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Identifying selection in the presence of gene flow

English title Identifying selection in the presence of gene flow
Applicant Wegmann Daniel
Number 173062
Funding scheme Project funding (Div. I-III)
Research institution Département de Biologie Faculté des Sciences Université de Fribourg
Institution of higher education University of Fribourg - FR
Main discipline Genetics
Start/End 01.06.2017 - 30.09.2021
Approved amount 849'557.00
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All Disciplines (2)

Discipline
Genetics
Ecology

Keywords (6)

Machiene learning; Ecological speciation; Evolutionary genetics; Locus-specific inference; Hidden Markov Model; Demographic inference

Lay Summary (German)

Lead
Stehen Populationen im genetischen Austausch, können lokale Anpassungen nur dank natürlicher Selektion aufrecht erhalten werden. In diesem Projekt werden neue statistische Verfahren entwickelt, um von diesem Mechanismus beeinflusste Gene zu identifizieren.
Lay summary

Inhalt und Ziele des Forschungsprojekts

Viele Populationen sind lokal angepasst. Zum Beispiel widerstehen Populationen der Meeresschnecken Littorina saxatilis an Steilküsten dem Wellengang mit kleinen, abgerundeten Häusern, während sich die Populationen im Geröll mit grossen Häusern gegen Krabben verteidigen. Solche Unterschiede sind oft genetisch basiert in dem relevante Mutationen in einer Population sehr häufig, in der anderen aber selten sind. Stehen solche Populationen im Austausch, werden kontinuierlich schlecht angepasste Mutationen eingeführt, und die beiden Populationen bleiben nur auf Grund der natürlichen Selektion gegen die eingewanderten Mutationen angepasst. Obwohl dieser Mechanismus bestens bekannt ist, bleibt die Identifikation von betroffenen Genen schwierig. Die Identifikation solcher Gene würde aber Aufschluss geben über die Häufigkeit von lokale Anpassung in der Natur, und aufzeigen, welche Merkmale an einer Artaufspaltung beteiligt sind. In dieses Projekt sollen deshalb neue statistische Methoden für eine solche Identifikation entwickelt werden. Hierfür machen wir uns die Eigenschaft zu nutze, dass die Selektion gegen eingewanderte Mutationen zu einer Reduktionen der effektiven Migrationsrate an diesen im Vergleich zu anderen Stellen im Genom führt.

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts

Das Projekt befasst sich mit Grundlagenforschung der Evolutionsbiologie mit dem Ziel, mehr über die Prozesse zu erfahren, welche die heutige Biodiversität hervorgebracht haben. Insbesondere wollen wir besser verstehen, wie sich Arten aufspalten und lokal anpassen können.

 

Direct link to Lay Summary Last update: 09.05.2017

Responsible applicant and co-applicants

Employees

Publications

Publication
A sparse observation model to quantify species distributions and their overlap in space and time
Ait Kaci Azzou Sadoune, Singer Liam, Aebischer Thierry, Caduff Madleina, Wolf Beat, Wegmann Daniel (2021), A sparse observation model to quantify species distributions and their overlap in space and time, in Ecography, 44(6), 928-940.
Identifying loci under selection via explicit demographic models
Luqman Hirzi, Widmer Alex, *Fior Simone, *Wegmann Daniel (2021), Identifying loci under selection via explicit demographic models, in Molecular Ecology Resources, 21(8), 2719-2737.
Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
Louis Marie, Galimberti Marco, Archer Frederick, Berrow Simon, Brownlow Andrew, Fallon Ramon, Nykänen Milaja, O’Brien Joanne, Roberston Kelly M., Rosel Patricia E., Simon-Bouhet Benoit, Wegmann Daniel, Fontaine Michael C., Foote Andrew D., Gaggiotti Oscar E. (2021), Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins, in Science Advances, 7(44), 1245-1245.
Detecting selection from linked sites using an F-model
Galimberti Marco, Leuenberger Christoph, Wolf Beat, Szilágyi Sándor Miklós, Foll Matthieu, Wegmann Daniel (2020), Detecting selection from linked sites using an F-model, in Genetics, 216(4), 1205-1215.
Estimating and accounting for genotyping errors in RAD-seq experiments
Bresadola Luisa, Link Vivian, Buerkle C. Alex, Lexer Christian, Wegmann Daniel (2020), Estimating and accounting for genotyping errors in RAD-seq experiments, in Molecular Ecology Resources, 20(4), 856-870.
Low Prevalence of lactase persistence in Bronze Age Europe indicates ongoing strong selection over the last 3,000 years
*Burger Joachim, *Link Vivian, Blöcher Jens, Schulz Anna, Sell Christian, Pochon Zoé, Diekmann Yoan, Žegarac Aleksandra, Hofmanová Zuzana, Winkelbach Laura, Reyna-Blanco Carlos S., Bieker Vanessa, Orschiedt Jörg, Brinker Ute, Scheu Amelie, Leuenberger Christoph, Bertino Thomas S., Bollongino Ruth, Lidke Gundula, Stefanović Sofija, Jantzen Detlef, Kaiser Elke, Terberger Thomas, Thomas Mark G., Veeramah Krishna R., Wegmann Daniel (2020), Low Prevalence of lactase persistence in Bronze Age Europe indicates ongoing strong selection over the last 3,000 years, in Current Biology, 30(21), 4307-4315.

Collaboration

Group / person Country
Types of collaboration
Palaeogenetics Group Mainz Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Probabilistic Modeling in Genomics Poster A New Isolation with Migration Model using whole-genome sequences 06.10.2019 Aussoi, France Ait Kaci Azzou Sadoune; Wegmann Daniel;
Probabilistic Modeling in genomics Poster Go low with ATLAS: maximizing population genetic insight from minimal sequencing depth 06.10.2019 Aussoi, France Link Vivian; Wegmann Daniel; Reyna Carlos Stefano;
Probabilistic Modeling in Genomics Poster An improved recalibration model for accurately estimating genetic diversity from low and ancient sequencing data 06.10.2019 Aussoi, France Reyna Carlos Stefano; Wegmann Daniel; Link Vivian;
SMBE 2018 Poster An improved recalibration model for accurately estimating genetic diversity from low and ancient sequencing data 08.07.2018 Yokohama, Japan Link Vivian; Reyna Carlos Stefano; Wegmann Daniel;
SMBE 2018 Poster A New Isolation with Migration Model using whole-genome sequences 08.07.2018 Yokohama, Japan Wegmann Daniel; Ait Kaci Azzou Sadoune;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Ancient genes vital for dolphin survival, research involving Bangor University suggests North Wales Chronicle International 2021
Media relations: radio, television 120 générations pour tolérer le lait RTS Western Switzerland 2020
Media relations: print media, online media Digérer le lactose, un facteur de survie Le Matin Dimanche Western Switzerland 2020
Media relations: print media, online media Lactose tolerance spread throughout Europe in a few thousand years, says study Metro International 2020
Media relations: print media, online media Milchtrinker waren den anderen gegenüber klar im Vorteil Tagesanzeiger German-speaking Switzerland 2020
Media relations: print media, online media Mitteleuropäer waren in Bronzezeit noch keine Milchtrinker Blick German-speaking Switzerland 2020
Media relations: print media, online media Mitteleuropäer wurden spät und schnell zu Milchtrinkern Der Standard International 2020
Media relations: print media, online media Wann und wieso Erwachsene zu Milchtrinkern wurden Kurier International 2020

Awards

Title Year
Vigener Prize for the best PhD thesis 2020

Associated projects

Number Title Start Funding scheme
200420 Better genotype likelihoods for ancient DNA 01.06.2021 Project funding (Div. I-III)
149920 Joint Inference of Selection and Demography 01.11.2013 Project funding (Div. I-III)
171131 Computational optimization of a model-based inference algorithm for circadian oscillators 01.09.2016 International short research visits

Abstract

Migration is a major evolutionary force homogenizing evolutionary trajectories of populations by promoting the exchange of genetic material. The influx of new genetic material may be facilitated or hampered by selection. In case of strong local adaptation, for instance, migrants may carry maladapted alleles that are selected against. This way, selection results in reduced effective gene flow between populations. But selection can also favor immigrant alleles if they confer a local fitness advantage, as has been shown for several loci that introgressed from archaic into modern humans, including a haplotype conferring adaptation to high altitude in Tibetans. While the rate of migration is the same for all loci, at least on autosomes, selection is likely to vary across loci. As a consequence, and due to to genetic drift, the effective gene flow is expected to vary along the genome in organisms undergoing recombination.Identifying loci affecting the effective rate of gene flow is of major interests in evolutionary biology. Loci at which gene flow is strongly reduced between ecologically diverse populations, for instance, are the drivers of local adaptation and are thought to constitute the first step towards ecological speciation. Identifying these loci is key to understand the role of selection in shaping phenotypic differences between populations.The classic way to identify such loci is by means of outlier scans using statistics that quantify divergence between populations or assessing incongruence between genealogies at different a loci. However, outlier scans based on such summary statistics are likely to ignore valuable information present in the full data, do not model linkage explicitly and require arbitrary choices to identify outliers. There is thus considerable interest in developing methods to quantify locus-specific rates of gene flow and / or selection coefficients while accounting for the effects of demography, and ideally also account for physical linkage between loci. However, due to both statistical and computational challenges, available methods available either assume loci to be independent, do not account for population splits, or require detailed haplotype information from multiple species. Here I propose to complement these approaches with new methods to infer locus-specific migration rates (or selection coefficients) under three important scenarios:Scenario 1: Rich population divergence models.Scenario 2: Ancestral introgression.Scenario 3: From time-series frequency data.To achieve this, I will build upon existing tools and extend these by explicitly modeling correlation in evolutionary parameters along the genome using Hidden Markov Models (HMM). For Scenario 1 I will in this way extend an efficient approach to samples genealogies under isolation-with-migration models used previously. For Scenario 2 I will extend methods using Gaussian processes to describe the evolution of allele frequencies in related populations, for which I describe here an efficient inference strategy. For Scenario 3, finally, I will build upon an computationally efficient approximation to the Wright-Fisher diffusion we recently introduced.All newly developed methods will then be carefully evaluated using simulations. But this project goes beyond tool development by identifying loci conferring local adaptation in several important system: domesticated date palms, Darwin finches, and Littorina snails. For this we will team up with groups that have studied these systems in detail for years and have assembled impressive data sets to learn about the genetic architecture of phenotypic divergence in that prevails in the presence of gene flow. Inferring and comparing the genetic architectures underlying those divergent phenotypes will contribute significantly to our understanding of how ecological divergence may initiate speciation.
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