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Mancuso M, Zaman S, Maddock ST, Kamei RG, Salazar-Valenzuela D, Wilkinson M, Roelants K, Fry BG. Resistance Is Not Futile: Widespread Convergent Evolution of Resistance to Alpha-Neurotoxic Snake Venoms in Caecilians (Amphibia: Gymnophiona). Int J Mol Sci 2023; 24:11353. [PMID: 37511112 PMCID: PMC10379402 DOI: 10.3390/ijms241411353] [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: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory innovations impose reciprocal selection pressures upon prey. The evolution of snake venom alpha-neurotoxins has triggered the corresponding evolution of resistance in the post-synaptic nicotinic acetylcholine receptors of prey in a complex chemical arms race. All other things being equal, animals like caecilians (an Order of legless amphibians) are quite vulnerable to predation by fossorial elapid snakes and their powerful alpha-neurotoxic venoms; thus, they are under strong selective pressure. Here, we sequenced the nicotinic acetylcholine receptor alpha-1 subunit of 37 caecilian species, representing all currently known families of caecilians from across the Americas, Africa, and Asia, including species endemic to the Seychelles. Three types of resistance were identified: (1) steric hindrance from N-glycosylated asparagines; (2) secondary structural changes due to the replacement of proline by another amino acid; and (3) electrostatic charge repulsion of the positively charged neurotoxins, through the introduction of a positively charged amino acid into the toxin-binding site. We demonstrated that resistance to alpha-neurotoxins convergently evolved at least fifteen times across the caecilian tree (three times in Africa, seven times in the Americas, and five times in Asia). Additionally, as several species were shown to possess multiple resistance modifications acting synergistically, caecilians must have undergone at least 20 separate events involving the origin of toxin resistance. On the other hand, resistance in non-caecilian amphibians was found to be limited to five origins. Together, the mutations underlying resistance in caecilians constitute a robust signature of positive selection which strongly correlates with elapid presence through both space (sympatry with caecilian-eating elapids) and time (Cenozoic radiation of elapids). Our study demonstrates the extent of convergent evolution that can be expected when a single widespread predatory adaptation triggers parallel evolutionary arms races at a global scale.
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Affiliation(s)
- Marco Mancuso
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Shabnam Zaman
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Simon T Maddock
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- School of Life Sciences, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé P.O. Box 1348, Seychelles
| | - Rachunliu G Kamei
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Amphibians and Reptiles Division, The Field Museum of Natural History, 1400 S Lake Shore Dr., Chicago, IL 60605, USA
| | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Indoamérica, Machala y Sabanilla, Quito EC170301, Ecuador
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Bryan G Fry
- Venom Evolutionary Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
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Ceríaco LMP, Marques MP, de Sousa ACA, Veríssimo J, Beja P, Ferreira S. Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa). Zookeys 2023; 1168:41-75. [PMID: 37415718 PMCID: PMC10320720 DOI: 10.3897/zookeys.1168.101334] [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: 02/03/2023] [Accepted: 04/18/2023] [Indexed: 07/08/2023] Open
Abstract
The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authorities in the identification of the country's herpetofauna: an illustrated key to the herpetofauna of the two islands and surroundings islets and a DNA barcode reference library. The keys allow a rapid and unambiguous morphological identification of all occurring species. The DNA barcodes for the entire herpetofauna of the country were produced from 79 specimens, all of which are deposited in museum collections. The barcodes generated are available in online repositories and can be used to provide unambiguous molecular identification of most of the species. Future applications and use of these tools are briefly discussed.
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Affiliation(s)
- Luis Miguel Pires Ceríaco
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Av. Bartolomeu de Gusmão 875, São Cristóvão, 20941-160 Rio de Janeiro, Brasil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana Pimentel Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 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, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | | | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 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, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | - Pedro Beja
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Kazzaz SA, Giani Tagliabue S, Franks DG, Denison MS, Hahn ME, Bonati L, Powell WH. An aryl hydrocarbon receptor from the caecilian Gymnopis multiplicata suggests low dioxin affinity in the ancestor of all three amphibian orders. Gen Comp Endocrinol 2020; 299:113592. [PMID: 32858041 PMCID: PMC7771225 DOI: 10.1016/j.ygcen.2020.113592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/31/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022]
Abstract
The aryl hydrocarbon receptor (AHR) plays pleiotropic roles in the development and physiology of vertebrates in conjunction with xenobiotic and endogenous ligands. It is best known for mediating the toxic effects of dioxin-like pollutants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While most vertebrates possess at least one AHR that binds TCDD tightly, amphibian AHRs bind TCDD with very low affinity. Previous analyses of AHRs from Xenopus laevis (a frog; order Anura) and Ambystoma mexicanum (a salamander; order Caudata) identified three amino acid residues in the ligand-binding domain (LBD) that underlie low-affinity binding. In X. laevis AHR1β, these are A354, A370, and N325. Here we extend the analysis of amphibian AHRs to the caecilian Gymnopis multiplicata, representing the remaining extant amphibian order, Gymnophiona. G. multiplicata AHR groups with the monophyletic vertebrate AHR/AHR1 clade. The LBD includes all three signature residues of low TCDD affinity, and a structural homology model suggests that its architecture closely resembles those of other amphibians. In transactivation assays, the EC50 for reporter gene induction by TCDD was 17.17 nM, comparable to X. laevis AhR1β (26.23 nM) and Ambystoma AHR (34.09 nM) and dramatically higher than mouse AhR (0.13 nM), a trend generally reflected in direct measures of TCDD binding. These shared properties distinguish amphibian AHRs from the high-affinity proteins typical of both vertebrate groups that diverged earlier (teleost fish) and those that appeared more recently (other tetrapods). These findings suggest the hypothesis that AHRs with low TCDD affinity represent a characteristic that evolved in a common ancestor of all three extant amphibian groups.
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Affiliation(s)
- Sarah A Kazzaz
- Biology Department, Kenyon College, Gambier, OH 43022, USA
| | - Sara Giani Tagliabue
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Diana G Franks
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Michael S Denison
- Department of Environmental Toxicology, University of California-Davis, Davis, CA 95616, USA
| | - Mark E Hahn
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Wade H Powell
- Biology Department, Kenyon College, Gambier, OH 43022, USA.
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Santos RO, Laurin M, Zaher H. A review of the fossil record of caecilians (Lissamphibia: Gymnophionomorpha) with comments on its use to calibrate molecular timetrees. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Gymnophiona, popularly known as caecilians, the most poorly known major taxon of extant amphibians, are elongate and limbless tetrapods, with compact ossified skulls and reduced eyes, mainly adapted to fossorial life as adults. Caecilians are poorly represented in the fossil record, but despite the scarcity of fossil specimens described (only four named taxa, in addition to indeterminate fragmentary material), their fossils play a key role in our knowledge of the origin and evolution of Lissamphibia, as well as contribute directly to a better understanding of the phylogeny, taxonomy and biogeography of extant gymnophionan taxa. These records are scattered throughout geological time (from the Jurassic to the sub-Recent) and space (North and South America and Africa). Here, we revisit the caecilian fossil record, providing a brief description of all known extinct taxa described so far, along with general remarks about their impact on systematics, time range, and geographical distribution of the clade, as well as prospects for future research. Possible calibration constraints based on the caecilian fossil record are provided.
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Affiliation(s)
| | - Michel Laurin
- Centre de Recherches sur la Paléobiologie et les Paléoenvironnements (CR2P), Centre national de la Recherche scientifique (CNRS)/Muséum national d’Histoire naturelle (MNHN)/Sorbonne Université, Paris, France
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, Brazil
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5
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Serrano-Perez CA, Ramírez-Pinilla MP. Morphology and histology of the male reproductive tract of Caecilia thompsoni (amphibia: Gymnophiona). Anat Rec (Hoboken) 2020; 304:1119-1135. [PMID: 33022119 DOI: 10.1002/ar.24527] [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: 04/28/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 11/06/2022]
Abstract
We studied the male reproductive tract of individuals of different body sizes of Caecilia thompsoni to describe morphological characteristics in comparison to other Gymnophiona. The reproductive tract consists of paired testes segmented into chains of primary and secondary lobes, sperm ducts that empty to Wolffian ducts, the cloaca that receives the Wolffian ducts and possesses a phallodeum. Müllerian ducts are present and develop into paired glands that empty into the cloacal urodeum. Testicular secondary lobes contain lobules with cysts of the entire germinal cell line, whereas primary lobes, in the terminal ends of the chains, only have spermagonia, Sertoli cells, and connective tissue. The smallest individual examined (21 cm body length) was immature and only possessed a few testicular primary lobes. Once the individuals reach sexual maturity, the morphological characteristics are quite consistent at macroscopic and histological level among males of very different body sizes. The histological features of the Wolffian and Müllerian glands suggest a complementary secretory role between the two ducts. In the cloaca we found the propulsor muscle, venous sinuses, and blind sacs in the phallodeum, which differentiate C. thompsoni from other species of the genus. Despite these slight differences, the general morphological characteristics, both macroscopic and microscopic, of the reproductive tracts of adult males of C. thompsoni follow the pattern known for the reproductively active males of Gymnophiona.
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Affiliation(s)
- Carlos A Serrano-Perez
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Martha Patricia Ramírez-Pinilla
- Laboratorio de Biología Reproductiva de Vertebrados, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia.,Colección Herpetológica, Museo de Historia Natural, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
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6
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Acosta-Galvis AR, Torres M, Pulido-Santacruz P. A new species of Caecilia (Gymnophiona, Caeciliidae) from the Magdalena valley region of Colombia. Zookeys 2019; 884:135-157. [PMID: 31723330 PMCID: PMC6834723 DOI: 10.3897/zookeys.884.35776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/12/2019] [Indexed: 11/21/2022] Open
Abstract
A new species of the genus Caecilia (Caeciliidae) from the western foothills of the Serranía de los Yariguíes in Colombia is described. Caeciliapulchraserranasp. nov. is similar to C.degenerata and C.corpulenta but differs from these species in having fewer primary annular grooves and a shorter body length. With this new species, the currently recognized species in the genus are increased to 35. Mitochondrial DNA sequences, including newly sequenced terminals representing two additional, previously unanalyzed species, corroborate the phylogenetic position of the new species within Caecilia and the monophyly of the genus. This analysis also included newly sequenced terminals of Epicrionopsaff.parkeri (Rhinatrematidae) and trans-Andean Microcaecilianicefori (Siphonopidae). Evidence was found for the non-monophyly of the family Siphonopidae and the siphonopid genera Microcaecilia and Siphonops. The implications of these results for caecilian systematics are discussed and the status of the trans-Andean populations of Caeciliadegenerata is commented upon.
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7
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Maciel AO, de Castro TM, Sturaro MJ, Costa Silva IE, Ferreira JG, dos Santos R, Risse-Quaioto B, Barboza BA, Oliveira JC, Sampaio I, Schneider H. Phylogenetic systematics of the Neotropical caecilian amphibian Luetkenotyphlus (Gymnophiona: Siphonopidae) including the description of a new species from the vulnerable Brazilian Atlantic Forest. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Diaz RE, Shylo NA, Roellig D, Bronner M, Trainor PA. Filling in the phylogenetic gaps: Induction, migration, and differentiation of neural crest cells in a squamate reptile, the veiled chameleon (Chamaeleo calyptratus). Dev Dyn 2019; 248:709-727. [DOI: 10.1002/dvdy.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Raul E. Diaz
- Department of Biological Sciences, Southeastern Louisiana University Hammond Louisiana
- Natural History Museum of Los Angeles CountyDivision of Herpetology Los Angeles California
| | | | - Daniela Roellig
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena California
| | - Marianne Bronner
- Division of Biology and Biological Engineering, California Institute of Technology Pasadena California
| | - Paul A. Trainor
- Stowers Institute for Medical Research Kansas City Missouri
- Department of Anatomy and Cell Biology, University of Kansas Medical Center Kansas City Kansas
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Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia. Proc Natl Acad Sci U S A 2017. [PMID: 28630337 DOI: 10.1073/pnas.1706752114] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of the limbless caecilians remains a lasting question in vertebrate evolution. Molecular phylogenies and morphology support that caecilians are the sister taxon of batrachians (frogs and salamanders), from which they diverged no later than the early Permian. Although recent efforts have discovered new, early members of the batrachian lineage, the record of pre-Cretaceous caecilians is limited to a single species, Eocaecilia micropodia The position of Eocaecilia within tetrapod phylogeny is controversial, as it already acquired the specialized morphology that characterizes modern caecilians by the Jurassic. Here, we report on a small amphibian from the Upper Triassic of Colorado, United States, with a mélange of caecilian synapomorphies and general lissamphibian plesiomorphies. We evaluated its relationships by designing an inclusive phylogenetic analysis that broadly incorporates definitive members of the modern lissamphibian orders and a diversity of extinct temnospondyl amphibians, including stereospondyls. Our results place the taxon confidently within lissamphibians but demonstrate that the diversity of Permian and Triassic stereospondyls also falls within this group. This hypothesis of caecilian origins closes a substantial morphologic and temporal gap and explains the appeal of morphology-based polyphyly hypotheses for the origins of Lissamphibia while reconciling molecular support for the group's monophyly. Stem caecilian morphology reveals a previously unrecognized stepwise acquisition of typical caecilian cranial apomorphies during the Triassic. A major implication is that many Paleozoic total group lissamphibians (i.e., higher temnospondyls, including the stereospondyl subclade) fall within crown Lissamphibia, which must have originated before 315 million years ago.
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Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, San Mauro D, Day JJ, Littlewood DTJ, Foster PG, Nussbaum RA, Gower DJ. Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. PLoS One 2016; 11:e0156757. [PMID: 27280454 PMCID: PMC4900593 DOI: 10.1371/journal.pone.0156757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 05/19/2016] [Indexed: 01/06/2023] Open
Abstract
Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina’s HiSeq and MiSeq, Roche’s 454 GS FLX, and Life Technologies’ Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.
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Affiliation(s)
- Simon T. Maddock
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
- Department of Animal Management, Reaseheath College, Nantwich, CW5 6DF, United Kingdom
- * E-mail:
| | - Andrew G. Briscoe
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Andrea Waeschenbach
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Diego San Mauro
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Julia J. Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - D. Tim J. Littlewood
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
| | - Ronald A. Nussbaum
- Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109–1079, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109–1079, United States of America
| | - David J. Gower
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom
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Kupfer A, Maxwell E, Reinhard S, Kuehnel S. The evolution of parental investment in caecilian amphibians: a comparative approach. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12805] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Kupfer
- Staatliches Museum für Naturkunde Stuttgart; Rosenstein 1 Stuttgart 70191 Germany
- Institut für Biochemie und Biologie; Allgemeine Zoologie und Evolutionsgenomik; Universität Potsdam; Karl-Liebknecht-Strasse 24-25 Haus 26 Potsdam 14476 Germany
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich Schiller-Universität Jena; Erbertstrasse 1 Jena 07743 Germany
| | - Erin Maxwell
- Staatliches Museum für Naturkunde Stuttgart; Rosenstein 1 Stuttgart 70191 Germany
| | - Sandy Reinhard
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich Schiller-Universität Jena; Erbertstrasse 1 Jena 07743 Germany
- Naturhistorisches Museum; Thüringer Landesmuseum Heidecksburg; Schlossbezirk 1 Rudolstadt 07407 Germany
| | - Susanne Kuehnel
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich Schiller-Universität Jena; Erbertstrasse 1 Jena 07743 Germany
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12
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Héritier L, Badets M, Du Preez LH, Aisien MS, Lixian F, Combes C, Verneau O. Evolutionary processes involved in the diversification of chelonian and mammal polystomatid parasites (Platyhelminthes, Monogenea, Polystomatidae) revealed by palaeoecology of their hosts. Mol Phylogenet Evol 2015; 92:1-10. [DOI: 10.1016/j.ympev.2015.05.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 11/16/2022]
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13
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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14
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Phylogeography of the harvestman genus Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0233-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I. acuminatus Taylor, 1960, I. youngorum Taylor, 1960 and I. laosensis Taylor, 1969. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0190-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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du Preez LH, Badets M, Verneau O. Assessment of platyhelminth diversity within amphibians of French Guiana revealed a new species of Nanopolystoma (Monogenea: Polystomatidae) in the caecilian Typhlonectes compressicauda. Folia Parasitol (Praha) 2014. [DOI: 10.14411/fp.2014.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Stoelting RE, Measey GJ, Drewes RC. Population genetics of the São Tomé caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) reveals strong geographic structuring. PLoS One 2014; 9:e104628. [PMID: 25171066 PMCID: PMC4149351 DOI: 10.1371/journal.pone.0104628] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities.
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Affiliation(s)
- Ricka E. Stoelting
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
| | - G. John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert C. Drewes
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
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18
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19
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Pyron RA. Biogeographic Analysis Reveals Ancient Continental Vicariance and Recent Oceanic Dispersal in Amphibians. Syst Biol 2014; 63:779-97. [DOI: 10.1093/sysbio/syu042] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington, DC 20052, USA
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20
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Maddin HC, Sherratt E. Influence of fossoriality on inner ear morphology: insights from caecilian amphibians. J Anat 2014; 225:83-93. [PMID: 24762299 DOI: 10.1111/joa.12190] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2014] [Indexed: 12/01/2022] Open
Abstract
It is widely accepted that a relationship exists between inner ear morphology and functional aspects of an animal's biology, such as locomotor behaviour. Animals that engage in agile and spatially complex behaviours possess semicircular canals that morphologically maximise sensitivity to correspondingly complex physical stimuli. Stemming from the prediction that fossorial tetrapods require a well-developed sense of spatial awareness, we investigate the hypothesis that fossoriality leads to inner ear morphology that is convergent with other spatially adept tetrapods. We apply morphometrics to otic capsule endocasts of 26 caecilian species to quantify aspects of inner ear shape, and compare these with a sample of frog and salamander species. Our results reveal caecilians (and also frogs) possess strongly curved canals, a feature in common with spatially adept species. However, significantly shorter canals in caecilians suggest reduced sensitivity, possibly associated with reduced reliance on vestibulo-ocular reflexes in this group of visually degenerate tetrapods. An elaboration of the sacculus of caecilians is interpreted as a unique adaptation among amphibians to increase sensitivity to substrate-borne vibrations transmitted through the head. This study represents the first quantitative analyses of inner ear morphology of limbless fossorial tetrapods, and identifies features within a new behavioural context that will contribute to our understanding of the biological consequences of physical stimuli on sensory function and associated morphological evolution.
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Affiliation(s)
- Hillary C Maddin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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21
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Xu T, Tang D, Cheng Y, Wang R. Mitogenomic perspectives into sciaenid fishes' phylogeny and evolution origin in the New World. Gene 2014; 539:91-8. [DOI: 10.1016/j.gene.2014.01.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 12/26/2013] [Accepted: 01/15/2014] [Indexed: 10/25/2022]
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22
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Mohun SM, Wilkinson M. The eye of the caecilianRhinatrema bivittatum(Amphibia: Gymnophiona: Rhinatrematidae). ACTA ZOOL-STOCKHOLM 2014. [DOI: 10.1111/azo.12061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samantha M. Mohun
- Herpetology Research Group; Department of Life Sciences; Natural History Museum; London SW7 5BD UK
- UCL Institute of Ophthalmology; 11-43 Bath Street London EC1V 9EL UK
| | - Mark Wilkinson
- Herpetology Research Group; Department of Life Sciences; Natural History Museum; London SW7 5BD UK
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23
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San Mauro D, Gower DJ, Müller H, Loader SP, Zardoya R, Nussbaum RA, Wilkinson M. Life-history evolution and mitogenomic phylogeny of caecilian amphibians. Mol Phylogenet Evol 2014; 73:177-89. [PMID: 24480323 DOI: 10.1016/j.ympev.2014.01.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/13/2014] [Accepted: 01/16/2014] [Indexed: 11/27/2022]
Abstract
We analyze mitochondrial genomes to reconstruct a robust phylogenetic framework for caecilian amphibians and use this to investigate life-history evolution within the group. Our study comprises 45 caecilian mitochondrial genomes (19 of them newly reported), representing all families and 27 of 32 currently recognized genera, including some for which molecular data had never been reported. Support for all relationships in the inferred phylogenetic tree is high to maximal, and topology tests reject all investigated alternatives, indicating an exceptionally robust molecular phylogenetic framework of caecilian evolution consistent with current morphology-based supraspecific classification. We used the mitogenomic phylogenetic framework to infer ancestral character states and to assess correlation among three life-history traits (free-living larvae, viviparity, specialized pre-adult or vernal teeth), each of which occurs only in some caecilian species. Our results provide evidence that an ancestor of the Seychelles caecilians abandoned direct development and re-evolved a free-living larval stage. This study yields insights into the concurrent evolution of direct development and of vernal teeth in an ancestor of Teresomata that likely gave rise to skin-feeding (maternal dermatophagy) behavior and subsequently enabled evolution of viviparity, with skin feeding possibly a homologous precursor of oviduct feeding in viviparous caecilians.
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Affiliation(s)
- Diego San Mauro
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Hendrik Müller
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller-Universität Jena, Erbertstrasse 1, 07743 Jena, Germany
| | - Simon P Loader
- University of Basel, Biogeography Research Group, Department of Environmental Sciences, Basel 4056, Switzerland
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales - CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Ronald A Nussbaum
- Museum of Zoology, University of Michigan, 1109 Geddes Ave., Ann Arbor, MI 48109-1079, United States
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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24
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Donnelly MA, Wake MH. A New Microcaecilia (Amphibia: Gymnophiona) from Guyana with Comments on Epicrionops niger. COPEIA 2013. [DOI: 10.1643/ch-12-094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Zhang P, Liang D, Mao RL, Hillis DM, Wake DB, Cannatella DC. Efficient sequencing of Anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs. Mol Biol Evol 2013; 30:1899-915. [PMID: 23666244 DOI: 10.1093/molbev/mst091] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mitochondrial DNAs (mtDNAs) by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Based on this method, we generated 47 nearly complete, new anuran mitochondrial genomes and discovered nine novel gene arrangements. By combining the new data and published anuran mitochondrial genomes, we assembled a large mitogenomic data set (11,007 nt) including 90 frog species, representing 39 of 53 recognized anuran families, to investigate their phylogenetic relationships and evolutionary history. The resulting tree strongly supported a paraphyletic arrangement of archaeobatrachian (=nonneobatrachian) frogs, with Leiopelmatoidea branching first, followed by Discoglossoidea, Pipoidea, and Pelobatoidea. Within Neobatrachia, the South African Heleophrynidae is the sister-taxon to all other neobatrachian frogs and the Seychelles-endemic Sooglossidae is recovered as the sister-taxon to Ranoidea. These phylogenetic relationships agree with many nuclear gene studies. The chronogram derived from two Bayesian relaxed clock methods (MultiDivTime and BEAST) suggests that modern frogs (Anura) originated in the early Triassic about 244 Ma and the appearance of Neobatrachia took place in the late Jurassic about 163 Ma. The initial diversifications of two species-rich superfamilies Hyloidea and Ranoidea commenced 110 and 133 Ma, respectively. These times are older than some other estimates by approximately 30-40 My. Compared with nuclear data, mtDNA produces compatible time estimates for deep nodes (>150 Ma), but apparently older estimates for more shallow nodes. Our study shows that, although it evolves relatively rapidly and behaves much as a single locus, mtDNA performs well for both phylogenetic and divergence time inferences and will provide important reference hypotheses for the phylogeny and evolution of frogs.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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26
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Venu G, Venkatachalaiah G. Chromosomal homology of Uraeotyphlus oxyurus group of species (Amphibia, Gymnophiona, Ichthyophiidae). COMPARATIVE CYTOGENETICS 2013; 7:11-23. [PMID: 24260686 PMCID: PMC3833749 DOI: 10.3897/compcytogen.v7i1.3603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 12/27/2012] [Indexed: 06/02/2023]
Abstract
Uraeotyphlus oxyurus (Dumeril et Bibron, 1841), Uraeotyphlus interruptus Pillai et Ravichandran, 1999, Uraeotyphlus narayani Seshachar, 1939 and Uraeotyphlus menoni Annandale, 1913 were cytogenetically analysed following conventional and differential staining techniques. These species show similar karyotypes with 2n=36 (FN=58). There were no traces of species-specific features in regard to C-banding and NOR staining. The comparative study of karyotypes shows chromosomal homologies among the four species. Chromosomal data seem to support the concept that two species groups exist in the genus Uraeotyphlus.
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Affiliation(s)
- G. Venu
- Centre for Applied Genetics, Department of Zoology, Bangalore University, Bangalore 560 056, India
| | - G. Venkatachalaiah
- Centre for Applied Genetics, Department of Zoology, Bangalore University, Bangalore 560 056, India
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27
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Kotharambath R, Wilkinson M, Oommen O, George S, Nussbaum R, Gower D. On the systematics, distribution and conservation status ofIchthyophis longicephalusPillai, 1986 (Amphibia: Gymnophiona: Ichthyophiidae). J NAT HIST 2012. [DOI: 10.1080/00222933.2012.717972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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MADDIN HILLARYC, RUSSELL ANTHONYP, ANDERSON JASONS. Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona). Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00838.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland. Mol Phylogenet Evol 2012; 63:714-23. [DOI: 10.1016/j.ympev.2012.02.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 02/12/2012] [Accepted: 02/15/2012] [Indexed: 11/19/2022]
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30
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Kleinteich T, Maddin HC, Herzen J, Beckmann F, Summers AP. Is solid always best? Cranial performance in solid and fenestrated caecilian skulls. J Exp Biol 2012; 215:833-44. [DOI: 10.1242/jeb.065979] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Caecilians (Lissamphibia: Gymnophiona) are characterized by a fossorial lifestyle that appears to play a role in the many anatomical specializations in the group. The skull, in particular, has been the focus of previous studies because it is driven into the substrate for burrowing. There are two different types of skulls in caecilians: (1) stegokrotaphic, where the squamosal completely covers the temporal region and the jaw closing muscles, and (2) zygokrotaphic, with incomplete coverage of the temporal region by the squamosal. We used 3-D imaging and modeling techniques to explore the functional consequences of these skull types in an evolutionary context. We digitally converted stegokrotaphic skulls into zygokrotaphic skulls and vice versa. We also generated a third, akinetic skull type that was presumably present in extinct caecilian ancestors. We explored the benefits and costs of the different skull types under frontal loading at different head angles with finite element analysis (FEA). Surprisingly, the differences in stress distributions and bending between the three tested skull types were minimal and not significant. This suggests that the open temporal region in zygokrotaphic skulls does not lead to poorer performance during burrowing. However, the results of the FEA suggest a strong relationship between the head angle and skull performance, implying there is an optimal head angle during burrowing.
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Affiliation(s)
- Thomas Kleinteich
- Christian-Albrechts-Universität Kiel, Department of Zoology – Functional Morphology and Biomechanics, Am Botanischen Garten 1-9, 24098 Kiel, Germany
- University of Washington, Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250, USA
| | - Hillary C. Maddin
- University of Calgary, 2500 University Drive, Calgary, Alberta, T2N 1N4, Canada
| | - Julia Herzen
- Helmholtz Zentrum Geesthacht, Institute of Materials Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - Felix Beckmann
- Helmholtz Zentrum Geesthacht, Institute of Materials Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - Adam P. Summers
- University of Washington, Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250, USA
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31
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San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M, Massingham T. Experimental Design in Phylogenetics: Testing Predictions from Expected Information. Syst Biol 2012; 61:661-74. [DOI: 10.1093/sysbio/sys028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Diego San Mauro
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - David J. Gower
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - James A. Cotton
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales—CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Mark Wilkinson
- Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Tim Massingham
- EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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32
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Alexander Pyron R, Wiens JJ. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phylogenet Evol 2011; 61:543-83. [DOI: 10.1016/j.ympev.2011.06.012] [Citation(s) in RCA: 936] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 06/10/2011] [Accepted: 06/12/2011] [Indexed: 11/27/2022]
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33
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Gower DJ, Mauro DS, Giri V, Bhatta G, Govindappa V, Kotharambath R, Oommen OV, Fatih FA, Mackenzie-Dodds JA, Nussbaum RA, Biju S, Shouche YS, Wilkinson M. Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India. Mol Phylogenet Evol 2011; 59:698-707. [DOI: 10.1016/j.ympev.2011.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 02/28/2011] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
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Pyron RA. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol 2011; 60:466-81. [PMID: 21540408 DOI: 10.1093/sysbio/syr047] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.
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Affiliation(s)
- R Alexander Pyron
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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35
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Maddin HC. Deciphering morphological variation in the braincase of caecilian amphibians (Gymnophiona). J Morphol 2011; 272:850-71. [PMID: 21538474 DOI: 10.1002/jmor.10953] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 01/10/2011] [Accepted: 02/10/2011] [Indexed: 11/12/2022]
Abstract
High levels of morphological homoplasy have hindered progress in understanding morphological evolution within gymnophione lissamphibians. Stemming from the hypothesis that the braincase has the potential to yield phylogenetic information, the braincases of 27 species (23 genera) of gymnophione amphibians were examined using high-resolution micro-computed tomography and histologically prepared specimens. Morphology of the brain and its relationship to features of the braincase is described, and it is shown that eight different patterns exist in the distribution of foramina in the antotic region. The distribution of variants is congruent with molecule-based phylogeny. Additionally, all variants are shown to correspond directly to stages along developmental continua, suggesting that the evolutionary truncation of development in the antotic region at various stages has driven the evolution of morphology in this region. Attempts to correlate the observed morphology with proxies of putative heterochronic events (including those attributable to burrowing, life history, and size) fail to explain the distribution of morphology if each proxy is considered separately. Thus, it is concluded that either currently unrecognized causes of heterochrony or combinations thereof have influenced morphology in different lineages independently. These data identify clades whose morphology can now be reconsidered in light of previously unrecognized heterochronic events, thereby providing a foundation for future analyses of the evolution of morphology within Gymnophiona as a whole. Most significantly, these data confirm, for the first time in a lissamphibian group, that the braincase can preserve important phylogenetic information that is otherwise obscured in regions of the skull that experience strong influences from functional constraints.
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Affiliation(s)
- Hillary C Maddin
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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36
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Doherty-Bone TM, Ndifon RK, San Mauro D, Wilkinson M, LeGrand GN, Gower DJ. Systematics and ecology of the caecilianCrotaphatrema lamottei(Nussbaum) (Amphibia: Gymnophiona: Scolecomorphidae). J NAT HIST 2011. [DOI: 10.1080/00222933.2010.535921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Kleinteich T, Haas A. The hyal and ventral branchial muscles in caecilian and salamander larvae: Homologies and evolution. J Morphol 2011; 272:598-613. [DOI: 10.1002/jmor.10940] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/31/2010] [Accepted: 11/29/2010] [Indexed: 01/25/2023]
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38
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Kuehnel S, Herzen J, Kleinteich T, Beckmann F, Kupfer A. The female cloaca of an oviparous caecilian amphibian (Gymnophiona): functional and seasonal aspects. ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2010.00499.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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A multilocus timescale for the origin of extant amphibians. Mol Phylogenet Evol 2010; 56:554-61. [DOI: 10.1016/j.ympev.2010.04.019] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 04/06/2010] [Accepted: 04/13/2010] [Indexed: 11/15/2022]
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