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Mattila TM, Aalto EA, Toivainen T, Niittyvuopio A, Piltonen S, Kuittinen H, Savolainen O. Selection for population-specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post-glacial colonization. Mol Ecol 2016; 25:581-97. [PMID: 26600237 DOI: 10.1111/mec.13489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022]
Abstract
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population-specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population-specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.
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Affiliation(s)
- Tiina M Mattila
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Esa A Aalto
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Tuomas Toivainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Susanna Piltonen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Outi Savolainen
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
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Paul P, Chaturvedi P, Selymesi M, Ghatak A, Mesihovic A, Scharf KD, Weckwerth W, Simm S, Schleiff E. The membrane proteome of male gametophyte in Solanum lycopersicum. J Proteomics 2016; 131:48-60. [DOI: 10.1016/j.jprot.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
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Krämer U. Planting molecular functions in an ecological context with Arabidopsis thaliana. eLife 2015; 4:e06100. [PMID: 25807084 PMCID: PMC4373673 DOI: 10.7554/elife.06100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/13/2015] [Indexed: 12/31/2022] Open
Abstract
The vascular plant Arabidopsis thaliana is a central genetic model and universal reference organism in plant and crop science. The successful integration of different fields of research in the study of A. thaliana has made a large contribution to our molecular understanding of key concepts in biology. The availability and active development of experimental tools and resources, in combination with the accessibility of a wealth of cumulatively acquired knowledge about this plant, support the most advanced systems biology approaches among all land plants. Research in molecular ecology and evolution has also brought the natural history of A. thaliana into the limelight. This article showcases our current knowledge of the natural history of A. thaliana from the perspective of the most closely related plant species, providing an evolutionary framework for interpreting novel findings and for developing new hypotheses based on our knowledge of this plant.
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Affiliation(s)
- Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Bochum, Germany
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Ellstrand NC. Is gene flow the most important evolutionary force in plants? AMERICAN JOURNAL OF BOTANY 2014; 101:737-53. [PMID: 24752890 DOI: 10.3732/ajb.1400024] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/17/2014] [Indexed: 05/02/2023]
Abstract
Although theory has demonstrated rather low levels of gene flow are sufficient to counteract opposing mutation, drift, and selection, widespread recognition of the evolutionary importance of gene flow has come slowly. The perceived role of gene flow as an evolutionary force has vacillated over the last century. In the last few decades, new methods and analyses have demonstrated that plant gene flow rates vary tremendously-from nil to very high-depending on the species and specific populations involved, and sometimes over time for individual populations. In many cases, the measured gene flow rates are evolutionarily significant at distances of hundreds and sometimes thousands of meters, occurring at levels sufficient to counteract drift, spread advantageous alleles, or thwart moderate levels of opposing local selection. Gene flow in plants is likely to often act as a cohesive force, uniting individual plant species into real evolutionary units. Also, gene flow can evolve under natural selection, decreasing or increasing. The fact of frequent, but variable, plant gene flow has important consequences for applied issues in which the presence or absence of gene flow might influence the outcome of a policy, regulatory, or management decision. Examples include the unintended spread of engineered genes, the evolution of invasiveness, and conservation. New data-rich genomic techniques allow closer scrutiny of the role of gene flow in plant evolution. Most plant evolutionists now recognize the importance of gene flow, and it is receiving increased recognition from other areas of plant biology as well.
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Affiliation(s)
- Norman C Ellstrand
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124 USA
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Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, Holderegger R, Widmer A. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Mol Ecol 2013; 22:5594-607. [PMID: 24102711 PMCID: PMC4274019 DOI: 10.1111/mec.12521] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 09/02/2013] [Accepted: 09/09/2013] [Indexed: 12/27/2022]
Abstract
Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
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Affiliation(s)
- Martin C Fischer
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
| | - Christian Rellstab
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Andrew Tedder
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of ZurichWinterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Stefan Zoller
- ETH Zürich, Genetic Diversity CentreUniversitätstrasse 16, 8092, Zürich, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of ZurichWinterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Rolf Holderegger
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Alex Widmer
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
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Hanikenne M, Kroymann J, Trampczynska A, Bernal M, Motte P, Clemens S, Krämer U. Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptation. PLoS Genet 2013; 9:e1003707. [PMID: 23990800 PMCID: PMC3749932 DOI: 10.1371/journal.pgen.1003707] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/22/2013] [Indexed: 12/27/2022] Open
Abstract
Among the rare colonizers of heavy-metal rich toxic soils, Arabidopsis halleri is a compelling model extremophile, physiologically distinct from its sister species A. lyrata, and A. thaliana. Naturally selected metal hypertolerance and extraordinarily high leaf metal accumulation in A. halleri both require Heavy Metal ATPase4 (HMA4) encoding a PIB-type ATPase that pumps Zn(2+) and Cd(2+) out of specific cell types. Strongly enhanced HMA4 expression results from a combination of gene copy number expansion and cis-regulatory modifications, when compared to A. thaliana. These findings were based on a single accession of A. halleri. Few studies have addressed nucleotide sequence polymorphism at loci known to govern adaptations. We thus sequenced 13 DNA segments across the HMA4 genomic region of multiple A. halleri individuals from diverse habitats. Compared to control loci flanking the three tandem HMA4 gene copies, a gradual depletion of nucleotide sequence diversity and an excess of low-frequency polymorphisms are hallmarks of positive selection in HMA4 promoter regions, culminating at HMA4-3. The accompanying hard selective sweep is segmentally eclipsed as a consequence of recurrent ectopic gene conversion among HMA4 protein-coding sequences, resulting in their concerted evolution. Thus, HMA4 coding sequences exhibit a network-like genealogy and locally enhanced nucleotide sequence diversity within each copy, accompanied by lowered sequence divergence between paralogs in any given individual. Quantitative PCR corroborated that, across A. halleri, three genomic HMA4 copies generate overall 20- to 130-fold higher transcript levels than in A. thaliana. Together, our observations constitute an unexpectedly complex profile of polymorphism resulting from natural selection for increased gene product dosage. We propose that these findings are paradigmatic of a category of multi-copy genes from a broad range of organisms. Our results emphasize that enhanced gene product dosage, in addition to neo- and sub-functionalization, can account for the genomic maintenance of gene duplicates underlying environmental adaptation.
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Affiliation(s)
- Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Liège, Belgium
| | - Juergen Kroymann
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud/CNRS, Orsay, France
| | | | - María Bernal
- Department of Plant Physiology, Ruhr University Bochum, Bochum, Germany
| | - Patrick Motte
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, Liège, Belgium
| | - Stephan Clemens
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, Bochum, Germany
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Koch MA, German DA. Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples. FRONTIERS IN PLANT SCIENCE 2013; 4:267. [PMID: 23914192 PMCID: PMC3728732 DOI: 10.3389/fpls.2013.00267] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/02/2013] [Indexed: 05/20/2023]
Abstract
Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella.
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Affiliation(s)
- Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Center for Organismal Studies Heidelberg, Heidelberg UniversityHeidelberg, Germany
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics, Center for Organismal Studies Heidelberg, Heidelberg UniversityHeidelberg, Germany
- South-Siberian Botanical Garden, Altai State UniversityBarnaul, Russia
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Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea. PLoS One 2013; 8:e58916. [PMID: 23554957 PMCID: PMC3595216 DOI: 10.1371/journal.pone.0058916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.
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Roux C, Castric V, Pauwels M, Wright SI, Saumitou-Laprade P, Vekemans X. Does speciation between Arabidopsis halleri and Arabidopsis lyrata coincide with major changes in a molecular target of adaptation? PLoS One 2011; 6:e26872. [PMID: 22069475 PMCID: PMC3206069 DOI: 10.1371/journal.pone.0026872] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 10/05/2011] [Indexed: 11/19/2022] Open
Abstract
Ever since Darwin proposed natural selection as the driving force for the origin of species, the role of adaptive processes in speciation has remained controversial. In particular, a largely unsolved issue is whether key divergent ecological adaptations are associated with speciation events or evolve secondarily within sister species after the split. The plant Arabidopsis halleri is one of the few species able to colonize soils highly enriched in zinc and cadmium. Recent advances in the molecular genetics of adaptation show that the physiology of this derived ecological trait involves copy number expansions of the AhHMA4 gene, for which orthologs are found in single copy in the closely related A. lyrata and the outgroup A. thaliana. To gain insight into the speciation process, we ask whether adaptive molecular changes at this candidate gene were contemporary with important stages of the speciation process. We first inferred the scenario and timescale of speciation by comparing patterns of variation across the genomic backgrounds of A. halleri and A. lyrata. Then, we estimated the timing of the first duplication of AhHMA4 in A. halleri. Our analysis suggests that the historical split between the two species closely coincides with major changes in this molecular target of adaptation in the A. halleri lineage. These results clearly indicate that these changes evolved in A. halleri well before industrial activities fostered the spread of Zn- and Cd-polluted areas, and suggest that adaptive processes related to heavy-metal homeostasis played a major role in the speciation process.
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Affiliation(s)
- Camille Roux
- Université Lille Nord de France, Lille, France
- FRE 3268 CNRS Université Lille 1, Villeneuve d'Ascq, France
| | - Vincent Castric
- Université Lille Nord de France, Lille, France
- FRE 3268 CNRS Université Lille 1, Villeneuve d'Ascq, France
| | - Maxime Pauwels
- Université Lille Nord de France, Lille, France
- FRE 3268 CNRS Université Lille 1, Villeneuve d'Ascq, France
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Pierre Saumitou-Laprade
- Université Lille Nord de France, Lille, France
- FRE 3268 CNRS Université Lille 1, Villeneuve d'Ascq, France
| | - Xavier Vekemans
- Université Lille Nord de France, Lille, France
- FRE 3268 CNRS Université Lille 1, Villeneuve d'Ascq, France
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Shimizu KK, Kudoh H, Kobayashi MJ. Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology. ANNALS OF BOTANY 2011; 108:777-87. [PMID: 21852275 PMCID: PMC3170158 DOI: 10.1093/aob/mcr180] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 05/18/2011] [Indexed: 05/19/2023]
Abstract
BACKGROUND It is essential to understand and predict the effects of changing environments on plants. This review focuses on the sexual reproduction of plants, as previous studies have suggested that this trait is particularly vulnerable to climate change, and because a number of ecologically and evolutionarily relevant genes have been identified. SCOPE It is proposed that studying gene functions in naturally fluctuating conditions, or gene functions in natura, is important to predict responses to changing environments. First, we discuss flowering time, an extensively studied example of phenotypic plasticity. The quantitative approaches of ecological and evolutionary systems biology have been used to analyse the expression of a key flowering gene, FLC, of Arabidopsis halleri in naturally fluctuating environments. Modelling showed that FLC acts as a quantitative tracer of the temperature over the preceding 6 weeks. The predictions of this model were verified experimentally, confirming its applicability to future climate changes. Second, the evolution of self-compatibility as exemplifying an evolutionary response is discussed. Evolutionary genomic and functional analyses have indicated that A. thaliana became self-compatible via a loss-of-function mutation in the male specificity gene, SCR/SP11. Self-compatibility evolved during glacial-interglacial cycles, suggesting its association with mate limitation during migration. Although the evolution of self-compatibility may confer short-term advantages, it is predicted to increase the risk of extinction in the long term because loss-of-function mutations are virtually irreversible. CONCLUSIONS Recent studies of FLC and SCR have identified gene functions in natura that are unlikely to be found in laboratory experiments. The significance of epigenetic changes and the study of non-model species with next-generation DNA sequencers is also discussed.
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Affiliation(s)
- Kentaro K Shimizu
- Institute of Plant Biology, University Research Priority Program in Systems Biology/Functional Genomics & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.
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