adaptive genetic variation; adaptation; natural selection; alpine flora; environmental heterogeneity
Novikova Polina Yu, Hohmann Nora, Nizhynska Viktoria, Tsuchimatsu Takashi, Ali Jamshaid, Muir Graham, Guggisberg Alessia, Paape Tim, Schmid Karl, Fedorenko Olga M, Holm Svante, Säll Torbjörn, Schlötterer Christian, Marhold Karol, Widmer Alex, Sese Jun, Shimizu Kentaro K, Weigel Detlef, Krämer Ute, Koch Marcus A, Nordborg Magnus (2016), Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism., in Nature genetics
, 48(9), 1077-82.
Rellstab Christian, Gugerli Felix, Eckert Andrew J., Hancock Angela M., Holderegger Rolf (2015), A practical guide to environmental association analysis in landscape genomics, in Molecular Ecology
, 24(17), 4348-4370.
Stockenhuber Reinhard, Zoller Stefan, Shimizu-Inatsugi Rie, Gugerli Felix, Shimizu Kentaro K., Widmer Alex, Fischer Martin C. (2015), Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing, in PLOS One
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Tedder Andrew, Carleial Samuel, Gołębiewska Martyna, Kappel Christian, Shimizu Kentaro K, Stift Marc (2015), Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)., in PloS one
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Tedder A., Helling M., Pannell J. R., Shimizu-Inatsugi R., Kawagoe T., van Campen J., Sese J., Shimizu K. K. (2015), Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae), in Annals of Botany
, 115(5), 763-776.
Akama Satoru, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Sese Jun (2014), Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis., in Nucleic acids research
Seehausen Ole, Butlin Roger K., Keller Irene, Wagner Catherine E., Boughman Janette W., Hohenlohe Paul A., Peichel Catherine L., Saetre Glenn-Peter, Bank Claudia, Braennstroem Ake, Brelsford Alan, Clarkson Chris S., Eroukhmanoff Fabrice, Feder Jeffrey L., Fischer Martin C., Foote Andrew D., Franchini Paolo, Jiggins Chris D., Jones Felicity C., Lindholm Anna K., Lucek Kay, Maan Martine E., Marques David A., Martin Simon H., Matthews Blake (2014), Genomics and the origin of species, in NATURE REVIEWS GENETICS
, 15(3), 176-192.
Buehler Dominique, Brodbeck Sabine, Holderegger Rolf, Schnyder Elvira, Gugerli Felix (2014), Validation of outlier loci through replication in independent data sets: a test on Arabis alpina, in Ecology and Evolution
, 4(22), 4296-4306.
Andrew Rose L., Bernatchez Louis, Bonin Aurélie, Buerkle C. Alex, Carstens Bryan C., Emerson Brent C., Garant Dany, Giraud Tatiana, Kane Nolan C., Rogers Sean M., Slate Jon, Smith Harry, Sork Victoria L., Stone Graham N., Vines Timothy H., Waits Lisette, Widmer Alex, Rieseberg Loren H. (2013), A road map for molecular ecology, in Molecular Ecology
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Kobayashi Masaki J., Shimizu Kentaro K. (2013), Challenges in the studies on flowering time: interfaces between phenological researches and the molecular network of flowering genes, in Ecological Research
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Shimizu Kentaro K. (2013), Pollen, Pollen tube, Selfing, Pistil, Ovule, Endosperm, Embryo sac, Sporangium, Stamen, in Iwasa Yoh, Kuratani Shigeru, Saitou Naruya, Tsukaya Hirokazu (ed.), Iwanami, Tokyo, 1.
Fischer Martin C., Rellstab Christian, Tedder Andrew, Zoller Stefan, Gugerli Felix, Shimizu Kentaro K., Widmer Alex (2013), Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps, in Molecular Ecology
, 22(22), 5594-5607.
Manel Stéphanie, Holderegger Rolf (2013), Ten years of landscape genetics, in Trends in Ecology & Evolution
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Mandáková Terezie, Kovarík Ales, Zozomová-Lihová Judita, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Mummenhoff Klaus, Marhold Karol, Lysak Martin A (2013), The more the merrier: recent hybridization and polyploidy in cardamine., in The Plant cell
, 25(9), 3280-95.
Rellstab Christian, Zoller Stefan, Tedder Andrew, Gugerli Felix, Fischer Martin C. (2013), Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species, in PLoS One
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Parisod Christian, Holderegger Rolf (2012), Adaptive landscape genetics: pitfalls and benefits, in Molecular Ecology
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Manel S., Gugerli F., Thuiller W., Alvarez N., Legendre P., Holderegger F., Gielly L., Taberlet P., IntraBioDiv Consortium (2012), Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation, in Molecular Ecology
, 21(15), 3729-3738.
Shimizu Kentaro K. (2012), Chapter 12 Overview: the evolution of genes responsible for adaptation, in Morinaga Shinichi, Kudoh Hiroshi (ed.), Kyoritsu, Tokyo, 189-196.
Shimizu-Inatsugi Rie, Shimizu Kentaro K. (2012), Chapter 16: Genome duplication: speciation and ecogenomics of polyploid species, in Morinaga Shinichi, Kudoh Hiroshi (ed.), Kyoritsu, Tokyo, 246-262.
Jay Flora, Manel Stéphanie, Alvarez Nadir, Durand Eric Y., Thuiller Wilfried, Holderegger Rolf, Taberlet Pierre, François Olivier (2012), Forecasting changes in population genetic structure of Alpine plants in response to global warming, in Molecular Ecology
, 21, 2354-2368.
Tsuchimatsu Takashi, Kaiser Pascal, Yew Chow-Lih, Bachelier Julien, Shimizu Kentaro (2012), Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica, in PLoS Genetics
, 8(7), e1002838.
Kawagoe T., Shimizu K.K., Kakutani T., Kudoh H. (2011), Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches, in PLoS One
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Shimizu K.K., Kudoh H., Kobayashi M.J. (2011), Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology, in Annals of Botany
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Holderegger R, Buehler D, Gugerli F, Manel S (2010), Landscape genetics of plants, in TRENDS IN PLANT SCIENCE
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Zulliger Deborah, Schnyder Elvira, Gugerli Felix, Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species, in Molecular Ecology
, 22(6), 1626-1639.
Liu Xuanyu, Widmer Alex, Genome-wide Comparative Analysis of the GRAS Gene Family in Populus, Arabidopsis and Rice, in Plant Molecular Biology Reporter
Rellstab Christian, Fischer Martin C., Zoller Stefan, Graf René, Tedder Andrew, Shimizu Kentaro K., Widmer Alex, Holderegger Rolf, Gugerli Felix, Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri, in Heredity
Natural variation is ubiqitous and forms the target of selection. In sessile organisms, such as plants, strong selection can be imposed by environmental conditions, both biotic and abiotic. These environmental conditions can change over small geographic scales in some landscapes, such as mountain areas and the Alps. Here, sites with contrasting environmental conditions, brought about for example by differences in exposure, snow cover or bedrock, are often located in close physical proximity and within the reach of contemporary gene-flow. In the face of such environmental heterogeneity, natural variation is essential for the adaptation of plants to their environment.The genetic basis of adaptation is one of the central and most hotly debated topics in evolutionary biology. Recent theoretical and empirical work has shed new light on the number and relative effects of genes underlying adaptation. In contrast to earlier views of adaptation being a slow process mediated by large numbers of genes of minor effect, it has become clear that adaptation is often due to a finite number of genes, some of which are of major effect. Empirical studies on adaptation and its underlying adaptive variation in plants have used both forward and reverse genetic approaches, mostly in model organisms, to identify candidate genes for adaptation. The current adaptive value of such candidate genes can in principle be assessed experimentally in transplant experiments. Yet, this ecological work has often been neglected or carried out under highly artificial conditions, mainly because of a lack of collaboration between ecologists and plant molecular biologists. Only a small number of studies, mostly on the model plant species Arabidopsis thaliana, have carefully investigated the adaptive value of candidate genes in different, ecologically realistic environments. These studies have provided new insights into the genetic basis of adaptation, and the role of epistasis, pleiotropy and gene-by-environment interactions in the maintenance of adaptive genetic variation.The presented project builds on the insights gained from such studies to investigate adaptation to environmental heterogeneity from an ecological, landscape genetic and functional genomic perspective. Environmental heterogeneity is pronounced in alpine areas, where conditions often change over small geographic distances as a consequence of differences for example in altitude, exposition, bedrock, snow cover or water availability. Alpine areas are centers of biodiversity in Europe and around the world, and are particularly affected by climate change, yet plant species native to these alpine areas remain poorly investigated with respect to the genetics of adaptation.We here propose to investigate adaptive genetic variation in the model plant species Arabidopsis thaliana and several related species with contrasting mating systems, life histories or altitudinal distributions. We will assess natural genetic variation at 500 loci in multiple populations of six plant species collected in a landscape with high environmental heterogeneity. The 500 loci include 100 candidate genes from A. thaliana and 400 randomly chosen genes that provide approximately homogeneous genome coverage in A. thaliana. This comparative approach is supported by the application of ultra-high throughput sequencing technology, which allows for genome-wide analyses of genetic variation in multiple species.The overarching questions we address are:1.What is the genetic basis of adaptation to environmental heterogeneity ?2.Do the same genes contribute to adaptation in related species ?3.What is the adaptive value of candidate genes ?With respect to these questions we hypothesize that 1.major genes contribute substantially to adaptation2.the same genes (or gene families) are involved in adaptation to the same enviornmental factor in different species3.some of the identified candidate genes cause above-average fitness in their native environment, but below- average fitness in other environments (i.e. display genetic trade-offs).Results from this study will provide new insights into the genetic basis of adaptation and the nature of adaptive genetic variation. This knowledge not only contributes to our understanding of natural variation and adaptation per se, but helps us to predict the effects of climate change on alpine plants and provides a scientifically informed foundation for the conservation of alpine plant biodiversity.