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Vieu JC, Koubínová D, Grant JR. Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1710. [PMID: 37111932 PMCID: PMC10145315 DOI: 10.3390/plants12081710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.
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2
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Griswold CK. The effects of migration load, selfing, inbreeding depression, and the genetics of adaptation on autotetraploid versus diploid establishment in peripheral habitats. Evolution 2020; 75:39-55. [PMID: 33259069 DOI: 10.1111/evo.14127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/22/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
The distribution and abundance of polyploids has intrigued biologists since their discovery in the early 20th century. A pattern in nature that may give insight to processes that shape the distribution and abundance of polyploids is that polyploid populations are sometimes associated with peripheral habitats within the range of a species of mixed ploidy. Here, adaptation and competition of a diploid versus an autotetraploid population in a peripheral habitat are examined theoretically. It is shown that a nascent autotetraploid population adapts to and outcompetes a diploid population in the periphery when the rate of gamete dispersal is high, and when the mode of gene action is recessive for moderate to high rates of selfing. With additive or dominant modes of gene action, the conditions for an autotetraploid to outcompete a diploid in the periphery appear determined more by the rate of selfing and less by gamete dispersal. All of these results are based on empirical work that suggests inbreeding depression is higher in diploids versus autotetraploids. Generally, the results indicate that, although autotetraploids incur minority cytotype exclusion, diploids face burdens themselves. In the case of adaptation to a peripheral habitat, this burden is migration load from gamete and propagule dispersal.
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3
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Reisch C, Rosbakh S. Patterns of genetic variation in European plant species depend on altitude. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Christoph Reisch
- Institute of Plant Sciences University of Regensburg Regensburg Germany
| | - Sergey Rosbakh
- Institute of Plant Sciences University of Regensburg Regensburg Germany
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4
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Kitavi M, Cashell R, Ferguson M, Lorenzen J, Nyine M, McKeown PC, Spillane C. Heritable epigenetic diversity for conservation and utilization of epigenetic germplasm resources of clonal East African Highland banana (EAHB) accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2605-2625. [PMID: 32719910 PMCID: PMC7419381 DOI: 10.1007/s00122-020-03620-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 05/20/2020] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Genetically identical East African Highland banana (EAHB) clones are epigenetically diverse with heritable epialleles that can contribute to morphological diversity. Heritable epigenetic variation can contribute to agronomic traits in crops and should be considered in germplasm conservation. Despite the genetic uniformity arising from a genetic bottleneck of one ancestral clone, followed by subsequent vegetative propagation, East African Highland bananas (EAHBs) display significant phenotypic diversity potentially arising from somatic mutations, heritable epialleles and/or genotype-by-environment interactions. Here, we use DNA methylation profiling across EAHB accessions representing most of the primary EAHB genepool to demonstrate that the genetically uniform EAHB genepool harbours significant epigenetic diversity. By analysing 724 polymorphic DNA methylation sites by methylation-sensitive AFLP across 90 EAHB cultivars, we could differentiate the EAHB varieties according to their regions (Kenya and Uganda). In contrast, there was minimal association of DNA methylation variation with the five morphological groups that are used to classify EAHBs. We further analysed DNA methylation patterns in parent-offspring cohort, which were maintained in offspring generated by sexual (seed) and asexual (vegetative) propagation, with higher levels of altered DNA methylation observed in vegetatively generated offspring. Our results indicate that the phenotypic diversity of near-isogenic EAHBs is mirrored by considerable DNA methylation variation, which is transmitted between generations by both vegetative reproduction and seed reproduction. Genetically uniform vegetatively propagated crops such as EAHBs harbour considerable heritable epigenetic variation, where heritable epialleles could arise in offspring and contribute to functional traits. This study provides a basis for developing strategies for conservation of epigenetic resources and for integration of epimarkers into crop breeding programmes.
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Affiliation(s)
- M Kitavi
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - R Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - M Ferguson
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - J Lorenzen
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
- Crop R&D, Agricultural Development, Bill & Melinda Gates Foundation, PO Box 23350, Seattle, WA, 98102, USA
| | - M Nyine
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - P C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - C Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
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Cisneros‐de la Cruz DJ, Martínez‐Castillo J, Herrera‐Silveira J, Yáñez‐Espinosa L, Ortiz‐García M, Us‐Santamaria R, Andrade JL. Short-distance barriers affect genetic variability of Rhizophora mangle L. in the Yucatan Peninsula. Ecol Evol 2018; 8:11083-11099. [PMID: 30519427 PMCID: PMC6262909 DOI: 10.1002/ece3.4575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 11/22/2022] Open
Abstract
The environmental variability at local scale results in different physiognomic types of mangrove forest. However, this variability has never been considered in studies of mangrove genetic variability. This study analyzed the genetic and morphological variability and structure of Rhizophora mangle at regional and local scales in the Yucatan Peninsula. Thirteen mangrove populations (eight scrub and five tall), located in seven sites, were sampled, and their morphological variability and relationship with the availability of phosphorus and salinity were analyzed. The diversity and genetic structure were estimated at different hierarchical levels with nine microsatellites, also Bayesian inference and Principal Coordinates Analysis were used. We found a great morphological variability of R. mangle that responded to local environmental variability and not to the precipitation gradient of the peninsula. The genetic diversity found in the peninsula was greater than that reported for other populations in Mexico and was grouped into two regions: the Gulf of Mexico and the Caribbean Sea. At a local scale, tall and scrub mangroves had significant genetic differentiation suggesting that ecological barriers promote genetic differentiation within sites. These results need to be considered in future population genetic studies and for mangrove management and conservation.
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Affiliation(s)
| | | | | | - Laura Yáñez‐Espinosa
- Instituto de Investigaciones de Zonas DesérticasUniversidad Autónoma de San Luis Potosí (UASLP)San Luis PotosíMexico
| | | | | | - José L. Andrade
- Centro de Investigación Científica de Yucatán (CICY)MéridaMéxico
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6
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Leempoel K, Parisod C, Geiser C, Joost S. Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata. Ecol Evol 2018; 8:1794-1806. [PMID: 29435254 PMCID: PMC5792616 DOI: 10.1002/ece3.3778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 01/15/2023] Open
Abstract
Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine-scale models to evaluate environmental heterogeneity may help detecting adaptation to micro-habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1-km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine-scale topography. Using a large panel of DEM-derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high-resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.
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Affiliation(s)
- Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG)School of Civil and Environmental Engineering (ENAC)École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Christian Parisod
- Laboratory of Evolutionary BotanyUniversity of NeuchâtelNeuchâtelSwitzerland
- Institute of Plant SciencesUniversity of BernBernSwitzerland
| | - Céline Geiser
- Laboratory of Evolutionary BotanyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG)School of Civil and Environmental Engineering (ENAC)École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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7
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Ma K, Sun L, Cheng T, Pan H, Wang J, Zhang Q. Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume. FRONTIERS IN PLANT SCIENCE 2018; 9:41. [PMID: 29441078 PMCID: PMC5797549 DOI: 10.3389/fpls.2018.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/09/2018] [Indexed: 05/23/2023]
Abstract
Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.
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Affiliation(s)
- Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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8
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Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu YX. Ten Years of Landscape Genomics: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:2136. [PMID: 29312391 PMCID: PMC5733015 DOI: 10.3389/fpls.2017.02136] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/01/2017] [Indexed: 05/06/2023]
Abstract
Landscape genomics is a relatively new discipline that aims to reveal the relationship between adaptive genetic imprints in genomes and environmental heterogeneity among natural populations. Although the interest in landscape genomics has increased since this term was coined, studies on this topic remain scarce. Landscape genomics has become a powerful method to scan and determine the genes responsible for the complex adaptive evolution of species at population (mostly) and individual (more rarely) level. This review outlines the sampling strategies, molecular marker types and research categories in 37 articles published during the first 10 years of this field (i.e., 2007-2016). We also address major challenges and future directions for landscape genomics. This review aims to promote interest in conducting additional studies in landscape genomics.
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Affiliation(s)
- Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xue-Xia Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Run-Li Mao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Jie Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Cai-Yun Miao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Zhuo Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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9
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Morgan EJ, Kaiser-Bunbury CN, Edwards PJ, Fleischer-Dogley F, Kettle CJ. Keeping it in the family: strong fine-scale genetic structure and inbreeding in Lodoicea maldivica, the largest-seeded plant in the world. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0982-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Listl D, Poschlod P, Reisch C. Do seed transfer zones for ecological restoration reflect the spatial genetic variation of the common grassland species Lathyrus pratensis
? Restor Ecol 2017. [DOI: 10.1111/rec.12613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Listl
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
| | - Peter Poschlod
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
| | - Christoph Reisch
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
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11
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Coughlan JM, Han S, Stefanović S, Dickinson TA. Widespread generalist clones are associated with range and niche expansion in allopolyploids of Pacific Northwest Hawthorns (Crataegus
L.). Mol Ecol 2017; 26:5484-5499. [DOI: 10.1111/mec.14331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023]
Affiliation(s)
- J. M. Coughlan
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario Canada
- Department of Biology; University of Toronto; Mississauga; Mississauga Ontario Canada
- Green Plant Herbarium (TRT); Department of Natural History; Royal Ontario Museum; Toronto Ontario Canada
- Department of Biology; Duke University; Durham NC USA
| | - S. Han
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - S. Stefanović
- Department of Biology; University of Toronto; Mississauga; Mississauga Ontario Canada
| | - T. A. Dickinson
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario Canada
- Green Plant Herbarium (TRT); Department of Natural History; Royal Ontario Museum; Toronto Ontario Canada
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12
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Abstract
Phylogeographic analyses of plants in Europe have revealed common glacial refugia and migration routes for several trees and herbs with arctic-alpine distributions. The postglacial histories of dry grassland species in central Europe have rarely been analyzed, even though the extremely species-rich habitat is threatened. Sedum album (Crassulaceae) is a common inhabitant of rocky sites in central European dry grasslands. We inferred the phylogeographic history of S. album over its distribution range in Europe. Genetic diversity within and differentiation between 34 S. album populations was examined using AFLP markers. Population isolation was indicated based on the rarity of the fragments and by isolation-by-distance effects. We sequenced the trnL-trnF region in 32 populations and used chloroplast microsatellites to analyze chloroplast haplotype distributions. Two distinct S. album lineages were detected. One lineage was comprised of populations from eastern and central parts of central Europe, and the Apennine Peninsula. A second lineage was comprised of populations from the Iberian Peninsula and western and northern parts of central Europe. Glacial refugia were identified based on the accumulation of ancient chloroplast haplotypes, high diversity of AFLP fragments within populations, and high levels of rare fragments in Liguria, Serbia, the Apennine and Iberian peninsulas. Cryptic refugia were detected in the Czech Republic and Slovakia. Isolation by distance was present all over the distribution range, and it was separately detected in southwestern and central Europe. In western Europe, where a contact zone between the two lineages can be expected, no isolation by distance was detected. Our results suggest migration routes of S. album northeastward from glacial refugia in southern Iberia, northward from the Apennine Peninsula, and northward and westward from the southeastern parts of central Europe. Therefore, central European grasslands were recently colonized by northern cryptic populations and source populations originating in the east and the Apennine Peninsula.
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Li J, Xu H, Song Y, Tang L, Gong Y, Yu R, Shen L, Wu X, Liu Y, Zeng W. Geography Plays a More Important Role than Soil Composition on Structuring Genetic Variation of Pseudometallophyte Commelina communis. FRONTIERS IN PLANT SCIENCE 2016; 7:1085. [PMID: 27499758 PMCID: PMC4956667 DOI: 10.3389/fpls.2016.01085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/11/2016] [Indexed: 05/14/2023]
Abstract
Pseudometallophytes are excellent models to study microevolution and local adaptation to soil pollution, as they can grow both on metalliferous and contrasting non-metalliferous soils. Although, there has been accumulating evidence for the effects of edaphic conditions and geographical isolation on the genetic structure of pesudometallophytes, it is still a difficult problem in evolutionary biology to assess their relative importance. In this study, we investigated the spatial patterns of genetic variability, population differentiation and genetic groups in pseudometallophyte Commelina communis with 12 microsatellite loci. Eight metallicolous and six non-metallicolous populations of C. communis were sampled from cupriferous sites and surrounding non-contaminated areas in China. Neither significant reduction in genetic diversity nor apparent founder and bottleneck effects were observed in metallicolous populations of C. communis. Based on Bayesian and Neighbor-Joining clustering analyses and a principal coordinates analysis, all sampled populations were found to be mainly separated into three genetic groups, corresponding well to their geographical locations rather than edaphic origins. Moreover, a significant and strong correlation between population genetic divergence and geographical distance were detected by Mantel test (r = 0.33; P < 0.05) and multiple matrix regression with randomization (MMRR; βD = 0.57, P < 0.01). However, the effect of copper concentration on genetic patterns of C. communis was not significant (MMRR; βE = -0.17, P = 0.12). Our study clearly demonstrated that the extreme edaphic conditions in metalliferous areas had limited effects on the genetic variability in C. communis. Geographic distance played a more important role in affecting the genetic structure of C. communis than soil composition did. In C. communis, the geographically disjunctive populations on metalliferous soils had multiple origins and evolved independently from nearby non-metallicolous populations.
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Affiliation(s)
- Jiaokun Li
- School of Metallurgy and Environment, Central South University, ChangshaChina
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Hui Xu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Yunpeng Song
- College of Life Sciences, Central China Normal University, WuhanChina
| | - Lulu Tang
- School of Life Sciences, Central South University, ChangshaChina
| | - Yanbing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, WuhanChina
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, ChangshaChina
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14
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Yang AH, Wei N, Fritsch PW, Yao XH. AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect. FRONTIERS IN PLANT SCIENCE 2016; 7:698. [PMID: 27303414 PMCID: PMC4880593 DOI: 10.3389/fpls.2016.00698] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/06/2016] [Indexed: 05/27/2023]
Abstract
Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.
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Affiliation(s)
- Ai-Hong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Na Wei
- Department of Ecology and Evolutionary Biology, University of MichiganAnn Arbor, MI, USA
| | | | - Xiao-Hong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
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15
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Jiang Q, Li Q, Yu H, Kong L. Inheritance and Variation of Genomic DNA Methylation in Diploid and Triploid Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:124-132. [PMID: 26585587 DOI: 10.1007/s10126-015-9674-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
DNA methylation is an important epigenetic mechanism that could be responsive to environmental changes indicating a potential role in natural selection and adaption. In order to evaluate an evolutionary role of DNA methylation, it is essential to first gain a better insight into inheritability. To address this question, this study investigated DNA methylation variation from parents to offspring in the Pacific oyster Crassostrea gigas using fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) analysis. Most of parental methylated loci were stably transmitted to offspring segregating following Medelian expectation. However, methylated loci deviated more often than non-methylated loci and offspring showed a few de novo methylated loci indicating DNA methylation changes from parents to offspring. Interestingly, some male-specific methylated loci were found in this study which might help to explore sex determination in oyster. Despite environmental stimuli, genomic stresses such as polyploidization also can induce methylation changes. This study also compared global DNA methylation level and individual methylated loci between diploid and triploid oysters. Results showed no difference in global methylation state but a few ploidy-specific loci were detected. DNA methylation variation during polyploidization was less than autonomous methylation variation from parents to offspring.
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Affiliation(s)
- Qun Jiang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Hong Yu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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16
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Ci D, Song Y, Du Q, Tian M, Han S, Zhang D. Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:723-37. [PMID: 26552881 DOI: 10.1093/jxb/erv485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.
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Affiliation(s)
- Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Min Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Shuo Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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17
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Ravenscroft CH, Whitlock R, Fridley JD. Rapid genetic divergence in response to 15 years of simulated climate change. GLOBAL CHANGE BIOLOGY 2015; 21:4165-76. [PMID: 26311135 PMCID: PMC4975715 DOI: 10.1111/gcb.12966] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/05/2015] [Indexed: 05/05/2023]
Abstract
Genetic diversity may play an important role in allowing individual species to resist climate change, by permitting evolutionary responses. Our understanding of the potential for such responses to climate change remains limited, and very few experimental tests have been carried out within intact ecosystems. Here, we use amplified fragment length polymorphism (AFLP) data to assess genetic divergence and test for signatures of evolutionary change driven by long-term simulated climate change applied to natural grassland at Buxton Climate Change Impacts Laboratory (BCCIL). Experimental climate treatments were applied to grassland plots for 15 years using a replicated and spatially blocked design and included warming, drought and precipitation treatments. We detected significant genetic differentiation between climate change treatments and control plots in two coexisting perennial plant study species (Festuca ovina and Plantago lanceolata). Outlier analyses revealed a consistent signature of selection associated with experimental climate treatments at individual AFLP loci in P. lanceolata, but not in F. ovina. Average background differentiation at putatively neutral AFLP loci was close to zero, and genomewide genetic structure was associated neither with species abundance changes (demography) nor with plant community-level responses to long-term climate treatments. Our results demonstrate genetic divergence in response to a suite of climatic environments in reproductively mature populations of two perennial plant species and are consistent with an evolutionary response to climatic selection in P. lanceolata. These genetic changes have occurred in parallel with impacts on plant community structure and may have contributed to the persistence of individual species through 15 years of simulated climate change at BCCIL.
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Affiliation(s)
| | - Raj Whitlock
- Institute of Integrative BiologyUniversity of LiverpoolThe Biosciences Building, Crown StreetLiverpoolL69 7ZBUK
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jason D. Fridley
- Department of BiologySyracuse University107 College PlaceSyracuseNY 13244USA
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18
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Chai J, Su Y, Huang F, Liu S, Tao M, Murphy RW, Luo J. The gap in research on polyploidization between plants and vertebrates: model systems and strategic challenges. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-015-0879-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Leempoel K, Parisod C, Geiser C, Daprà L, Vittoz P, Joost S. Very high‐resolution digital elevation models: are multi‐scale derived variables ecologically relevant? Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12427] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG) School of Civil and Environmental Engineering (ENAC) École Polytechnique Fédérale de Lausanne (EPFL) Bâtiment GC Station 18 1015 Lausanne Switzerland
| | - Christian Parisod
- Laboratory of evolutionary botany University of Neuchâtel CH‐2000 Neuchâtel Switzerland
| | - Céline Geiser
- Laboratory of evolutionary botany University of Neuchâtel CH‐2000 Neuchâtel Switzerland
| | - Lucas Daprà
- Laboratory of evolutionary botany University of Neuchâtel CH‐2000 Neuchâtel Switzerland
| | - Pascal Vittoz
- Institut des dynamiques de la surface terrestre University of Lausanne Géopolis CH‐1015 Lausanne Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG) School of Civil and Environmental Engineering (ENAC) École Polytechnique Fédérale de Lausanne (EPFL) Bâtiment GC Station 18 1015 Lausanne Switzerland
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20
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Pošćić F, Fellet G, Vischi M, Casolo V, Schat H, Marchiol L. Variation in Heavy Metal Accumulation and Genetic Diversity at a Regional Scale Among Metallicolous and Non-Metallicolous Populations of the Facultative Metallophyte Biscutella laevigata subsp. laevigata. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2015; 17:464-475. [PMID: 25495937 DOI: 10.1080/15226514.2014.922921] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biscutella laevigata is a facultative metallophyte, with populations on non-metalliferous and metalliferous soils. Some of its metallicolous populations have been shown to hyperaccumulate thallium or lead in nature. Only Tl hyperaccumulation has been experimentally confirmed. We aimed to compare the patterns of metal (hyper)accumulation and genetic diversity among populations of B. laevigata subsp. laevigata in NE Italy. None of the populations exhibited foliar hyperaccumulation of Cu, Zn, or Pb. The root-to-shoot accumulation rates for these metals were unchanged or decreased rather than enhanced in the metallicolous populations, in comparison with the non-metallicolous ones. Hyperaccumulation of Tl was confined to the population of the Cave del Predil mine. This population was genetically very distinct from the others, as demonstrated by AFLP-based cluster analysis. The two other mine populations did not surpass the threshold for Tl hyperaccumulation, but showed enhanced foliar Tl concentrations and root-to-shoot translocation rates, in comparison with the non-metallicolous populations. Genetic analysis suggested that adaptation to metalliferous soil must have been independently evolved in the metallicolous populations.
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Affiliation(s)
- Filip Pošćić
- a Department of Agricultural and Environmental Sciences , Università degli Studi di Udine , Via delle Scienze , Udine , Italy
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21
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Ray A, Ray R. Rapid divergence of ecotypes of an invasive plant. AOB PLANTS 2014; 6:plu052. [PMID: 25165061 PMCID: PMC4215188 DOI: 10.1093/aobpla/plu052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/07/2014] [Indexed: 06/03/2023]
Abstract
Invasive species demonstrate rapid evolution within a very short period of time allowing one to understand the underlying mechanism(s). Lantana camara, a highly invasive plant of the tropics and subtropics, has expanded its range and successfully established itself almost throughout India. In order to uncover the processes governing the invasion dynamics, 218 individuals from various locations across India were characterized with six microsatellites. By integrating genetic data with niche modelling, we examined the effect of drift and environmental selection on genetic divergence. We found multiple genetic clusters that were non-randomly distributed across space. Spatial autocorrelation revealed a strong fine-scale structure, i.e. isolation by distance. In addition, we obtained evidence of inhibitory effects of selection on gene flow, i.e. isolation by environmental distance. Perhaps, local adaptation in response to selection is offsetting gene flow and causing the populations to diverge. Niche models suggested that temperature and precipitation play a major role in the observed spatial distribution of this plant. Based on a non-random distribution of clusters, unequal gene flow among them and different bioclimatic niche requirements, we concluded that the emergence of ecotypes represented by two genetic clusters is underway. They may be locally adapted to specific climatic conditions, and perhaps at the very early stages of ecological divergence.
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Affiliation(s)
- Avik Ray
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India Present address: Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Sriramapura, Jakkur Post, Bangalore 560064, India, and Center for Interdisciplinary Studies (CIS), Basudha, Kolkata 700078, India
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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Grdiša M, Liber Z, Radosavljević I, Carović-Stanko K, Kolak I, Satovic Z. Genetic diversity and structure of Dalmatian pyrethrum (Tanacetum cinerariifolium Trevir./Sch./Bip., Asteraceae) within the Balkan refugium. PLoS One 2014; 9:e105265. [PMID: 25121763 PMCID: PMC4133326 DOI: 10.1371/journal.pone.0105265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/22/2014] [Indexed: 12/16/2022] Open
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium Trevir. /Sch./ Bip.) is an outcrossing, perennial insecticidal plant, restricted to the eastern Adriatic coast (Mediterranean). Amplified fragment-length polymorphisms (AFLP) were used to investigate the genetic diversity and structure within and among 20 natural plant populations. The highest level of gene diversity, the number of private alleles and the frequency down-weighted marker values (DW) were found in northern Adriatic populations and gradually decreased towards the southern boundary of the species range. Genetic impoverishment of these southern populations is most likely the result of human-related activities. An analysis of molecular variance (AMOVA) indicated that most of the genetic diversity was attributed to differences among individuals within populations (85.78%), which are expected due to the outcrossing nature of the species. A Bayesian analysis of the population structure identified two dominant genetic clusters. A spatial analysis of the genetic diversity indicated that 5.6% of the genetic differentiation resulted from isolation by distance (IBD), while 12.3% of the genetic differentiation among populations followed the pattern of isolation by environmental distance (IBED). Knowledge of the genetic diversity patterns of the natural populations and the mechanism behind these patterns is required for the exploitation and possible conservation management of this endemic and economically important species.
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Affiliation(s)
- Martina Grdiša
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- * E-mail:
| | - Zlatko Liber
- Department of Botany, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Radosavljević
- Department of Botany, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Klaudija Carović-Stanko
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ivan Kolak
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Zlatko Satovic
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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23
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Genetic variation of Sherardia arvensis L. – How land use and fragmentation affect an arable weed. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Vazačová K, Münzbergová Z. The importance of species traits for species distribution on oceanic islands. PLoS One 2014; 9:e101046. [PMID: 25003737 PMCID: PMC4086896 DOI: 10.1371/journal.pone.0101046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/03/2014] [Indexed: 11/25/2022] Open
Abstract
Understanding species' ability to colonize new habitats is a key knowledge allowing us to predict species' survival in the changing landscapes. However, most studies exploring this topic observe distribution of species in landscapes which are under strong human influence being fragmented only recently and ignore the fact that the species distribution in these landscapes is far from equilibrium. Oceanic islands seem more appropriate systems for studying the relationship between species traits and its distribution as they are fragmented without human contribution and as they remained unchanged for a long evolutionary time. In our study we compared the values of dispersal as well as persistence traits among 18 species pairs from the Canary Islands differing in their distribution within the archipelago. The data were analyzed both with and without phylogenetic correction. The results demonstrate that no dispersal trait alone can explain the distribution of the species in the system. They, however, also suggest that species with better dispersal compared to their close relatives are better colonizers. Similarly, abundance of species in the archipelago seems to be an important predictor of species colonization ability only when comparing closely related species. This implies that analyses including phylogenetic correction may provide different insights than analyses without such a correction and both types of analyses should be combined to understand the importance of various plant traits for species colonization ability.
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Affiliation(s)
- Kristýna Vazačová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
- * E-mail:
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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25
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Steane DA, Potts BM, McLean E, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Genome-wide scans detect adaptation to aridity in a widespread forest tree species. Mol Ecol 2014; 23:2500-13. [DOI: 10.1111/mec.12751] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/21/2014] [Accepted: 04/30/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and National Centre for Future Forest Industries; University of Tasmania; Private Bag 55 Hobart TAS 7000 Australia
- Faculty of Science, Health, Education and Engineering and Collaborative Research Network; University of the Sunshine Coast; Locked Bag 4 Maroochydore QLD 4558 Australia
| | - Brad M. Potts
- School of Biological Sciences and National Centre for Future Forest Industries; University of Tasmania; Private Bag 55 Hobart TAS 7000 Australia
| | - Elizabeth McLean
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104 Bentley Delivery Centre Perth WA 6983 Australia
| | | | - William D. Stock
- Centre for Ecosystem Management; School of Natural Sciences; Edith Cowan University; Perth WA Australia
| | - René E. Vaillancourt
- School of Biological Sciences and National Centre for Future Forest Industries; University of Tasmania; Private Bag 55 Hobart TAS 7000 Australia
| | - Margaret Byrne
- Science and Conservation Division; Department of Parks and Wildlife; Locked Bag 104 Bentley Delivery Centre Perth WA 6983 Australia
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26
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Senerchia N, Felber F, Parisod C. Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats. THE NEW PHYTOLOGIST 2014; 202:975-985. [PMID: 24548250 DOI: 10.1111/nph.12731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.
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Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Musée et Jardins botaniques cantonaux, Avenue de Cour 14bis, 1007, Lausanne, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
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Genetics of cryptic speciation within an Arctic mustard, Draba nivalis. PLoS One 2014; 9:e93834. [PMID: 24691072 PMCID: PMC3972243 DOI: 10.1371/journal.pone.0093834] [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: 10/11/2013] [Accepted: 03/09/2014] [Indexed: 01/13/2023] Open
Abstract
Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.
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28
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Zhao Y, Vrieling K, Liao H, Xiao M, Zhu Y, Rong J, Zhang W, Wang Y, Yang J, Chen J, Song Z. Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild riceOryza rufipogon? Mol Ecol 2013; 22:5531-47. [DOI: 10.1111/mec.12517] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 08/28/2013] [Accepted: 08/30/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Yao Zhao
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Klaas Vrieling
- Plant Ecology and Phytochemistry; Institute of Biology; Leiden University; PO Box 9505 2300 RA Leiden The Netherlands
| | - Hui Liao
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Manqiu Xiao
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Yongqing Zhu
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Jun Rong
- Center for Watershed Ecology; Institute of Life Science and Key Laboratory of Poyang Lake Environment and Resource Utilization; Ministry of Education; Nanchang University; Nanchang 330031 China
| | - Wenju Zhang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Yuguo Wang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Ji Yang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering; Institute of Biodiversity Science; Fudan University; Shanghai 200433 China
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29
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Ma K, Song Y, Yang X, Zhang Z, Zhang D. Variation in genomic methylation in natural populations of chinese white poplar. PLoS One 2013; 8:e63977. [PMID: 23704963 PMCID: PMC3660595 DOI: 10.1371/journal.pone.0063977] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/07/2013] [Indexed: 11/29/2022] Open
Abstract
Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.
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Affiliation(s)
- Kaifeng Ma
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Xiaohui Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Zhiyi Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- * E-mail:
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30
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Jiang Q, Li Q, Yu H, Kong LF. Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0114-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Zulliger D, Schnyder E, Gugerli F. Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species. Mol Ecol 2013; 22:1626-39. [PMID: 23398479 DOI: 10.1111/mec.12199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 11/27/2022]
Abstract
Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify markers potentially under directional selection, we performed outlier and environmental association analyses using a set of topo-climatic variables available as GIS layers. Several AFLP loci showed signatures of adaptation, of which one, found in Cardamine resedifolia (Cre_P1_212.5), was associated with precipitation. We sequence-characterized this candidate locus and genotyped single nucleotide polymorphisms (SNPs) found within this locus for all species. Testing for environmental associations of SNPs revealed the same association of this locus in Arabis alpina but not in other study species. Cumulative statistical evidence indicates that locus Cre_P1_212.5 is environmentally relevant or is linked to a gene under selection in our study range. Furthermore, the locus shows an association to the same potentially selective factor in at least one other related species. These findings help to identify trends in plant adaptation in Alpine ecosystems in response to particular environmental parameters.
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Affiliation(s)
- Deborah Zulliger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
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Temunović M, Franjić J, Satovic Z, Grgurev M, Frascaria-Lacoste N, Fernández-Manjarrés JF. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl. PLoS One 2012; 7:e42764. [PMID: 22905171 PMCID: PMC3414449 DOI: 10.1371/journal.pone.0042764] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/12/2012] [Indexed: 11/18/2022] Open
Abstract
Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.
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Affiliation(s)
- Martina Temunović
- Department of Forest Genetics, Faculty of Forestry, University of Zagreb, Zagreb, Croatia.
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Liu S, Sun K, Jiang T, Ho JP, Liu B, Feng J. Natural epigenetic variation in the female great roundleaf bat (Hipposideros armiger) populations. Mol Genet Genomics 2012; 287:643-50. [DOI: 10.1007/s00438-012-0704-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 06/18/2012] [Indexed: 01/01/2023]
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Holderegger R, Buehler D, Gugerli F, Manel S. Landscape genetics of plants. TRENDS IN PLANT SCIENCE 2010; 15:675-683. [PMID: 20940103 DOI: 10.1016/j.tplants.2010.09.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/31/2010] [Accepted: 09/08/2010] [Indexed: 05/30/2023]
Abstract
Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.
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Affiliation(s)
- Rolf Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
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Poncet BN, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L, Rioux D, Thuiller W, Aubert S, Manel S. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 2010; 19:2896-907. [PMID: 20609082 DOI: 10.1111/j.1365-294x.2010.04696.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.
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Affiliation(s)
- Bénédicte N Poncet
- Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, Grenoble Université, BP 53, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
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Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J, González-Martínez SC, Neale DB. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 2010; 185:969-82. [PMID: 20439779 PMCID: PMC2907212 DOI: 10.1534/genetics.110.115543] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 04/20/2010] [Indexed: 12/21/2022] Open
Abstract
Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F(ST) outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes.
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Affiliation(s)
- Andrew J. Eckert
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Joost van Heerwaarden
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Jill L. Wegrzyn
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - C. Dana Nelson
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - Santíago C. González-Martínez
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
| | - David. B. Neale
- Section of Evolution and Ecology, Center for Population Biology, and Department of Plant Sciences, University of California, Davis, California 95616, Southern Institute of Forest Genetics, U. S. Department of Agriculture Forest Service, Saucier, Mississippi 39574, Department of Forest Systems and Resources, Forest Research Institute, Center of Forest Research, Institito Nacional de Investigacion y Tecnologia Agraria y Alimentaria, 28040 Madrid, Spain, and Institute of Forest Genetics, Pacific Southwest Research Station, U. S. Department of Agriculture, Davis, California 95616
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Lira-Medeiros CF, Parisod C, Fernandes RA, Mata CS, Cardoso MA, Ferreira PCG. Epigenetic variation in mangrove plants occurring in contrasting natural environment. PLoS One 2010; 5:e10326. [PMID: 20436669 PMCID: PMC2859934 DOI: 10.1371/journal.pone.0010326] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 03/26/2010] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Epigenetic modifications, such as cytosine methylation, are inherited in plant species and may occur in response to biotic or abiotic stress, affecting gene expression without changing genome sequence. Laguncularia racemosa, a mangrove species, occurs in naturally contrasting habitats where it is subjected daily to salinity and nutrient variations leading to morphological differences. This work aims at unraveling how CpG-methylation variation is distributed among individuals from two nearby habitats, at a riverside (RS) or near a salt marsh (SM), with different environmental pressures and how this variation is correlated with the observed morphological variation. PRINCIPAL FINDINGS Significant differences were observed in morphological traits such as tree height, tree diameter, leaf width and leaf area between plants from RS and SM locations, resulting in smaller plants and smaller leaf size in SM plants. Methyl-Sensitive Amplified Polymorphism (MSAP) was used to assess genetic and epigenetic (CpG-methylation) variation in L. racemosa genomes from these populations. SM plants were hypomethylated (14.6% of loci had methylated samples) in comparison to RS (32.1% of loci had methylated samples). Within-population diversity was significantly greater for epigenetic than genetic data in both locations, but SM also had less epigenetic diversity than RS. Frequency-based (G(ST)) and multivariate (beta(ST)) methods that estimate population structure showed significantly greater differentiation among locations for epigenetic than genetic data. Co-Inertia analysis, exploring jointly the genetic and epigenetic data, showed that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment, suggesting that CpG-methylation changes may be associated with environmental heterogeneity. CONCLUSIONS In spite of significant morphological dissimilarities, individuals of L. racemosa from salt marsh and riverside presented little genetic but abundant DNA methylation differentiation, suggesting that epigenetic variation in natural plant populations has an important role in helping individuals to cope with different environments.
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Affiliation(s)
- Catarina Fonseca Lira-Medeiros
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Christian Parisod
- Laboratoire de Biologie Cellulaire, Institut J.-P. Bourgin - INRA Centre de Versailles, Versailles, France
| | - Ricardo Avancini Fernandes
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Camila Souza Mata
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Monica Aires Cardoso
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Paulo Cavalcanti Gomes Ferreira
- Diretoria de Pesquisa Científica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brasil
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Abstract
Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.
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Affiliation(s)
- Christian Parisod
- National Centre for Biosystematics, University of Oslo, 0318 Oslo, Norway.
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Parisod C, Joost S. Divergent selection in trailing- versus leading-edge populations of Biscutella laevigata. ANNALS OF BOTANY 2010; 105:655-60. [PMID: 20181567 PMCID: PMC2850798 DOI: 10.1093/aob/mcq014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/23/2009] [Accepted: 01/04/2010] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Knowledge on how climate-induced range shifts might affect natural selection is crucial to understand the evolution of species ranges. METHODS Using historical demographic perspectives gathered from regional-scale phylogeography on the alpine herb Biscutella laevigata, indirect inferences on gene flow and signature of selection based on AFLP genotyping were compared between local populations persisting at the trailing edge and expanding at the leading edge. KEY RESULTS Spatial autocorrelation revealed that gene flow was two times more restricted at the trailing edge and genome scans indicated divergent selection in this persisting population. In contrast, no pattern of selection emerged in the expanding population at the leading edge. CONCLUSIONS Historical effects may determine different architecture of genetic variation and selective patterns within local populations, what is arguably important to understand evolutionary processes acting across the species ranges.
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Affiliation(s)
- Christian Parisod
- National Center for Biosystematics (NCB), Natural History Museum, University of Oslo, 0318 Oslo, Norway.
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Pleistocene distribution range shifts were accompanied by breeding system divergence within Hornungia alpina (Brassicaceae) in the Alps. Mol Phylogenet Evol 2009; 54:571-82. [PMID: 19695334 DOI: 10.1016/j.ympev.2009.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/03/2009] [Accepted: 08/07/2009] [Indexed: 11/20/2022]
Abstract
Impact of glacial history on the phylogeography of silicate-dwelling plants of the European Alps has been particularly well studied, whereas virtually no data are available for species growing on different bedrock types, as for Hornungia alpina. Bayesian clustering of AFLP data only partly support the distinction of three subspecies as morphologically defined. Whereas the phylogeographical N-group corresponds to subsp. alpina, the congruence of the SW-group and SE-group with subsp. brevicaulis, and subsp. austroalpina, respectively, is limited. High levels of rarity and genetic diversity in the N-group suggest Pleistocene survival along the outer margin of the Alpine arc. For subsp. brevicaulis we suggest a single origin from a refugium in the Southwestern Alps, whereas subsp. austroalpina might have originated twice in the Southern and Southeastern Alps. Different levels of genetic diversity and partitioning of genetic variation indicate a divergence in breeding system, which is corroborated by pollinator exclusion experiments revealing self-incompatibility in the N-group and autonomous selfing in the SE-group.
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Riba M, Mayol M, Giles BE, Ronce O, Imbert E, Van Der Velde M, Chauvet S, Ericson L, Bijlsma R, Vosman B, Smulders MJM, Olivieri I. Darwin's wind hypothesis: does it work for plant dispersal in fragmented habitats? THE NEW PHYTOLOGIST 2009; 183:667-677. [PMID: 19659587 DOI: 10.1111/j.1469-8137.2009.02948.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Using the wind-dispersed plant Mycelis muralis, we examined how landscape fragmentation affects variation in seed traits contributing to dispersal. Inverse terminal velocity (Vt(-1)) of field-collected achenes was used as a proxy for individual seed dispersal ability. We related this measure to different metrics of landscape connectivity, at two spatial scales: in a detailed analysis of eight landscapes in Spain and along a latitudinal gradient using 29 landscapes across three European regions. In the highly patchy Spanish landscapes, seed Vt(-1)increased significantly with increasing connectivity. A common garden experiment suggested that differences in Vt(-1) may be in part genetically based. The Vt(-1) was also found to increase with landscape occupancy, a coarser measure of connectivity, on a much broader (European) scale. Finally, Vt(-1)was found to increase along a south-north latitudinal gradient. Our results for M. muralis are consistent with 'Darwin's wind dispersal hypothesis' that high cost of dispersal may select for lower dispersal ability in fragmented landscapes, as well as with the 'leading edge hypothesis' that most recently colonized populations harbour more dispersive phenotypes.
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Affiliation(s)
- Miquel Riba
- CREAF (Center for Ecological Research and Forestry Applications), Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Maria Mayol
- CREAF (Center for Ecological Research and Forestry Applications), Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Barbara E Giles
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Ophélie Ronce
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Eric Imbert
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Marco Van Der Velde
- Animal Ecology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, PO Box 14, NL-9750 AA Haren, The Netherlands
| | - Stéphanie Chauvet
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
- Association Tela Botanica, Institut de Botanique, 163 Rue Auguste Broussonnet, F-34090 Montpellier, France
| | - Lars Ericson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - R Bijlsma
- Population and Conservation Genetics, Theoretical Biology, University of Groningen, PO Box 14, NL-9750 AA Haren, The Netherlands
| | - Ben Vosman
- Plant Research International, Wageningen UR, PO Box 16, NL-6700 AA Wageningen, The Netherlands
| | - M J M Smulders
- Plant Research International, Wageningen UR, PO Box 16, NL-6700 AA Wageningen, The Netherlands
| | - Isabelle Olivieri
- Université Montpellier 2, Institut des Sciences de l'Evolution, UMR CNRS 5554, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
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HERRERA CM, BAZAGA P. Quantifying the genetic component of phenotypic variation in unpedigreed wild plants: tailoring genomic scan for within-population use. Mol Ecol 2009; 18:2602-14. [DOI: 10.1111/j.1365-294x.2009.04229.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Affiliation(s)
- Patrik Nosil
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver BC, Canada.
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Jombart T, Pontier D, Dufour AB. Genetic markers in the playground of multivariate analysis. Heredity (Edinb) 2009; 102:330-41. [PMID: 19156164 DOI: 10.1038/hdy.2008.130] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multivariate analyses such as principal component analysis were among the first statistical methods employed to extract information from genetic markers. From their early applications to current innovations, these approaches have proven to be efficient for the analysis of the genetic variability in various contexts such as human genetics, conservation and adaptation studies. However, because multivariate analysis is a wide and diversified area of statistics, choosing a method appropriate to both the data and to the question being asked can be difficult. Moreover, some particularities of genetic markers need to be taken into account when using multivariate methods. As a consequence, multivariate analyses are often used as black boxes, which results in frequent mistakes in the literature. In this review, we provide a critical analysis of the application of multivariate methods to genetic markers, using a general framework that unifies all these methods for the sake of clarity. First, we focus on some common mistakes in these applications and ways to avoid these pitfalls. We then detail the most critical particularities of allele frequencies that demand adaptations of multivariate methods, and we propose solutions to the subsequent problems. Finally, we tackle several questions of interest in which multivariate analysis has a great role to play, such as the study of the typological coherence of different genetic markers, or the investigation of spatial genetic patterns.
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Fine-scale genetic structure and marginal processes in an expanding population of Biscutella laevigata L. (Brassicaceae). Heredity (Edinb) 2008; 101:536-42. [PMID: 18781166 DOI: 10.1038/hdy.2008.95] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Evolutionary processes acting at the expanding margins of a species' range are still poorly understood. Genetic drift is considered prevalent in marginal populations, and the maintenance of genetic diversity during recolonization might seem puzzling. To investigate such processes, a fine-scale investigation of 219 individuals was performed within a population of Biscutella laevigata (Brassicaceae), located at the leading edge of its range. The survey used amplified fragment length polymorphisms (AFLPs). As commonly reported across the whole species distribution range, individual density and genetic diversity decreased along the local axis of recolonization of this expanding population, highlighting the enduring effect of the historical colonization on present-day diversity. The self-incompatibility system of the plant may have prevented local inbreeding in newly found patches and sustained genetic diversity by ensuring gene flow from established populations. Within the more continuously populated region, spatial analysis of genetic structure revealed restricted gene flow among individuals. The distribution of genotypes formed a mosaic of relatively homogenous patches within the continuous population. This pattern could be explained by a history of expansion by long-distance dispersal followed by fine-scale diffusion (that is, a stratified dispersal combination). The secondary contact among expanding patches apparently led to admixture among differentiated genotypes where they met (that is, a reshuffling effect). This type of dynamics could explain the maintenance of genetic diversity during recolonization.
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