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de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, do Nascimento Vieira L, Guerra MP, Pacca Luna Mattar E, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.). PLANT MOLECULAR BIOLOGY 2021; 105:559-574. [PMID: 33386578 DOI: 10.1007/s11103-020-01109-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Coelho GM, Santos AS, de Menezes IPP, Tarazi R, Souza FMO, Silva MDGCPC, Gaiotto FA. Genetic structure among morphotypes of the endangered Brazilian palm Euterpe edulis Mart (Arecaceae). Ecol Evol 2020; 10:6039-6048. [PMID: 32607211 PMCID: PMC7319139 DOI: 10.1002/ece3.6348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/04/2020] [Accepted: 04/14/2020] [Indexed: 11/07/2022] Open
Abstract
Euterpe edulis (Arecaceae) Mart has high ecological and economic importance providing food resources for more than 58 species of birds and 20 species of mammals, including humans. E. edulis is the second most exploited nontimber product from Brazilian Atlantic Forest. Due to overexploitation and destruction of habitats, E. edulis is threatened by extinction. Euterpe edulis populations have large morphological variations, with individuals having green, red, or yellow leaf sheath. However, no study has related phenotypic distinctions between populations and their levels of genetic structure. Thus, this study aimed to evaluate the diversity and genetic structure of different E. edulis morphotypes. We sampled 250 adult individuals in eight populations with the different morphotypes. Using 14 microsatellite markers, we access genetic diversity through population genetic parameters calculated in the GenAlex program and the diveRsity package in R. We used the Wilcoxon test to verify population bottlenecks and the genetic distance of Nei and Bayesian analysis for genetic clusters. The eight populations showed low allele richness, low observed heterozygosity, and high inbreeding values (f). In addition, six of the eight populations experienced genetic bottlenecks, which would partly explain the low genetic diversity in populations. Cluster analysis identified two clusters (K = 2), with green morphotype genetically distinguishing from yellow and red morphotypes. Thus, we show, for the first time, a strong genetic structure among E. edulis morphotypes even for geographically close populations.
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Affiliation(s)
- Gislaine Mendes Coelho
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | - Alesandro Souza Santos
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
| | | | | | - Fernanda Maria Oliveira Souza
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
| | | | - Fernanda Amato Gaiotto
- Departamento de Ciências BiológicasCentro de Biotecnologia e GenéticaUniversidade Estadual de Santa CruzIlhéusBrazil
- Laboratório de Ecologia Aplicada à ConservaçãoUniversidade Estadual de Santa CruzIlhéusBrazil
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Soares LASS, Cazetta E, Santos LR, França DDS, Gaiotto FA. Anthropogenic Disturbances Eroding the Genetic Diversity of a Threatened Palm Tree: A Multiscale Approach. Front Genet 2019; 10:1090. [PMID: 31788000 PMCID: PMC6855268 DOI: 10.3389/fgene.2019.01090] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/09/2019] [Indexed: 12/02/2022] Open
Abstract
Habitat loss and the illegal exploitation of natural resources are among the main drivers of species extinction around the world. These disturbances act at different scales, once changes in the landscape composition and configuration operate at large scales and exploitation of natural resources at local scales. Evidence suggests that both scales are capable of triggering genetic erosion in the remaining populations. However, most of the studies so far did not evaluate simultaneously the effects of these disturbances on genetic diversity and structure of plants. In this study, we used a multiple scale approach to empirically evaluate the impacts caused by local and landscape scale disturbances in the genetic diversity and structure of an endangered palm tree, Euterpe edulis. We sampled and genotyped with microsatellite markers 544 juveniles of E. edulis in 17 fragments of Atlantic Forest in Brazil. In addition, we estimated the local logging rate and the forest cover and isolation at landscape scale. We found that the palm populations have not undergone any recent bottleneck events and that only logging intensification had affected the fixation index and the number of private alleles. Additionally, we did not detect any evidence of spatial genetic structure or genetic divergence associated with environmental disturbance variables at different scales. However, we identified distinct genetic clusters, which may indicate a reduction of gene flow between fragments that were previously a continuous habitat. Our results show that local disturbances, which act directly on population size reduction, such as logging, modified the genetic diversity more rapidly, whereas genetic structure is probably more influenced by large-scale modifications. In this way, to maximize the conservation efforts of economically exploited species, we recommend to increase the inspection to reduce the illegal exploitation, and reforestation of degraded areas, in order to increase the gene flow in Atlantic Forest fragments.
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Affiliation(s)
- Leiza Aparecida Souza Serafim Soares
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Eliana Cazetta
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Larissa Rocha Santos
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Daniele de Souza França
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Fernanda Amato Gaiotto
- Applied Ecology and Conservation Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, Brazil.,Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
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Santos JD, Varassin IG, Muschner VC, Ovaskainen O. Estimating seed and pollen dispersal kernels from genetic data demonstrates a high pollen dispersal capacity for an endangered palm species. AMERICAN JOURNAL OF BOTANY 2018; 105:1802-1812. [PMID: 30347429 DOI: 10.1002/ajb2.1176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Seed and pollen dispersal are key processes shaping plant population dynamics and maintaining genetic diversity. The essence of these processes is the movement of propagules from a parental tree to the site of propagule establishment. The estimation of plant dispersal kernels has remained challenging due to the difficulty of making direct observations. We estimated the dispersal capacity of the endangered palm Euterpe edulis, whose seeds are dispersed by vertebrates and pollen by insects. METHODS We used a hierarchical Bayesian model with genetic data from reproductive plants, juveniles, and embryos to estimate dispersal kernels. Our analyses account for genotyping error and uncertainty in parental assignment. KEY RESULTS We found that seeds were dispersed at most a few hundred meters, but pollen was dispersed up to several kilometers. We hypothesize that this long-distance pollen dispersal is generated mainly by euglossine bees, whereas the main dispersal vectors for short-distance seed dispersal are thrushes. The long-distance dispersal of pollen suggests a high level of gene flow that should maintain genetic diversity of E. edulis. Despite the relation between long-distance dispersal and genetic diversity, we observed low genetic diversity and inbreeding within the local population, which are probably due to restricted gene flow due to the low density of this population and its aggregated spatial distribution. CONCLUSIONS We conclude that if conservation actions are able to restore the population density of E. edulis, the recovery of its genetic diversity will be facilitated because of its high dispersal capacity, especially with regard to pollen.
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Affiliation(s)
- Jaqueline Dos Santos
- Laboratório de Ecologia Molecular Vegetal, Departamento de Botânica, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Caixa Postal 19031, CEP: 81531-990, Curitiba, PR, Brazil
- Laboratório de Interações e Biologia Reprodutiva, Departamento de Botânica, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Caixa Postal 19031, CEP: 81531-990, Curitiba, PR, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação - UFPR
| | - Isabela Galarda Varassin
- Laboratório de Interações e Biologia Reprodutiva, Departamento de Botânica, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Caixa Postal 19031, CEP: 81531-990, Curitiba, PR, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação - UFPR
| | - Valéria Cunha Muschner
- Laboratório de Ecologia Molecular Vegetal, Departamento de Botânica, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Caixa Postal 19031, CEP: 81531-990, Curitiba, PR, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação - UFPR
| | - Otso Ovaskainen
- Department of Biosciences, University of Helsinki, Viikinkaari 1, Helsinki, 00014, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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Montagna T, Silva JZ, Pikart TG, Reis MS. Reproductive ecology of Ocotea catharinensis, an endangered tree species. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:926-935. [PMID: 29786924 DOI: 10.1111/plb.12847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Ocotea catharinensis (Lauraceae) is an endangered tree species from the Brazilian Atlantic Rainforest. Currently, little is known about the reproductive ecology of this species. Aiming to propose conservation measures, we described aspects related to phenology, floral biology, pollination, seed dispersal and mating system of O. catharinensis. We conducted phenological observations in 62 individuals for 2 years. In one reproductive event, we evaluated nectar production, stigmatic receptivity and pollen viability. Floral visitors were observed, identified and classified on a scale of pollination effectiveness. Seed dispersers were observed and identified using camera traps. Finally, the mating system was evaluated through pollen/ovule ratios, experimental pollination treatments and genetic analysis with molecular markers. Ocotea catharinensis presented a supra-annual fruiting pattern with a substantial reduction of reproducing individuals from bud phase to ripe fruit phase. Several mechanisms prompting cross-fertilisation were identified, such as attractive, herkogamic and protogynic flowers. The main floral visitors and pollinators were from the Diptera order, and all seed dispersers were birds. The species presented a predominantly outcrossed mixed mating system with significant selfing rate (17.3%). Although based on restricted evidence, we hypothesised that selfing is an escape mechanism for situations unfavourable to cross-fertilisation. Specifically, for the studied population selfing is a response to reduced population size, which is caused by the non-reproduction of all potentially reproductive individuals and by past exploitation events. Therefore, conservation efforts should be able to enhance population sizes, as well as prevent overexploitation.
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Affiliation(s)
- T Montagna
- Núcleo de Pesquisas em Florestas Tropicais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - J Z Silva
- Núcleo de Pesquisas em Florestas Tropicais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - T G Pikart
- Laboratório de Entomologia, Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco, Acre, Brazil
| | - M S Reis
- Núcleo de Pesquisas em Florestas Tropicais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Escobar S, Pintaud J, Balslev H, Bernal R, Moraes Ramírez M, Millán B, Montúfar R. Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis-scenario. Ecol Evol 2018; 8:8030-8042. [PMID: 30250682 PMCID: PMC6144996 DOI: 10.1002/ece3.4216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/22/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022] Open
Abstract
Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.
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Affiliation(s)
- Sebastián Escobar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | | | - Henrik Balslev
- Department of Bioscience, Ecoinformatics and Biodiversity GroupAarhus UniversityAarhusDenmark
| | - Rodrigo Bernal
- Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | | | - Betty Millán
- Museo de Historia NaturalUniversidad Nacional Mayor de San Marcos (UNMSM)LimaPerú
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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Understanding genetic diversity, spatial genetic structure, and mating system through microsatellite markers for the conservation and sustainable use of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1061-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hoeltgebaum MP, dos Reis MS. Genetic Diversity and Population Structure of Varronia curassavica: A Medicinal Polyploid Species in a Threatened Ecosystem. J Hered 2017; 108:415-423. [DOI: 10.1093/jhered/esx010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/08/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marcia Patricia Hoeltgebaum
- From the Núcleo de Pesquisa em Florestas Tropicais, Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Rodovia Admar Gonzaga, 1346, Itacorubi, Florianópolis/SC, CEP: 88034-001, Brazil
| | - Maurício Sedrez dos Reis
- From the Núcleo de Pesquisa em Florestas Tropicais, Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Rodovia Admar Gonzaga, 1346, Itacorubi, Florianópolis/SC, CEP: 88034-001, Brazil
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Araújo MRG, Melo Júnior AFD, Menezes EV, Brandão MM, Cota LG, Oliveira DAD, Royo VDA, Vieira FA. Fine-scale spatial genetic structure and gene flow in Acrocomia aculeata (Arecaceae): Analysis in an overlapping generation. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Carvalho CDS, Ballesteros-Mejia L, Ribeiro MC, Côrtes MC, Santos AS, Collevatti RG. Climatic stability and contemporary human impacts affect the genetic diversity and conservation status of a tropical palm in the Atlantic Forest of Brazil. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0921-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gene flow and fine-scale spatial genetic structure in Cabralea canjerana (Meliaceae), a common tree species from the Brazilian Atlantic forest. JOURNAL OF TROPICAL ECOLOGY 2016. [DOI: 10.1017/s0266467416000067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:The Atlantic forest is the biome most severely affected by deforestation in Brazil. Cabralea canjerana spp. canjerana is a dioecious tree species with widespread distribution in the Neotropical region. This species is considered a model to ascertain population ecology parameters for endangered plant species from the Atlantic forest. Fine-scale spatial genetic structure and pollen-mediated gene flow are crucial information in landscape genetics and evolutionary ecology. A total of 192 adults and 121 offspring were sampled in seven C. canjerana populations in the Southern Minas Gerais State, Brazil, to assess whether pollen-mediated gene flow is able to prevent spatial genetic structure within and among Atlantic forest fragments. Several molecular ecology parameters were estimated using microsatellite loci. High levels of genetic diversity (HE = 0.732) and moderate population structure (θ = 0.133) were recorded. No significant association between kinship and spatial distance amongst individuals within each population (Sp = 0.000109) was detected. Current pollen-mediated gene flow occurs mainly within forest fragments, probably due to short-distance flights of the pollinator of C. canjerana, and also the forest fragmentation may have restricted flight distance. The high levels of genetic differentiation found amongst the seven sites sampled demonstrated how habitat fragmentation affects the gene flow process in natural areas.
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Santos AS, Cazetta E, Morante Filho JC, Baumgarten J, Faria D, Gaiotto FA. Lessons from a palm: genetic diversity and structure in anthropogenic landscapes from Atlantic Forest, Brazil. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0740-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Picanço-Rodrigues D, Astolfi-Filho S, Lemes MR, Gribel R, Sebbenn AM, Clement CR. Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers. Genet Mol Biol 2015; 38:59-66. [PMID: 25983626 PMCID: PMC4415557 DOI: 10.1590/s1415-475738120140022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 07/28/2014] [Indexed: 11/21/2022] Open
Abstract
Peach palm (Bactris gasipaes) is cultivated by many indigenous and
traditional communities from Amazonia to Central America for its edible fruits, and
is currently important for its heart-of-palm. The objective of this study was to
investigate the mating system of peach palm, as this is important for conservation
and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated
progenies from three populations of the Pampa Hermosa landrace maintained in a
progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95
to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high,
indicating that peach palm is predominantly allogamous. The outcrossing rates among
relatives were significantly different from zero (0.101 to 0.202), providing evidence
for considerable biparental inbreeding within populations, probably due to farmers
planting seeds of a small number of open-pollinated progenies in the same plot. The
correlations of paternity estimates were low (0.051 to 0.112), suggesting a large
number of pollen sources (9 to 20) participating in pollination of individual fruit
bunches. Effective population size estimates suggest that current germplasm
collections are insufficient for long-term ex situ conservation. As
with most underutilized crops, on farm conservation is the most important component
of an integrated conservation strategy.
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Affiliation(s)
- Doriane Picanço-Rodrigues
- Laboratório de Evolução Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Spartaco Astolfi-Filho
- Laboratório de Evolução Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Maristerra R Lemes
- Laboratório de Genética e Biologia Reprodutiva de Plantas, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil . ; Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rogerio Gribel
- Laboratório de Genética e Biologia Reprodutiva de Plantas, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil . ; Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alexandre M Sebbenn
- Estação Experimental de Tupi, Instituto Florestal de São Paulo, São Paulo, SP, Brazil
| | - Charles R Clement
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil . ; Laboratório de Evolução Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, AM, Brazil
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14
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Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm. Heredity (Edinb) 2015; 115:216-24. [PMID: 25873150 DOI: 10.1038/hdy.2015.30] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/03/2015] [Accepted: 03/12/2015] [Indexed: 11/08/2022] Open
Abstract
Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.
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Mariot A, Mantovani A, Reis MSD. Bark harvesting systems of Drimys brasiliensis Miers in the Brazilian Atlantic rainforest. AN ACAD BRAS CIENC 2014; 86:1315-26. [PMID: 25119732 DOI: 10.1590/0001-3765201420130180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/28/2013] [Indexed: 11/22/2022] Open
Abstract
Drimys brasiliensis Miers, locally known as cataia or casca-de-anta, is a native tree species of the Atlantic Rainforest. Its bark is harvested from natural populations. This study examined the recovery capacity of the bark of D. brasiliensis under different bark harvesting methods, as well as the influence of these approaches on its population dynamics and reproductive biology. While none of these treatments resulted in changes in phenological behavior or the rate of increase of diameter at breast height and tree height, the removal of wider bark strips resulted in lower rates of bark recovery and higher rates of insect attack and diseases. Accordingly, the results recommend using strips of bark 2 cm wide and 2 m long, with 4 cm between strips, for effective rates of bark regrowth and for lower susceptibility to insect attack and diseases. From these studies, we concluded that D. brasiliensis has a high potential for sustainable management of its natural populations, demonstrating the possibility of generating an important supplementary income for farmers and contributing to the use and conservation of the Atlantic Rainforest.
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Affiliation(s)
- Alexandre Mariot
- Núcleo de Pesquisas em Florestas Tropicais, Departamento de Fitotecnia, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
| | - Adelar Mantovani
- Departamento de Engenharia Florestal, Centro Agroveterinário, Universidade do Estado de Santa Catarina, Lages, SC, Brasil
| | - Maurício S dos Reis
- Núcleo de Pesquisas em Florestas Tropicais, Departamento de Fitotecnia, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, SC, Brasil
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The discovery of microsatellite markers for Hardenbergia violacea (Fabaceae), using next-generation sequencing. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9707-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nazareno AG, Reis MSD. Linking phenology to mating system: exploring the reproductive biology of the threatened palm species Butia eriospatha. ACTA ACUST UNITED AC 2012; 103:842-52. [PMID: 23077230 DOI: 10.1093/jhered/ess070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The reproductive biology of the vulnerable palm species Butia eriospatha was studied to provide important information that contributes to our understanding and conservation of the species. In order to determine when and how B. erisopatha reproduces, we combined data from 7 nuclear microsatellite loci with ecological data on flowering and fruiting phenology collected between 2009 and 2011 from a population (N = 515) in the Atlantic Rainforest, Southern Brazil. Periods of flowering and fruit production were seasonal and variable across reproductive events. Mating system analyses indicate that B. eriospatha is a predominantly outcrossing species, ((m) = 0.961), since a certain degree of biparental inbreeding does occur. The species is self-compatible and reproduction may also occur by geitonogamy, indicating the ability of isolated populations to survive and persist. Open-pollinated seeds varied in relatedness, including mainly half-sibs and full-sibs. The effective population size was lower than that expected for panmictic populations. Hence, seeds for conservation programs must be collected from a large number of seed-trees to ensure an adequate effective population in the sample. The collection of germplasm is a high-priority strategy that should be employed to maintain the genetic variability that remains.
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Affiliation(s)
- Alison Gonçalves Nazareno
- Núcleo de Pesquisas em Florestas Tropicais, Federal University of Santa Catarina, CP 476, 88040-900, Florianópolis, Santa Catarina, Brazil.
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Namoff S, Veloz A, Jiménez F, Rodríguez-Peña RA, Peguero B, Lewis C, Moynihan J, Abdo M, Maunder M, Von Wettberg E, Meerow AW, Griffith MP, Francisco-Ortega J. Sweet drinks are made of this: conservation genetics of an endemic palm species from the Dominican Republic. J Hered 2011; 102:1-10. [PMID: 21172825 DOI: 10.1093/jhered/esq118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pseudophoenix ekmanii is a threatened palm species endemic to the Dominican Republic. Sap from trees is extracted to make a local drink; once they are tapped the individual usually dies. Plants are also illegally harvested for the nursery trade and destroyed by poachers hunting the endemic and threatened Hispaniolan parrot. We used 7 DNA microsatellite markers to assist land managers in developing conservation strategies for this palm. We sampled 4 populations along the known distribution range of this species (3 populations from the mainland and 1 from the small island of Isla Beata), for a total sample of n = 104. We found strong evidence for genetic drift, inbreeding, and moderate gene flow (i.e., all populations had at least 4 loci that were not in Hardy-Weinberg equilibrium, at least 9 loci pairs were in linkage disequilibrium, the pairwise F(ST) values ranged from 0.069 to 0.266, and had positive F(IS) values). Data supported an isolation-by-distance model, and cluster analyses based on genetic distances resolved 2 groups that match a north-south split. The population from Isla Beata had the lowest levels of genetic diversity and was the only one in which we found pairs of individuals with identical shared multilocus genotypes.
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Affiliation(s)
- Sandra Namoff
- Center for Tropical Plant Conservation, Fairchild Tropical Botanic Garden, Coral Gables, Miami, FL 33156, USA
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Jones JM, Gibson JP. Population genetic diversity and structure within and among disjunct populations of Alnus maritima (seaside alder) using microsatellites. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0203-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Genetic structure and long-distance dispersal in populations of the wingless pest springtail, Sminthurus viridis (Collembola: Sminthuridae). Genet Res (Camb) 2011; 93:1-12. [DOI: 10.1017/s0016672310000510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SummaryThe lucerne flea, Sminthurus viridis (Collembola: Sminthuridae) (L.) is a major pest of broadacre agriculture across southern Australia. Few molecular studies have been conducted on S. viridis and none have examined its population genetics, despite the importance for developing effective control strategies. Here, we characterize the genetic structure of Australian populations using three allozyme and eight microsatellite loci, as well as sequencing a fragment of the mitochondrial DNA cytochrome oxidase I gene. We found that S. viridis in Australia are diploid, sexually reproducing and exhibit significant population structure as a result of limited gene flow. Despite significant differentiation between populations, there was very low cytochrome oxidase subunit I (COI) gene sequence variation, indicating the presence of a single species in Australia. The observed structure only marginally complied with an ‘isolation by distance’ model with human-mediated long-distance dispersal likely occurring. Allozymes and microsatellites gave very similar FST estimates, although differences found for novel alternative estimates of differentiation suggest that the allozymes did not capture the full extent of the population structure. These results highlight that control strategies may need to vary for locally adapted S. viridis populations and strategies aimed at limiting the spread of any future pesticide resistance will need to manage the effects of human-mediated dispersal.
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Fine-scale spatial genetic structure and allozymic diversity in natural populations of Ocotea catharinensis Mez. (Lauraceae). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9939-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Clement CR, Santos RP, Desmouliere SJM, Ferreira EJL, Neto JTF. Ecological adaptation of wild peach palm, its in situ conservation and deforestation-mediated extinction in southern Brazilian Amazonia. PLoS One 2009; 4:e4564. [PMID: 19238213 PMCID: PMC2642997 DOI: 10.1371/journal.pone.0004564] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Accepted: 01/13/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Arc of Fire across southern Amazonia seasonally attracts worldwide attention as forests are cut and burned for agricultural expansion. These forests contain numerous wild relatives of native South American crops, such as peach palm. METHODOLOGY/PRINCIPAL FINDINGS Our prospecting expeditions examined critical areas for wild peach palm in the Arc of Fire in Mato Grosso, Pará, Maranhão and Tocantins, as well as areas not previously examined in Amazonas and Amapá states. Recent digitization of the RADAM Brasil project permitted comparison among RADAM's parataxonomists' observations, previous botanical collections and our prospecting. Mapping on soils and vegetation types enabled us to hypothesize a set of ecological preferences. Wild peach palm is best adapted to Ultisols (Acrisols) in open forests across the Arc of Fire and westward into the more humid western Amazonia. Populations are generally small (fewer than 10 plants) on slopes above watercourses. In northern Mato Grosso and southern Pará soybean fields and pastures now occupy numerous areas where RADAM identified wild peach palm. The controversial BR-163 Highway is already eroding wild peach palm as deforestation expands. CONCLUSIONS/SIGNIFICANCE Many of these populations are now isolated by increasing forest fragmentation, which will lead to decreased reproduction via inbreeding depression and eventual extinction even without complete deforestation. Federal conservation areas are less numerous in the Arc of Fire than in other parts of Brazilian Amazonia, although there are indigenous lands; these conservation areas contain viable populations of wild peach palm and require better protection than they are currently receiving. Ex situ conservation of these populations is not viable given the relative lack of importance of domesticated peach palm and the difficulty of maintaining even economically interesting genetic resources.
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Affiliation(s)
- Charles R. Clement
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brasil
- * E-mail:
| | - Ronaldo P. Santos
- Instituto Nacional de Colonização e Reforma Agrária, Manaus, Amazonas, Brasil
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