1
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Wheeler WC. Much ado about nothing: inapplicable data as insertion-deletion events. Cladistics 2023; 39:475-478. [PMID: 37466458 DOI: 10.1111/cla.12553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/27/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023] Open
Abstract
The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feature, and its variation when present, in a reasonable manner. Three basic issues have presented themselves: (i) impossible states at internal nodes; (ii) action at a distance among disparate parts of the tree; and (iii) "secondary" (i.e. aspect variation) characters overwhelming "primary" (i.e. character presence/absence) patterns in grouping taxa. Multiple methods have been proposed to deal with these issues in the context of standard character coding with varying levels of complexity. Here, I show that these issues can be dealt with in a direct fashion by treating presence/absence not as a character, but as insertion/deletion of a character with all its potential variation. This approach removes these three problems in simple, straightforward manner.
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Affiliation(s)
- Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA
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2
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Anganoy-Criollo M, Viuche-Lozano A, Enciso-Calle MP, Bernal MH, Grant T. The Enigmatic Hyloxalus edwardsi Species Group (Anura: Dendrobatidae): Phylogenetic Position, a New Species, and New Putative Morphological Synapomorphies. HERPETOLOGICA 2022. [DOI: 10.1655/herpetologica-d-21-00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marvin Anganoy-Criollo
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Andres Viuche-Lozano
- Grupo de Herpetología, Eco-Fisiología and Etología, Departamento de Biología, Universidad del Tolima, 730006299 Ibagué, Colombia
| | - Maria Paula Enciso-Calle
- Grupo de Herpetología, Eco-Fisiología and Etología, Departamento de Biología, Universidad del Tolima, 730006299 Ibagué, Colombia
| | - Manuel Hernando Bernal
- Grupo de Herpetología, Eco-Fisiología and Etología, Departamento de Biología, Universidad del Tolima, 730006299 Ibagué, Colombia
| | - Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, SP, Brazil
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3
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Ospina Sarria JJ, Velásquez Trujillo DA, Castaño Saavedra CO, Castillo LF, Bolívar-García W. A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus. PeerJ 2022; 10:e12765. [PMID: 35186452 PMCID: PMC8833226 DOI: 10.7717/peerj.12765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/17/2021] [Indexed: 01/07/2023] Open
Abstract
A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus-Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II-IV and toes II-IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
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Affiliation(s)
- Jhon Jairo Ospina Sarria
- Calima, Fundación Para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali, Valle del Cauca, Colombia
| | | | | | - Luis Fernando Castillo
- Calidris, Asociación Para el Estudio y Conservación de las Aves Acuáticas en Colombia, Cali, Valle del Cauca, Colombia
| | - Wilmar Bolívar-García
- Calima, Fundación Para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali, Valle del Cauca, Colombia,Universidad del Valle, Departamento de Biología, Grupo de Investigación en Ecología Animal, Cali, Valle del Cauca, Colombia
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4
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Jacob Machado D, Scott R, Guirales S, Janies DA. Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2. Cladistics 2021; 37:461-488. [PMID: 34570933 PMCID: PMC8239696 DOI: 10.1111/cla.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.
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Affiliation(s)
- Denis Jacob Machado
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Rachel Scott
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Sayal Guirales
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Daniel A. Janies
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
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5
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Gueratto C, Benedetti A, Pinto-da-Rocha R. Phylogenetic relationships of the genus Mischonyx Bertkau, 1880, with taxonomic changes and three new species description (Opiliones: Gonyleptidae). PeerJ 2021; 9:e11682. [PMID: 34692238 PMCID: PMC8485841 DOI: 10.7717/peerj.11682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/06/2021] [Indexed: 11/30/2022] Open
Abstract
The type species of Mischonyx Bertkau 1880, Mischonyx squalidus, was described based on a juvenile. The holotype is lost. Based on a revision of publications, the genus includes 12 species, all in Brazil. The objectives of this research are: to propose a phylogenetic hypothesis for Mischonyx based on Total Evidence (TE); propose taxonomic changes based on the phylogeny; and analyze the phylogenetic hypothesis biogeographically. Using the exemplar approach to taxon selection, we studied 54 specimens, 15 outgroups and 39 ingroup taxa using seven molecular markers (28S, 12S and 16S ribosomal genes, citochrome oxidase subunit I gene, carbamoyl-phosphate synthetase gene, internal transcribed spacer subunit 2 and histone H3 gene), totaling 3,742 bp, and 128 morphological characters. We analyzed the dataset under three optimality criteria: Maximum likelihood (ML), Maximum parsimony (MP) and Bayesian. We discuss the transformation of character states throughout the phylogeny, the different phylogenetic hypotheses using different datasets and the congruence of evidence between the clades obtained by the phylogenetic analysis and the biogeographical hypothesis for the Atlantic Forest areas of endemism. We estimate that Mischonyx clade diverged 50.53 Mya, and inside the genus there are two major clades. One of them cointains species from Paraná, Santa Catarina, South of São Paulo and Serra do Mar Areas of Endemism and the other has species from Espinhaço, Bocaina, South coast of Rio de Janeiro and Serra dos Órgãos Areas of Endemism. The first split inside these two clades occurred at 48.94 and 44.80 Mya, respectively. We describe three new species from Brazil: Mischonyx minimus sp. nov. (type locality: Petrópolis, Rio de Janeiro), Mischonyx intervalensis sp. nov. (type locality: Ribeirão Grande, São Paulo) and Mischonyx tinguaensis sp. nov (type locality: Nova Iguaçu, Rio de Janeiro). The genus Urodiabunus Mello-Leitão, 1935 is considered a junior synonym of Mischonyx. Weyhia spinifrons Mello-Leitão, 1923; Weyhia clavifemur Mello-Leitão, 1927 and Geraeocormobius reitzi Vasconcelos, 2005 were transferred to Mischonyx. Mischonyx cuspidatus (Roewer, 1913) is a junior synonym of M. squalidus Bertkau, 1880. In the results of the phylogenetic analyses, Gonyleptes antiquus Mello-Leitão, 1934 (former Mischonyx antiquus) does not belong in Mischonyx and its original combination is re-established. As it is now defined, Mischonyx comprises 17 species, with seven new combinations.
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Affiliation(s)
- Caio Gueratto
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Alípio Benedetti
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Centro Universitário Metodista Izabela Hendrix, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo Pinto-da-Rocha
- Departamento de Zoologia/Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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6
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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] [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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7
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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: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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8
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Moura PHAG, Costa FR, Anelli LE, Nunes I. A new genus of fossil frog (Anura) from lower Cretaceous deposits in South America. AN ACAD BRAS CIENC 2021; 93:e20191560. [PMID: 34161447 DOI: 10.1590/0001-3765202120201560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/20/2021] [Indexed: 11/21/2022] Open
Abstract
The frog clade Neobatrachia or "advanced frogs" represents more than 95% of the diversity within Anura. The neobatrachian fossil record is incomplete due to the small size and fragile nature of their bones but provides some clues on the time and rate of the current diversification of modern-day amphibians. The Crato Formation (Aptian) of northeastern Brazil is known for the presence of, at least, five species of neobatrachian fossils. Herein, we describe a well-preserved fossil that represents a new neobatrachian taxon from the Crato Formation (Cretaceous) in the Araripe Basin, northeastern Brazil, and perform phylogenetic analysis to assess its higher-level relationships. The new specimen is an almost complete and articulated skeleton with soft tissue preservation. Phylogenetic analysis recovered the specimen nested in the clade Hyloidea and our results highlight the remarkable value of the Crato Formation as a Laggerstätte.
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Affiliation(s)
- Pedro Henrique A G Moura
- Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Laboratory of Herpetology, Institute of Biosciences, Campus do Litoral Paulista, Pça. Infante D. Henrique, s/n, Parque Bitaru, 11330-900 São Vicente, SP, Brazil
| | - Fabiana R Costa
- Universidade Federal do ABC (UFABC), Laboratory of Vertebrate Paleontology and Animal Behavior (LAPC), Center of Natural and Human Sciences, Campus São Bernardo do Campo, Alameda da Universidade, s/n, Anchieta, 09606-045 São Bernardo do Campo, SP, Brazil
| | - Luiz E Anelli
- Universidade de São Paulo (USP), Department of Sedimentary and Environmental Geology, Geosciences Institute, Rua do Lago, 562, Butantã, 05508-900 São Paulo, SP, Brazil
| | - Ivan Nunes
- Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Laboratory of Herpetology, Institute of Biosciences, Campus do Litoral Paulista, Pça. Infante D. Henrique, s/n, Parque Bitaru, 11330-900 São Vicente, SP, Brazil
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9
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Blotto BL, Pereyra MO, Grant T, Faivovich J. Hand and Foot Musculature of Anura: Structure, Homology, Terminology, and Synapomorphies for Major Clades. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.1206/0003-0090.443.1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Boris L. Blotto
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil; División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires, Argentina
| | - Martín O. Pereyra
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”–CONICET, Buenos Aires, Argentina; Laboratorio de Genética Evolutiva “Claudio J. Bidau,” Instituto de Biología Subtropical–CONICET, Facultad de Ciencias Exactas Químic
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil; Coleção de Anfíbios, Museu de Zoologia, Universidade de São Paulo, São Paulo, Brazil; Research Associate, Herpetology, Division of Vertebrate Zoology, A
| | - 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
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10
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Phylogenetic relationships of the Boana pulchella Group (Anura: Hylidae). Mol Phylogenet Evol 2020; 155:106981. [PMID: 33059068 DOI: 10.1016/j.ympev.2020.106981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 11/24/2022]
Abstract
In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test of its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included>300 specimens of 37 of the 38 species currently included in the group, plus 36 outgroups, exemplars of the diversity of Boana and the other genera of the hylid tribe Cophomantini. The dataset included eight mitochondrial genes (12S, 16S, CytB, COI, ND1, tRNAIle, tRNALeu, and tRNAVal) and five nuclear genes (RHO, TYR, RAG-1, CXCR4, SIAH1). The phylogenetic analyses recover the monophyly of the B. pulchella Group with lower support than previous studies, as a result of the inclusion of the B. claresignata Group, which is recovered as its sister taxon. Within the B. pulchella Group, the inclusion of almost all species of the group had little impact on previous notions of its phylogeny, except for the rejection of the hypothesized B. polytaenia Clade (B. goiana and B. phaeopleura are nested in the clade here called the B. prasina Clade), which is redefined. Phylogenetic support is strong for five major clades, which collectively include all but three of the species sampled: the B. balzani Clade (B. aguilari, B. balzani, B. gladiator, B. melanopleura, B. palaestes), the redefined B. polytaenia Clade (B. botumirim, B. buriti, B. cipoensis, B. jaguariaivensis, B. leptolineata, B. polytaenia, B. stenocephala, and two undescribed species), the B. prasina Clade (B. bischoffi, B. caingua, B. cordobae, B. goiana, B. guentheri, B. marginata, B. phaeopleura, B. prasina, B. pulchella, and one undescribed species), the B. riojana Clade (B. callipleura, B. marianitae, B. riojana), and the B. semiguttata Clade (B. caipora, B. curupi, B. joaquini, B. poaju, B. semiguttata, B. stellae, and two undescribed species). The monophyly of the B. prasina + B. riojana Clades, and that of the B. polytaenia + B. semiguttata Clades are well-supported. The relationships among these two clades, the B. balzani Clade, B. ericae + B. freicanecae, and B. cambui (representing the deepest phylogenetic splits within the B. pulchella Group) are recovered with weak support. We discuss the phenotypic evidence supporting the monophyly of the B. pulchella Group, and the taxonomy of several species, identifying three new synonyms of Boana polytaenia, one new synonym of Boana goiana, and one new synonym of B. riojana.
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11
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de Bernadi Schneider A, Jacob Machado D, Guirales S, Janies DA. FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. Viruses 2020; 12:E892. [PMID: 32824044 PMCID: PMC7472247 DOI: 10.3390/v12080892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus, named "Fast Loci Annotation of Viruses" (FLAVi; http://flavi-web.com/), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.
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Affiliation(s)
- Adriano de Bernadi Schneider
- AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA;
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Sayal Guirales
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
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12
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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] [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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13
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Jaramillo AF, De La Riva I, Guayasamin JM, Chaparro JC, Gagliardi-Urrutia G, Gutiérrez RC, Brcko I, Vilà C, Castroviejo-Fisher S. Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification. Mol Phylogenet Evol 2020; 149:106841. [PMID: 32305511 DOI: 10.1016/j.ympev.2020.106841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 11/29/2022]
Abstract
We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23-49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10-15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.
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Affiliation(s)
- Andrés F Jaramillo
- Pos-Graduação em Ecologia e Evolução da Biodiversidade, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil.
| | | | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA-USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito (USFQ), Ecuador; University of North Carolina at Chapel Hill, Department of Biology, USA
| | - Juan C Chaparro
- Museo de Biodiversidad del Perú (MUBI), Peru; Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Peru
| | - Giussepe Gagliardi-Urrutia
- Pos-Graduação em Ecologia e Evolução da Biodiversidade, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Peruvian Center for Biodiversity and Conservation (PCB&C), Peru; Dirección de Investigación en Diversidad Biológica Terrestre Amazónica, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Peru
| | - Roberto C Gutiérrez
- Museo de Historia Natural de la Universidad Nacional de San Agustín de Arequipa (MUSA), Peru
| | - Isabela Brcko
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Brazil
| | - Carles Vilà
- Estación Biológica de Doñana (EBD-CSIC), Spain
| | - Santiago Castroviejo-Fisher
- Pos-Graduação em Ecologia e Evolução da Biodiversidade, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Department of Herpetology, American Museum of Natural History, USA
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14
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Cabra-García J, Hormiga G. Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.
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Affiliation(s)
- Jimmy Cabra-García
- Departamento de Biología, Universidad del Valle, Cali, AA, Colombia
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo Hormiga
- The George Washington University, Department of Biological Sciences, Washington, DC, USA
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15
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Araujo-Vieira K, Blotto BL, Caramaschi U, Haddad CFB, Faivovich J, Grant T. A total evidence analysis of the phylogeny of hatchet-faced treefrogs (Anura: Hylidae: Sphaenorhynchus). Cladistics 2019; 35:469-486. [PMID: 34618945 DOI: 10.1111/cla.12367] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 12/26/2022] Open
Abstract
The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group.
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Affiliation(s)
- Katyuscia Araujo-Vieira
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Boris L Blotto
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina.,Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, 05508-090, Brazil
| | - Ulisses Caramaschi
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, Rio de Janeiro, Rio de Janeiro, 20940-040, Brazil
| | - Celio F B Haddad
- Departamento de Zoologia and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Avenida 24A, 1515, Bela Vista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Ángel 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
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, 05508-090, Brazil
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16
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Grant T. Outgroup sampling in phylogenetics: Severity of test and successive outgroup expansion. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Taran Grant
- Department of Zoology, Institute of Biosciences University of São Paulo São Paulo Brazil
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17
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Ospina-Sarria JJ, Cabra-García J. Parsimony analysis of unaligned sequence data: some clarifications. Cladistics 2018; 34:574-577. [PMID: 34706480 DOI: 10.1111/cla.12229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 11/29/2022] Open
Abstract
De Laet (2015) claimed that minimization of ad hoc hypotheses of homoplasy does not lead to a preference for trivial optimizations when analysing unaligned sequence data, as claimed by Wheeler (2012; see also Kluge and Grant, 2006). In addition, De Laet asserted that Kluge and Grant's (2006) parsimony rationale is internally inconsistent in terms of Baker's (2003) theoretical framework. We argue that De Laet used extraneous presuppositions to critique Wheeler's position and, as such, his criticism should be considered cautiously in terms of its scope. Finally, we demonstrate that considering Kluge and Grant's parsimony rationale as inconsistent rests on De Laet's misunderstanding of the ideographic character concept and the consequences of relating it to Baker's rationale.
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Affiliation(s)
- Jhon Jairo Ospina-Sarria
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Jimmy Cabra-García
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.,Departamento de Biología, Universidad del Valle, Cali, AA 25360, Colombia
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18
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Sánchez-Pacheco SJ, Torres-Carvajal O, Aguirre-Peñafiel V, Nunes PMS, Verrastro L, Rivas GA, Rodrigues MT, Grant T, Murphy RW. Phylogeny of Riama (Squamata: Gymnophthalmidae), impact of phenotypic evidence on molecular datasets, and the origin of the Sierra Nevada de Santa Marta endemic fauna. Cladistics 2018; 34:260-291. [PMID: 34645080 DOI: 10.1111/cla.12203] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2017] [Indexed: 02/02/2023] Open
Abstract
Riama is the most speciose genus of the Neotropical lizard family Gymnophthalmidae. Its more than 30 montane species occur throughout the northern Andes, the Cordillera de la Costa (CC) in Venezuela, and Trinidad. We present the most comprehensive phylogenetic analysis of Riama to date based on a total evidence (TE) approach and direct optimization of molecular and morphological evidence. Analyses use DNA sequences from four loci and 35 phenotypic characters. The dataset consists of 55 ingroup terminals representing 25 of the 30 currently recognized species of Riama plus five undescribed taxa, including an endemic species from the Sierra Nevada de Santa Marta (SNSM) in Colombia, and 66 outgroup terminals of 47 species. Analysis results in a well-supported hypothesis in which Riama is polyphyletic, with its species falling into three clades. The Tepuian Anadia mcdiarmidi nests within one clade of Riama, and the recently resurrected Pantodactylus nests within Cercosaura. Accordingly, we propose a monophyletic taxonomy that reflects historical relationships. Analysis of character evolution indicates that the presence/absence of prefrontals-a cornerstone of the early genus-level taxonomy of cercosaurines-is optimally explained as having been plesiomorphically present in the most recent common ancestor of Cercosaurinae and lost in that of the immediately less inclusive clade. Multiple independent reversals to present and subsequent returns to absent occur within this clade. To evaluate the impact of phenotypic evidence on our results, we compare our TE results with results obtained from analyses using only molecular data. Although phenotypic evidence comprises only 1.2% of the TE matrix, its inclusion alters both the topology and support values of the clades that do not differ. Finally, current phylogenetic evidence reveals a SNSM-CC-Trinidad-tepuis biogeographical link. We hypothesize that an ancient connection facilitated the exchange of species between the SNSM and the CC.
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Affiliation(s)
- Santiago J Sánchez-Pacheco
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.,Laboratorio de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
| | - Omar Torres-Carvajal
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca apartado 17-01-2184, Quito, Ecuador
| | - Vanessa Aguirre-Peñafiel
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca apartado 17-01-2184, Quito, Ecuador
| | - Pedro M Sales Nunes
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.,Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. Professor Moraes Rego S/n, Cidade Universitaria 50670-901, Recife, PE, Brazil
| | - Laura Verrastro
- Laboratorio de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS 91540-000, Brazil
| | - Gilson A Rivas
- Museo de Biología, Facultad Experimental de Ciencias, Universidad del Zulia, Apartado Postal 526, Maracaibo, 4011, Estado Zulia, Venezuela
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Taran Grant
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada
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19
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Faivovich J, Pereyra MO, Luna MC, Hertz A, Blotto BL, Vásquez-Almazán CR, McCranie JR, Sánchez DA, Baêta D, Araujo-Vieira K, Köhler G, Kubicki B, Campbell JA, Frost DR, Wheeler WC, Haddad CF. On the Monophyly and Relationships of Several Genera of Hylini (Anura: Hylidae: Hylinae), with Comments on Recent Taxonomic Changes in Hylids. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2018. [DOI: 10.2994/sajh-d-17-00115.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julián Faivovich
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Martín O. Pereyra
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - María Celeste Luna
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Andreas Hertz
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Boris L. Blotto
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090 São Paulo, São Paulo, Brazil
| | - Carlos R. Vásquez-Almazán
- Museo de Historia Natural, Escuela de Biología, Universidad de San Carlos de Guatemala, Calle Mariscal Cruz 1-56 zona 10, Ciudad de Guatemala, Guatemala
| | | | - David A. Sánchez
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Délio Baêta
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Katyuscia Araujo-Vieira
- Division Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” —Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Brian Kubicki
- Costa Rican Amphibian Research Center, Guayacán, Provincia de Limón, Costa Rica
| | - Jonathan A. Campbell
- Department of Biology, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Darrel R. Frost
- Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79 Street, New York, NY 10024, USA
| | - Célio F.B. Haddad
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de Zoologia and Centro de Aquicultura, Av. 24A 1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
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20
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Grant T, Rada M, Anganoy-Criollo M, Batista A, Dias PH, Jeckel AM, Machado DJ, Rueda-Almonacid JV. Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea). SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2017. [DOI: 10.2994/sajh-d-17-00017.1] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Amphibian Collection, Museum of Zoology of the University of São Paulo, 04263-000, São Paulo, SP, Brazil
| | - Marco Rada
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Marvin Anganoy-Criollo
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Abel Batista
- Universidad Autónoma de Chiriquí, David, Republic of Panama
- Los Naturalistas, David 0426-01459, Chiriquí, Panama
| | - Pedro Henrique Dias
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Adriana Moriguchi Jeckel
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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21
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Caetano-Anollés D, Caetano-Anollés G. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. Life (Basel) 2016; 6:life6040043. [PMID: 27918435 PMCID: PMC5198078 DOI: 10.3390/life6040043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 01/10/2023] Open
Abstract
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, 24306 Plön, Germany.
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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22
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Goicoechea N, Frost DR, De la Riva I, Pellegrino KCM, Sites J, Rodrigues MT, Padial JM. Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree‐alignment and similarity‐alignment. Cladistics 2016; 32:624-671. [DOI: 10.1111/cla.12150] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 02/02/2023] Open
Affiliation(s)
- Noemí Goicoechea
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales‐CSIC C/ José Gutiérrez Abascal 2 28006 Madrid Spain
| | - Darrel R. Frost
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales‐CSIC C/ José Gutiérrez Abascal 2 28006 Madrid Spain
| | - Katia C. M. Pellegrino
- Departamento de Ciências Biológicas Universidade Federal de São Paulo Avenida Professor Artur Riedel 275 Diadema São Paulo CEP 09972‐270 Brazil
| | - Jack Sites
- Departament of Biology and M.L. Bean Life Science Museum Brigham Young University Provo UT 84602 USA
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo São Paulo CEP: 05508‐090 Brazil
| | - José M. Padial
- Section of Amphibians and Reptiles Carnegie Museum of Natural History 4400 Forbes Avenue Pittsburgh PA 15213 USA
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23
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Caetano-Anollés D, Caetano-Anollés G. Ribosomal accretion, apriorism and the phylogenetic method: a response to Petrov and Williams. Front Genet 2015; 6:194. [PMID: 26082795 PMCID: PMC4451634 DOI: 10.3389/fgene.2015.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
Historical (ideographic) and non-historical (nomothetic) studies of ribosomal accretion appear to arrive at diametrically opposite conclusions. Phylogenetic analysis of thousands of RNA molecules and protein structures in hundreds of genomes supports the structural origin of the ribosome in RNA decoding and ribosomal mechanics. Predictions from extant features in a handful of rRNA structural models of the large ribosomal subunit support its origin in protein biosynthesis. In recent correspondence, one of us reported that correcting dismissals of conflicting data and avoiding unwarranted assumptions of the nomothetic method reconciled conclusions. In response, Petrov and Williams dismissed our arguments claiming we did not understand their algorithmic model of ribosomal apical growth. Instead, they controverted the historical approach. Here we show that their objections to the phylogenetic method are unjustified, that their algorithm subjectively guarantees back-in-time molecular deconstructions toward the protein biosynthetic core, and that processes of ribosomal growth are much more complex. We prompt abandoning apriorism, decreasing ad hoc hypotheses and integrating historical and non-historical scientific methods.
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Affiliation(s)
- Derek Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Gustavo Caetano-Anollés
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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24
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Peloso PL, Frost DR, Richards SJ, Rodrigues MT, Donnellan S, Matsui M, Raxworthy CJ, Biju S, Lemmon EM, Lemmon AR, Wheeler WC. The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae). Cladistics 2015; 32:113-140. [DOI: 10.1111/cla.12118] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 02/02/2023] Open
Affiliation(s)
- Pedro L.V. Peloso
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
- Richard Gilder Graduate School American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Darrel R. Frost
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Stephen J. Richards
- Herpetology Department South Australian Museum North Terrace Adelaide SA 5000 Australia
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo, Rua do Matão Trav. 14, n 321, Cidade Universitária, Caixa Postal 11461 CEP 05422‐970 São Paulo São Paulo Brazil
| | - Stephen Donnellan
- Centre for Evolutionary Biology and Biodiversity The University of Adelaide Adelaide SA 5005 Australia
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Sakyo‐ku Kyoto 606‐8501 Japan
| | - Cristopher J. Raxworthy
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - S.D. Biju
- Systematics Lab Department of Environmental Studies University of Delhi Delhi 110 007 India
| | | | - Alan R. Lemmon
- Department of Scientific Computing Florida State University Dirac Science Library Tallahassee FL 32306‐4120 USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
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25
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Faivovich J, Nicoli L, Blotto BL, Pereyra MO, Baldo D, Barrionuevo JS, Fabrezi M, Wild ER, Haddad CF. Big, Bad, and Beautiful: Phylogenetic Relationships of the Horned Frogs (Anura: Ceratophryidae). SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2014. [DOI: 10.2994/sajh-d-14-00032.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Laura Nicoli
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Boris L. Blotto
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Martín O. Pereyra
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de Misiones), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N
| | - J. Sebastián Barrionuevo
- División Herpetología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”—Consejo Nacional de Investigaciones Científicas y Técnicas, Ángel Gallardo 470, C1405DJR, Buenos Aires, Argentina
| | - Marissa Fabrezi
- Instituto de Bio y Geociencias del NOA, Centro Científico Tecnológico-Salta, Consejo Nacional de Investigaciones Científicas y Técnicas, 9 de Julio 14, 4405, Rosario de Lerma, Salta, Argentina
| | - Erik R. Wild
- Department of Biology and Museum of Natural History, University of Wisconsin-Stevens Point. Stevens Point, Wisconsin, 54022, USA
| | - Célio F.B. Haddad
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Avenida 24A1515, CEP 13506-900, Rio Claro, São Paulo, Brazil
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26
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De Laet J. Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations. Cladistics 2014; 31:550-567. [DOI: 10.1111/cla.12098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jan De Laet
- Göteborgs Botaniska Trädgård; Carl Skottsbergs Gata 22A SE-413 19 Göteborg Sweden
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27
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Sá ROD, Grant T, Camargo A, Heyer WR, Ponssa ML, Stanley E. Systematics of the Neotropical GenusLeptodactylusFitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2014. [DOI: 10.2994/sajh-d-13-00022.1] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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28
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Peloso PL, Sturaro MJ, Forlani MC, Gaucher P, Motta AP, Wheeler WC. Phylogeny, Taxonomic Revision, and Character Evolution of the GeneraChiasmocleisandSyncope(Anura, Microhylidae) in Amazonia, with Descriptions of Three New Species. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2014. [DOI: 10.1206/834.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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29
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Faivovich J, Mcdiarmid RW, Myers CW. Two New Species ofMyersiohyla(Anura: Hylidae) from Cerro De La Neblina, Venezuela, with Comments on Other Species of the Genus. AMERICAN MUSEUM NOVITATES 2013. [DOI: 10.1206/3792.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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30
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Jungfer KH, Faivovich J, Padial JM, Castroviejo-Fisher S, Lyra MM, V. M. Berneck B, Iglesias PP, Kok PJR, MacCulloch RD, Rodrigues MT, Verdade VK, Torres Gastello CP, Chaparro JC, Valdujo PH, Reichle S, Moravec J, Gvoždík V, Gagliardi-Urrutia G, Ernst R, De la Riva I, Means DB, Lima AP, Señaris JC, Wheeler WC, F. B. Haddad C. Systematics of spiny-backed treefrogs (Hylidae:Osteocephalus): an Amazonian puzzle. ZOOL SCR 2013. [DOI: 10.1111/zsc.12015] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karl-Heinz Jungfer
- División Herpetología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’-CONICET; Angel Gallardo 470; C1405DJR; Buenos Aires; Argentina
| | | | - José M. Padial
- Section of Amphibians and Reptiles; Carnegie Museum of Natural History; 4400 Forbes Avenue; Pittsburgh; PA; 15213-4080; USA
| | | | - Mariana M. Lyra
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
| | - Bianca V. M. Berneck
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
| | - Patricia P. Iglesias
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Instituto de Ecología, Genética y Evolución de Buenos Aires; IEGEBA-CONICET; Universidad de Buenos Aires; Ciudad Universitaria Pab. II; C1428EHA; Buenos Aires; Argentina
| | | | - Ross D. MacCulloch
- Department of Natural History; Royal Ontario Museum; 100 Queens Park; Toronto; ON; M5S 2C6; Canada
| | - Miguel T. Rodrigues
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11461; CEP 05508-090; São Paulo; Brazil
| | - Vanessa K. Verdade
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; Av. dos Estados; 5001; CEP 09210-971; Santo André; São Paulo; Brazil
| | - Claudia P. Torres Gastello
- Departamento de Herpetología; Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos; Av. Arenales 1256; Apto. 14-0434; Lima 14; Peru
| | - Juan Carlos Chaparro
- Museo de Historia Natural; Universidad Nacional de San Antonio Abad del Cusco; Cusco; Peru
| | - Paula H. Valdujo
- Departamento de Ecologia; Instituto de Biociências; Universidade de São Paulo; Rua do Matão, travessa 14; 05508-900; São Paulo; SP; Brazil
| | - Steffen Reichle
- Fundación para la Conservación del Bosque Chiquitano; Av. Ejército Nacional No 160; Santa Cruz de la Sierra; Bolivia
| | - Jiří Moravec
- Department of Zoology; National Museum; Prague 9; Czech Republic
| | - Václav Gvoždík
- Department of Zoology; National Museum; Prague 9; Czech Republic
| | - Giussepe Gagliardi-Urrutia
- Programa de Investigación en Biodiversidad Amazónica del Instituto de Investigaciones de la Amazonia Peruana; Av. Quiñonez Km 2.5; Iquitos; Perú
| | - Raffael Ernst
- Museum für Tierkunde; Senckenberg Natural History Collections Dresden; Königsbrücker Landstr. 159; D-01109; Dresden; Germany
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology; Museo Nacional de Ciencias Naturales-CSIC; C/José Gutiérrez Abascal 2; 28006; Madrid; Spain
| | - Donald Bruce Means
- Coastal Plains Institute and Land Conservancy; 1313 Milton Street; Tallahassee; FL; 32303; USA
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia; Caixa Postal 478; CEP 69011-970; Manaus; Amazonas; Brazil
| | - J. Celsa Señaris
- Laboratorio de Ecología y Genética de Poblaciones; Centro de Ecología; Instituto Venezolano de Investigaciones Científicas; Apartado 21827; Caracas; 1020-A; Venezuela
| | - Ward C. Wheeler
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street; New York; NY; 10024-5192; USA
| | - Célio F. B. Haddad
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; Av. 24A 1515; CEP 13506-900; Rio Claro; São Paulo; Brazil
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31
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Peloso PL, Faivovich J, Grant T, Gasparini JL, Haddad CF. An Extraordinary New Species ofMelanophryniscus(Anura, Bufonidae) from Southeastern Brazil. AMERICAN MUSEUM NOVITATES 2012. [DOI: 10.1206/3762.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Faivovich J, Ferraro DP, Basso NG, Haddad CF, Rodrigues MT, Wheeler WC, Lavilla EO. A phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae) based on mitochondrial and nuclear gene sequences, with comments on the evolution of anuran foam nests. Cladistics 2012; 28:460-482. [DOI: 10.1111/j.1096-0031.2012.00406.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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34
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REP provides meaningful measurement of support across datasets. Mol Phylogenet Evol 2009; 55:340-342. [PMID: 19874907 DOI: 10.1016/j.ympev.2009.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 10/22/2009] [Accepted: 10/22/2009] [Indexed: 11/20/2022]
Abstract
The relative optimality of the best and next-best hypotheses indicates the strength of support for the optimal hypothesis and may be calculated as either the difference or ratio of their optimality scores. The Goodman-Bremer support measure (GB) calculates the support for a given clade in the most parsimonious tree as the difference between the length of the optimal tree and the optimal tree that lacks that clade. The ratio of explanatory power (REP) support measure calculates support as the ratio of optimality scores, which simplifies to the ratio of observed GB and the maximum possible GB, GB/GB(max). In this paper we show that REP support provides a logical basis for comparison of support across datasets and that recent claims to the contrary are incorrect.
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