1
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Altamirano-Ponce L, Dávila-Játiva M, Pozo G, Pozo MJ, Terán-Velástegui M, Cadena CD, Cisneros-Heredia DF, Torres MDL. First genetic insights of Gonatodescaudiscutatus (Reptilia, Gekkota) in the Galapagos Islands and mainland Ecuador. Biodivers Data J 2023; 11:e113396. [PMID: 38028240 PMCID: PMC10680088 DOI: 10.3897/bdj.11.e113396] [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: 09/27/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Studies on genetic variability amongst native and introduced species contribute to a better understanding of the genetic diversity of species along their autochthonous distribution and identify possible routes of introduction. Gonatodescaudiscutatus is a gecko native to western Ecuador and introduced to the Galapagos Islands. Despite being a successful species in human-modified habitats along its native and non-native ranges, neither the colonisation process nor the genetic diversity of this gecko is known. In this study, we analysed 55 individuals from 14 localities in western Ecuador and six localities in San Cristobal Island, Galapagos - the only island with a large, self-sustaining population. We amplified and analysed the genetic variability of two nuclear genes (Cmos and Rag2) and one mitochondrial gene (16S). Cmos and Rag2 sequences presented little to none genetic variability, while 16S allowed us to build a haplotype network. We identified nine haplotypes across mainland Ecuador, two of which are also present in Galapagos. Low genetic diversity between insular and continental populations suggests that the introduction of G.caudiscutatus on the Islands is relatively recent. Due to the widespread geographical distribution of mainland haplotypes, it was not possible to determine the source population of the introduction. This study represents the first exploration of the genetic diversity of Gonatodescaudiscutatus, utilising genetic tools to gain insights into its invasion history in the Galapagos.
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Affiliation(s)
- Lía Altamirano-Ponce
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Mateo Dávila-Játiva
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Universidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de Vertebrados, Bogotá, ColombiaUniversidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de VertebradosBogotáColombia
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
| | - Gabriela Pozo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - María José Pozo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Martín Terán-Velástegui
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
| | - Carlos Daniel Cadena
- Universidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de Vertebrados, Bogotá, ColombiaUniversidad de los Andes, Departamento de Ciencias Biológicas, Laboratorio de Biología Evolutiva de VertebradosBogotáColombia
| | - Diego F. Cisneros-Heredia
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología TerrestreQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
| | - Maria de Lourdes Torres
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología Vegetal, Quito, EcuadorUniversidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalQuitoEcuador
- Universidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San Cristóbal, Galápagos, EcuadorUniversidad San Francisco de Quito USFQ, extensión Galápagos GAIAS, Puerto Baquerizo Moreno, San CristóbalGalápagosEcuador
- Galápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNC, Galápagos, EcuadorGalápagos Science Center, Universidad San Francisco de Quito USFQ & University of North Carolina at Chapel Hill UNCGalápagosEcuador
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2
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Chou MH, Chu IH, Lau D, Huang JP. Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: a case study on. INVERTEBR SYST 2022. [DOI: 10.1071/is22011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alpha taxonomy is fundamental for many biological fields. Delineation of the species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets, and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialisation, and further corroborate that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can occur at a small geographic scale, even in a winged insect like tiger beetles. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered. ZooBank LSID: urn:lsid:zoobank.org:pub:9DEC1432-365C-4872-8D06-73B95F30624F
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3
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Vázquez-Miranda H, Zink RM, Pinto BJ. Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence. Mol Phylogenet Evol 2022; 171:107466. [DOI: 10.1016/j.ympev.2022.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
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4
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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5
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Douglas J. UglyTrees: a browser-based multispecies coalescent tree visualizer. Bioinformatics 2021; 37:268-269. [PMID: 32717041 PMCID: PMC8055222 DOI: 10.1093/bioinformatics/btaa679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 01/20/2023] Open
Abstract
SUMMARY Visualization is a vital task in phylogenetics and yet there is a deficit in programs which visualize the multispecies coalescent (MSC) model. UglyTrees (UT) is an easy-to-use program for visualizing multiple gene trees embedded within a single species trees. The mapping between gene and species nodes is automatically detected allowing for ready access to the program. UT can scrape the contents of a website for MSC analyses, enabling the sharing of interactive MSC figures through optional parameters in the URL. If a posterior distribution is uploaded, the transitions between MSC states are animated allowing the visual tracking of trees throughout the sequence. AVAILABILITY AND IMPLEMENTATION UT runs in all major web browsers including mobile devices, and is hosted at www.uglytrees.nz. The MIT-licensed code is available at https://github.com/UglyTrees/uglytrees.github.io.
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Affiliation(s)
- Jordan Douglas
- School of Computer Science, University of Auckland, Auckland 1010, New Zealand
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6
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Baroni S, Damasceno RP, Almeida-Toledo LFD. Paraphyly and evolutionary independent lineages in Gymnotus pantherinus (Gymnotiformes: Gymnotidae) in the Brazilian Atlantic Forest Coastal Streams. Mol Phylogenet Evol 2021; 161:107159. [PMID: 33794394 DOI: 10.1016/j.ympev.2021.107159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022]
Abstract
In the Brazilian Atlantic Forest (AF), many terrestrial species with broad geographical distributions show high diversity and endemism of intraspecific lineages, as revealed by molecular genetic data. This pattern, however, is less explored in freshwater fishes. Gymnotus pantherinus is an electric fish endemic to the Brazilian coastal drainages that shows a wide distribution, ranging from the states of Bahia to Santa Catarina, an unusual pattern for AF fishes. It has been hypothesized that G. pantherinus is a species complex because distinct morphotypes were described for the species based on morphometric and meristic features. We used mitochondrial and nuclear data to test this hypothesis. Based on phylogenetic inference and multi-locus, multispecies coalescent methods, we identified six independent lineages, flagging them as candidate species. One such lineage is the recently described species G. refugio that is nested within G. pantherinus and renders it paraphyletic, showing it is a species complex. We named G. pantherinus stricto sensu the lineage that includes samples from the type locality (Santos, SP). Our results show that genetic lineages correspond only partially and far exceed the number of previously reported morphotypes. Genetic breaks in the group correspond to landscape features associated with the Serra do Mar mountain range and with riverine dynamics caused by sea level changes during the last glacial maximum. Moreover, we found evidence of river capture events affecting phylogeographic structure in the group. We uncovered an important dimension of diversity in the group and encourage further integration of genetic and phenotypic data. Such integration is a fruitful approach not only to reduce the gap between taxonomy and evolutionary history in Gymnotidae, but also to uncover the real AF biodiversity.
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Affiliation(s)
- Sabrina Baroni
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.
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7
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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8
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Freitas TMB, Sales JBL, Sampaio I, Piorski NM, Weber LN. Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers. BRAZ J BIOL 2020; 81:855-866. [PMID: 33111926 DOI: 10.1590/1519-6984.225646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 05/04/2020] [Indexed: 11/22/2022] Open
Abstract
The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.
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Affiliation(s)
- T M B Freitas
- Universidade Federal do Maranhão - UFMA, Departamento de Biologia, Laboratório de Ecologia e Sistemática de Peixes, Programa de Pós-graduação Bionorte, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, São Luís, MA, Brasil
| | - J B L Sales
- Universidade Federal do Pará - UFPA, Centro de Estudos Avançados da Biodiversidade - CEABIO, Programa de Pós-graduação em Ecologia Aquática e Pesca - PPGEAP, Grupo de Investigação Biológica Integrada - GIBI, Belém, PA, Brasil
| | - I Sampaio
- Universidade Federal do Pará - UFPA, Instituto de Estudos Costeiros - IECOS, Laboratório e Filogenomica e Bioinformatica, Programa de Pós-graduação Biologia Ambiental - PPBA, Grupo de Estudos em Genética e Filogenômica, Bragança, PA, Brasil
| | - N M Piorski
- Universidade Federal do Maranhão - UFMA, Departamento de Biologia, Laboratório de Ecologia e Sistemática de Peixes, Programa de Pós-graduação Bionorte, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, São Luís, MA, Brasil
| | - L N Weber
- Universidade Federal do Sul da Bahia - UFSB, Centro de Formação em Ciências Ambientais, Instituto Sosígenes Costa de Humanidades, Artes e Ciências, Departamento de Ciências Biológicas, Laboratório de Zoologia, Programa de Pós-graduação Bionorte, Grupo Biodiversidade da Fauna do Sul da Bahia, Porto Seguro, BA, Brasil
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9
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Keating SE, Griffing AH, Nielsen SV, Scantlebury DP, Gamble T. Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (
Aristelliger
: Sphaerodactylidae). J Evol Biol 2020; 33:1316-1326. [DOI: 10.1111/jeb.13682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 01/04/2023]
Affiliation(s)
| | - Aaron H. Griffing
- Department of Biological Sciences Marquette University Milwaukee WI USA
| | - Stuart V. Nielsen
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Florida Museum of Natural HistoryUniversity of Florida Gainesville FL USA
| | | | - Tony Gamble
- Department of Biological Sciences Marquette University Milwaukee WI USA
- Milwaukee Public Museum Milwaukee WI USA
- Bell Museum of Natural HistoryUniversity of Minnesota Saint Paul MN USA
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10
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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11
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Ramírez-Reyes T, Blair C, Flores-Villela O, Piñero D, Lathrop A, Murphy R. Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico. Mol Phylogenet Evol 2020; 150:106880. [PMID: 32512192 DOI: 10.1016/j.ympev.2020.106880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.
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Affiliation(s)
- Tonatiuh Ramírez-Reyes
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510 Ciudad de México, Mexico; Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico; Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico.
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA; Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico
| | - Amy Lathrop
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada
| | - Robert Murphy
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
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12
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Torres-Carvajal O, Hinojosa KC. Hidden diversity in two widespread snake species (Serpentes: Xenodontini: Erythrolamprus) from South America. Mol Phylogenet Evol 2020; 146:106772. [PMID: 32087331 DOI: 10.1016/j.ympev.2020.106772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
The spatial distribution of genetic diversity of widely distributed Neotropical tetrapods has been an active research field during the last decade, although it has focused on lowland (mostly Amazonian) taxa. In this paper we use phylogenetic analyses to explore the diversity within two widely distributed snake species, Erythrolamprus epinephelus and E. reginae. Specifically, we focus on Andean populations of the former and lowland samples of the latter. Our results show that Erythrolamprus epinephelus is paraphyletic and support recognition of the subspecies albiventris, fraseri and lamonae as distinct species. Regarding E. reginae, our results are in conflict with recent taxonomic proposals in that (1) E. reginae is paraphyletic, and (2) E. zweifeli from Trinidad and E. reginae from Amazonian Ecuador are not reciprocally monophyletic. Finally, we recommend caution when proposing taxonomic changes based on incomplete geographic and/or character sampling of widespread Neotropical taxa.
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Affiliation(s)
- Omar Torres-Carvajal
- Museo de Zoología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador.
| | - Katherin C Hinojosa
- Museo de Zoología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Avenida 12 de Octubre y Roca, Apartado 17-01-2184, Quito, Ecuador
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13
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Local adaptation fuels cryptic speciation in terrestrial annelids. Mol Phylogenet Evol 2020; 146:106767. [PMID: 32081763 DOI: 10.1016/j.ympev.2020.106767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/13/2020] [Indexed: 11/23/2022]
Abstract
Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between 17 populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.
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14
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A phylogenetic and biogeographic study of Rafflesia (Rafflesiaceae) in the Philippines: Limited dispersal and high island endemism. Mol Phylogenet Evol 2019; 139:106555. [DOI: 10.1016/j.ympev.2019.106555] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 01/12/2023]
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15
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Evidence for cryptic diversification in a rupicolous forest-dwelling gecko (Gekkonidae: Afroedura pondolia) from a biodiversity hotspot. Mol Phylogenet Evol 2019; 139:106549. [DOI: 10.1016/j.ympev.2019.106549] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
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16
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Pinto BJ, Titus-McQuillan J, Daza JD, Gamble T. Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos. J Hered 2019; 110:523-534. [PMID: 30859222 DOI: 10.1093/jhered/esz015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, WI
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN.,Milwaukee Public Museum, Milwaukee, WI
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17
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Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
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Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Life Science, Jilin Agricultural University, Changchun, China.
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18
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Russell AP, Stark AY, Higham TE. The Integrative Biology of Gecko Adhesion: Historical Review, Current Understanding, and Grand Challenges. Integr Comp Biol 2019; 59:101-116. [DOI: 10.1093/icb/icz032] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Geckos are remarkable in their ability to reversibly adhere to smooth vertical, and even inverted surfaces. However, unraveling the precise mechanisms by which geckos do this has been a long process, involving various approaches over the last two centuries. Our understanding of the principles by which gecko adhesion operates has advanced rapidly over the past 20 years and, with this knowledge, material scientists have attempted to mimic the system to create artificial adhesives. From a biological perspective, recent studies have examined the diversity in morphology, performance, and real-world use of the adhesive apparatus. However, the lack of multidisciplinarity is likely a key roadblock to gaining new insights. Our goals in this paper are to 1) present a historical review of gecko adhesion research, 2) discuss the mechanisms and morphology of the adhesive apparatus, 3) discuss the origin and performance of the system in real-world contexts, 4) discuss advancement in bio-inspired design, and 5) present grand challenges in gecko adhesion research. To continue to improve our understanding, and to more effectively employ the principles of gecko adhesion for human applications, greater intensity and scope of interdisciplinary research are necessary.
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Affiliation(s)
- Anthony P Russell
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Alyssa Y Stark
- Department of Biology, Villanova University, Villanova, PA 19085, USA
| | - Timothy E Higham
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA 92521, USA
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19
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Higham TE, Russell AP, Niewiarowski PH, Wright A, Speck T. The Ecomechanics of Gecko Adhesion: Natural Surface Topography, Evolution, and Biomimetics. Integr Comp Biol 2019; 59:148-167. [DOI: 10.1093/icb/icz013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
The study of gecko adhesion is necessarily interdisciplinary due to the hierarchical nature of the adhesive system and the complexity of interactions between the animals and their habitats. In nature, geckos move on a wide range of surfaces including soft sand dunes, trees, and rocks, but much of the research over the past two decades has focused on their adhesive performance on artificial surfaces. Exploring the complex interactions between geckos and their natural habitats will reveal aspects of the adhesive system that can be applied to biomimetic research, such as the factors that facilitate movement on dirty and rough surfaces with varying microtopography. Additionally, contrasting suites of constraints and topographies are found on rocks and plants, likely driving differences in locomotion and morphology. Our overarching goals are to bring to light several aspects of ecology that are important for gecko–habitat interactions, and to propose a framework for how they can inspire material scientists and functional ecologists. We also present new data on surface roughness and topography of a variety of surfaces, and adhesive performance of Phelsuma geckos on surfaces of varying roughness. We address the following key questions: (1) why and how should ecology be incorporated into the study of gecko adhesion? (2) What topographical features of rocks and plants likely drive adhesive performance? (3) How can ecological studies inform material science research? Recent advances in surface replication techniques that eliminate confounding factors among surface types facilitate the ability to address some of these questions. We pinpoint gaps in our understanding and identify key initiatives that should be adopted as we move forward. Most importantly, fine details of locomotor microhabitat use of both diurnal and nocturnal geckos are needed.
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Affiliation(s)
- Timothy E Higham
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92506, USA
| | - Anthony P Russell
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Peter H Niewiarowski
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, USA
| | - Amber Wright
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Thomas Speck
- Plant Biomechanics Group and Botanic Garden, University of Freiburg, 79085 Freiburg, Germany
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