Projekt

Zurück zur Übersicht

Genome-wide patterns of nucleotide diversity and divergence in wild tomatoes (Solanum section Lycopersicon): inferences on demographic history, speciation, and natural selection

Titel Englisch Genome-wide patterns of nucleotide diversity and divergence in wild tomatoes (Solanum section Lycopersicon): inferences on demographic history, speciation, and natural selection
Gesuchsteller/in Städler Thomas
Nummer 130702
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Institut für Integrative Biologie Departement Umweltwissenschaften ETHZ
Hochschule ETH Zürich - ETHZ
Hauptdisziplin Botanik
Beginn/Ende 01.09.2010 - 31.08.2013
Bewilligter Betrag 331'000.00
Alle Daten anzeigen

Alle Disziplinen (3)

Disziplin
Botanik
Genetik
Molekularbiologie

Keywords (12)

speciation; introgression; reproductive isolation; demographic history; selection; coalescent simulations; recombination rates; Population genetics; wild tomatoes; gene flow; divergence; natural selection

Lay Summary (Englisch)

Lead
Lay summary
This project aims to establish genome-wide patterns of diversity and divergence between several closely related, ecologically diverged wild tomato species. Of particular interest is the relative importance of various evolutionary processes that have shaped these patterns, such as demographic history, mutation, and natural selection.Understanding speciation processes is a central goal in population genetics and evolutionary biology, not least because they represent the origin of biodiversity. However, they are difficult to study in many natural systems because species often have diverged sufficiently to erode signatures of evolutionary processes that caused the initial divergence. Under a genealogical perspective, DNA sequence data from multiple genomic fragments contain footprints of species' demographic history and may reveal cases of interspecific gene flow during the process of divergence. Wild tomatoes are ideally suited for these purposes because of their recent divergence, diversity of mating systems, and valuable genomic resources that include a draft genome sequence. Three subprojects will be pursued that all rest on a common data set generated by sequencing 60 nuclear loci from seven wild tomato species.A major project goal is building a speciation/demographic model for the seven species: to what extent did these species experience changes in population size after divergence, and is there genomic evidence for speciation with ongoing gene flow? A second goal is to estimate the strength of correlation(s) between levels of nucleotide diversity, divergence to a non-tomato outgroup, and levels of recombination. Finally, we aim to identify genomic regions that show either elevated or reduced divergence among the focal tomato species, given their inferred demographic history. Nuclear genes from genomic regions of normal versus very low recombination rate will be sequenced with next-generation sequencing technology.Extensive analyses of the genome-wide sequence data and their comparison to results from computer simulations will provide reliable inferences on many aspects of the historical divergence process among the wild tomato species. Molecular evolutionary analyses of the sequence data will assess the relative importance of "positive" and "negative" selection on nucleotide diversity and divergence in linked regions, compared to neutral factors such as mutations and random genetic drift. Moreover, we can also test the potential role of suppressed recombination in facilitating divergence and the build-up of reproductive barriers between species. These issues are of fundamental evolutionary interest and can now be studied at a genome-wide scale.
Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Genomic imprinting in the endosperm is systematically perturbed in abortive hybrid tomato seeds
Florez-Rueda Ana M., Paris Margot, Schmidt Anja, Widmer Alex, Grossniklaus Ueli, Städler Thomas (2016), Genomic imprinting in the endosperm is systematically perturbed in abortive hybrid tomato seeds, in Molecular Biology and Evolution, 33(11), 2935-2946.
Genomic analyses provide insights into the history of tomato breeding
Lin Tao, 26 other coauthors, Städler Thomas, Li Jingfu, Ye Zhibiao, Du Yongchen, Huang Sanwen (2014), Genomic analyses provide insights into the history of tomato breeding, in Nature Genetics, 46(11), 1220-1226.
A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity
Qi Jianjian, Liu Xin, Shen Di, Miao Han, 18 other authors, Städler Thomas, Renner Susanne S., Kamoun Sophien, Lucas William J., Zhang Zhonghua, Huang Sanwen (2013), A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity, in Nature Genetics, 45(12), 1510-1515.
Molecular ecology in Vienna: hot topics in a chilly place
Städler Thomas (2012), Molecular ecology in Vienna: hot topics in a chilly place, in EMBO REPORTS, 13(6), 475-477.
Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates
Städler Thomas, Florez-Rueda Ana Marcela, Paris Margot (2012), Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates, in Molecular Biology and Evolution, 29(1), 31-34.
Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum
Tellier A, Pfaffelhuber P, Haubold B, Naduvilezhath L, Rose LE, Städler T, Stephan W, Metzler D (2011), Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum, in PLOS ONE, 6(5), keine-keine.
Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure
Tellier A, Fischer I, Merino C, Xia H, Camus-Kulandaivelu L, Städler T, Stephan W (2011), Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure, in HEREDITY, 107(3), 189-199.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Prof. Kentaro Shimizu, University of Zurich Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Prof. Aurelien Tellier, TU Munich Deutschland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Prof. Ueli Grossniklaus, University of Zurich Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
Prof. Sanwen Huang, Chinese Academy of Agricultural Sciences China (Asien)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
The 3rd Plant Genomics Congress: Asia Vortrag im Rahmen einer Tagung Exploring genomic imprinting and endosperm transcriptomes in abortive hybrid wild tomato seeds 11.04.2016 Kuala Lumpur, Malaysia Städler Thomas;
SOL 2015 - The 12th Solanaceae Conference Vortrag im Rahmen einer Tagung Using molecular diversity in wild tomatoes for inferences on evolution and speciation 25.10.2015 Bordeaux, Frankreich Städler Thomas;
SMBE 2015, Annual Meeting of the Society for Molecular Biology and Evolution Vortrag im Rahmen einer Tagung Genomic imprinting and its systematic perturbation in abortive interspecific tomato seeds 12.07.2015 Wien, Österreich Städler Thomas;
VISCEA Conference "Molecular Ecology and Evolution" Vortrag im Rahmen einer Tagung Inference of natural selection from genome-wide sequence data in wild tomatoes 22.06.2015 Wien, Österreich Städler Thomas;
14th Congress of the European Society for Evolutionary Biology Poster Evolutionary inferences using nucleotide polymorphism and divergence data in the tomato clade 19.08.2013 Lisbon, Portugal Paris Margot;
SMBE 2013, Annual Meeting of the Society for Molecular Biology and Evolution Poster Speciation in wild tomatoes: inference from genome-wide sequence data 07.07.2013 Chicago, Vereinigte Staaten von Amerika Städler Thomas;
Second European Conference on Speciation Research Vortrag im Rahmen einer Tagung Speciation in wild tomatoes 27.05.2013 Montpellier, Frankreich Paris Margot;
First Joint Congress on Evolutionary Biology Poster Characterizing the molecular basis of hybrid seed failure between two wild tomato species 06.07.2012 Ottawa, Kanada Städler Thomas;
SMBE 2012, Annual Meeting of the Society for Molecular Biology and Evolution Poster Assessing the impacts of mating system and natural selection on genome-wide patterns of nucleotide diversity in wild tomatoes 23.06.2012 Dublin, Irland Paris Margot;
Adaptive Landscape Genetics - A Joint Workshop with SUSO Poster Population genomics of wild tomatoes (Solanum section Lycopersicon) 07.02.2012 Neuchatel, Schweiz Paris Margot;
VIPCA International Conference "Molecular Ecology" Vortrag im Rahmen einer Tagung Evolutionary inference from sequence data: why the spatial sampling scheme matters 04.02.2012 Vienna, Austria, Österreich Städler Thomas;
Next Generation Plant Ecology & Evolution Workshop 2011 Poster Population genomics of wild tomatoes (Solanum section Lycopersicon): inferences on demographic history, speciation and reproductive isolation 18.10.2011 Edinburgh, Grossbritannien und Nordirland Paris Margot;
13th Congress of the European Society for Evolutionary Biology Vortrag im Rahmen einer Tagung Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates 20.08.2011 Tübingen, Deutschland Städler Thomas;


Selber organisiert

Titel Datum Ort
SOL 2012 - 9th Solanaceae Conference 26.08.2012 Neuchatel, Schweiz

Abstract

Lineage divergence and processes of speciation are of fundamental interest in evolutionary biology and population genetics, but are difficult to address in many natural systems because extant species may have diverged sufficiently to erode signatures of evolutionary processes that accompanied and/or caused the initial divergence. Under a genealogical (coalescent) perspective, DNA sequence data obtained from multiple unlinked loci contain footprints of demographic history and may reveal incidences of interspecific gene flow during the process of divergence. Understanding the demographic history of species is also of considerable importance for interpreting patterns of nucleotide polymorphism, site frequency spectra (SFS), and linkage disequilibrium (LD) at “candidate” loci that might be involved in adaptive traits or reproductive isolation. Moreover, recombination rates can vary dramatically across genomic regions, providing opportunities to test evolutionary models invoking the effects of directional and/or purifying selection. Finally, regions of very low recombination may facilitate the build-up of reproductive barriers and adaptive differentiation, but empirical data in plants to address these issues are still scarce. Here I propose a research project that builds on my previous studies in wild tomatoes (Solanum section Lycopersicon) with a similar focus, but that were limited to fewer species and markedly fewer loci. Wild tomatoes are ideally suited for such a project because of their recent divergence, differences in their mating system, and abundant genomic resources including estimates of recombination rate for hundreds of mapped nuclear markers. I plan to pursue three subprojects that each have their own conceptual framework, but rest on a common data set generated by sequencing 50-60 nuclear loci from seven nominal wild tomato species, two of them with a highly selfing mating system. Due to population subdivision and its genealogical consequences, the aim of characterizing nucleotide diversity and the SFS can be accomplished in the least biased manner by a scattered sampling scheme across each species’ geographic range. Nuclear loci from known regions of normal versus very low recombination rate, but without regard to putative function, will be sequenced with next-generation sequencing technology (454) to provide the raw data for the three subprojects. Project 1 concerns the demographic history and divergence processes of the seven nominal species, to be evaluated with extensive coalescent simulations under an approximate Bayesian computation (ABC) framework. Project 2 focuses on the direction and strength of correlation(s) between levels of silent nucleotide diversity, divergence to a non-tomato outgroup, and levels of recombination; these analyses assess the relative importance of directional and/or purifying selection on nucleotide diversity and divergence in linked regions, compared to neutral factors such as mutation and random genetic drift. By screening for genomic regions showing either higher or lower divergence levels between the focal species than expected given their inferred demographic history, project 3 aims to test the potential role of suppressed recombination in facilitating divergence and reproductive isolation. The proposed research will provide new insights into genome-wide patterns of diversity and divergence between multiple closely related, ecologically diverged plant species, as well as into the evolutionary processes generating those patterns. These issues are of fundamental biological interest and have now become amenable to study at a genome-wide scale, due to recent innovations in sequencing technology and theoretical advances in understanding the genealogical implications of different sampling schemes in subdivided species.
-