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Santos LS, Roseno RS, Sol M, Dias IR. Another new species (and its not over yet) of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of southern Bahia, northeastern Brazil. Zootaxa 2023; 5374:519-532. [PMID: 38220845 DOI: 10.11646/zootaxa.5374.4.4] [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: 11/17/2023] [Indexed: 01/16/2024]
Abstract
The genus Phyllodytes, endemic to the Atlantic Forest, stands out for its life cycle being closely associated with bromeliads. Since the 2000s, the number of species in the group has more than doubled and the number is still increasing, a fact proven here with the description of Phyllodytes iuna sp. nov. This species, herein described using morphological and molecular evidence, is endemic to the Atlantic Forest of southern Bahia, in the northern portion of the Atlantic Forest Central Corridor. Phyllodytes iuna differs from both its sister species and most of its congeners by the color pattern on the dorsum and by the presence of a single tubercle in the tibiotarsal region. The genetic distance for a fragment of the 16S gene ranged from 4.4% to 5.0% between Phyllodytes iuna and its sister species (P. brevirostris and P. edelmoi), and from 5.8% to 14.2% with its congeners. The description of a new species of Phyllodytes serves as a reminder that our understanding of the groups diversity is far from complete. Despite the alarming rates of deforestation, the Atlantic Forest continues to hold significant untapped potential for unexplored biodiversity.
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Affiliation(s)
- Laisa S Santos
- Programa de Ps-Graduao em Zoologia; Departamento de Cincias Biolgicas; Universidade Estadual de Santa Cruz; Ilhus; Bahia; Brasil.
| | - Rafaella S Roseno
- Programa de Ps-Graduao em Zoologia; Departamento de Cincias Biolgicas; Universidade Estadual de Santa Cruz; Ilhus; Bahia; Brasil.
| | - Mirco Sol
- Herpetology Section; Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160; D-53113 Bonn; Germany.
| | - Iuri Ribeiro Dias
- Programa de Ps-Graduao em Zoologia; Departamento de Cincias Biolgicas; Universidade Estadual de Santa Cruz; Ilhus; Bahia; Brasil.
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Rees M, Neaves LE, Lewis GP, de Lima HC, Gagnon E. Phylogenomic and morphological data reveal hidden patterns of diversity in the national tree of Brazil, Paubrasilia echinata. AMERICAN JOURNAL OF BOTANY 2023; 110:e16241. [PMID: 37672601 DOI: 10.1002/ajb2.16241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
PREMISE Paubrasilia echinata (common names, pau brasil, brazilwood) is the national tree of Brazil and an endangered species endemic to the Brazilian Atlantic Forest. Over its wide distribution of 2000 km, its leaflets morphology exhibits extensive plasticity. Three morphotypes are commonly identified based on leaf size, but it is unclear if they represent distinct taxa or a single polymorphic species. This study aims to clarify the taxonomic position of the three morphotypes to inform conservation decisions. METHODS A morphometric study of leaf characters of herbarium specimens was coupled with genetic analyses using genotype-by-sequencing data. We used maximum-likelihood and coalescent methods to evaluate the phylogenetic and population structure of the species. We compared these with a morphological dendrogram built from hierarchical clustering. RESULTS Two of the three morphotypes formed separately evolving lineages, the third morphotype formed two geographically separate lineages, and northern trees with intermediate leaf morphology formed a separate fifth lineage. Leaflet size varied by over 35-fold, and although morphological clustering generally matched the genetic patterns, there were some overlaps, highlighting the cryptic diversity within this group. CONCLUSIONS Our genetic and morphological results provide some evidence that cultivated trees from different states in Brazil seem to have a limited genetic origin and do not reflect the broader genetic and geographical diversity of the species. As a result, more care is likely needed to preserve the overall genomic diversity of this endangered and iconic species.
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Affiliation(s)
- Mathew Rees
- Tropical Diversity, Royal Botanic Garden Edinburgh, Edinburgh, EH5 3LR, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Linda E Neaves
- Tropical Diversity, Royal Botanic Garden Edinburgh, Edinburgh, EH5 3LR, UK
- Fenner School of Environment & Society, Australian National University, Australian Capital Territory, Australia
| | - Gwilym P Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - Haroldo C de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915, Rio de Janeiro, RJ, 22460-030, Brazil
- Instituto Nacional da Mata Atlântica/INMA-MCTI, Av. José Ruschi, 4, Centro, Santa Teresa, Espírito Santo, Brazil
| | - Edeline Gagnon
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, 85352, Freising-Weihenstephan, Germany
- Department of Integrative BIology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
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3
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Fouquet A, Réjaud A, Rodrigues MT, Ron SR, Chaparro JC, Osorno M, Werneck FP, Hrbek T, Lima AP, Camacho-Badani T, Jaramillo-Martinez AF, Chave J. Diversification of the Pristimantis conspicillatus group (Anura: Craugastoridae) within distinct neotropical areas throughout the Neogene. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2130464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Universidade de São Paulo Instituto de Biociências, São Paulo, SP, Brazil
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Juan C. Chaparro
- Museo de Biodiversidad del Perú, Urbanización Mariscal Gamarra A-61, Zona 2, Cusco, Peru
- Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Paraninfo Universitario (Plaza de Armas s/n), Cusco, Perú
| | - Mariela Osorno
- Instituto Amazónico de Investigaciones Científicas SINCHI, Sede enlace. Calle 20 # 5-44, Bogotá, Colombia
| | - Fernanda P. Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, 69080-971, AM, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, 69080-900, AM, Brazil
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, Manaus, 69080-971, AM, Brazil
| | | | - Andres F. Jaramillo-Martinez
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Prédio 40, sala 110, Porto Alegre, 90619-900, RS, Brazil
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse, 31077, France
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4
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Skorinov DV, Bozkurt E, Olgun K, Litvinchuk SN. Ventral and lateral spot patterns differentiation between three smooth newt species (Amphibia: Salamandridae: Lissotriton). ACTA ZOOL ACAD SCI H 2022. [DOI: 10.17109/azh.68.3.261.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The location, shape and area of dark spots on the belly, throat and sides of the body of three closely related species of smooth newts (Lissotriton kosswigi, L. schmidtleri and L. vulgaris) were analysed. Differences were found between species and sexes in the location and shape of dark spots on the belly, throat and lateral surfaces of the body. Discriminant analysis of these spot characteristics allows to identificate of males of all three species with a high degree of confidence (85–91%). In females, only L. vulgaris was correctly distinguished from the other two species (accuracy 81–94%). Anatolian and Thracian populations of L. schmidtleri have very similar patterns of dark spots, which confirm their conspecificity. The differences in the location and size of dark spots make possible successful identification of the species during field research and study of museum specimens. The developed method could be useful for comparative studies of other animal species which have spotted camouflage or aposematic colouration.
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Fouquet A, Peloso P, Jairam R, Lima AP, Mônico AT, Ernst R, Kok PJR. Back from the deaf: integrative taxonomy revalidates an earless and mute species, Hylodes grandoculis van Lidth de Jeude, 1904, and confirms a new species of Pristimantis Jiménez de la Espada, 1870 (Anura: Strabomantidae) from the Eastern Guiana Shield. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00564-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Barbo FE, Grazziotin FG, Pereira-Filho GA, Freitas MA, Abrantes SH, Kokubum MNDC. Isolated by dry lands: integrative analyses unveil the existence of a new species and a previously unknown evolutionary lineage of Brazilian Lanceheads (Serpentes: Viperidae: Bothrops) from a Caatinga moist-forest enclave. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2021-0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Here we describe a new species of Lancehead (Bothrops jabrensis sp. nov.) based on three individuals sampled from a previously unknown population from Pico do Jabre, an isolated and small Caatinga moist-forest enclave (CMFE) located in northeastern Brazil. Although this new species has an external morphology resembling those found in representatives of the Bothrops jararaca (Wied-Neuwied, 1824) species group, B. jabrensis can be diagnosed by a combination of meristic and color characters. Molecular phylogenetic analysis indicates the new species represents a unique and highly divergent lineage within Bothrops revealing the existence of a previously unknown phylogenetic lineage that has been evolving as an independent unit for more than 8 million years. Additionally, the estimated divergence time of this lineage conflicts with some proposed scenarios of historical processes associated with the evolution of CMFEs. Finally, the uniqueness of this species indicates its relevance for the maintenance of the phylogenetic diversity of Lanceheads in South America. Like other CMFEs, Pico do Jabre is consistently threatened by poaching, illegal fires, deforestation for agricultural purposes, and illegal logging. The restricted distribution of B. jabrensis, in a small and disturbed CMFE, strongly suggests that this species is critically endangered and is likely approaching extinction as a natural population.
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Affiliation(s)
- Fausto E. Barbo
- Laboratório de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brazil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Gentil A. Pereira-Filho
- Laboratório de Ecologia Animal, Departamento de Engenharia e Meio Ambiente, Centro de Ciências Aplicadas e Educação, Universidade Federal da Paraíba, 58297-000, Rio Tinto, PB, Brazil
| | - Marco A. Freitas
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Estação Ecológica de Murici, Rua Marino Vieira de Araújo, 32, 57820-000, Cidade Alta, Murici, AL, Brazil
| | - Stephenson H.F. Abrantes
- Laboratório de Ecomorfologia Animal, Centro de Saúde e Tecnologia Rural, Universidade Federal de Campina Grande, Avenida Universitária, s/n, 58708-110, Patos, PB, Brazil
| | - Marcelo N. de C. Kokubum
- Laboratório de Herpetologia, Centro de Saúde e Tecnologia Rural, Universidade Federal de Campina Grande, Avenida Universitária, s/n, 58708-110, Patos, PB, Brazil
- Programa de Pós-graduação em Ecologia e Conservação, Universidade Estadual da Paraíba, 58429-500, Campina Grande, PB, Brazil
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Borges LMS, Treneman NC, Haga T, Shipway JR, Raupach MJ, Altermark B, Carlton JT. Out of taxonomic crypsis: A new trans-arctic cryptic species pair corroborated by phylogenetics and molecular evidence. Mol Phylogenet Evol 2021; 166:107312. [PMID: 34530118 DOI: 10.1016/j.ympev.2021.107312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/06/2021] [Accepted: 09/09/2021] [Indexed: 01/17/2023]
Abstract
Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Shipworms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentagonalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.
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Affiliation(s)
- Luísa M S Borges
- L(3) Scientific Solutions, Runder Berg 7e, 21502 Geesthacht, Germany.
| | - Nancy C Treneman
- Oregon Institute of Marine Biology, P.O. Box 5389, Charleston, OR 97420, USA.
| | - Takuma Haga
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan.
| | - J Reuben Shipway
- Institute of Marine Sciences, University of Portsmouth, Ferry Rd, Portsmouth, UK. & Microbiology Department, University of Massachusetts, Amherst, MA, USA.
| | - Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany.
| | - Bjørn Altermark
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, PB 6050 Langnes, 9037 Tromsø, Norway.
| | - James T Carlton
- Ocean & Coastal Studies Program, Williams College-Mystic Seaport, Mystic, CT 06355, USA.
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Onn Chan K, Hutter CR, Wood PL, Su YC, Brown RM. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). Syst Biol 2021; 71:40-57. [PMID: 33964168 DOI: 10.1093/sysbio/syab034] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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9
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Motta AP, Taucce PPG, Haddad CFB, Canedo C. A new terraranan genus from the Brazilian Atlantic Forest with comments on the systematics of Brachycephaloidea (Amphibia: Anura). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Paula Motta
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Pedro Paulo Goulart Taucce
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Célio Fernando Baptista Haddad
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP) Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Clarissa Canedo
- Departamento de Zoologia Instituto de Biologia Roberto Alcantara Gomes Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil
- Setor de Herpetologia Departamento de Vertebrados Museu Nacional Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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Oliveira PMDA, Mello AVAD, Dubeux MJM, Oliveira SBDA, Lourenço GF, Nunes PMS. Herpetofauna of Matas de Água Azul, an Atlantic Forest remnant in Serra do Mascarenhas, Pernambuco state, Brazil. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2020-1063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: The northern most portion of Atlantic Forest is currently considered as the most vulnerable and threatened in this ecoregion, while also harboring the ecoregion’s least studied biota. Herein we present results of a herpetofaunistic survey in Refúgio de Vida Silvestre (Wildlife Refuge) Matas de Água Azul (RVSMAA), in the mountain range Serra do Mascarenhas, northeastern state of Pernambuco, Brazil, one of the largest forest remnants in the northern Atlantic Forest. The sampling was carried out in four expeditions using methods of visual searching and pitfall traps. A total of 43 species of amphibians and 40 species of reptiles were registered, including anurans, caecilians, lizards, snakes and chelonians. The richness recorded represented 56% of amphibians and 20% of reptiles registered in the Atlantic Forest north of the São Francisco River. The RVSMAA holds a high diversity of amphibians and reptiles, representing one of the highest levels of richness in the northern Atlantic Forest. The record of seven species included in some of the threatened species lists reinforces the importance of the area for the conservation of the Atlantic Forest herpetofauna and adds relevant information to our knowledge of northern Atlantic Forest biodiversity and aids in its assessment of conservation.
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Alves-dos-Santos TFSS, Forti LR, Napoli MF. Feeding habits of the Robber Frog Pristimantis paulodutrai (Bokermann, 1975) in northeastern Brazil. BIOTA NEOTROPICA 2021. [DOI: 10.1590/1676-0611-bn-2020-1098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Studying feeding habits is crucial to understand complex predator-prey interactions. Even though anurans play a fundamental role in the control of arthropods populations, the diet of several Neotropical species is poorly known. We describe the frequency and occurrence of prey items and their dry mass in stomach contents of the Robber Frog Pristimantis paulodutrai in the north east of the state of Bahia, Brazil. Based on the stomach contents of 30 individuals, Araneae, Isopoda, and Formicidae were found to be the most important food items. The generalist diet of this frog, which seems to be phylogenetically conserved among Pristimantis, is likely to be linked to its ecological dominance in the habitats surveyed. Our study corroborates the high trophic relevance of Robber Frogs in tropical forests as generalist predators.
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Menezes L, Batalha‐Filho H, Garda AA, Napoli M. Tiny treefrogs in the Pleistocene: Phylogeography of
Dendropsophus oliveirai
in the Atlantic Forest and associated enclaves in northeastern Brazil. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lucas Menezes
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | - Henrique Batalha‐Filho
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis ‐ LAR Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Marcelo Napoli
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
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13
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Damasceno RP, Carnaval AC, Sass C, Sousa Recoder R, Moritz C, Trefaut Rodrigues M. Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata). Mol Phylogenet Evol 2020; 154:106993. [PMID: 33148523 DOI: 10.1016/j.ympev.2020.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.
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Affiliation(s)
- Roberta P Damasceno
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil; Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York and the Biology Program at the Graduate Center of CUNY, 160 Convent Avenue, Marshak Life Science Building J-526, New York, NY 10031, USA.
| | - Chodon Sass
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Renato Sousa Recoder
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia.
| | - Miguel Trefaut Rodrigues
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
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Merckelbach LM, Borges LMS. Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species. Mol Ecol Resour 2020; 20:1761-1768. [PMID: 32623815 DOI: 10.1111/1755-0998.13222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022]
Abstract
Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.
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Affiliation(s)
- Lucas M Merckelbach
- Centre for Materials and Coastal Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
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