Project
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Speciation Genomics of the Swiss Alpine Whitefish Radiation
English title |
Speciation Genomics of the Swiss Alpine Whitefish Radiation |
Applicant |
Feulner Philine
|
Number |
163446 |
Funding scheme |
Project funding (Div. I-III)
|
Research institution |
Fischökologie und Evolution Eawag
|
Institution of higher education |
Swiss Federal Institute of Aquatic Science and Technology - EAWAG |
Main discipline |
Molecular Biology |
Start/End |
01.10.2016 - 30.11.2020 |
Approved amount |
337'316.00 |
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Keywords (5)
adaptive radiation; Coregonus; speciation genomics; genome evolution; genomic architecture
Lay Summary (German)
Lead
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Die Felchen der Schweiz sind enorm vielfältig und die verschieden Felchen-Arten unterscheiden sich in einer Reihe von Merkmalen, wie beispielsweise Körperform und Größe, Ernährungsweise, Lebensraum und Fortpflanzungszeitraum. Sehr wahrscheinlich hat sich diese Vielfalt mehrfach in der unterschiedlichen Schweizer Seen entwickelt. Die parallele Entstehung ähnlicher Arten in den verschiedenen Seen deutet darauf hin, dass dies durch Anpassungen an verschiedene Lebensräume innerhalb der Seen geschehen ist. Die genetische Grundlage hierfür ist bisher jedoch wenig verstanden und untersucht.
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Lay summary
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Die korrekte Interpretation genomischer Muster, die durch das Sequenzieren ganzer Genome ermöglicht wurde, wird jedoch dadurch erschwert, dass eine Vielzahl von Prozessen, wie Drift, Selektion, Genefluss, und Rekombination, alle simultan das Genom formen und die Heterogenität entlang des Genoms beeinflussen. In diesem Projekt untersuchen wir die Genomevolution innerhalb der Schweizer Felchen und ihr Einhergehen mit der Differenzierung in unterschiedlichste Arten. Hierfür erstellen wir zunächst ein Referenzgenom. Felchen sind Salmoniden und haben ein großes stark dupliziertes Genome. Dies ist eine große Herausforderung, erlaubt uns aber auch einen Einblick in die Rolle der Genomduplikation während der Artentstehung. Des Weiteren werden wir die genetische Architektur bedeutender ökologischer und fortpflanzungsrelevanter Merkmale im Detail untersuchen. Außerdem werden wir die Differenzierung im Genom zwischen Arten innerhalb eines Sees (sympatrisch) und zwischen verschiedenen Seen (allopatrisch) miteinander vergleichen. Diese Grundlagenforschung wird unser Verständnis der Rolle des Erbgutes für die Artenstehung verbessern. Ein besseres Verständnis der Artenvielfalt und ihrer genetischen Grundlage wird auch dazu beitragen können diese Vielfalt bestmöglich zu erhalten.
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Responsible applicant and co-applicants
Employees
Publications
De-Kayne Rishi, Zoller Stefan, Feulner Philine G.D. (2020), A de novo chromosome‐level genome assembly of Coregonus sp. “Balchen ”: One representative of the Swiss Alpine whitefish radiation, in
Molecular Ecology Resources, 1-17.
Feulner Philine G.D., Seehausen Ole (2018), Genomic insights into the vulnerability of sympatric whitefish species flocks, in
Molecular Ecology, mec.14977-mec.14977.
De-Kayne Rishi, Feulner Philine G. D. (2018), A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication, in
G3: Genes, Genomes, Genetics, 8(12), 3745-3755.
Datasets
Supplemental Material for De-Kayne and Feulner, 2018
Author |
Feulner, Philine |
Publication date |
08.10.2018 |
Persistent Identifier (PID) |
DOI: 10.25387/g3.7093799.v1 |
Repository |
figshare
|
|
Coregonus sp. 'Albock' Raw sequence reads
Author |
Feulner, Philine |
Publication date |
27.06.2018 |
Persistent Identifier (PID) |
NCBI SRA Accession: PRJNA478121 |
Repository |
SRA
|
|
Data from: Genomic insights into the vulnerability of sympatric whitefish species flocks
Author |
Feulner, Philine |
Publication date |
29.11.2018 |
Persistent Identifier (PID) |
DOI:10.1111/mec.14977 |
Repository |
Dryad
|
|
Raw sequence reads: Genomic insights into the vulnerability of sympatric whitefish species flocks
Author |
Feulner, Philine |
Publication date |
08.08.2018 |
Persistent Identifier (PID) |
PRJNA485027 |
Repository |
SRA
|
|
Data from: A de novo chromosome-level genome assembly of Coregonus sp. “Balchen”: one representative of the Swiss Alpine whitefish radiation
Author |
Feulner, Philine |
Publication date |
15.05.2020 |
Persistent Identifier (PID) |
DOI: 10.5061/dryad.xd2547ddf |
Repository |
Dryad
|
|
Raw reads: WFgenomePacBioRawdata
Author |
Feulner, Philine |
Persistent Identifier (PID) |
Run accession: ERR4085732 |
Repository |
ENA
|
|
Raw reads: WFgenomeIlluminaRawdata
Author |
Feulner, Philine |
Persistent Identifier (PID) |
Run accession: ERR4093748 |
Repository |
ENA
|
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Assembly: GCA_902810595.1
Author |
Feulner, Philine |
Persistent Identifier (PID) |
GCA_902810595.1 |
Repository |
ENA
|
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Associated projects
Number |
Title |
Start |
Funding scheme |
183566
|
20,000 years of evolution and ecosystem dynamics in the world’s largest tropical lake reconstructed from sediment cores, fossils and ancient DNA |
01.03.2019 |
Sinergia |
160812
|
Host virus coevolution - demography versus selection |
01.01.2016 |
Project funding (Div. I-III) |
179637
|
Host virus coevolution - demography versus selection in the face of multiple stressors |
01.01.2019 |
Project funding (Div. I-III) |
169211
|
Parasite radiations: Domino effect of host radiations? |
01.07.2017 |
Project funding (Div. I-III) |
Abstract
Fuelled by the recent technological advancements in sequencing technology, speciation research has started to address long-standing questions on the genomic basis underlying and the genome evolution accompanying the speciation process. The first studies of this kind on established model systems of speciation research have revealed that patterns of divergence are not necessarily consistent across systems. In addition, the accurate interpretation of genomic patterns is challenged by a variety of different processes, such as drift, selection, gene flow, and recombination, all acting simultaneously in shaping the genome and contributing to the heterogeneity of divergence observed along the genome. The Swiss whitefish radiation (Coregonus lavaretus complex) exhibits great species diversity across different Alpine lakes. Alpine whitefish species, which partially evolved and are maintained in sympatry, are differentiated in body shape, size, feeding morphology, habitat choice, and phenology of reproduction. This adaptive radiation permits us to assess genomic divergence along a continuum of geographic, genetic, and ecological differentiation, in order to understand which evolutionary processes drive divergence and to gain insights on the genomic basis of speciation. Here we propose to study the genome evolution within the C. lavaretus complex accompanying the divergence of morphs and species within and across Alpine lakes. We aim to fulfill three major objectives towards ultimately understanding the properties of the genome structure and the genomic architecture of traits facilitating the adaptive radiation of Alpine whitefish. (1) We will build a reference genome backbone and assess the variation in genome structure across whitefish species. We will evaluate the evolution of the largely duplicated genome resulting from a relatively recent whole genome duplication at the base of the salmonid lineage. (2) We will investigate the genetic architecture of ecological and reproductive traits differing across whitefish species. (3) We will compare patterns of genomic divergence across different sympatric and allopatric species. Finally, integrating divergence patterns, trait architecture, and genome structure will address key outstanding questions on how species diversity can evolve and be maintained in sympatry. The study proposed here will greatly contribute towards ongoing research questions in the field of speciation genomics, provide a valuable genomic resource for an economically important group of fishes, and allow training of a PhD student.
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