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Genomic divergence in plants: exploring the consequences of ecological adaptation for plant divergence and speciation

Titel Englisch Genomic divergence in plants: exploring the consequences of ecological adaptation for plant divergence and speciation
Gesuchsteller/in Widmer Alexander
Nummer 141260
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Institut für Integrative Biologie Departement Umweltwissenschaften ETHZ
Hochschule ETH Zürich - ETHZ
Hauptdisziplin Oekologie
Beginn/Ende 01.05.2012 - 30.04.2015
Bewilligter Betrag 564'000.00
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Alle Disziplinen (2)

Disziplin
Oekologie
Botanik

Keywords (5)

next-generation sequencing; ecological adaptation; natural selection; genomic divergence; speciation

Lay Summary (Englisch)

Lead
Lay summary

Studies of adaptation and speciation in plants are currently experiencing a major revolution. First, new sequencing technologies and conceptual advances open the doors to truly genome-wide analyses of adaptation, selection and genomic divergence in natural populations. Second, the concept of ecological speciation puts ecological adaptation into the spotlight of speciation research because it provides a direct link between ecological adaptation, divergent selection and speciation. To date, however, relevant examples of ecological speciation are scarce and empirical data on the genetic basis of the process is largely lacking.

This project explores the genetic basis of ecological adaptation and its consequences for genome-wide divergence in two plant study systems, an evolutionary young and an older system. The first study system is wild carnation, Dianthus sylvestris, where natural populations occur over a large altitudinal gradient in the Alps and show strong phenotypic divergence in the absence of neutral genetic divergence. This pattern suggests that divergent natural selection underlies phenotypic divergence and has led to ecological adaptation. The second study system includes two closely related Silene species, S. latifolia and S. dioica. These species show incomplete morphological, ecological and reproductive isolation and often hybridize upon secondary contact, yet remain distinct outside of contact zones.

The goal of this project is to gain a novel perspective on links between ecological adaptation, divergent selection and speciation in plants and to provide a test of the ecological speciation scenario. Developing a better understanding of the genetic basis of adaptation and its consequences for genomic divergence and speciation is not only of fundamental interest for basic science, but is also highly relevant for a society that is concerned about the consequences of climate change and associated threats to biodiversity.

Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment
Favre Adrien, Widmer Alex, Karrenberg Sophie (2016), Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment, in New Phytologist, 1-13.
Evolution of sex-biased gene expression in a dioecious plant
Zemp Niklaus, Tavares Raquel, Muyle Aline, Charlesworth Deborah, Marais Gabriel A. B., Widmer Alex (2016), Evolution of sex-biased gene expression in a dioecious plant, in Nature Plants, 2, 1-7.
Genomics and the challenging translation into conservation practice
Shafer Aaron, Fior Simone, Zielinski Piotr (2015), Genomics and the challenging translation into conservation practice, in Trends in Ecology & Evolution, 30(2), 78-87.
Genomics and the origin of species
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.
Identification of Internal Reference Genes for Gene Expression Normalization between the Two Sexes in Dioecious White Campion
Zemp Niklaus, Minder Aria, Widmer Alex (2014), Identification of Internal Reference Genes for Gene Expression Normalization between the Two Sexes in Dioecious White Campion, in Plos One, 9(3), e92893.
A road map for molecular ecology
Andrew Rose L., Bernatchez Louis, Bonin Aurelie, 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, 22(10), 2605-2626.
Patterns of molecular evolution in dioecious and non-dioecious Silene
Kaefer J., Talianova M., Bigot T., Michu E., Gueguen L., Widmer A., Zluvova J., Glemin S., Marais G. A. B. (2013), Patterns of molecular evolution in dioecious and non-dioecious Silene, in Journal of Evolutionary Biology, 26(2), 335-346.
Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes
Muyle Aline, Zemp Niklaus, Deschamps Clothilde, Mousset Sylvain, Widmer Alex, Marais Gabriel A. B. (2012), Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes, in Plos Biology, 10(4), 1308-1308.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Dr. Stefan Zoller, Genetic Diversity Centre, ETH Zurich Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Prof. Dr. Gabriel AB Marais, University of Lyon Frankreich (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Dr. Konrad Paszkiewicz, Wellcome Trust Biomedical Informatics Hub Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Prof. Dr. Andreas Erhardt, University of Basel Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Prof. Dr. Lars Hennig, Swedish University of Agricultural Sciences Schweden (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Dr. Ramon Dolcet, IRTA - Centre de Recerca en Agrigenòmica Spanien (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Seminar series Einzelvortrag Genomic signature of selection reveals loci involved in altitudinal adaptation in carnation (Dianthus) 15.03.2015 Norwegian Institute for Nature Research (NINA) - Trondheim, Norwegen Fior Simone;
Seminar series Einzelvortrag Genomic patterns reveal genes involved in altitudinal adaptation in carnation (Dianthus) 11.02.2015 National Research Council - Institute of Ecosystem Study (CNR - ISE) - Pallanza (VB), Italien Fior Simone;
Genomics of the Speciation Continuum Vortrag im Rahmen einer Tagung Towards a genomic perspective on altitudinal adaptation and divergence in two species of carnation (Dianthus) 04.09.2014 Fribourg, Schweiz Fior Simone;
Systems genetics and evolution of non-human (model) organism Poster Fungal infection induces sex-specific transcriptional changes in a dioecious host plant 19.05.2014 Ascona, Schweiz Zemp Niklaus;
108° Congress of the Italian Botanical Society Vortrag im Rahmen einer Tagung Ecological speciation in plants 18.09.2013 Baselga di Piné , Italien Widmer Alexander;
Seminar series Einzelvortrag Next-generation sequencing in non-model organisms - insights from plants and sex chromosomes 21.01.2013 University of Trier, Deutschland Widmer Alexander;
Plant and Animal Genome (PAG) 2013 Vortrag im Rahmen einer Tagung Dosage compensation and sex-biased gene expression in a dioecious plant 11.01.2013 San Diego, Vereinigte Staaten von Amerika Zemp Niklaus;
PreSol Symposium Einzelvortrag Express yourself: Evolution of sex chromosomes and sex-biased gene expression in a dioecious plant 24.08.2012 Zürich, Schweiz Widmer Alexander;
Molecular Ecology Symposium Vortrag im Rahmen einer Tagung Reproductive isolation, hybridisation and genomic divergence in a dioecious plant group 06.07.2012 Ottawa, Kanada Widmer Alexander;


Selber organisiert

Titel Datum Ort
Genomics of the Speciation Continuum 04.09.2014 Fribourg, Schweiz

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
127155 Adaptive genetic variation and plant adaptation to environmental heterogeneity (AVE) 01.04.2010 Sinergia
116455 Porous genomes and the nature of plant species differences in a pair of hybridizing silence species 01.07.2007 Projektförderung (Abt. I-III)
160123 Genomics of adaptation in the context of a rapid plant radiation 01.06.2015 Projektförderung (Abt. I-III)

Abstract

Studies of adaptation and speciation in plants are currently experiencing a major revolution. First, new sequencing technologies and conceptual advances open the doors to truly genome-wide analyses of adaptation, selection and genomic divergence in natural populations. Second, the concept of ecological speciation puts ecological adaptation into the spotlight of speciation research because it provides a direct link between ecological adaptation, divergent selection and speciation, and because it implies that speciation can occur over ecological time scales. To date, however, relevant examples of ecological speciation are scarce and empirical data on the genetic basis of the process is largely lacking.This project sets out to explore the genetic basis of ecological adaptation and its consequences for genome-wide divergence in two plant study systems, an evolutionary young and an older system. The first study system is wild carnation, Dianthus sylvestris, where natural populations occur over a large altitudinal gradient in the Alps and show strong phenotypic divergence in the absence of neutral genetic divergence. This pattern suggests that divergent natural selection underlies phenotypic divergence and has led to ecological adaptation. I propose to explore the association between ecological adaptation and incipient genomic divergence in Dianthus. The second study system includes two closely related Silene species, S. latifolia and S. dioica. These species show incomplete morphological, ecological and reproductive isolation and often hybridize upon secondary contact, yet remain distinct outside of contact zones. I propose to explore the contribution of ecological adaptation to present day reproductive isolation and genomic divergence between these two species.To assess genomic divergence between high and low altitude populations of D. sylvestris, as well as between S. latifolia and S. dioica, we will use RAD sequencing, a recently developed method that uses next-generation sequencing (NGS) to assess nucleotide variation at a genome-wide scale. Genomic regions associated with ecological adaptation will be identified using a combination of classical ecological transplant experiments and high-density QTL mapping in experimental populations. This genotyping information will be further used to study the frequency and genomic position of intrinsic reproductive barriers (incompatibilities). Together, these results will provide a novel perspective on the associations between ecological adaptation, divergent selection and speciation in plants and provide a test of the ecological speciation scenario.Developing a better understanding of the genetic basis of adaptation and its consequences for genomic divergence and speciation is not only of fundamental interest for basic science, but is also highly relevant for a society that is anxious about the consequences of climate change and the threats to biodiversity.
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