1
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Brunetti AE, Lyra ML, Monteiro JPC, Zurano JP, Baldo D, Haddad CFB, Moeller AH. Convergence of gut microbiota in myrmecophagous amphibians. Proc Biol Sci 2023; 290:20232223. [PMID: 37964521 PMCID: PMC10646458 DOI: 10.1098/rspb.2023.2223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023] Open
Abstract
The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.
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Affiliation(s)
- Andrés E. Brunetti
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Juliane P. C. Monteiro
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Juan P. Zurano
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Puerto Iguazú, Misiones 3370, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones 3300, Argentina
| | - Celio F. B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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2
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Brunetti AE, Lyra ML, Bauermeister A, Bunk B, Boedeker C, Müsken M, Neto FC, Mendonça JN, Caraballo-Rodríguez AM, Melo WG, Pupo MT, Haddad CF, Cabrera GM, Overmann J, Lopes NP. Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome. iScience 2023; 26:108109. [PMID: 37867936 PMCID: PMC10587524 DOI: 10.1016/j.isci.2023.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/23/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023] Open
Abstract
The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.
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Affiliation(s)
- Andrés E. Brunetti
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones N3300LQH, Argentina
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745 Jena, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates
| | - Anelize Bauermeister
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Christian Boedeker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Niedersachsen, Germany
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Jacqueline Nakau Mendonça
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weilan G.P. Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Mônica T. Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Célio F.B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Gabriela M. Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos aplicados a la Química Orgánica (UMYMFOR), Buenos Aires C1428EGA, Argentina
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Norberto P. Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
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3
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Becker CG, Greenspan SE, Martins RA, Lyra ML, Prist P, Metzger JP, São Pedro V, Haddad CFB, Le Sage EH, Woodhams DC, Savage AE. Habitat split as a driver of disease in amphibians. Biol Rev Camb Philos Soc 2023; 98:727-746. [PMID: 36598050 DOI: 10.1111/brv.12927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]
Abstract
Anthropogenic habitat disturbance is fundamentally altering patterns of disease transmission and immunity across the vertebrate tree of life. Most studies linking anthropogenic habitat change and disease focus on habitat loss and fragmentation, but these processes often lead to a third process that is equally important: habitat split. Defined as spatial separation between the multiple classes of natural habitat that many vertebrate species require to complete their life cycles, habitat split has been linked to population declines in vertebrates, e.g. amphibians breeding in lowland aquatic habitats and overwintering in fragments of upland terrestrial vegetation. Here, we link habitat split to enhanced disease risk in amphibians (i) by reviewing the biotic and abiotic forces shaping elements of immunity and (ii) through a spatially oriented field study focused on tropical frogs. We propose a framework to investigate mechanisms by which habitat split influences disease risk in amphibians, focusing on three broad host factors linked to immunity: (i) composition of symbiotic microbial communities, (ii) immunogenetic variation, and (iii) stress hormone levels. Our review highlights the potential for habitat split to contribute to host-associated microbiome dysbiosis, reductions in immunogenetic repertoire, and chronic stress, that often facilitate pathogenic infections and disease in amphibians and other classes of vertebrates. We highlight that targeted habitat-restoration strategies aiming to connect multiple classes of natural habitats (e.g. terrestrial-freshwater, terrestrial-marine, marine-freshwater) could enhance priming of the vertebrate immune system through repeated low-load exposure to enzootic pathogens and reduced stress-induced immunosuppression.
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Affiliation(s)
- C Guilherme Becker
- Department of Biology, The Pennsylvania State University, 208 Curtin Road, University Park, PA, 16802, USA
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Renato A Martins
- Programa de Pós-graduação em Conservação da Fauna, Universidade Federal de São Carlos, Rodovia Washington Luís, km 235, São Carlos, 13565-905, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Avenida 24 A, 1515, C.P. 199, Rio Claro, SP, 13506-900, Brazil.,New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Paula Prist
- EcoHealth Aliance, 520 Eighth Avenue, Suite 1200, New York, NY, 10018, USA
| | - Jean Paul Metzger
- Departamento do Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 321, trav. 14, São Paulo, SP, 05508-090, Brazil
| | - Vinicius São Pedro
- Centro de Ciências da Natureza, Universidade Federal de São Carlos, campus Lagoa do Sino, Rodovia Lauri Simões de Barros, km 12, Buri, SP, 18290-000, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Avenida 24 A, 1515, C.P. 199, Rio Claro, SP, 13506-900, Brazil
| | - Emily H Le Sage
- Vanderbilt University Medical Center, Vanderbilt University, 1211 Medical Center Drive, Nashville, TN, 37232, USA
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA.,Smithsonian Tropical Research Institute, Roosevelt Avenue, Tupper Building - 401, 0843-03092, Panamá, Panama
| | - Anna E Savage
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL, 32816, USA
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4
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Carvalho TR, Fouquet A, Lyra ML, Giaretta AA, Costa-Campos CE, Rodrigues MT, Haddad CFB, Ron SR. Species diversity and systematics of the Leptodactylus melanonotus group (Anura, Leptodactylidae): review of diagnostic traits and a new species from the Eastern Guiana Shield. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2089269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Thiago R. Carvalho
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Mariana L. Lyra
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Ariovaldo A. Giaretta
- Laboratório de Taxonomia e Evolução de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | - C. Eduardo Costa-Campos
- Laboratório de Herpetologia, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, AP, Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Célio F. B. Haddad
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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5
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Greenspan SE, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J, Becker CG. Low microbiome diversity in threatened amphibians from two biodiversity hotspots. Anim Microbiome 2022; 4:69. [PMID: 36582011 PMCID: PMC9801548 DOI: 10.1186/s42523-022-00220-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.
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Affiliation(s)
- Sasha E. Greenspan
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Pedro Peloso
- grid.452671.30000 0001 2175 1274Programa de Pós Gradução em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, Pará 66077-530 Brazil ,Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Jesualdo A. Fuentes-González
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - Molly Bletz
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Mariana L. Lyra
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Ibere F. Machado
- Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Renato A. Martins
- grid.411247.50000 0001 2163 588XPrograma de Pós-Graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 Brazil
| | - Daniel Medina
- Sistema Nacional de Investigación, SENACYT; City of Knowledge, Clayton, Panama, Republic of Panama ,grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
| | - Diego Moura-Campos
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil ,grid.1001.00000 0001 2180 7477Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Wesley J. Neely
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Jackson Preuss
- grid.412292.e0000 0004 0417 7532Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel Do Oeste, Santa Catarina 89900-000 Brazil
| | - Marcelo J. Sturaro
- grid.411249.b0000 0001 0514 7202Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo 09972-270 Brazil
| | - Renata I. Vaz
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Carlos A. Navas
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Luís Felipe Toledo
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil
| | - Alexandro M. Tozetti
- grid.412302.60000 0001 1882 7290Programa de Pos-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, Rio Grande Do Sul 93022-750 Brazil
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Brunswick, Germany
| | - Douglas C. Woodhams
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Célio F. B. Haddad
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Jason Pienaar
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - C. Guilherme Becker
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
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6
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Andrade P, Lyra ML, Zina J, Bastos DFO, Brunetti AE, Baêta D, Afonso S, Brunes TO, Taucce PPG, Carneiro M, Haddad CFB, Sequeira F. Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana. G3 (Bethesda) 2022; 12:jkac270. [PMID: 36205610 PMCID: PMC9713437 DOI: 10.1093/g3journal/jkac270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022]
Abstract
Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Juliana Zina
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Deivson F O Bastos
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, Brazil
| | - Andrés E Brunetti
- Laboratory of Evolutionary Genetics, Institute of Subtropical Biology, National University of Misiones (UNaM-CONICET) Posadas N3300LQH, Misiones, Argentina
| | - Délio Baêta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Tuliana O Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Pedro P G Taucce
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão 4485-661, Portugal
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7
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Novaes-e-Fagundes G, Lyra ML, Loredam VSA, Carvalho TR, Haddad CFB, Rodrigues MT, Baldo D, Barrasso DA, Loebmann D, Ávila RW, Brusquetti F, Prudente ALC, Wheeler WC, Goyannes Dill Orrico V, Peloso P. A tale of two bellies: systematics of the oval frogs (Anura: Microhylidae: Elachistocleis Parker, 1927). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.
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Affiliation(s)
- Gabriel Novaes-e-Fagundes
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Vinicius S A Loredam
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Thiago R Carvalho
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Célio F B Haddad
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo , São Paulo , Brazil
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical `Claudio Juan Bidau’ (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones , Posadas, Misiones , Argentina
| | - Diego A Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Puerto Madryn, Chubut , Argentina
- Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia `San Juan Bosco’ , Puerto Madryn, Chubut , Argentina
| | - Daniel Loebmann
- Laboratório de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande , Rio Grande, Rio Grande do Sul , Brazil
| | - Robson W Ávila
- Departamento de Biologia, Núcleo Regional de Ofiologia da UFC, Universidade Federal do Ceará , Fortaleza, Ceará , Brazil
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay , Del Escudo, Asunción , Paraguay
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History , New York, NY , USA
| | - Victor Goyannes Dill Orrico
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Pedro Peloso
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
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8
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Rocha FP, Ronque MUV, Lyra ML, Bacci M, Oliveira PS. Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants. Microb Ecol 2022:10.1007/s00248-022-02064-y. [PMID: 35802173 DOI: 10.1007/s00248-022-02064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.
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Affiliation(s)
- Felipe P Rocha
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
- The University of Hong Kong, Pokfulam Road, Hong Kong Island, SAR, Hong Kong
| | - Mariane U V Ronque
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
- Universidade Estadual do Norte do Paraná, Ciências Biológicas, Cornélio Procópio, PR, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista - Campus Rio Claro, Rio Claro, SP, 13506-900, Brazil
- New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista - Campus Rio Claro, Rio Claro, SP, 13506-900, Brazil
| | - Paulo S Oliveira
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil.
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9
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Martins RA, Greenspan SE, Medina D, Buttimer S, Marshall VM, Neely WJ, Siomko S, Lyra ML, Haddad CFB, São-Pedro V, Becker CG. Signatures of functional bacteriome structure in a tropical direct-developing amphibian species. Anim Microbiome 2022; 4:40. [PMID: 35672870 PMCID: PMC9172097 DOI: 10.1186/s42523-022-00188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.
Results
Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.
Conclusions
Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.
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10
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de Araújo CB, de Oliveira EJL, Lyra ML, Mirantsev LV, de Oliveira IN. Formation of topological defects in nematic shells with a dumbbell-like shape. Soft Matter 2022; 18:4189-4196. [PMID: 35605981 DOI: 10.1039/d2sm00378c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The present study investigates dumbbell-shaped nematic liquid crystal shells. Using molecular dynamics (MD) simulations, we consider the effects of an external electric field on nematic ordering by computing the average molecular alignment's time evolution and equilibrium configuration. We show that the number and location of topological defects are strongly affected by the external field, with the orientational ordering's equilibrium configuration depending on field direction about the shell's long axis. For a transverse external field, it is verified that the defect rearrangement presents a non-linear dynamics, with a field independent characteristic time scale delimiting the short and long time regimes. Effects associated with varying the shell's Gaussian curvature are also analyzed.
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Affiliation(s)
- C B de Araújo
- Instituto de Física, Universidade Federal de Alagoas, Maceió, AL, Brazil.
| | - E J L de Oliveira
- Instituto de Física, Universidade Federal de Alagoas, Maceió, AL, Brazil.
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, Maceió, AL, Brazil.
| | - L V Mirantsev
- Institute for Problems of Mechanical Engineering, Russian Academy of Sciences, St. Petersburg, Russia
| | - I N de Oliveira
- Instituto de Física, Universidade Federal de Alagoas, Maceió, AL, Brazil.
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11
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Sinai N, Glos J, Mohan AV, Lyra ML, Riepe M, Thöle E, Zummach C, Ruthsatz K. Developmental plasticity in amphibian larvae across the world: Investigating the roles of temperature and latitude. J Therm Biol 2022; 106:103233. [DOI: 10.1016/j.jtherbio.2022.103233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/23/2022] [Accepted: 03/26/2022] [Indexed: 01/04/2023]
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12
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de Sá FP, Condez TH, Lyra ML, Haddad CFB, Malagoli LR. Unveiling the diversity of Giant Neotropical Torrent frogs (Hylodidae): phylogenetic relationships, morphology, and the description of two new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2039318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fábio P. de Sá
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-862, São Paulo, Brazil
- Laboratório de Herpetologia, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | | | - Mariana L. Lyra
- Laboratório de Herpetologia, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | - Célio F. B. Haddad
- Laboratório de Herpetologia, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
| | - Leo R. Malagoli
- Laboratório de Herpetologia, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, 13506-900, São Paulo, Brazil
- Núcleo São Sebastião, Parque Estadual da Serra do Mar, Fundação para a Conservação e a Produção Florestal do Estado de São Paulo, São Sebastião, 11600-000, São Paulo, Brazil
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13
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Brunetti AE, Bunk B, Lyra ML, Fuzo CA, Marani MM, Spröer C, Haddad CFB, Lopes NP, Overmann J. Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing. ISME J 2022; 16:788-800. [PMID: 34601502 PMCID: PMC8857215 DOI: 10.1038/s41396-021-01121-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023]
Abstract
The molecular bases for the symbiosis of the amphibian skin microbiome with its host are poorly understood. Here, we used the odor-producer Pseudomonas sp. MPFS and the treefrog Boana prasina as a model to explore bacterial genome determinants and the resulting mechanisms facilitating symbiosis. Pseudomonas sp. MPFS and its closest relatives, within a new clade of the P. fluoresens Group, have large genomes and were isolated from fishes and plants, suggesting environmental plasticity. We annotated 16 biosynthetic gene clusters from the complete genome sequence of this strain, including those encoding the synthesis of compounds with known antifungal activity and of odorous methoxypyrazines that likely mediate sexual interactions in Boana prasina. Comparative genomics of Pseudomonas also revealed that Pseudomonas sp. MPFS and its closest relatives have acquired specific resistance mechanisms against host antimicrobial peptides (AMPs), specifically two extra copies of a multidrug efflux pump and the same two-component regulatory systems known to trigger adaptive resistance to AMPs in P. aeruginosa. Subsequent molecular modeling indicated that these regulatory systems interact with an AMP identified in Boana prasina through the highly acidic surfaces of the proteins comprising their sensory domains. In agreement with a symbiotic relationship and a highly selective antibacterial function, this AMP did not inhibit the growth of Pseudomonas sp. MPFS but inhibited the growth of another Pseudomonas species and Escherichia coli in laboratory tests. This study provides deeper insights into the molecular interaction of the bacteria-amphibian symbiosis and highlights the role of specific adaptive resistance toward AMPs of the hosts.
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Affiliation(s)
- Andrés E. Brunetti
- grid.11899.380000 0004 1937 0722Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, SP Brazil ,grid.412223.40000 0001 2179 8144Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET – UNaM), Facultad de Ciencias Exactas, Universidad Nacional de Misiones, N3300 Posadas, Argentina
| | - Boyke Bunk
- grid.420081.f0000 0000 9247 8466Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Mariana L. Lyra
- grid.410543.70000 0001 2188 478XDepartamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, SP Brazil
| | - Carlos A. Fuzo
- grid.11899.380000 0004 1937 0722Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, SP Brazil
| | - Mariela M. Marani
- grid.423606.50000 0001 1945 2152IPEEC-CONICET, Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas, U9120ACD Puerto Madryn, Argentina
| | - Cathrin Spröer
- grid.420081.f0000 0000 9247 8466Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Célio F. B. Haddad
- grid.410543.70000 0001 2188 478XDepartamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, SP Brazil
| | - Norberto P. Lopes
- grid.11899.380000 0004 1937 0722Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, SP Brazil
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany. .,Mikrobiologie, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
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14
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Magalhães FDM, Camurugi F, Lyra ML, Baldo D, Gehara M, Haddad CFB, Garda AA. Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex. Mol Phylogenet Evol 2022; 169:107398. [PMID: 35031468 DOI: 10.1016/j.ympev.2022.107398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/31/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022]
Abstract
Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.
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Affiliation(s)
- Felipe de M Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba-UFPB, Centro de Ciências Exatas e da Natureza, Cidade Universitária, 58000-000 João Pessoa, Paraiba, Brazil; Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark 195 University Ave, Newark, NJ 07102, USA.
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Cx. Postal 199, 13506-900 Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, Félix de Azara 1552, CPA N3300LQF Posadas, Misiones, Argentina
| | - Marcelo Gehara
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark 195 University Ave, Newark, NJ 07102, USA
| | - Célio F B Haddad
- Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Cx. Postal 199, 13506-900 Rio Claro, São Paulo, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis (LAR), Departamento de Botânica e Zoologia da Universidade Federal do Rio Grande do Norte, Campus Universitário. Lagoa Nova, 59078-900 Natal, Rio Grande do Norte, Brazil
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15
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Haddad CF, Lopes CM, Becker CG, da Silva FR, Lyra ML. From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil. Biota Neotrop 2022. [DOI: 10.1590/1676-0611-bn-2022-1375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract Here, we summarize examples of significant advances in amphibian research supported by the São Paulo Research Foundation (FAPESP), focusing on recent discoveries in the fields of community ecology, habitat change, infection diseases, and multipurpose DNA sequencing. We demonstrated that FAPESP has been fundamental not only by directly funding research projects and scholarships, but also through its science training policy, fostering international collaborations with world-class research institutions, improving and consolidating new lines of research that often depended on a synergetic combination of different knowledge and complex tools. We emphasized that future studies will continue to focus on basic questions, such as description of new species, as well as taxonomic and systematic corrections. Furthermore, we also expect that there will be a strong integration among different disciplines using novel bioinformatics tools and modeling approaches, such as machine learning. These new approaches will be critical to further develop our understanding of foundational questions of amphibian life-history trait variation, disease transmission, community assembly, biogeography, and population forecasts under different global change scenarios such as agricultural expansion, agrochemical use, habitat loss, and climate change.
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16
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Falcão PRN, Buarque ARC, Dias WS, Almeida GMA, Lyra ML. Universal dynamical scaling laws in three-state quantum walks. Phys Rev E 2021; 104:054106. [PMID: 34942820 DOI: 10.1103/physreve.104.054106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]
Abstract
We perform a finite-time scaling analysis over the detrapping point of a three-state quantum walk on the line. The coin operator is parametrized by ρ that controls the wave packet spreading velocity. The input state prepared at the origin is set as a symmetric linear combination of two eigenstates of the coin operator with a characteristic mixing angle θ, one of them being the component that results in full spreading occurring at θ_{c}(ρ) for which no fraction of the wave packet remains trapped near the initial position. We show that relevant quantities, such as the survival probability and the participation ratio assume single parameter scaling forms at the vicinity of the detrapping angle θ_{c}. In particular, we show that the participation ratio grows linearly in time with a logarithmic correction, thus, shedding light on previous reports of sublinear behavior.
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Affiliation(s)
- P R N Falcão
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, Alagoas, Brazil
| | - A R C Buarque
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, Alagoas, Brazil
| | - W S Dias
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, Alagoas, Brazil
| | - G M A Almeida
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, Alagoas, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, Alagoas, Brazil
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17
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Lyra ML, Monteiro JPC, Rancilhac L, Irisarri I, Künzel S, Sanchez E, Condez TH, Rojas-Padilla O, Solé M, Toledo LF, Haddad CFB, Vences M. Initial Phylotranscriptomic Confirmation of Homoplastic Evolution of the Conspicuous Coloration and Bufoniform Morphology of Pumpkin-Toadlets in the Genus Brachycephalus. Toxins (Basel) 2021; 13:816. [PMID: 34822600 PMCID: PMC8620806 DOI: 10.3390/toxins13110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
The genus Brachycephalus is a fascinating group of miniaturized anurans from the Brazilian Atlantic Forest, comprising the conspicuous, brightly colored pumpkin-toadlets and the cryptic flea-toads. Pumpkin-toadlets are known to contain tetrodotoxins and therefore, their bright colors may perform an aposematic function. Previous studies based on a limited number of mitochondrial and nuclear-encoded markers supported the existence of two clades containing species of pumpkin-toadlet phenotype, but deep nodes remained largely unresolved or conflicting between data sets. We use new RNAseq data of 17 individuals from nine Brachycephalus species to infer their evolutionary relationships from a phylogenomic perspective. Analyses of almost 5300 nuclear-encoded ortholog protein-coding genes and full mitochondrial genomes confirmed the existence of two separate pumpkin-toadlet clades, suggesting the convergent evolution (or multiple reversals) of the bufoniform morphology, conspicuous coloration, and probably toxicity. In addition, the study of the mitochondrial gene order revealed that three species (B. hermogenesi, B. pitanga, and B. rotenbergae) display translocations of different tRNAs (NCY and CYA) from the WANCY tRNA cluster to a position between the genes ATP6 and COIII, showing a new mitochondrial gene order arrangement for vertebrates. The newly clarified phylogeny suggests that Brachycephalus has the potential to become a promising model taxon to understand the evolution of coloration, body plan and toxicity. Given that toxicity information is available for only few species of Brachycephalus, without data for any flea-toad species, we also emphasize the need for a wider screening of toxicity across species, together with more in-depth functional and ecological study of their phenotypes.
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Affiliation(s)
- Mariana L. Lyra
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Juliane P. C. Monteiro
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Iker Irisarri
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goldschmidtstr, 1, 37077 Göttingen, Germany;
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
| | - Eugenia Sanchez
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Thais H. Condez
- Unidade Passos, Universidade do Estado de Minas Gerais (UEMG), Avenida Juca Stockler 1130, Passos 37900-106, MG, Brazil;
| | - Omar Rojas-Padilla
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, Porto Alegre 90619-900, RS, Brazil;
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, SP, Brazil;
| | - Célio F. B. Haddad
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
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18
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Gippner S, Travers SL, Scherz MD, Colston TJ, Lyra ML, Mohan AV, Multzsch M, Nielsen SV, Rancilhac L, Glaw F, Bauer AM, Vences M. A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation. Mol Phylogenet Evol 2021; 165:107311. [PMID: 34530117 DOI: 10.1016/j.ympev.2021.107311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/22/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.
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Affiliation(s)
- Sven Gippner
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany; State Natural History Museum of Braunschweig, Pockelsstr. 10, 38106 Braunschweig, Germany
| | - Scott L Travers
- Department of Biological Sciences, Rutgers University-Newark, 195 University Avenue, Newark, NJ 07102, USA
| | - Mark D Scherz
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Timothy J Colston
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP CEP13506-900, Brazil
| | - Ashwini V Mohan
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Malte Multzsch
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Stuart V Nielsen
- Santa Fe College, 3000 NW 83rd St., Gainesville, FL 32606, USA; Florida Museum of Natural History, Division of Herpetology, 1659 Museum Road - Dickinson Hall, Gainesville, FL 32611, USA
| | - Loïs Rancilhac
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Miguel Vences
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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19
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Blotto BL, Lyra ML, Cardoso MCS, Trefaut Rodrigues M, R Dias I, Marciano-Jr E, Dal Vechio F, Orrico VGD, Brandão RA, Lopes de Assis C, Lantyer-Silva ASF, Rutherford MG, Gagliardi-Urrutia G, Solé M, Baldo D, Nunes I, Cajade R, Torres A, Grant T, Jungfer KH, da Silva HR, Haddad CFB, Faivovich J. The phylogeny of the Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini). Cladistics 2021; 37:36-72. [PMID: 34478174 DOI: 10.1111/cla.12409] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2019] [Indexed: 12/24/2022] Open
Abstract
The South American and West Indian Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present a phylogenetic analysis of this hylid tribe based on sequence fragments of up to five mitochondrial (12S, 16S, ND1, COI, Cytb) and six nuclear genes (POMC, RAG-1, RHOD, SIAH, TNS3, TYR). We included most of its species (> 96%), in addition to a number of new species. Our results indicate: (i) the paraphyly of Trachycephalus with respect to Aparasphenodon venezolanus; (ii) the nonmonophyly of Aparasphenodon, with Argenteohyla siemersi, Corythomantis galeata and Nyctimantis rugiceps nested within it, and Ap. venezolanus nested within Trachycephalus; (iii) the polyphyly of Corythomantis; (iv) the nonmonophyly of the recognized species groups of Phyllodytes; and (v) a pervasive low support for the deep relationships among the major clades of Lophyohylini, including C. greeningi and the monotypic genera Itapotihyla and Phytotriades. To remedy the nonmonophyly of Aparasphenodon, Corythomantis, and Trachycephalus, we redefined Nyctimantis to include Aparasphenodon (with the exception of Ap. venezolanus, which we transferred to Trachycephalus), Argenteohyla, and C. galeata. Additionally, our results indicate the need for taxonomic work in the following clades: (i) Trachycephalus dibernardoi and Tr. imitatrix; (ii) Tr. atlas, Tr. mambaiensis and Tr. nigromaculatus; and (iii) Phyllodytes. On the basis of our phylogenetic results, we analyzed the evolution of skull hyperossification and reproductive biology, with emphasis on the multiple independent origins of phytotelm breeding, in the context of Anura. We also analyzed the inter-related aspects of chemical defences, venom delivery, phragmotic behaviour, co-ossification, and prevention of evaporative water loss.
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Affiliation(s)
- Boris L Blotto
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Monica C S Cardoso
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, CEP 20940-040, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Iuri R Dias
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Euvaldo Marciano-Jr
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Francisco Dal Vechio
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Victor G D Orrico
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Reuber A Brandão
- Laboratório de Fauna e Unidades de Conservação, Departamento de Engenharia Florestal, Universidade de Brasília, 70910-900, Brasília, Distrito Federal, Brazil
| | - Clodoaldo Lopes de Assis
- Museu de Zoologia João Moojen, Departamento de Biologia Animal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Amanda S F Lantyer-Silva
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Mike G Rutherford
- Department of Life Sciences, The University of The West Indies Zoology Museum, The University of The West Indies, St. Augustine, Trinidad & Tobago
| | - Giussepe Gagliardi-Urrutia
- Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Prédio 40, sala 110, 90619-900, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mirco Solé
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP 45662-900, Ilhéus, Bahia, Brazil
| | - Diego Baldo
- Laboratorio de Genetica Evolutiva "Claudio Juan Bidau", Instituto de Biologıa Subtropical (CONICET-UNaM), Félix de Azara, 1552, CPA N3300LQF Posadas, Misiones, Argentina
| | - Ivan Nunes
- Laboratório de Herpetologia, Instituto de Biociências, Universidade Estadual Paulista, Campus do Litoral Paulista, CEP 11330-900, São Vicente, São Paulo, Brazil
| | - Rodrigo Cajade
- Laboratorio de Herpetología, Departamento de Biología, Facultad de Ciencias Exactas y Naturales y Agrimensura, CONICET, Universidad Nacional del Nordeste, Av. Libertad 5470, 3400, Corrientes, Argentina
| | - Ambrosio Torres
- Unidad Ejecutora Lillo, CONICET - Fundación Miguel Lillo, Miguel Lillo 251, 4000, San Miguel de Tucumán, Argentina
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, São Paulo, Brazil
| | - Karl-Heinz Jungfer
- Department of Biology, Institute of Integrated Sciences, University of Koblenz-Landau, Universitätsstr. 1, 56070, Koblenz, Germany
| | - Helio R da Silva
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Federal Rural do Rio de Janeiro, Caixa Postal 74524, 23851-970, Seropédica, Rio de Janeiro, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A 1515, 13506-900, Rio Claro, São Paulo, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Angel Gallardo 470, C1405DJR, Buenos Aires, Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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20
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Orrico VGD, Grant T, Faivovich J, Rivera-Correa M, Rada MA, Lyra ML, Cassini CS, Valdujo PH, Schargel WE, Machado DJ, Wheeler WC, Barrio-Amorós C, Loebmann D, Moravec J, Zina J, Solé M, Sturaro MJ, Peloso PLV, Suarez P, Haddad CFB. The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae). Cladistics 2021; 37:73-105. [PMID: 34478175 DOI: 10.1111/cla.12429] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 11/29/2022] Open
Abstract
The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.
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Affiliation(s)
- Victor G D Orrico
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, CEP 45662-900, Brazil
| | - Taran Grant
- Laboratório de Anfíbios, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, CEP 05508-090, Brazil
| | - Julian Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Angel Gallardo 470, Buenos Aires, C1405DJR, Argentina.,Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio Rivera-Correa
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Marco A Rada
- Laboratório de Anfíbios, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, CEP 05508-090, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Av. 24A 1515, Rio Claro, CEP 13506-900, Brazil
| | - Carla S Cassini
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, CEP 45662-900, Brazil
| | - Paula H Valdujo
- Laboratório de Ecologia da Paisagem - Superintendência de Conservação, WWF-Brasil, Entre Quadra SHIS EQL 6/8 Conjunto E, Setor de Habitações Individuais Sul, Brasília, CEP 71620-430, Brazil
| | - Walter E Schargel
- Department of Biology, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Denis J Machado
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC, 28223, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West, New York, NY, 10024, USA
| | | | - Daniel Loebmann
- Laboratório de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Av. Itália, km 8, Rio Grande, CEP 96.203-900, Brazil
| | - Jiří Moravec
- Department of Zoology, National Museum, Cirkusová 1740, 193 00 Prague 9, Prague, Czech Republic
| | - Juliana Zina
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Av. José Moreira Sobrinho, Jequié, CEP 45205-490, Brazil
| | - Mirco Solé
- Tropical Herpetology Laboratory, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, CEP 45662-900, Brazil
| | - Marcelo J Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Av. Professor Artur Riedel, 275, Jardim Eldorado, Diadema, CEP 09972-270, Brazil.,Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Avenida Perimetral 1901, Terra Firme, Belém, CEP 66017-970, Brazil
| | - Pedro L V Peloso
- Instituto de Ciências Biológicas, Universidade Federal do Pará, R. Augusto Corrêa, 1, Guamá, Belém, 66075-110, Brazil
| | - Pablo Suarez
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Bertoni 85, Puerto Iguazú, (3370), Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Av. 24A 1515, Rio Claro, CEP 13506-900, Brazil
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21
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Brunes TO, Lyra ML, Maldonado JA, Pellegrino KCM, Rodrigues MT, Fujita MK. The first mitochondrial genome of a South America parthenogenetic lizard (Squamata: Gymnophthalmidae). Mitochondrial DNA B Resour 2021; 6:2393-2395. [PMID: 34345705 PMCID: PMC8284125 DOI: 10.1080/23802359.2021.1951132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The mitogenome of the South American parthenogenetic lizard Loxopholis percarinatum Müller, 1923 (Squamata: Gymnophthalmidae), a uni-bisexual species complex, was recovered for three individuals from Rio Negro region, Amazonas, Brazil. The content and order of genes are typical for vertebrate mitochondrial genomes, and we recovered 13 protein-coding genes, 22 tRNA, and two rRNA (12S and 16S), in addition to partial fragments of the Control Region. A maximum likelihood phylogenetic analysis with mitogenomes of selected lizard families recovered L. percarinatum with Iphisa elegans Gray, 1851, the only other Gymnophthalmidae species available in GenBank.
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Affiliation(s)
- Tuliana O Brunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, Brazil
| | - José A Maldonado
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Katia C M Pellegrino
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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22
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Belasen AM, Riolo MA, Bletz MC, Lyra ML, Toledo LF, James TY. Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiota of Fragmented Brazilian Atlantic Forest Frog Populations. Ecol Evol 2021; 11:9293-9307. [PMID: 34306622 PMCID: PMC8293785 DOI: 10.1002/ece3.7594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/31/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). While bacterial alpha diversity varied by both site type and host MHC IIB genotype, microeukaryotic alpha diversity varied only by site type. However, bacteria and microeukaryote composition showed variation according to both site type and host MHC IIB genotype. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions may occur among domains. Lastly, anti-Bd bacteria were not broadly negatively co-associated with the fungal microbiome and were positively associated with potential amphibian parasites. Our findings emphasize the importance of considering both domains in microbiome research and suggest that for effective probiotic strategies for amphibian disease management, considering potential interactions among all members of the microbiome is crucial.
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Affiliation(s)
- Anat M. Belasen
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Maria A. Riolo
- Center for Complex SystemsUniversity of MichiganAnn ArborMIUSA
| | - Molly C. Bletz
- Department of BiologyUniversity of Massachusetts BostonBostonMAUSA
| | - Mariana L. Lyra
- Instituto de BiociênciasUniversidade Estadual PaulistaRio ClaroBrazil
| | - L. Felipe Toledo
- Laboratório de História Natural de Anfíbios BrasileirosDepartamento de Biologia AnimalInstituto de BiologiaUniversidade Estadual de CampinasCampinasBrazil
| | - Timothy Y. James
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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23
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Falcão PRN, Lyra ML. Asymmetric acoustic wave scattering by a nonreciprocal and position-dependent mass defect. J Phys Condens Matter 2021; 33:325402. [PMID: 34044370 DOI: 10.1088/1361-648x/ac05e6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
We investigate the asymmetric wave scattering in a phononic one-dimensional lattice with a nonreciprocal defect and position dependent masses coupled by the defect spring. The nonreciprocal interaction is characterized by a single parameter Δ while the nonlinear contribution due to position-dependent masses are controlled by a parameterχ. The transmission and reflection coefficients are analytically computed and the effects of the nonreciprocity and nonlinearity are detailed. We show that, in opposite with the linear case, the rectification factor has a frequency dependence, which leads to a more efficient diode-like action at large wavevectors. Further, the nonlinearity leads to an asymmetry of the reflected component, absent in the linear regime. We extend our analysis to a system with frictional forces which suppresses the multistability window promoted by the nonlinear mass contribution without compromising the rectification action.
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Affiliation(s)
- P R N Falcão
- Instituto de Física, Universidade Federal de Alagoas, 57072-900, Maceió-AL, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-900, Maceió-AL, Brazil
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24
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Rojas O, de Souza SM, Torrico J, Veríssimo LM, Pereira MSS, Lyra ML. Low-temperature pseudo-phase-transition in an extended Hubbard diamond chain. Phys Rev E 2021; 103:042123. [PMID: 34006009 DOI: 10.1103/physreve.103.042123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/25/2021] [Indexed: 11/07/2022]
Abstract
We consider the extended Hubbard diamond chain with an arbitrary number of particles driven by chemical potential. The interaction between dimer diamond chain and nodal couplings is considered in the atomic limit (no hopping), whereas the dimer interaction includes the hopping term. We demonstrate that this model exhibits a pseudo-transition effect in the low-temperature regime. Here, we explore the pseudo-transition rigorously by analyzing several physical quantities. The internal energy and entropy depict sudden, although continuous, jumps which closely resembles discontinuous or first-order phase-transition. At the same time, the correlation length and specific heat exhibit astonishing strong sharp peaks quite similar to a second-order phase-transition. We associate the ascending and descending parts of the peak with power-law "pseudo-critical" exponents. We determine the pseudo-critical exponents in the temperature range where these peaks are developed, namely, ν=1 for the correlation length and α=3 for the specific heat. We also study the behavior of the electron density and isothermal compressibility around the pseudo-critical temperature.
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Affiliation(s)
- Onofre Rojas
- Departamento de Física, Universidade Federal de Lavras, 37200-900 Lavras, Minas Gerais, Brazil
| | - S M de Souza
- Departamento de Física, Universidade Federal de Lavras, 37200-900 Lavras, Minas Gerais, Brazil
| | - Jordana Torrico
- Departamento de Física, Universidade Federal de Minas Gerais, Caixa Postale 702, 30123-970 Belo Horizonte, Minas Gerais, Brazil
| | - L M Veríssimo
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
| | - M S S Pereira
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
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Kirchhof S, Lyra ML, Rodríguez A, Ineich I, Müller J, Rödel MO, Trape JF, Vences M, Boissinot S. Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophile lizard genus Acanthodactylus. Sci Rep 2021; 11:4858. [PMID: 33649347 PMCID: PMC7921649 DOI: 10.1038/s41598-021-83422-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022] Open
Abstract
Climate has a large impact on diversity and evolution of the world's biota. The Eocene-Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene-Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them-and especially A. guineensis-as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene-Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.
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Affiliation(s)
- Sebastian Kirchhof
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates.
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP, CEP 13506-900, Brazil
| | - Ariel Rodríguez
- Institute of Zoology, University of Veterinary Medicine of Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Ivan Ineich
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, CP 30, 57 rue Cuvier, 75005, Paris, France
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jean-François Trape
- Laboratoire de Paludologie et Zoologie médicale, IRD, UMR MIVEGEC, B. P. 1386, Dakar, Senegal
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Stéphane Boissinot
- New York University Abu Dhabi, Abu Dhabi, Saadiyat Island, United Arab Emirates
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Gazoni T, Lyra ML, Ron SR, Strüssmann C, Baldo D, Narimatsu H, Pansonato A, Schneider RG, Giaretta AA, Haddad CF, Parise-Maltempi PP, Carvalho TR. Revisiting the systematics of the Leptodactylus melanonotus group (Anura: Leptodactylidae): Redescription of L. petersii and revalidation of its junior synonyms. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2020.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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28
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Ruthsatz K, Lyra ML, Lambertini C, Belasen AM, Jenkinson TS, da Silva Leite D, Becker CG, Haddad CFB, James TY, Zamudio KR, Toledo LF, Vences M. Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil's Atlantic Forest treefrogs. Sci Rep 2020; 10:22311. [PMID: 33339839 PMCID: PMC7749163 DOI: 10.1038/s41598-020-79130-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
In Brazil’s Atlantic Forest (AF) biodiversity conservation is of key importance since the fungal pathogen Batrachochytrium dendrobatidis (Bd) has led to the rapid loss of amphibian populations here and worldwide. The impact of Bd on amphibians is determined by the host's immune system, of which the skin microbiome is a critical component. The richness and diversity of such cutaneous bacterial communities are known to be shaped by abiotic factors which thus may indirectly modulate host susceptibility to Bd. This study aimed to contribute to understanding the environment-host–pathogen interaction determining skin bacterial communities in 819 treefrogs (Anura: Hylidae and Phyllomedusidae) from 71 species sampled across the AF. We investigated whether abiotic factors influence the bacterial community richness and structure on the amphibian skin. We further tested for an association between skin bacterial community structure and Bd co-occurrence. Our data revealed that temperature, precipitation, and elevation consistently correlate with richness and diversity of the skin microbiome and also predict Bd infection status. Surprisingly, our data suggest a weak but significant positive correlation of Bd infection intensity and bacterial richness. We highlight the prospect of future experimental studies on the impact of changing environmental conditions associated with global change on environment-host–pathogen interactions in the AF.
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Affiliation(s)
- Katharina Ruthsatz
- Institute of Zoology, Universität Hamburg, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany. .,Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Brunswick, Germany.
| | - Mariana L Lyra
- Laboratório de Herpetologia, Depto de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Carolina Lambertini
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Anat M Belasen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Thomas S Jenkinson
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, Davis, CA, USA
| | - Domingos da Silva Leite
- Laboratório de Antígenos Bacterianos II, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, São Paulo, CEP 13083-862, Brazil
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35847, USA
| | - Célio F B Haddad
- Laboratório de Herpetologia, Depto de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Brunswick, Germany
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29
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Magalhães FDM, Lyra ML, de Carvalho TR, Baldo D, Brusquetti F, Burella P, Colli GR, Gehara MC, Giaretta AA, Haddad CF, Langone JA, López JA, Napoli MF, Santana DJ, de Sá RO, Garda AA. Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae). Herpetological Monographs 2020. [DOI: 10.1655/0733-1347-31.4.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Felipe de M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
| | - Mariana L. Lyra
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Thiago R. de Carvalho
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, CP N3300LQF, Posadas, Misiones, Argentina
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay (IIBP), Del Escudo 1607, CP 1425 Asunción, Paraguay
| | - Pamela Burella
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília (UNB), CEP 70910-900, Brasília, Distrito Federal, Brazil
| | - Marcelo C. Gehara
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, 07102, USA
| | - Ariovaldo A. Giaretta
- Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN), Instituto de Ciências Exatas e Naturais do Pontal (ICENP), Universidade Federal de Uberlândia (UFU), Ituiutaba, Minas Gerais, Brazil
| | - Célio F.B. Haddad
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - José A. Langone
- Departamento de Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, CP 11.000, Montevideo, Uruguay
| | - Javier A. López
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Marcelo F. Napoli
- Laboratório de Taxonomia e História Natural de Anfíbios (AMPHIBIA), Museu de História Natural, Instituto de Biologia, Universidade Federal da Bahia (UFBA), CEP 40170–115, Salvador, Bahia, Brazil
| | - Diego J. Santana
- Mapinguari – Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul (UFMS), CEP 79002-970 Campo Grande, Mato Grosso, Brazil
| | - Rafael O. de Sá
- Department of Biology, University of Richmond, Richmond, Virginia, 23173, USA
| | - Adrian A. Garda
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
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30
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Santos FL, Almeida ML, Albuquerque EL, Macedo-Filho A, Lyra ML, Fulco UL. Critical properties of the SIS model on the clustered homophilic network. Physica A 2020; 559:125067. [PMID: 32834437 PMCID: PMC7427564 DOI: 10.1016/j.physa.2020.125067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The spreading of epidemics in complex networks has been a subject of renewed interest of several scientific branches. In this regard, we have focused our attention on the study of the susceptible-infected-susceptible (SIS) model, within a Monte Carlo numerical simulation approach, representing the spreading of epidemics in a clustered homophilic network. The competition between infection and recovery that drives the system either to an absorbing or to an active phase is analyzed. We estimate the static critical exponents β ∕ ν , 1 ∕ ν and γ ∕ ν , through finite-size scaling (FSS) analysis of the order parameter ρ and its fluctuations, showing that they differ from those associated with the contact process on a scale-free network, as well as those predicted by the heterogeneous mean-field theory.
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Affiliation(s)
- F L Santos
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - M L Almeida
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - E L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - A Macedo-Filho
- Universidade Estadual do Piauí, 64260-000, Piripiri-PI, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-900, Maceió-AL, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
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31
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Taboada C, Brunetti AE, Lyra ML, Fitak RR, Faigón Soverna A, Ron SR, Lagorio MG, Haddad CFB, Lopes NP, Johnsen S, Faivovich J, Chemes LB, Bari SE. Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin. Proc Natl Acad Sci U S A 2020; 117:18574-18581. [PMID: 32661155 PMCID: PMC7414155 DOI: 10.1073/pnas.2006771117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations-a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism-the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.
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Affiliation(s)
- Carlos Taboada
- Department of Biology, Duke University, Durham, NC 27708;
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
| | - Andrés E Brunetti
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
- Laboratorio de Genética Evolutiva "Claudio Juan Bidau," Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Universidad Nacional de Misiones, 3300 Posadas, Misiones, Argentina
| | - Mariana L Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, São Paulo, Brazil
| | - Robert R Fitak
- Department of Biology, Duke University, Durham, NC 27708
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816
| | - Ana Faigón Soverna
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Aptdo. 17-01-2184, Quito, Ecuador
| | - María G Lagorio
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, São Paulo, Brazil
| | - Norberto P Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
| | - Sönke Johnsen
- Department of Biology, Duke University, Durham, NC 27708
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
| | - Lucía B Chemes
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1405BWE, Argentina;
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Buenos Aires, Argentina
| | - Sara E Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina;
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32
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Anjos FCD, Lyra ML, Gléria I, Argolo C, de Souza AJF. Emerging extreme value and Fermi-Dirac distributions in the Lévy branching and annihilating process. Phys Rev E 2020; 101:052136. [PMID: 32575329 DOI: 10.1103/physreve.101.052136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 11/07/2022]
Abstract
We study the dynamics of the branching and annihilating process with long-range interactions. Static particles generate an offspring and annihilate upon contact. The branching distance is supposed to follow a Lévy-like power-law distribution with P(r)∝1/r^{α}. We analyze the long term behavior of the mean particles number and its fluctuations as a function of the parameter α that controls the range of the branching process. We show that the dynamic exponent associated with the particle number fluctuations varies continuously for α<4 while the particle number exponent only changes for α<3. A crossover from extreme value Frechet (at α=3) and Gumbell (for 2<α<3) distributions is developed, similar to the one reported in recent experiments with cw-pumped random fiber lasers presenting underlying gain and Lévy processes. We report the dependence of the relevant dynamical power-law exponents on α showing that explosive growth takes place for α≤2. Further, the average occupation number distribution is shown to evolve from the standard Fermi-Dirac form to the generalized one within the context of nonextensive statistics.
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Affiliation(s)
- F C Dos Anjos
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL, Brazil
| | - Iram Gléria
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL, Brazil
| | - C Argolo
- Instituto Federal de Ciência e Tecnologia do Estado de Alagoas, 57020-510 Maceió-AL, Brazil and Núcleo de Ciências Exatas - NCEx, Universidade Federal de Alagoas, 57309-005 Arapiraca-AL, Brazil
| | - Adauto J F de Souza
- Departamento de Física, Universidade Federal Rural de Pernambuco, 52171-900 Recife-PE, Brazil
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Ronque MUV, Lyra ML, Migliorini GH, Bacci M, Oliveira PS. Symbiotic bacterial communities in rainforest fungus-farming ants: evidence for species and colony specificity. Sci Rep 2020; 10:10172. [PMID: 32576863 PMCID: PMC7311517 DOI: 10.1038/s41598-020-66772-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 05/19/2020] [Indexed: 12/22/2022] Open
Abstract
Animals may host diverse bacterial communities that can markedly affect their behavioral physiology, ecology, and vulnerability to disease. Fungus-farming ants represent a classical example of mutualism that depends on symbiotic microorganisms. Unraveling the bacterial communities associated with fungus-farming ants is essential to understand the role of these microorganisms in the ant-fungus symbiosis. The bacterial community structure of five species of fungus-farmers (non-leaf-cutters; genera Mycocepurus, Mycetarotes, Mycetophylax, and Sericomyrmex) from three different environments in the Brazilian Atlantic rainforest (lowland forest, restinga forest, and sand dunes) was characterized with amplicon-based Illumina sequencing of 16 S ribosomal RNA gene. Possible differences in bacterial communities between ants internal to the nest (on the fungus garden) and external foragers were also investigated. Our results on the richness and diversity of associated bacteria provide novel evidence that these communities are host- and colony-specific in fungus-farming ants. Indeed, the bacterial communities associated with external foragers differ among the five species, and among colonies of the same species. Furthermore, bacterial communities from internal ants vs. foragers do not differ or differ only slightly within each ant species. This study highlights the importance of describing ant-associated bacterial communities to better understand this host-bacterial interaction in the social environment of insect colonies and provides the foundation for future studies on the ecological and evolutionary processes that drive the success of fungus-farming ants.
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Affiliation(s)
- Mariane U V Ronque
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, C.P. 6109, Universidade Estadual de Campinas, 13083-862, Campinas, SP, Brazil.
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista - Campus Rio Claro, 13506-900, Rio Claro, SP, Brazil
| | - Gustavo H Migliorini
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual Paulista - Campus São José do Rio Preto, 15054-000, São José do Rio Preto, SP, Brazil
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, Universidade Estadual Paulista - Campus Rio Claro, 13506-900, Rio Claro, SP, Brazil
| | - Paulo S Oliveira
- Departamento de Biologia Animal, C.P. 6109, Universidade Estadual de Campinas, 13083-862, Campinas, SP, Brazil
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Lyra ML, Lourenço ACC, Pinheiro PDP, Pezzuti TL, Baêta D, Barlow A, Hofreiter M, Pombal JP, Haddad CFB, Faivovich J. High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that make this group a crucial missing piece that hinders our understanding of Cophomantini phylogenetics and character evolution. We obtained DNA sequences from a museum larval specimen of Bok. claresignata, using specialized extraction methods and high-throughput DNA sequencing, and combined the molecular phylogenetic results with available phenotypic information to provide new insights into the taxonomy and phylogenetic relationships of its species group. Our phylogenetic results place Bok. claresignata as sister to the Boana pulchella group, supporting its inclusion in Boana, together with Bokermannohyla clepsydra. In light of this new finding, we recognize a newly defined Boana claresignata group to accommodate these species, thus resolving both the polyphyly of Bokermannohyla and the paraphyly of Boana. Considering the phylogenetic relationships of the Boana claresignata group, we also discuss the evolution of suctorial tadpoles and mature oocyte/egg pigmentation in Cophomantini.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
| | - Ana Carolina C Lourenço
- Departamento de Ciências Biológicas, Universidade do Estado de Minas Gerais, Campus Ubá, Avenida Olegário Maciel, Ubá, Minas Gerais, CEP, Brazil
| | - Paulo D P Pinheiro
- Laboratório de Anfíbios, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa, Sala, Cidade Universitária, São Paulo, São Paulo, CEP, Brazil
| | - Tiago L Pezzuti
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos, Pampulha, Belo Horizonte, Minas Gerais, CEP, Brazil
| | - Délio Baêta
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista,, Rio de Janeiro, Rio de Janeiro, CEP, Brazil
| | - Axel Barlow
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Straße, Potsdam, Germany
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Straße, Potsdam, Germany
| | - José P Pombal
- Setor de Herpetologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista,, Rio de Janeiro, Rio de Janeiro, CEP, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista (UNESP), Rio Claro, São Paulo, CEP, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’-CONICET, Ángel Gallardo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biologia Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Falcão PRN, Lyra ML. Rectification of acoustic phonons in harmonic chains with nonreciprocal spring defects. J Phys Condens Matter 2020; 32:245401. [PMID: 32100725 DOI: 10.1088/1361-648x/ab7a0f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The scattering of acoustic phonons by nonreciprocal spring defects inserted in an harmonic chain is investigated. The degree of nonreciprocity of the forces mediated by the defect springs is parameterized by a single quantity Δ that effectively takes into account the interaction of the coupled masses with hidden degrees of freedom of an underlying nonequilibrium system. We demonstrate a pronounced rectification effect with transmission having a preferential direction. Nonreciprocity also allows energy exchange between the system and the medium. Further, we show a cooperative action between defects mediated by resonant cavity modes. The influence of damping forces is also explored and shown to promote the rectification of the reflected vibrational wave component.
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Affiliation(s)
- P R N Falcão
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió-AL, Brazil
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Rancilhac L, Bruy T, Scherz MD, Pereira EA, Preick M, Straube N, Lyra ML, Ohler A, Streicher JW, Andreone F, Crottini A, Hutter CR, Randrianantoandro JC, Rakotoarison A, Glaw F, Hofreiter M, Vences M. Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus). J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1748243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Teddy Bruy
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Mark D. Scherz
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Elvis Almeida Pereira
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
- Programa de Pós-Graduação em Biologia Animal, Departamento de Biologia Animal, Laboratório de Herpetologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nicolas Straube
- Department of Natural History, University Museum of Bergen, Bergen, Norway
| | - Mariana L. Lyra
- Depto de Zoologia, Instituto de Biologia, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Annemarie Ohler
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Jeffrey W. Streicher
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
| | - Franco Andreone
- Sezione zoologia, Museo Regionale di Scienze Naturali, Torino, Italy
| | - Angelica Crottini
- Cibio, Research Centre in Biodiversity, Genetics and Evolution, InBio, Universidade do Porto, Vairão, Portugal
| | - Carl R. Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Andolalao Rakotoarison
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d’Antananarivo, Antananarivo, Madagascar
| | - Frank Glaw
- Sektion Herpetologie, Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
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Ribeiro JW, Siqueira T, DiRenzo GV, Lambertini C, Lyra ML, Toledo LF, Haddad CFB, Becker CG. Assessing amphibian disease risk across tropical streams while accounting for imperfect pathogen detection. Oecologia 2020; 193:237-248. [DOI: 10.1007/s00442-020-04646-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 04/07/2020] [Indexed: 12/23/2022]
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Zornosa-Torres C, Augusto-Alves G, Lyra ML, Silva Júnior JCD, Garcia PC, Leite F, Verdade V, Rodrigues MT, Gasparini JL, Haddad CF, Toledo LF. Anurans of the Caparaó National Park and surroundings, southeast Brazil. Biota Neotrop 2020. [DOI: 10.1590/1676-0611-bn-2019-0882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract The Atlantic Forest (AF) is one of the biodiversity hotspots of the world, and the most fragmented biome of Brazil. This biome includes different phytophysiognomies, as riparian, slope, cloudy forests, and grasslands. Such complexity, allied to huge latitudinal and high elevational range, provides diverse habitats and conditions for amphibian speciation. As a result, there are over 600 amphibian species known to occur in the AF. Within this biome the Caparaó National Park (CNP) is relevant, as it includes the highest peak of the biome, the Pico da Bandeira at almost 3,000 m above sea level, as well as different phytophysiognomies as rocky fields and humid forests. In spite of that, its amphibian fauna is still poorly described. We inventoried amphibians at the CNP and surrounding areas from 2016 to 2018 and recorded 47 anuran species, of which two are locally endemic and at least six have not been described yet. Additionally, we compiled data from previous surveys (2004 to 2008) and secondary data from scientific collections. All together, we registered a total of 61 anuran species from 12 families for the CNP and surroundings, placing this area among the 10 amphibian richest sites in the AF. Some of these species are represented by only one or two collected specimens and have not been registered in the CNP since the 1980’s, such as Thoropa lutzi and Hylodes vanzolinii. These species could be examples of population declines or even past local extinctions, highlighting the need of further sampling efforts in that highly biodiverse site.
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Affiliation(s)
- Camila Zornosa-Torres
- Universidade Estadual de Campinas, Brasil; Universidade Estadual de Campinas, Brasil
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Baldo D, Araujo-Vieira K, Cardozo D, Borteiro C, Leal F, Pereyra MO, Kolenc F, Lyra ML, Garcia PCA, Haddad CFB, Faivovich J. Correction: A review of the elusive bicolored iris Snouted Treefrogs (Anura: Hylidae:Scinax uruguayus group). PLoS One 2019; 14:e0225543. [PMID: 31725800 PMCID: PMC6855439 DOI: 10.1371/journal.pone.0225543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Baldo D, Araujo-Vieira K, Cardozo D, Borteiro C, Leal F, Pereyra MO, Kolenc F, Lyra ML, Garcia PCA, Haddad CFB, Faivovich J. A review of the elusive bicolored iris Snouted Treefrogs (Anura: Hylidae:Scinax uruguayus group). PLoS One 2019; 14:e0222131. [PMID: 31553727 PMCID: PMC6760762 DOI: 10.1371/journal.pone.0222131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022] Open
Abstract
The genus Scinax currently includes more than 120 species, recovered in two major clades, the S. catharinae and the S. ruber clades. The latter comprises 75 species, most of which remain unassigned to any species groups, while 12 are included in the S. rostratus and S. uruguayus groups. In this paper we present a taxonomic review of the two species currently included in the S. uruguayus group, discussing some putative phenotypic synapomorphies of this group. Although S. pinima and S. uruguayus have been considered as distinct species, this has been based on scant evidence, and several authors doubted of their distinctiveness. Our study of available specimens of S. pinima and S. uruguayus corroborates that both are valid and diagnosable species based on phenotypic evidence. Furthermore, our results show that S. pinima previously known only from its type locality, has a much widespread distribution than previously thought (including the Brazilian states of Paraná, Santa Catarina, and Rio Grande do Sul), which, added to the biological information presented here allows to suggest the removal of this species from the "Data Deficient" IUCN Red List category to "Least Concern". Also, we describe a new species formerly reported as S. aff. pinima and S. uruguayus from NE Argentina and some localities from the Brazilian State of Rio Grande do Sul. All species are diagnosed and characterized using adult and larval morphology, osteology, vocalizations, cytogenetics, and natural history.
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Affiliation(s)
- Diego Baldo
- Laboratório de Genética Evolutiva, Instituto de Biología Subtropical “Claudio Juan Bidau” (CONICET-UNaM), Posadas, Misiones, Argentina
| | - Katyuscia Araujo-Vieira
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—CONICET, Buenos Aires, Argentina
| | - Dario Cardozo
- Laboratório de Genética Evolutiva, Instituto de Biología Subtropical “Claudio Juan Bidau” (CONICET-UNaM), Posadas, Misiones, Argentina
| | - Claudio Borteiro
- Sección Herpetología, Museo Nacional de Historia Natural, Montevideo, Uruguay
| | - Fernando Leal
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Martín O. Pereyra
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—CONICET, Buenos Aires, Argentina
| | - Francisco Kolenc
- Sección Herpetología, Museo Nacional de Historia Natural, Montevideo, Uruguay
| | - Mariana L. Lyra
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Paulo C. A. Garcia
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Célio F. B. Haddad
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—CONICET, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Greenspan SE, Lyra ML, Migliorini GH, Kersch-Becker MF, Bletz MC, Lisboa CS, Pontes MR, Ribeiro LP, Neely WJ, Rezende F, Romero GQ, Woodhams DC, Haddad CFB, Toledo LF, Becker CG. Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense. Proc Biol Sci 2019; 286:20190924. [PMID: 31238845 DOI: 10.1098/rspb.2019.0924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.
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Affiliation(s)
- Sasha E Greenspan
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Mariana L Lyra
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Gustavo H Migliorini
- 3 Programa de Pós-graduação em Biologia Animal, Universidade Estadual Paulista 'Júlio de Mesquita Filho' , São José do Rio Preto SP 15054-000 , Brazil
| | - Mônica F Kersch-Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Molly C Bletz
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | | | - Mariana R Pontes
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Luisa P Ribeiro
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Wesley J Neely
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Felipe Rezende
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Gustavo Q Romero
- 7 Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas SP 13083-862 , Brazil
| | - Douglas C Woodhams
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | - Célio F B Haddad
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Luís Felipe Toledo
- 8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - C Guilherme Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
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Mendes CVC, Almeida GMA, Lyra ML, de Moura FABF. Localization-delocalization transition in discrete-time quantum walks with long-range correlated disorder. Phys Rev E 2019; 99:022117. [PMID: 30934307 DOI: 10.1103/physreve.99.022117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 11/07/2022]
Abstract
We study the effects of spatially long-range correlated phase disorder on the Hadamard quantum walk on a line. The shift operator is built to exhibit an intrinsic disorder distribution featuring long-range correlations. To impose such, we resort to fractional Brownian motion with power-law spectrum 1/k^{2α} with α≥0 being the exponent that controls the degree of correlations. We discuss the scaling behavior of the walker's wave packet and report a localization-delocalization transition controlled by α. We unveil two intermediate dynamical regimes between exponential localization and full delocalization.
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Affiliation(s)
- C V C Mendes
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, AL, Brazil
| | - G M A Almeida
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, AL, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, AL, Brazil
| | - F A B F de Moura
- Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió, AL, Brazil
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Bergamo LW, Fresia P, Lyra ML, Azeredo-Espin AML. High Genetic Diversity and No Population Structure of the New World Screwworm Fly Cochliomyia hominivorax (Diptera: Calliphoridae) on a Microgeographic Scale: Implications for Management Units. J Econ Entomol 2018; 111:2476-2482. [PMID: 30256994 DOI: 10.1093/jee/toy171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 06/08/2023]
Abstract
The New World screwworm fly Cochliomyia hominivorax (Coquerel, 1858) (Diptera: Calliphoridae) is an important livestock pest endemic to the Americas that has been eradicated from North and continental Central America with a control program based on the Sterile Insect Technique (SIT). The establishment of target management units is a strategic step in the implementation of new control programs, which can be achieved using genetic studies of natural populations. Previous studies of New World screwworm fly populations were conducted on the continental scale and identified four main groups: two in South America and two in the Caribbean. However, studies within these groups are needed to determine which smaller geographic areas can be treated as management units. Here, we analyze the genetic variability distribution and the population demographic signals of the New World screwworm fly in a 6,000 km2 area located along the border of Brazil and Uruguay. This area was the subject of the first control pilot program conducted in South America. We studied eight microsatellite loci and sequences from two mitochondrial DNA regions in individuals sampled at 20-25 livestock breeding farms. We observed no population structure and found high genetic variability on the geographical scale sampled for both molecular markers. Our microsatellite data suggest that these populations are not in equilibrium, and demographic analyses based on mitochondrial data indicate population expansion. These results suggest that this geographic scale is not adequate for future New World screwworm fly management in South America.
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Affiliation(s)
- Luana W Bergamo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Pablo Fresia
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana L Lyra
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Ana Maria L Azeredo-Espin
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
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Lyra ML, Bletz MC, Haddad CFB, Vences M. The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates. Microb Ecol 2018; 76:121-124. [PMID: 29159493 DOI: 10.1007/s00248-017-1109-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 11/13/2017] [Indexed: 06/07/2023]
Abstract
Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Zoologia, Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil.
| | - Molly C Bletz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
| | - Célio F B Haddad
- Departamento de Zoologia, Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil
- Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106, Braunschweig, Germany
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Sousa HS, Pereira MSS, de Oliveira IN, Strečka J, Lyra ML. Phase diagram and re-entrant fermionic entanglement in a hybrid Ising-Hubbard ladder. Phys Rev E 2018; 97:052115. [PMID: 29906985 DOI: 10.1103/physreve.97.052115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Indexed: 06/08/2023]
Abstract
The degree of fermionic entanglement is examined in an exactly solvable Ising-Hubbard ladder, which involves interacting electrons on the ladder's rungs described by Hubbard dimers at half-filling on each rung, accounting for intrarung hopping and Coulomb terms. The coupling between neighboring Hubbard dimers is assumed to have an Ising-like nature. The ground-state phase diagram consists of four distinct regions corresponding to the saturated paramagnetic, the classical antiferromagnetic, the quantum antiferromagnetic, and the mixed classical-quantum phase. We have exactly computed the fermionic concurrence, which measures the degree of quantum entanglement between the pair of electrons on the ladder rungs. The effects of the hopping amplitude, the Coulomb term, temperature, and magnetic fields on the fermionic entanglement are explored in detail. It is shown that the fermionic concurrence displays a re-entrant behavior when quantum entanglement is being generated at moderate temperatures above the classical saturated paramagnetic ground state.
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Affiliation(s)
- H S Sousa
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió, Alagoas, Brazil
- Instituto Federal do Piauí, Campus Pedro II, 64255-000 Pedro II-Piauí, Brazil
| | - M S S Pereira
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió, Alagoas, Brazil
| | - I N de Oliveira
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió, Alagoas, Brazil
| | - J Strečka
- Department of Theoretical Physics and Astrophysics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 040 01 Košice, Slovakia
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió, Alagoas, Brazil
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Sabbag AF, Lyra ML, Zamudio KR, Haddad CF, Feio RN, Leite FS, Gasparini JL, Brasileiro CA. Molecular phylogeny of Neotropical rock frogs reveals a long history of vicariant diversification in the Atlantic forest. Mol Phylogenet Evol 2018; 122:142-156. [DOI: 10.1016/j.ympev.2018.01.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/19/2018] [Accepted: 01/20/2018] [Indexed: 11/16/2022]
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Carvalho RCP, Pereira MSS, de Oliveira IN, Strečka J, Lyra ML. Ground-state phase diagram, fermionic entanglement and kinetically-induced frustration in a hybrid ladder with localized spins and mobile electrons. J Phys Condens Matter 2017; 29:365801. [PMID: 28675150 DOI: 10.1088/1361-648x/aa7d61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We introduce an exactly solvable hybrid spin-ladder model containing localized nodal Ising spins and interstitial mobile electrons, which are allowed to perform a quantum-mechanical hopping between the ladder's legs. The quantum-mechanical hopping process induces an antiferromagnetic coupling between the ladder's legs that competes with a direct exchange coupling of the nodal spins. The model is exactly mapped onto the Ising spin ladder with temperature-dependent two- and four-spin interactions, which is subsequently solved using the transfer-matrix technique. We report the ground-state phase diagram and compute the fermionic concurrence to characterize the quantum entanglement between the pair of interstitial mobile electrons. We further provide a detailed analysis of the local spin ordering including the pair and four-spin correlation functions around an elementary plaquette, as well as, the local ordering diagrams. It is shown that a complex sequence of distinct local orderings and frustrated correlations takes place when the model parameters drive the investigated system close to a zero-temperature triple coexistence point.
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Affiliation(s)
- R C P Carvalho
- Instituto de Física, Universidade Federal de Alagoas 57072-970 Maceió-AL, Brazil
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Dias WS, Bertrand D, Lyra ML. Bose-Einstein condensation in chains with power-law hoppings: Exact mapping on the critical behavior in d-dimensional regular lattices. Phys Rev E 2017; 95:062105. [PMID: 28709254 DOI: 10.1103/physreve.95.062105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 11/07/2022]
Abstract
Recent experimental progress on the realization of quantum systems with highly controllable long-range interactions has impelled the study of quantum phase transitions in low-dimensional systems with power-law couplings. Long-range couplings mimic higher-dimensional effects in several physical contexts. Here, we provide the exact relation between the spectral dimension d at the band bottom and the exponent α that tunes the range of power-law hoppings of a one-dimensional ideal lattice Bose gas. We also develop a finite-size scaling analysis to obtain some relevant critical exponents and the critical temperature of the BEC transition. In particular, an irrelevant dangerous scaling field has to be taken into account when the hopping range is sufficiently large to make the effective dimensionality d>4.
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Affiliation(s)
- W S Dias
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
| | - D Bertrand
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
| | - M L Lyra
- Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió, Alagoas, Brazil
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Lyra ML, Sanchez E, Künzel S, Lötters S, Haddad CF, Vences M. The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates). Mitochondrial DNA B Resour 2017; 2:397-399. [PMID: 33473839 PMCID: PMC7800569 DOI: 10.1080/23802359.2017.1347830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/24/2017] [Indexed: 10/31/2022] Open
Abstract
We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas, and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus, being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%.
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Affiliation(s)
- Mariana L. Lyra
- Department of Zoology and Aquiculture Centre (CAUNESP), Campus Rio Claro, São Paulo State University – UNESP, Biosciences Institute, Rio Claro, SP, Brazil
| | - Eugenia Sanchez
- Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Stefan Lötters
- Biogeography Department, Trier University, Trier, Germany
| | - Célio F.B. Haddad
- Department of Zoology and Aquiculture Centre (CAUNESP), Campus Rio Claro, São Paulo State University – UNESP, Biosciences Institute, Rio Claro, SP, Brazil
| | - Miguel Vences
- Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany
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Lyra ML, Haddad CFB, de Azeredo-Espin AML. Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers. Mol Ecol Resour 2017; 17:966-980. [PMID: 28029226 DOI: 10.1111/1755-0998.12648] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 01/17/2023]
Abstract
Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Ana Maria L de Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Cândido Rondon No. 400, CEP 13083-875, Campinas, São Paulo, Brazil
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