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Rosas-Espinoza VC, Álvarez-Grzybowska E, Godoy González AA, Santiago-Pérez AL, Peña-Joya KE, Rodríguez-Zaragoza FA, Díaz Pérez L, Huerta Martínez FM. Taxonomic diversity of amphibians (Amphibia, Anura) and reptiles (Reptilia, Testudines, Squamata) in a heterogeneous landscape in west-central Mexico: a checklist and notes on geographical distributions. Zookeys 2024; 1211:29-55. [PMID: 39262608 PMCID: PMC11384138 DOI: 10.3897/zookeys.1211.122565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/18/2024] [Indexed: 09/13/2024] Open
Abstract
In Mexico, land use changes have significantly impacted the diversity of amphibians and reptiles in a negative way. In light of this, we evaluate the alpha and beta components of the taxonomic diversity of amphibians and reptiles in a heterogeneous landscape in west-central Mexico. Additionally, we provide a checklist of amphibian and reptile species recorded over nine years of observations within the studied landscape and surrounding areas. The land cover/use types with the highest species richness and alpha taxonomic diversity differed between amphibians and reptiles. Overall beta taxonomic diversity was high for both groups, but slightly higher in reptiles. This taxonomic differentiation mainly corresponded to a difference in the turnover component and was greater in pristine habitats compared to disturbed ones. The checklist records 20 species of amphibians (ten of which are endemic) and 48 of reptiles (30 endemics). Additionally, the study expands the known geographical distribution range of one species of frog and three species of snakes. Our findings suggest that heterogeneous landscapes with diverse land cover/use types can provide essential habitats for the conservation of amphibian and reptile species.
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Affiliation(s)
- Verónica Carolina Rosas-Espinoza
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Eliza Álvarez-Grzybowska
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Arquímedes Alfredo Godoy González
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Ana Luisa Santiago-Pérez
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Karen Elizabeth Peña-Joya
- Departamento de Producción Forestal, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Puerto Vallarta Mexico
| | - Fabián Alejandro Rodríguez-Zaragoza
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Leopoldo Díaz Pérez
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
| | - Francisco Martín Huerta Martínez
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada,, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ramón Padilla Sánchez 2100, CP 45200, Zapopan, Jalisco, Mexico Universidad de Guadalajara Zapopan Mexico
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2
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Roberts JR, Bernstein JM, Austin CC, Hains T, Mata J, Kieras M, Pirro S, Ruane S. Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics. J Hered 2024; 115:487-497. [PMID: 38722259 DOI: 10.1093/jhered/esae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/08/2024] [Indexed: 08/21/2024] Open
Abstract
We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.
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Affiliation(s)
- Jackson R Roberts
- Division of Zoology, Sternberg Museum of Natural History, Fort Hays State University, Hays, KS 67601, United States
- Division of Herpetology, Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, United States
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Justin M Bernstein
- Center for Genomics, University of Kansas, Lawrence, KS 66045, United States
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010, United States
| | - Christopher C Austin
- Division of Herpetology, Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, United States
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, United States
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, IL 60637, United States
| | - Joshua Mata
- Amphibian and Reptile Collection, The Field Museum of Natural History, Chicago, IL 60605, United States
| | - Michael Kieras
- Iridian Genomes, Inc., Bethesda, MD 20817, United States
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD 20817, United States
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, IL 60637, United States
- Amphibian and Reptile Collection, The Field Museum of Natural History, Chicago, IL 60605, United States
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3
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Gable SM, Bushroe NA, Mendez JM, Wilson A, Pinto BJ, Gamble T, Tollis M. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles. Genome Biol Evol 2024; 16:evae157. [PMID: 39031594 PMCID: PMC11303007 DOI: 10.1093/gbe/evae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/22/2024] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas A Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine M Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan J Pinto
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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4
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Weinell JL, Burbrink FT, Das S, Brown RM. Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240064. [PMID: 39113776 PMCID: PMC11303032 DOI: 10.1098/rsos.240064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 08/10/2024]
Abstract
Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.
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Affiliation(s)
- Jeffrey L. Weinell
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Lawrence, KS66045, USA
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY10024, USA
| | - Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY10024, USA
| | - Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki00014, Finland
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Lawrence, KS66045, USA
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5
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Goldenberg J, Bisschop K, Bruni G, Di Nicola MR, Banfi F, Faraone FP. Melanin-based color variation in response to changing climates in snakes. Ecol Evol 2024; 14:e11627. [PMID: 38952653 PMCID: PMC11213819 DOI: 10.1002/ece3.11627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Abstract
Melanism, the process of heavier melanin deposition, can interact with climate variation at both micro and macro scales, ultimately influencing color evolution in organisms. While the ecological processes regulating melanin production in relation to climate have been extensively studied, intraspecific variations of melanism are seldom considered. Such scientific gap hampers our understanding of how species adapt to rapidly changing climates. For example, dark coloration may lead to higher heat absorption and be advantageous in cool climates, but also in hot environments as a UV or antimicrobial protection mechanism. To disentangle such opposing predictions, here we examined the effect of climate on shaping melanism variation in 150 barred grass snakes (Natrix helvetica) and 383 green whip snakes (Hierophis viridiflavus) across Italy. By utilizing melanistic morphs (charcoal and picturata in N. helvetica, charcoal and abundistic in H. viridiflavus) and compiling observations from 2002 to 2021, we predicted that charcoal morphs in H. viridiflavus would optimize heat absorption in cold environments, while offering protection from excessive UV radiation in N. helvetica within warm habitats; whereas picturata and abundistic morphs would thrive in humid environments, which naturally have a denser vegetation and wetter substrates producing darker ambient light, thus providing concealment advantages. While picturata and abundistic morphs did not align with our initial humidity expectations, the charcoal morph in N. helvetica is associated with UV environments, suggesting protection mechanisms against damaging solar radiation. H. viridiflavus is associated with high precipitations, which might offer antimicrobial protection. Overall, our results provide insights into the correlations between melanin-based color morphs and climate variables in snake populations. While suggestive of potential adaptive responses, future research should delve deeper into the underlying mechanisms regulating this relationship.
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Affiliation(s)
- J. Goldenberg
- Division of Biodiversity and Evolution, Department of BiologyLund UniversityLundSweden
- Evolution and Optics of Nanostructures Group, Department of BiologyGhent UniversityGhentBelgium
| | - K. Bisschop
- Division of Biodiversity and Evolution, Department of BiologyLund UniversityLundSweden
- Laboratory of Aquatic BiologyKU Leuven KulakKortrijkBelgium
- Terrestrial Ecology Unit, Department of BiologyGhent UniversityGhentBelgium
| | - G. Bruni
- Independent Researcher, Viale Palmiro TogliattiSesto FiorentinoFlorenceItaly
| | - M. R. Di Nicola
- Faculty of Veterinary Medicine, Department of Pathobiology, Pharmacology and Zoological Medicine, Wildlife Health GhentGhent UniversityMerelbekeBelgium
- Unit of Dermatology and CosmetologyIRCCS San Raffaele HospitalMilanItaly
| | - F. Banfi
- Laboratory of Functional Morphology, Department of BiologyUniversity of AntwerpWilrijkBelgium
| | - F. P. Faraone
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversity of PalermoPalermoItaly
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6
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Crowell HL, Curlis JD, Weller HI, Davis Rabosky AR. Ecological drivers of ultraviolet colour evolution in snakes. Nat Commun 2024; 15:5213. [PMID: 38890335 PMCID: PMC11189474 DOI: 10.1038/s41467-024-49506-4] [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: 06/15/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Ultraviolet (UV) colour patterns invisible to humans are widespread in nature. However, research bias favouring species with conspicuous colours under sexual selection can limit our assessment of other ecological drivers of UV colour, like interactions between predators and prey. Here we demonstrate widespread UV colouration across Western Hemisphere snakes and find stronger support for a predator defence function than for reproduction. We find that UV colouration has evolved repeatedly in species with ecologies most sensitive to bird predation, with no sexual dichromatism at any life stage. By modelling visual systems of potential predators, we find that snake conspicuousness correlates with UV colouration and predator cone number, providing a plausible mechanism for selection. Our results suggest that UV reflectance should not be assumed absent in "cryptically coloured" animals, as signalling beyond human visual capacities may be a key outcome of species interactions in many taxa for which UV colour is likely underreported.
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Affiliation(s)
- Hayley L Crowell
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA
| | - John David Curlis
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hannah I Weller
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI, 02912, USA
- Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Uusimaa, 00790, Finland
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, MI, 48109, USA.
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7
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Silva FM, Guerra-Fuentes RA, Blackburn DC, Prudente ALC. Embryonic development of the neotropical pit viper Bothrops atrox (Serpentes: Viperidae: Crotalinae), with emphasis on pit organ morphogenesis and its evolution in snakes. Dev Dyn 2024; 253:606-623. [PMID: 38157161 DOI: 10.1002/dvdy.677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Bothrops atrox is a pit viper with a loreal pit organ, and its embryological development remains undescribed. Here, we provide a comprehensive description of the embryology of B. atrox, focusing on the loreal pit organ and cephalic scales. RESULTS We characterized 13 developmental stages of B. atrox based on external features consistent with the embryogenesis of previously described snake species. The loreal pit organ originates from the circumorbital region and migrates to its final position. In Crotalinae, the pit organ first becomes visible at stage 28, whereas in Pythonidae labial, pit organs appear at Stage 35. Pit organs evolved independently three times in Serpentes, encompassing Boidae, Pythonidae, and Crotalinae. Boidae lacks embryological information for pit organs. Furthermore, we observed that head scalation onset occurs at Stage 33 in B. atrox, with fusion of scales surrounding the loreal pit organ. CONCLUSIONS The embryology of pit organs in Pythonidae and Boidae species remains poorly understood. Our detailed embryological descriptions are critical for proposing developmental scenarios for pit organs and guiding future research on these structures.
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Affiliation(s)
- Fernanda Magalhães Silva
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará e Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Ricardo Arturo Guerra-Fuentes
- Faculdade de Ciências Naturais, Campus Universitário do Tocantins-Cametá, Universidade Federal do Pará, Cametá, Brazil
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Ana L Costa Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará e Museu Paraense Emílio Goeldi, Belém, Brazil
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8
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Dashevsky D, Harris RJ, Zdenek CN, Benard-Valle M, Alagón A, Portes-Junior JA, Tanaka-Azevedo AM, Grego KF, Sant'Anna SS, Frank N, Fry BG. Red-on-Yellow Queen: Bio-Layer Interferometry Reveals Functional Diversity Within Micrurus Venoms and Toxin Resistance in Prey Species. J Mol Evol 2024; 92:317-328. [PMID: 38814340 PMCID: PMC11168994 DOI: 10.1007/s00239-024-10176-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024]
Abstract
Snakes in the family Elapidae largely produce venoms rich in three-finger toxins (3FTx) that bind to the α 1 subunit of nicotinic acetylcholine receptors (nAChRs), impeding ion channel activity. These neurotoxins immobilize the prey by disrupting muscle contraction. Coral snakes of the genus Micrurus are specialist predators who produce many 3FTx, making them an interesting system for examining the coevolution of these toxins and their targets in prey animals. We used a bio-layer interferometry technique to measure the binding interaction between 15 Micrurus venoms and 12 taxon-specific mimotopes designed to resemble the orthosteric binding region of the muscular nAChR subunit. We found that Micrurus venoms vary greatly in their potency on this assay and that this variation follows phylogenetic patterns rather than previously reported patterns of venom composition. The long-tailed Micrurus tend to have greater binding to nAChR orthosteric sites than their short-tailed relatives and we conclude this is the likely ancestral state. The repeated loss of this activity may be due to the evolution of 3FTx that bind to other regions of the nAChR. We also observed variations in the potency of the venoms depending on the taxon of the target mimotope. Rather than a pattern of prey-specificity, we found that mimotopes modeled after snake nAChRs are less susceptible to Micrurus venoms and that this resistance is partly due to a characteristic tryptophan → serine mutation within the orthosteric site in all snake mimotopes. This resistance may be part of a Red Queen arms race between coral snakes and their prey.
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Affiliation(s)
- Daniel Dashevsky
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia.
| | - Richard J Harris
- Venom Evolution Lab, School of the Environment, The University of Queensland, Saint Lucia, QLD, 4072, Australia
- Australian Institute of Marine Science, Cape Cleveland, QLD, 4810, Australia
| | - Christina N Zdenek
- Celine Frere Group, School of the Environment, The University of Queensland, Saint Lucia, QLD, 4072, Australia
| | - Melisa Benard-Valle
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Region Hovedstaden, Denmark
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - José A Portes-Junior
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, São Paulo, 05503-900, Brazil
| | - Anita M Tanaka-Azevedo
- Laboratório de Herpetologia, Instituto Butantan, São Paulo, São Paulo, 05503-900, Brazil
| | - Kathleen F Grego
- Laboratório de Herpetologia, Instituto Butantan, São Paulo, São Paulo, 05503-900, Brazil
| | - Sávio S Sant'Anna
- Laboratório de Herpetologia, Instituto Butantan, São Paulo, São Paulo, 05503-900, Brazil
| | - Nathaniel Frank
- MToxins Venom Lab, 717 Oregon Street, Oshkosh, WI, 54902, USA
| | - Bryan G Fry
- Venom Evolution Lab, School of the Environment, The University of Queensland, Saint Lucia, QLD, 4072, Australia
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9
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Chuliver M, Scanferla A. Paedomorphosis and retention of juvenile diet lead speciation in a group of Neotropical snakes (Colubroides-Philodryadini). Sci Rep 2024; 14:10071. [PMID: 38698134 PMCID: PMC11066030 DOI: 10.1038/s41598-024-60885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024] Open
Abstract
Dipsadidae is one of the largest clades of extant reptiles, showing an impressive morphological and ecological diversity. Despite this fact, the developmental processes behind its diversity are still largely unknown. In this study, we used 3D reconstructions based on micro-CT data and geometric morphometrics to evaluate the skull morphology of Philodryas agassizii, a small, surface-dwelling dipsadid that consume spiders. Adult individuals of P. agassizii exhibit a cranial morphology frequently observed in juveniles of other surface-dwelling colubroideans, represented in our analysis by its close relative Philodryas patagoniensis. Large orbits, gibbous neurocranial roof and a relatively short jaw complex are features present in juveniles of the latter species. Furthermore, we performed an extensive survey about diet of P. patagoniensis in which we detected an ontogenetic dietary shift, indicating that arthropods are more frequently consumed by juveniles of this dietary generalist. Thus, we infer that P. agassizzii retained not only the ancestral juvenile skull morphology but also dietary preferences. This study reveals that morphological changes driven by heterochronic changes, specifically paedomorphosis, influenced the retention of ancestral life history traits in P. agassizii, and therefore promoted cladogenesis. In this way, we obtained first evidence that heterochronic processes lead speciation in the snake megadiverse clade Dipsadidae.
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Affiliation(s)
- Mariana Chuliver
- Fundación de Historia Natural "Félix de Azara", Hidalgo 775, C1405BCK, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Agustín Scanferla
- Fundación de Historia Natural "Félix de Azara", Hidalgo 775, C1405BCK, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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10
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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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11
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de Oliveira L, Gower DJ, Wilkinson M, Segall M. Comparative morphology of oral glands in snakes of the family Homalopsidae reveals substantial variation and additional independent origins of salt glands within Serpentes. J Anat 2024; 244:708-721. [PMID: 38234265 PMCID: PMC11021688 DOI: 10.1111/joa.14005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/24/2023] [Accepted: 12/29/2023] [Indexed: 01/19/2024] Open
Abstract
Using diffusible iodine-based contrast-enhanced computed tomography (diceCT), we examined the morphology of the oral glands of 12 species of the family Homalopsidae. Snakes of this family exhibit substantial interspecific morphological variation in their oral glands. Particular variables are the venom glands, ranging from large (e.g., Subsessor bocourti) to small (e.g., Erpeton tentaculatum). The supra- and infralabial glands are more uniform in morphology, being the second most developed in almost all the sampled species. Premaxillary glands distinct from the supralabial glands were observed in five species (Myron richardsonii, Bitia hydroides, Cantoria violacea, Fordonia leucobalia, and Gerarda prevostiana), in addition to Cerberus rynchops, the only species in which this condition was previously documented associated with the excretion of salt. In the three species of the saltwater group of homalopsids (C. violacea, F. leucobalia, and G. prevostiana), the premaxillary glands also extend posteriorly, occupying a large area above the supralabial gland, a condition not observed in any other species of snake studied thus far. Character evolution analyses indicate that premaxillary glands differentiated from the supralabial gland and evolved independently three or four times in the family, always in lineages that invaded marine habitats. Our results suggest that the differentiated premaxillary glands are likely salt glands, as is the case in C. rynchops. If corroborated, this increases to six or seven the number of independent evolutionary origins of salt glands in snakes that have undergone an evolutionary transition to marine life.
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Affiliation(s)
- Leonardo de Oliveira
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
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12
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Das S, Greenbaum E, Brecko J, Pauwels OSG, Ruane S, Pirro S, Merilä J. Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family. Sci Rep 2024; 14:9489. [PMID: 38664489 PMCID: PMC11045840 DOI: 10.1038/s41598-024-60215-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.
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Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX, 79968, USA
| | - Jonathan Brecko
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium
- Royal Museum for Central Africa, Tervuren, Belgium
| | - Olivier S G Pauwels
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, Chicago, IL, USA
| | - Stacy Pirro
- Iridian Genomes Inc., Bethesda, MD, 20817, USA
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
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13
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Kojima Y, Ito RK, Fukuyama I, Ohkubo Y, Durso AM. Foraging predicts the evolution of warning coloration and mimicry in snakes. Proc Natl Acad Sci U S A 2024; 121:e2318857121. [PMID: 38437547 PMCID: PMC10945821 DOI: 10.1073/pnas.2318857121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/16/2024] [Indexed: 03/06/2024] Open
Abstract
Warning coloration and Batesian mimicry are classic examples of Darwinian evolution, but empirical evolutionary patterns are often paradoxical. We test whether foraging costs predict the evolution of striking coloration by integrating genetic and ecological data for aposematic and mimetic snakes (Elapidae and Dipsadidae). Our phylogenetic comparison on a total of 432 species demonstrated that dramatic changes in coloration were well predicted by foraging strategy. Multiple tests consistently indicated that warning coloration and conspicuous mimicry were more likely to evolve in species where foraging costs of conspicuous appearance were relaxed by poor vision of their prey, concealed habitat, or nocturnal activity. Reversion to crypsis was also well predicted by ecology for elapids but not for dipsadids. In contrast to a theoretical prediction and general trends, snakes' conspicuous coloration was correlated with secretive ecology, suggesting that a selection regime underlies evolutionary patterns. We also found evidence that mimicry of inconspicuous models (pitvipers) may have evolved in association with foraging demand for crypsis. These findings demonstrate that foraging is an important factor necessary to understand the evolution, persistence, and diversity of warning coloration and mimicry of snakes, highlighting the significance of additional selective factors in solving the warning coloration paradox.
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Affiliation(s)
- Yosuke Kojima
- Department of Biology, Toho University, Funabashi274-8510, Japan
| | - Ryosuke K. Ito
- Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Ibuki Fukuyama
- Division of Earth, Life and Environment, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto606-8501, Japan
| | - Yusaku Ohkubo
- Department of Human Ecology, Graduate School of Environmental and Life Science, Okayama University, Okayama700-8530, Japan
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL33965
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14
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Gable SM, Bushroe N, Mendez J, Wilson A, Pinto B, Gamble T, Tollis M. Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579686. [PMID: 38405926 PMCID: PMC10888918 DOI: 10.1101/2024.02.09.579686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.
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Affiliation(s)
- Simone M. Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Nicholas Bushroe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Jasmine Mendez
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam Wilson
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Brendan Pinto
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
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16
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Ludington AJ, Hammond JM, Breen J, Deveson IW, Sanders KL. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 2023; 21:284. [PMID: 38066641 PMCID: PMC10709897 DOI: 10.1186/s12915-023-01772-2] [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: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates. RESULTS Here, we generate four new annotated sea snake genomes, three of these at chromosome-scale (Hydrophis major, H. ornatus and H. curtus), and perform detailed comparative genomic analyses of sea snakes and their closest terrestrial relatives. Phylogenomic analyses highlight the possibility of near-simultaneous speciation at the root of Hydrophis, and synteny maps show intra-chromosomal variations that will be important targets for future adaptation and speciation genomic studies of this system. We then used a strict screen for positive selection in sea snakes (against a background of seven terrestrial snake genomes) to identify genes over-represented in hypoxia adaptation, sensory perception, immune response and morphological development. CONCLUSIONS We provide the best reference genomes currently available for the prolific and medically important elapid snake radiation. Our analyses highlight the phylogenetic complexity and conserved genome structure within Hydrophis. Positively selected marine-associated genes provide promising candidates for future, functional studies linking genetic signatures to the marine phenotypes of sea snakes and other vertebrates.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia
- John Curtin School of Medical Research, College of Health & Medicine, Australian National University, Canberra, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- The South Australian Museum, Adelaide, Australia.
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17
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Frynta D, Elmi HSA, Janovcová M, Rudolfová V, Štolhoferová I, Rexová K, Král D, Sommer D, Berti DA, Landová E, Frýdlová P. Are vipers prototypic fear-evoking snakes? A cross-cultural comparison of Somalis and Czechs. Front Psychol 2023; 14:1233667. [PMID: 37928591 PMCID: PMC10620321 DOI: 10.3389/fpsyg.2023.1233667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/08/2023] [Indexed: 11/07/2023] Open
Abstract
Snakes are known as highly fear-evoking animals, eliciting preferential attention and fast detection in humans. We examined the human fear response to snakes in the context of both current and evolutionary experiences, conducting our research in the cradle of humankind, the Horn of Africa. This region is characterized by the frequent occurrence of various snake species, including deadly venomous viperids (adders) and elapids (cobras and mambas). We conducted experiments in Somaliland and compared the results with data from Czech respondents to address the still unresolved questions: To which extent is human fear of snakes affected by evolutionary or current experience and local culture? Can people of both nationalities recognize venomous snakes as a category, or are they only afraid of certain species that are most dangerous in a given area? Are respondents of both nationalities equally afraid of deadly snakes from both families (Viperidae, Elapidae)? We employed a well-established picture-sorting approach, consisting of 48 snake species belonging to four distinct groups. Our results revealed significant agreement among Somali as well as Czech respondents. We found a highly significant effect of the stimulus on perceived fear in both populations. Vipers appeared to be the most salient stimuli in both populations, as they occupied the highest positions according to the reported level of subjectively perceived fear. The position of vipers strongly contrasts with the fear ranking of deadly venomous elapids, which were in lower positions. Fear scores of vipers were significantly higher in both populations, and their best predictor was the body width of the snake. The evolutionary, cultural, and cognitive aspects of this phenomenon are discussed.
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Affiliation(s)
- Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Hassan Sh Abdirahman Elmi
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Department of Biology, Faculty of Education, Amoud University, Borama, Somalia
| | - Markéta Janovcová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Veronika Rudolfová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Iveta Štolhoferová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Kateřina Rexová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - David Král
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - David Sommer
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Daniel Alex Berti
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Eva Landová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Petra Frýdlová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
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18
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Štolhoferová I, Frynta D, Janovcová M, Rudolfová V, Elmi HSA, Rexová K, Berti DA, Král D, Sommer D, Landová E, Frýdlová P. The bigger the threat, the longer the gaze? A cross-cultural study of Somalis and Czechs. Front Psychol 2023; 14:1234593. [PMID: 37829068 PMCID: PMC10565226 DOI: 10.3389/fpsyg.2023.1234593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023] Open
Abstract
High fear reaction, preferential attention, or fast detection are only a few of the specific responses which snakes evoke in humans. Previous research has shown that these responses are shared amongst several distinct cultures suggesting the evolutionary origin of the response. However, populations from sub-Saharan Africa have been largely missing in experimental research focused on this issue. In this paper, we focus on the effect of snake threat display on human spontaneous attention. We performed an eye-tracking experiment with participants from Somaliland and the Czechia and investigated whether human attention is swayed towards snakes in a threatening posture. Seventy-one Somalis and 71 Czechs were tested; the samples were matched for gender and comparable in age structure and education level. We also investigated the effect of snake morphotype as snakes differ in their threat display. We found that snakes in a threatening posture were indeed gazed upon more than snakes in a relaxed (non-threatening) posture. Further, we found a large effect of snake morphotype as this was especially prominent in cobras, less in vipers, and mostly non-significant in other morphotypes. Finally, despite highly different cultural and environmental backgrounds, the overall pattern of reaction towards snakes was similar in Somalis and Czechs supporting the evolutionary origin of the phenomenon. We concluded that human attention is preferentially directed towards snakes, especially cobras and vipers, in threatening postures.
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Affiliation(s)
- Iveta Štolhoferová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Markéta Janovcová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Veronika Rudolfová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Hassan Sh Abdirahman Elmi
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Department of Biology, Faculty of Education, Amoud University, Borama, Somalia
| | - Kateřina Rexová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Daniel Alex Berti
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - David Král
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - David Sommer
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Eva Landová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Petra Frýdlová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
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19
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Pandelis GG, Grundler MC, Rabosky DL. Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes. BMC Ecol Evol 2023; 23:48. [PMID: 37679675 PMCID: PMC10485986 DOI: 10.1186/s12862-023-02157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species. RESULTS We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data. CONCLUSIONS Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.
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Affiliation(s)
- Gregory G Pandelis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA.
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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20
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Koludarov I, Senoner T, Jackson TNW, Dashevsky D, Heinzinger M, Aird SD, Rost B. Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily. Nat Commun 2023; 14:4861. [PMID: 37567881 PMCID: PMC10421932 DOI: 10.1038/s41467-023-40550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.
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Affiliation(s)
- Ivan Koludarov
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany.
| | - Tobias Senoner
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel Dashevsky
- Australian National Insect Collection, Commonwealth Scientific & Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Heinzinger
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
| | - Steven D Aird
- 7744-23 Hotaka Ariake, 399-8301, Azumino-shi, Nagano-ken, Japan
| | - Burkhard Rost
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology-i12, Boltzmannstr. 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
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21
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Guo P, Wang P, Lyu B, Liu Q, Zheng J, Fu C, Wu Y, Shu G, Hou S. Molecular phylogeny reveals cryptic diversity in Sibynophis from China (Serpentes: Sibynophiidae). Ecol Evol 2023; 13:e10367. [PMID: 37529581 PMCID: PMC10375455 DOI: 10.1002/ece3.10367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
The elucidation of species diversity and distribution is critical within the fields of evolution, genetics, and conservation. The genus Sibynophis contains rare snakes that have historically received little attention. In this study, we conducted comprehensive sampling and use both mitochondrial and nuclear genetic markers to explore Sibynophis species diversity within China. Our findings revealed that S. c. miyiensis should be considered synonymous with S. c. grahami, and S. c. grahami should be gave a specific rank as S. grahami. In addition, we discovered S. triangularis was new to China and Myanmar. Based on the specimens and molecular phylogeny results, we redefined the species distribution boundaries of each Chinese species.
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Affiliation(s)
- Peng Guo
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Ping Wang
- Sichuan Academy of ForestryChengduChina
| | - Bing Lyu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Qin Liu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Jieyu Zheng
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Chunmei Fu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Yayong Wu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Guocheng Shu
- Faculty of Agriculture, Forest and Food EngineeringYibin UniversityYibinChina
| | - Shaobing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong MountainKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
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22
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Tiatragul S, Brennan IG, Broady ES, Keogh JS. Australia's hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes. Mol Phylogenet Evol 2023; 185:107812. [PMID: 37207892 DOI: 10.1016/j.ympev.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/24/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023]
Affiliation(s)
- Sarin Tiatragul
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Elizabeth S Broady
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
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23
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Jowers MJ, Smart U, Sánchez-Ramírez S, Murphy JC, Gómez A, Bosque RJ, Sarker GC, Noonan BP, Faria JF, Harris DJ, da Silva NJ, Prudente ALC, Weber J, Kok PJR, Rivas GA, Jadin RC, Sasa M, Muñoz-Mérida A, Moreno-Rueda G, Smith EN. Unveiling underestimated species diversity within the Central American Coralsnake, a medically important complex of venomous taxa. Sci Rep 2023; 13:11674. [PMID: 37468518 DOI: 10.1038/s41598-023-37734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 06/27/2023] [Indexed: 07/21/2023] Open
Abstract
Coralsnakes of the genus Micrurus are a diverse group of venomous snakes ranging from the southern United States to southern South America. Much uncertainty remains over the genus diversity, and understanding Micrurus systematics is of medical importance. In particular, the widespread Micrurus nigrocinctus spans from Mexico throughout Central America and into Colombia, with a number of described subspecies. This study provides new insights into the phylogenetic relationships within M. nigrocinctus by examining sequence data from a broad sampling of specimens from Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, and Panama. The recovered phylogenetic relationships suggest that M. nigrocinctus is a species complex originating in the Pliocene and composed of at least three distinct species-level lineages. In addition, recovery of highly divergent clades supports the elevation of some currently recognized subspecies to the full species rank while others may require synonymization.
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Affiliation(s)
- Michael J Jowers
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.
| | - Utpal Smart
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX, 78666, USA
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
| | - John C Murphy
- Science and Education, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Aarón Gómez
- Facultad de Microbiología, Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Renan J Bosque
- Department of Biological Sciences, Southwestern Oklahoma State University, Weatherford, OK, 73096, USA
| | - Goutam C Sarker
- Department of Biology and Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, 76019, USA
- Department of Biology, Cottey College, 1000 W. Austin Blvd, Nevada, MO, 64772, USA
| | - Brice P Noonan
- Department of Biology, The University of Mississippi, Oxford, MS, 38677, USA
| | - J Filipe Faria
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4099-002, Porto, Portugal
| | - D James Harris
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Nelson Jorge da Silva
- Pontifícia Universidade Católica de Goiás - Programa de Pós-Graduação em Ciências Ambientais e Saúde, Goiânia, Goiás, 74605140, Brazil
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi (MPEG), Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia (UFPA/MPEG) and Biodiversidade e Evolução (MPEG), Belém, Pará, Brazil
| | - John Weber
- Department of Geology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, 90-237, Lodz, Poland
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Gilson A Rivas
- Museo de Biología, Facultad Experimental de Ciencias, Universidad del Zulia, Maracaibo, Venezuela
| | - Robert C Jadin
- Department of Biology and Museum of Natural History, University of Wisconsin Stevens Point, Stevens Point, WI, 54481, USA
| | - Mahmood Sasa
- Facultad de Microbiología, Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, San José, Costa Rica
| | - Antonio Muñoz-Mérida
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Gregorio Moreno-Rueda
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Eric N Smith
- Department of Biology and Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, 76019, USA
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24
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Comparative cytogenetics of Hemorrhois hippocrepis and Malpolon monspessulanus highlights divergent karyotypes in Colubridae and Psammophiidae (Squamata: Serpentes). THE EUROPEAN ZOOLOGICAL JOURNAL 2023. [DOI: 10.1080/24750263.2023.2180547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
- M. Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - E. Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - G. Odierna
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - F. M. Guarino
- Department of Biology, University of Naples Federico II, Naples, Italy
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25
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Yang S, Savitzky AH, Gower DJ, Deepak V, Mori A, Khot R, Shi J, Ding L, Hou M, Xu H, Wang Q, Zhu G. Identity of the holotype and type locality of Rhabdophis leonardi (Wall, 1923) (Colubridae: Natricinae), with notes on the morphology and natural history of the species in southwestern China. Ecol Evol 2023; 13:e10032. [PMID: 37153019 PMCID: PMC10154373 DOI: 10.1002/ece3.10032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
The original description of Natrix leonardi (currently Rhabdophis leonardi) by Frank Wall in 1923, based on a specimen from the "Upper Burma Hills," lacked important morphological details that have complicated the assignment of recently collected material. Furthermore, although the holotype was never lost, its location has been misreported in one important taxonomic reference, leading to further confusion. We report the correct repository of the holotype (Natural History Museum, London), together with its current catalog number. We also describe key features of that specimen that were omitted from the original description, and provide new details on the morphology of the species, including sexual dichromatism unusual for the genus, based upon specimens from southern Sichuan, China. Rhabdophis leonardi is distinguished from its congeners by the following characters: 15 or 17 DSR at midbody and 6 supralabials; distinct annulus around the neck, broad and red in males, and narrow and orange with a black border in females; dorsal ground color light green or olive; some lateral and dorsal scales possessing black edges, the frequency of black edges gradually increasing from anterior to posterior, forming irregular and ill-defined transverse black bands; eye with prominent green iris; black ventral spots with a red edge, most numerous at midbody but extending halfway down the length of the tail. In southwestern China, this species is frequently found at 1730-2230 m elevation. It has been documented to prey upon anuran amphibians, including toads. A recently published phylogenetic analysis showed this species to be deeply nested with the genus Rhabdophis, as a member of the R. nuchalis Group. That analysis also revealed the existence of two closely related but geographically distinct subclades in the molecular analysis, one of which may represent an unnamed taxon.
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Affiliation(s)
- Shi‐Jun Yang
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | | | | | - V. Deepak
- Senckenberg Natural History CollectionsDresdenGermany
| | - Akira Mori
- Department of Zoology, Graduate School of ScienceKyoto UniversitySakyoKyotoJapan
| | - Rahul Khot
- Bombay Natural History SocietyFort, MumbaiIndia
| | - Jing‐Song Shi
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of SciencesInstitute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of ScienceBeijingChina
| | - Li Ding
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Mian Hou
- Sichuan Normal UniversityChengduChina
| | - Hai‐Yuan Xu
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | - Qin Wang
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
| | - Guang‐Xiang Zhu
- College of Life ScienceSichuan Agricultural UniversityYa'anChina
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26
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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27
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Das S, Greenbaum E, Meiri S, Bauer AM, Burbrink FT, Raxworthy CJ, Weinell JL, Brown RM, Brecko J, Pauwels OSG, Rabibisoa N, Raselimanana AP, Merilä J. Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family. Mol Phylogenet Evol 2023; 180:107700. [PMID: 36603697 DOI: 10.1016/j.ympev.2022.107700] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023]
Abstract
The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.
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Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX 79968, USA
| | - Shai Meiri
- School of Zoology, Tel Aviv University, Tel Aviv, Israel; The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Jeffrey L Weinell
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jonathan Brecko
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium; Royal Museum for Central Africa, Tervuren, Belgium
| | - Olivier S G Pauwels
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Campus Universitaire d'Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland; Area of Ecology and Biodiversity, School of Biological Sciences, Kadoorie Biological Sciences Building, Pokfulam Road, The University of Hong Kong, Hong Kong Special Administrative Region
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28
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Mirza ZA, H. T. Lalremsanga EO, Bhosale H, Gowande G, Patel H, Idiatullina SS, Poyarkov NA. Systematics of Trimeresurus popeiorum Smith, 1937 with a revised molecular phylogeny of Asian pitvipers of the genus Trimeresurus Lacépède, 1804 sensu lato. EVOLUTIONARY SYSTEMATICS 2023. [DOI: 10.3897/evolsyst.7.97026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The pit viper snake genus Trimeresurus Lacépède, 1804 sensu lato, is a diverse group of nocturnal serpents comprising over 61 species. The genus is morphologically heterogeneous and has been divided into several subgenera. We present an updated phylogeny of Asian pitvipers and propose a revised classification. Additionally, we revise the taxonomy of T. popeiorum Smith, 1937 and propose taxonomic changes with support from molecular and morphological data. We restrict T. popeiorumsensu stricto to northeastern India, Bangladesh, southern China, and northern Myanmar; populations beyond these areas require further assessment. We also synonymize T. yingjiangensisChen et al., 2019 with T. popeiorum based on overlapping morphological characters, molecular data, and distribution. The findings shed new light on the taxonomy of T. popeiorum, warranting the need for assessing the population of T. popeiorum from southeast Asia.
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29
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Vieira SEM, Grego KF, Blank MH, Novaes GA, Rodrigues FDS, Silveira GPMD, Castro RAD, Sant'Anna SS, Pereira RJG. Ejaculate characteristics over seasons in five species of lancehead pitvipers (Bothrops spp) kept in captivity. Zoo Biol 2023; 42:119-132. [PMID: 35652411 DOI: 10.1002/zoo.21713] [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: 10/14/2021] [Revised: 04/01/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Abstract
Due to their major medical importance in Latin America, lancehead pitvipers are frequently kept and bred in captivity for venom extraction to the production of antivenom serums. Nevertheless, despite the great contribution given to captive breeding, much of the knowledge of Bothrops' reproductive biology derived from sporadic and insufficient data provided by zoological collections. Thus, we aimed to investigate seasonal changes in gonadosomatic index (GSI) and seminal parameters (e.g., volume, concentration, motility, viability, and acrosome integrity) of five species of lancehead pitvipers from different biomes and phylogenetic groups, maintained in the indoors serpentarium at Butantan Institute (Brazil). Patterns of variation in GSI and semen parameters differed from one species to another, suggesting that captive populations should perhaps be managed distinctly to maximize reproductive success. Furthermore, in none of the studied species did changes in GSI occur concomitantly with seminal variations. GSI remained unaltered year-round for Jararaca (Bothrops jararaca) and Brazilian lancehead (Bothrops moojeni), whereas it peaked in the autumn for Common lancehead (Bothrops atrox), Jararacussu (Bothrops jararacussu), and Whitetail lancehead (Bothrops leucurus). But surprisingly, the scenario was inverted when we estimated the total number of motile spermatozoa per season, as Jararaca and Brazilian lancehead displayed seasonal differences and the other species did not vary throughout the year. Potential ecological and evolutionary factors underlying these differences were also discussed in the present article. Together, these findings can help to better define breeding management strategies for each species in captivity, in addition to optimizing the future use of artificial insemination and semen cryopreservation.
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Affiliation(s)
- Samira E M Vieira
- Laboratory of Herpetology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Kathleen F Grego
- Laboratory of Herpetology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Marcel H Blank
- Study Group for Avian Multiplication-GEMA, Department of Animal Reproduction, College of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Gabriel A Novaes
- Study Group for Avian Multiplication-GEMA, Department of Animal Reproduction, College of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | | | - Rafael A de Castro
- Laboratory of Herpetology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Sávio S Sant'Anna
- Laboratory of Herpetology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Ricardo J G Pereira
- Study Group for Avian Multiplication-GEMA, Department of Animal Reproduction, College of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
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30
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Abegg AD, Santos AP, Costa HC, Battilana J, Graboski R, Vianna FSL, Azevedo WS, Fagundes NJR, Castille CM, Prado PC, Bonatto SL, Zaher H, Grazziotin FG. Increasing taxon sampling suggests a complete taxonomic rearrangement in Echinantherini (Serpentes: Dipsadidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.969263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although the recent advances on the relationship of its major groups, the systematics of the rich fauna of Neotropical snakes is far from being a consensus. In this sense, derived groups presenting continental distributions have represented a main challenge. The taxonomy of the snake tribe Echinantherini is one of the most contentious among the diverse family known as Dipsadidae. The tribe is poorly sampled in phylogenetic studies, resulting in conflicting hypotheses of relationships among its taxa. Moreover, several rare and micro endemic species of Echinantherini have never been evaluated within a comprehensive phylogenetic framework. Here, we assess for the first time the phylogenetic position of the rare Echinanthera amoena within Echinantherini. We based our analyses on a comprehensive multilocus dataset including 14 of the 16 species described for the tribe. Our results support the monophyly of Echinantherini and strongly indicate E. amoena as a unique lineage, phylogenetically positioned apart from all other congeners. From the three current genera (Echinanthera, Taeniophallus, and Sordellina) our results indicate that Echinanthera and Taeniophallus are paraphyletic, since the T. affinis species group is positioned as sister to Echinanthera (except E. amoena) clustering apart from the clade formed by the T. brevirostris and T. occipitalis groups. We describe new genera for the T. affinis and T. occipitalis species groups and an additional monospecific genus for E. amoena. Although we did not evaluate the phylogenetic position of T. nebularis, we described a new genus and removed it from Echinantherini since its morphology strikingly departs from all species now included in the tribe. Finally, we redefine the genera Echinanthera and Taeniophallus and we provide comments about further directions to study the biogeography and the evolution of morphological traits in Echinantherini.
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Shan S, Wang Y. Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications. Zookeys 2022; 1124:191-206. [PMID: 36762359 PMCID: PMC9836618 DOI: 10.3897/zookeys.1124.87861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/25/2022] [Indexed: 11/12/2022] Open
Abstract
The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boigakraepelini and Hebiuscraspedogaster were sequenced and characterized for the first time. The lengths of the B.kraepelini and H.craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B.kraepelini and H.craspedogaster. In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B.kraepelini and the genus Lycodon. Moreover, H.craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae.
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Affiliation(s)
- Shuangshuang Shan
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, ChinaZhejiang Normal UniversityJinhuaChina
| | - Yu Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, ChinaZhejiang Normal UniversityJinhuaChina
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Ophidiomyces ophidiicola detection and infection: a global review on a potential threat to the world’s snake populations. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01612-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOphidiomyces ophidiicola (Oo) is one of the most relevant fungal pathogens for snakes. It is the etiological agent of ophidiomycosis, an emerging disease causing dysecdysis, skin abnormalities, crusting cutaneous lesions, and ulcerations. Despite this major tegumentary “tropism”, Oo infection can be systemic and it is capable of inducing visceral lesions. Moreover, ophidiomycosis may lead to abnormalities of reproductive physiology, hunting behavior, and thermoregulation, thus increasing the risks of sublethal effects and predation on affected snakes. Oo seems horizontally transmitted and can induce postnatal mortality. This article reviews published data on Oo detection and infection in all snake species in countries around the world and categorizes these data using new classification parameters. The presence of this fungus has been recorded in 11 states (considering the USA as a whole); however, in four states, the mycosis has only been reported in snakes held in captivity. Detection and/or infection of Oo has been ascertained in 62 snake species, divided into nine families. The taxa have been categorized with diagnostic criteria in order to report, for each species, the highest rank of categorization resulting from all cases. Therefore, 20 species have been included within the class “Ophidiomycosis and Oo shedder”, 11 within “Ophidiomycosis”, 16 in “Apparent ophidiomycosis”, and 15 within “Ophidiomyces ophidiicola present”. We also discuss the significance and limits of case classifications and Oo’s impact on wild populations, and we suggest methods for preliminary surveillance. Standardized methods, interdisciplinary studies, and cooperation between various research institutions may facilitate further Oo screening studies, elucidate the unclear aspects of the disease, and protect ophidiofauna from this emerging threat at the global level.
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YANG DIANCHENG, HUANG RUYI, JIANG KE, BURBRINK FRANKT, GONG YANAN, YU JING, ZHANG YI, HUANG TIANQI, HUANG SONG. A new species of the genus Achalinus (Squamata: Xenodermidae) from Ningshan County, Shaanxi Province, China. Zootaxa 2022; 5190:127-140. [PMID: 37045178 DOI: 10.11646/zootaxa.5190.1.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 11/04/2022]
Abstract
A new species of odd-scaled snake in the genus Achalinus is described from Ningshan County, Shaanxi Province, China, based on seven female specimens. Morphologically, the new species can be distinguished from its congeners by the following combination of characters: (1) dorsum iridescent and uniformly dark brown in preservative, longitudinal vertebral line absent; (2) light brown beneath; (3) dotted black streak in the middle of the subcaudals absent; (4) tail length relatively short, TaL/ToL 12–16%, in females; (5) fewer subcaudals, 41–46 in females; (6) dorsal scales 23 rows throughout, strongly keeled; the outer-most rows on both sides are also keeled and slightly enlarged; (7) one loreal; (8) internasal not fused to prefrontal; (9) suture between internasals is similar in size when compared to the suture between prefrontals; (10) preocular and postocular absent; (11) 6 supralabials; (12) 5 infralabials, the first 3 (rarely 2) touching the first pair of chin shields; (13) 3 pairs of chin shields. A phylogenetic analysis using mitochondrial gene, cytochrome c oxidase subunit 1 (CO1), showed that this new species forms a monophyletic group with strong support. In addition, the uncorrected p-distances between the new species and other known congeners ranged from 3.4% to 13.0%. The recognition of the new species increases the number of described Achalinus species to 21.
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Conradie W, Keates C, Baptista NL, Lobón-Rovira J. Taxonomical review of Prosymnaangolensis Boulenger, 1915 (Elapoidea, Prosymnidae) with the description of two new species. Zookeys 2022; 1121:97-143. [PMID: 36760759 PMCID: PMC9848606 DOI: 10.3897/zookeys.1121.85693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/15/2022] [Indexed: 11/12/2022] Open
Abstract
African Shovel-snout snakes (Prosymna Gray, 1849) are small, semi-fossorial snakes with a unique compressed and beak-like snout. Prosymna occur mainly in the savanna of sub-Saharan Africa. Of the 16 currently recognised species, four occur in Angola: Prosymnaambigua Bocage, 1873, P.angolensis Boulenger, 1915, P.frontalis (Peters, 1867), and P.visseri FitzSimons, 1959. The taxonomical status and evolutionary relationships of P.angolensis have never been assessed due to the lack of genetic material. This species is known to occur from western Angola southwards to Namibia, and eastwards to Zambia, Botswana and Zimbabwe. The species shows considerable variation in dorsal colouration across its range, and with the lower ventral scales count, an 'eastern race' was suggested. In recent years, Prosymna material from different parts of Angola has been collected, and with phylogenetic analysis and High Resolution X-ray Computed Tomography, the taxonomic status of these populations can be reviewed. Strong phylogenetic evidence was found to include the angolensis subgroup as part of the larger sundevalli group, and the existence of three phylogenetic lineages within the angolensis subgroup were identified, which each exhibit clear morphological and colouration differences. One of these lineages is assigned to the nominotypical P.angolensis and the other two described as new species, one of which corroborates the distinct eastern population previously detected. These results reinforce that a considerable part of Angolan herpetological diversity is still to be described and the need for further studies.
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Affiliation(s)
- Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood 6013, Gqeberha, South AfricaNelson Mandela UniversityGeorgeSouth Africa,Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South AfricaPort Elizabeth Museum (Bayworld)GqeberhaSouth Africa,National Geographic Okavango Wilderness Project, Wild Bird Trust, Sandton, South AfricaNational Geographic Okavango Wilderness Project, Wild Bird TrustSandtonSouth Africa
| | - Chad Keates
- Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South AfricaPort Elizabeth Museum (Bayworld)GqeberhaSouth Africa,National Geographic Okavango Wilderness Project, Wild Bird Trust, Sandton, South AfricaNational Geographic Okavango Wilderness Project, Wild Bird TrustSandtonSouth Africa,South African Institute for Aquatic Biodiversity (SAIAB), Makhanda, South AfricaSouth African Institute for Aquatic Biodiversity (SAIAB)MakhandaSouth Africa,Department of Zoology and Entomology, Rhodes University, Makhanda, South AfricaRhodes UniversityMakhandaSouth Africa
| | - Ninda L. Baptista
- National Geographic Okavango Wilderness Project, Wild Bird Trust, Sandton, South AfricaNational Geographic Okavango Wilderness Project, Wild Bird TrustSandtonSouth Africa,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, AngolaUniversidade do PortoVairaoPortugal,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, PortugalUniversidade do PortoPortoPortugal,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, PortugalInstituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento RodriguesLubangoAngola,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, PortugalBiodiversity and Land Planning, CIBIOVairaoPortugal
| | - Javier Lobón-Rovira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, PortugalUniversidade do PortoPortoPortugal,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, PortugalInstituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento RodriguesLubangoAngola,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, PortugalBiodiversity and Land Planning, CIBIOVairaoPortugal
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Trevine VC, Grazziotin FG, Giraudo A, Sallesbery‐Pinchera N, Vianna JA, Zaher H. The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence. ZOOL SCR 2022. [DOI: 10.1111/zsc.12565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Vivian C. Trevine
- Laboratório de Coleções Zoológicas Instituto Butantan São Paulo Brazil
- Programa de Pós‐Graduação de Zoologia, Insituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Alejandro Giraudo
- Instituto Nacional de Limnología (CONICET – UNL) Ciudad Universitaria Santa Fe Argentina
- Facultad de Humanidades y Ciencias (FHUC – UNL) Ciudad Universitaria Santa Fe Argentina
| | - Nicole Sallesbery‐Pinchera
- Escuela Medicina Veterinaria, Facultad Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Juliana A. Vianna
- Millennium Institute Center for Genome Regulation (CRG), Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Hussam Zaher
- Laboratório de Herpetologia, Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
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36
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Schield DR, Perry BW, Card DC, Pasquesi GIM, Westfall AK, Mackessy SP, Castoe TA. The Rattlesnake W Chromosome: A GC-Rich Retroelement Refugium with Retained Gene Function Across Ancient Evolutionary Strata. Genome Biol Evol 2022; 14:evac116. [PMID: 35867356 PMCID: PMC9447483 DOI: 10.1093/gbe/evac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a "refugium" for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
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37
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Cabral H, Cacciali P, Santana DJ. Evolution of the rostral scale and mimicry in the genus Xenodon Boie, 1826 (Serpentes: Dipsadidae: Xenodontinae). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Snakes are a stimulating life form from an evolutionary perspective. Despite the basic morphological body shape (limbless, with a tubular body), these vertebrates are extremely diverse. The Neotropical region is one of the most diverse regions for snakes in the world, with >650 known species. Within this great diversity, the genus Xenodon includes 12 species with interesting adaptations to terrestrial and semi-fossorial habitats. Members of this genus are mostly diurnal and terrestrial, feed mainly on anurans and exhibit Batesian mimicry of venomous snakes of the genera Bothrops or Micrurus. Here, through phylogenetic analysis and ancestral state estimation, we explore the evolution of the rostral scale and mimicry within the genus Xenodon. Our results suggest that the ancestral lineage of Xenodon had a rounded rostral scale and exhibited Bothrops mimicry. The evolution of the rostral scale in Xenodon might be related to abiotic factors, as an adaptation for open and forested habitats, and mimicry is likely to be related to biotic factors, as a defensive strategy resembling those of venomous snakes.
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Affiliation(s)
- Hugo Cabral
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual Paulista , São José do Rio Preto, SP , Brazil
- Instituto de Investigación Biológica del Paraguay , Del Escudo 1607, Asunción , Paraguay
- Asociación Guyra Paraguay , Avenida Coronel Carlos Bóveda, Parque Asunción Verde, Viñas Cué , Paraguay
| | - Pier Cacciali
- Instituto de Investigación Biológica del Paraguay , Del Escudo 1607, Asunción , Paraguay
- Asociación Guyra Paraguay , Avenida Coronel Carlos Bóveda, Parque Asunción Verde, Viñas Cué , Paraguay
| | - Diego José Santana
- Mapinguari Lab, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul , 79002-970, Campo Grande, MS , Brazil
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38
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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Li J, Liang D, Zhang P. Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.969581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.
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40
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VenomMaps: Updated species distribution maps and models for New World pitvipers (Viperidae: Crotalinae). Sci Data 2022; 9:232. [PMID: 35614080 PMCID: PMC9132920 DOI: 10.1038/s41597-022-01323-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022] Open
Abstract
Beyond providing critical information to biologists, species distributions are useful for naturalists, curious citizens, and applied disciplines including conservation planning and medical intervention. Venomous snakes are one group that highlight the importance of having accurate information given their cosmopolitan distribution and medical significance. Envenomation by snakebite is considered a neglected tropical disease by the World Health Organization and venomous snake distributions are used to assess vulnerability to snakebite based on species occurrence and antivenom/healthcare accessibility. However, recent studies highlighted the need for updated fine-scale distributions of venomous snakes. Pitvipers (Viperidae: Crotalinae) are responsible for >98% of snakebites in the New World. Therefore, to begin to address the need for updated fine-scale distributions, we created VenomMaps, a database and web application containing updated distribution maps and species distribution models for all species of New World pitvipers. With these distributions, biologists can better understand the biogeography and conservation status of this group, researchers can better assess vulnerability to snakebite, and medical professionals can easily discern species found in their area. Measurement(s) | Species Distributions | Technology Type(s) | Geographic Information System • Species Distribution Model (MaxEnt/kuenm) | Factor Type(s) | Occurrence Records • Environmental Data | Sample Characteristic - Organism | Crotalinae | Sample Characteristic - Location | North America • South America |
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Costa JCL, Graboski R, Grazziotin FG, Zaher H, Rodrigues MT, Prudente ALDC. Reassessing the systematics of
Leptodeira
(Serpentes, Dipsadidae) with emphasis in the South American species. ZOOL SCR 2022. [DOI: 10.1111/zsc.12534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- João C. L. Costa
- Laboratório de Herpetologia Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém Pará Brazil
| | - Roberta Graboski
- Laboratório de Herpetologia Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém Pará Brazil
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas Instituto Butantan São Paulo City São Paulo Brazil
| | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo São Paulo City São Paulo Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo São Paulo City São Paulo Brazil
| | - Ana Lúcia da C. Prudente
- Laboratório de Herpetologia Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém Pará Brazil
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de Albuquerque NR, dos Santos FM, Borges-Nojosa DM, Ávila RW. A New Species of Parrot-Snake of the Genus Leptophis Bell, 1825 (Serpentes, Colubridae) from the Semi-Arid Region of Brazil. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2022. [DOI: 10.2994/sajh-d-19-00113.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Nelson Rufino de Albuquerque
- Laboratório de Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Fernanda Martins dos Santos
- Laboratório de Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Diva Maria Borges-Nojosa
- Núcleo Regional de Ofiologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Bloco 905, 60440-554, Fortaleza, Ceará, Brazil
| | - Robson Waldemar Ávila
- Núcleo Regional de Ofiologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, Bloco 905, 60440-554, Fortaleza, Ceará, Brazil
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Johnston CI, Tasoulis T, Isbister GK. Australian Sea Snake Envenoming Causes Myotoxicity and Non-Specific Systemic Symptoms - Australian Snakebite Project (ASP-24). Front Pharmacol 2022; 13:816795. [PMID: 35387331 PMCID: PMC8977552 DOI: 10.3389/fphar.2022.816795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Background: Sea snakes are venomous snakes found in the warm parts of the Indo-Pacific, including around Australia. Most sea snake envenoming causes myotoxicity, but previous Australian case reports describe neurotoxicity. We aimed to describe the epidemiology and clinical presentation of Australian sea snake envenoming and the effectiveness of antivenom. Methods: Patients were recruited to the Australian Snakebite Project (ASP), an Australia-wide prospective observational study recruiting all patients with suspected or confirmed snakebite >2 years. Information about demographics, bite circumstances, species involved, clinical and laboratory features of envenoming, and treatment is collected and entered into a purpose-built database. Results: Between January 2002 and August 2020, 13 patients with suspected sea snake bite were recruited to ASP, 11 were male; median age was 30 years. Bites occurred in Queensland and Western Australia. All patients were in or around, coastal waters at the time of bite. The species involved was identified in two cases (both Hydrophis zweifeli). Local effects occurred in 9 patients: pain (5), swelling (5), bleeding (2), bruising (1). Envenoming occurred in eight patients and was characterised by non-specific systemic features (6) and myotoxicity (2). Myotoxicity was severe (peak CK 28200 and 48100 U/L) and rapid in onset (time to peak CK 13.5 and 15.1 h) in these two patients. Non-specific systemic features included nausea (6), headache (6), abdominal pain (3), and diaphoresis (2). Leukocytosis, neutrophilia, and lymphopenia occurred in both patients with myotoxicity and was evident on the first blood test. No patients developed neurotoxicity or coagulopathy. Early Seqirus antivenom therapy was associated with a lower peak creatine kinase. Conclusion: While relatively rare, sea snake envenoming is associated with significant morbidity and risk of mortality. Early antivenom appears to have a role in preventing severe myotoxicity and should be a goal of therapy.
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Affiliation(s)
| | - Theo Tasoulis
- Clinical Toxicology Research Group, University of Newcastle, Newcastle, NSW, Australia
| | - Geoffrey K Isbister
- Clinical Toxicology Research Group, University of Newcastle, Newcastle, NSW, Australia.,National Poison Centre Network, Westmead Children's Hospital, Sydney, NSW, Australia
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44
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Abstract
The venom glands of reptiles, particularly those of front-fanged advanced snakes, must satisfy conflicting biological demands: rapid synthesis of potentially labile and highly toxic proteins, storage in the gland lumen for long periods, stabilization of the stored secretions, immediate activation of toxins upon deployment and protection of the animal from the toxic effects of its own venom. This dynamic system could serve as a model for the study of a variety of different phenomena involving exocrine gland activation, protein synthesis, stabilization of protein products and secretory mechanisms. However, these studies have been hampered by a lack of a long-term model that can be propagated in the lab (as opposed to whole-animal studies). Numerous attempts have been made to extend the lifetime of venom gland secretory cells, but only recently has an organoid model been shown to have the requisite qualities of recapitulation of the native system, self-propagation and long-term viability (>1 year). A tractable model is now available for myriad cell- and molecular-level studies of venom glands, protein synthesis and secretion. However, venom glands of reptiles are not identical, and many differ very extensively in overall architecture, microanatomy and protein products produced. This Review summarizes the similarities among and differences between venom glands of helodermatid lizards and of rear-fanged and front-fanged snakes, highlighting those areas that are well understood and identifying areas where future studies can fill in significant gaps in knowledge of these ancient, yet fascinating systems.
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Affiliation(s)
- Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th St., CB 92, Greeley, CO 80639-0017, USA
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45
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Senter PJ. Phylogeny of Courtship and Male-male Combat Behavior in Snakes: An Updated Analysis. CURRENT HERPETOLOGY 2022. [DOI: 10.5358/hsj.41.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Philip J. Senter
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, North Carolina, 28301 UNITED STATES
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46
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Georgalis GL, Szyndlar Z. First occurrence of Psammophis (Serpentes) from Europe witnesses another Messinian herpetofaunal dispersal from Africa - biogeographic implications and a discussion of the vertebral morphology of psammophiid snakes. Anat Rec (Hoboken) 2022; 305:3263-3282. [PMID: 35139258 DOI: 10.1002/ar.24892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 11/08/2022]
Abstract
We here describe abundant new snake material from the late Miocene (MN 13) of Salobreña, Spain. Vertebral morphology suggests a referral of the specimens to the extant psammophiid Psammophis, documenting the first occurrence of this genus in Europe. The diversity and disparity across the vertebral morphology of different psammophiid genera is discussed. We identify vertebral features that could diagnose Psammophis and therefore enable the recognition of the genus in the fossil record. A comparison of the new Spanish form with other taxa is conducted. We provide a detailed review of the psammophiid fossil record. Material previously described from the middle Miocene of Beni Mellal, Morocco is here tentatively referred to as? Psammophis sp., an action that renders that occurrence as the oldest (probable) record of the genus and Psammophiidae as a whole, providing thus a potential calibration point. On the other hand, Eastern European Pliocene material that had been previously supposedly referred to Psammophis is here discarded as being rather fragmentary, not affording any more precise determination. The two psammophiid genera Psammophis and Malpolon appear almost simultaneously in the European fossil record (MN 13), with the former achieving only a short-lived and apparently geographically limited distribution in the continent, while the latter still exists in its modern herpetofauna. We assess biogeographic implications of the new find, suggesting a direct dispersal event from northwestern Africa to the Iberian Peninsula during the late Miocene, facilitated by the Messinian Salinity Crisis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Georgios L Georgalis
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Zbigniew Szyndlar
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
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47
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Das S, Brecko J, Pauwels OSG, Merilä J. Cranial osteology of
Hypoptophis
(Aparallactinae: Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations. J Morphol 2022; 283:510-538. [PMID: 35094424 PMCID: PMC9305546 DOI: 10.1002/jmor.21457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI‐00014 University of Helsinki Finland
| | - Jonathan Brecko
- Department of Recent Vertebrates Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, B‐1000 Brussels Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren Belgium
| | - Olivier S. G. Pauwels
- Department of Recent Vertebrates Royal Belgian Institute of Natural Sciences (RBINS), Rue Vautier 29, B‐1000 Brussels Belgium
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI‐00014 University of Helsinki Finland
- Division of Ecology and Biodiversity, Faculty of Science The University of Hong Kong, KBSB 3N19 Hong Kong SAR
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48
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Barbo FE, Grazziotin FG, Pereira-Filho GA, Freitas MA, Abrantes SH, Kokubum MNDC. Isolated by dry lands: integrative analyses unveil the existence of a new species and a previously unknown evolutionary lineage of Brazilian Lanceheads (Serpentes: Viperidae: Bothrops) from a Caatinga moist-forest enclave. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2021-0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Here we describe a new species of Lancehead (Bothrops jabrensis sp. nov.) based on three individuals sampled from a previously unknown population from Pico do Jabre, an isolated and small Caatinga moist-forest enclave (CMFE) located in northeastern Brazil. Although this new species has an external morphology resembling those found in representatives of the Bothrops jararaca (Wied-Neuwied, 1824) species group, B. jabrensis can be diagnosed by a combination of meristic and color characters. Molecular phylogenetic analysis indicates the new species represents a unique and highly divergent lineage within Bothrops revealing the existence of a previously unknown phylogenetic lineage that has been evolving as an independent unit for more than 8 million years. Additionally, the estimated divergence time of this lineage conflicts with some proposed scenarios of historical processes associated with the evolution of CMFEs. Finally, the uniqueness of this species indicates its relevance for the maintenance of the phylogenetic diversity of Lanceheads in South America. Like other CMFEs, Pico do Jabre is consistently threatened by poaching, illegal fires, deforestation for agricultural purposes, and illegal logging. The restricted distribution of B. jabrensis, in a small and disturbed CMFE, strongly suggests that this species is critically endangered and is likely approaching extinction as a natural population.
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Affiliation(s)
- Fausto E. Barbo
- Laboratório de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Gentil A. Pereira-Filho
- Laboratório de Ecologia Animal, Departamento de Engenharia e Meio Ambiente, Centro de Ciências Aplicadas e Educação, Universidade Federal da Paraíba, 58297-000, Rio Tinto, PB, Brazil
| | - Marco A. Freitas
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Estação Ecológica de Murici, Rua Marino Vieira de Araújo, 32, 57820-000, Cidade Alta, Murici, AL, Brazil
| | - Stephenson H.F. Abrantes
- Laboratório de Ecomorfologia Animal, Centro de Saúde e Tecnologia Rural, Universidade Federal de Campina Grande, Avenida Universitária, s/n, 58708-110, Patos, PB, Brazil
| | - Marcelo N. de C. Kokubum
- Laboratório de Herpetologia, Centro de Saúde e Tecnologia Rural, Universidade Federal de Campina Grande, Avenida Universitária, s/n, 58708-110, Patos, PB, Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Universidade Estadual da Paraíba, 58429-500, Campina Grande, PB, Brazil
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49
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Poyarkov NA, Nguyen TV, Pawangkhanant P, Yushchenko PV, Brakels P, Nguyen LH, Nguyen HN, Suwannapoom C, Orlov N, Vogel G. An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina. PeerJ 2022; 10:e12713. [PMID: 35047234 PMCID: PMC8757378 DOI: 10.7717/peerj.12713] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
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Affiliation(s)
- Nikolay A. Poyarkov
- Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam,Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Tan Van Nguyen
- Department of Species Conservation, Save Vietnam’s Wildlife, Ninh Binh, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Platon V. Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | | | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
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50
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Dubeux MJM, Araújo Neto JVD, Triburcio ICS, Lisboa BS, Torquato S, Freitas MAD, Freire EMX, Guarnieri MC, Mott T. A “hotspot” within a hotspot: the reptiles of the Estação Ecológica and Área de Proteção Ambiental de Murici, Atlantic Forest of northeastern Brazil. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Currently the Atlantic Forest hotspot has less than 11% of its original coverage. However approximately 300 species of reptiles are known to inhabit this ecoregion, of which 34% are endemic. The creation of protected areas represents a strategy for preserving ecosystems and managing land use, and for attaining the proper management of these protected areas, information on local biodiversity is essential. Herein we provide the first list of reptile species for the Estação Ecológica and Área de Proteção Ambiental de Murici, two overlapping protected areas located in the state of Alagoas, one of the most important sets of forest remnants for the conservation of the Atlantic Forest in the northeast of Brazil. The species list was constructed based on expeditions and occasional encounters in the area between 1994 and 2022. A total of 89 reptile species were obtained during the 28 years of collection, being two species of Crocodylia, three species of Testudines and 84 species of Squamata. This richness is by far one of the greatest ever documented for the Atlantic Forest. Additionally, two species registered in the area are considered threatened according to the national list (Amerotyphlops paucisquamus and Bothrops muriciensis) and six are defined as data deficient for the assessment of their conservation status. Three species are recorded for the first time in the Atlantic Forest north of the São Francisco River: Dipsas indica, Trilepida salgueiroi and Cercophis auratus. We claim that the species list provided here will serve as a starting point for further studies in this rich reptile “hotspot” within the Atlantic Forest.
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Affiliation(s)
- Marcos Jorge Matias Dubeux
- Universidade Federal de Pernambuco, Brasil; Universidade Federal de Alagoas, Brasil; Universidade Federal de Alagoas, Brasil
| | | | | | - Barnagleison Silva Lisboa
- Universidade Federal de Pernambuco, Brasil; Universidade Federal de Alagoas, Brasil; Instituto Federal de Alagoas, Brasil
| | | | | | | | | | - Tamí Mott
- Universidade Federal de Alagoas, Brasil; Universidade Federal de Alagoas, Brasil
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