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Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
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Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
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2
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Tse TC, Tsai IH, Chan YY, Tsai TS. Venom Proteomics of Trimeresurus gracilis, a Taiwan-Endemic Pitviper, and Comparison of Its Venom Proteome and VEGF and CRISP Sequences with Those of the Most Related Species. Toxins (Basel) 2023; 15:408. [PMID: 37505677 PMCID: PMC10467061 DOI: 10.3390/toxins15070408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023] Open
Abstract
Trimeresurus gracilis is an endemic alpine pitviper in Taiwan with controversial phylogeny, and its venom proteome remains unknown. In this study, we conducted a proteomic analysis of T. gracilis venom using high-performance liquid chromatography-tandem mass spectrometry and identified 155 toxin proteoforms that belong to 13 viperid venom toxin families. By searching the sequences of trypsin-digested peptides of the separated HPLC fractions against the NCBI database, T. gracilis venom was found to contain 40.3% metalloproteases (SVMPs), 15.3% serine proteases, 6.6% phospholipases A2, 5.0% L-amino acid oxidase, 4.6% Cys-rich secretory proteins (CRISPs), 3.2% disintegrins, 2.9% vascular endothelial growth factors (VEGFs), 1.9% C-type lectin-like proteins, and 20.2% of minor toxins, nontoxins, and unidentified peptides or compounds. Sixteen of these proteoforms matched the toxins whose full amino-acid sequences have been deduced from T. gracilis venom gland cDNA sequences. The hemorrhagic venom of T. gracilis appears to be especially rich in PI-class SVMPs and lacks basic phospholipase A2. We also cloned and sequenced the cDNAs encoding two CRISP and three VEGF variants from T. gracilis venom glands. Sequence alignments and comparison revealed that the PI-SVMP, kallikrein-like proteases, CRISPs, and VEGF-F of T. gracilis and Ovophis okinavensis are structurally most similar, consistent with their close phylogenetic relationship. However, the expression levels of some of their toxins were rather different, possibly due to their distinct ecological and prey conditions.
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Affiliation(s)
- Tsz-Chun Tse
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Inn-Ho Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan;
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106319, Taiwan
| | - Yuen-Ying Chan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
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3
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Carrasco PA, Koch C, Grazziotin FG, Venegas PJ, Chaparro JC, Scrocchi GJ, Salazar-Valenzuela D, Leynaud GC, Mattoni CI. Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae). Cladistics 2023; 39:71-100. [PMID: 36701490 DOI: 10.1111/cla.12522] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 01/27/2023] Open
Abstract
Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of Bothrops lojanus, which may lead to the paraphyly of either Bothrops or Bothrocophias. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.
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Affiliation(s)
- Paola A Carrasco
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Centro de Zoología Aplicada, Rondeau 798, Córdoba, 5000, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Diversidad y Ecología Animal (IDEA-CONICET), Rondeau, 798, Córdoba, 5000, Argentina
| | - Claudia Koch
- Leibniz Institute for the Analysis of Biodiversity Change/Zoologisches Forschungsinstitute und Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, 1500, São Paulo, SP, Brazil
| | - Pablo J Venegas
- Instituto Peruano de Herpetología, Salazar Bondy 136, Santiago de Surco 15038, Lima, Peru.,Rainforest Partnership, 4005 Guadalupe St, Austin, TX, 78751, USA
| | - Juan C Chaparro
- Museo de Biodiversidad del Perú, Urbanización Mariscal Gamarra A-61, Zona 2, Cusco, Peru.,Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Paraninfo Universitario (Plaza de Armas s/n), Cusco, Peru
| | - Gustavo J Scrocchi
- UEL-CONICET and Fundación Miguel Lillo, Miguel Lillo 251, San Miguel de Tucumán, Tucumán, Argentina
| | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, EC170301, Quito, Ecuador
| | - Gerardo C Leynaud
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Centro de Zoología Aplicada, Rondeau 798, Córdoba, 5000, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Diversidad y Ecología Animal (IDEA-CONICET), Rondeau, 798, Córdoba, 5000, Argentina
| | - Camilo I Mattoni
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Centro de Zoología Aplicada, Rondeau 798, Córdoba, 5000, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Diversidad y Ecología Animal (IDEA-CONICET), Rondeau, 798, Córdoba, 5000, Argentina
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4
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Tsai TS, Tsai IH. Full sequencing and comparison of five venom metalloproteases of Trimeresurus gracilis: The PI-enzyme is most similar to okinalysin but the PIII-enzyme is most similar to Crotalus venom enzymes. Toxicon 2023; 225:107053. [PMID: 36758773 DOI: 10.1016/j.toxicon.2023.107053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
The cDNAs encoding the Zn+2-metalloproteases (SVMPs) of Trimeresurus gracilis (abbreviated as Tgc), a pitviper endemic to Taiwan, were cloned from venom glands and sequenced. The amino-acid sequences of five novel SVMPs, including one P-III, three P-II and one P-I class enzymes, were thus deduced and subjected to BLAST-analyses. The P-III enzyme (designated as Tgc-PIII) is structurally most similar to the PIII-SVMPs of New World pitvipers but not similar to the PIII-SVMP of Ovophis okinavensis. Sequence-similarity analysis of 22 homologous PIII-SVMPs reveal three major structural subtypes of the pitviper PIII-SVMPs, which possibly have different substrate specificities. In addition, Tgc-PIII and the PI-class SVMP (named Tgc-MP) were isolated from the venom and verified by mass spectrometry. All the three deduced sequences of PII-SVMPs (Tgc-PIIs) contain an abnormal Zn+2-binding-site in their catalytic-domain, and an identical "long-disintegrin" domain. The predicted 85-residues disintegrin, gracilisin, bears high similarities to some long-disintegrins of the New-World pitvipers and salmosin3. By BLAST search and comparison, Tgc-MP is 96% similar to okinalysin, the hemorrhagic PI-SVMP of O. okinavensis, rather than any other PI-SVMPs in the databanks. Our results confirm the fast evolution of Tgc-SVMPs as well as their structural similarities to different SVMP-classes of the New-World pitvipers and of O. okinavensis, respectively. The implications of our findings are discussed along with our previous sequence comparisons of venom phospholipases A2 and ten venom serine proteases of Tgc.
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Affiliation(s)
- Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Inn-Ho Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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5
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Grabowsky ER, Saviola AJ, Alvarado-Díaz J, Mascareñas AQ, Hansen KC, Yates JR, Mackessy SP. Montane Rattlesnakes in México: Venoms of Crotalus tancitarensis and Related Species within the Crotalus intermedius Group. Toxins (Basel) 2023; 15:72. [PMID: 36668891 PMCID: PMC9867100 DOI: 10.3390/toxins15010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
The Crotalus intermedius group is a clade of rattlesnakes consisting of several species adapted to a high elevation habitat, primarily in México. Crotalus tancitarensis was previously classified as C. intermedius, until individuals occurring on Cerro Tancítaro in Michoacán, México, were reevaluated and classified as a new species (C. tancitarensis) based on scale pattern and geographic location. This study aimed to characterize the venom of C. tancitarensis and compare the venom profile to those of other species within the Crotalus intermedius group using gel electrophoresis, biochemical assays, reverse-phase high performance liquid chromatography, mass spectrometry, and lethal toxicity (LD50) assays. Results show that the venom profiles of species within the Crotalus intermedius group are similar, but with distinct differences in phospholipase A2 (PLA2), metalloproteinase PI (SVMP PI), and kallikrein-like serine proteinase (SVSP) activity and relative abundance. Proteomic analysis indicated that the highland forms produce venoms with 50-60 protein isoforms and a composition typical of type I rattlesnake venoms (abundant SVMPs, lack of presynaptic PLA2-based neurotoxins), as well as a diversity of typical Crotalus venom components such as serine proteinases, PLA2s, C-type lectins, and less abundant toxins (LAAOs, CRiSPs, etc.). The overall venom profile of C. tancitarensis appears most similar to C. transversus, which is consistent with a previous mitochondrial DNA analysis of the Crotalus intermedius group. These rattlesnakes of the Mexican highlands represent a radiation of high elevation specialists, and in spite of divergence of species in these Sky Island habitats, venom composition of species analyzed here has remained relatively conserved. The majority of protein family isoforms are conserved in all members of the clade, and as seen in other more broadly distributed rattlesnake species, differences in their venoms are largely due to relative concentrations of specific components.
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Affiliation(s)
- Emily R. Grabowsky
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Javier Alvarado-Díaz
- INIRENA (Instituto de Investigaciones sobre los Recursos Naturales), Morelia CP 58330, Michoacán, Mexico
| | | | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John R. Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen P. Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
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6
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Muñoz-Mora VH, Suárez-Atilano M, Maltagliati F, Ramírez-Corona F, Carbajal-Saucedo A, Percino-Daniel R, Langeneck J, D’Addario M, Sunny A. A tale about vipers’ tails: phylogeography of black-tailed rattlesnakes. HERPETOZOA 2022. [DOI: 10.3897/herpetozoa.35.e84297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The phylogenetic relationships among black-tailed rattlesnakes remain poorly understood and some authors indicated that the diversity of this group has been underestimated and additional analyses are required to clarify the biogeographic patterns throughout its distribution in Mexico. Therefore, the aim of this study was to elucidate the phylogenetic relationships among black-tailed rattlesnakes across their range, identifying relative divergence times among the main clades and reconstructing the biogeographical history of the group. Three partial mitochondrial genes (ND4, cytb and ATPase6) and one nuclear gene (RAG1) were sequenced to infer the phylogenetic relationships, through the maximum likelihood and Bayesian inference-based methods; demographic history reconstruction was investigated through Bayesian Skyline plot analysis and the ancestral area reconstruction was carried out considering a Bayesian framework. We found strong evidence that the black-tailed rattlesnakes’ group is composed of six clades, which is in agreement with subspecies previously reported. Divergence time estimation indicated that the origin of the C. molossus group could be traced to the middle of the Miocene (~7.71 Mya). Ancestral area reconstruction indicated that early divergence events occurred in Central Mexico, probably related to the geological dynamics of the Trans-Mexican Volcanic Belt. The lineage C. m. oaxacus is the basal member of the C. molossus group. Furthermore, the combination of geological events and changes in Quaternary vegetation may have contributed to the divergence of C. molossus clades. Our results suggest several clades within C. molossus complex could be potentially recognized as separate species.
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7
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Bernarde PS, Pucca MB, Mota-da-Silva A, da Fonseca WL, de Almeida MRN, de Oliveira IS, Cerni FA, Gobbi Grazziotin F, Sartim MA, Sachett J, Wen FH, Moura-da-Silva AM, Monteiro WM. Bothrops bilineatus: An Arboreal Pitviper in the Amazon and Atlantic Forest. Front Immunol 2021; 12:778302. [PMID: 34975866 PMCID: PMC8714932 DOI: 10.3389/fimmu.2021.778302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
The two-striped forest-pitviper (Bothrops bilineatus) is an arboreal snake that is currently represented by two subspecies (B. b. bilineatus and B. b. smaragdinus) that comprise a species complex, and its distribution is in the Amazon and the Atlantic Forest. The rarity of encounters with this snake is reflected in the low occurrence of cases of snakebites throughout its geographic distribution and the resulting low number of published clinical reports. However, in some areas, B. bilineatus proves to be more frequent and causes envenomations in a greater proportion. Herein, we review the main aspects of the species complex B. bilineatus, including its biology, ecology, taxonomy, morphology, genetic and molecular studies, geographic distribution, conservation status, venom, pathophysiology and clinical aspects, and epidemiology. In addition, the different antivenoms available for the treatment of envenomations caused by B. bilineatus are presented along with suggestions for future studies that are needed for a better understanding of the snakebites caused by this snake.
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Affiliation(s)
- Paulo Sérgio Bernarde
- Laboratório de Herpetologia, Universidade Federal do Acre, Cruzeiro do Sul, Brazil
- *Correspondence: Paulo Sérgio Bernarde, ; Wuelton M. Monteiro,
| | - Manuela Berto Pucca
- Curso de Medicina, Universidade Federal de Roraima, Boa Vista, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Roraima, Boa Vista, Brazil
| | | | | | | | - Isadora Sousa de Oliveira
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Felipe Augusto Cerni
- Programa de Pós-graduação em Ciências da Saúde, Universidade Federal de Roraima, Boa Vista, Brazil
| | | | - Marco A. Sartim
- Departamento de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
- Departamento de Pós-Graduação, Universidade Nilton Lins, Manaus, Brazil
| | - Jacqueline Sachett
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Departamento de Ensino e Pesquisa, Fundação Alfredo da Matta, Manaus, Brazil
| | - Fan Hui Wen
- Núcleo Estratégico de Venenos e Antivenenos, Instituto Butantan, São Paulo, Brazil
| | - Ana Maria Moura-da-Silva
- Departamento de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
| | - Wuelton M. Monteiro
- Departamento de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- *Correspondence: Paulo Sérgio Bernarde, ; Wuelton M. Monteiro,
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8
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Shi JS, Liu JC, Giri R, Owens JB, Santra V, Kuttalam S, Selvan M, Guo KJ, Malhotra A. Molecular phylogenetic analysis of the genus Gloydius (Squamata, Viperidae, Crotalinae), with description of two new alpine species from Qinghai-Tibet Plateau, China. Zookeys 2021; 1061:87-108. [PMID: 34707454 PMCID: PMC8505391 DOI: 10.3897/zookeys.1061.70420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/20/2021] [Indexed: 11/25/2022] Open
Abstract
We provide a molecular phylogeny of Asian pit vipers (the genus Gloydius) based on four mitochondrial genes (12S, 16S, ND4, and cytb). Sequences of Gloydiushimalayanus, the only member of the genus that occurs south of the Himalayan range, are included for the first time. In addition, two new species of the genus Gloydius are described based on specimens collected from Zayu, Tibet, west of the Nujiang River and Heishui, Sichuan, east of the Qinghai-Tibet Plateau. The new species, Gloydiuslipipengi sp. nov., can be differentiated from its congeners by the combination of the following characters: the third supralabial not reaching the orbit (separated from it by a suborbital scale); wide, black-bordered greyish postorbital stripe extending from the posterior margin of the orbit (not separated by the postoculars, covering most of the anterior temporal scale) to the ventral surface of the neck; irregular black annular crossbands on the mid-body; 23-21-15 dorsal scales; 165 ventral scales, and 46 subcaudal scales. Gloydiusswildsp. nov. can be differentiated from its congeners by the narrower postorbital stripe (only half the width of the anterior temporal scale, the lower edge is approximately straight and bordered with white); a pair of arched stripes on the occiput; lateral body lakes black spots; a pair of round spots on the parietal scales; 21 rows of mid-body dorsal scales; zigzag dark brown stripes on the dorsum; 168–170 ventral scales, and 43–46 subcaudal scales. The molecular phylogeny in this study supports the sister relationship between G.lipipengisp. nov. and G.rubromaculatus, another recently described species from the Qinghai-Tibet Plateau, more than 500 km away, and indicate the basal position of G.himalayanus within the genus and relatively distant relationship to its congeners.
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Affiliation(s)
- Jing-Song Shi
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,Institute of Herpetology, Shenyang Normal University, Shenyang 110034, China
| | - Jin-Cheng Liu
- Institute of Herpetology, Shenyang Normal University, Shenyang 110034, China
| | - Rohit Giri
- Department of Zoology, Prithvi Narayan Campus, Bhimkalipatan-1, Pokhara 33700, Nepal
| | - John Benjamin Owens
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.,Captive and Field Herpetology, Wales, UK
| | - Vishal Santra
- Captive and Field Herpetology, Wales, UK.,Society for Nature Conservation, Research and Community Engagement (CONCERN), Nalikul, Hooghly, West Bengal, India
| | - Sourish Kuttalam
- Captive and Field Herpetology, Wales, UK.,Society for Nature Conservation, Research and Community Engagement (CONCERN), Nalikul, Hooghly, West Bengal, India
| | - Melvin Selvan
- Endangered Wildlife Trust, Dindigull, Tamil Nadu, India
| | - Ke-Ji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, College of Life Sciences and Technology, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Anita Malhotra
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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9
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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10
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Molecular Phylogenetics and Morphometrics Reveal a New Endemic Jumping Pitviper (Serpentes: Viperidae: Metlapilcoatlus) from the Sierra Madre Oriental of Mexico. J HERPETOL 2021. [DOI: 10.1670/20-028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Xu G, Zhu P, Zhu W, Ma B, Li X, Li W. Characterization of the complete mitochondrial genome of Notocotylus sp. (Trematoda, Notocotylidae) and its phylogenetic implications. Parasitol Res 2021; 120:1291-1301. [PMID: 33559042 DOI: 10.1007/s00436-021-07075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/28/2021] [Indexed: 01/20/2023]
Abstract
The parasite genus Notocotylus comprises at least 50 species colonizing mainly aquatic birds and to a lesser extent some mammals, particularly rodents. Here trematode specimens isolated from a wild black swan were characterized and identified to belong to the genus Notocotylus via morphological and molecular analyses. Phylogenetic position of the isolate among other trematodes was determined based on the ribosomal internal transcribed spacer (ITS) 1 and 2. The complete mitochondrial (mt) genome of the isolate was amplified, sequenced, assembled, analyzed, and annotated. The isolate has an AT-rich mt genome (14,317 bp in length) that comprises 12 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The Notocotylus isolate identified in this study has relatively high mt genome sequence identity and identical gene content and arrangement to a known Notocotylidae species, Ogmocotyle sikae. The isolate formed a genetic clade with O. sikae in phylogenetic analysis of the concatenated PCG amino acid sequences. Compared to the ITS, the trematode mt genome appears more informative for resolving high-level phylogenies. To the best of our knowledge, this is the first study exploring the complete mt genome for the genus Notocotylus, and it offers a novel genomic resource that has important implications for trematode phylogenetics.
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Affiliation(s)
- Guoliang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China.,Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Peng Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Weining Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Bo Ma
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaoyun Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.
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Li JN, Liang D, Wang YY, Guo P, Huang S, Zhang P. A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system. Mol Phylogenet Evol 2020; 148:106807. [PMID: 32268200 DOI: 10.1016/j.ympev.2020.106807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/05/2020] [Accepted: 03/23/2020] [Indexed: 01/04/2023]
Abstract
Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increasing the compatibility of the data from different researches is thus important, which can be facilitated by standardization of the loci used in systematic analyses. In this study, we proposed a unified multilocus marker system for snake systematics by conflating 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers. This marker system is an addition to the large squamate conserved locus set (SqCL) for studies preferring a medium-scale data set. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematic framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on the multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple types of markers to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the nuclear data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into many snake phylogenetic relationships. Suggestions are made for the current Chinese snake taxonomy.
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Affiliation(s)
- Jiang-Ni Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Yong Wang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin, China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China.
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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Characterization of the complete mitogenome of Centrorhynchus clitorideus (Meyer, 1931) (Palaeacanthocephala: Centrorhynchidae), the largest mitochondrial genome in Acanthocephala, and its phylogenetic implications. Mol Biochem Parasitol 2020; 237:111274. [PMID: 32243910 DOI: 10.1016/j.molbiopara.2020.111274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/23/2020] [Accepted: 03/04/2020] [Indexed: 11/22/2022]
Abstract
Species of Centrorhynchus (Polymorphida: Centrorhynchidae) commonly parasitize various falconiform and strigiform birds worldwide. In the present study, the complete mitochondrial (mt) genome sequences of Centrorhynchus clitorideus was sequenced and annotated for the first time based on specimens collected from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. The complete mt genome sequences of C. clitorideus is 15,884 bp in length, and contained 36 genes [two rRNA genes (rrnL and rrnS), 22 tRNA genes and 12 protein-coding genes (PCGs) (lacking atp8)] and two non-coding regions (NCR1 and NCR2), which represents the largest mt genome of acanthocephalan reported so far. In order to assess the systematic position of C. clitorideus and the interrelationship of the family Centrorhynchidae and the other families in order Polymorphida, the phylogenetic tree was constructed using Bayesian inference (BI) based on amino acid sequences of 12 PCGs. Phylogenetic results supported C. clitorideus formed a sister relationship to C. milvus in Centrorhynchidae, which has a sister relationship to the representatives of Polymorphidae + Plagiorhynchidae. Our results revealed the monophyly of Polymorphida and paraphyly of Echinorhynchida in the class Palaeacanthocephala. The validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) was also challenged by our phylogenetic results, which seems to be a synonym of Centrorhynchus. Moreover, the present phylogenetic analysis indicated that the family Quadrigyridae and subfamily Pallisentinae (A. cheni and P. celatus) are polyphyletic.
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14
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Muhammad N, Li L, Suleman, Zhao Q, Bannai MA, Mohammad ET, Khan MS, Zhu XQ, Ma J. Characterization of the complete mitochondrial genome of Cavisoma magnum () (Acanthocephala: Palaeacanthocephala), first representative of the family Cavisomidae, and its phylogenetic implications. INFECTION GENETICS AND EVOLUTION 2020; 80:104173. [PMID: 31917357 DOI: 10.1016/j.meegid.2020.104173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/26/2019] [Accepted: 01/02/2020] [Indexed: 11/29/2022]
Abstract
The phylum Acanthocephala is a small group of endoparasites occurring in the alimentary canal of all major lineages of vertebrates worldwide. In the present study, the complete mitochondrial (mt) genome of Cavisoma magnum (Southwell, 1927) (Palaeacanthocephala: Echinorhynchida) was determined and annotated, the representative of the family Cavisomidae with the characterization of the complete mt genome firstly decoded. The mt genome of this acanthocephalan is 13,594 bp in length, containing 36 genes plus two non-coding regions. The positions of trnV and SNCR (short non-coding region) in the mt genome of C. magnum are different comparing to those of the other acanthocephalan species available in GenBank. Phylogenetic analysis based on amino acid sequences of 12 protein-coding genes using Bayesian inference (BI) supported the class Palaeacanthocephala and its included order Polymorphida to be monophyletic, but rejected monophyly of the order Echinorhynchida. Our phylogenetic results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae). The novel mt genomic data of C. magnum are very useful for understanding the evolutionary history of this group of parasites and establishing a natural classification of Acanthocephala.
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Affiliation(s)
- Nehaz Muhammad
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Liang Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, PR China.
| | - Suleman
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Qing Zhao
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, PR China
| | - Majid A Bannai
- Marine Vertebrate, Marine Science Center, University of Basrah, Basrah, Iraq
| | - Essa T Mohammad
- Marine Vertebrate, Marine Science Center, University of Basrah, Basrah, Iraq
| | - Mian Sayed Khan
- Department of Zoology, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; Jiangsu Co-innovation Centre for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu Province 225009, PR China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China.
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15
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Grabowsky ER, Mackessy SP. Predator-prey interactions and venom composition in a high elevation lizard specialist, Crotalus pricei (Twin-spotted Rattlesnake). Toxicon 2019; 170:29-40. [DOI: 10.1016/j.toxicon.2019.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 01/31/2023]
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16
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Kadota Y, Kurita K, Inoue E. Development of Polymorphic Microsatellite Markers for the Okinawa Pit Viper, Ovophis okinavensis. CURRENT HERPETOLOGY 2019. [DOI: 10.5358/hsj.38.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Yohei Kadota
- 1Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, JAPAN
| | - Kazuki Kurita
- 2Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Saky
| | - Eiji Inoue
- 3Department of Biology, Faculty of Science, Toho University, Funabashi City, Chiba, 274-8510, JAPAN
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Abstract
Rare species tend to be especially sensitive to habitat disturbance, making them important conservation targets. Thus, rarity patterns might be an important guide to conservation efforts. Rabinowitz’s approach defines rarity using a combination of geographical range, habitat specificity, and local abundance, and is frequently used in conservation prioritization. Herein, we use Rabinowitz’s approach to classify the New World (NW) pitvipers (family Viperidae) regarding rarity. We tested whether body size and latitude could predict rarity, and we compared rarity patterns with extinction risk assessments and other prioritization methods in order to detect rare species not classified as threatened or prioritized. Most NW pitvipers have large geographical ranges, high local abundances, and narrow habitat breadths. There are 11.8% of NW pitviper species in the rarest category and they occur along the Pacific coast of Mexico, in southern Central America, in the Andean region of Ecuador, and in eastern Brazil. Rarity in NW pitvipers is inversely related to latitude but is not related to body size. Our results indicate that additional species of NW pitvipers are threatened and/or should be prioritized for conservation. Combining complementary approaches to detect rare and threatened species may substantially improve our knowledge on the conservation needs of NW pitvipers.
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Jadin RC, Mihaljevic JR, Orlofske SA. Do New World pitvipers "scale-down" at high elevations? Macroecological patterns of scale characters and body size. Ecol Evol 2019; 9:9362-9375. [PMID: 31463027 PMCID: PMC6706185 DOI: 10.1002/ece3.5486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022] Open
Abstract
Bergmann's rule describes the macroecological pattern of increasing body size in response to higher latitudes and elevations. This pattern is extensively documented in endothermic vertebrates, within and among species; however, studies involving ectotherms are less common and suggest no consistent pattern for amphibians and reptiles. Moreover, adaptive traits, such as epidermal features like scales, have not been widely examined in conjunction with Bergmann's rule, even though these traits affect physiological processes, such as thermoregulation, which are hypothesized as underlying mechanisms for the pattern. Here, we investigate how scale characters correlate with elevation among 122 New World pitviper species, representing 15 genera. We found a contra-Bergmann's pattern, where body size is smaller at higher elevations. This pattern was mainly driven by the presence of small-bodied clades at high elevations and large-bodied clades at low elevations, emphasizing the importance of taxonomic scope in studying macroecological patterns. Within a subset of speciose clades, we found that only Crotalus demonstrated a significant negative relationship between body size and elevation, perhaps because of its wide elevational range. In addition, we found a positive correlation between scale counts and body size but no independent effect of elevation on scale numbers. Our study increases our knowledge of Bergmann's rule in reptiles by specifically examining characters of squamation and suggests a need to reexamine macroecological patterns for this group.
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Affiliation(s)
- Robert C. Jadin
- Department of BiologyUniversity of Wisconsin Eau ClaireEau ClaireWIUSA
| | - Joseph R. Mihaljevic
- School of Informatics, Computing, and Cyber SystemsNorthern Arizona UniversityFlagstaffAZUSA
| | - Sarah A. Orlofske
- Department of BiologyUniversity of Wisconsin Stevens PointStevens PointWIUSA
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Muhammad N, Suleman, Ma J, Khan MS, Wu SS, Zhu XQ, Li L. Characterization of the complete mitochondrial genome of Centrorhynchus milvus (Acanthocephala: Polymorphida) and its phylogenetic implications. INFECTION GENETICS AND EVOLUTION 2019; 75:103946. [PMID: 31279002 DOI: 10.1016/j.meegid.2019.103946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/17/2019] [Accepted: 06/29/2019] [Indexed: 10/26/2022]
Abstract
The phylum Acanthocephala is a small group of obligate parasites of animals. However, the current classifications of Acanthocephala are still under debate. Moreover, our present knowledge of the complete mitochondrial genome of this parasite group remains limited. To fill this knowledge gap, the complete mitochondrial (mt) genome of Centrorhynchus milvusWard, 1956 (Palaeacanthocephala: Polymorphida) was firstly sequenced and determined based on specimens collected from the red kite (Milvus milvus) in Pakistan. The mitochondrial genome of C. milvus is 14,314 bp in length and contains 36 genes, including 12 protein-coding (PCGs) genes, 22 transfer RNA (tRNA) genes and ribosomal RNA (rRNA) genes (rrnL and rrnS). To elucidate the phylogenetic relationships of the four classes of Acanthocephala and the systematic position of C. milvus, phylogenetic analysis based on concatenated amino acid sequences of 12 PCGs was performed using Bayesian inference (BI). The results supported the monophyly of Archiacanthocephala and Palaeacanthocephala with strong support (BPP = 1) and also indicated that Archiacanthocephala is the sister clade to the remaining classes of Acanthocephala (Palaeacanthocephala, Eoacanthocephala and Polyacanthocephala). However, Polyacanthocephala with only one representative species (P. caballeroi) is nested within Eoacanthocephala. Our phylogenetic analysis also confirmed C. milvus as the member of the family Centrorhynchidae with a sister relationship to C. aluconis. Our present mt genomic data are very useful for studying the molecular epidemiology, population genetics and systematics of acanthocephalans.
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Affiliation(s)
- Nehaz Muhammad
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Suleman
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China.
| | - Mian Sayed Khan
- Department of Zoology, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Shan-Shan Wu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, PR China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu Province 225009, PR China
| | - Liang Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, 050024 Shijiazhuang, Hebei Province, PR China.
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Characterization of the mitochondrial genome sequences of the liver fluke Amphimerus sp. (Trematoda: Opisthorchiidae) from Ecuador and phylogenetic implications. Acta Trop 2019; 195:90-96. [PMID: 31022381 DOI: 10.1016/j.actatropica.2019.04.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 01/25/2023]
Abstract
Amphimerus Barker, 1911 is a liver fluke infecting several animal species and humans. Being a digenetic trematode of the Opisthorchiidae family, Amphimerus is closely related to the genera Metorchis, Clonorchis and Opisthorchis. Recently, a high prevalence of Amphimerus infection in humans, cats, and dogs had been demonstrated in a tropical Pacific region of Ecuador. Hence, we determined and characterized the entire mt genome sequences of adult liver flukes, morphologically identified as Amphimerus, collected in the endemic region of Ecuador, and examined its phylogenetic relationships with flukes in the Opisthorchiidae family using Bayesian inference (BI) based on the concatenated amino acid sequences and partial cox1 sequences. The complete mt genome sequence (15, 151 bp in length) of the Amphimerus sp. contains 35 genes, including 12 protein-coding genes (PCGs, without atp8), two rRNAs (rrnL and rrnS) and 21 tRNAs, lacking trnG. The gene content and arrangement of the Ecuadorian Amphimerus mt genome was similar to those of other trematodes in the Opisthorchiidae family. All genes in the circular mt genome of Amphimerus sp. are transcribed from the same strand in one direction, with the A + T content of 60.77%. Genetic distances between Amphimerus sp. and other genera in Opisthorchiidae were rather high, ranging from 26.86% to 28.75% at nucleotide level and 29.37%-31.12% at amino acid level. Phylogenetic analysis placed the Ecuadorian Amphimerus within the branch of Opisthorchiidae, but very distinct from Opisthorchis. Our results indicate that the liver fluke Amphimerus from Ecuador does not belong to the genus Opisthorchis, and that it should be assigned under the genus Amphimerus. The determination of the mt genome of the Ecuadorian Amphimerus provides a new genetic resource for future studies on taxonomy and molecular epidemiology of Opisthorchiidae trematodes.
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Muhammad N, Suleman, Ma J, Khan MS, Li L, Zhao Q, Ahmad MS, Zhu XQ. Characterization of the complete mitochondrial genome of Sphaerirostris picae (Rudolphi, 1819) (Acanthocephala: Centrorhynchidae), representative of the genus Sphaerirostris. Parasitol Res 2019; 118:2213-2221. [PMID: 31183599 DOI: 10.1007/s00436-019-06356-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/15/2019] [Indexed: 10/26/2022]
Abstract
The Centrorhynchidae (Acanthocephala: Palaeacanthocephala) is a cosmopolitan family commonly found in various avian and mammalian hosts. Within Centrorhynchidae, species of the genus Sphaerirostris Golvan, 1956 are usually parasitic in the digestive tract of various passerine birds. In the present study, adult specimens of Sphaerirostris picae (Rudolphi, 1819), the type species of this genus, were recovered from the small intestine of Acridotheres tristis (Sturnidae) and Dendrocitta vagabunda (Corvidae) in Pakistan. Molecular data from the nuclear or mitochondrial genome is either very limited or completely absent from this phylogenetically understudied group of acanthocephalans. To fill this knowledge gap, we sequenced and determined the internal transcribed spacers of ribosomal DNA (ITS rDNA) and the complete mitochondrial (mt) genome of S. picae. The ITS rDNA of S. picae was 95.2% similar to that of Sphaerirostris lanceoides which is the only member of the Centrorhynchidae whose ITS rDNA is available in GenBank. The phylogenetic tree based on the amino acid sequences of 12 mt protein-coding genes (PCGs) placed S. picae close to Centrorhynchus aluconis in a monophyletic clade of Polymorphida which also contain members of the families Polymorphidae and Plagiorhynchidae on separate branches. The mt gene arrangement, nucleotide composition and codon usage of 12 PCGs were discussed and compared with those of other acanthocephalan mt genomes. Within the Centrorhynchidae, S. picae and C. aluconis showed 67.7-86.8% similarity in the nucleotide sequences of 12 PCGs and 2 rRNAs, where nad4L is the most conserved gene while atp6 is the least conserved. The similarity in amino acid sequences ranged from 68.1 to 91.8%, where cox1 was recorded as the most conserved gene, while atp6 is highly variable among 12 PCGs. This novel mt genome of S. picae provides genetic resources for further studies of phylogenetics and molecular epidemiology of acanthocephalans.
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Affiliation(s)
- Nehaz Muhammad
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Suleman
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China.
| | - Mian Sayed Khan
- Department of Zoology, University of Swabi, Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Liang Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Qing Zhao
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | | | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, People's Republic of China.
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22
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Whittington AC, Mason AJ, Rokyta DR. A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin. Mol Biol Evol 2019; 35:887-898. [PMID: 29329419 DOI: 10.1093/molbev/msx334] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases. Type II venoms are highly neurotoxic and lack snake venom metalloproteinase expression and associated hemorrhagic activity. This dichotomy hinges on Mojave toxin (MTx), a phospholipase A2 (PLA2) based β-neurotoxin expressed in Type II venoms. MTx is comprised of a nontoxic acidic subunit that undergoes extensive proteolytic processing and allosterically regulates activity of a neurotoxic basic subunit. Evolution of the acidic subunit presents an evolutionary challenge because the need for high expression of a nontoxic venom component and the proteolytic machinery required for processing suggests genetic changes of seemingly little immediate benefit to fitness. We showed that MTx evolved through a cascading series of exaptations unlocked by a single nucleotide change. The evolution of one new cleavage site in the acidic subunit unmasked buried cleavage sites already present in ancestral PLA2s, enabling proteolytic processing. Snake venom serine proteases, already present in the venom to disrupt prey hemostasis, possess the requisite specificities for MTx acidic subunit proteolysis. The dimerization interface between MTx subunits evolved by exploiting a latent, but masked, hydrophobic interaction between ancestral PLA2s. The evolution of MTx through exaptation of existing functional and structural features suggests complex phenotypes that depend on evolutionary innovations can arise from minimal genetic change enabled by prior evolution.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Andrew J Mason
- Department of Biology, University of Central Florida, Orlando, FL
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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23
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Hill N. Description of cranial elements and ontogenetic change within Tropidolaemus wagleri (Serpentes: Crotalinae). PLoS One 2019; 14:e0206023. [PMID: 30785876 PMCID: PMC6382112 DOI: 10.1371/journal.pone.0206023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022] Open
Abstract
Tropidolaemus wagleri is a species of Asian pitviper with a geographic range including Thailand, Vietnam, Malaysia, Singapore, Bruniei, parts of Indonesia, and the Philippines. Tropidolaemus is a member of the Crotalinae subfamily, within Viperidae. The genus Tropidolaemus includes five species, and was once included within the genus Trimeresurus. While some osteologic characteristics have been noted a comprehensive description of cranial elements has not been produced for T. wagleri. An in-depth description of the cranial skeleton of Tropidolaemus wagleri lays the foundation for future projects to compare and contrast other taxa within Crotalinae and Viperidae. The chosen reference specimen was compared to the presumed younger specimens to note any variation in ontogeny. The study here provides a comprehensive description of isolated cranial elements as well as a description of ontogenetic change within the specimens observed. This study contributes to the knowledge of osteological characters in T. wagleri and provides a foundation for a long term project to identify isolated elements in the fossil record.
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Affiliation(s)
- Nicolette Hill
- Department of Geosciences, East Tennessee State University, Johnson City, Tennessee, United States of America
- * E-mail:
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Mitochondrial and nuclear ribosomal DNA dataset suggests that Hepatiarius sudarikovi Feizullaev, 1961 is a member of the genus Opisthorchis Blanchard, 1895 (Digenea: Opisthorchiidae). Parasitol Res 2019; 118:807-815. [DOI: 10.1007/s00436-019-06227-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/24/2019] [Indexed: 11/29/2022]
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25
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Blair C, Bryson RW, Linkem CW, Lazcano D, Klicka J, McCormack JE. Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus). Mol Ecol Resour 2018; 19:349-365. [PMID: 30565862 DOI: 10.1111/1755-0998.12970] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 01/28/2023]
Abstract
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
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Affiliation(s)
- Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York.,Biology PhD Program, CUNY Graduate Center, New York, New York
| | - Robert W Bryson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington.,Moore Laboratory of Zoology, Occidental College, Los Angeles, California
| | - Charles W Linkem
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - David Lazcano
- Laboratorio de Herpetología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California
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26
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DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms. Biotechniques 2018; 65:339-345. [PMID: 30477329 DOI: 10.2144/btn-2018-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].
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Takeuchi H, Savitzky AH, Ding L, de Silva A, Das I, Nguyen TT, Tsai T, Jono T, Zhu G, Mahaulpatha D, Tang Y, Mori A. Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny. Ecol Evol 2018; 8:10219-10232. [PMID: 30397460 PMCID: PMC6206205 DOI: 10.1002/ece3.4497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 06/22/2018] [Accepted: 07/24/2018] [Indexed: 01/25/2023] Open
Abstract
A large body of evidence indicates that evolutionary innovations of novel organs have facilitated the subsequent diversification of species. Investigation of the evolutionary history of such organs should provide important clues for understanding the basis for species diversification. An Asian natricine snake, Rhabdophis tigrinus, possesses a series of unusual organs, called nuchal glands, which contain cardiotonic steroid toxins known as bufadienolides. Rhabdophis tigrinus sequesters bufadienolides from its toad prey and stores them in the nuchal glands as a defensive mechanism. Among more than 3,500 species of snakes, only 17 Asian natricine species are known to possess nuchal glands or their homologues. These 17 species belong to three nominal genera, Balanophis, Macropisthodon, and Rhabdophis. In Macropisthodon and Rhabdophis, however, species without nuchal glands also exist. To infer the evolutionary history of the nuchal glands, we investigated the molecular phylogenetic relationships among Asian natricine species with and without nuchal glands, based on variations in partial sequences of Mt-CYB, Cmos, and RAG1 (total 2,767 bp). Results show that all species with nuchal glands belong to a single clade (NGC). Therefore, we infer that the common ancestor of this clade possessed nuchal glands with no independent origins of the glands within the members. Our results also imply that some species have secondarily lost the glands. Given the estimated divergence time of related species, the ancestor of the nuchal gland clade emerged 19.18 mya. Our study shows that nuchal glands are fruitful subjects for exploring the evolution of novel organs. In addition, our analysis indicates that reevaluation of the taxonomic status of the genera Balanophis and Macropisthodon is required. We propose to assign all species belonging to the NGC to the genus Rhabdophis, pending further study.
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Affiliation(s)
- Hirohiko Takeuchi
- Seto Marine Biological LaboratoryField Science Education and Research CenterKyoto UniversityShirahamaJapan
- Present address:
College of Bioresource ScienceNihon UniversityFujisawaKanagawaJapan
| | | | - Li Ding
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | | | - Indraneil Das
- Institute of Biodiversity and Environmental ConservationUniversity Malaysia SarawakSarawakMalaysia
| | - Tao Thien Nguyen
- Vietnam National Museum of NatureVietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and TechnologyHanoiVietnam
| | - Tein‐Shun Tsai
- Department of Biological Science and TechnologyNational Pingtung University of Science and TechnologyNeipu TownshipTaiwan
| | - Teppei Jono
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
- Present address:
Tropical Biosphere Research CenterUniversity of the RyukyusNishiharaOkinawaJapan
| | - Guang‐Xiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | | | - Yezhong Tang
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Akira Mori
- Department of ZoologyGraduate School of ScienceKyoto UniversityKyotoJapan
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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] [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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Venom Ontogeny in the Mexican Lance-Headed Rattlesnake ( Crotalus polystictus). Toxins (Basel) 2018; 10:toxins10070271. [PMID: 29970805 PMCID: PMC6070973 DOI: 10.3390/toxins10070271] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
As trophic adaptations, rattlesnake venoms can vary in composition depending on several intrinsic and extrinsic factors. Ontogenetic changes in venom composition have been documented for numerous species, but little is known of the potential age-related changes in many rattlesnake species found in México. In the current study, venom samples collected from adult and neonate Crotalus polystictus from Estado de México were subjected to enzymatic and electrophoretic analyses, toxicity assays (LD50), and MALDI-TOF mass spectrometry, and a pooled sample of adult venom was analyzed by shotgun proteomics. Electrophoretic profiles of adult males and females were quite similar, and only minor sex-based variation was noted. However, distinct differences were observed between venoms from adult females and their neonate offspring. Several prominent bands, including P-I and P-III snake venom metalloproteinases (SVMPs) and disintegrins (confirmed by MS/MS) were present in adult venoms and absent/greatly reduced in neonate venoms. Age-dependent differences in SVMP, kallikrein-like, phospholipase A2 (PLA2), and L-amino acid oxidase (LAAO) activity levels were confirmed by enzymatic activity assays, and like many other rattlesnake species, venoms from adult snakes have higher SVMP activity than neonate venoms. Conversely, PLA2 activity was approximately 2.5 × greater in venoms from neonates, likely contributing to the increased toxicity (neonate venom LD50 = 4.5 μg/g) towards non-Swiss albino mice when compared to adult venoms (LD50 = 5.5 μg/g). Thrombin-like (TLE) and phosphodiesterase activities did not vary significantly with age. A significant effect of sex (between adult male and adult female venoms) was also observed for SVMP, TLE, and LAAO activities. Analysis of pooled adult venom by LC-MS/MS identified 14 toxin protein families, dominated by bradykinin-inhibitory peptides, SVMPs (P-I, P-II and P-III), disintegrins, PLA2s, C-type-lectins, CRiSPs, serine proteinases, and LAAOs (96% of total venom proteins). Neonate and adult C. polystictus in this population consume almost exclusively mammals, suggesting that age-based differences in composition are related to physical differences in prey (e.g., surface-to-volume ratio differences) rather than taxonomic differences between prey. Venoms from adult C. polystictus fit a Type I pattern (high SVMP activity, lower toxicity), which is characteristic of many larger-bodied rattlesnakes of North America.
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Comparison of biological and biochemical characteristics of venom from rattlesnakes in the southern Baja California Peninsula. Toxicon 2018; 148:197-201. [DOI: 10.1016/j.toxicon.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/28/2018] [Accepted: 04/25/2018] [Indexed: 11/22/2022]
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31
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Gibbs HL, Sovic M, Amazonas D, Chalkidis H, Salazar-Valenzuela D, Moura-Da-Silva AM. Recent lineage diversification in a venomous snake through dispersal across the Amazon River. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
- Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH, USA
| | - Michael Sovic
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Diana Amazonas
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
| | | | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Ecuador
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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] [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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Tracing the evolution of venom phospholipases A 2 in Gloydius strauchii and related pitvipers: A tale of two acidic isozymes. Toxicon 2017; 141:65-72. [PMID: 29191388 DOI: 10.1016/j.toxicon.2017.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/29/2023]
Abstract
Two acidic Asp49-PLA2s with Glu6 substitution and a neutral Lys49-PLA (designated Gst-K49) were cloned from G. strauchii venom glands, their full amino acid sequences were deduced. The predominant acidic PLA2 (designated Gst-E6a) contains 124 residues and the M18W30 substitutions, while the minor acidic PLA2 (designated Gst-E6b) contains 122 residues and the V18A30 substitutions. Their sequences are most similar to those of the respective orthologous PLA2s of G. intermedius venom. Gst-E6a and Gst-E6b appear to be paralogs and possibly have different predatory targets or functions. The LC-MS/MS results indicate the presence of only three PLA2 gene products in the crude venom, the relative expression levels were in the order of Gst-E6a ≫ Gst-E6b > Gst-K49, as confirmed by qPCR results. In contrast to other Gloydius, G. strauchii venom does not contain neurotoxic or basic anticoagulant Asp49-PLA2s, but Gst-K49 is the first Lys49-PLA2 identified in Gloydius venoms. However, its venom content is relatively low and its pI value 7.3 is much lower than those of other Lys49-PLA2s and. The Lys49-PLA2 genes appear to regress in the venom of most of Gloydius and related rattlesnake, and this evolutionary regression occurred before the dispersal of Asian pitvipers to the New World.
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Durban J, Sanz L, Trevisan-Silva D, Neri-Castro E, Alagón A, Calvete JJ. Integrated Venomics and Venom Gland Transcriptome Analysis of Juvenile and Adult Mexican Rattlesnakes Crotalus simus, C. tzabcan, and C. culminatus Revealed miRNA-modulated Ontogenetic Shifts. J Proteome Res 2017; 16:3370-3390. [PMID: 28731347 DOI: 10.1021/acs.jproteome.7b00414] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Adult rattlesnakes within genus Crotalus express one of two distinct venom phenotypes, type I (hemorrhagic) and type II (neurotoxic). In Costa Rican Central American rattlesnake, ontogenetic changes in the concentration of miRNAs modulate venom type II to type I transition. Venomics and venom gland transcriptome analyses showed that adult C. simus and C. tzabcan expressed intermediate patterns between type II and type I venoms, whereas C. culminatus had a canonical type I venom. Neonate/juvenile and adult Mexican rattlesnakes showed notable inter- and intraspecific variability in the number, type, abundance and ontogenetic shifts of the transcriptional and translational venom gland activities. These results support a role for miRNAs in the ontogenetic venom compositional changes in the three congeneric Mexican rattlesnakes. It is worth noting the finding of dual-action miRNAs, which silence the translation of neurotoxic heterodimeric PLA2 crotoxin and acidic PLA2 mRNAs while simultaneously up-regulating SVMP-targeting mRNAs. Dual transcriptional regulation potentially explains the existence of mutually exclusive crotoxin-rich (type-II) and SVMP-rich (type-I) venom phenotypic dichotomy among rattlesnakes. Our results support the hypothesis that alterations of the distribution of miRNAs, modulating the translational activity of venom gland toxin-encoding mRNAs in response to an external cue, may contribute to the mechanism generating adaptive venom variability.
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Affiliation(s)
- Jordi Durban
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
| | - Libia Sanz
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
| | - Dilza Trevisan-Silva
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain.,Department of Cell Biology, Federal University of Paraná , Jardim das Américas, Curitiba, Paraná, Brazil
| | - Edgar Neri-Castro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, México
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, México
| | - Juan J Calvete
- Instituto de Biomedicina de Valencia , Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
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35
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Sulca M, Remuzgo C, Cárdenas J, Kiyota S, Cheng E, Bemquerer M, Machini M. Venom of the Peruvian snake Bothriopsis oligolepis : Detection of antibacterial activity and involvement of proteolytic enzymes and C-type lectins in growth inhibition of Staphylococcus aureus. Toxicon 2017; 134:30-40. [DOI: 10.1016/j.toxicon.2017.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 10/19/2022]
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Hague MT, Feldman CR, Brodie ED, Brodie ED. Convergent adaptation to dangerous prey proceeds through the same first‐step mutation in the garter snake
Thamnophis sirtalis. Evolution 2017; 71:1504-1518. [DOI: 10.1111/evo.13244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Michael T.J. Hague
- Department of Biology University of Virginia Charlottesville Virginia 22904
| | | | | | - Edmund D. Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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Ma J, Sun MM, He JJ, Liu GH, Ai L, Chen MX, Zhu XQ. Fasciolopsis buski (Digenea: Fasciolidae) from China and India may represent distinct taxa based on mitochondrial and nuclear ribosomal DNA sequences. Parasit Vectors 2017; 10:101. [PMID: 28228149 PMCID: PMC5322651 DOI: 10.1186/s13071-017-2039-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/15/2017] [Indexed: 11/10/2022] Open
Abstract
Background Fasciolopsis buski is a zoonotic intestinal fluke infecting humans and pigs, but it has been seriously neglected. It is yet to know whether there is any genetic diversity among F. buski from different geographical locations, particularly in sequences of nuclear ribosomal DNA (rDNA) and mitochondrial (mt) DNA. Therefore, we determined the sequences of partial 18S, the complete internal transcribed spacer (ITS) rDNA and the complete mt genome of F. buski from China, compared the rDNA and mtDNA sequences with those of isolates from India and Vietnam, and assessed the phylogenetic relationships of this fluke and related fasciolid trematodes based on the mtDNA dataset. Results The complete mt genome sequence of F. buski from China is 14,833 bp, with 36 genes, including 12 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes (rrnL and rrnS). The AT content of F. buski from China is 65.12%. The gene content and arrangement of the F. buski mt genome is similar to that of Fascioloides magna. Genetic distances between isolates of F. buski from China and India were high (28.2% in mtDNA, 13.2% in ITS-1 and 9.8% in ITS-2) and distinctly higher than the interspecific differences between Fasciola hepatica and Fasciola gigantica. The rDNA and mtDNA datasets for F. buski from China (isolate from pigs) and Vietnam (isolates from humans) were identical. The intergeneric differences in amino acid and nucleotide sequences among the genera Fasciolopsis, Fascioloides and Fasciola ranged between 24.64–25.56% and 26.35–28.46%, respectively. Conclusions Our results indicate that F. buski from China and India may represent distinct taxa, while F. buski in Vietnam and China represent the same species. These findings might have implications for the implementation of appropriate control strategies in different regions. Further studies are needed to decode mtDNA and rDNA sequences of F. buski from various geographical isolates for the better understanding of the species complex of F. buski. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2039-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Miao-Miao Sun
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, 230036, People's Republic of China
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, People's Republic of China
| | - Lin Ai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China
| | - Mu-Xin Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China. .,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu Province, 225009, People's Republic of China.
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38
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Venomics: integrative venom proteomics and beyond*. Biochem J 2017; 474:611-634. [DOI: 10.1042/bcj20160577] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 01/15/2023]
Abstract
Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection. Reconstructing the natural history of venoms, particularly those of snakes, which will be dealt with in more detail in this review, requires the integration of different levels of knowledge into a meaningful and comprehensive evolutionary framework for separating stochastic changes from adaptive evolution. The application of omics technologies and other disciplines have contributed to a qualitative and quantitative advance in the road map towards this goal. In this review we will make a foray into the world of animal venoms, discuss synergies and complementarities of the different approaches used in their study, and identify current bottlenecks that prevent inferring the evolutionary mechanisms and ecological constraints that molded snake venoms to their present-day variability landscape.
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Sun MM, Liu GH, Ando K, Woo HC, Ma J, Sohn WM, Sugiyama H, Zhu XQ. Complete mitochondrial genomes of Gnathostoma nipponicum and Gnathostoma sp., and their comparison with other Gnathostoma species. INFECTION GENETICS AND EVOLUTION 2016; 48:109-115. [PMID: 28025097 DOI: 10.1016/j.meegid.2016.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/12/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
Gnathostomiasis is a foodborne zoonotic parasitosis caused by Gnathostoma nematodes. It has caused significant public problems worldwide, but its molecular biology is limited. The purpose of this study was to decode the complete mitochondrial (mt) genomes of Gnathostoma nipponicum and Gnathostoma sp., and compare their mt sequences with other Gnathostoma species. The complete mt genome sequences were amplified by long-range PCR and determined by subsequent primer walking. The complete mt genomes of G. nipponicum and Gnathostoma sp. were 14,093bp and 14,391bp, respectively. Both of the two mt genomes contain 12 protein-coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes. The gene order and transcription direction are the same as G. spinigerum and G. doloresi. The sequence difference across the entire mt genomes varied from 14.4% to 18.2% between G. nipponicum, Gnathostoma sp., G. spinigerum and G. doloresi of Japan and China isolates. Phylogenetic analyses by Bayesian inference (BI) using concatenated amino acid sequences of 12 PCGs showed that G. nipponicum and Gnathostoma sp. are two distinctive species of Gnathostoma, and G. nipponicum are more closely related to Gnathostoma sp. than to G. spinigerum. The mtDNA datasets provide abundant resources of novel markers, which can be used for the studies of molecular epidemiology and diagnosis of Gnathostoma spp.
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Affiliation(s)
- Miao-Miao Sun
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province 230036, PR China
| | - Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
| | - Katsuhiko Ando
- Department of Medical Zoology, Mie University School of Medicine, Mie 514-8507, Japan
| | - Ho-Choon Woo
- Department of Veterinary Parasitology, Jeju National University College of Veterinary Medicine, Jeju 690-756, Republic of Korea
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Woon-Mok Sohn
- Department Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju 52727, Republic of Korea
| | - Hiromu Sugiyama
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province 230036, PR China; College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
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Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates. Mol Phylogenet Evol 2016; 105:50-62. [DOI: 10.1016/j.ympev.2016.07.029] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 04/01/2016] [Accepted: 07/28/2016] [Indexed: 11/17/2022]
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Sun DS, Ho PH, Chang HH. Soluble P-selectin rescues viper venom-induced mortality through anti-inflammatory properties and PSGL-1 pathway-mediated correction of hemostasis. Sci Rep 2016; 6:35868. [PMID: 27779216 PMCID: PMC5078805 DOI: 10.1038/srep35868] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/03/2016] [Indexed: 01/24/2023] Open
Abstract
Venomous snakebites are lethal and occur frequently worldwide each year, and receiving the antivenom antibody is currently the most effective treatment. However, the specific antivenom might be unavailable in remote areas. Snakebites by Viperidae usually lead to hemorrhage and mortality if untreated. In the present study, challenges of rattlesnake (Crotalus atrox) venom markedly increased the circulating soluble P-selectin (sP-sel) level, but not P-selectin (P-sel, Selp−/−) mutants, in wild-type mice. Because sP-sel enhances coagulation through the P-selectin ligand 1 (PSGL-1, Selplg) pathway to produce tissue factor–positive microparticles, we hypothesized that increasing the plasma sP-sel level can be a self-rescue response in hosts against snake venom–mediated suppression of the coagulation system. Confirming our hypothesis, our results indicated that compared with wild-type mice, Selp−/− and Selplg−/− mice were more sensitive to rattlesnake venom. Additionally, administration of recombinant sP-sel could effectively reduce the mortality rate of mice challenged with venoms from three other Viperidae snakes. The antivenom property of sP-sel is associated with improved coagulation activity in vivo. Our data suggest that the elevation of endogenous sP-sel level is a self-protective response against venom-suppressed coagulation. The administration of recombinant sP-sel may be developed as a new strategy to treat Viperidae snakebites.
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Affiliation(s)
- Der-Shan Sun
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien 970, Taiwan.,Center for Vascular Medicine, Tzu-Chi University, Hualien 970, Taiwan
| | - Pei-Hsun Ho
- Center for Vascular Medicine, Tzu-Chi University, Hualien 970, Taiwan
| | - Hsin-Hou Chang
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, Hualien 970, Taiwan.,Center for Vascular Medicine, Tzu-Chi University, Hualien 970, Taiwan
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Pla D, Sanz L, Sasa M, Acevedo ME, Dwyer Q, Durban J, Pérez A, Rodriguez Y, Lomonte B, Calvete JJ. Proteomic analysis of venom variability and ontogeny across the arboreal palm-pitvipers (genus Bothriechis). J Proteomics 2016; 152:1-12. [PMID: 27777178 DOI: 10.1016/j.jprot.2016.10.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 01/17/2023]
Abstract
Bothriechis is a genus of eleven currently recognized slender and arboreal venomous snakes, commonly called palm-pitvipers that range from southern Mexico to northern South America. Despite dietary studies suggesting that palm-pitvipers are generalists with an ontogenetic shift toward endothermic prey, venom proteomic analyses have revealed remarkable divergence between the venoms of the Costa Rican species, B. lateralis, B. schlegelii, B. supraciliaris, and B. nigroviridis. To achieve a more complete picture of the venomic landscape across Bothriechis, the venom proteomes of biodiversity of the northern Middle American highland palm-pitvipers, B. thalassinus, B. aurifer, and B. bicolor from Guatemala, B. marchi from Honduras, and neonate Costa Rican B. lateralis and B. schlegelii, were investigated. B. thalassinus and B. aurifer venoms are comprised by similar toxin arsenals dominated by SVMPs (33-39% of the venom proteome), CTLs (11-16%), BPP-like molecules (10-13%), and CRISPs (5-10%), and are characterized by the absence of PLA2 proteins. Conversely, the predominant (35%) components of B. bicolor are D49-PLA2 molecules. The venom proteome of B. marchi is similar to B. aurifer and B. thalassinus in that it is rich in SVMPs and BPPs, but also contains appreciable amounts (14.3%) of PLA2s. The major toxin family found in the venoms of both neonate B. lateralis and B. schlegelii, is serine proteinase (SVSP), comprising about 20% of their toxin arsenals. The venom of neonate B. schlegelii is the only palm-pitviper venom where relative high amounts of Kunitz-type (6.3%) and γPLA2 (5.2%) inhibitors have been identified. Despite notable differences between their proteomes, neonate venoms are more similar to each other than to adults of their respective species. However, the ontogenetic changes taking place in the venom of B. lateralis strongly differ from those that occur in the venom of B. schlegelii. Thus, the ontogenetic change in B. lateralis produces a SVMP-rich venom, whereas in B. schlegelii the age-dependent compositional shift generates a PLA2-rich venom. Overall, genus-wide venomics illustrate the high evolvability of palm-pitviper venoms. The integration of the pattern of venom variation across Bothriechis into a phylogenetic and biogeographic framework may lay the foundation for assessing, in future studies, the evolutionary path that led to the present-day variability of the venoms of palm-pitvipers. SIGNIFICANCE Bothriechis represents a monophyletic basal genus of eleven arboreal palm-pitvipers that range from southern Mexico to northern South America. Despite palm-pitvipers' putative status as diet generalists, previous proteomic analyses have revealed remarkable divergence between the venoms of Costa Rican species, B. lateralis, B. schlegelii, B. supraciliaris, and B. nigroviridis. Our current proteomic study of Guatemalan species, B. thalassinus, B. aurifer, and B. bicolor, Honduran B. marchi, and neonate B. lateralis and B. schlegelii from Costa Rica was undertaken to deepen our understanding of the evolutionary pattern of venom proteome diversity across Bothriechis. Ancestral characters are often, but not always, preserved in an organism's development. Venoms of neonate B. lateralis and B. schlegelii are more similar to each other than to adults of their respective species, suggesting that the high evolvability of palm-pitviper venoms may represent an inherent feature of Bothriechis common ancestor. Our genus-wide data identified four nodes of venom phenotype differentiation across the phylogeny of Bothriechis. Integrated into a phylogenetic and biogeographic framework, the pattern of venom variation across Bothriechis may lay the groundwork to establish whether divergence was driven by selection for efficient resource exploitation in arboreal 'islands', thereby contributing to the ecological speciation of the genus.
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Affiliation(s)
- Davinia Pla
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Libia Sanz
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Manuel E Acevedo
- Centro de Estudios Conservacionistas, Centro de Datos para la Conservacion, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Quetzal Dwyer
- Parque Reptilandia, Platanillo between Dominical & San Isidro, 8000 Dominical, Puntarenas, Costa Rica
| | - Jordi Durban
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Alicia Pérez
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Yania Rodriguez
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
| | - Juan J Calvete
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
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Zainal Abidin SA, Rajadurai P, Chowdhury MEH, Ahmad Rusmili MR, Othman I, Naidu R. Proteomic Characterization and Comparison of Malaysian Tropidolaemus wagleri and Cryptelytrops purpureomaculatus Venom Using Shotgun-Proteomics. Toxins (Basel) 2016; 8:toxins8100299. [PMID: 27763534 PMCID: PMC5086659 DOI: 10.3390/toxins8100299] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 12/02/2022] Open
Abstract
Tropidolaemus wagleri and Cryptelytrops purpureomaculatus are venomous pit viper species commonly found in Malaysia. Tandem mass spectrometry analysis of the crude venoms has detected different proteins in T. wagleri and C. purpureomaculatus. They were classified into 13 venom protein families consisting of enzymatic and nonenzymatic proteins. Enzymatic families detected in T. wagleri and C. purpureomaculatus venom were snake venom metalloproteinase, phospholipase A2, l-amino acid oxidase, serine proteases, 5′-nucleotidase, phosphodiesterase, and phospholipase B. In addition, glutaminyl cyclotransferase was detected in C. purpureomaculatus. C-type lectin-like proteins were common nonenzymatic components in both species. Waglerin was present and unique to T. wagleri—it was not in C. purpureomaculatus venom. In contrast, cysteine-rich secretory protein, bradykinin-potentiating peptide, and C-type natriuretic peptide were present in C. purpureomaculatus venom. Composition of the venom proteome of T. wagleri and C. purpureomaculatus provides useful information to guide production of effective antivenom and identification of proteins with potential therapeutic applications.
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Affiliation(s)
- Syafiq Asnawi Zainal Abidin
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Pathmanathan Rajadurai
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
- Ramsay Sime Darby Healthcare, Sime Darby Medical Centre, No. 1, Jalan SS12/1A, Subang Jaya, Selangor Darul Ehsan 47500, Malaysia.
| | - Md Ezharul Hoque Chowdhury
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Muhamad Rusdi Ahmad Rusmili
- Kuliyyah of Pharmacy, International Islamic University Malaysia, Kuantan Campus, Bandar Indera Mahkota, Kuantan, Pahang Darul Makmur 25200, Malaysia.
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia.
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Figueroa A, McKelvy AD, Grismer LL, Bell CD, Lailvaux SP. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus. PLoS One 2016; 11:e0161070. [PMID: 27603205 PMCID: PMC5014348 DOI: 10.1371/journal.pone.0161070] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/28/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). RESULTS Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. CONCLUSION Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.
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Affiliation(s)
- Alex Figueroa
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Alexander D. McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, United States of America
- Department of Biology, 6S-143, College of Staten Island, 2800 Victory Boulevard, Staten Island, NY, United States of America
| | - L. Lee Grismer
- Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, United States of America
| | - Charles D. Bell
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
| | - Simon P. Lailvaux
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America
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Ma J, He JJ, Liu GH, Leontovyč R, Kašný M, Zhu XQ. Complete mitochondrial genome of the giant liver fluke Fascioloides magna (Digenea: Fasciolidae) and its comparison with selected trematodes. Parasit Vectors 2016; 9:429. [PMID: 27492461 PMCID: PMC4973546 DOI: 10.1186/s13071-016-1699-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022] Open
Abstract
Background Representatives of the trematode family Fasciolidae are responsible for major socio-economic losses worldwide. Fascioloides magna is an important pathogenic liver fluke of wild and domestic ungulates. To date, only a limited number of studies concerning the molecular biology of F. magna exist. Therefore, the objective of the present study was to determine the complete mitochondrial (mt) genome sequence of F. magna, and assess the phylogenetic relationships of this fluke with other trematodes based on the mtDNA dataset. Findings The complete F. magna mt genome sequence is 14,047 bp. The gene content and arrangement of the F. magna mt genome is similar to those of Fasciola spp., except that trnE is located between trnG and the only non-coding region in F. magna mt genome. Phylogenetic relationships of F. magna with selected trematodes using Bayesian inference (BI) was reconstructed based on the concatenated amino acid sequences for 12 protein-coding genes, which confirmed that the genus Fascioloides is closely related to the genus Fasciola; the intergeneric differences of amino acid composition between the genera Fascioloides and Fasciola ranged 17.97–18.24 %. Conclusions The determination of F. magna mt genome sequence provides a valuable resource for further investigations of the phylogeny of the family Fasciolidae and other trematodes, and represents a useful platform for designing appropriate molecular markers. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1699-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, PR China
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
| | - Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China
| | - Roman Leontovyč
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic
| | - Martin Kašný
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 44, Czech Republic. .,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, PR China. .,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, PR China.
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Debono J, Cochran C, Kuruppu S, Nouwens A, Rajapakse NW, Kawasaki M, Wood K, Dobson J, Baumann K, Jouiaei M, Jackson TNW, Koludarov I, Low D, Ali SA, Smith AI, Barnes A, Fry BG. Canopy Venom: Proteomic Comparison among New World Arboreal Pit-Viper Venoms. Toxins (Basel) 2016; 8:toxins8070210. [PMID: 27399777 PMCID: PMC4963843 DOI: 10.3390/toxins8070210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 05/28/2016] [Accepted: 06/16/2016] [Indexed: 11/16/2022] Open
Abstract
Central and South American pitvipers, belonging to the genera Bothrops and Bothriechis, have independently evolved arboreal tendencies. Little is known regarding the composition and activity of their venoms. In order to close this knowledge gap, venom proteomics and toxin activity of species of Bothriechis, and Bothrops (including Bothriopsis) were investigated through established analytical methods. A combination of proteomics and bioactivity techniques was used to demonstrate a similar diversification of venom composition between large and small species within Bothriechis and Bothriopsis. Increasing our understanding of the evolution of complex venom cocktails may facilitate future biodiscoveries.
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Affiliation(s)
- Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Chip Cochran
- Department of Earth and Biological Sciences, Loma Linda University, Loma Linda, CA 92350, USA.
| | - Sanjaya Kuruppu
- Department of Biochemistry & Molecular Biology, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Niwanthi W Rajapakse
- Baker IDI Heart and Diabetes Institute, 75 Commercial Road, Melbourne, Victoria 3004, Australia.
- Department of Physiology, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Minami Kawasaki
- Aquatic Animal Health, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072 Australia.
| | - Kelly Wood
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - James Dobson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Kate Baumann
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Mahdokht Jouiaei
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Timothy N W Jackson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Ivan Koludarov
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Dolyce Low
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Syed A Ali
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
- HEJ Research Institute of Chemistry, ICCBS, University of Karachi, Karachi-75270, Pakistan.
| | - A Ian Smith
- Department of Biochemistry & Molecular Biology, Biomedical Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Andrew Barnes
- Aquatic Animal Health, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072 Australia
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
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Andrade-Silva D, Zelanis A, Kitano ES, Junqueira-de-Azevedo ILM, Reis MS, Lopes AS, Serrano SMT. Proteomic and Glycoproteomic Profilings Reveal That Post-translational Modifications of Toxins Contribute to Venom Phenotype in Snakes. J Proteome Res 2016; 15:2658-75. [DOI: 10.1021/acs.jproteome.6b00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Débora Andrade-Silva
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
| | - André Zelanis
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
- Instituto de Ciência
e Tecnologia, Universidade Federal de São Paulo (ICT-UNIFESP), São José dos Campos 12231-280, Brazil
| | - Eduardo S. Kitano
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
| | - Inácio L. M. Junqueira-de-Azevedo
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
| | - Marcelo S. Reis
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
| | - Aline S. Lopes
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
- Departamento
de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema 04021-001, Brazil
| | - Solange M. T. Serrano
- Laboratório
Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo 05503-000, Brazil
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48
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Sun MM, Ma J, Sugiyama H, Ando K, Li WW, Xu QM, Liu GH, Zhu XQ. The complete mitochondrial genomes of Gnathostoma doloresi from China and Japan. Parasitol Res 2016; 115:4013-20. [PMID: 27301404 DOI: 10.1007/s00436-016-5171-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/07/2016] [Indexed: 11/29/2022]
Abstract
Gnathostoma doloresi is one of the neglected pathogens causing gnathostomiasis. Although this zoonotic parasite leads to significant socioeconomic concerns globally, little is known of its genetics and systematics. In the present study, we sequenced and characterized the complete mitochondrial (mt) genomes of G. doloresi isolates from China and Japan. The lengths of the mt genomes of the G. doloresi China and Japan isolates are 13,809 and 13,812 bp, respectively. Both mt genomes encode 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene order, transcription direction, and genome content are identical with its congener G. spinigerum. Phylogenetic analyses based on concatenated amino acid sequences of 12 PCGs by Bayesian inference (BI) indicated that G. doloresi are closely related to G. spinigerum. Our data provide an invaluable resource for studying the molecular epidemiology, phylogenetics, and population genetics of Gnathostoma spp. and should have implications for further studies of the diagnosis, prevention, and control of gnathostomiasis in humans and animals.
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Affiliation(s)
- Miao-Miao Sun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, 230036, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, China
| | - Hiromu Sugiyama
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Katsuhiko Ando
- Department of Medical Zoology, Mie University School of Medicine, Mie, 514-8507, Japan
| | - Wen-Wen Li
- Department of Animal Experiment Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Qian-Ming Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, 230036, China
| | - Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, China.
| | - Xing-Quan Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, 230036, China. .,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, China.
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49
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Carrasco PA, Venegas PJ, Chaparro JC, Scrocchi GJ. Nomenclatural instability in the venomous snakes of the Bothrops complex: Implications in toxinology and public health. Toxicon 2016; 119:122-8. [PMID: 27242040 DOI: 10.1016/j.toxicon.2016.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/24/2016] [Accepted: 05/26/2016] [Indexed: 11/18/2022]
Abstract
Since nomenclature is intended to reflect the evolutionary history of organisms, advances in our understanding of historical relationships may lead to changes in classification, and thus potentially in taxonomic instability. An unstable nomenclature for medically important animals like venomous snakes is of concern, and its implications in venom/antivenom research and snakebite treatment have been extensively discussed since the 90´s. The taxonomy of the pitvipers of the Bothrops complex has been historically problematic and different genus-level rearrangements were proposed to rectify the long-standing paraphyly of the group. Here we review the toxinological literature on the Bothrops complex to estimate the impact of recent proposals of classification in non-systematic research. This assessment revealed moderate levels of nomenclatural instability in the last five years, and the recurrence of some practices discussed in previous studies regarding the use of classifications and the information provided about the origin of venom samples. We briefly comment on a few examples and the implications of different proposals of classifications for the Bothrops complex. The aim of this review is to contribute to the reduction of adverse effects of current taxonomic instability in a group of medical importance in the Americas.
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Affiliation(s)
- Paola Andrea Carrasco
- Centro de Zoología Aplicada, Instituto de Diversidad y Ecología Animal (IDEA-CONICET), Universidad Nacional de Córdoba, Rondeau 798, 5000 Córdoba, Argentina.
| | - Pablo Javier Venegas
- División de Herpetología, Centro de Ornitología y Biodiversidad (CORBIDI), Santa Rita, 10536, Of. 202, Huertos de San Antonio, Surco, Lima, Perú
| | - Juan Carlos Chaparro
- Departamento de Herpetología del Museo de Historia Natural del Cusco, Universidad Nacional de San Antonio Abad del Cusco, Plaza de Armas del Cusco s/n, Cusco, Perú
| | - Gustavo José Scrocchi
- CONICET and Instituto de Herpetología, Fundación Miguel Lillo, Miguel Lillo 251, 4000 San Miguel de Tucumán, Argentina
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50
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Tsai IH, Wang YM, Huang KF. Structures of Azemiops feae venom phospholipases and cys-rich-secretory protein and implications for taxonomy and toxinology. Toxicon 2016; 114:31-9. [DOI: 10.1016/j.toxicon.2016.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/31/2016] [Accepted: 02/11/2016] [Indexed: 11/28/2022]
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