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Vekemans X, Poux C, Goubet PM, Castric V. The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S-locus? J Evol Biol 2014; 27:1372-85. [PMID: 24725152 DOI: 10.1111/jeb.12372] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Evolutionary transitions between mating systems have occurred repetitively and independently in flowering plants. One of the most spectacular advances of the recent empirical literature in the field was the discovery of the underlying genetic machinery, which provides the opportunity to retrospectively document the scenario of the outcrossing to selfing transitions in a phylogenetic perspective. In this review, we explore the literature describing patterns of polymorphism and molecular evolution of the locus controlling self-incompatibility (S-locus) in selfing species of the Brassicaceae family in order to document the transition from outcrossing to selfing, a retrospective approach that we describe as the 'mating system genes approach'. The data point to strikingly contrasted scenarios of transition from outcrossing to selfing. We also perform original analyses of the fully sequenced genomes of four species showing self-compatibility, to compare the orthologous S-locus region with that of functional S-locus haplotypes. Phylogenetic analyses suggest that all species we investigated evolved independently towards loss of self-incompatibility, and in most cases almost intact sequences of either of the two S-locus genes suggest that these transitions occurred relatively recently. The S-locus region in Aethionema arabicum, representing the most basal lineage of Brassicaceae, showed unusual patterns so that our analysis could not determine whether self-incompatibility was lost secondarily, or evolved in the core Brassicaceae after the split with this basal lineage. Although the approach we detail can only be used when mating system genes have been identified in a clade, we suggest that its integration with phylogenetic and population genetic approaches should help determine the main routes of this predominant mating system shift in plants.
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Affiliation(s)
- X Vekemans
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université Lille 1, Villeneuve d'Ascq Cedex, France
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Hay AS, Pieper B, Cooke E, Mandáková T, Cartolano M, Tattersall AD, Ioio RD, McGowan SJ, Barkoulas M, Galinha C, Rast MI, Hofhuis H, Then C, Plieske J, Ganal M, Mott R, Martinez-Garcia JF, Carine MA, Scotland RW, Gan X, Filatov DA, Lysak MA, Tsiantis M. Cardamine hirsuta: a versatile genetic system for comparative studies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1-15. [PMID: 24460550 DOI: 10.1111/tpj.12447] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/14/2014] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
A major goal in biology is to identify the genetic basis for phenotypic diversity. This goal underpins research in areas as diverse as evolutionary biology, plant breeding and human genetics. A limitation for this research is no longer the availability of sequence information but the development of functional genetic tools to understand the link between changes in sequence and phenotype. Here we describe Cardamine hirsuta, a close relative of the reference plant Arabidopsis thaliana, as an experimental system in which genetic and transgenic approaches can be deployed effectively for comparative studies. We present high-resolution genetic and cytogenetic maps for C. hirsuta and show that the genome structure of C. hirsuta closely resembles the eight chromosomes of the ancestral crucifer karyotype and provides a good reference point for comparative genome studies across the Brassicaceae. We compared morphological and physiological traits between C. hirsuta and A. thaliana and analysed natural variation in stamen number in which lateral stamen loss is a species characteristic of C. hirsuta. We constructed a set of recombinant inbred lines and detected eight quantitative trait loci that can explain stamen number variation in this population. We found clear phylogeographic structure to the genetic variation in C. hirsuta, thus providing a context within which to address questions about evolutionary changes that link genotype with phenotype and the environment.
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Affiliation(s)
- Angela S Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany
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53
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Brennan AC, Méndez-Vigo B, Haddioui A, Martínez-Zapater JM, Picó FX, Alonso-Blanco C. The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe. BMC PLANT BIOLOGY 2014; 14:17. [PMID: 24411008 PMCID: PMC3890648 DOI: 10.1186/1471-2229-14-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown. RESULTS To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia. CONCLUSIONS The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia.
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Affiliation(s)
- Adrian C Brennan
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Belén Méndez-Vigo
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Abdelmajid Haddioui
- Faculté des Sciences et Techniques, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | - José M Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja), Logroño, Spain
| | - F Xavier Picó
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Carlos Alonso-Blanco
- Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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54
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Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2013; 110:21077-82. [PMID: 24324156 DOI: 10.1073/pnas.1316773110] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organisms inhabiting different environments are often locally adapted, and yet despite a considerable body of theory, the genetic basis of local adaptation is poorly understood. Unanswered questions include the number and effect sizes of adaptive loci, whether locally favored loci reduce fitness elsewhere (i.e., fitness tradeoffs), and whether a lack of genetic variation limits adaptation. To address these questions, we mapped quantitative trait loci (QTL) for total fitness in 398 recombinant inbred lines derived from a cross between locally adapted populations of the highly selfing plant Arabidopsis thaliana from Sweden and Italy and grown for 3 consecutive years at the parental sites (>40,000 plants monitored). We show that local adaptation is controlled by relatively few genomic regions of small to modest effect. A third of the 15 fitness QTL we detected showed evidence of tradeoffs, which contrasts with the minimal evidence for fitness tradeoffs found in previous studies. This difference may reflect the power of our multiyear study to distinguish conditionally neutral QTL from those that reflect fitness tradeoffs. In Sweden, but not in Italy, the local genotype underlying fitness QTL was often maladaptive, suggesting that adaptation there is constrained by a lack of adaptive genetic variation, attributable perhaps to genetic bottlenecks during postglacial colonization of Scandinavia or to recent changes in selection regime caused by climate change. Our results suggest that adaptation to markedly different environments can be achieved through changes in relatively few genomic regions, that fitness tradeoffs are common, and that lack of genetic variation can limit adaptation.
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55
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Carlson AL, Gong H, Toomajian C, Swanson RJ. Parental genetic distance and patterns in nonrandom mating and seed yield in predominately selfing Arabidopsis thaliana. PLANT REPRODUCTION 2013; 26:317-28. [PMID: 23843176 PMCID: PMC3825607 DOI: 10.1007/s00497-013-0228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/03/2013] [Indexed: 05/09/2023]
Abstract
In this study, we ask two questions: (1) Is reproductive success independent of parental genetic distance in predominately selfing plants? (2) In the absence of early inbreeding depression, is there substantial maternal and/or paternal variation in reproductive success in natural populations? Seed yield in single pollinations and proportion of seeds sired in mixed pollinations were studied in genetically defined accessions of the predominately selfing plant Arabidopsis thaliana by conducting two diallel crosses. The first diallel was a standard, single pollination design that we used to examine variance in seed yield. The second diallel was a mixed pollination design that utilized a standard pollen competitor to examine variance in proportion of seeds sired. We found no correlation between reproductive success and parental genetic distance, and self-pollen does not systematically differ in reproductive success compared to outcross pollen, suggesting that Arabidopsis populations do not experience embryo lethality due to early-acting inbreeding or outbreeding depression. We used these data to partition the contributions to total phenotypic variation from six sources, including maternal contributions, paternal contributions and parental interactions. For seed yield in single pollinations, maternal effects accounted for the most significant source of variance (16.6 %). For proportion of seeds sired in mixed pollinations, the most significant source of variance was paternal effects (17.9 %). Thus, we show that population-level genetic similarities, including selfing, do not correlate with reproductive success, yet there is still significant paternal variance under competition. This suggests two things. First, since these differences are unlikely due to early-acting inbreeding depression or differential pollen viability, this implicates natural variation in pollen germination and tube growth dynamics. Second, this strongly supports a model of fixation of pollen performance genes in populations, offering a focus for future genetic studies in differential reproductive success.
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Affiliation(s)
- Ann L. Carlson
- Department of Biology, Valparaiso University, Valparaiso, IN 46383 USA
| | - Hui Gong
- Department of Mathematics and Computer Science, Valparaiso University, Valparaiso, IN 46383 USA
| | | | - Robert J. Swanson
- Department of Biology, Valparaiso University, Valparaiso, IN 46383 USA
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56
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Shimono Y, Hayakawa H, Kurokawa S, Nishida T, Ikeda H, Futagami N. Phylogeography of mugwort (Artemisia indica), a native pioneer herb in Japan. J Hered 2013; 104:830-41. [PMID: 24023252 DOI: 10.1093/jhered/est054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many phylogeographic studies of various tree species have been conducted to elucidate the locations of refugia and the colonization patterns during the Pleistocene. However, only a few large-scale phylogeographic studies have been conducted on herbaceous plants, especially scarce on herbs that are adapted to disturbance. Artemisia indica is a fast-growing perennial herb found in open habitats. To examine the basic information on the genetic structure of this species, we investigated the chloroplast DNA variation within and among populations across Japan. We detected 26 haplotypes in 604 individuals from 28 Japanese populations. The haplotype A1 had wide geographic distribution, and its close relatives were locally present. Some putative ancestral lineages were found mainly in the Kyushu region. This may be because several lineages migrated from the Eurasian continent to the northern coast in Kyushu via the Korean peninsula during the Pleistocene, and the A1 haplotype expanded northward, whereas others remained in southern areas. Phylogenetic distant haplotypes were present mainly in the Kanto region. Because the geographic distribution pattern of these haplotypes in this region is believed to be unnatural, these haplotypes may be derived from commercial sources for re-vegetation during the last few decades.
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Affiliation(s)
- Yoshiko Shimono
- the National Institute for Agro-Environmental Sciences, Tsukuba, Japan
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57
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Stearns FW, Fenster CB. Evidence for parallel adaptation to climate across the natural range of Arabidopsis thaliana. Ecol Evol 2013; 3:2241-50. [PMID: 23919166 PMCID: PMC3728961 DOI: 10.1002/ece3.622] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 11/23/2022] Open
Abstract
How organisms adapt to different climate habitats is a key question in evolutionary ecology and biological conservation. Species distributions are often determined by climate suitability. Consequently, the anthropogenic impact on earth's climate is of key concern to conservation efforts because of our relatively poor understanding of the ability of populations to track and evolve to climate change. Here, we investigate the ability of Arabidopsis thaliana to occupy climate space by quantifying the extent to which different climate regimes are accessible to different A. thaliana genotypes using publicly available data from a large-scale genotyping project and from a worldwide climate database. The genetic distance calculated from 149 single-nucleotide polymorphisms (SNPs) among 60 lineages of A. thaliana was compared to the corresponding climate distance among collection localities calculated from nine different climatic factors. A. thaliana was found to be highly labile when adapting to novel climate space, suggesting that populations may experience few constraints when adapting to changing climates. Our results also provide evidence of a parallel or convergent evolution on the molecular level supporting recent generalizations regarding the genetics of adaptation.
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Affiliation(s)
- Frank W Stearns
- Department of Biology, Biology-Psychology Building, University of Maryland College Park, Maryland, 20742
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58
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Co-variation between seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana. PLoS One 2013; 8:e61075. [PMID: 23717385 PMCID: PMC3662791 DOI: 10.1371/journal.pone.0061075] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/05/2013] [Indexed: 01/20/2023] Open
Abstract
Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.
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59
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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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60
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Olson-Manning CF, Lee CR, Rausher MD, Mitchell-Olds T. Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. Mol Biol Evol 2013; 30:14-23. [PMID: 22923463 PMCID: PMC3525143 DOI: 10.1093/molbev/mss204] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Network characteristics of biochemical pathways are believed to influence the rate of evolutionary change in constituent enzymes. One characteristic that may affect rate heterogeneity is control of the amount of product produced by a biochemical pathway or flux control. In particular, theoretical analyses suggest that adaptive substitutions should be concentrated in the enzyme(s) that exert the greatest control over flux. Although a handful of studies have found a correlation between position in a pathway and evolutionary rate, these investigations have not examined the relationship between evolutionary rate and flux control. Given that genes with greater control will experience stronger selection and that the probability of fixation is proportional to the selective advantage, we ask the following: 1) do upstream enzymes have majority flux control, 2) do enzymes with majority flux control accumulate adaptive substitutions, and 3) are upstream enzymes under higher selective constraint? First, by perturbing the enzymes in the aliphatic glucosinolate pathway in Arabidopsis thaliana with gene insertion lines, we show that flux control is focused in the first enzyme in the pathway. Next, by analyzing several sequence signatures of selection, we also show that this enzyme is the only one in the pathway that shows convincing evidence of selection. Our results support the hypothesis that natural selection preferentially acts on enzymes with high flux control.
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61
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Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nat Commun 2012; 3:1319. [DOI: 10.1038/ncomms2333] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/26/2012] [Indexed: 11/08/2022] Open
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Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana. PLoS Genet 2012; 8:e1002923. [PMID: 22969436 PMCID: PMC3435251 DOI: 10.1371/journal.pgen.1002923] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 07/13/2012] [Indexed: 11/19/2022] Open
Abstract
Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. Cadmium (Cd) is a potentially toxic metal pollutant that threatens food quality and human health in many regions of the world. Plants have evolved mechanisms for the acquisition of essential metals such as zinc and iron from the soil. Though often quite specific, such mechanisms can also lead to the accumulation of Cd by plants. Understanding natural variation in the processes that contribute to Cd accumulation in food crops could help minimize the human health risk posed. We have discovered that DNA sequence changes at a single gene, which encodes the Heavy Metal ATPase 3 (HMA3), drives the variation in Cd accumulation we observe in a world-wide sample of Arabidopsis thaliana. We identified 10 major HMA3 protein variants, of which five contribute to reduce Cd accumulation in leaves of A. thaliana.
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63
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Schmickl R, Paule J, Klein J, Marhold K, Koch MA. The evolutionary history of the Arabidopsis arenosa complex: diverse tetraploids mask the Western Carpathian center of species and genetic diversity. PLoS One 2012; 7:e42691. [PMID: 22880083 PMCID: PMC3411824 DOI: 10.1371/journal.pone.0042691] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 07/11/2012] [Indexed: 01/02/2023] Open
Abstract
The Arabidopsis arenosa complex is closely related to the model plant Arabidopsis thaliana. Species and subspecies in the complex are mainly biennial, predominantly outcrossing, herbaceous, and with a distribution range covering most parts of latitudes and the eastern reaches of Europe. In this study we present the first comprehensive evolutionary history of the A. arenosa species complex, covering its natural range, by using chromosome counts, nuclear AFLP data, and a maternally inherited marker from the chloroplast genome [trnL intron (trnL) and trnL/F intergenic spacer (trnL/F-IGS) of tRNA(Leu) and tRNA(Phe), respectively]. We unravel the broad-scale cytogeographic and phylogeographic patterns of diploids and tetraploids. Diploid cytotypes were exclusively found on the Balkan Peninsula and in the Carpathians while tetraploid cytotypes were found throughout the remaining distribution range of the A. arenosa complex. Three centers of genetic diversity were identified: the Balkan Peninsula, the Carpathians, and the unglaciated Eastern and Southeastern Alps. All three could have served as long-term refugia during Pleistocene climate oscillations. We hypothesize that the Western Carpathians were and still are the cradle of speciation within the A. arenosa complex due to the high species number and genetic diversity and the concurrence of both cytotypes there.
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Affiliation(s)
- Roswitha Schmickl
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Juraj Paule
- Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Johannes Klein
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Karol Marhold
- Department of Vascular Plant Taxonomy, Institute of Botany SAS, Bratislava, Slovakia
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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Lasky JR, Des Marais DL, McKay JK, Richards JH, Juenger TE, Keitt TH. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate. Mol Ecol 2012; 21:5512-29. [PMID: 22857709 DOI: 10.1111/j.1365-294x.2012.05709.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well-studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large-scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.
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Affiliation(s)
- Jesse R Lasky
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78712-0253, USA.
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65
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Tsuchimatsu T, Kaiser P, Yew CL, Bachelier JB, Shimizu KK. Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica. PLoS Genet 2012; 8:e1002838. [PMID: 22844253 PMCID: PMC3405996 DOI: 10.1371/journal.pgen.1002838] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/04/2012] [Indexed: 01/01/2023] Open
Abstract
The evolutionary transition from outcrossing to self-fertilization (selfing) through the loss of self-incompatibility (SI) is one of the most prevalent events in flowering plants, and its genetic basis has been a major focus in evolutionary biology. In the Brassicaceae, the SI system consists of male and female specificity genes at the S-locus and of genes involved in the female downstream signaling pathway. During recent decades, much attention has been paid in particular to clarifying the genes responsible for the loss of SI. Here, we investigated the pattern of polymorphism and functionality of the female specificity gene, the S-locus receptor kinase (SRK), in allotetraploid Arabidopsis kamchatica. While its parental species, A. lyrata and A. halleri, are reported to be diploid and mainly self-incompatible, A. kamchatica is self-compatible. We identified five highly diverged SRK haplogroups, found their disomic inheritance and, for the first time in a wild allotetraploid species, surveyed the geographic distribution of SRK at the two homeologous S-loci across the species range. We found intact full-length SRK sequences in many accessions. Through interspecific crosses with the self-incompatible and diploid congener A. halleri, we found that the female components of the SI system, including SRK and the female downstream signaling pathway, are still functional in these accessions. Given the tight linkage and very rare recombination of the male and female components on the S-locus, this result suggests that the degradation of male components was responsible for the loss of SI in A. kamchatica. Recent extensive studies in multiple Brassicaceae species demonstrate that the loss of SI is often derived from mutations in the male component in wild populations, in contrast to cultivated populations. This is consistent with theoretical predictions that mutations disabling male specificity are expected to be more strongly selected than mutations disabling female specificity, or the female downstream signaling pathway.
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Affiliation(s)
| | | | | | | | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, Institute of Plant Biology, and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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Poormohammad Kiani S, Trontin C, Andreatta M, Simon M, Robert T, Salt DE, Loudet O. Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient. PLoS Genet 2012; 8:e1002814. [PMID: 22807689 PMCID: PMC3395621 DOI: 10.1371/journal.pgen.1002814] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/21/2012] [Indexed: 11/24/2022] Open
Abstract
As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness. Plants are studied for their ability to adapt to their environment and especially to the physical constraints to which they are subjected. It is expected that they evolve in promoting genetic variants favorable under their native conditions, which could lead to negative consequences in other conditions. One approach to study the mechanisms and dynamics of these adaptations is to discover genetic variants that control potentially adaptive traits, and to study directly these variants in wild populations to try to reveal their evolutionary trajectory. We have identified a new polymorphism in a gene coding for a transporter of molybdenum (an essential micronutrient for the plant) in Arabidopsis; we show that this variant has strong phenotypic consequences at the level of plant growth and reproductive value in specific conditions, and that it explains a lot of the species diversity for these traits. Especially, the variant is associated with a clear negative effect under molybdenum-deficient conditions (caused by soil acidity) and with a subtle positive effect under molybdenum-plethoric conditions. Interestingly, the landscape distribution of the variant is not random among Asian populations and correlates well with the availability of molybdenum in the soil at the precise location where the plants are growing in the wild.
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Affiliation(s)
| | | | - Matthew Andreatta
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana United States of America
| | - Matthieu Simon
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Versailles, France
| | - Thierry Robert
- Laboratoire d'Ecologie, Systématique, et Evolution, Université Paris-Sud XI, Orsay, France
| | - David E. Salt
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana United States of America
| | - Olivier Loudet
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Versailles, France
- * E-mail:
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67
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Ågren J, Schemske DW. Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range. THE NEW PHYTOLOGIST 2012; 194:1112-1122. [PMID: 22432639 DOI: 10.1111/j.1469-8137.2012.04112.x] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To quantify adaptive differentiation in the model plant Arabidopsis thaliana, we conducted reciprocal transplant experiments for five years between two European populations, one near the northern edge of the native range (Sweden) and one near the southern edge (Italy). We planted seeds (years 1-3) and seedlings (years 4-5), and estimated fitness as the number of fruits produced per seed or seedling planted. In eight of the 10 possible site × year comparisons, the fitness of the local population was significantly higher than that of the nonlocal population (3.1-22.2 times higher at the southern site, and 1.7-3.6 times higher at the northern site); in the remaining two comparisons no significant difference was recorded. At both sites, the local genotype had higher survival than the nonlocal genotype, and at the Italian site, the local genotype also had higher fecundity. Across years, the relative survival of the Italian genotype at the northern site decreased with decreasing winter soil temperature. The results provide evidence of strong adaptive differentiation between natural populations of A. thaliana and indicate that differences in tolerance to freezing contributed to fitness variation at the northern site. In ongoing work, we explore the functional and genetic basis of this adaptive differentiation.
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Affiliation(s)
- Jon Ågren
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Douglas W Schemske
- Department of Plant Biology and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
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Bloomer RH, Juenger TE, Symonds VV. Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana. Mol Ecol 2012; 21:3501-15. [PMID: 22625421 DOI: 10.1111/j.1365-294x.2012.05630.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ultimate understanding of how biological diversity arises, is maintained, and lost depends on identifying the genes responsible. Although a good deal has been discovered about gene function over the past few decades, far less is understood about gene effects, that is, how natural variation in a gene contributes to natural variation in phenotypes. Trichome density in Arabidopsis thaliana is an ideal trait for studies of natural molecular and phenotypic variation, as trichome initiation is genetically well-characterized and trichome density is highly variable in and among natural populations. Here, we show that variation at GLABRA1 (GL1), an R2R3 MYB transcription factor gene, which has a role in trichome initiation, has qualitative and likely quantitative effects on trichome density in natural accessions of A. thaliana. Specifically, we characterize four independent loss-of-function alleles for GL1, each of which yields a glabrous phenotype. Further, we find that a pattern of common polymorphisms confined to the GL1 locus is associated with quantitative variation for trichome density. While mutations resulting in a glabrous phenotype are primarily coding changes, the pattern resulting in quantitative variation spans both coding and regulatory regions. These data show that GL1 is an important source of trichome density variation within A. thaliana and, along with recent reports, suggest that the TTG1 epidermal cell fate pathway generally may be the key molecular genetic source of natural trichome density variation and an important model for the study of molecular evolution.
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Affiliation(s)
- R H Bloomer
- Institute of Molecular BioSciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
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69
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Huang CC, Hung KH, Wang WK, Ho CW, Huang CL, Hsu TW, Osada N, Hwang CC, Chiang TY. Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae). Gene 2012; 499:194-201. [DOI: 10.1016/j.gene.2012.02.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/31/2012] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. PLANT PHYSIOLOGY 2012; 158:2-22. [PMID: 22147517 PMCID: PMC3252104 DOI: 10.1104/pp.111.189845] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Affiliation(s)
- Detlef Weigel
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany.
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71
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Španiel S, Marhold K, Passalacqua NG, Zozomová-Lihová J. Intricate variation patterns in the diploid-polyploid complex of Alyssum montanum-A. repens (Brassicaceae) in the Apennine Peninsula: evidence for long-term persistence and diversification. AMERICAN JOURNAL OF BOTANY 2011; 98:1887-904. [PMID: 22052961 DOI: 10.3732/ajb.1100147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The Apennine Peninsula, one of the three peninsulas of the European Mediterranean, is an important hotspot of genetic and species diversity, but studies devoted to plant evolution are still very scarce in this region. We studied the diploid-polyploid complex of Alyssum montanum-A. repens, focusing on Apennine and adjacent southwestern Alpine populations from southeastern France, with the aim of examining their taxonomic position and evolutionary patterns. METHODS We employed AFLP markers and cpDNA sequences, along with cytotype determination using flow cytometry, and a multivariate morphometric approach. KEY RESULTS The Italian and French populations formed two well-delimited groupings within the studied complex that were, in contrast to previous taxonomic treatments, clearly distinct from A. montanum. Populations from southeastern France represent A. orophilum, a previously described but abandoned species. Those from central and southern Italy correspond to A. diffusum, exhibiting high, geographically structured variation (central Apennines, Gargano, and southern Apennines/Calabria). This pattern coincides with hotspot refugial regions, in congruence with the "refugia-within-refugia" hypothesis, and is reflected here in the recognition of three subspecies within A. diffusum. CONCLUSIONS We provide evidence for the presence of Mediterranean refugia for the studied Alyssum montanum-A. repens complex located in central and southern Italy, which, however, did not contribute to the postglacial colonization of Central Europe. Past extinctions, genetic bottlenecks, and recent expansion were inferred in Central Europe, while long-term accumulation of diversity as well as polyploidization occurred in the Apennines.
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Affiliation(s)
- Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic.
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Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biol 2011; 9:64. [PMID: 21951689 PMCID: PMC3193812 DOI: 10.1186/1741-7007-9-64] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 09/27/2011] [Indexed: 11/12/2022] Open
Abstract
Background The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene MSH1 (MutS 1 homolog), lending itself to detailed study of de novo mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution. Results We obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and msh1 mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the msh1 mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. De novo asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes. Conclusions Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.
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73
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Hou Y, Lou A. Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae). PLoS One 2011; 6:e24497. [PMID: 21909437 PMCID: PMC3164725 DOI: 10.1371/journal.pone.0024497] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 08/11/2011] [Indexed: 11/24/2022] Open
Abstract
Aims Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. Methods Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. Important Findings The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.
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Affiliation(s)
- Yan Hou
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Anru Lou
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing, China
- * E-mail:
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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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75
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Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 2011; 43:956-63. [PMID: 21874002 DOI: 10.1038/ng.911] [Citation(s) in RCA: 629] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 07/26/2011] [Indexed: 12/20/2022]
Abstract
The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
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76
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Qiu S, Zeng K, Slotte T, Wright S, Charlesworth D. Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species. Genome Biol Evol 2011; 3:868-80. [PMID: 21856647 PMCID: PMC3296465 DOI: 10.1093/gbe/evr085] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (N(e)) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in N(e). Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.
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Affiliation(s)
- Suo Qiu
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-Sen University, Guangzhou, China
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77
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Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. Source verification of mis-identified Arabidopsis thaliana accessions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:554-66. [PMID: 21481029 DOI: 10.1111/j.1365-313x.2011.04606.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A major strength of Arabidopsis thaliana as a model lies in the availability of a large number of naturally occurring inbred lines. Recent studies of A. thaliana population structure, using thousands of accessions from stock center and natural collections, have revealed a robust pattern of isolation by distance at several spatial scales, such that genetically identical individuals are generally found close to each other. However, some individual accessions deviate from this pattern. While some of these may be the products of rare long-distance dispersal events, many deviations may be the result of mis-identification, in the sense that the data regarding location of origin data are incorrect. Here, we aim to identify such discrepancies. Of the 5965 accessions examined, we conclude that 286 deserve special attention as being potentially mis-identified. We describe these suspicious accessions and their possible origins, and advise caution with regard to their use in experiments in which accurate information on geographic origin is important. Finally, we discuss possibilities for maintaining the integrity of stock lines.
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78
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Strasburg JL, Kane NC, Raduski AR, Bonin A, Michelmore R, Rieseberg LH. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Mol Biol Evol 2011; 28:1569-80. [PMID: 20952500 PMCID: PMC3080132 DOI: 10.1093/molbev/msq270] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.
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Natural variation in Arabidopsis thaliana revealed a genetic network controlling germination under salt stress. PLoS One 2010; 5:e15198. [PMID: 21188145 PMCID: PMC3004798 DOI: 10.1371/journal.pone.0015198] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 10/29/2010] [Indexed: 11/20/2022] Open
Abstract
Plant responses to environmental stresses are polygenic and complex traits. In this study quantitative genetics using natural variation in Arabidopsis thaliana was used to investigate the genetic architecture of plant responses to salt stress. Eighty seven A. thaliana accessions were screened and showed a large variation for root development and seed germination under 125 and 200 mM NaCl, respectively. Twenty two quantitative trait loci for these traits have been detected by phenotyping two recombinants inbred line populations, Sha x Col and Sha x Ler. Four QTLs controlling germination under salt were detected in the Sha x Col population. Interestingly, only one allelic combination at these four QTLs inhibits germination under salt stress, implying strong epistatic interactions between them. In this interacting context, we confirmed the effect of one QTL by phenotyping selected heterozygous inbred families. We also showed that this QTL is involved in the control of germination under other stress conditions such as KCl, mannitol, cold, glucose and ABA. Our data highlights the presence of a genetic network which consists of four interacting QTLs and controls germination under limiting environmental conditions.
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80
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Wilczek AM, Burghardt LT, Cobb AR, Cooper MD, Welch SM, Schmitt J. Genetic and physiological bases for phenological responses to current and predicted climates. Philos Trans R Soc Lond B Biol Sci 2010; 365:3129-47. [PMID: 20819808 PMCID: PMC2981944 DOI: 10.1098/rstb.2010.0128] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We are now reaching the stage at which specific genetic factors with known physiological effects can be tied directly and quantitatively to variation in phenology. With such a mechanistic understanding, scientists can better predict phenological responses to novel seasonal climates. Using the widespread model species Arabidopsis thaliana, we explore how variation in different genetic pathways can be linked to phenology and life-history variation across geographical regions and seasons. We show that the expression of phenological traits including flowering depends critically on the growth season, and we outline an integrated life-history approach to phenology in which the timing of later life-history events can be contingent on the environmental cues regulating earlier life stages. As flowering time in many plants is determined by the integration of multiple environmentally sensitive gene pathways, the novel combinations of important seasonal cues in projected future climates will alter how phenology responds to variation in the flowering time gene network with important consequences for plant life history. We discuss how phenology models in other systems--both natural and agricultural--could employ a similar framework to explore the potential contribution of genetic variation to the physiological integration of cues determining phenology.
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Affiliation(s)
- A M Wilczek
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
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81
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Lewandowska-Sabat AM, Fjellheim S, Rognli OA. Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes. Mol Ecol 2010; 19:4753-64. [PMID: 20887360 DOI: 10.1111/j.1365-294x.2010.04840.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genetic diversity and population structure of Arabidopsis thaliana populations from Norway were studied and compared to a worldwide sample of A. thaliana to investigate the demographic history and elucidate possible colonization routes of populations at the northernmost species limit. We genotyped 282 individuals from 31 local populations using 149 single nucleotide polymorphism markers. A high level of population subdivision (F(ST) = 0.85 ± 0.007) was found indicating that A. thaliana is highly structured at the regional level. Significant relationships between genetic and geographical distances were found, suggesting an isolation by distance mode of evolution. Genetic diversity was much lower, and the level of linkage disequilibrium was higher in populations from the north (65-68°N) compared to populations from the south (59-62°N); this is consistent with a northward expansion pattern. A neighbour-joining tree showed that populations from northern Norway form a separate cluster, while the remaining populations are distributed over a few minor clusters. Minimal gene flow seems to have occurred between populations in different regions, especially between the geographically distant northern and southern populations. Our data suggest that northern populations represent a homogenous group that may have been established from a few founders during northward expansions, while populations in the central part of Norway constitute an admixed group established by founders of different origins, most probably as a result of human-mediated gene flow. Moreover, Norwegian populations appeared to be homogenous and isolated compared to a worldwide sample of A. thaliana, but they are still grouped with Swedish populations, which may indicate common colonization histories.
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Affiliation(s)
- A M Lewandowska-Sabat
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
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Moison M, Roux F, Quadrado M, Duval R, Ekovich M, Lê DH, Verzaux M, Budar F. Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:728-38. [PMID: 20553420 DOI: 10.1111/j.1365-313x.2010.04275.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In recent years Arabidopsis thaliana has become a model species for genomic variability and adaptation studies. Although impressive quantities of data have been gathered on the nuclear genomic diversity of this species, little has been published regarding its cytoplasmic diversity. We analyzed the diversity of plastid (pt) and mitochondrial (mt) genomes among 95 accessions, covering most Arabidopsis geographic origins. Four intergenic regions of the pt genome were sequenced, and a total of 68 polymorphisms and 65 pt haplotypes were identified. Several strategies were developed to identify mt polymorphisms among a subset of 14 accessions. Fifteen polymorphisms were further developed as PCR-based markers and used to analyze the whole set of 95 accessions. Using statistical parsimony, we built pt and mt phylogenetic networks of haplotype groups. To root the pt network, the pt intergenic regions of two related Arabidopsis species, Arabidopsis lyrata and Arabidopsis arenosa, were also sequenced. The mt and pt phylogenies are highly congruent and could be combined into a single cytoplasmic phylogeny. To estimate whether co-adaptation between nuclear and cytoplasmic genomes exists in A. thaliana, we tested the germination capacity in challenging conditions of 27 pairs of reciprocal F(2) families. We found that the cytoplasm donor had a significant effect on the germination capacity of some F(2) families.
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Affiliation(s)
- Michaël Moison
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, Versailles Cedex, France
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Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gene array. Genetics 2010; 186:263-76. [PMID: 20551443 DOI: 10.1534/genetics.110.116392] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tandemly arrayed genes that belong to gene families characterize genomes of many organisms. Gene duplication and subsequent relaxation of selection can lead to the establishment of paralogous cluster members that may evolve along different trajectories. Here, we report on the structural variation in MADS AFFECTING FLOWERING 2 (MAF2) gene, one member of the tandemly duplicated cluster of MADS-box-containing transcription factors in Arabidopsis thaliana. The altered gene structure at the MAF2 locus is present as a moderate-frequency polymorphism in Arabidopsis and leads to the extensive diversity in transcript patterns due to alternative splicing. Rearrangements at the MAF2 locus are associated with an early flowering phenotype in BC(5) lines. The lack of suppression of flowering time in a MAF2-insertion line expressing the MAF2-specific artificial miRNA suggests that these MAF2 variants are behaving as loss-of-function alleles. The variation in gene architecture is also associated with segregation distortion, which may have facilitated the spread and the establishment of the corresponding alleles throughout the Eurasian range of the A. thaliana population.
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84
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Lihová J, Kudoh H, Marhold K. Genetic structure and phylogeography of a temperate-boreal herb, Cardamine scutata (Brassicaceae), in northeast Asia inferred from AFLPs and cpDNA haplotypes. AMERICAN JOURNAL OF BOTANY 2010; 97:1058-1070. [PMID: 21622475 DOI: 10.3732/ajb.0900361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Studies on genetic structure of plant populations help us understand the history of local flora and vegetation. In this study, we focus on the temperate-boreal herb Cardamine scutata from northeast Asia, an area with scarce phylogeographic studies. We explore patterns of genetic variation within this species, with an aim to infer its (post-) glacial history with reference to colonization routes and migrations via land bridges. • METHODS We analyzed 46 populations sampled in Japan, Kamchatka, and Korea using AFLP and cpDNA sequence data. • KEY RESULTS Two intraspecific genetic groups were resolved, distributed in the northeastern and southwestern part of the study area, most likely reflecting lineages isolated from each other during (at least) the last glaciation. A zone of secondary contacts was found in central/northern Honshu, and a few cases of long-distance dispersal were observed. We detected efficient gene flow across the marine straits, supporting the role of land bridges created by sea level decline during the last glacial period. The cpDNA data indicated extensive recent expansion and diversification within both lineages. We inferred recent colonization of Kamchatka from Hokkaido, associated with genetic impoverishment. • CONCLUSIONS The pattern of north-south genetic differentiation found in C. scutata is rather common among several other plant species studied in Japan, despite their distinct biological features. We assume that different processes and factors may have brought about this similarity. Overall, this study contributes to better understanding of the biogeography of northeast Asia.
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Affiliation(s)
- Judita Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
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85
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Willis CG, Brock MT, Weinig C. Genetic variation in tolerance of competition and neighbour suppression in Arabidopsis thaliana. J Evol Biol 2010; 23:1412-24. [PMID: 20492094 DOI: 10.1111/j.1420-9101.2010.02003.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Intraspecific competitive interactions can profoundly influence phenotypic evolution. However, prior studies have rarely evaluated the evolutionary potential of the two components of competitive ability, tolerance of competition and suppression of neighbours. Here, we grow a set of 20 Arabidopsis thaliana recombinant inbred lines in three competitive treatments (noncompetitive, intra-genotypic competition and inter-genotypic competition) to examine if there is genetic variation for the components of competitive ability and whether neighbour relatedness has an effect on fitness. We find evidence for genetic variation in tolerance of competition and neighbour suppression and that these two competitive strategies are correlated, such that genotypes that tolerate competition will also strongly suppress neighbours. We further observe that the effect of neighbour relatedness on fitness of target individuals depends on neighbour identity, i.e. whether target individuals perform better when competing against self vs. nonself individuals depends on the genotypic identity of the nonself neighbour. The results are particularly relevant to evolutionary responses under multi-level selection.
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Affiliation(s)
- C G Willis
- Department of Biology, Duke University, Durham, NC, USA
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86
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Kronholm I, Loudet O, de Meaux J. Influence of mutation rate on estimators of genetic differentiation--lessons from Arabidopsis thaliana. BMC Genet 2010; 11:33. [PMID: 20433762 PMCID: PMC2888750 DOI: 10.1186/1471-2156-11-33] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 05/01/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high. Alternative estimators of F(ST) have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q(ST), a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators. RESULTS If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Phi(ST) depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q(ST) has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology. CONCLUSIONS We find that alternative measures of differentiation like F'(ST) and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be taken as evidence for homogenising selection as has been traditionally thought.
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Affiliation(s)
- Ilkka Kronholm
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France
| | - Juliette de Meaux
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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87
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Liao PC, Kuo DC, Lin CC, Ho KC, Lin TP, Hwang SY. Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehirae Hay. (Lauraceae) in Taiwan inferred from nuclear genes. BMC Evol Biol 2010; 10:124. [PMID: 20433752 PMCID: PMC2880300 DOI: 10.1186/1471-2148-10-124] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Accepted: 04/30/2010] [Indexed: 11/23/2022] Open
Abstract
Background Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species. Results Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples. Conclusions Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.
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Affiliation(s)
- Pei-Chun Liao
- Department of Life Science, Pingtung University of Science and Technology, Pingtung, Taiwan
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88
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Schmickl R, Jørgensen MH, Brysting AK, Koch MA. The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier. BMC Evol Biol 2010; 10:98. [PMID: 20377907 PMCID: PMC2858744 DOI: 10.1186/1471-2148-10-98] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 04/08/2010] [Indexed: 02/28/2023] Open
Abstract
BACKGROUND The genomes of higher plants are, on the majority, polyploid, and hybridisation is more frequent in plants than in animals. Both polyploidisation and hybridisation contribute to increased variability within species, and may transfer adaptations between species in a changing environment. Studying these aspects of evolution within a diversified species complex could help to clarify overall spatial and temporal patterns of plant speciation. The Arabidopsis lyrata complex, which is closely related to the model plant Arabidopsis thaliana, is a perennial, outcrossing, herbaceous species complex with a circumpolar distribution in the Northern Hemisphere as well as a disjunct Central European distribution in relictual habitats. This species complex comprises three species and four subspecies, mainly diploids but also several tetraploids, including one natural hybrid. The complex is ecologically, but not fully geographically, separated from members of the closely related species complex of Arabidopsis halleri, and the evolutionary histories of both species compexes have largely been influenced by Pleistocene climate oscillations. RESULTS Using DNA sequence data from the nuclear encoded cytosolic phosphoglucoisomerase and Internal Transcribed Spacers 1 and 2 of the ribosomal DNA, as well as the trnL/F region from the chloroplast genome, we unravelled the phylogeography of the various taxonomic units of the A. lyrata complex. We demonstrate the existence of two major gene pools in Central Europe and Northern America. These two major gene pools are constructed from different taxonomic units. We also confirmed that A. kamchatica is the allotetraploid hybrid between A. lyrata and A. halleri, occupying the amphi-Beringian area in Eastern Asia and Northern America. This species closes the large distribution gap of the various other A. lyrata segregates. Furthermore, we revealed a threefold independent allopolyploid origin of this hybrid species in Japan, China, and Kamchatka. CONCLUSIONS Unglaciated parts of the Eastern Austrian Alps and arctic Eurasia, including Beringia, served as major glacial refugia of the Eurasian A. lyrata lineage, whereas A. halleri and its various subspecies probably survived in refuges in Central Europe and Eastern Asia with a large distribution gap in between. The North American A. lyrata lineage probably survived the glaciation in the southeast of North America. The dramatic climatic changes during glaciation and deglaciation cycles promoted not only secondary contact and formation of the allopolyploid hybrid A. kamchatica, but also provided the environment that allowed this species to fill a large geographic gap separating the two genetically different A. lyrata lineages from Eurasia and North America. With our example focusing on the evolutionary history of the A. lyrata species complex, we add substantial information to a broad evolutionary framework for future investigations within this emerging model system in molecular and evolutionary biology.
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Affiliation(s)
- Roswitha Schmickl
- Heidelberg University, Heidelberg Institute of Plant Sciences, Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Marte H Jørgensen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Marcus A Koch
- Heidelberg University, Heidelberg Institute of Plant Sciences, Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
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89
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Bomblies K, Yant L, Laitinen RA, Kim ST, Hollister JD, Warthmann N, Fitz J, Weigel D. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana. PLoS Genet 2010; 6:e1000890. [PMID: 20361058 PMCID: PMC2845663 DOI: 10.1371/journal.pgen.1000890] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 03/01/2010] [Indexed: 11/19/2022] Open
Abstract
As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.
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Affiliation(s)
- Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Levi Yant
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Roosa A. Laitinen
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sang-Tae Kim
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jesse D. Hollister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Joffrey Fitz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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90
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Ansell SW, Stenøien HK, Grundmann M, Schneider H, Hemp A, Bauer N, Russell SJ, Vogel JC. Population structure and historical biogeography of European Arabidopsis lyrata. Heredity (Edinb) 2010; 105:543-53. [PMID: 20160758 DOI: 10.1038/hdy.2010.10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Understanding the natural history of model organisms is important for the effective use of their genomic resources. Arabidopsis lyrata has emerged as a useful plant for studying ecological and evolutionary genetics, based on its extensive natural variation, sequenced genome and close relationship to A. thaliana. We studied genetic diversity across the entire range of European Arabidopsis lyrata ssp. petraea, in order to explore how population history has influenced population structure. We sampled multiple populations from each region, using nuclear and chloroplast genome markers, and combined population genetic and phylogeographic approaches. Within-population diversity is substantial for nuclear allozyme markers (mean P=0.610, A(e)=1.580, H(e)=0.277) and significantly partitioned among populations (F(ST)=0.271). The Northern populations have modestly increased inbreeding (F(IS)=0.163 verses F(IS)=0.093), but retain comparable diversity to central European populations. Bottlenecks are common among central and northern Europe populations, indicating recent demographic history as a dominant factor in structuring the European diversity. Although the genetic structure was detected at all geographic scales, two clear differentiated units covering northern and central European areas (F(CT) =0.155) were identified by Bayesian analysis and supported by regional pairwise F(CT) calculations. A highly similar geographic pattern was observed from the distribution of chloroplast haplotypes, with the dominant northern haplotypes absent from central Europe. We conclude A. l. petraea's cold-tolerance and preference for disturbed habitats enabled glacial survival between the alpine and Nordic glaciers in central Europe and an additional cryptic refugium. While German populations are probable peri-glacial leftovers, Eastern Austrian populations have diversity patterns possibly compatible with longer-term survival.
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Affiliation(s)
- S W Ansell
- Department of Botany, Natural History Museum, Cromwell Road, London, UK.
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91
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The scale of population structure in Arabidopsis thaliana. PLoS Genet 2010; 6:e1000843. [PMID: 20169178 PMCID: PMC2820523 DOI: 10.1371/journal.pgen.1000843] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 01/12/2010] [Indexed: 12/04/2022] Open
Abstract
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales. Much of the modern field of population genetics is premised on particular models of what an organism's population structure is and how it behaves. The classic models generally start with the idea of a single randomly mating population that has reached an evolutionary equilibrium. Many models relax some of these assumptions, allowing for phenomena such as assortative mating, discrete sub-populations with migration, self-fertilization, and sex-ratio distortion. Virtually all models, however, have as their core premise the notion that there exist classes of exchangeable individuals each of which represents an identical, independent sample from that class' distribution. For certain organisms, such as Drosophila melanogaster, these models do an excellent job of describing how populations work. For other organisms, such as humans, these models can be reasonable approximations but require a great deal of care in assembling samples and can begin to break down as sampling becomes locally dense. For the vast majority of organisms the applicability of these models has never been investigated.
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92
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Yin P, Kang J, He F, Qu LJ, Gu H. The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences. BMC PLANT BIOLOGY 2010; 10:22. [PMID: 20141622 PMCID: PMC2827422 DOI: 10.1186/1471-2229-10-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Accepted: 02/08/2010] [Indexed: 05/08/2023]
Abstract
BACKGROUND In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China. RESULTS A data set comprising 77 accessions of A. thaliana, including 19 field-collected Chinese accessions together with three related species (A. arenosa, A. suecica, and Olimarabidopsis cabulica) as the out-group, was compiled. The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). The estimated divergence time of the two MDHCs was about 0.39 mya. Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (pi) of 0.00169. The Chinese populations along the Yangtze River were characterized by five haplotypes, and the two accessions collected from the middle range of the Altai Mountains in China shared six specific variable sites. CONCLUSIONS The dimorphism in the chloroplast DNA could be due to founder effects during late Pleistocene glaciations and interglacial periods, although introgression cannot be ruled out. The Chinese populations along the Yangtze River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two accessions collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections.
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Affiliation(s)
- Ping Yin
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Juqing Kang
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Fei He
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Hongya Gu
- National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- National Plant Gene Research Center (Beijing), Beijing 100101, China
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93
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Katori T, Ikeda A, Iuchi S, Kobayashi M, Shinozaki K, Maehashi K, Sakata Y, Tanaka S, Taji T. Dissecting the genetic control of natural variation in salt tolerance of Arabidopsis thaliana accessions. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:1125-38. [PMID: 20080827 PMCID: PMC2826654 DOI: 10.1093/jxb/erp376] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Many accessions (ecotypes) of Arabidopsis have been collected. Although few differences exist among their nucleotide sequences, these subtle differences induce large genetic variation in phenotypic traits such as stress tolerance and flowering time. To understand the natural variability in salt tolerance, large-scale soil pot experiments were performed to evaluate salt tolerance among 350 Arabidopsis thaliana accessions. The evaluation revealed a wide variation in the salt tolerance among accessions. Several accessions, including Bu-5, Bur-0, Ll-1, Wl-0, and Zu-0, exhibited marked stress tolerance compared with a salt-sensitive experimental accession, Col-0. The salt-tolerant accessions were also evaluated by agar plate assays. The data obtained by the large-scale assay correlated well with the results of a salt acclimation (SA) assay, in which plants were transferred to high-salinity medium following placement on moderate-salinity medium for 7 d. Genetic analyses indicated that the salt tolerance without SA is a quantitative trait under polygenic control, whereas salt tolerance with SA is regulated by a single gene located on chromosome 5 that is common among the markedly salt-tolerant accessions. These results provide important information for understanding the mechanisms underlying natural variation of salt tolerance in Arabidopsis.
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Affiliation(s)
- Taku Katori
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Akiro Ikeda
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Satoshi Iuchi
- RIKEN Bioresource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masatomo Kobayashi
- RIKEN Bioresource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazuo Shinozaki
- RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kenji Maehashi
- Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Yoichi Sakata
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Shigeo Tanaka
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
- To whom correspondence should be addressed. E-mail:
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94
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Montesinos A, Tonsor SJ, Alonso-Blanco C, Picó FX. Demographic and genetic patterns of variation among populations of Arabidopsis thaliana from contrasting native environments. PLoS One 2009; 4:e7213. [PMID: 19787050 PMCID: PMC2746291 DOI: 10.1371/journal.pone.0007213] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 08/24/2009] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana. METHODOLOGY/PRINCIPAL FINDINGS We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected. CONCLUSIONS/SIGNIFICANCE Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations.
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Affiliation(s)
- Alicia Montesinos
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephen J. Tonsor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F. Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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95
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Shimizu-Inatsugi R, Lihová J, Iwanaga H, Kudoh H, Marhold K, Savolainen O, Watanabe K, Yakubov VV, Shimizu KK. The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Mol Ecol 2009; 18:4024-48. [PMID: 19754506 DOI: 10.1111/j.1365-294x.2009.04329.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low-copy nuclear genes WER and CHS by designing homeolog-specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial-interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins.
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96
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VRANCKEN JÉRÔME, BROCHMANN CHRISTIAN, WESSELINGH RENATEA. How did an annual plant react to Pleistocene glaciations? Postglacial history of Rhinanthus angustifolius in Europe. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01261.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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97
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Lefebvre V, Kiani SP, Durand-Tardif M. A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana. Int J Mol Sci 2009; 10:3547-82. [PMID: 20111677 PMCID: PMC2812820 DOI: 10.3390/ijms10083547] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 08/04/2009] [Accepted: 08/11/2009] [Indexed: 11/30/2022] Open
Abstract
Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented.
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Affiliation(s)
- Valérie Lefebvre
- INRA/IJPB, Genetics and Plant Breeding Laboratory, UR 254, Route de St Cyr, F-78000 Versailles, France; E-Mails:
(V.L.);
(S.P.K.)
| | - Seifollah Poormohammad Kiani
- INRA/IJPB, Genetics and Plant Breeding Laboratory, UR 254, Route de St Cyr, F-78000 Versailles, France; E-Mails:
(V.L.);
(S.P.K.)
| | - Mylène Durand-Tardif
- INRA/IJPB, Genetics and Plant Breeding Laboratory, UR 254, Route de St Cyr, F-78000 Versailles, France; E-Mails:
(V.L.);
(S.P.K.)
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98
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Fogelqvist J, Niittyvuopio A, Agren J, Savolainen O, Lascoux M. Cryptic population genetic structure: the number of inferred clusters depends on sample size. Mol Ecol Resour 2009; 10:314-23. [PMID: 21565026 DOI: 10.1111/j.1755-0998.2009.02756.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5-10 individuals per population should be enough. The results argue for abandoning the concept of 'accessions' in partially selfing organisms.
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Affiliation(s)
- Johan Fogelqvist
- Evolutionary Functional Genomics, Department of Evolution, Genomics and Systematics, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden Department of Biology, University of Oulu, 90014 Oulu, Finland Plant Ecology, Department of Ecology and Evolution, Uppsala University, Villavägen 14, SE-752 36 Uppsala, Sweden
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99
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Kover PX, Rowntree JK, Scarcelli N, Savriama Y, Eldridge T, Schaal BA. Pleiotropic effects of environment-specific adaptation in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2009; 183:816-825. [PMID: 19594694 DOI: 10.1111/j.1469-8137.2009.02943.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Local adaptation may be important for the preservation of genetic diversity and the promotion of speciation. However, local adaptation may also constrain establishment in different environments. The consequences of local adaptation depend strongly on the pleiotropic effects of the genes involved in adaptation. Here, we investigated the pleiotropic effects of the genetic response to selection in outbred lines of Arabidopsis artificially selected to flower earlier under both winter- and spring-annual simulated conditions. The consequences of adaptation were evaluated by reciprocally transplanting selected and control lines between the two conditions. Selected lines always flower earlier than their controls, independent of growing conditions. However, selected lines, growing in the same condition in which they were selected, flower earlier than plants selected in the alternative environment. Plants selected to flower earlier in spring produce more fruits than controls when growing in the spring, and less fruits when growing in the winter; indicating that local adaptation has negative pleiotropic effects in another environment. Our results indicate that local adaptation can arise even when selection targets the same trait in the same direction. Furthermore, it suggests that adaptation under the two different environments can generate fitness trade-offs that can maintain genetic variation for flowering time.
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Affiliation(s)
- P X Kover
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
| | - J K Rowntree
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
| | - N Scarcelli
- IRD Montpellier, 911, Avenue Agropolis, F-34394 Montpellier cedex 5, France
| | - Y Savriama
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
| | - T Eldridge
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
| | - B A Schaal
- Department of Biology, Washington University, St. Louis, One Brookings Drive, St. Louis, MO 63110, USA
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100
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Durand E, Chen C, Francois O. Comment on 'On the inference of spatial structure from population genetics data'. Bioinformatics 2009; 25:1802-4; author reply 1805-6. [DOI: 10.1093/bioinformatics/btp337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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