male mating strategies respond to female availability such that variation in resources that affect spatial distribution can also alter cost–benefit tradeoffs within a population. In arid‐adapted species, rainfall alters reproduction, behavior, morphology, and population density such that populations differing in resource availability may also differ in successful reproductive strategies. Here, we compare two populations of Cape ground squirrels (Xerus inauris), a sub‐Saharan species with year‐round breeding and intense mating competition. Unlike most mammals where males resort to aggressive interactions over females, male X. inauris are tolerant of one another, relying instead on other nonaggressive pre‐ and postcopulatory strategies to determine reproductive success. Our findings suggest that differences in resource availability affect female distribution, which ultimately leads to intraspecific variation in male reproductive tactics and sexual morphology. Sperm competition, assessed by reproductive morphometrics, was more pronounced in our high resource site where females were distributed evenly across the landscape, whereas dominance seemed to be an important determinant of success in our low resource site where females were more aggregated. Both sites had similar mating intensities, and most males did not sire any offspring. However, our low resource site had a higher variance in fertilization success with fewer males siring multiple offspring compared with our high resource site where more individuals were successful. Our results lend support to resource models where variations in female spatial distribution attributed to environmental resources ultimately impact male reproductive behaviors and morphology.
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Affiliation(s)
- Mary Beth Manjerovic
- Department of BiologyVirginia Military InstituteLexingtonVirginiaUSA
- Department of BiologyUniversity of Central FloridaOrlandoFloridaUSA
| | - Eric A. Hoffman
- Department of BiologyUniversity of Central FloridaOrlandoFloridaUSA
| | - Christopher L. Parkinson
- Department of BiologyUniversity of Central FloridaOrlandoFloridaUSA
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
| | - Jane M. Waterman
- Department of BiologyUniversity of Central FloridaOrlandoFloridaUSA
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
- Department of Zoology and EntomologyMammal Research Institute, University of PretoriaPretoriaSouth Africa
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9
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Myers EA, Strickland JL, Rautsaw RM, Mason AJ, Schramer TD, Nystrom GS, Hogan MP, Yooseph S, Rokyta DR, Parkinson CL. De Novo Genome Assembly Highlights the Role of Lineage-Specific Duplications in the Evolution of Venom in Fea’s Viper. Genome Biol Evol 2022; 14:6603630. [PMID: 35670514 PMCID: PMC9256536 DOI: 10.1093/gbe/evac082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
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, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
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Affiliation(s)
- Edward A. Myers
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Biology, University of South Alabama , Mobile, AL 36688, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA
| | - Tristan D. Schramer
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, 4000 Central Florida Blvd , Orlando, FL, 32816, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University , Clemson, SC 29634, USA
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10
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King KL, Wilson S, Napolitano JM, Sell KJ, Rennert L, Parkinson CL, Dean D. SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva. PLoS One 2022; 17:e0267750. [PMID: 35536777 PMCID: PMC9089873 DOI: 10.1371/journal.pone.0267750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/16/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. METHODS AND FINDINGS In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72-28.51), followed by Alpha (23.93, 18.36-28.49), Gamma (24.74, 18.84-30.64), and the more historic clade 20G (25.21, 20.50-29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n = 1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n = 167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. CONCLUSIONS COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.
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Affiliation(s)
- Kylie L. King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Stevin Wilson
- Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
| | - Justin M. Napolitano
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Keegan J. Sell
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher L. Parkinson
- Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Department of Biological Sciences and Department of Forestry and Environmental Conservation, Clemson University, Clemson, South Carolina, United States of America
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
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11
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Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation 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 the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
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Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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12
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King KL, Wilson S, Napolitano JM, Sell KJ, Rennert L, Parkinson CL, Dean D. SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva.. [PMID: 35194615 PMCID: PMC8863157 DOI: 10.1101/2022.02.10.22270797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. Methods and Findings In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72–28.51), followed by Alpha (23.93, 18.36–28.49), Gamma (24.74, 18.84–30.64), and the more historic clade 20G (25.21, 20.50–29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n=1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n=167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. Conclusions COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.
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13
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Schramer TD, Rautsaw RM, Bayona-Serrano JD, Nystrom GS, West TR, Ortiz-Medina JA, Sabido-Alpuche B, Meneses-Millán M, Borja M, Junqueira-de-Azevedo ILM, Rokyta DR, Parkinson CL. An integrative view of the toxic potential of Conophis lineatus (Dipsadidae: Xenodontinae), a medically relevant rear-fanged snake. Toxicon 2021; 205:38-52. [PMID: 34793822 DOI: 10.1016/j.toxicon.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/25/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
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 to historical inertia and methodological challenges, the toxin repertoires of non-front-fanged snake families (e.g., Colubridae, Dipsadidae, and Natricidae) have been heavily neglected despite the knowledge of numerous species capable of inflicting medically relevant envenomations. Integrating proteomic data for validation, we perform a de novo assembly and analysis of the Duvernoy's venom gland transcriptome of the Central American Road Guarder (Dipsadidae: Xenodontinae: Conophis lineatus), a species known for its potent bite. We identified 28 putative toxin transcripts from 13 toxin families in the Duvernoy's venom gland transcriptome, comprising 63.7% of total transcriptome expression. In addition to ubiquitous snake toxin families, we proteomically confirmed several atypical venom components. The most highly expressed toxins (55.6% of total toxin expression) were recently described snake venom matrix metalloproteases (svMMPs), with 48.0% of svMMP expression contributable to a novel svMMP isoform. We investigate the evolution of the new svMMP isoform in the context of rear-fanged snakes using phylogenetics. Finally, we examine the morphology of the venom apparatus using μCT and explore how the venom relates to autecology and the highly hemorrhagic effects seen in human envenomations. Importantly, we provide the most complete venom characterization of this medically relevant snake species to date, producing insights into the effects and evolution of its venom, and point to future research directions to better understand the venoms of 'harmless' non-front-fanged snakes.
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Affiliation(s)
- Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | | | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Taylor R West
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Javier A Ortiz-Medina
- Departamento de Sistemática y Ecología Acuática, El Colegio de La Frontera Sur, Unidad Chetumal, Chetumal, Quintana Roo, Mexico; Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico; HERP.MX A.C., Villa de Álvarez, Colima, Mexico
| | - Bianca Sabido-Alpuche
- Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico
| | - Marcos Meneses-Millán
- Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez Del Estado de Durango, Gómez Palacio, Durango, Mexico
| | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil; Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA.
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14
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Colis-Torres A, Neri-Castro E, Strickland JL, Olvera-Rodríguez A, Borja M, Calvete J, Jones J, Parkinson CL, Bañuelos J, López de León J, Alagón A. Intraspecific venom variation of Mexican West Coast Rattlesnakes (Crotalus basiliscus) and its implications for antivenom production. Biochimie 2021; 192:111-124. [PMID: 34656669 DOI: 10.1016/j.biochi.2021.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Accepted: 10/11/2021] [Indexed: 11/02/2022]
Abstract
Intraspecific variation in snake venoms has been widely documented worldwide. However, there are few studies on this subject in Mexico. Venom characterization studies provide important data used to predict clinical syndromes, to evaluate the efficacy of antivenoms and, in some cases, to improve immunogenic mixtures in the production of antivenoms. In the present work, we evaluated the intraspecific venom variation of Crotalus basiliscus, a rattlesnake of medical importance and whose venom is used in the immunization of horses to produce one of the Mexican antivenoms. Our results demonstrate that there is variation in biological and biochemical activities among adult venoms and that there is an ontogenetic change from juvenile to adult venoms. Juvenile venoms were more lethal and had higher percentages of crotamine and crotoxin, while adult venoms had higher percentages of snake venom metalloproteases (SVMPs). Additionally, we documented crotoxin-like PLA2 variation in which specimens from Zacatecas, Sinaloa and Michoacán (except 1) lacked the neurotoxin, while the rest of the venoms had it. Finally, we evaluated the efficacy of three lots of Birmex antivenom and all three were able to neutralize the lethality of four representative venoms but were not able to neutralize crotamine. We also observed significant differences in the LD50 values neutralized per vial among the different lots. Based on these results, we recommend including venoms containing crotamine in the production of antivenom for a better immunogenic mixture and to improve the homogeneity of lots.
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Affiliation(s)
- Andrea Colis-Torres
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Neri-Castro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jason L Strickland
- Department of Biology, University of South Alabama, 5871 USA Dr. N, Mobile, AL, 36688, USA
| | - Alejandro Olvera-Rodríguez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel Borja
- Facultad Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo, Mexico
| | - Juan Calvete
- Laboratorio de Venómica Evolutiva y Traslacional, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010, Valencia, Spain
| | - Jason Jones
- Herp.mx A.C, Villa del Álvarez, Colima, Mexico
| | - Christopher L Parkinson
- Department of Biological Sciences and Department of Forestry, and Environmental Conservation, Clemson University, 190 Collings St. Clemson, SC, 29631, USA
| | - Jorge Bañuelos
- Herp.mx A.C, Villa del Álvarez, Colima, Mexico; Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Edificio de Biología Campus II Ave. Preparatoria S/N, Col. Agronómica, 98066, ZacatecasZacatecas, Mexico
| | - Jorge López de León
- Hospital General Norberto Treviño Zapata, Ciudad Victoria, Tamaulipas, Mexico
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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15
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Rautsaw RM, Schramer TD, Acuña R, Arick LN, DiMeo M, Mercier KP, Schrum M, Mason AJ, Margres MJ, Strickland JL, Parkinson CL. Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes. Mol Biol Evol 2021; 38:745-760. [PMID: 33035326 PMCID: PMC7947766 DOI: 10.1093/molbev/msaa266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.
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Affiliation(s)
- Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | | | - Rachel Acuña
- Department of Biology, University of Central Florida, Orlando, FL
| | - Lindsay N Arick
- Department of Biology, University of Central Florida, Orlando, FL
| | - Mark DiMeo
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Kathryn P Mercier
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, City College of New York, New York, NY.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, NY
| | - Michael Schrum
- Department of Biology, University of Central Florida, Orlando, FL
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, University of South Alabama, Mobile, AL
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
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16
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Hofmann EP, Rautsaw RM, Mason AJ, Strickland JL, Parkinson CL. Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes. Toxins (Basel) 2021; 13:toxins13050336. [PMID: 34066626 PMCID: PMC8148590 DOI: 10.3390/toxins13050336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The venoms of small rear-fanged snakes (RFS) remain largely unexplored, despite increased recognition of their importance in understanding venom evolution more broadly. Sequencing the transcriptome of venom-producing glands has greatly increased the ability of researchers to examine and characterize the toxin repertoire of small taxa with low venom yields. Here, we use RNA-seq to characterize the Duvernoy’s gland transcriptome of the Plains Black-headed Snake, Tantilla nigriceps, a small, semi-fossorial colubrid that feeds on a variety of potentially dangerous arthropods including centipedes and spiders. We generated transcriptomes of six individuals from three localities in order to both characterize the toxin expression of this species for the first time, and to look for initial evidence of venom variation in the species. Three toxin families—three-finger neurotoxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)—dominated the transcriptome of T. nigriceps; 3FTx themselves were the dominant toxin family in most individuals, accounting for as much as 86.4% of an individual’s toxin expression. Variation in toxin expression between individuals was also noted, with two specimens exhibiting higher relative expression of c-type lectins than any other sample (8.7–11.9% compared to <1%), and another expressed CRISPs higher than any other toxin. This study provides the first Duvernoy’s gland transcriptomes of any species of Tantilla, and one of the few transcriptomic studies of RFS not predicated on a single individual. This initial characterization demonstrates the need for further study of toxin expression variation in this species, as well as the need for further exploration of small RFS venoms.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; (E.P.H.); (R.M.R.); (A.J.M.); (J.L.S.)
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
- Correspondence:
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17
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Holding ML, Strickland JL, Rautsaw RM, Hofmann EP, Mason AJ, Hogan MP, Nystrom GS, Ellsworth SA, Colston TJ, Borja M, Castañeda-Gaytán G, Grünwald CI, Jones JM, Freitas-de-Sousa LA, Viala VL, Margres MJ, Hingst-Zaher E, Junqueira-de-Azevedo ILM, Moura-da-Silva AM, Grazziotin FG, Gibbs HL, Rokyta DR, Parkinson CL. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proc Natl Acad Sci U S A 2021; 118:e2015579118. [PMID: 33875585 PMCID: PMC8092465 DOI: 10.1073/pnas.2015579118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.
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Affiliation(s)
- Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, C.P. 35010 Gómez Palacio, Dgo., Mexico
| | | | - Jason M Jones
- HERP.MX A.C., Villa del Álvarez, Colima 28973, Mexico
| | | | - Vincent Louis Viala
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil
- Center of Toxins, Immune-Response and Cell Signaling, São Paulo 05503-900, Brazil
| | - Ana M Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus 69040, Brazil
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, Brazil
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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Nachtigall PG, Rautsaw RM, Ellsworth SA, Mason AJ, Rokyta DR, Parkinson CL, Junqueira-de-Azevedo ILM. ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. Brief Bioinform 2021; 22:6235957. [PMID: 33866357 DOI: 10.1093/bib/bbab095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/15/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
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-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide. RESULTS Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time ($>20x$ faster), coding sequence prediction ($>3x$ more accurate) and the number of toxins predicted (generating $>4x$ less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP 05503-900, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA
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19
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Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer TD, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proc Natl Acad Sci U S A 2021; 118:e2014634118. [PMID: 33468678 PMCID: PMC7848695 DOI: 10.1073/pnas.2014634118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variation in gene regulation is ubiquitous, yet identifying the mechanisms producing such variation, especially for complex traits, is challenging. Snake venoms provide a model system for studying the phenotypic impacts of regulatory variation in complex traits because of their genetic tractability. Here, we sequence the genome of the Tiger Rattlesnake, which possesses the simplest and most toxic venom of any rattlesnake species, to determine whether the simple venom phenotype is the result of a simple genotype through gene loss or a complex genotype mediated through regulatory mechanisms. We generate the most contiguous snake-genome assembly to date and use this genome to show that gene loss, chromatin accessibility, and methylation levels all contribute to the production of the simplest, most toxic rattlesnake venom. We provide the most complete characterization of the venom gene-regulatory network to date and identify key mechanisms mediating phenotypic variation across a polygenic regulatory network.
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Affiliation(s)
- Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
- Department of Biology, University of South Alabama, Mobile, AL 36688
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Erin Stiers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC 29634;
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634
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20
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Bayona-Serrano JD, Viala VL, Rautsaw RM, Schramer TD, Barros-Carvalho GA, Nishiyama MY, Freitas-de-Sousa LA, Moura-da-Silva AM, Parkinson CL, Grazziotin FG, Junqueira-de-Azevedo ILM. Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes. Mol Biol Evol 2020; 37:3563-3575. [PMID: 32722789 PMCID: PMC8525196 DOI: 10.1093/molbev/msaa192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an "SVMP-like" function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.
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Affiliation(s)
| | - Vincent Louis Viala
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC
| | | | | | - Milton Yutaka Nishiyama
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | | | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
| | | | - Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
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21
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Reyes-Velasco J, Adams RH, Boissinot S, Parkinson CL, Campbell JA, Castoe TA, Smith EN. Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae). Mol Phylogenet Evol 2020; 147:106770. [PMID: 32084510 DOI: 10.1016/j.ympev.2020.106770] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/06/2020] [Accepted: 02/14/2020] [Indexed: 01/04/2023]
Abstract
New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity and prominence as model systems, surprisingly little is known about species boundaries and phylogenetic relationships within Micrurus, which has substantially hindered meaningful analyses of their evolutionary history. Here we use mitochondrial genes together with thousands of nuclear genomic loci obtained via ddRADseq to study the phylogenetic relationships and population genomics of a subclade of the genus Micrurus: The M. diastema species complex. Our results indicate that prior species and species-group inferences based on morphology and color pattern have grossly misguided taxonomy, and that the M. diastema complex is not monophyletic. Based on our analyses of molecular data, we infer the phylogenetic relationships among species and populations, and provide a revised taxonomy for the group. Two non-sister species-complexes with similar color patterns are recognized, the M. distans and the M. diastema complexes, the first being basal to the monadal Micrurus and the second encompassing most North American monadal taxa. We examined all 13 species, and their respective subspecies, for a total of 24 recognized taxa in the M. diastema species complex. Our analyses suggest a reduction to 10 species, with no subspecific designations warranted, to be a more likely estimate of species diversity, namely, M. apiatus, M. browni, M. diastema, M. distans, M. ephippifer, M. fulvius, M. michoacanensis, M. oliveri, M. tener, and one undescribed species.
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Affiliation(s)
- Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA; New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA
| | - Stephane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Christopher L Parkinson
- Department of Biological Sciences and Department of Forestry and Environmental Conservation, Clemson University, 190 Collins St., Clemson, SC 29634, USA
| | - Jonathan A Campbell
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA
| | - Eric N Smith
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, 337 Life Science, Arlington, TX 76010, USA.
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Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. Trait differentiation and modular toxin expression in palm-pitvipers. BMC Genomics 2020; 21:147. [PMID: 32046632 PMCID: PMC7014597 DOI: 10.1186/s12864-020-6545-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
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 trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis nigroviridis) and Talamancan Palm-Pitvipers (B. nubestris). Results We assembled 1517 coding sequences, including 43 toxins for B. nigroviridis and 1787 coding sequences including 42 toxins for B. nubestris. The venom gland transcriptomes were extremely divergent between these two species with one B. nigroviridis exhibiting a primarily neurotoxic pattern of expression, both B. nubestris expressing primarily hemorrhagic toxins, and a second B. nigroviridis exhibiting a mixed expression phenotype. Weighted gene coexpression analyses identified six submodules of transcript expression variation, one of which was highly associated with SVMPs and a second which contained both subunits of the neurotoxic PLA2 complex. The sub-module association of these toxins suggest common regulatory pathways underlie the variation in their expression and is consistent with known patterns of inheritance of similar haplotypes in other species. We also find evidence that module associated toxin families show fewer gene duplications and transcript losses between species, but module association did not appear to affect sequence diversification. Conclusion Sub-modular regulation of expression likely contributes to the diversification of venom phenotypes within and among species and underscores the role of modularity in facilitating rapid evolution of complex traits.
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Affiliation(s)
- Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 24105, USA
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA. .,Department of Forestry, and Environmental Conservation, Clemson University, Clemson, SC, USA.
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23
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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: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Borja M, Neri-Castro E, Pérez-Morales R, Strickland JL, Ponce-López R, Parkinson CL, Espinosa-Fematt J, Sáenz-Mata J, Flores-Martínez E, Alagón A, Castañeda-Gaytán G. Ontogenetic Change in the Venom of Mexican Black-Tailed Rattlesnakes ( Crotalus molossus nigrescens). Toxins (Basel) 2018; 10:toxins10120501. [PMID: 30513722 PMCID: PMC6315878 DOI: 10.3390/toxins10120501] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Ontogenetic changes in venom composition have important ecological implications due the relevance of venom in prey acquisition and defense. Additionally, intraspecific venom variation has direct medical consequences for the treatment of snakebite. However, ontogenetic changes are not well documented in most species. The Mexican Black-tailed Rattlesnake (Crotalus molossus nigrescens) is large-bodied and broadly distributed in Mexico. To document venom variation and test for ontogenetic changes in venom composition, we obtained venom samples from twenty-seven C. m. nigrescens with different total body lengths (TBL) from eight states in Mexico. The primary components in the venom were detected by reverse-phase HPLC, western blot, and mass spectrometry. In addition, we evaluated the biochemical (proteolytic, coagulant and fibrinogenolytic activities) and biological (LD50 and hemorrhagic activity) activities of the venoms. Finally, we tested for recognition and neutralization of Mexican antivenoms against venoms of juvenile and adult snakes. We detected clear ontogenetic venom variation in C. m. nigrescens. Venoms from younger snakes contained more crotamine-like myotoxins and snake venom serine proteinases than venoms from older snakes; however, an increase of snake venom metalloproteinases was detected in venoms of larger snakes. Venoms from juvenile snakes were, in general, more toxic and procoagulant than venoms from adults; however, adult venoms were more proteolytic. Most of the venoms analyzed were hemorrhagic. Importantly, Mexican antivenoms had difficulties recognizing low molecular mass proteins (<12 kDa) of venoms from both juvenile and adult snakes. The antivenoms did not neutralize the crotamine effect caused by the venom of juveniles. Thus, we suggest that Mexican antivenoms would have difficulty neutralizing some human envenomations and, therefore, it may be necessary improve the immunization mixture in Mexican antivenoms to account for low molecular mass proteins, like myotoxins.
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Affiliation(s)
- Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010 Gómez Palacio, Dgo., Mexico.
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 s/n. Fracc. Filadelfia, Apartado Postal No. 51, C.P. 35010 Gómez Palacio, Dgo., Mexico.
| | - Edgar Neri-Castro
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210 Cuernavaca, Mor., Mexico.
- Programa de Doctorado en Ciencias Biomédicas UNAM, C.P. 04510 México D.F., Mexico.
| | - Rebeca Pérez-Morales
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 s/n. Fracc. Filadelfia, Apartado Postal No. 51, C.P. 35010 Gómez Palacio, Dgo., Mexico.
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC 29634, USA.
| | - Roberto Ponce-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210 Cuernavaca, Mor., Mexico.
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC 29634, USA.
- Department of Forestry and Environmental Conservation, Clemson University, 190 Collings St., Clemson, SC 29634, USA.
| | - Jorge Espinosa-Fematt
- Facultad de Ciencias de la Salud, Universidad Juárez del Estado de Durango, Calz. Palmas 1, Revolución, 35050 Gómez Palacio, Dgo., Mexico.
| | - Jorge Sáenz-Mata
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010 Gómez Palacio, Dgo., Mexico.
| | - Esau Flores-Martínez
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010 Gómez Palacio, Dgo., Mexico.
| | - Alejandro Alagón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Chamilpa, C.P. 62210 Cuernavaca, Mor., Mexico.
| | - Gamaliel Castañeda-Gaytán
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010 Gómez Palacio, Dgo., Mexico.
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25
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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: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, García GC, Bouzid NM, Strickland JL, Parkinson CL, Borja M, Castañeda-Gaytán G, Bryson RW, Flores-Villela OA, Mackessy SP, Castoe TA. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Mol Phylogenet Evol 2018; 127:669-681. [DOI: 10.1016/j.ympev.2018.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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Kalkvik HM, Stout IJ, Hoffman EA, Parkinson CL. Colonization and divergence: phylogeography and population genetics of the Atlantic coast beach mice. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1486339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Håkon M. Kalkvik
- Department of Biology, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
| | - I. Jack Stout
- Department of Biology, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
| | - Eric A. Hoffman
- Department of Biology, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
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Lawrance MF, Muthukrishnan G, Deichen J, Deichen M, Schaus J, Cole AM, Parkinson CL. Genetic assessment of Staphylococcus aureus in an underreported locality: Ambulatory care clinic. J Infect Public Health 2018; 11:648-656. [PMID: 29716844 DOI: 10.1016/j.jiph.2018.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 03/29/2018] [Accepted: 04/08/2018] [Indexed: 10/17/2022] Open
Abstract
BACKGROUND Staphylococcus aureus has strong association with anthropogenic environments. This association has not been well supported by use of genetic tools. The aim of this study was to phylogenetically relate numerous isolates from three environments - NCBI samples from hospitals, a community, and a previously unexplored healthcare environment: an ambulatory care clinic (ACC). METHODS This study incorporated hospital samples from NCBI, a community database from the University of Central Florida (UCF), and newly added samples taken from employees of an ambulatory care clinic located at UCF. Samples were collected from nasal swabs of employees, and positive samples were cultured, extracted, and sequenced at seven MLST loci and one virulence locus (spa). MLST sequences were used in eBURST and TCS population structure analyses and all sequences were incorporated into a phylogenetic reconstruction of relationships. RESULTS A total of 185 samples were incorporated in this study (15 NCBI sequences from hospital infections, 29 from the ACC, and 141 from the community). In both phylogenetic and population genetics analyses, samples proved to be panmixic, with samples not segregating monophyletically based on sample origin. CONCLUSION Samples isolated from ambulatory care clinics are not significantly differentiated from either community or hospital samples at the representative loci chosen. These results strengthen previous conclusions that S. aureus may exhibit high genetic similarity across anthropogenic environments.
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Affiliation(s)
- Matthew F Lawrance
- Department of Biology, University of Central Florida, Orlando, FL, United States
| | - Gowrishankar Muthukrishnan
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, United States
| | - John Deichen
- Department of Economics, University of Florida College of Liberal Arts and Sciences, Orlando, FL, United States; Department of Statistics, University of Central Florida, Orlando, FL, United States
| | - Michael Deichen
- UCF Health Services, University of Central Florida, Orlando, FL, United States
| | - James Schaus
- UCF Health Services, University of Central Florida, Orlando, FL, United States
| | - Alexander M Cole
- Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, United States
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Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. Phenotypic Variation in Mojave Rattlesnake (Crotalus scutulatus) Venom Is Driven by Four Toxin Families. Toxins (Basel) 2018; 10:toxins10040135. [PMID: 29570631 PMCID: PMC5923301 DOI: 10.3390/toxins10040135] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 02/04/2023] Open
Abstract
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, which is under strong selection due to its role in prey acquisition and defense. Rattlesnake venom can be characterized by the presence (Type A) or absence (Type B) of a type of neurotoxic phospholipase A2 (PLA2), such as Mojave toxin, that increases venom toxicity. Mojave rattlesnakes (Crotalus scutulatus), represent this diversity as both venom types are found within this species and within a single panmictic population in the Sonoran Desert. We used comparative venom gland transcriptomics of nine specimens of C. scutulatus from this region to test whether expression differences explain diversity within and between venom types. Type A individuals expressed significantly fewer toxins than Type B individuals owing to the diversity of C-type lectins (CTLs) and snake venom metalloproteinases (SVMPs) found in Type B animals. As expected, both subunits of Mojave toxin were exclusively found in Type A individuals but we found high diversity in four additional PLA2s that was not associated with a venom type. Myotoxin a expression and toxin number variation was not associated with venom type, and myotoxin a had the highest range of expression of any toxin class. Our study represents the most comprehensive transcriptomic profile of the venom type dichotomy in rattlesnakes and C. scutulatus. Even intra-specifically, Mojave rattlesnakes showcase the diversity of snake venoms and illustrate that variation within venom types blurs the distinction of the venom dichotomy.
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Affiliation(s)
- Jason L Strickland
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC 29634, USA.
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.
| | - Christopher L Parkinson
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
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Rautsaw RM, Martin SA, Vincent BA, Lanctot K, Bolt MR, Seigel RA, Parkinson CL. Stopped Dead in Their Tracks: The Impact of Railways on Gopher Tortoise (Gopherus polyphemus) Movement and Behavior. COPEIA 2018. [DOI: 10.1643/ce-17-635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Saldarriaga-Córdoba M, Parkinson CL, Daza JM, Wüster W, Sasa M. Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE). PLoS One 2017; 12:e0187969. [PMID: 29176806 PMCID: PMC5703453 DOI: 10.1371/journal.pone.0187969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/30/2017] [Indexed: 11/18/2022] Open
Abstract
The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species’ distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O´Higgins, Santiago, Chile
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Juan M. Daza
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Wolfgang Wüster
- School of Biological Sciences, Bangor University, Bangor, United states of Kingdom
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
- Organization for Tropical Studies, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- * E-mail:
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Martin SA, Rautsaw RM, Robb F, Bolt MR, Parkinson CL, Seigel RA. Set AHDriFT: Applying game cameras to drift fences for surveying herpetofauna and small mammals. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott A. Martin
- Department of Biological Sciences; Towson University; 8000 York Road Towson MD 21252 USA
| | - Rhett M. Rautsaw
- Department of Biology; University of Central Florida; 4000 Central Florida Boulevard Orlando FL 32816 USA
| | - Frank Robb
- Biomedical Science; Eastern Florida State College; 1311US HWY 1, Titusville FL 32796 USA
| | - M. Rebecca Bolt
- Integrated Mission Support Services; Mail Code IMSS-200; Kennedy Space Center FL 32899 USA
| | - Christopher L. Parkinson
- Department of Biology; University of Central Florida; 4000 Central Florida Boulevard Orlando FL 32816 USA
| | - Richard A. Seigel
- Department of Biological Sciences; Towson University; 8000 York Road Towson MD 21252 USA
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Martin SA, Rautsaw RM, Bolt R, Parkinson CL, Seigel RA. Adapting coastal management to climate change: Mitigating our shrinking shorelines. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Scott A. Martin
- Department of Biological Sciences; Towson University; 8000 York Road Towson MD 21252 USA
| | - Rhett M. Rautsaw
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| | - Rebecca Bolt
- Integrated Mission Support Services; Mail Code IMSS-200; Kennedy Space Center FL 32899 USA
| | - Christopher L. Parkinson
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| | - Richard A. Seigel
- Department of Biological Sciences; Towson University; 8000 York Road Towson MD 21252 USA
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Doan TM, Mason AJ, Castoe TA, Sasa M, Parkinson CL. A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridis. Zootaxa 2016; 4138:271-90. [PMID: 27470764 DOI: 10.11646/zootaxa.4138.2.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 11/04/2022]
Abstract
Middle America is one of the most biodiverse regions in the world, harboring an exceptional number of rare and endemic species. This is especially true of Middle American cloud forests, where montane specialists occupy restricted, high-elevation ranges making them attractive candidates for investigating historical biogeography and speciation. One such highland-restricted species, the black speckled palm-pitviper (Bothriechis nigroviridis), occupies the Central, Tilarán, and Talamanca Cordilleras in Costa Rica and Panama. In this study, we investigate the genetic and morphological variation among populations of B. nigroviridis by inferring a multilocus phylogeny (21 individuals) and analyzing meristic scale characters with a principal component analysis (64 individuals). We find B. nigroviridis sensu stricto to be composed of two deeply divergent lineages, one with a restricted range in the northern and central Cordillera Talamanca and the other ranging throughout the Central, Tilarán, and Talamanca Cordilleras. Furthermore, these two lineages are morphologically distinct, with previously unrecognized differences in several characters allowing us to name and diagnose a new species B. nubestris sp. nov. We also examine the genetic and morphological variation within B. nigroviridis and discuss biogeographic hypotheses that may have led to the diversification of Bothriechis lineages.
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Affiliation(s)
- Tiffany M Doan
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.;
| | - Andrew J Mason
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.;
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA.; unknown
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, and Palo Verde Biological Station, Organization for Tropical Studies, San José, Costa Rica.;
| | - Christopher L Parkinson
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.;
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Streicher JW, McEntee JP, Drzich LC, Card DC, Schield DR, Smart U, Parkinson CL, Jezkova T, Smith EN, Castoe TA. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution 2016; 70:1435-49. [DOI: 10.1111/evo.12967] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/30/2016] [Accepted: 05/16/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Jeffrey W. Streicher
- Department of Life Sciences The Natural History Museum London United Kingdom
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Jay P. McEntee
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
- Department of Biology University of Florida Gainesville Florida
| | - Laura C. Drzich
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Daren C. Card
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Drew R. Schield
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Utpal Smart
- Department of Biology University of Texas at Arlington Arlington Texas
| | | | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona
| | - Eric N. Smith
- Department of Biology University of Texas at Arlington Arlington Texas
| | - Todd A. Castoe
- Department of Biology University of Texas at Arlington Arlington Texas
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Strickland JL, Carter S, Kraus F, Parkinson CL. Snake evolution in Melanesia: origin of the Hydrophiinae (Serpentes, Elapidae), and the evolutionary history of the enigmatic New Guinean elapidToxicocalamus. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jason L. Strickland
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| | - Sharon Carter
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology; University of Michigan; 830 North University Ann Arbor MI 48109 USA
| | - Christopher L. Parkinson
- Department of Biology; University of Central Florida; 4000 Central Florida Blvd. Orlando FL 32816 USA
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Strickland JL, Parkinson CL, McCoy JK, Ammerman LK. Phylogeography ofAgkistrodon piscivoruswith Emphasis on the Western Limit of Its Range. COPEIA 2014. [DOI: 10.1643/cg-13-123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Muthukrishnan G, Lamers RP, Ellis A, Paramanandam V, Persaud AB, Tafur S, Parkinson CL, Cole AM. Longitudinal genetic analyses of Staphylococcus aureus nasal carriage dynamics in a diverse population. BMC Infect Dis 2013; 13:221. [PMID: 23679038 PMCID: PMC3673815 DOI: 10.1186/1471-2334-13-221] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/08/2013] [Indexed: 02/03/2023] Open
Abstract
Background Staphylococcus aureus (SA) nasal colonization plays a critical role in the pathogenesis of staphylococcal infections and SA eradication from the nares has proven to be effective in reducing endogenous infections. To understand SA nasal colonization and its relation with consequent disease, assessment of nasal carriage dynamics and genotypic diversity among a diverse population is a necessity. Results We have performed extensive longitudinal monitoring of SA nasal carriage isolates in 109 healthy individuals over a period of up to three years. Longitudinal sampling revealed that 24% of the individuals were persistent SA nasal carriers while 32% were intermittent. To assess the genetic relatedness between different SA isolates within our cohort, multi locus sequence typing (MLST) was performed. MLST revealed that not only were strains colonizing intermittent and persistent nasal carriers genetically similar, belonging to the same clonal complexes, but strain changes within the same host were also observed over time for both types of carriers. More highly discriminating genetic analyses using the hypervariable regions of staphylococcal protein A and clumping factor B virulence genes revealed no preferential colonization of specific SA strains in persistent or intermittent carriers. Moreover, we observed that a subset of persistent and intermittent carriers retained clinically relevant community-acquired methicillin-resistant SA (CA-MRSA) strains in their nares over time. Conclusions The findings of this study provides added perspective on the nasal carriage dynamics between strains colonizing persistent and intermittent carriers; an area currently in need of assessment given that persistent carriers are at greater risk of autoinfection than intermittent carriers.
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Affiliation(s)
- Gowrishankar Muthukrishnan
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
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Lamers RP, Muthukrishnan G, Castoe TA, Tafur S, Cole AM, Parkinson CL. Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data. BMC Evol Biol 2012; 12:171. [PMID: 22950675 PMCID: PMC3464590 DOI: 10.1186/1471-2148-12-171] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 08/30/2012] [Indexed: 11/17/2022] Open
Abstract
Background Estimates of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies based largely on single gene analyses incorporating only a limited taxon sample. As such, the evolutionary relationships and hierarchical classification schemes among species have not been confidently established. Here, we address these points through analyses of DNA sequence data from multiple loci (16S rRNA gene, dnaJ, rpoB, and tuf gene fragments) using multiple Bayesian and maximum likelihood phylogenetic approaches that incorporate nearly all recognized Staphylococcus taxa. Results We estimated the phylogeny of fifty-seven Staphylococcus taxa using partitioned-model Bayesian and maximum likelihood analysis, as well as Bayesian gene-tree species-tree methods. Regardless of methodology, we found broad agreement among methods that the current cluster groups require revision, although there was some disagreement among methods in resolution of higher order relationships. Based on our phylogenetic estimates, we propose a refined classification for Staphylococcus with species being classified into 15 cluster groups (based on molecular data) that adhere to six species groups (based on phenotypic properties). Conclusions Our findings are in general agreement with gene tree-based reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships among species. Our results support the general importance of such multilocus assessments as a standard in microbial studies to more robustly infer relationships among recognized and newly discovered lineages.
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Affiliation(s)
- Ryan P Lamers
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
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Castoe TA, Streicher JW, Meik JM, Ingrasci MJ, Poole AW, de Koning APJ, Campbell JA, Parkinson CL, Smith EN, Pollock DD. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Mol Ecol Resour 2012; 12:1105-13. [PMID: 22938699 DOI: 10.1111/1755-0998.12000] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/18/2012] [Accepted: 07/28/2012] [Indexed: 11/29/2022]
Abstract
Studies of population genetics increasingly use next-generation DNA sequencing to identify microsatellite loci in nonmodel organisms. There are, however, relatively few studies that validate the feasibility of transitioning from marker development to experimental application across populations and species. North American coralsnakes of the Micrurus fulvius species complex occur in the United States and Mexico, and little is known about their population structure and phylogenetic relationships. This absence of information and population genetics markers is particularly concerning because they are highly venomous and have important implications on human health. To alleviate this problem in coralsnakes, we investigated the feasibility of using 454 shotgun sequences for microsatellite marker development. First, a genomic shotgun library from a single individual was sequenced (approximately 7.74 megabases; 26,831 reads) to identify potentially amplifiable microsatellite loci (PALs). We then hierarchically sampled 76 individuals from throughout the geographic distribution of the species complex and examined whether PALs were amplifiable and polymorphic. Approximately half of the loci tested were readily amplifiable from all individuals, and 80% of the loci tested for variation were variable and thus informative as population genetic markers. To evaluate the repetitive landscape characteristics across multiple snakes, we also compared microsatellite content between the coralsnake and two other previously sampled snakes, the venomous copperhead (Agkistrodon contortrix) and Burmese python (Python molurus).
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Affiliation(s)
- Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Lamers RP, Stinnett JW, Muthukrishnan G, Parkinson CL, Cole AM. Evolutionary analyses of Staphylococcus aureus identify genetic relationships between nasal carriage and clinical isolates. PLoS One 2011; 6:e16426. [PMID: 21283661 PMCID: PMC3025037 DOI: 10.1371/journal.pone.0016426] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 12/16/2010] [Indexed: 11/18/2022] Open
Abstract
Nasal carriage of Staphylococcus aureus has long been hypothesized to be a major vector for the transmission of virulent strains throughout the community. To address this hypothesis, we have analyzed the relatedness between a cohort of nasal carriage strains and clinical isolates to understand better the genetic conformity therein. To assess the relatedness between nasal carriage and clinical isolates of S. aureus, a genetic association study was conducted using multilocus sequence typing (MLST) and typing of the hypervariable regions of clumping factor and fibronectin binding protein genes. At all loci analyzed, genetic associations between both nasal carriage and clinical isolates were observed. Computational analyses of MLST data indicate that nasal carriage and clinical isolates belong to the same genetic clusters (clades), despite differences in sequence type assignments. Genetic analyses of the hypervariable regions from the clumping factor and fibronectin binding protein genes revealed that not only do clinically relevant strains belong to identical genetic lineages as the nasal carriage isolates within our cohort, but they also exhibit 100% sequence similarity within these regions. The findings of this report indicate that strains of S. aureus being carried asymptomatically throughout the community via nasal colonization are genetically related to those responsible for high levels of morbidity and mortality.
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Affiliation(s)
- Ryan P. Lamers
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Jason W. Stinnett
- School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Gowrishankar Muthukrishnan
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Alexander M. Cole
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
- * E-mail:
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Abstract
A definitive long-term decrease in the extent of antarctic sea ice is not detectable from 9 years (1973 to 1981) of year-round satellite observations and limited prior data. Regional interannual variability is large, with sea ice decreasing in some regions while increasing in others. A significant decrease in overall ice extent during the mid-1970's, previously suggested to reflect warming induced by carbon dioxide, has not been maintained. In particular, the extent of ice in the Weddell Sea region has rebounded after a large decrease concurrent with a major oceanographic anomaly, the Weddell polynya. Over the 9 years, the trends are nearly the same in all seasons, but for periods of 3 to 5 years, greater winter ice maxima are associated with lesser summer ice minima. The decrease of the mid-1970's was preceded by an increase in ice extent from 1966 to 1972, further indicating the presence of cyclical components of variation that obscure any long-term trends that might be caused by a warming induced by carbon dioxide.
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Castoe TA, Gu W, de Koning APJ, Daza JM, Jiang ZJ, Parkinson CL, Pollock DD. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenet Genome Res 2010; 127:112-27. [PMID: 20215734 DOI: 10.1159/000295342] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the approximately 200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models.
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Affiliation(s)
- T A Castoe
- Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Metzger GA, Kraus F, Allison A, Parkinson CL. Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): Evidence from mitochondrial and nuclear markers. Mol Phylogenet Evol 2010; 54:405-16. [DOI: 10.1016/j.ympev.2009.07.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/21/2009] [Accepted: 07/26/2009] [Indexed: 11/15/2022]
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Castoe TA, Spencer CL, Parkinson CL. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Mol Phylogenet Evol 2006; 42:193-212. [PMID: 16934495 DOI: 10.1016/j.ympev.2006.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Revised: 06/21/2006] [Accepted: 07/03/2006] [Indexed: 11/16/2022]
Abstract
The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American desert and semi-arid ecosystems, and its importance extends from its impact on the region's ecology and imagery, to its medical relevance as a large deadly venomous snake. We used mtDNA sequences to identify population genetic structure and historical demographic patterns across the range of this species, and relate these to broader patterns of historical biogeography of desert and semi-arid regions of the southwestern USA and adjacent Mexico. We inferred a Late Pliocene divergence between peninsular and continental lineages of Crotalus, followed by an Early Mid Pleistocene divergence across the continental divide within C. atrox. Within desert regions (Sonoran and Chihuahuan Deserts, Southern Plains, and Tamaulipan Plain) we observed population structure indicating isolation of populations in multiple Pleistocene refugia on either side of the continental divide, which we attempt to identify. Evidence of post-glacial population growth and range expansion was inferred, particularly in populations east of the continental divide. We observed clear evidence of (probably recent) gene flow across the continental divide and secondary contact of haplotype lineages. This recent gene flow appears to be particularly strong in the West-to-East direction. Our results also suggest that Crotalus tortugensis (Tortuga Island rattlesnake) and a population of 'C. atrox' inhabiting Santa Cruz Island (in the Gulf of California) previously suggested to be an unnamed species, are in fact deeply phylogenetically nested within continental lineages of C. atrox. Accordingly, we suggest C. tortugensis and 'C. atrox' from Santa Cruz Island be placed in the synonymy of C. atrox.
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Affiliation(s)
- Todd A Castoe
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA
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Abstract
How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships. We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S). Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete. Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree. Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis. The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family. They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera. A new classification of hylid frogs is proposed. Several potentially misleading signals in the morphological data are discussed.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA.
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Castoe TA, Parkinson CL. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Mol Phylogenet Evol 2006; 39:91-110. [PMID: 16504544 DOI: 10.1016/j.ympev.2005.12.014] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 12/02/2005] [Accepted: 12/26/2005] [Indexed: 11/24/2022]
Abstract
The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3kb) per individual, to estimate the phylogeny of pitvipers based on maximum parsimony and Bayesian phylogenetic methods. Our Bayesian analyses incorporated complex mixed models of nucleotide evolution that allocated independent models to various partitions of the dataset within combined analyses. We compared results of unpartitioned versus partitioned Bayesian analyses to investigate how much unpartitioned (versus partitioned) models were forced to compromise estimates of model parameters, and whether complex models substantially alter phylogenetic conclusions to the extent that they appear to extract more phylogenetic signal than simple models. Our results indicate that complex models do extract more phylogenetic signal from the data. We also address how differences in phylogenetic results (e.g., bipartition posterior probabilities) obtained from simple versus complex models may be interpreted in terms of relative credibility. Our estimates of pitviper phylogeny suggest that nearly all recently proposed generic reallocations appear valid, although certain Old and New World genera (Ovophis, Trimeresurus, and Bothrops) remain poly- or paraphyletic and require further taxonomic revision. While a majority of nodes were resolved, we could not confidently estimate the basal relationships among New World genera and which lineage of Old World species is most closely related to this New World group.
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Affiliation(s)
- Todd A Castoe
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, USA
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Reece JS, Ehrhart LM, Parkinson CL. Mixed stock analysis of juvenile loggerheads (Caretta caretta) in Indian River Lagoon, Florida: implications for conservation planning. CONSERV GENET 2006. [DOI: 10.1007/s10592-005-9046-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, dePamphilis CW, Palmer JD. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol 2005; 5:73. [PMID: 16368004 PMCID: PMC1343592 DOI: 10.1186/1471-2148-5-73] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 12/20/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago. RESULTS We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, approximately 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent approximately 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history. CONCLUSION The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and--consistent with the lack of RNA editing--exceptionally high levels of "mutagenic" retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria.
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Affiliation(s)
- Christopher L Parkinson
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Jeffrey P Mower
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
| | - Yin-Long Qiu
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew J Shirk
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
- Department of Otolaryngology, University of Washington, Seattle, WA, 98195, USA
| | - Keming Song
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
- Sigma Chemical Co., 3300 S. 2nd St., St. Louis, MO, 63118, USA
| | - Nelson D Young
- Department of Biology, Holyoke Community College, Holyoke, MA 01040, USA
| | - Claude W dePamphilis
- Department of Biology, Penn State University, University Park, PA 16802-0001, USA
| | - Jeffrey D Palmer
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
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