1
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Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
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Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
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2
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Arantes FM, de Paula LF, Forzza RC. Checklist of vascular plant species on inselbergs in the Monumento Natural dos Pontões Capixabas, Espírito Santo State, Brazil. Biodivers Data J 2024; 12:e105688. [PMID: 38235164 PMCID: PMC10793112 DOI: 10.3897/bdj.12.e105688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024] Open
Abstract
Background Inselbergs are granitic and/or gneissic rocky outcrops and, in Brazil, the dome-shaped ones in the Atlantic Forest Domain are called sugarloaves (pães de açúcar). They have an extremely specialised vegetation with high levels of endemism. Even though, they are poorly studied and highly degraded. In north-eastern Espírito Santo State, south-eastern Brazil, the Monumento Natural dos Pontões Capixabas (MONAPC) is a federal protected area created to guard some inselbergs mainly threatened by mining, which is one of the main economic activities in the State. In this work, we provide the first checklist of the vascular plant species in this protected area. New information We recorded 108 species in 36 families and 75 genera that inhabit the vegetation islands on the inselbergs within the official limits of MONAPC. A new species of Pleroma (Melastomataceae) and a new species of Cololobus (Asteraceae) were discovered as new to science and they are being described in other articles.
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Affiliation(s)
- Fabiula Moreno Arantes
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilJardim Botânico do Rio de JaneiroRio de JaneiroBrazil
| | - Luiza F.A. de Paula
- Universidade Federal de Minas Gerais, Belo Horizonte, BrazilUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Rafaela Campostrini Forzza
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, BrazilJardim Botânico do Rio de JaneiroRio de JaneiroBrazil
- Instituto Chico Mendes de Conservação da Biodiversidade, Prado, BrazilInstituto Chico Mendes de Conservação da BiodiversidadePradoBrazil
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3
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Jiménez-López FJ, Arista M, Talavera M, Cerdeira Morellato LP, Pannell JR, Viruel J, Ortiz Ballesteros PL. Multiple pre- and postzygotic components of reproductive isolation between two co-occurring Lysimachia species. THE NEW PHYTOLOGIST 2023; 238:874-887. [PMID: 36683441 DOI: 10.1111/nph.18767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Genetic divergence between species depends on reproductive isolation (RI) due to traits that reduce interspecific mating (prezygotic isolation) or are due to reduced hybrid fitness (postzygotic isolation). Previous research found that prezygotic barriers tend to be stronger than postzygotic barriers, but most studies are based on the evaluation of F1 hybrid fitness in early life cycle stages. We combined field and experimental data to determine the strength of 17 prezygotic and postzygotic reproductive barriers between two Lysimachia species that often co-occur and share pollinators. We assessed postzygotic barriers up to F2 hybrids and backcrosses. The two species showed near complete RI due to the cumulative effect of multiple barriers, with an uneven and asymmetric contribution to isolation. In allopatry, prezygotic barriers contributed more to reduce gene flow than postzygotic barriers, but their contributions were more similar in sympatry. The strength of postzygotic RI was up to three times lower for F1 progeny than for F2 or backcrossed progenies, and RI was only complete when late F1 stages and either F2 or backcrosses were accounted for. Our results thus suggest that the relative strength of postzygotic RI may be underestimated when its effects on late stages of the life cycle are disregarded.
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Affiliation(s)
- Francisco Javier Jiménez-López
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Apdo. 1095, 41080, Seville, Spain
- Phenology Lab, Department of Biodiversity, Biosciences Institute, UNESP - São Paulo State University, São Paulo, Brazil
| | - Montserrat Arista
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Apdo. 1095, 41080, Seville, Spain
| | - María Talavera
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Apdo. 1095, 41080, Seville, Spain
| | | | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, CH-1015, Switzerland
| | - Juan Viruel
- Royal Botanic Gardens, Kew, TW9 3DS, Richmond, UK
| | - Pedro L Ortiz Ballesteros
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Apdo. 1095, 41080, Seville, Spain
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Zhu X, Liang H, Jiang H, Kang M, Wei X, Deng L, Shi Y. Phylogeographic structure of Heteroplexis (Asteraceae), an endangered endemic genus in the limestone karst regions of southern China. FRONTIERS IN PLANT SCIENCE 2022; 13:999964. [PMID: 36388513 PMCID: PMC9647136 DOI: 10.3389/fpls.2022.999964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.
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Affiliation(s)
- Xianliang Zhu
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Hui Liang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
- College of Life Science, Guangxi Normal University, Guilin, China
| | - Haolong Jiang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Ming Kang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Wei
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Lili Deng
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Yancai Shi
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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5
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Changes in plant biodiversity facets of rocky outcrops and their surrounding rangelands across precipitation and soil gradients. Sci Rep 2022; 12:9022. [PMID: 35637253 PMCID: PMC9151709 DOI: 10.1038/s41598-022-13123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Climate and soil factors induce substantial controls over plant biodiversity in stressful ecosystems. Despite of some studies on plant biodiversity in extreme ecosystems including rocky outcrops, simultaneous effects of climate and soil factors have rarely been studied on different facets of biodiversity including taxonomic and functional diversity in these ecosystems. In addition, we know little about plant biodiversity variations in such extreme ecosystems compared to natural environments. It seems that environmental factors acting in different spatial scales specifically influence some facets of plant biodiversity. Therefore, we studied changes in taxonomic and functional diversity along precipitation and soil gradients in both landscapes (i) rocky outcrops and (ii) their nearby rangeland sites in northeast of Iran. In this regard, we considered six sites across precipitation and soil gradients in each landscape, and established 90 1m2 quadrates in them (i.e. 15 quadrats in each site; 15 × 6 = 90 in each landscape). Then, taxonomic and functional diversity were measured using RaoQ index, FDis and CWM indices. Finally, we assessed impacts of precipitation and soil factors on biodiversity indices in both landscapes by performing regression models and variation partitioning procedure. The patterns of taxonomic diversity similarly showed nonlinear changes along the precipitation and soil factors in both landscapes (i.e. outcrop and rangeland). However, we found a more negative and significant trends of variation in functional diversity indices (except for CWMSLA) across precipitation and soil factors in outcrops than their surrounding rangelands. Variations of plant biodiversity were more explained by precipitation factors in surrounding rangelands, whereas soil factors including organic carbon had more consistent and significant effects on plant biodiversity in outcrops. Therefore, our results represent important impacts of soil factors in structuring plant biodiversity facets in stressful ecosystems. While, environmental factors acting in regional and broad scales such as precipitation generally shape vegetation and plant biodiversity patterns in natural ecosystems. We can conclude that rocky outcrops provide suitable microenvironments to present plant species with similar yields that are less able to be present in rangeland ecosystems.
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6
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Tavares MM, Ferro M, Leal BSS, Palma‐Silva C. Speciation with gene flow between two Neotropical sympatric species (
Pitcairnia
spp.: Bromeliaceae). Ecol Evol 2022; 12:e8834. [PMID: 35509614 PMCID: PMC9055293 DOI: 10.1002/ece3.8834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Marília Manuppella Tavares
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Milene Ferro
- Departamento de Biologia Geral e Aplicada Universidade Estadual Paulista Rio Claro Brazil
| | - Bárbara Simões Santos Leal
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Clarisse Palma‐Silva
- Departamento de Biologia Vegetal Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
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7
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Leal BSS, Chaves CJN, Graciano VA, Boury C, Huacre LAP, Heuertz M, Palma-Silva C. Evidence of local adaptation despite strong drift in a Neotropical patchily distributed bromeliad. Heredity (Edinb) 2021; 127:203-218. [PMID: 33953353 PMCID: PMC8322333 DOI: 10.1038/s41437-021-00442-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Both genetic drift and divergent selection are predicted to be drivers of population differentiation across patchy habitats, but the extent to which these forces act on natural populations to shape traits is strongly affected by species' ecological features. In this study, we infer the genomic structure of Pitcairnia lanuginosa, a widespread herbaceous perennial plant with a patchy distribution. We sampled populations in the Brazilian Cerrado and the Central Andean Yungas and discovered and genotyped SNP markers using double-digest restriction-site associated DNA sequencing. In addition, we analyzed ecophysiological traits obtained from a common garden experiment and compared patterns of phenotypic and genetic divergence (PST-FST comparisons) in a subset of populations from the Cerrado. Our results from molecular analyses pointed to extremely low genetic diversity and a remarkable population differentiation, supporting a major role of genetic drift. Approximately 0.3% of genotyped SNPs were flagged as differentiation outliers by at least two distinct methods, and Bayesian generalized linear mixed models revealed a signature of isolation by environment in addition to isolation by distance for high-differentiation outlier SNPs among the Cerrado populations. PST-FST comparisons suggested divergent selection on two ecophysiological traits linked to drought tolerance. We showed that these traits vary among populations, although without any particular macro-spatial pattern, suggesting local adaptation to differences in micro-habitats. Our study shows that selection might be a relevant force, particularly for traits involved in drought stress, even for populations experiencing strong drift, which improves our knowledge on eco-evolutionary processes acting on non-continuously distributed species.
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Affiliation(s)
- Bárbara Simões Santos Leal
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Cleber Juliano Neves Chaves
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Vanessa Araujo Graciano
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil
| | - Christophe Boury
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Luis Alberto Pillaca Huacre
- grid.10800.390000 0001 2107 4576Departamento de Ecología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Myriam Heuertz
- grid.412041.20000 0001 2106 639XINRAE, Univ. Bordeaux, Biogeco, Cestas France
| | - Clarisse Palma-Silva
- grid.410543.70000 0001 2188 478XDepartamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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8
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Loiseau O, Mota Machado T, Paris M, Koubínová D, Dexter KG, Versieux LM, Lexer C, Salamin N. Genome Skimming Reveals Widespread Hybridization in a Neotropical Flowering Plant Radiation. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.668281] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The tropics hold at least an order of magnitude greater plant diversity than the temperate zone, yet the reasons for this difference are still subject to debate. Much of tropical plant diversity is in highly speciose genera and understanding the drivers of such high species richness will help solve the tropical diversity enigma. Hybridization has recently been shown to underlie many adaptive radiations, but its role in the evolution of speciose tropical plant genera has received little attention. Here, we address this topic in the hyperdiverse Bromeliaceae genus Vriesea using genome skimming data covering the three genomic compartments. We find evidence for hybridization in ca. 11% of the species in our dataset, both within the genus and between Vriesea and other genera, which is commensurate with hybridization underlying the hyperdiversity of Vriesea, and potentially other genera in Tillandsioideae. While additional genomic research will be needed to further clarify the contribution of hybridization to the rapid diversification of Vriesea, our study provides an important first data point suggesting its importance to the evolution of tropical plant diversity.
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9
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Caeiro-Dias G, Brelsford A, Kaliontzopoulou A, Meneses-Ribeiro M, Crochet PA, Pinho C. Variable levels of introgression between the endangered Podarcis carbonelli and highly divergent congeneric species. Heredity (Edinb) 2021; 126:463-476. [PMID: 33199832 PMCID: PMC8027454 DOI: 10.1038/s41437-020-00386-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Recent empirical studies have demonstrated that speciation with gene flow is more common than previously thought. From a conservation perspective, the potential negative effects of hybridization raise concerns on the genetic integrity of endangered species. However, introgressive hybridization has also been growingly recognized as a source of diversity and new advantageous alleles. Carbonell's wall lizard (Podarcis carbonelli) is an endangered species whose distribution overlaps with four other congeneric species. Our goal here was to determine whether P. carbonelli is completely reproductively isolated from its congeners and to evaluate the relevance of hybridization and interspecific gene flow for developing a conservation plan. We used restriction site associated DNA (RAD) sequencing to discover SNPs in samples from four contact zones between P. carbonelli and four other species. Principal component analysis, multilocus genotype assignment and interspecific heterozygosity suggest incomplete reproductive isolation and ongoing gene flow between species. However, hybridization dynamics vary across all pairs, suggesting complex interactions between multiple intrinsic and extrinsic barriers. Despite seemingly ubiquitous interspecific gene flow, we found evidence of strong reproductive isolation across most contact zones. Instead, indirect effects of hybridization like waste of reproductive effort in small isolated populations may be more problematic. Our results highlight the need to further evaluate the consequences of introgression for P. carbonelli, both on a geographic and genomic level and included in a comprehensive and urgently needed conservation plan. Besides, those findings will add important insights on the potential effects of hybridization and introgression for endangered species.
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Affiliation(s)
- Guilherme Caeiro-Dias
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France.
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, CA, USA
| | - Antigoni Kaliontzopoulou
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
| | - Mariana Meneses-Ribeiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
| | - Pierre-André Crochet
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Catarina Pinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
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10
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De Paula LFA, Forzza RC, Azevedo LO, Bueno ML, Solar RRC, Vanschoenwinkel B, Porembski S. Climatic control of mat vegetation communities on inselberg archipelagos in south-eastern Brazil. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Granite and/or gneiss inselbergs are excellent examples of geomorphologically stable island habitats, considered as old, climatically buffered, infertile landscapes (OCBILs). However, unlike oceanic islands, their underlying drivers of diversity patterns remain to be investigated. Here, we studied 24 inselbergs in south-eastern Brazil, aiming to understand the role of landscape variables and environmental conditions in the assembly of the characteristic extremophilic mat vegetation communities. We found that beta diversity was largely explained by climatic variables, whereas species richness did not vary among inselbergs. Classic determinants of the diversity of island communities do not generally seem to apply to these plant assemblages. Overall, these communities change along a coast-to-inland gradient that captures increased seasonality with a replacement of more hydrophilic taxa by more drought-tolerant taxa. Changes in species composition in space involved strong species replacement, with several widespread genera locally represented on distinct inselbergs by different narrowly distributed species. Despite the deterministic sorting of taxa based on climatic conditions, a substantial fraction of the beta diversity remained unexplained. This underlines the importance of historical processes, which are easier to notice in stable OCBIL regions, such as range expansion, local extinction, dispersal constraints and allopatric speciation.
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Affiliation(s)
- Luiza F A De Paula
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Avenida. Antônio Carlos, Belo Horizonte, MG, Brazil
| | | | - Luísa O Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Avenida. Antônio Carlos, Belo Horizonte, MG, Brazil
| | - Marcelo L Bueno
- Laboratory of Macroecology & Evolution, Universidade Estadual de Mato Grosso do Sul, Unidade Mundo Novo, Mato Grosso do Sul, MS, Brazil
| | - Ricardo R C Solar
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Avenida. Antônio Carlos, Belo Horizonte, MG, Brazil
| | - Bram Vanschoenwinkel
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), Pleinlaan, Brussels, Belgium
| | - Stefan Porembski
- Institut für Biowissenschaften, Allgemeine und Spezielle Botanik, Universität Rostock, Wismarsche Straße, Rostock, Germany
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11
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Vargas OM, Goldston B, Grossenbacher DL, Kay KM. Patterns of speciation are similar across mountainous and lowland regions for a Neotropical plant radiation (Costaceae: Costus). Evolution 2020; 74:2644-2661. [PMID: 33047821 DOI: 10.1111/evo.14108] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/28/2020] [Accepted: 09/21/2020] [Indexed: 01/05/2023]
Abstract
High species richness and endemism in tropical mountains are recognized as major contributors to the latitudinal diversity gradient. The processes underlying mountain speciation, however, are largely untested. The prevalence of steep ecogeographic gradients and the geographic isolation of populations by topographic features are predicted to promote speciation in mountains. We evaluate these processes in a species-rich Neotropical genus of understory herbs that range from the lowlands to montane forests and have higher species richness in topographically complex regions. We ask whether climatic niche divergence, geographic isolation, and pollination shifts differ between mountain-influenced and lowland Amazonian sister pairs inferred from a 756-gene phylogeny. Neotropical Costus ancestors diverged in Central America during a period of mountain formation in the last 3 million years with later colonization of Amazonia. Although climatic divergence, geographic isolation, and pollination shifts are prevalent in general, these factors do not differ between mountain-influenced and Amazonian sister pairs. Despite higher climatic niche and species diversity in the mountains, speciation modes in Costus appear similar across regions. Thus, greater species richness in tropical mountains may reflect differences in colonization history, diversification rates, or the prevalence of rapidly evolving plant life forms, rather than differences in speciation mode.
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Affiliation(s)
- Oscar M Vargas
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California, 95060.,Department of Biological Sciences, Humboldt State University, Arcata, California, 95521
| | - Brittany Goldston
- Department of Biology, California Polytechnic State University, San Luis Obispo, California, 93401
| | - Dena L Grossenbacher
- Department of Biology, California Polytechnic State University, San Luis Obispo, California, 93401
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California, 95060
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12
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From micro- to macroevolution: insights from a Neotropical bromeliad with high population genetic structure adapted to rock outcrops. Heredity (Edinb) 2020; 125:353-370. [PMID: 32681156 DOI: 10.1038/s41437-020-0342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Geographic isolation and reduced population sizes can lead to local extinction, low efficacy of selection and decreased speciation. However, population differentiation is an essential step of biological diversification. In allopatric speciation, geographically isolated populations differentiate and persist until the evolution of reproductive isolation and ecological divergence completes the speciation process. Pitcairnia flammea allows us to study the evolutionary consequences of habitat fragmentation on naturally disjoint rock-outcrop species from the Brazilian Atlantic Rainforest (BAF). Our main results showed low-to-moderate genetic diversity within populations, and deep population structuring caused by limited gene flow, low connectivity, genetic drift and inbreeding of long-term isolation and persistence of rock-outcrop populations throughout Quaternary climatic oscillations. Bayesian phylogenetic and model-based clustering analyses found no clear northern and southern phylogeographic structure commonly reported for many BAF organisms. Although we found two main lineages diverging by ~2 Mya during the early Pleistocene, species' delimitation analysis assigned most of the populations as independent evolving entities, suggesting an important role of disjoint rock outcrops in promoting high endemism in this rich biome. Lastly, we detected limited gene flow in sympatric populations although some hybridization and introgression were observed, suggesting a continuous speciation process in this species complex. Our data not only inform us about the extensive differentiation and limited gene flow found among Pitcairnia flammea species complex, but they also contain information about the mechanisms that shape the genetic architecture of small and fragmented populations of isolated rock outcrop of recently radiated plants.
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13
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Ling SJ, Qin XT, Song XQ, Zhang LN, Ren MX. Genetic delimitation of Oreocharis species from Hainan Island. PHYTOKEYS 2020; 157:59-81. [PMID: 32934448 PMCID: PMC7467941 DOI: 10.3897/phytokeys..32427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/12/2019] [Indexed: 06/11/2023]
Abstract
Hainan Island harbours an extraordinary diversity of Gesneriaceae with 14 genera and 23 species, amongst which two species and one variety are recognised in the genus Oreocharis. These three Oreocharis taxa are all Hainan-endemics and show a complex geographical distribution pattern with considerable morphological intermixtures. In this study, we combined DNA (nuclear ITS sequences and cpDNAtrnL-trnF and ycf1b) to evaluate genetic delimitation for 12 Oreocharis populations from the island, together with morphological similarity analysis using 16 morphological traits. The results showed Hainan Oreocharis taxa were monophyletic with relative low genetic diversity within populations, highly significant genetic differentiation amongst populations and a significant phylogeographical structure. The 12 populations formed three genetically distinct groups, roughly correspondent to the currently recognised two species and one unknown lineage. The PCA analyses of morphological traits indicate three distinctive groups, differing mainly in petal colour and corolla shapes. The roles of river and mountain isolations in the origin and distribution of these three lineages are discussed.
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Affiliation(s)
- Shao-Jun Ling
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaHainan UniversityHaikouChina
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, ChinaHainan UniversityHaikouChina
| | - Xin-Ting Qin
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaHainan UniversityHaikouChina
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, ChinaHainan UniversityHaikouChina
| | - Xi-Qiang Song
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaHainan UniversityHaikouChina
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, ChinaHainan UniversityHaikouChina
| | - Li-Na Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaHainan UniversityHaikouChina
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, ChinaHainan UniversityHaikouChina
| | - Ming-Xun Ren
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, ChinaHainan UniversityHaikouChina
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, ChinaHainan UniversityHaikouChina
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14
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de Paula LFA, Azevedo LO, Mauad LP, Cardoso LJT, Braga JMA, Kollmann LJC, Fraga CN, Menini Neto L, Labiak PH, Mello-Silva R, Porembski S, Forzza RC. Sugarloaf Land in south-eastern Brazil: a tropical hotspot of lowland inselberg plant diversity. Biodivers Data J 2020; 8:e53135. [PMID: 32617070 PMCID: PMC7320030 DOI: 10.3897/bdj.8.e53135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/07/2020] [Indexed: 11/17/2022] Open
Abstract
Background Isolated monoliths of granitic and/or gneissic rock rising abruptly from the surrounding landscape are known as inselbergs. Dome-shaped inselbergs are common throughout the Atlantic Forest in south-eastern Brazil, a region known as Sugarloaf Land (SLL). This study aimed to create the first checklist of vascular plant species occurring on lowland inselbergs in SLL, with a focus on vegetation islands. We used information from online databases, our own field sampling and data from previously-published studies. We found 548 vascular plant species (505 angiosperms; 43 ferns and lycophytes) belonging to 69 families and 212 genera. Of all identified species, 536 are native and 12 are naturalised. New information We updated the information currently available in Flora do Brasil 2020, as 59% of the angiosperms and 63% of the ferns and lycophytes on our checklist were not previously characterised as occurring on rock outcrops. As a first step towards generating a Virtual Herbarium of lowland inselberg vascular plants, we added barcode vouchers with images available online for 75% of the total number of vascular species. In the official lists of endangered species, 115 angiosperms and five ferns and lycophytes are mentioned. However, the conservation status of many species have not yet been evaluated (77% angiosperms; 88% ferns and lycophytes), thus this list is an important step towards their conservation. The information provided herein is essential for management programmes related to rock outcrops in Brazil as they are facing serious threats to conservation.
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Affiliation(s)
- Luiza F A de Paula
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Luísa O Azevedo
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Luana Paula Mauad
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
| | - Leandro Jorge Telles Cardoso
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
| | - João Marcelo Alvarenga Braga
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
| | - Ludovic J C Kollmann
- Instituto Nacional da Mata Atlântica, Museu de Biologia Prof. Mello Leitão, Santa Teresa, Brazil Instituto Nacional da Mata Atlântica, Museu de Biologia Prof. Mello Leitão Santa Teresa Brazil
| | - Claudio N Fraga
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
| | - Luiz Menini Neto
- Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil Universidade Federal de Juiz de Fora Juiz de Fora Brazil
| | - Paulo H Labiak
- Universidade Federal do Paraná, Curitiba, Brazil Universidade Federal do Paraná Curitiba Brazil
| | - Renato Mello-Silva
- Universidade de São Paulo, São Paulo, Brazil Universidade de São Paulo São Paulo Brazil
| | - Stefan Porembski
- Universität Rostock, Rostock, Germany Universität Rostock Rostock Germany
| | - Rafaela Campostrini Forzza
- Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
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15
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McCulloch JB, Owen JP, Hinkle NC, Mullens BA, Busch JW. Genetic Structure of Northern Fowl Mite (Mesostigmata: Macronyssidae) Populations Among Layer Chicken Flocks and Local House Sparrows (Passeriformes: Passeridae). JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:122-130. [PMID: 31504688 DOI: 10.1093/jme/tjz136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Indexed: 06/10/2023]
Abstract
The northern fowl mite (NFM) Ornithonyssus sylviarum Canestrini and Fanzago is a blood-feeding ectoparasite found on many wild bird species and is a pest of poultry in the United States. It is unknown where NFM infestations of poultry originate, which has made it difficult to establish preventative biosecurity or effective control. We used microsatellite markers to evaluate genetic variation within and among NFM populations to determine routes of introduction onto farms and long-term persistence. We compared NFM from flocks of chickens (Gallus gallus) on different farms in California, Washington, and Georgia, and we compared NFM collected over a 5-yr interval. On three farms we collected NFM from chickens and house sparrows (Passer domesticus) nesting on each farm, which we used to assess movement between host species. There was strong genetic structure among mites from different poultry farms and low estimates of migration between farms. There were significant differences between mites on chickens and house sparrows on two farms where sparrows nested near flocks, indicating no exchange of mites. Only one farm showed evidence of NFM movement between chickens and sparrows. There was high genetic similarity between mites collected 5 yr apart on each of two farms, indicating that NFM infestations can persist for long periods. The genetic patterns did not reveal sources of NFM infestations on chicken farms. The data suggest that NFMs are strongly differentiated, which likely reflects periodic population declines with flock turnover and pesticide pressure.
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Affiliation(s)
| | - Jeb P Owen
- Department of Entomology, Washington State University, Pullman, WA
| | - Nancy C Hinkle
- Department of Entomology University of Georgia, Athens, GA
| | - Bradley A Mullens
- Department of Entomology, University of California, Riverside, Riverside, CA
| | - Jeremiah W Busch
- School of Biological Sciences, Washington State University, Pullman, WA
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16
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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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17
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Manhães VDC, de Miranda FD, Clarindo WR, Carrijo TT. Genetic diversity and karyotype of Pitcairnia azouryi: an endangered species of Bromeliaceae endemic to Atlantic Forest inselbergs. Mol Biol Rep 2019; 47:179-189. [PMID: 31587186 DOI: 10.1007/s11033-019-05118-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Abstract
Plant species of various families, such as those of Bromeliaceae, occur on inselbergs where they are subject to geographic isolation and environmental conditions that can lead to genetic erosion. This, in turn, can result in the loss of natural populations due to homozygosis, or changes in ploidy that may lead to reproductive isolation. The genetic diversity of five natural populations of Pitcairnia azouryi was measured using nine microsatellite markers transferred from P. albiflos and P. geyskesii. Chromosome numbers and nuclear DNA content were also evaluated. The results indicated moderate genetic differentiation among populations (FST = 0.188), and significant gene flow (Nm = 1.073) in four of the five populations. P. azouryi has, predominantly, 2n = 50 chromosomes and DNA content of 2C = 1.16 pg, but the tetraploid condition was found (2n = 100 and 2C = 2.32 pg) in seedlings of an individual of the most geographically isolated population. The moderate level of genetic structuring observed for P. azouryi seems to be related to its disjoint geographical distribution and the locally aggregated spatial structure of the populations, which are isolated from each other, hindering the inter and intrapopulational gene flow. This interpretation was also evidenced by the mantel test (r = 0.777, P < 0.05). The occurrence of diploid individuals with tetraploid seedlings is indicative of events of eupolyploidization, possibly due to the environmental conditions of this geographically isolated population.
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Affiliation(s)
- Vitor da Cunha Manhães
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil.
- Programa de Pós-graduação em Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, Rio De Janeiro, Rio de Janeiro, 20940-040, Brazil.
| | - Fábio Demolinari de Miranda
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
| | - Wellington Ronildo Clarindo
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
| | - Tatiana Tavares Carrijo
- Programa de Pós-graduação em Genética e Melhoramento, Universidade Federal do Espírito Santo, Centro de Ciências Agrárias e Engenharias, Alto Universitário s.n., Guararema, Alegre, ES, CEP 29500-000, Brazil
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18
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Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Huang L, Wang H, Hwa TY, Kao SM, Choi JY, Sharma A, Song J, Wang L, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung CW, Wang ML, Coppens d'Eeckenbrugge G, Sanewski GM, Purugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R. The bracteatus pineapple genome and domestication of clonally propagated crops. Nat Genet 2019; 51:1549-1558. [PMID: 31570895 DOI: 10.1038/s41588-019-0506-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
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Affiliation(s)
- Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Robert VanBuren
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Margot Paris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Hongye Zhou
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hansong Yan
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Liu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jishan Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mahpara Fatima
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lixian Huang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Teh-Yang Hwa
- Department of Agronomy, National Taiwan University, Taipei, ROC
| | - Shu-Min Kao
- Department of Agronomy, National Taiwan University, Taipei, ROC
| | - Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA
| | - Jian Song
- Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Lulu Wang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA
| | - Robert E Paull
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Tracie Matsumoto
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Yuan Qin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingsong Wu
- South Subtropical Crops Research Institute, CATAS, Zhanjiang, China
| | - Jianping Wang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Qingyi Yu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.,Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Peter Boches
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, Taipei, ROC
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI, USA
| | - Geo Coppens d'Eeckenbrugge
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Garth M Sanewski
- Queensland Department of Agriculture and Fisheries, Nambour, Queensland, Australia
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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19
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Rifkin JL, Castillo AS, Liao IT, Rausher MD. Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Mol Ecol 2019; 28:1709-1729. [PMID: 30451335 DOI: 10.1111/mec.14945] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/03/2018] [Accepted: 11/01/2018] [Indexed: 02/03/2023]
Abstract
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
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Affiliation(s)
- Joanna L Rifkin
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Irene T Liao
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
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20
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Bombonato JR, Bonatelli IAS, Silva GAR, Moraes EM, Zappi DC, Taylor NP, Franco FF. Cross-genera SSR transferability in cacti revealed by a case study using Cereus (Cereeae, Cactaceae). Genet Mol Biol 2019; 42:87-94. [PMID: 30794719 PMCID: PMC6428128 DOI: 10.1590/1678-4685-gmb-2017-0293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/13/2018] [Indexed: 11/22/2022] Open
Abstract
The study of transferability of simple sequence repeats (SSR) among closely
related species is a well-known strategy in population genetics, however
transferability among distinct genera is less common. We tested cross-genera SSR
amplification in the family Cactaceae using a total of 20 heterologous primers
previously developed for the genera Ariocarpus, Echinocactus,
Polaskia and Pilosocereus, in four taxa of the
genus Cereus: C. fernambucensis subsp.
fernambucensis, C. fernambucensis subsp.
sericifer, C. jamacaru and C.
insularis. Nine microsatellite loci were amplified in
Cereus resulting in 35.2% of success in transferability,
which is higher than the average rate of 10% reported in the literature for
cross-genera transferability in eudicots. The genetic variation in the
transferred markers was sufficient to perform standard clustering analysis,
indicating each population as a cohesive genetic cluster. Overall, the amount of
genetic variation found indicates that the transferred SSR markers might be
useful in large-scale population studies within the genus
Cereus.
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Affiliation(s)
- Juliana Rodrigues Bombonato
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil.,Programa de Pós-graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Evandro Marsola Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
| | - Daniela Cristina Zappi
- Instituto Tecnológico Vale, Museu Paraense Emilio Goeldi, Coord. Botânica, Belém, PA, Brazil
| | - Nigel P Taylor
- Singapore Botanic Gardens (National Parks Board), Singapore, Republic of Singapore
| | - Fernando Faria Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos, Sorocaba, SP, Brazil
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21
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Mota MR, Pinheiro F, Leal BSS, Wendt T, Palma-Silva C. The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:122-132. [PMID: 30195257 DOI: 10.1111/plb.12909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/06/2018] [Indexed: 05/02/2023]
Abstract
Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.
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Affiliation(s)
- M R Mota
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - F Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - B S S Leal
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
| | - T Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C Palma-Silva
- Departamento de Ecologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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22
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Hurbath F, Leal BÁSS, Da Silva OLM, Palma-Silva C, Cordeiro IN. A new species and molecular phylogeny of Brazilian succulent Euphorbia sect. Brasilienses. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1473897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Fernanda Hurbath
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
| | - BÁrbara SimÕes Santos Leal
- Laboratório de Ecologia Molecular, Departamento de Ecologia, Universidade Estadual Paulista – Rio Claro, Avenida 24A 1515, Rio Claro, 13506-900, SP, Brazil
| | - Otávio Luis Marques Da Silva
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
| | - Clarisse Palma-Silva
- Laboratório de Ecologia Molecular, Departamento de Ecologia, Universidade Estadual Paulista – Rio Claro, Avenida 24A 1515, Rio Claro, 13506-900, SP, Brazil
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz – Barão Geraldo, Campinas, 13083-863, SP, Brazil
| | - INês Cordeiro
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
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23
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Leal BSS, Medeiros LR, Peres EA, Sobral-Souza T, Palma-Silva C, Romero GQ, Carareto CMA. Insights into the evolutionary dynamics of Neotropical biomes from the phylogeography and paleodistribution modeling of Bromelia balansae. AMERICAN JOURNAL OF BOTANY 2018; 105:1725-1734. [PMID: 30324691 DOI: 10.1002/ajb2.1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/04/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Historical abiotic and biotic factors have strongly affected species diversification and speciation. Although pre-Pleistocene events have been linked to the divergence of several Neotropical organisms, studies have highlighted a more prominent role of Pleistocene climatic oscillations in shaping current patterns of genetic variation of plants. METHODS We performed phylogeographic analyses based on plastidial markers and modeled the current distribution and paleodistribution of Bromelia balansae (Bromeliaceae), an herbaceous species with a wide geographical distribution in South America, to infer the processes underlying its evolutionary history. KEY RESULTS Combined molecular and paleodistributional modeling analyses indicated retraction during the Last Glacial Maximum followed by interglacial expansion. Populations occurring in the semideciduous Atlantic Forest and the Cerrado formed two distinct genetic clusters, which have been historically or ecologically isolated since late Pliocene to early Pleistocene. Populations located in the transition zone had higher levels of genetic diversity, as expected by the long-term climatic stability in the region detected in our ecological niche models. CONCLUSIONS Our study adds important information on how herbaceous species have been affected by past climate in Central and Southeast Brazil, helping to disentangle the complex processes that have triggered the evolution of Neotropical biota.
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Affiliation(s)
- Bárbara S S Leal
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
| | - Lilian R Medeiros
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, 15054-000, Brazil
| | - Elen A Peres
- Universidade de São Paulo (USP), Instituto de Biociências, São Paulo, SP, 05508-090, Brazil
| | - Thadeu Sobral-Souza
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
| | - Clarisse Palma-Silva
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Câmpus de Rio Claro, SP, 13506-900, Brazil
- Universidade Estadual de Campinas (Unicamp), Instituto de Biologia, Campinas, SP, 13083-862, Brazil
| | - Gustavo Q Romero
- Universidade Estadual de Campinas (Unicamp), Instituto de Biologia, Campinas, SP, 13083-862, Brazil
| | - Claudia M A Carareto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, 15054-000, Brazil
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24
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Zenk FL, Firmer C, Wöhrmann T, da Silva LV, Weising K, Huettel B, Paggi GM. Development of 15 nuclear microsatellite markers in Deuterocohnia (Pitcairnioideae; Bromeliaceae) using 454 pyrosequencing. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1147. [PMID: 30131889 PMCID: PMC5947610 DOI: 10.1002/aps3.1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed in Deuterocohnia longipetala (Bromeliaceae) to investigate species and subspecies boundaries within the genus and the genetic diversity of natural populations. METHODS AND RESULTS We used 454 pyrosequencing to isolate 835 microsatellite loci in D. longipetala. Of 64 loci selected for primer design, 15 were polymorphic among 23 individuals of D. longipetala and 76 individuals of the heterologous subspecies D. meziana subsp. meziana and D. meziana subsp. carmineo-viridiflora. Twelve and 13 of these loci were also polymorphic in one population each of D. brevispicata and D. seramisiana, respectively. Numbers of alleles per locus varied from two to 14 in D. longipetala, two to 12 in D. meziana, one to nine in D. brevispicata, and one to 10 in D. seramisiana. STRUCTURE analyses clearly separated the taxa from each other. CONCLUSIONS The 15 new microsatellite markers are promising tools for studying population genetics in Deuterocohnia species.
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Affiliation(s)
- Fides Lea Zenk
- Max Planck Institute of Immunobiology and EpigeneticsStübeweg 5179108Freiburg im BreisgauGermany
| | - Cynthia Firmer
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Tina Wöhrmann
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Luciana Vicente da Silva
- Ecology and Conservation Postgraduate ProgramFederal University of Mato Grosso do Sul State79070‐900Campo GrandeBrazil
| | - Kurt Weising
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Bruno Huettel
- Max Planck‐Genome‐centre CologneMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
| | - Gecele Matos Paggi
- Biological SciencesPantanal Campus/Federal University of Mato Grosso do Sul StateC.P. 25279304‐902CorumbáBrazil
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25
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Males J. Geography, environment and organismal traits in the diversification of a major tropical herbaceous angiosperm radiation. AOB PLANTS 2018; 10:ply008. [PMID: 29479409 PMCID: PMC5814923 DOI: 10.1093/aobpla/ply008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
The generation of plant diversity involves complex interactions between geography, environment and organismal traits. Many macroevolutionary processes and emergent patterns have been identified in different plant groups through the study of spatial data, but rarely in the context of a large radiation of tropical herbaceous angiosperms. A powerful system for testing interrelated biogeographical hypotheses is provided by the terrestrial bromeliads, a Neotropical group of extensive ecological diversity and importance. In this investigation, distributional data for 564 species of terrestrial bromeliads were used to estimate variation in the position and width of species-level hydrological habitat occupancy and test six core hypotheses linking geography, environment and organismal traits. Taxonomic groups and functional types differed in hydrological habitat occupancy, modulated by convergent and divergent trait evolution, and with contrasting interactions with precipitation abundance and seasonality. Plant traits in the Bromeliaceae are intimately associated with bioclimatic differentiation, which is in turn strongly associated with variation in geographical range size and species richness. These results emphasize the ecological relevance of structural-functional innovation in a major plant radiation.
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Affiliation(s)
- Jamie Males
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
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26
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Neri J, Wendt T, Palma-Silva C. Natural hybridization and genetic and morphological variation between two epiphytic bromeliads. AOB PLANTS 2018; 10:plx061. [PMID: 29308124 PMCID: PMC5751037 DOI: 10.1093/aobpla/plx061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/22/2017] [Indexed: 05/18/2023]
Abstract
Reproductive isolation is of fundamental importance for maintaining species boundaries in sympatry. Here, we examine the genetic and morphological differences between two closely related bromeliad species: Vriesea simplex and Vriesea scalaris. Furthermore, we examined the occurrence of natural hybridization and discuss the action of reproductive isolation barriers. Nuclear genomic admixture suggests hybridization in sympatric populations, although interspecific gene flow is low among species in all sympatric zones (Nem < 0.5). Thus, morphological and genetic divergence (10.99 %) between species can be maintained despite ongoing natural hybridization. Cross-evaluation of our genetic and morphological data suggests that species integrity is maintained by the simultaneous action of multiple barriers, such as divergent reproductive systems among species, differences in floral traits and low hybrid seed viability.
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Affiliation(s)
- Jordana Neri
- Programa de Pós Graduação em Botânica, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, São Cristóvão, Rio de Janeiro, RJ, Brazil
| | - Tânia Wendt
- Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Clarisse Palma-Silva
- Programa de Pós Graduação em Ecologia, Departamento de Ecologia – Universidade Estadual Paulista Julio Mesquita Filho, Rio Claro, SP, Brazil
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27
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Wang J, Feng C, Jiao T, Von Wettberg EB, Kang M. Genomic Signature of Adaptive Divergence despite Strong Nonadaptive Forces on Edaphic Islands: A Case Study of Primulina juliae. Genome Biol Evol 2017; 9:3495-3508. [PMID: 29272422 PMCID: PMC5751081 DOI: 10.1093/gbe/evx263] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2017] [Indexed: 12/28/2022] Open
Abstract
Both genetic drift and divergent selection are expected to be strong evolutionary forces driving population differentiation on edaphic habitat islands. However, the relative contribution of genetic drift and divergent selection to population divergence has rarely been tested simultaneously. In this study, restriction-site associated DNA-based population genomic analyses were applied to assess the relative importance of drift and divergent selection on population divergence of Primulina juliae, an edaphic specialist from southern China. All populations were found with low standing genetic variation, small effective population size (NE), and signatures of bottlenecks. Populations with the lowest genetic variation were most genetically differentiated from other populations and the extent of genetic drift increased with geographic distance from other populations. Together with evidence of isolation by distance, these results support neutral drift as a critical evolutionary driver. Nonetheless, redundancy analysis revealed that genomic variation is significantly associated with both edaphic habitats and climatic factors independently of spatial effects. Moreover, more genomic variation was explained by environmental factors than by geographic variables, suggesting that local adaptation might have played an important role in driving population divergence. Finally, outlier tests and environment association analyses identified 31 single-nucleotide polymorphisms as candidates for adaptive divergence. Among these candidates, 26 single-nucleotide polymorphisms occur in/near genes that potentially play a role in adaptation to edaphic specialization. This study has important implications that improve our understanding of the joint roles of genetic drift and adaptation in generating population divergence and diversity of edaphic specialists.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tenglong Jiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
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28
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Hmeljevski KV, Nazareno AG, Leandro Bueno M, dos Reis MS, Forzza RC. Do plant populations on distinct inselbergs talk to each other? A case study of genetic connectivity of a bromeliad species in an Ocbil landscape. Ecol Evol 2017; 7:4704-4716. [PMID: 28690800 PMCID: PMC5496560 DOI: 10.1002/ece3.3038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/09/2017] [Accepted: 01/28/2017] [Indexed: 11/10/2022] Open
Abstract
Here, we explore the historical and contemporaneous patterns of connectivity among Encholirium horridum populations located on granitic inselbergs in an Ocbil landscape within the Brazilian Atlantic Forest, using both nuclear and chloroplast microsatellite markers. Beyond to assess the E. horridum population genetic structure, we built species distribution models across four periods (current conditions, mid-Holocene, Last Glacial Maximum [LGM], and Last Interglacial) and inferred putative dispersal corridors using a least-cost path analysis to elucidate biogeographic patterns. Overall, high and significant genetic divergence was estimated among populations for both nuclear and plastid DNA (ΦST(n) = 0.463 and ΦST(plastid) = 0.961, respectively, p < .001). For nuclear genome, almost total absence of genetic admixture among populations and very low migration rates were evident, corroborating with the very low estimates of immigration and emigration rates observed among E. horridum populations. Based on the cpDNA results, putative dispersal routes in Sugar Loaf Land across cycles of climatic fluctuations in the Quaternary period revealed that the populations' connectivity changed little during those events. Genetic analyses highlighted the low genetic connectivity and long-term persistence of populations, and the founder effect and genetic drift seemed to have been very important processes that shaped the current diversity and genetic structure observed in both genomes. The genetic singularity of each population clearly shows the need for in situ conservation of all of them.
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Affiliation(s)
| | | | - Marcelo Leandro Bueno
- Department of BotanyLaboratory of Ecology and Evolution of PlantsUniversity of ViçosaViçosaMGBrazil
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29
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Wang J, Ai B, Kong H, Kang M. Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot. Evol Appl 2017; 10:919-934. [PMID: 29151883 PMCID: PMC5680421 DOI: 10.1111/eva.12495] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022] Open
Abstract
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species tree reconstruction, Structure and Neighbor‐Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Bin Ai
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou China.,Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Nay Pyi Taw Myanmar
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30
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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31
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Flores-Rentería L, Rymer PD, Riegler M. Unpacking boxes: Integration of molecular, morphological and ecological approaches reveals extensive patterns of reticulate evolution in box eucalypts. Mol Phylogenet Evol 2017; 108:70-87. [DOI: 10.1016/j.ympev.2017.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/26/2022]
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32
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André T, Salzman S, Wendt T, Specht CD. Speciation dynamics and biogeography of Neotropical spiral gingers (Costaceae). Mol Phylogenet Evol 2016; 103:55-63. [PMID: 27400627 DOI: 10.1016/j.ympev.2016.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
Abstract
Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts.
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Affiliation(s)
- Thiago André
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
| | - Shayla Salzman
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
| | - Tânia Wendt
- Departamento de Botânica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Sala A1-050, Bloco A, CCS, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Chelsea D Specht
- Departments of Plant and Microbial Biology and Integrative Biology, University of California at Berkeley, 431 Koshland Hall, Berkeley, CA 94720-3102, USA.
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Díaz Infante S, Lara C, Arizmendi MDC, Eguiarte LE, Ornelas JF. Reproductive ecology and isolation of Psittacanthus calyculatus and P. auriculatus mistletoes (Loranthaceae). PeerJ 2016; 4:e2491. [PMID: 27703848 PMCID: PMC5045876 DOI: 10.7717/peerj.2491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/25/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Relationships between floral biology and pollinator behavior are important to understanding species diversity of hemiparasitic Psittacanthus mistletoes (c. 120 species). We aimed to investigate trait divergence linked to pollinator attraction and reproductive isolation (RI) in two hummingbird-pollinated and bird-dispersed Psittacanthus species with range overlap. METHODS We investigated the phylogenetic relationships, floral biology, pollinator assemblages, seed dispersers and host usage, and the breeding system and female reproductive success of two sympatric populations of P. calyculatus and P. auriculatus, and one allopatric population of P. calyculatus. Flowers in sympatry were also reciprocally pollinated to assess a post-mating component of RI. RESULTS Hummingbird assemblages differed between calyculatus populations, while allopatric plants of calyculatus opened more but smaller flowers with longer lifespans and produced less nectar than those in sympatry. Bayesian-based phylogenetic analysis indicated monophyly for calyculatus populations (i.e. both populations belong to the same species). In sympatry, calyculatus plants opened more and larger flowers with longer lifespans and produced same nectar volume than those of auriculatus; populations shared pollinators but seed dispersers and host usage differed between species. Nectar standing crops differed between sympatric populations, with lower visitation in calyculatus. Hand pollination experiments indicated a predominant outcrossing breeding system, with fruit set after interspecific pollination two times higher from calyculatus to auriculatus than in the opposite direction. CONCLUSIONS Given the low genetic differentiation between calyculatus populations, observed trait divergence could have resulted from changes regarding the local communities of pollinators and, therefore, expected divergence for peripheral, allopatric populations. Using RI estimates, there were fewer heterospecific matings than expected by chance in P. calyculatus (RI4A = 0.629) as compared to P. auriculatus (RI4A = 0.20). When considering other factors of ecological isolation that affect co-occurrence, the RI4C values indicate that isolation by hummingbird pollinators was less effective (0.20) than isolation by host tree species and seed dispersers (0.80 and 0.60, respectively), suggesting that host usage is the most important ecological isolation factor between the two species. Accordingly, the absolute and relative cumulative strength values indicated that the host tree species' barrier is currently contributing the most to maintaining these species in sympatry.
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Affiliation(s)
- Sergio Díaz Infante
- Laboratorio de Ecología, UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - María del Coro Arizmendi
- Laboratorio de Ecología, UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Estado de México, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Distrito Federal, Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
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Pinheiro F, Zanfra de Melo E Gouveia TM, Cozzolino S, Cafasso D, Cardoso-Gustavson P, Suzuki RM, Palma-Silva C. Strong but permeable barriers to gene exchange between sister species of Epidendrum. AMERICAN JOURNAL OF BOTANY 2016; 103:1472-1482. [PMID: 27519428 DOI: 10.3732/ajb.1600064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The investigation of reproductive barriers between sister species can provide insights into how new lineages arise, and how species integrity is maintained in the face of interspecific gene flow. Different pre- and postzygotic barriers can limit interspecific gene exchange in sympatric populations, and different sources of evidence are often required to investigate the role of multiple reproductive isolation (RI) mechanisms. METHODS We tested the hypothesis of hybridization and potential introgression between Epidendrum secundum and Epidendrum xanthinum, two Neotropical food-deceptive orchid species, using nuclear and plastid microsatellites, experimental crosses, pollen tube growth observations, and genome size estimates. KEY RESULTS A large number of hybrids between E. secundum and E. xanthinum were detected, suggesting weak premating barriers. The low fertility of hybrid plants and the absence of haplotype sharing between parental species indicated strong postmating barriers, reducing interspecific gene exchange and the development of advanced generation hybrids. Despite the strength of reproductive barriers, fertile seeds were produced in some backcrossing experiments, and the existence of interspecific gene exchange could not be excluded. CONCLUSIONS Strong but permeable barriers were found between E. secundum and E. xanthinum. Indeed, haplotype sharing was not detected between parental species, suggesting that introgression is limited by a combination of genic incompatibilities, including negative cytonuclear interactions. Most taxonomic uncertainties in this group were potentially influenced by incomplete RI barriers between species, which mainly occurred sympatrically.
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Affiliation(s)
- Fábio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas 13083-862, Campinas, SP, Brazil Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado04301-902, São Paulo, SP, Brazil
| | | | - Salvatore Cozzolino
- Dipartimento di Biologia, Complesso Universitario di Monte S. Ângelo, Università degli Studidi Napoli Federico II 80100 Napoli, Italy Institute for Sustenible Plant Protection, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, I-50019 Sesto Fiorentino (FI), Italy
| | - Donata Cafasso
- Dipartimento di Biologia, Complesso Universitario di Monte S. Ângelo, Università degli Studidi Napoli Federico II 80100 Napoli, Italy
| | | | - Rogério Mamoru Suzuki
- Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado04301-902, São Paulo, SP, Brazil
| | - Clarisse Palma-Silva
- Departamento de Ecologia, Universidade Estadual Paulista 13506-900, Rio Claro, SP, Brazil
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Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests. PLoS One 2016; 11:e0156913. [PMID: 27305092 PMCID: PMC4909291 DOI: 10.1371/journal.pone.0156913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/20/2016] [Indexed: 01/24/2023] Open
Abstract
Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species’ gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees’ lifetimes.
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Palma-Silva C, Ferro M, Bacci M, Turchetto-Zolet AC. De novo assembly and characterization of leaf and floral transcriptomes of the hybridizing bromeliad species (Pitcairnia spp.) adapted to Neotropical Inselbergs. Mol Ecol Resour 2016; 16:1012-22. [PMID: 26849180 DOI: 10.1111/1755-0998.12504] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 02/06/2023]
Abstract
We present the leaf and floral transcriptomes of two hybridizing bromeliad species that differ in their major pollinator systems. Here we identified candidate genes responsible for pollinator attraction and reproductive isolation in these two species. We searched for candidate genes involved in floral traits, such as colour. Approximately 34 Gbp of cDNA sequence data were produced from both tissues and species, resulting in a total of 424 506 914 raw reads. The de novo-assembled transcriptomes consisted of a total of 263 955 contigs, further clustered into 110 977 unigenes. Over 58% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The transcriptomes revealed 144 unique transcripts that encode key enzymes in the flavonoid and anthocyanin biosynthesis pathways. The domain/family annotation and phylogenetic analysis allowed us to infer, by homology, potential functions of the genes encoding MYB, HD-ZIP and bZIP-HY5 transcription factors, as well as WD40 protein, which may be involved in anthocyanin and flavonoid regulation in these species. These candidate genes are associated with natural regulation in flower colour in other plant species and will facilitate future studies aimed at elucidating the molecular basis of adaptive differentiation and the evolution of mechanisms of pollinator-mediated reproductive isolation in these two bromeliads. In addition, we identified a total of 49 439 microsatellite loci. These resources will assist future research into adaptation and speciation events in bromeliad species, thus providing a starting point for investigation of the molecular mechanisms of the traits responsible for their reproductive isolation.
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Affiliation(s)
- C Palma-Silva
- Departamento de Ecologia, Programa de Pós-graduação em Ecologia e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - M Ferro
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - M Bacci
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho, 13506-900, Rio Claro, SP, Brazil
| | - A C Turchetto-Zolet
- Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
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Alves M, Trovó M, Forzza RC, Viana P. Overview of the systematics and diversity of Poales in the Neotropics with emphasis on the Brazilian flora. RODRIGUÉSIA 2015. [DOI: 10.1590/2175-7860201566203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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Palma-Silva C, Cozzolino S, Paggi GM, Lexer C, Wendt T. Mating system variation and assortative mating of sympatric bromeliads (Pitcairnia spp.) endemic to neotropical inselbergs. AMERICAN JOURNAL OF BOTANY 2015; 102:758-764. [PMID: 26022489 DOI: 10.3732/ajb.1400513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY The mating system is an important component of the complex set of reproductive isolation barriers causing plant speciation. However, empirical evidence showing that the mating system may promote reproductive isolation in co-occurring species is limited. The mechanisms by which the mating system can act as a reproductive isolation barrier are also largely unknown. METHODS Here we studied progeny arrays genotyped with microsatellites and patterns of stigma-anther separation (herkogamy) to understand the role of mating system shifts in promoting reproductive isolation between two hybridizing taxa with porous genomes, Pitcairnia albiflos and P. staminea (Bromeliaceae). KEY RESULTS In P. staminea, we detected increased selfing and reduced herkogamy in one sympatric relative to two allopatric populations, consistent with mating system shifts in sympatry acting to maintain the species integrity of P. staminea when in contact with P. albiflos. CONCLUSIONS Mating system variation is a result of several factors acting simultaneously in these populations. We report mating system shifts as one possible reproductive barrier between these species, acting in addition to numerous other prezygotic (i.e., flower phenology and pollination syndromes) and postzygotic barriers (Bateson-Dobzhansky-Muller genetic incompatibilities).
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Affiliation(s)
- Clarisse Palma-Silva
- Departamento de Ecologia, IB/UNESP, Rio Claro, SP, 13506-900 Brazil Instituto de Botânica, São Paulo, SP, 04301-012 Brazil
| | - Salvatore Cozzolino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, 80126 Italy CNR Istituto per la Protezione Sostenibile delle Piante, Firenze, I-50019 Italy
| | | | - Christian Lexer
- Department of Biology, University of Fribourg, Fribourg, Switzerland Department of Botany and Biodiversity Research, University of Vienna, Vienna, A-1030 Austria
| | - Tânia Wendt
- Departamento de Botânica, CCS/IB/UFRJ, Rio de Janeiro, RJ, 21941-590 Brazil
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Yan W, Hou B, Xue Q, Geng L, Ding X. Different evolutionary processes in shaping the genetic composition of Dendrobium nobile in southwest China. Genetica 2015; 143:361-71. [PMID: 25838240 DOI: 10.1007/s10709-015-9835-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/25/2015] [Indexed: 11/25/2022]
Abstract
Knowledge of population genetic structure and intrapopulation genetic variation is important for understanding population dynamics and evolutionary processes. Dendrobium nobile is an endangered traditional Chinese tonic medicine. In order to analyze the population differentiation and genetic diversity in D. nobile and propose proper conservation measurements, we genotyped 102 individual plants from 7 natural populations distributed across southwest China at 9 microsatellite loci. Seven pairs of genomic SSR primers were newly designed, and two pairs were chosen from the EST-SSRs. According to the results, the genetic process of D. nobile on Hainan Island and the Chinese mainland might be affected by different evolutionary processes, the genetic drift caused by founder effect has played an important role in shaping the genetic constitution of the Island population. The population of D. nobile in Hainan Island was highly differentiated and displayed low levels of genetic diversity. For the conservation management plans of D. nobile, we propose that individuals in Hainan Island with rare alleles need to be conserved with top priority, and those individuals with rare alleles and the most common alleles also should be concerned. The seven new microsatellite loci may be informative for further evaluation and conservation of the genetic diversity of D. nobile.
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Affiliation(s)
- Wenjin Yan
- College of Life Sciences, Nanjing Normal University, No. 1, Wenyuan Road, Nanjing, 210046, China
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Leles B, Chaves AV, Russo P, Batista JAN, Lovato MB. Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the Iron Quadrangle, southeastern Brazil. PLoS One 2015; 10:e0120645. [PMID: 25756994 PMCID: PMC4355488 DOI: 10.1371/journal.pone.0120645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/25/2015] [Indexed: 12/03/2022] Open
Abstract
Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.
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Affiliation(s)
- Bruno Leles
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Anderson V. Chaves
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Philip Russo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - João A. N. Batista
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Maria Bernadete Lovato
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
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Neri J, Nazareno AG, Wendt T, Palma-Silva C. Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Genetic variation in Aechmea winkleri, a bromeliad from an inland Atlantic rainforest fragment in Southern Brazil. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Strong postzygotic isolation prevents introgression between two hybridizing Neotropical orchids, Epidendrum denticulatum and E. fulgens. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9753-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Hmeljevski KV, dos Reis MS, Forzza RC. Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil. J Hered 2014; 106:93-101. [PMID: 25472982 DOI: 10.1093/jhered/esu067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F(ij) = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species.
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Affiliation(s)
- Karina Vanessa Hmeljevski
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza).
| | - Maurício Sedrez dos Reis
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza)
| | - Rafaela Campostrini Forzza
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza)
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Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL. Speciation and introgression between Mimulus nasutus and Mimulus guttatus. PLoS Genet 2014; 10:e1004410. [PMID: 24967630 PMCID: PMC4072524 DOI: 10.1371/journal.pgen.1004410] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/11/2014] [Indexed: 12/30/2022] Open
Abstract
Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued genomic signatures of the transition to predominant selfing, including an elevated proportion of nonsynonymous variants, an accumulation of premature stop codons, and extended levels of linkage disequilibrium. Despite clear biological differentiation, we document genomic signatures of ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.
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Affiliation(s)
- Yaniv Brandvain
- Department of Evolution and Ecology & Center for Population Biology, University of California - Davis, Davis, California, United States of America
- Department of Plant Biology, University of Minnesota – Twin Cities. St. Paul, Minnesota, United States of America
| | - Amanda M. Kenney
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Lex Flagel
- Monsanto Company, Chesterfield, Missouri, United States of America
| | - Graham Coop
- Department of Evolution and Ecology & Center for Population Biology, University of California - Davis, Davis, California, United States of America
| | - Andrea L. Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
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McIntosh EJ, Rossetto M, Weston PH, Wardle GM. Maintenance of strong morphological differentiation despite ongoing natural hybridization between sympatric species of Lomatia (Proteaceae). ANNALS OF BOTANY 2014; 113:861-872. [PMID: 24489011 PMCID: PMC3962242 DOI: 10.1093/aob/mct314] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
BACKGROUND AND AIMS When species cohesion is maintained despite ongoing natural hybridization, many questions are raised about the evolutionary processes operating in the species complex. This study examined the extensive natural hybridization between the Australian native shrubs Lomatia myricoides and L. silaifolia (Proteaceae). These species exhibit striking differences in morphology and ecological preferences, exceeding those found in most studies of hybridization to date. METHODS Nuclear microsatellite markers (nSSRs), genotyping methods and morphometric analyses were used to uncover patterns of hybridization and the role of gene flow in morphological differentiation between sympatric species. KEY RESULTS The complexity of hybridization patterns differed markedly between sites, however, signals of introgression were present at all sites. One site provided evidence of a large hybrid swarm and the likely presence of multiple hybrid generations and backcrosses, another site a handful of early generational hybrids and a third site only traces of admixture from a past hybridization event. The presence of cryptic hybrids and a pattern of morphological bimodality amongst hybrids often disguised the extent of underlying genetic admixture. CONCLUSIONS Distinct parental habitats and phenotypes are expected to form barriers that contribute to the rapid reversion of hybrid populations to their parental character state, due to limited opportunities for hybrid/intermediate advantage. Furthermore, strong genomic filters may facilitate continued gene flow between species without the danger of assimilation. Stochastic fire events facilitate temporal phenological isolation between species and may partly explain the bi-directional and site-specific patterns of hybridization observed. Furthermore, the findings suggest that F1 hybrids are rare, and backcrosses may occur rapidly following these initial hybridization events.
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Affiliation(s)
- Emma J. McIntosh
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- School of Biological Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - Maurizio Rossetto
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
| | - Peter H. Weston
- The Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
| | - Glenda M. Wardle
- School of Biological Sciences, the University of Sydney, Sydney, New South Wales, Australia
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Pinheiro F, Cozzolino S, Draper D, de Barros F, Félix LP, Fay MF, Palma-Silva C. Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil. BMC Evol Biol 2014; 14:49. [PMID: 24629134 PMCID: PMC4004418 DOI: 10.1186/1471-2148-14-49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/07/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as most of them display a marked ecological isolation from the surrounding area. The isolation of these rock outcrops is reflected in the high number of recorded endemic species and the strong floristic differences between individual inselbergs and adjacent habitats. We examined the genetic connectivity of orchids Epidendrum cinnabarinum and E. secundum adapted to Neotropical inselbergs of northeastern Brazil. Our goals were to identify major genetic divergences or disjunctions across the range of the species and to investigate potential demographic and evolutionary mechanisms leading to lineage divergence in Neotropical mountain ecosystems. RESULTS Based on plastid markers, high genetic differentiation was found for E. cinnabarinum (FST = 0.644) and E. secundum (FST = 0.636). Haplotypes were not geographically structured in either taxon, suggesting that restricted gene flow and genetic drift may be significant factors influencing the diversification of these inselberg populations. Moreover, strong differentiation was found between populations over short spatial scales, indicating substantial periods of isolation among populations. For E. secundum, nuclear markers indicated higher gene flow by pollen than by seeds. CONCLUSIONS The comparative approach adopted in this study contributed to the elucidation of patterns in both species. Our results confirm the ancient and highly isolated nature of inselberg populations. Both species showed similar patterns of genetic diversity and structure, highlighting the importance of seed-restricted gene flow and genetic drift as drivers of plant diversification in terrestrial islands such as inselbergs.
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Affiliation(s)
- Fábio Pinheiro
- Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado, Avenida Miguel Estéfano 3687, 04301-012 São Paulo, SP, Brazil.
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49
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Aoki-Gonçalves F, Louzada RB, De Souza LM, Palma-Silva C. Microsatellite loci for Orthophytum ophiuroides (Bromelioideae, Bromeliaceae) species adapted to neotropical rock outcrops. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300073. [PMID: 25202607 PMCID: PMC4103101 DOI: 10.3732/apps.1300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed for Orthophytum ophiuroides, a rupicolous bromeliad species endemic to neotropical rocky fields. These microsatellite loci will be used to investigate population differentiation and species cohesion in such fragmented environments. The loci were tested for cross-amplification in related bromeliad species. • METHODS AND RESULTS Eleven polymorphic microsatellite markers were isolated and characterized from an enriched library of O. ophiuroides. The loci were tested on 42 individuals from two populations of this species. The number of alleles per locus ranged from three to nine and the expected and observed heterozygosities ranged from 0.167 to 0.870 and from 0.369 to 0.958, respectively. Seven loci successfully amplified in other related bromeliad species. • CONCLUSIONS Our results suggest that the microsatellite loci developed here will be useful to assess genetic diversity and gene flow in O. ophiuroides for the investigation of population differentiation and species cohesion in neotropical mountainous habitats.
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Affiliation(s)
- Felipe Aoki-Gonçalves
- Instituto de Botânica, 3687 Miguel Stéfano Avenue, 04301-902 São Paulo, São Paulo, Brazil
| | - Rafael B. Louzada
- Departamento de Botânica, Universidade Federal de Pernambuco, 1235 Prof. Moraes Rego Avenue, 50670-901 Recife, Pernambuco, Brazil
| | - Lívia Moura De Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 400 Cândido Rondon Avenue, 13083-970 Campinas, São Paulo, Brazil
| | - Clarisse Palma-Silva
- Instituto de Botânica, 3687 Miguel Stéfano Avenue, 04301-902 São Paulo, São Paulo, Brazil
- Departamento de Ecologia, Universidade Estadual Paulista Júlio de Mesquita Filho, 1514 24-A Avenue, 13506-900 Rio Claro, São Paulo, Brazil
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Moraes AP, Chinaglia M, Palma-Silva C, Pinheiro F. Interploidy hybridization in sympatric zones: the formation of Epidendrum fulgens × E. puniceoluteum hybrids (Epidendroideae, Orchidaceae). Ecol Evol 2013; 3:3824-37. [PMID: 24198942 PMCID: PMC3810877 DOI: 10.1002/ece3.752] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 11/11/2022] Open
Abstract
Interspecific hybridization is a primary cause of extensive morphological and chromosomal variation and plays an important role in plant species diversification. However, the role of interploidal hybridization in the formation of hybrid swarms is less clear. Epidendrum encompasses wide variation in chromosome number and lacks strong premating barriers, making the genus a good model for clarifying the role of chromosomes in postzygotic barriers in interploidal hybrids. In this sense, hybrids from the interploidal sympatric zone between E. fulgens (2n = 2x = 24) and E. puniceoluteum (2n = 4x = 56) were analyzed using cytogenetic techniques to elucidate the formation and establishment of interploidal hybrids. Hybrids were not a uniform group: two chromosome numbers were observed, with the variation being a consequence of severe hybrid meiotic abnormalities and backcrossing with E. puniceoluteum. The hybrids were triploids (2n = 3x = 38 and 40) and despite the occurrence of enormous meiotic problems associated with triploidy, the hybrids were able to backcross, producing successful hybrid individuals with broad ecological distributions. In spite of the nonpolyploidization of the hybrid, its formation is a long-term evolutionary process rather than a product of a recent disturbance, and considering other sympatric zones in Epidendrum, these events could be recurrent.
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Affiliation(s)
- Ana P Moraes
- Laboratório de Biossistemática e Evolução de Plantas, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas/UNICAMP Campinas, São Paulo, Brasil ; Programa de Pós Graduação em Evolução e Diversidade, Universidade Federal do ABC/UFABC Santo André, São Paulo, Brasil
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