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Fonseca EM, Pope NS, Peterman WE, Werneck FP, Colli GR, Carstens BC. Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae). Heredity (Edinb) 2024; 132:284-295. [PMID: 38575800 PMCID: PMC11166928 DOI: 10.1038/s41437-024-00682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Nathaniel S Pope
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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Arantes ÍC, Vasconcellos MM, Smith ML, Garrick RC, Colli GR, Noonan BP. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Mol Phylogenet Evol 2023:107843. [PMID: 37286064 DOI: 10.1016/j.ympev.2023.107843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.
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Affiliation(s)
- Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
| | - Mariana M Vasconcellos
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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5
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Estupiñán RA, Torres de Farias S, Gonçalves EC, Camargo M, Cruz Schneider MP. Performance of intron 7 of the β-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae). Zookeys 2023; 1149:145-169. [DOI: 10.3897/zookeys.1149.85627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/22/2022] [Indexed: 02/24/2023] Open
Abstract
Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 – FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.
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Souza TO, Luna LW, Araripe J, Silva WADEGE, Rego PSDO. Peripheral isolation and demographic stability are reflected in the genetic diversity of the populations of the Helmeted Manakin: a bird endemic to the gallery forests. AN ACAD BRAS CIENC 2022; 94:e20201206. [PMID: 36541971 DOI: 10.1590/0001-3765202220201206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
The Cerrado encompasses a complex network of hydrographic basins, which is responsible for the formation and maintenance of the riparian and gallery forests. Alterations in the vegetation resulting from the paleoclimatic changes that occurred during the Pleistocene influenced the current distribution of these humid forests. To understand of the evolutionary dynamics of this landscape on the population structure of the associated organisms, we studied the population genetics of the Antilophia galeata (Pipridae), a bird endemic to the gallery forests of the Cerrado. For this, we evaluated the variability of the mitochondrial control region of 71 A. galeata specimens from 18 localities distributed throughout the Cerrado. The results indicated the existence of significant substructure among the populations located in the peripheral areas of the Cerrado, in comparison with the populations found in the central portion, reflecting historical changes in the environment. We also found high levels of diversity in all the populations, while the analysis of the demographic history revealed a scenario of stability. Overall, then, these findings indicate that the historical modifications of the gallery forest distribution may have been most accentuated in the peripheral zones, with a greater stability and connectivity persisting in the central portion of the biome.
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Affiliation(s)
- Thainara O Souza
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil
| | - Leilton W Luna
- Universidade Federal do Pará, Departamento de Zoologia, Museu Paraense Emílio Goeldi, Avenida Perimetral, 1901/1907, 66040-170 Belém, PA, Brazil
| | - Juliana Araripe
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal
| | - Weber A DE G E Silva
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Avenida Pintor João Figueiredo - SESC - Iparana, 61627-250 Caucaia, CE, Brazil
| | - Péricles S DO Rego
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal
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7
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Porto CR, Fazolato CP, Marques R, Batalha-Filho H, Napoli MF, Garda AA, de Carvalho MLS, de Campos Fernandes FM. Unravelling the cryptic diversity and evolution of the dwarf swamp frog Pseudopaludicola mystacalis (Anura, Leptodactylidae) in open habitats of South America. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Many studies on the diversity of the South American biota support the role of ecological and geological events as main drivers of species diversification. For many groups, geomorphological events are the key drivers of diversification, while the influence of Pleistocene climate oscillations is prominent for others. To precisely indicate which events were key for the development of the astonishing biodiversity in South America, studies on widely distributed species are paramount. One such species, the dwarf swamp frog Pseudopaludicola mystacalis (Leptodactylidae, Leiuperinae), is widely distributed in open habitats of South America and we herein investigate population differentiation and diversification in this species across its geographic range. We sequenced a 1374 bp mtDNA fragment from 64 specimens across 25 localities. We used population assignment and species delimitation methods to assess genetic structure and lineage limits across the species distribution. We estimated, for each lineage, intraspecific diversity, divergence times, and demographic histories. Our results recovered ten lineages with up to 5% of genetic divergence among them. Diversification occurred mainly during the Tertiary, suggesting that Miocene-Pliocene topographic events had a major influence on the diversification of P. mystacalis. Pleistocene climatic oscillations also played a role on evolutionary history of P. mystacalis, causing demographic changes in one lineage.
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Affiliation(s)
- Clara Ribeiro Porto
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Cecil Pergentino Fazolato
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Ricardo Marques
- Universidade do Estado de Mato Grosso, 78690-000, Nova Xavantina, Mato Grosso, Brazil
| | - Henrique Batalha-Filho
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Marcelo Felgueiras Napoli
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica e Zoologia, Avenida Senador Salgado Filho, S/N, Lagoa Nova, 59078-900, Natal, RN, Brazil
| | - Maria Luiza Silveira de Carvalho
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
| | - Flora Maria de Campos Fernandes
- Universidade Federal da Bahia, Programa de Pós-Graduação em Genética e Biodiversidade, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
- Universidade Federal da Bahia, Programa de Pós-Graduação em Biodiversidade e Evolução, Instituto de Biologia, Rua Barão de Jeremoabo, s/n, 40170-115, Ondina, Salvador, Bahia, Brazil
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Mittan CS, Zamudio KR, Thomé MTC, Camurugi F, Colli GR, Garda AA, Haddad CFB, Prado CPA. Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group. Mol Phylogenet Evol 2022; 175:107579. [PMID: 35835425 DOI: 10.1016/j.ympev.2022.107579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.
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Affiliation(s)
- Cinnamon S Mittan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - M Tereza C Thomé
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Cynthia P A Prado
- Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
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9
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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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10
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Freitas TMB, Abreu JMS, Sampaio I, Piorski NM, Weber LN. Molecular data reveal multiple lineages of Scinax nebulosus (Spix, 1824) (Anura: Hylidae) with Plio-Pleistocene diversification in different Brazilian regions. AN ACAD BRAS CIENC 2022; 94:e20200733. [PMID: 35544846 DOI: 10.1590/0001-3765202220200733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/06/2020] [Indexed: 11/21/2022] Open
Abstract
To understand the organism's history, we can start assessing the complexity of the biome where they occur. In this study, we used a region of the mitochondrial genome, the rRNA 16S, to evaluate the genetic differentiation in Scinax nebulosus along with its geographical range highlighting important Brazilian biomes as Restinga, Cerrado, Amazon, and Atlantic Forest. Geographically structured genetic divergence was observed within the species S. nebulosus. The values of the fixation index (Фst) and the pairwise Fst index were high and significant regarding this structuring. Besides, the haplotype network corroborates these results with the haplotypes arrangement found by separating the S. nebulosus populations in two major groups: North and Northeast. The lineage delimitation analyses indicate the occurrence of several lineages with divergence mainly between the samples from the Northeast group. Thus, we can suggest that S. nebulosus may present itself as a group of cryptic species due to the genetic characteristics found. The existence of a mosaic of heterogeneous habitats may explain the genetic divergence found, which justifies the existence of cryptic species in this group. However, this hypothesis needs more detail in molecular studies, including large sample sizes and other population and demographic analyses.
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Affiliation(s)
- Tatiana M B Freitas
- Programa de Pós-Graduação Bionorte, Universidade Federal do Maranhão (UFMA), Departamento de Biologia, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, Laboratório de Ecologia e Sistemática de Peixes, Av. dos Portugueses, 1966, Campus do Bacanga, 65080-805 São Luís, MA, Brazil
| | - João M S Abreu
- Programa de Pós-Graduação Bionorte, Universidade Federal do Maranhão (UFMA), Departamento de Biologia, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, Laboratório de Ecologia e Sistemática de Peixes, Av. dos Portugueses, 1966, Campus do Bacanga, 65080-805 São Luís, MA, Brazil
| | - Iracilda Sampaio
- Programa de Pós-Graduação Biologia Ambiental (PPBA), Universidade Federal do Pará (UFPA), Instituto de Estudos Costeiros (IECOS), Grupo de Estudos em Genética e Filogenômica, Laboratório e Filogenomica e Bioinformatica, Alameda Leandro Ribeiro, s/n, Campus de Bragança, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Nivaldo M Piorski
- Programa de Pós-Graduação Bionorte, Universidade Federal do Maranhão (UFMA), Departamento de Biologia, Grupo de Taxonomia, Biogeografia, Ecologia e Conservação de Peixes do Maranhão, Laboratório de Ecologia e Sistemática de Peixes, Av. dos Portugueses, 1966, Campus do Bacanga, 65080-805 São Luís, MA, Brazil
| | - Luiz N Weber
- Programa de Pós-Graduação Bionorte, Universidade Federal do Sul da Bahia (UFSB), Instituto Sosígenes Costa de Humanidades, Artes e Ciências, Centro de Formação em Ciências Ambientais, Departamento de Ciências Biológicas, Grupo Biodiversidade da Fauna do Sul da Bahia, Laboratório de Zoologia, Rod. Porto Seguro, BR 367, Km 10, Eunápolis, 45810-000 Porto Seguro, BA, Brazil
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11
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Pezzuti TL, Fortes Leite FS, Rossa-Feres DDC, Anchietta Garcia PC. The Tadpoles of the Iron Quadrangle, Southeastern Brazil: A Baseline for Larval Knowledge and Anuran Conservation in a Diverse and Threatened Region. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2021. [DOI: 10.2994/sajh-d-20-00042.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Tiago Leite Pezzuti
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais. Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Sá Fortes Leite
- Sagarana Lab, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Campus Florestal. Florestal, Minas Gerais, Brazil
| | - Denise de C. Rossa-Feres
- Departamento de Zoologia e Botânica, Universidade Estadual de São Paulo, Campus São José do Rio Preto. São José do Rio Preto, São Paulo, Brazil
| | - Paulo Christiano Anchietta Garcia
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais. Belo Horizonte, Minas Gerais, Brazil
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12
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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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13
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Bonatelli IAS, Gehara M, Carstens BC, Colli GR, Moraes EM. Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography. Mol Ecol 2021; 31:331-342. [PMID: 34614269 DOI: 10.1111/mec.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.
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Affiliation(s)
- Isabel A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil.,Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, Brazil
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, Brazil
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14
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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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15
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Fonseca EM, Colli GR, Werneck FP, Carstens BC. Phylogeographic model selection using convolutional neural networks. Mol Ecol Resour 2021; 21:2661-2675. [PMID: 33973350 DOI: 10.1111/1755-0998.13427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non-model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genus Norops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population-level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non-sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Fernanda P Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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16
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Fouquet A, Marinho P, Réjaud A, Carvalho TR, Caminer MA, Jansen M, Rainha RN, Rodrigues MT, Werneck FP, Lima AP, Hrbek T, Giaretta AA, Venegas PJ, Chávez G, Ron S. Systematics and biogeography of the Boana albopunctata species group (Anura, Hylidae), with the description of two new species from Amazonia. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1873869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Pedro Marinho
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, Toulouse, 31077, France
| | - Thiago R. Carvalho
- Laboratório de Herpetologia, Departamento de Biodiversidade e Centro de Aquicultura, I.B., Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Marcel A. Caminer
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Germany
| | - Martin Jansen
- Department of Terrestrial Zoology, Research Institute and Nature Museum Senckenberg, Frankfurt, Germany
| | - Raíssa N. Rainha
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Universidade de São Paulo, Instituto de Biociências, São Paulo, SP, Brazil
| | - Fernanda P. Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Albertina P. Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Ariovaldo A. Giaretta
- Laboratório de Anuros Neotropicais, Instituto de Ciências Exatas e Naturais do Pontal, Universidade Federal de Uberlândia, Ituiutaba, MG, Brazil
| | | | | | - Santiago Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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17
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Gomes DF, Azevedo J, Murta-Fonseca R, Faurby S, Antonelli A, Passos P. Taxonomic revision of the genus Xenopholis Peters, 1869 (Serpentes: Dipsadidae): Integrating morphology with ecological niche. PLoS One 2020; 15:e0243210. [PMID: 33306700 PMCID: PMC7732082 DOI: 10.1371/journal.pone.0243210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
A reliable identification and delimitation of species is an essential pre-requisite for many fields of science and conservation. The Neotropical herpetofauna is the world's most diverse, including many taxa of uncertain or debated taxonomy. Here we tackle one such species complex, by evaluating the taxonomic status of species currently allocated in the snake genus Xenopholis (X. scalaris, X. undulatus, and X. werdingorum). We base our conclusions on concordance between quantitative (meristic and morphometric) and qualitative (color pattern, hemipenes and skull features) analyses of morphological characters, in combination with ecological niche modeling. We recognize all three taxa as valid species and improve their respective diagnosis, including new data on color in life, pholidosis, bony morphology, and male genitalia. We find low overlap among the niches of each species, corroborating the independent source of phenotypic evidence. Even though all three species occur in the leaf litter of distinct forested habitats, Xenopholis undulatus is found in the elevated areas of the Brazilian Shield (Caatinga, Cerrado and Chaco), whereas X. scalaris occurs in the Amazon and Atlantic rainforests, and X. werdingorum in the Chiquitanos forest and Pantanal wetlands. We discuss the disjunct distribution between Amazonian and Atlantic Forest snake species in the light of available natural history and ecological aspects. This study shows the advantages of combining multiple data sources for reliable identification and circumscription of ecologically similar species.
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Affiliation(s)
- Daniel Faustino Gomes
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia, Amazonas, Brazil
| | - Roberta Murta-Fonseca
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Zoologia, Campus do Pantanal, Universidade Federal de Mato Grosso do Sul, Bairro Universitário, Corumbá, Mato Grosso do Sul, Brasil
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Paulo Passos
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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18
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Nali RC, Becker CG, Zamudio KR, Prado CPA. Topography, more than land cover, explains genetic diversity in a Neotropical savanna tree frog. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Renato C. Nali
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Instituto de Biociências Universidade Estadual Paulista Rio Claro São Paulo Brazil
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | | | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Cynthia P. A. Prado
- Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Instituto de Biociências Universidade Estadual Paulista Rio Claro São Paulo Brazil
- Departamento de Morfologia e Fisiologia Animal Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista Jaboticabal São Paulo Brazil
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19
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Ledo RMD, Domingos FMCB, Giugliano LG, Sites JW, Werneck FP, Colli GR. Pleistocene expansion and connectivity of mesic forests inside the South American Dry Diagonal supported by the phylogeography of a small lizard*. Evolution 2020; 74:1988-2004. [DOI: 10.1111/evo.13978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Roger Maia D. Ledo
- Área de Meio Ambiente Instituto Federal de Educação, Ciência e Tecnologia de Brasília Campus Samambaia Samambaia DF 70860 Brazil
- Departamento de Zoologia Universidade de Brasília Brasília DF 70910 Brazil
| | | | - Lilian G. Giugliano
- Departamento de Genética e Morfologia Universidade de Brasília Brasília DF 70910‐900 Brazil
| | - Jack W. Sites
- Department of Biology and Bean Life Sciences Museum Brigham Young University Provo Utah 84602 USA
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus AM 69060 Brazil
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília DF 70910 Brazil
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20
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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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21
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Leal BSS, Graciano VA, Chaves CJN, Huacre LAP, Heuertz M, Palma-Silva C. Dispersal and local persistence shape the genetic structure of a widespread Neotropical plant species with a patchy distribution. ANNALS OF BOTANY 2019; 124:499-512. [PMID: 31219156 PMCID: PMC6798837 DOI: 10.1093/aob/mcz105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND AND AIMS Isolated populations constitute an ideal laboratory to study the consequences of intraspecific divergence, because intrinsic incompatibilities are more likely to accumulate under reduced gene flow. Here, we use a widespread bromeliad with a patchy distribution, Pitcairnia lanuginosa, as a model to infer processes driving Neotropical diversification and, thus, to improve our understanding of the origin and evolutionary dynamics of biodiversity in this highly speciose region. METHODS We assessed the timing of lineage divergence, genetic structural patterns and historical demography of P. lanuginosa, based on microsatellites, and plastid and nuclear sequence data sets using coalescent analyses and an Approximate Bayesian Computation framework. Additionally, we used species distribution models (SDMs) to independently estimate potential changes in habitat suitability. KEY RESULTS Despite morphological uniformity, plastid and nuclear DNA data revealed two distinct P. lanuginosa lineages that probably diverged through dispersal from the Cerrado to the Central Andean Yungas, following the final uplift of the Andes, and passed through long-term isolation with no evidence of migration. Microsatellite data indicate low genetic diversity and high levels of inbreeding within populations, and restricted gene flow among populations, which are likely to be a consequence of bottlenecks (or founder events), and high selfing rates promoting population persistence in isolation. SDMs showed a slight expansion of the suitable range for P. lanuginosa lineages during the Last Glacial Maximum, although molecular data revealed a signature of older divergence. Pleistocene climatic oscillations thus seem to have played only a minor role in the diversification of P. lanuginosa, which probably persisted through adverse conditions in riparian forests. CONCLUSIONS Our results imply drift as a major force shaping the evolution of P. lanuginosa, and suggest that dispersal events have a prominent role in connecting Neotropical open and forest biomes.
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Affiliation(s)
- Bárbara Simões Santos Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Vanessa Araujo Graciano
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Cleber Juliano Neves Chaves
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Luis Alberto Pillaca Huacre
- Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - Clarisse Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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22
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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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Vasconcellos MM, Colli GR, Weber JN, Ortiz EM, Rodrigues MT, Cannatella DC. Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Mol Ecol 2019; 28:1748-1764. [DOI: 10.1111/mec.15045] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Jesse N. Weber
- Department of Biological Sciences University of Alaska Anchorage Anchorage, Alaska
| | - Edgardo M. Ortiz
- Department of Integrative Biology The University of Texas at Austin Austin Texas
- Plant Biodiversity Research Department of Ecology and Ecosystem Management Technical University of Munich Freising Germany
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | - David C. Cannatella
- Department of Integrative Biology The University of Texas at Austin Austin Texas
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24
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Nguyen HN, Lu CW, Chu JH, Grismer LL, Hung CM, Lin SM. Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation. Mol Ecol 2018; 28:772-784. [PMID: 30580492 DOI: 10.1111/mec.14985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022]
Abstract
Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
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Affiliation(s)
- Hung N Nguyen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Zoology, Southern Institute of Ecology, Vietnam Academia of Science and Technology, Ho Chi Minh City, Vietnam.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Wei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Si-Min Lin
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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25
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Diversification of the widespread neotropical frog Physalaemus cuvieri in response to Neogene-Quaternary geological events and climate dynamics. Mol Phylogenet Evol 2018; 132:67-80. [PMID: 30508632 DOI: 10.1016/j.ympev.2018.11.003] [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: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/10/2018] [Indexed: 11/24/2022]
Abstract
Here we reconstructed the demographical history and the dispersal dynamics of Physalemus cuvieri through the Neogene-Quaternary periods by coupling DNA regions with different mutation rates, ecological niche modelling, reconstruction of spatio-temporal lineage dispersal and coalescent simulations. Still, to test alternative diversification scenarios we used approximate Bayesian computation. Molecular phylogenetic analysis recovered four deep and strongly supported clades, which we interpret as population lineages. The ancestral location reconstruction placed the root in southcentral Amazonia, and the dispersal events indicate that spatial displacement was widespread early in the diversification of this species. The demographical scenario of "Multiple Refugia" with recent lineage admixture was the most likely hypothesis to predict the observed genetic parameters of P. cuvieri. Our results revealed that Neogene orogenic events might have played a prominent role in the early diversification of P. cuvieri. The species shows deep divergences with strong regional population structure, despite its widespread distribution. Final uplift of the central Brazilian Plateau and formation of the river basins in Central South America played an important role in the origin, diversification and the maintenance of P. cuvieri lineages.
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26
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Pinheiro PDP, Cintra CED, Valdujo PH, Silva HLR, Martins IA, da Silva NJ, Garcia PCA. A New Species of theBoana albopunctataGroup (Anura: Hylidae) from the Cerrado of Brazil. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2018. [DOI: 10.2994/sajh-d-17-00040.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Paulo D. P. Pinheiro
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista “Julio de Mesquita Filho”, Rio Claro, São Paulo, Brazil
| | - Carlos E. D. Cintra
- Centro de Estudos e Pesquisas Biológicas, Pontifícia Universidade Católica de Goiás, Avenida Universitária, 1440, Setor Universitário. CEP 74605-010, Goiânia, Goiás, Brazil
| | - Paula H. Valdujo
- Programa de Ciências, WWF-Brasil. SGCV Lote 15 Sala 421, CEP 71620-430, Brasília, Distrito Federal, Brazil
| | - Hélder L. R. Silva
- Centro de Estudos e Pesquisas Biológicas, Pontifícia Universidade Católica de Goiás, Avenida Universitária, 1440, Setor Universitário. CEP 74605-010, Goiânia, Goiás, Brazil
| | - Itamar A. Martins
- Laboratório de Zoologia, Instituto Básico de Biociências, Universidade de Taubaté, Avenida Tiradentes, 500, CEP 12030-180, Taubaté, São Paulo, Brazil
| | - Nelson Jorge da Silva
- Centro de Estudos e Pesquisas Biológicas, Pontifícia Universidade Católica de Goiás, Avenida Universitária, 1440, Setor Universitário. CEP 74605-010, Goiânia, Goiás, Brazil
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Rua 232 n° 128, 3° andar, Área V, Setor Universitário, CEP 74605-140, Goiânia, Goiás, Brazil
| | - Paulo C. A. Garcia
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais. Avenida Antônio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
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27
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Costa WJ. Three new species of the killifish genus Melanorivulus from the Rio Paraná Basin, central Brazilian Cerrado (Cyprinodontiformes, Aplocheilidae). ZOOSYST EVOL 2018. [DOI: 10.3897/zse.94.21321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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28
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da Silva Santos A, Trigo TC, de Oliveira TG, Silveira L, Eizirik E. Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history. Genet Mol Biol 2018; 41:273-287. [PMID: 29668017 PMCID: PMC5913729 DOI: 10.1590/1678-4685-gmb-2017-0079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/07/2017] [Indexed: 11/22/2022] Open
Abstract
The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species' history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America.
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Affiliation(s)
- Anelisie da Silva Santos
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Tatiane Campos Trigo
- Setor de Mastozoologia, Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul. Porto Alegre, RS, Brazil
| | - Tadeu Gomes de Oliveira
- Universidade Estadual do Maranhão (UEMA), São Luís, MA, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | | | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
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29
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Ramos EKS, de Magalhães RF, Sari EHR, Rosa AHB, Garcia PCA, Santos FR. Population genetics and distribution data reveal conservation concerns to the sky island endemic Pithecopus megacephalus (Anura, Phyllomedusidae). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1013-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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30
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Costa WJEM. Three new species of the killifish genus Melanorivulus from the central Brazilian Cerrado savanna (Cyprinodontiformes, Aplocheilidae). Zookeys 2017:51-70. [PMID: 28228667 PMCID: PMC5299224 DOI: 10.3897/zookeys.645.10920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/12/2022] Open
Abstract
Three new species are described from the Neotropical region comprising the Cerrado savannas of the central Brazilian plateaus, which is among the most important biodiversity centres in the world. These species are considered closely related to Melanorivulusdapazi from the same region, with which they share the presence of a rudimentary interarcual cartilage and a dark reddish brown distal margin on the male anal fin. The group comprising Melanorivulusdapazi and the three new species is here named as the Melanorivulusdapazi species group. Melanorivulusignescenssp. n., from the upper Rio Araguaia basin, is distinguished from all other species of the Melanorivulusdapazi group by the anal-fin colour pattern in males; Melanorivulusflavipinnissp. n. and Melanorivulusregularissp. n. from the Rio Paraguai basin are distinguished from all other congeners of the Melanorivulusdapazi group by the colour pattern of the caudal fin and number of scales in the longitudinal series, respectively. All the new species are further unambiguously diagnosed by unique combinations of morphological characters, including meristic and morphometric data, and colour patterns. This study reinforces the importance of using live colour patterns to diagnose species and species groups of the genus Melanorivulus, but also indicates that osteological characters may be informative for species diagnosis. This study confirms the high diversity of species of Melanorivulus in the central Brazilian Cerrado plateaus already reported in previous studies, indicating that endemic species are often restricted to short segments of a single river drainage.
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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
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31
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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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32
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Souza HAVE, Collevatti RG, Lima-Ribeiro MS, Lemos-Filho JPD, Lovato MB. A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species. ANNALS OF BOTANY 2017; 119:239-252. [PMID: 27311573 PMCID: PMC5321056 DOI: 10.1093/aob/mcw096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/02/2015] [Accepted: 03/29/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated. METHODS A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM). KEY RESULTS Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium. CONCLUSIONS The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.
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Affiliation(s)
- Helena Augusta Viana E Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Caixa Postal 131, 74001-970 Goiânia, GO, Brazil
| | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Universidade Federal de Goiás, Campus Jataí, 75801-615 Jataí, GO, Brazil
| | - José Pires de Lemos-Filho
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
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33
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Guarnizo CE, Werneck FP, Giugliano LG, Santos MG, Fenker J, Sousa L, D’Angiolella AB, dos Santos AR, Strüssmann C, Rodrigues MT, Dorado-Rodrigues TF, Gamble T, Colli GR. Cryptic lineages and diversification of an endemic anole lizard (Squamata, Dactyloidae) of the Cerrado hotspot. Mol Phylogenet Evol 2016; 94:279-89. [DOI: 10.1016/j.ympev.2015.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 01/17/2023]
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34
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Langone JA, Camargo A, de Sá RO. High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America. Mol Phylogenet Evol 2015; 95:137-51. [PMID: 26639101 DOI: 10.1016/j.ympev.2015.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 11/03/2015] [Accepted: 11/07/2015] [Indexed: 11/16/2022]
Abstract
Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.
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Affiliation(s)
- José A Langone
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay.
| | - Arley Camargo
- Programa de Desarrollo Universitario, Centro Universitario de Rivera, Universidad de la República. Ituzaingó 667, Código Postal 40.000, Rivera, Uruguay.
| | - Rafael O de Sá
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay; Department of Biology, University of Richmond, Richmond, VA 23173, USA.
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35
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Perez MF, Carstens BC, Rodrigues GL, Moraes EM. Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America. Mol Phylogenet Evol 2015; 95:11-9. [PMID: 26582125 DOI: 10.1016/j.ympev.2015.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 11/30/2022]
Abstract
The Pilosocereus aurisetus complex consists of eight cactus species with a fragmented distribution associated to xeric enclaves within the Cerrado biome in eastern South America. The phylogeny of these species is incompletely resolved, and this instability complicates evolutionary analyses. Previous analyses based on both plastid and microsatellite markers suggested that this complex contained species with inherent phylogeographic structure, which was attributed to recent diversification and recurring range shifts. However, limitations of the molecular markers used in these analyses prevented some questions from being properly addressed. In order to better understand the relationship among these species and make a preliminary assessment of the genetic structure within them, we developed anonymous nuclear loci from pyrosequencing data of 40 individuals from four species in the P. aurisetus complex. The data obtained from these loci were used to identify genetic clusters within species, and to investigate the phylogenetic relationship among these inferred clusters using a species tree methodology. Coupled with a palaeodistributional modelling, our results reveal a deep phylogenetic and climatic disjunction between two geographic lineages. Our results highlight the importance of sampling more regions from the genome to gain better insights on the evolution of species with an intricate evolutionary history. The methodology used here provides a feasible approach to develop numerous genealogical molecular markers throughout the genome for non-model species. These data provide a more robust hypothesis for the relationship among the lineages of the P. aurisetus complex.
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Affiliation(s)
- Manolo F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Gustavo L Rodrigues
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo 18052780, Brazil.
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Teixeira M, Prates I, Nisa C, Silva-Martins NSC, Strüssmann C, Rodrigues MT. Molecular data reveal spatial and temporal patterns of diversification and a cryptic new species of lowland Stenocercus Duméril & Bibron, 1837 (Squamata: Tropiduridae). Mol Phylogenet Evol 2015; 94:410-23. [PMID: 26432394 DOI: 10.1016/j.ympev.2015.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 07/28/2015] [Accepted: 09/09/2015] [Indexed: 01/16/2023]
Abstract
Phylogenetic studies have uncovered biogeographic patterns and the associated diversification processes of Neotropical wet forest taxa, yet the extensive open and drier biomes have received much less attention. In the Stenocercus lizard radiation, restricted sampling and phylogenetic information have limited inferences about the timing, spatial context, and environmental drivers of diversification in the open and dry lowland settings of eastern and southern South America. Based on new DNA sequence data of previously unsampled species, we provide an updated historical biogeographic hypothesis of Stenocercus. We infer phylogenetic relationships, estimate divergence times, and track ancestral distributions, asking whether cladogenetic events within the genus correlate to reported shifts in South American landscapes during the past 30millionyears, focusing in the open and drier areas. To examine correlations between genetic and ecological divergence, we extracted environmental data from occurrence records and estimated climatic envelopes occupied by lowland taxa. Our results suggest that Stenocercus began to diversify around the South American Midwest by the late Oligocene. We recovered two main lowland and two main Andean clades within the genus; within both Andean clades, most cladogenetic events date back to the Miocene, synchronously with the most intense phase of Andean uplift. In the western clade of lowland Stenocercus, species ranges and divergence times are consistent with major landscape shifts at the upper Guaporé and Paraguay River basins as a result of Andean orogeny, suggesting vicariant speciation. By contrast, in the 'horned' lowland clade, we find evidence that dispersal and ecological differentiation have shaped species divergences and current ranges in the Brazilian Cerrado, Caatinga, Pampas and Atlantic Forest, possibly under a vanishing refuge scenario. Lastly, our phylogenetic results indicate two divergent clades within the formerly recognized taxon S. sinesaccus, and further evaluation of morphological data corroborates the existence of a distinct, new species of Stenocercus, here described. The new taxon occurs in the Chapada dos Parecis massif in the Brazilian states of Mato Grosso and Rondônia.
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Affiliation(s)
- Mauro Teixeira
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
| | - Ivan Prates
- Department of Biology, City College and Graduate Center, City University of New York, New York, NY 10031, USA
| | - Carolina Nisa
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
| | - Nathalia Suzan Camarão Silva-Martins
- Departamento de Ciências Básicas e Produção Animal, Faculdade de Agronomia, Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil
| | - Christine Strüssmann
- Departamento de Ciências Básicas e Produção Animal, Faculdade de Agronomia, Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil
| | - Miguel Trefaut Rodrigues
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil
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Emerson KJ, Conn JE, Bergo ES, Randel MA, Sallum MAM. Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region. PLoS One 2015; 10:e0130773. [PMID: 26172559 PMCID: PMC4501553 DOI: 10.1371/journal.pone.0130773] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/23/2015] [Indexed: 11/18/2022] Open
Abstract
The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector, Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based (Principal Components and Discriminant Analysis) analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province (= West Atlantic forest population, with one Chacoan population - SP); and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.
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Affiliation(s)
- Kevin J. Emerson
- Biology Department, St. Mary’s College of Maryland, St. Mary’s City, Maryland, United States of America
| | - Jan E. Conn
- The Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences—School of Public Health, SUNY Albany, Albany, New York, United States of America
| | - Eduardo S. Bergo
- Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, Araraquara, São Paulo, Brazil
| | - Melissa A. Randel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
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Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga. BMC Evol Biol 2015; 15:94. [PMID: 26001787 PMCID: PMC4494643 DOI: 10.1186/s12862-015-0368-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards. Results Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River. Conclusions The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0368-3) contains supplementary material, which is available to authorized users.
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Out of the deep: Cryptic speciation in a Neotropical gecko (Squamata, Phyllodactylidae) revealed by species delimitation methods. Mol Phylogenet Evol 2014; 80:113-24. [DOI: 10.1016/j.ympev.2014.07.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/21/2014] [Accepted: 07/29/2014] [Indexed: 11/23/2022]
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Damasceno R, Strangas ML, Carnaval AC, Rodrigues MT, Moritz C. Revisiting the vanishing refuge model of diversification. Front Genet 2014; 5:353. [PMID: 25374581 PMCID: PMC4205810 DOI: 10.3389/fgene.2014.00353] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/21/2014] [Indexed: 11/13/2022] Open
Abstract
Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and peripheral isolates can lead to genetic and functional (i.e., ecological and phenotypic) diversity, resulting in sister taxa that occupy contrasting habitats with abutting distributions. Here, we provide predictions for populations undergoing divergence according to the VRM that encompass habitat dynamics, phylogeography, and phenotypic differentiation across populations. Such integrative analyses can, in principle, differentiate the operation of the VRM from other speciation models. We applied these principles to a lizard species, Coleodactylus meridionalis, which was used to illustrate the model in the original paper. We incorporate data on inferred historic habitat dynamics, phylogeography and thermal physiology to test for divergence between coastal and inland populations in the Atlantic Forest of Brazil. Environmental and genetic analyses are concordant with divergence through the VRM, yet physiological data are not. We emphasize the importance of multidisciplinary approaches to test this and alternative speciation models while seeking to explain the extraordinarily high genetic and phenotypic diversity of tropical biomes.
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Affiliation(s)
- Roberta Damasceno
- Museum of Vertebrate Zoology, Integrative Biology Department, University of California Berkeley Berkeley, CA, USA ; Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo São Paulo, Brazil
| | - Maria L Strangas
- Biology Department, The Graduate Center, City University of New York New York, NY, USA
| | - Ana C Carnaval
- Biology Department, The Graduate Center, City University of New York New York, NY, USA ; Biology Department, City College, City University of New York New York, NY, USA
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo São Paulo, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, Integrative Biology Department, University of California Berkeley Berkeley, CA, USA ; Research School of Biology, The Australian National University Acton, ACT, Australia
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Brusquetti F, Jansen M, Barrio-Amorós C, Segalla M, Haddad CFB. Taxonomic review ofScinax fuscomarginatus(Lutz, 1925) and related species (Anura; Hylidae). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Francisco Brusquetti
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; UNESP, Cx. Postal 199 13506-906 Rio Claro SP Brazil
- Instituto de Investigación Biológica del Paraguay; Del Escudo 1607 CP 1429 Asunción Paraguay
| | - Martin Jansen
- Senckenberg Forschungsinstitut und Naturmuseum; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - César Barrio-Amorós
- Instituto de Biodiversidad Tropical; Apartado Postal 220-8000, San Jose, Perez Zeledon San Isidro del General 11901 Costa Rica
| | - Magno Segalla
- Laboratótio de Herpetologia; Museu de História Natural Capão da Imbuia; 82810-080 Curitiba PR Brazil
| | - Célio F. B. Haddad
- Departamento de Zoologia; Instituto de Biociências; Universidade Estadual Paulista; UNESP, Cx. Postal 199 13506-906 Rio Claro SP Brazil
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Bonatelli IAS, Perez MF, Peterson AT, Taylor NP, Zappi DC, Machado MC, Koch I, Pires AHC, Moraes EM. Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions forPilosocereus aurisetusand allies. Mol Ecol 2014; 23:3044-63. [DOI: 10.1111/mec.12780] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 04/21/2014] [Accepted: 04/23/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Isabel A. S. Bonatelli
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Manolo F. Perez
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | | | - Nigel P. Taylor
- National Parks Board; Singapore Botanic Gardens; 1 Cluny Road Singapore 259569 Singapore
- Royal Botanic Gardens; Kew Richmond Surrey TW9 3AB UK
| | - Daniela C. Zappi
- Royal Botanic Gardens; Kew Richmond Surrey TW9 3AB UK
- Gardens by the Bay; 18 Marina Gardens Drive Singapore Singapore
| | - Marlon C. Machado
- Departamento de Ciências Biológicas; Universidade Estadual de Feira de Santana; Rodovia BR 116 km 03 44031-460 Feira de Santana Bahia Brazil
| | - Ingrid Koch
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Adriana H. C. Pires
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
| | - Evandro M. Moraes
- Departamento de Biologia; Universidade Federal de São Carlos; Rodovia João Leme dos Santos km 110 18052780 Sorocaba São Paulo Brazil
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Reproductive Dynamics of the Neotropical TreefrogHypsiboas albopunctatus(Anura, Hylidae). J HERPETOL 2014. [DOI: 10.1670/12-193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Karyotypic diversity in seven Amazonian anurans in the genus Hypsiboas (family Hylidae). BMC Genet 2014; 15:43. [PMID: 24707932 PMCID: PMC4234493 DOI: 10.1186/1471-2156-15-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 03/24/2014] [Indexed: 01/28/2023] Open
Abstract
Background Hypsiboas species have been divided into seven groups using morphological and genetic characters, but for most of the species, there is no cytogenetic information available. A cytogenetic analysis using conventional staining, C-banding, silver staining, and fluorescence in situ hybridization (FISH) with telomeric sequence probes were used to investigate the karyotype of seven Amazon species of the genus Hypsiboas belonging to the following intrageneric groups: H. punctatus (H. cinerascens), H. semilineatus (H. boans, H. geographicus, and H. wavrini), and H. albopunctatus (H. lanciformis, H. multifasciatus, and H. raniceps). The aim was to differentiate between the karyotypes and use the chromosomal markers to distinguish between the Hypsiboas groups. The data were compared with a previous phylogenetic proposal for these anurans. In addition, H. lanciformis, H. boans, and H. wavrini are described here for the first time, and we characterize the diploid numbers for H. cinerascens, H. geographicus, H. multifasciatus, and H. raniceps. Results The diploid number for all of the species analyzed was 24, with the exception of Hypsiboas lanciformis, which had 2n = 22 chromosomes. The constitutive heterochromatin distribution, nucleolar organizer region locations, and interstitial telomeric sites differed between the species. A hypothesis that the heterochromatic patterns are evolving is proposed, with the divergence of the groups probably involving events such as an increase in the heterochromatin in the species of the H. semilineatus group. The FISH conducted with the telomeric probes detected sites in the terminal regions of all of the chromosomes of all species. Interstitial telomeric sites were detected in three species belonging to the H. semilineatus group: H. boans, H. geographicus, and H. wavrini. Conclusion The results of this study reinforce the complexity previously observed within the genus Hypsiboas and in the different groups that compose this taxon. More studies are needed focusing on this group and covering larger sampling areas, especially in the Brazilian Amazon, to improve our understanding of this fascinating and complex group.
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López-Uribe MM, Zamudio KR, Cardoso CF, Danforth BN. Climate, physiological tolerance and sex-biased dispersal shape genetic structure of Neotropical orchid bees. Mol Ecol 2014; 23:1874-90. [PMID: 24641728 DOI: 10.1111/mec.12689] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/20/2014] [Accepted: 02/03/2014] [Indexed: 11/26/2022]
Abstract
Understanding the impact of past climatic events on the demographic history of extant species is critical for predicting species' responses to future climate change. Palaeoclimatic instability is a major mechanism of lineage diversification in taxa with low dispersal and small geographical ranges in tropical ecosystems. However, the impact of these climatic events remains questionable for the diversification of species with high levels of gene flow and large geographical distributions. In this study, we investigate the impact of Pleistocene climate change on three Neotropical orchid bee species (Eulaema bombiformis, E. meriana and E. cingulata) with transcontinental distributions and different physiological tolerances. We first generated ecological niche models to identify species-specific climatically stable areas during Pleistocene climatic oscillations. Using a combination of mitochondrial and nuclear markers, we inferred calibrated phylogenies and estimated historical demographic parameters to reconstruct the phylogeographical history of each species. Our results indicate species with narrower physiological tolerance experienced less suitable habitat during glaciations and currently exhibit strong population structure in the mitochondrial genome. However, nuclear markers with low and high mutation rates show lack of association with geography. These results combined with lower migration rate estimates from the mitochondrial than the nuclear genome suggest male-biased dispersal. We conclude that despite large effective population sizes and capacity for long-distance dispersal, climatic instability is an important mechanism of maternal lineage diversification in orchid bees. Thus, these Neotropical pollinators are susceptible to disruption of genetic connectivity in the event of large-scale climatic changes.
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Machado T, Silva VX, Silva MJDJ. Phylogenetic relationships within Bothrops neuwiedi group (Serpentes, Squamata): Geographically highly-structured lineages, evidence of introgressive hybridization and Neogene/Quaternary diversification. Mol Phylogenet Evol 2014; 71:1-14. [DOI: 10.1016/j.ympev.2013.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 10/03/2013] [Accepted: 10/05/2013] [Indexed: 11/15/2022]
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Giugliano LG, de Campos Nogueira C, Valdujo PH, Collevatti RG, Colli GR. Cryptic diversity in South American Teiinae (Squamata, Teiidae) lizards. ZOOL SCR 2013. [DOI: 10.1111/zsc.12017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lilian G. Giugliano
- Departamento de Genética e Morfologia; Universidade de Brasília; Brasília; 70910-900; DF; Brazil
| | | | - Paula H. Valdujo
- Departamento de Ecologia Geral; Universidade de São Paulo; São Paulo 05508-900; SP; Brazil
| | - Rosane G. Collevatti
- Laboratório de Genetica & Biodiversidade; Instituto de Ciências Biológicas, Universidade Federal de Goiás; CP 131; Goiânia; 74001-970; GO, Brazil
| | - Guarino R. Colli
- Departamento de Zoologia; Universidade de Brasília Brasília 70910-900; DF; Brazil
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Nascimento FF, Lazar A, Menezes AN, Durans ADM, Moreira JC, Salazar-Bravo J, D′Andrea PS, Bonvicino CR. The role of historical barriers in the diversification processes in open vegetation formations during the Miocene/Pliocene using an ancient rodent lineage as a model. PLoS One 2013; 8:e61924. [PMID: 24349576 PMCID: PMC3630152 DOI: 10.1371/journal.pone.0061924] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022] Open
Abstract
The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.
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Affiliation(s)
- Fabrícia F. Nascimento
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Ana Lazar
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Albert N. Menezes
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Andressa da Matta Durans
- Programa de Pós Graduação em Biociências, Pavilhão Américo Piquet Carneiro, UERJ, Vila Isabel, Rio de Janeiro, RJ, Brazil
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Jânio C. Moreira
- Setor de Mastozoologia, Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristovão, Rio de Janeiro, RJ, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, UFRJ, Ilha do Fundão, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Jorge Salazar-Bravo
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Paulo S. D′Andrea
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Cibele R. Bonvicino
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Bisconti R, Canestrelli D, Salvi D, Nascetti G. A geographic mosaic of evolutionary lineages within the insular endemic newt Euproctus montanus. Mol Ecol 2012; 22:143-56. [PMID: 23163335 DOI: 10.1111/mec.12085] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 09/10/2012] [Accepted: 09/13/2012] [Indexed: 11/30/2022]
Abstract
Islands are hotspots of biodiversity, with a disproportionately high fraction of endemic lineages, often of ancient origin. Nevertheless, intra-island phylogeographies are surprisingly scarce, leading to a scanty knowledge about the microevolutionary processes induced on island populations by Plio-Pleistocene climatic oscillations, and the manner in which these processes contributed to shape their current genetic diversity. We investigated the phylogeography, historical demography and species distribution models of the Corsican endemic newt Euproctus montanus (north-western Mediterranean). As for many island endemics, the continuous distribution of E. montanus throughout its range has hitherto been considered as evidence for a single large population, a belief that also guided the species' categorization for conservation purposes. Instead, we found a geographic mosaic of ancient evolutionary lineages, with five main clades of likely Pliocene origin (2.6-5.8 My), all but one restricted to northern Corsica. Moreover, the copresence between main lineages in the same population was limited to a single case. As also suggested by growing literature on intra-island phylogeographic variation, it seems that the extensive use of simplifying assumption on the population structure and historical demography of island populations--both in theoretical and applicative studies--should be carefully reconsidered, a claim that is well exemplified by the case presented here.
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Affiliation(s)
- Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viale dell'Università s.n.c., I-01100, Viterbo, Italy
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