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Almeida-Silva D, Servino LM, Pontes-Nogueira M, Sawaya RJ. Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae). PeerJ 2024; 12:e17232. [PMID: 38646479 PMCID: PMC11027904 DOI: 10.7717/peerj.17232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a "south-north" or a "north-south" direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines' ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.
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Affiliation(s)
- Diego Almeida-Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Miguel Lillo, Unidad Ejecutora Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Leonardo Matheus Servino
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Matheus Pontes-Nogueira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Ricardo J. Sawaya
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
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2
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Xia L, Cai F, Chen S, Cai Y, Zhou K, Yan J, Li P. Phylogenetic Analysis and Genetic Structure of Schlegel's Japanese Gecko ( Gekko japonicus) from China Based on Mitochondrial DNA Sequences. Genes (Basel) 2022; 14:18. [PMID: 36672759 PMCID: PMC9858143 DOI: 10.3390/genes14010018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/07/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Gekko japonicus, i.e., Schlegel's Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations.
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Affiliation(s)
- Longjie Xia
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fengna Cai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shasha Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yao Cai
- School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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3
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Coelho FEA, Guillory WX, Gehara M. Coalescent simulations indicate that the São Francisco River is a biogeographic barrier for six vertebrates in a seasonally dry South American forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.983134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The riverine barrier hypothesis has been extensively explored in Neotropical rainforests, while its importance in drier regions such as the Caatinga, a seasonally dry tropical forest in northeastern Brazil, has only recently received more attention. The Caatinga is bisected by the São Francisco River (SFR), which has long been suggested to be an important biogeographic feature in the region. However, recent studies have found mixed support for the role of the SFR as a hard barrier, most of them relying on the presence or absence of genetic breaks congruent with its course. Here, we used published multilocus and next-generation data from six vertebrate species to test the SFR’s strength as a barrier. Using model-based approaches (approximate Bayesian computation and supervised machine learning), we tested demographic models incorporating full, intermediate, and zero migration across the SFR, estimating divergence times and migration rates for each species. We found support for the SFR’s role as a barrier, allowing gene flow for some species. Estimated divergence times varied among species but are limited to the late Pleistocene, coherent with one of several proposed paleocourse changes in the river’s geological history. Contrary to the mixed results of previous studies, our study supports the SFR as an important phylogeographic barrier across different taxonomic groups, driving diversification in the Caatinga.
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4
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Rossigalli-Costa N, Kohlsdorf T. Native Lizards Living in Brazilian Cities: Effects of Developmental Environments on Thermal Sensitivity and Morpho-Functional Associations of Locomotion. Front Physiol 2022; 13:891545. [PMID: 35910576 PMCID: PMC9335278 DOI: 10.3389/fphys.2022.891545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
Environmental conditions often affect developmental processes and consequently influence the range of phenotypic variation expressed at population level. Expansion of urban sites poses new challenges for native species, as urbanization usually affects the intensity of solar exposure and shade availability, determining the thermal regimes organisms are exposed to. In this study, we evaluate the effects of different developmental conditions in a Tropidurus lizard commonly found in Brazilian urban sites. After incubating embryos of Tropidurus catalanensis in two different thermal regimes (Developmental Environments [DE]: cold 24°C and warm 30°C), we measured morphological traits in the neonates and quantified locomotor performance in horizontal and vertical surfaces at three temperatures [Test Temperatures (TT) = 24°C, 30°C and 36°C]. Results indicate effects of developmental temperatures on morphological features, expressing functional implications that might be decisive for the viability of T. catalanensis in urbanized areas. Lizards ran similarly on horizontal and vertical surfaces, and isolated analyses did not identify significant effects of DE or TT on the sprint speeds measured. Absolute Vmax (i.e., the maximum sprint speed reached among all TTs) positively correlated with body size (SVL), and neonates from the warm DE (30°C) were larger than those from the cold DE (24°C). Morpho-functional associations of absolute Vmax also involved pelvic girdle width and forelimb, hindlimb, trunk, and tail lengths. Emerging discussions aim to understand how animals cope with abrupt environmental shifts, a likely common challenge in urbanized sites. Our findings add a new dimension to the topic, providing evidence that temperature, an environmental parameter often affected by urbanization, influences the thermal sensitivity of locomotion and the morphological profile of T. catalanensis neonates. Thermal sensitivity of specific developmental processes may influence the ability of these lizards to remain in habitats that change fast, as those suffering rapid urbanization due to city growth.
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5
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Camurugi F, Oliveira EF, Lima GS, Marques R, Magalhães FM, Colli GR, Mesquita DO, Garda AA. Isolation by distance and past climate resistance shaped the distribution of genealogical lineages of a neotropical lizard. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2084470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Eliana F. Oliveira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil
| | - Guilherme S. Lima
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Ricardo Marques
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Felipe M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark, Newark, New Jersey, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Daniel O. Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Adrian A. Garda
- Departamento Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal, Rio Grande do Norte, Brazil
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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7
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Pirani RM, Tonini JFR, Thomaz AT, Napoli MF, Encarnação LC, Knowles LL, Werneck FP. Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.765977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.
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8
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Rivera D, Prates I, Firneno TJ, Rodrigues MT, Caldwell JP, Fujita MK. Phylogenomics, introgression, and demographic history of South American true toads (Rhinella). Mol Ecol 2021; 31:978-992. [PMID: 34784086 DOI: 10.1111/mec.16280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/24/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.
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Affiliation(s)
- Danielle Rivera
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Janalee P Caldwell
- Sam Noble Museum & Department of Biology, University of Oklahoma, Norman, Oklahoma, 73072-7029, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, TX, USA
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9
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Thomé MTC, Carstens BC, Rodrigues MT, Galetti PM, Alexandrino J, Haddad CFB. A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad. Heredity (Edinb) 2021; 127:363-372. [PMID: 34304245 PMCID: PMC8478927 DOI: 10.1038/s41437-021-00460-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
The process of diversification can be studied at the phylogeographic level by attempting to identify the environmental features that promote and maintain population divergence. Here we investigate diversification in Rhinella granulosa, a Neotropical toad from northeastern Brazil, by testing a range of hypotheses that encompass different putative mechanisms reducing gene flow among populations. We sequenced single nucleotide polymorphisms and examined individual predictions related to the role of geographic barriers (rivers), ecological gradients, historical habitat stability, and spatial variation in climate seasonality, also known as the asynchrony of seasons hypothesis. This hypothesis postulates that temporal asynchrony of wet and dry seasons over short distances causes parapatric populations to become isolated by time. After determining genetic structure, inferring past distributions, ranking demographic models, and estimating the power of monthly climatic variables, our results identified two populations that are not associated with geographic barriers, biome gradients, or historical refugia. Instead, they are predicted by spatial variation in monthly rainfall and minimum temperature, consistent with the asynchrony of seasons hypothesis, supported also by our comparative framework using multiple matrix regression and linear mixed effects modeling. Due to the toad's life history, climate likely mediates gene flow directly, with genetic differentiation being provoked by neutral mechanisms related to climate driven population isolation, and/or by natural selection against migrants from populations with different breeding times. The asynchrony of seasons hypothesis is seldom considered in phylogeographic studies, but our results indicate that it should be tested in systems where breeding is tightly coupled with climate.
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Affiliation(s)
- Maria Tereza C Thomé
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - João Alexandrino
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
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10
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Rossigalli-Costa N, Cury de Barros F, Cipriano AP, Prado Prandini L, Medeiros de Andrade T, Rothier PS, Lofeu L, Brandt R, Kohlsdorf T. A guide to incubate eggs of Tropidurus lizards under laboratory conditions. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:576-584. [PMID: 34496131 DOI: 10.1002/jez.b.23095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 01/11/2023]
Abstract
Studies in Evo-Devo benefit from the use of a variety of organisms, as comparative approaches provide a better understanding of Biodiversity and Evolution. Standardized protocols to incubate eggs and manipulate embryo development enable postulation of additional species as suitable biological systems for research in the field. In the past decades, vertebrate lineages such as Squamata (lizards, snakes, and amphisbaenians) emerged as crucial study systems for addressing topics as diverse as phenotypic evolution and climate change. However, protocols for maintaining gravid females and incubating eggs in the lab under experimental conditions are available to only a few squamate species. This resource article presents a simple incubation guide that standardizes conditions to maintain embryos of Tropidurus catalanensis (Squamata: Tropiduridae) under different experimental conditions, manipulating relevant environmental factors like temperature and humidity. We identified associated effects relating the egg incubation condition to developmental stage, incubation time, hatching success, and resulting morphotypes. Temperature and humidity play a key role in development and require attention when establishing the experimental design. Current literature comprises information for Tropidurus lizards that ponders how general in Squamata are the ecomorphs originally described for Anolis. Studies evaluating phenotypic effects of developmental environments suggest plasticity in some of the traits that characterize the ecomorphological associations described for this family. We expect that this incubation guide encourages future studies using Tropidurus lizards to address Evo-Devo questions.
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Affiliation(s)
- Nathalia Rossigalli-Costa
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | - Fábio Cury de Barros
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Department of Ecology and Evolutionary Biology, ICAQF, Federal University of São Paulo. Rua Prof. Artur Riedel, Diadema, Brazil.,University of the Estate of Minas Gerais (UEMG/Passos). Av. Juca Stockler 1130, Passos, Brazil
| | - Ana Paula Cipriano
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | - Luísa Prado Prandini
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
| | | | - Priscila S Rothier
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, 55 Rue Buffon, Paris, France
| | - Leandro Lofeu
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Renata Brandt
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil.,Science North, Sudbury, Ontario, Canada
| | - Tiana Kohlsdorf
- Department of Biology, FFCLRP, University of São Paulo. Avenida Bandeirantes, Ribeirão Preto, Brazil
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11
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Fegies AC, Carmignotto AP, Perez MF, Guilardi MD, Lessinger AC. Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes. Mol Phylogenet Evol 2021; 162:107213. [PMID: 34029717 DOI: 10.1016/j.ympev.2021.107213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.
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Affiliation(s)
- Ana Cláudia Fegies
- Departamento de Engenharia Ambiental, Universidade Estadual Paulista (UNESP), Campus Sorocaba, Av. Três de Março 511, Sorocaba, São Paulo CEP 18087-180, Brazil
| | - Ana Paula Carmignotto
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
| | - Manolo Fernandez Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís km 235, São Carlos, São Paulo CEP 13565-905, Brazil
| | - Mariana Dias Guilardi
- Laboratório de Ecologia e Evolução, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, São Paulo CEP 05503-000, Brazil
| | - Ana Cláudia Lessinger
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
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12
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Carvalho AF, Menezes RST, Miranda EA, Costa MA, Del Lama MA. Comparative phylogeography and palaeomodelling reveal idiosyncratic responses to climate changes in Neotropical paper wasps. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The impact of the broad disjunction between Amazonia and the Atlantic Forest on biodiversity has been the theme of several discussions in recent decades. Here, we evaluate the effects of dependence on humid environments and the role of historical factors on the level, distribution and structuring of genetic variation in widely distributed Neotropical insects. For such, we test whether climatically stable zones (i.e. refuges) in both Amazonia and the Atlantic Forest concentrate higher genetic diversity in the social paper wasps Angiopolybia pallens and Synoeca surinama. We found that historical events have avoided the interchange of A. pallens between both rainforests at least since the Early Pliocene and that ancient colonization in north-western Amazonia and the Bahia refuge significantly predicts genetic diversity in populations of this species. Conversely, the split between the Atlantic Forest and remaining western populations of S. surinama is more recent (Plio-Pleistocene); this species has considerably lower genetic diversity than A. pallens and such diversity is mostly concentrated in Amazonia and in the cerrado biome (savanna) than in the Atlantic Forest. Finally, we propose that the occurrence of species that exhibit such distribution patterns should be taken into consideration when establishing areas for conservation.
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Affiliation(s)
- Antônio F Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Instituto Nacional da Mata Atlântica, Santa Teresa, Espírito Santo, Brazil
| | - Rodolpho S T Menezes
- Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Elder A Miranda
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
- Observatório UniFG do Semiárido Nordestino, Núcleo de Pesquisa da Conservação e Biodiversidade do Semiárido – CONBIOS, Centro Universitário de Guanambi – UniFG, Guanambi, Guanambi, Bahia, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Marco A Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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13
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Almeida JPFA, Thomé MTC, Sturaro MJ, Pereira RJ, Mott T. The relative role of glacial refugia and longstanding barriers in the diversification of a fossorial squamate. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783716] [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)
- João P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Maria Tereza C. Thomé
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Av. Professor Artur Riedel, 275, Jardim Eldorado, Diadema, São Paulo, CEP 09972-270, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig- Maximilians-Universität München, Grosshaderner Strasse 2, München, 82152, Germany
| | - Tamí Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
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14
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Rivera D, Prates I, Rodrigues MT, Carnaval AC. Effects of climate and geography on spatial patterns of genetic structure in tropical skinks. Mol Phylogenet Evol 2020; 143:106661. [DOI: 10.1016/j.ympev.2019.106661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
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15
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Mângia S, Oliveira EF, Santana DJ, Koroiva R, Paiva F, Garda AA. Revising the taxonomy of
Proceratophrys
Miranda‐Ribeiro, 1920 (Anura: Odontophrynidae) from the Brazilian semiarid Caatinga: Morphology, calls and molecules support a single widespread species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Mângia
- Departamento de Sistemática e Ecologia Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Universidade Federal da Paraı́ba João Pessoa Brazil
| | - Eliana Faria Oliveira
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Diego José Santana
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Ricardo Koroiva
- Laboratório de Citotaxonomia e Insetos Aquáticos Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Fernando Paiva
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
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16
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Hamdan B, Guedes TB, Carrasco PA, Melville J. A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes, Viperidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12398] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Breno Hamdan
- Departamento de Genética Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
- Laboratório de Coleções Biológicas e Biodiversidade Instituto Vital Brazil Niterói Brazil
| | - Thaís B. Guedes
- Programa de Pós‐Graduação em Biodiversidade, Ambiente e Saúde Centro de Estudos Superiores de Caxias Universidade Estadual do Maranhão Caxias Brazil
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Center University of Gothenburg Göteborg Sweden
| | - Paola A. Carrasco
- Facultad de Ciencias Exactas Físicas y Naturales Centro de Zoología Aplicada Universidad Nacional de Córdoba Córdoba Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Instituto de Diversidad y Ecología Animal (IDEA) Córdoba Argentina
| | - Jane Melville
- Sciences Department Museum Victoria Melbourne Vic. Australia
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17
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Lanna FM, Gehara M, Werneck FP, Fonseca EM, Colli GR, Sites JW, Rodrigues MT, Garda AA. Dwarf geckos and giant rivers: the role of the São Francisco River in the evolution of Lygodactylus klugei (Squamata: Gekkonidae) in the semi-arid Caatinga of north-eastern Brazil. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Species diversification can be strongly influenced by geomorphological features, such as mountains, valleys and rivers. Rivers can act as hard or soft barriers to gene flow depending on their size, speed of flow, historical dynamics and regional topographical characteristics. The São Francisco River (SFR) is the largest perennial river in the Caatinga biome in north-eastern Brazil and has been considered a barrier to gene flow and dispersal. Herein, we evaluated the role of the SFR on the evolution of Lygodactylus klugei, a small gecko from the Caatinga. Using a single-locus species delimitation method (generalized mixed Yule coalescent), we defined lineages (haploclades). Subsequently, we evaluated the role of the SFR in structuring genetic diversity in this species using a multilocus approach to quantify migration across margins. We also evaluated genetic structure based on nuclear markers, testing the number of populations found through an assignment test (STRUCTURE) across the species distribution. We recovered two mitochondrial lineages structured with respect to the SFR, but only a single population was inferred from nuclear markers. Given that we detected an influence of the SFR only on mitochondrial markers, we suggest that the current river course has acted as a relatively recent geographical barrier for L. klugei, for ~450 000 years.
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Affiliation(s)
- Flávia M Lanna
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Emanuel M Fonseca
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, USA
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal, RN, Brazil
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18
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Perez R, Borges-Martins M. Integrative taxonomy of small worm lizards from Southern South America, with description of three new species (Amphisbaenia: Amphisbaenidae). ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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20
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Bruschi DP, Peres EA, Lourenço LB, Bartoleti LFDM, Sobral-Souza T, Recco-Pimentel SM. Signature of the Paleo-Course Changes in the São Francisco River as Source of Genetic Structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) Treefrog. Front Genet 2019; 10:728. [PMID: 31475035 PMCID: PMC6702341 DOI: 10.3389/fgene.2019.00728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/11/2019] [Indexed: 11/13/2022] Open
Abstract
Historical processes that have interrupted gene flow between distinct evolutionary lineages have played a fundamental role in the evolution of the enormous diversity of species found in the Neotropical region. Numerous studies have discussed the role of geographic barriers and Pleistocene forest refugia in the diversification of the region's biodiversity. In the present study, we investigated the relative contribution of these different factors to the evolutionary history of Pithecopus nordestinus, a Neotropical tree frog, which is amply distributed in the Brazilian Atlantic Forest and adjacent areas of the Caatinga biome. We used an extensive sample and multilocus DNA sequences to provide an overview of the intraspecific genetic diversity of P. nordestinus, characterize historical diversification patterns, and identify possible phylogenetic splits. We tested different scenarios of diversification based on Pleistocene Refugia and river barrier models using approximate Bayesian computation (ABC) and ecological niche modeling (ENM). The phylogenetic approach indicate the occurrence of processes of phylogeographic divergence in both time and space, related to historical shifts in the course of the São Francisco River during Plio-Pleistocene period, resulting in two principal, highly divergent clades. The ABC model provided strong statistical support for this scenario, confirming the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus. We believe that the climatic changes that occurred during the Pleistocene also played a secondary role in the genetic signatures identified, reinforcing the divergence of populations isolated by physical barriers. These findings reinforce the conclusion that the two models of diversification (geographic barriers and refugia) are not mutually exclusive in the Neotropical domain but may interact extensively during the diversification of species on a regional scale.
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Affiliation(s)
| | - Elen Arroyo Peres
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luciana Bolsoni Lourenço
- Department of Structural and Functional Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Thadeu Sobral-Souza
- Spatial Ecology and Conservation Lab (LEEC), São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
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21
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Integrating phylogeography and ecological niche modelling to test diversification hypotheses using a Neotropical rodent. Evol Ecol 2019. [DOI: 10.1007/s10682-019-09968-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Passos JF, Nascimento DB, Menezes RST, Adaime R, Araujo EL, Lima KM, Zucchi RA, Teles BR, Nascimento RR, Arce RR, Barr NB, McPheron BA, Silva JG. Genetic structure and diversity in Brazilian populations of Anastrepha obliqua (Diptera: Tephritidae). PLoS One 2018; 13:e0208997. [PMID: 30571687 PMCID: PMC6301665 DOI: 10.1371/journal.pone.0208997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/28/2018] [Indexed: 11/26/2022] Open
Abstract
Anastrepha obliqua (Macquart), the West Indian fruit fly, is one of the most economically important pest species in the Neotropical region. It infests an extensive range of host plants that include over 60 species. The geographic range of A. obliqua is from northern Mexico to southern Brazil and includes the Caribbean Islands. Previous molecular studies have revealed significant genetic structure among populations. We used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate structure and genetic diversity of A. obliqua populations from Brazil. We analyzed a total of 153 specimens from the Amazon Forest, Atlantic Forest, Cerrado, and Caatinga biomes. Our study revealed weak genetic structure among the A. obliqua Brazilian populations sampled. Collections from the Amazon Forest had similar haplotype diversity compared to previously reported estimates for collections from the Caribbean and both populations are also closely related to each other, thus challenging the hypothesis that A. obliqua originated in the Caribbean and then moved to other regions of the Americas. Therefore, further evidence is necessary to draw a definite conclusion about the putative center of origin for A. obliqua. Additionally, we suggest a putative historical migration from the west to the east for the A. obliqua Brazilian populations, which could explain the high genetic diversity for this fly in the Amazon Forest and low genetic diversity in the other Brazilian biomes.
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Affiliation(s)
- Joseane F. Passos
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz. Ilhéus, Bahia, Brazil
| | - Danilo B. Nascimento
- Departamento de Ciências Biológicas, Universidade Federal do Amapá. Macapá, Amapá, Brazil
| | - Rodolpho S. T. Menezes
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras - Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ricardo Adaime
- Empresa Brasileira de Pesquisa Agropecuária, Macapá, Amapá, Brazil
| | - Elton L. Araujo
- Departamento de Ciências Biológicas. Universidade Federal Rural do Semi-Árido, Mossoró, Rio Grande do Norte, Brazil
| | - Kátia M. Lima
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz. Ilhéus, Bahia, Brazil
| | - Roberto A. Zucchi
- Departamento de Entomologia. Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Beatriz Ronchi Teles
- Departamento de Entomologia. Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Ruth R. Nascimento
- Departamento de Ciências Biológicas. Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Raul Ruiz Arce
- USDA APHIS Science and Technology, Mission Laboratory, Edinburg, Texas, United States of America
| | - Norman B. Barr
- USDA APHIS Science and Technology, Mission Laboratory, Edinburg, Texas, United States of America
| | - Bruce A. McPheron
- Department of Entomology, Ohio University, Columbus, Ohio, United States of America
| | - Janisete G. Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz. Ilhéus, Bahia, Brazil
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23
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Jacobina UP, Lima SMQ, Maia DG, Souza G, Batalha-Filho H, Torres RA. DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras. Genetica 2018; 146:505-515. [DOI: 10.1007/s10709-018-0043-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 10/09/2018] [Indexed: 02/04/2023]
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24
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Raposo do Amaral F, Maldonado‐Coelho M, Aleixo A, Luna LW, Rêgo PSD, Araripe J, Souza TO, Silva WAG, Thom G. Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in
Antilophia
manakins. Mol Ecol 2018; 27:4108-4120. [DOI: 10.1111/mec.14843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Fabio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Diadema SP Brazil
| | - Marcos Maldonado‐Coelho
- Departamento de Ecologia e Biologia Evolutiva Universidade Federal de São Paulo Diadema SP Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém PA Brazil
| | - Leilton W. Luna
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Péricles Sena do Rêgo
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Juliana Araripe
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Thainara O. Souza
- Laboratório de Genética e Conservação Instituto de Estudos Costeiros Universidade Federal do Pará Bragança PA Brazil
| | - Weber A. G. Silva
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos Fortaleza Brazil
| | - Gregory Thom
- Departamento de Genética e Biologia Evolutiva Universidade de São Paulo São Paulo SP Brazil
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25
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Costa WJEM, Amorim PF, Mattos JLO. Cryptic species diversity in the Hypsolebiasmagnificus complex, a clade of endangered seasonal killifishes from the São Francisco River basin, Brazilian Caatinga (Cyprinodontiformes, Aplocheilidae). Zookeys 2018:141-158. [PMID: 30100793 PMCID: PMC6079103 DOI: 10.3897/zookeys.777.25058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 11/29/2022] Open
Abstract
A great diversity of animal species adapted to life in the semi-arid Caatinga of northeastern Brazil, including seasonal killifishes, has been reported in the last three decades. More recently, field and molecular data have shown a high occurrence of cryptic species. The killifish group herein analysed, the Hypsolebiasmagnificus species complex, is endemic to the middle and southern portion of the Caatinga, occupying about 120 km along the floodplains of the middle São Francisco River and some adjacent tributaries. Species of this complex are rare and presently considered threatened with extinction, being uniquely found in pools protected by trees and bushes. Single-locus delimitation methods were used to test species limits of populations displaying different colour patterns along the whole distribution of the complex. All analyses consistently supported the three nominal species and two new, herein described: H.gardneri Costa, sp. n., from the floodplains of the middle São Francisco River and H.hamadryades Costa, sp. n., from the Gorotuba River floodplains. The phylogenetic analysis highly supports H.hamadryades as sister to a clade comprising H.gardneri and H.harmonicus. Our field observations suggest that H.hamadryades is a miniature species. This study indicates that the H.magnificus complex comprises cryptic species apparently endemic to small areas and extremely vulnerable to environmental changes, deserving high concern.
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Affiliation(s)
- Wilson J E M Costa
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Caixa Postal 68049, CEP 21941-971, Rio de Janeiro, Brazil Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Pedro F Amorim
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Caixa Postal 68049, CEP 21941-971, Rio de Janeiro, Brazil Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - José Leonardo O Mattos
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Caixa Postal 68049, CEP 21941-971, Rio de Janeiro, Brazil Federal University of Rio de Janeiro Rio de Janeiro Brazil
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26
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Lanna FM, Werneck FP, Gehara M, Fonseca EM, Colli GR, Sites JW, Rodrigues MT, Garda AA. The evolutionary history of Lygodactylus lizards in the South American open diagonal. Mol Phylogenet Evol 2018; 127:638-645. [PMID: 29906606 DOI: 10.1016/j.ympev.2018.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/05/2018] [Accepted: 06/06/2018] [Indexed: 11/16/2022]
Abstract
The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-supported monophyletic South American Lygodactylus, presumably resulting from a single trans-Atlantic dispersal event 29 Mya. Species delimitation analyses supported the existence of five putative species, three of them undescribed. Divergence times among L. klugei and the three putative undescribed species, all endemic to the SDTFs, are not congruent with the fragmentation of the PAH. However, fragmentation of the once broader and continuous SDTFs likely influenced the divergence of L. wetzeli in the Chaco and Lygodactylus sp. 3 (in a SDTF enclave in the Cerrado).
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Affiliation(s)
- Flávia M Lanna
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil.
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), 69067-375 Manaus, Amazonas, Brazil
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, 79th St. Central Park West, New York, NY 10024, United States
| | - Emanuel M Fonseca
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil
| | - Jack W Sites
- Department of Biology and Bean Life Science Museum, Brigham Young University, Provo, UT 84602, United States
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, 59078-900 Natal, RN, Brazil
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Sousa GA, Oliveira IS, Silva-Freitas FV, Viana AFSC, Neto BPS, Cunha FVM, Gonçalves RLG, Lima Filho ACM, Amaral MPM, Oliveira RDCM, Fernandes PD, Maciel JKS, da Silva TMS, Souza MDFV, Oliveira FA. Gastroprotective effect of ethanol extracts of cladodes and roots of Pilosocereus gounellei (A. Weber ex K. Schum.) Bly. Ex Rowl (Cactaceae) on experimental ulcer models. JOURNAL OF ETHNOPHARMACOLOGY 2018; 218:100-108. [PMID: 29471086 DOI: 10.1016/j.jep.2018.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 09/07/2017] [Accepted: 02/05/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Pilosocereus gounellei Cactaceae), popularly known as "xique xique", is a species native from Caatinga region of Northeast Brazil, which is used by traditional communities in folk medicine for a variety of health problems, especially inflammatory processes and gastritis. AIM OF THE STUDY The present study investigates the possible gastric antiulceractivity of ethanol extracts obtained from the cladodes and roots of Pilosocereus gounellei (EECPG and EERPG, respectively) and mechanisms of action underlying this effect. MATERIALS AND METHODS Mice were used for the evaluation of the acute toxicity, and mice and rats to study the gastroprotective activity. The gastroprotective action of EECPG and EERPG was analyzed in the absolute ethanol in mice, ischemia-reperfusion and cold restraint stress in rats. In the investigation of the gastroprotective mechanisms of EECPG and EERPG, the participation of the NO and prostaglandins, the levels of the non-protein sulfhydril groups (NP-SH) and the catalase activity using the ethanol-induced gastric mucosa lesion model and the quantification of the gastric mucus and the antisecretory activity through pylorus ligature model in rats were analyzed. RESULTS The animals did not present any signs of acute toxicity for the EECPG and EERPG, and it was not possible to calculate the DL50. EECPG and EERPG (200 and 400 mg/kg) exhibited a significant gastroprotective effect in absolute ethanol, ischemia-reperfusion-induced and cold restraint stress gastric lesion models. Gastroprotection of EECPG and EERPG (200 mg/kg) was significantly decreased in pre-treated mice with L-NAME. Our studies revealed that EECPG and EERPG (200 mg/kg) prevented the decrease of the non-protein sulfhydril groups (NPSH) and increased the catalase levels in ethanol-treated animals. However, the gastric secretion parameters (volume, [H+], pH) did not show any alteration. CONCLUSIONS Our results indicate that the ethanolic extract from the cladodes and roots of Pilosocereus gounellei exhibits a significant gastroprotection, because it inhibits the formation of gastric lesions using different models. The participation of the nitric oxide, prostaglandins, the non-protein sulfhydril groups (NP-SH), catalase seem to be involved in the gastroprotection activity of the EECPG and EERPG. Nevertheless, this activity does not seem to be related to antisecretory mechanisms.
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Affiliation(s)
- Glaubert A Sousa
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Irisdalva S Oliveira
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Francilene V Silva-Freitas
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Ana Flávia S C Viana
- Rua Capitao Francisco Pedro, 1016, Bairro: Rodolfo Teófilo, 60430372 Fortaleza, Ceará, Brazil.
| | - Benedito P S Neto
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Francisco Valmor M Cunha
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Rodrigo L G Gonçalves
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Antônio Carlos M Lima Filho
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Maurício P M Amaral
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Rita de Cássia M Oliveira
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
| | - Pedro D Fernandes
- Department of Agroecology and Agriculture, Center of Agricultural and Environmental Sciences, University of Paraiba State, 351, Baraúnas Street, Campina Grande, PB 58429-500, Brazil.
| | - Jéssica K S Maciel
- Post-Graduation Program in Development and Technological Innovation in Medicines, Health Science Center, Federal University of Paraiba, Campus I, João Pessoa PB 58051-900, Brazil.
| | - Tânia Maria S da Silva
- Postgraduate Program in Development and Technological Innovation in Medicines, Departmente of Molecular Sciences, Rural Federal University of Pernambuco, Campus Dois Irmãos Recife, PE 52171-900, Brazil.
| | - Maria de Fátima V Souza
- Post-Graduation Program in Development and Technological Innovation in Medicines, Health Science Center, Federal University of Paraiba, Campus I, João Pessoa PB 58051-900, Brazil.
| | - Francisco A Oliveira
- Medicinal Plants Research Center, Federal University of Piauí, (unnumbered), 64049-550 Teresina, Piauí, Brazil.
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Baranzelli MC, Cosacov A, Espíndola A, Iglesias MDR, Chan LM, Johnson LA, Sérsic AN. Echoes of the whispering land: interacting roles of vicariance and selection in shaping the evolutionary divergence of two Calceolaria (Calceolariaceae) species from Patagonia and Malvinas/Falkland Islands. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9938-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Costa WJEM, Amorim PF, Mattos JLO. Synchronic historical patterns of species diversification in seasonal aplocheiloid killifishes of the semi-arid Brazilian Caatinga. PLoS One 2018; 13:e0193021. [PMID: 29451915 PMCID: PMC5815601 DOI: 10.1371/journal.pone.0193021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/02/2018] [Indexed: 11/18/2022] Open
Abstract
The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography. We performed independent time-calibrated phylogenetic molecular analyses for two clades of sympatric and geographically widespread seasonal killifishes endemic to the Caatinga, the Hypsolebias antenori group and the Cynolebias alpha-clade. Our results consistently indicate that species diversification took place synchronically in both groups, as well as it is contemporary to diversification of other organisms adapted to life in the semi-arid Caatinga, including lizards and small mammals. Both groups originated during the Miocene, but species diversification started between the Late Miocene and Early Pliocene, when global cooling probably favoured the expansion of semi-arid areas. Synchronic diversification patterns found are chronologically related to Tertiary palaeogeographical reorganizations associated to continental drift and to Quaternary climatic changes, corroborating the recent proposal that South American biodiversity has been continuously shaped between the Late Paleogene and Pleistocene.
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Affiliation(s)
- Wilson J. E. M. Costa
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
- * E-mail:
| | - Pedro F. Amorim
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - José Leonardo O. Mattos
- Laboratory of Systematics and Evolution of Teleost Fishes, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
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30
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Oliveira EF, Martinez PA, São-Pedro VA, Gehara M, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Costa GC. Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard. Heredity (Edinb) 2017; 120:251-265. [PMID: 29238076 DOI: 10.1038/s41437-017-0017-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
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Affiliation(s)
- Eliana Faria Oliveira
- Pós-Graduação em Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil. .,Universidade Federal de Mato Grosso do Sul, Centro de Ciências Biológicas e da Saúde, Laboratório de Zoologia, Campo Grande, MS, Brazil.
| | - Pablo Ariel Martinez
- Universidade Federal de Sergipe, Laboratório de Pesquisas Integrativas em Biodiversidade (PIBi Lab), Pós-Graduação em Ecologia e Conservação, São Cristovão, SE, Brazil
| | - Vinícius Avelar São-Pedro
- Universidade Federal de São Carlos, Campus Lagoa do Sino, Centro de Ciências da Natureza, Buri, SP, Brazil
| | - Marcelo Gehara
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
| | | | - Daniel Oliveira Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Natal, RN, Brazil
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Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017; 1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
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Affiliation(s)
- Fabrícia F Nascimento
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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32
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The effects of Quaternary sea-level fluctuations on the evolutionary history of an endemic ground lizard (Tropidurus hygomi). ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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33
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Gehara M, Garda AA, Werneck FP, Oliveira EF, Fonseca EM, Camurugi F, Magalhães FDM, Lanna FM, Sites JW, Marques R, Silveira‐Filho R, São Pedro VA, Colli GR, Costa GC, Burbrink FT. Estimating synchronous demographic changes across populations using
hABC
and its application for a herpetological community from northeastern Brazil. Mol Ecol 2017; 26:4756-4771. [DOI: 10.1111/mec.14239] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/30/2017] [Accepted: 07/02/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Marcelo Gehara
- Department of Herpetology American Museum of Natural History New York NY USA
| | - Adrian A. Garda
- Departamento de Botânica e Zoologia Centro de Biociências Universidade Federal do Rio Grande do Norte Lagoa Nova Natal RN Brazil
| | - Fernanda P. Werneck
- Coordenação de Biodiversidade Programa de Coleções Científicas Biológicas Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus AM Brazil
| | - Eliana F. Oliveira
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências Biológicas e da Saúde Laboratório de Zoologia Cidade Universitária Universidade Federal do Mato Grosso do Sul Campo Grand MS Brazil
| | - Emanuel M. Fonseca
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Felipe Camurugi
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Felipe de M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Flávia M. Lanna
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Science Museum Brigham Young University Provo UT USA
| | - Ricardo Marques
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Ricardo Silveira‐Filho
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa PB Brazil
| | - Vinícius A. São Pedro
- Programa de Pós‐Graduação em Ecologia Universidade Federal do Rio Grande do Norte Lagoa Nova Natal, RN Brazil
- Centro de Ciências da Natureza Universidade Federal de São Carlos Buri SP Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Gabriel C. Costa
- Department of Biology Auburn University at Montgomery Montgomery AL USA
| | - Frank T. Burbrink
- Department of Herpetology American Museum of Natural History New York NY USA
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34
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The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps. Sci Rep 2017; 7:7689. [PMID: 28794485 PMCID: PMC5550474 DOI: 10.1038/s41598-017-07776-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species – the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.
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35
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Baranzelli MC, Cosacov A, Ferreiro G, Johnson LA, Sérsic AN. Travelling to the south: Phylogeographic spatial diffusion model in Monttea aphylla (Plantaginaceae), an endemic plant of the Monte Desert. PLoS One 2017; 12:e0178827. [PMID: 28582433 PMCID: PMC5459442 DOI: 10.1371/journal.pone.0178827] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/20/2017] [Indexed: 11/20/2022] Open
Abstract
Effects of Pleistocene climatic oscillations on plant phylogeographic patterns are relatively well studied in forest, savanna and grassland biomes, but such impacts remain less explored on desert regions of the world, especially in South America. Here, we performed a phylogeographical study of Monttea aphylla, an endemic species of the Monte Desert, to understand the evolutionary history of vegetation communities inhabiting the South American Arid Diagonal. We obtained sequences of three chloroplast (trnS–trnfM, trnH–psbA and trnQ–rps16) and one nuclear (ITS) intergenic spacers from 272 individuals of 34 localities throughout the range of the species. Population genetic and Bayesian coalescent analyses were performed to infer genealogical relationships among haplotypes, population genetic structure, and demographic history of the study species. Timing of demographic events was inferred using Bayesian Skyline Plot and the spatio-temporal patterns of lineage diversification was reconstructed using Bayesian relaxed diffusion models. Palaeo-distribution models (PDM) were performed through three different timescales to validate phylogeographical patterns. Twenty-five and 22 haplotypes were identified in the cpDNA and nDNA data, respectively. that clustered into two main genealogical lineages following a latitudinal pattern, the northern and the southern Monte (south of 35° S). The northern Monte showed two lineages of high genetic structure, and more relative stable demography than the southern Monte that retrieved three groups with little phylogenetic structure and a strong signal of demographic expansion that would have started during the Last Interglacial period (ca. 120 Ka). The PDM and diffusion models analyses agreed in the southeast direction of the range expansion. Differential effect of climatic oscillations across the Monte phytogeographic province was observed in Monttea aphylla lineages. In northern Monte, greater genetic structure and more relative stable demography resulted from a more stable climate than in the southern Monte. Pleistocene glaciations drastically decreased the species area in the southern Monte, which expanded in a southeastern direction to the new available areas during the interglacial periods.
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Affiliation(s)
- Matias C Baranzelli
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gabriela Ferreiro
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Leigh A Johnson
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
| | - Alicia N Sérsic
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
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36
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Miranda EA, Ferreira KM, Carvalho AT, Martins CF, Fernandes CR, Del Lama MA. Pleistocene climate changes shaped the population structure of Partamona seridoensis (Apidae, Meliponini), an endemic stingless bee from the Neotropical dry forest. PLoS One 2017; 12:e0175725. [PMID: 28410408 PMCID: PMC5391937 DOI: 10.1371/journal.pone.0175725] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/30/2017] [Indexed: 11/28/2022] Open
Abstract
Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup. The Mantel test revealed no isolation by distance. No evidence of a potential geographic barrier in the present that could explain the diversification between the P. seridoensis haplogroups was found. However, Pleistocene climatic changes may explain this differentiation, since the initial time for the P. seridoensis lineages diversification took place during the mid-Pleistocene, specifically the interglacial period, when the biota is presumed to have been more associated with dry conditions and had more restricted, fragmented geographical distribution. This event may have driven diversification by isolating the two haplogroups. Otherwise, the climatic changes in the late Pleistocene must not have drastically affected the population dynamics of P. seridoensis, since the Bayesian Skyline Plot did not reveal any substantial fluctuation in effective population size in either haplogroup. Considering its importance and the fact that it is an endemic bee from a very threatened Neotropical dry forest, the results herein could be useful to the development of conservation strategies for P. seridoensis.
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Affiliation(s)
- Elder Assis Miranda
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Kátia Maria Ferreira
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Airton Torres Carvalho
- Unidade Acadêmica de Serra Talhada, Universidade Federal Rural de Pernambuco, Serra Talhada, PE, Brazil
| | - Celso Feitosa Martins
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | | | - Marco Antonio Del Lama
- Laboratório de Genética Evolutiva de Himenópteros, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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Sturaro MJ, Avila-Pires TCS, Rodrigues MT. Molecular phylogenetic diversity in the widespread lizard Cercosaura ocellata (Reptilia: Gymnophthalmidae) in South America. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1284913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Marcelo José Sturaro
- Laboratório de Herpetologia, Museu Paraense Emílio Goeldi, CZO. C.P. 399, 66017-970, Belém, Pará, Brazil
- Programa de Pós-Graduação em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi
| | - Teresa C. S. Avila-Pires
- Laboratório de Herpetologia, Museu Paraense Emílio Goeldi, CZO. C.P. 399, 66017-970, Belém, Pará, Brazil
| | - Miguel T. Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, 05422-970, São Paulo, Brazil
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38
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In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 2017; 107:455-465. [DOI: 10.1016/j.ympev.2016.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022]
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Miranda EA, Batalha-Filho H, Congrains C, Carvalho AF, Ferreira KM, Del Lama MA. Phylogeography of Partamona rustica (Hymenoptera, Apidae), an Endemic Stingless Bee from the Neotropical Dry Forest Diagonal. PLoS One 2016; 11:e0164441. [PMID: 27723778 PMCID: PMC5056711 DOI: 10.1371/journal.pone.0164441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
The South America encompasses the highest levels of biodiversity found anywhere in the world and its rich biota is distributed among many different biogeographical regions. However, many regions of South America are still poorly studied, including its xeric environments, such as the threatened Caatinga and Cerrado phytogeographical domains. In particular, the effects of Quaternary climatic events on the demography of endemic species from xeric habitats are poorly understood. The present study uses an integrative approach to reconstruct the evolutionary history of Partamona rustica, an endemic stingless bee from dry forest diagonal in Brazil, in a spatial-temporal framework. In this sense, we sequenced four mitochondrial genes and genotyped eight microsatellite loci. Our results identified two population groups: one to the west and the other to the east of the São Francisco River Valley (SFRV). These groups split in the late Pleistocene, and the Approximate Bayesian Computation approach and phylogenetic reconstruction indicated that P. rustica originated in the west of the SFRV, subsequently colonising eastern region. Our tests of migration detected reduced gene flow between these groups. Finally, our results also indicated that the inferences both from the genetic data analyses and from the spatial distribution modelling are compatible with historical demographic stability.
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Affiliation(s)
- Elder Assis Miranda
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
- * E-mail:
| | - Henrique Batalha-Filho
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Antônio Freire Carvalho
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Kátia Maria Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marco Antonio Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Carvalho ALG. Three New Species of theTropidurus spinulosusGroup (Squamata: Tropiduridae) from Eastern Paraguay. AMERICAN MUSEUM NOVITATES 2016. [DOI: 10.1206/3853.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Carvalho AL, Sena MA, Peloso PL, Machado FA, Montesinos R, Silva HR, Campbell G, Rodrigues MT. A NewTropidurus(Tropiduridae) from the Semiarid Brazilian Caatinga: Evidence for Conflicting Signal between Mitochondrial and Nuclear Loci Affecting the Phylogenetic Reconstruction of South American Collared Lizards. AMERICAN MUSEUM NOVITATES 2016. [DOI: 10.1206/3852.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Oliveira EF, Gehara M, São-Pedro VA, Chen X, Myers EA, Burbrink FT, Mesquita DO, Garda AA, Colli GR, Rodrigues MT, Arias FJ, Zaher H, Santos RML, Costa GC. Speciation with gene flow in whiptail lizards from a Neotropical xeric biome. Mol Ecol 2015; 24:5957-75. [PMID: 26502084 DOI: 10.1111/mec.13433] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/15/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.
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Affiliation(s)
- Eliana F Oliveira
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Marcelo Gehara
- Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Vinícius A São-Pedro
- Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Xin Chen
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Edward A Myers
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA
| | - Frank T Burbrink
- Department of Biology, 6S-143, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY, 10314, USA.,Department of Biology, The Graduate School, City University of New York, New York, NY, 10016, USA.,Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, PB, 58000-00, Brazil
| | - Adrian A Garda
- Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Federico J Arias
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Rodrigo M L Santos
- Departamento de Zoologia, Universidade de São Paulo, São Paulo, SP, 05422-970, Brazil
| | - Gabriel C Costa
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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