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Unraveling the evolutionary origin and consequences of the largest known recent vertebrate radiation by a comprehensive analysis of complete cichlid genomes

English title Unraveling the evolutionary origin and consequences of the largest known recent vertebrate radiation by a comprehensive analysis of complete cichlid genomes
Applicant Seehausen Ole
Number 163338
Funding scheme Project funding (Div. I-III)
Research institution Institut für Ökologie und Evolution Universität Bern
Institution of higher education University of Berne - BE
Main discipline Zoology
Start/End 01.10.2016 - 31.03.2021
Approved amount 756'000.00
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Keywords (5)

adaptive radiation; cichlid fish; speciation; phylogenomics; population genomics

Lay Summary (German)

Lead
Bei weitem die schnellste Rate von Artbildung wurde bei Buntbarschen im afrikanischen Viktoriasee nachgewiesen. Sie ermöglichte die Entstehung eines der artenreichsten Ökosysteme der Welt in nur wenigen zehntausend Jahren. Die genomischen Grundlagen dieser jungen Artenvielfalt sind noch nie vergleichend untersucht worden. Unser Projekt leistet dazu einen Beitrag.
Lay summary

Grosse Artenradiationen sind Ikonen der Evolutionsbiologie, besonders dann wenn sie in geologisch junger Zeit entstanden sind. Ihr Studium kann uns über das Entstehen und Vergehen von Artenvielfalt lehren, und darüber warum einige Tier- und Pflanzengruppen viel artenreicher werden als andere. Seitdem die Vorfahren der Viktoriabuntbarsche vor nur 15'000 Jahren in den sich damals gerade füllenden Viktoriasee einwanderten, entstanden 500 neue Arten mit den verschiedensten Erscheinungsbildern, Verhaltensweisen und ökologischen Anpassungen. Das ist die schnellste Artbildungsrate, die je bei Tieren festgestellt wurde, und lies eines der artenreichsten Ökosysteme der Erde entstehen.

Ziel unseres Projektes ist es, Veränderungen in den Genomen der Buntbarsche zu charakterisieren, die mit dieser Diversifizierung einhergingen. Wir sequenzieren die gesamten Genome von mehreren hundert Buntbarschen verschiedenster Arten. Wir sequenzieren aber auch die Arten, die wahrscheinlich die direkten Nachkommen der damaligen Einwanderer sind und heute noch unverändert in anderen Gewässern leben, sowie Buntbarsche anderer Evolutionslinien, die in sehr ähnlichen Lebensräumen leben ohne sich aber in neue Arten aufgespalten zu haben.

Wir möchten herausfinden, welche Gene für die Artbildung, und welche für ökologische Anpassungen verantwortlich sind, und wie diese im Genom gekoppelt werden, eine Voraussetzung für die Entstehung und Koexistenz von Arten. Wir möchten auch wissen, was der Ursprung der grossen genetischen Vielfalt ist. Waren die Vorfahren vielleicht bereits ungewöhnlich genetisch variabel und wie kam das? Könnte das Fehlen entsprechender Variation das Ausbleiben von Artbildung bei anderen Gruppen erklären? Wir rekonstruieren auch die zeitliche Abfolge der Geschehnisse in der Radiation um die Interaktion ökologischer und evolutionärer Mechanismen zu verstehen. Letztlich wird unser Projekt zu einem besseren Verständnis eines global einmaligen Biodiversitätshotspots beitragen.

Direct link to Lay Summary Last update: 19.08.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
Reply to “Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin”
Marques David A., Lucek Kay, Sousa Vitor C., Excoffier Laurent, Seehausen Ole (2021), Reply to “Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin”, in Nature Communications, 12(1), 2807-2807.
Movement of transposable elements contributes to cichlid diversity
Carleton Karen L., Conte Matthew A., Malinsky Milan, Nandamuri Sri Pratima, Sandkam Benjamin A., Meier Joana I., Mwaiko Salome, Seehausen Ole, Kocher Thomas D. (2020), Movement of transposable elements contributes to cichlid diversity, in Molecular Ecology, 29(24), 4956-4969.
The ecological and genomic basis of explosive adaptive radiation
McGee Matthew D., Borstein Samuel R., Meier Joana I., Marques David A., Mwaiko Salome, Taabu Anthony, Kishe Mary A., O’Meara Brian, Bruggmann Rémy, Excoffier Laurent, Seehausen Ole (2020), The ecological and genomic basis of explosive adaptive radiation, in Nature, 586(7827), 75-79.
The propagation of admixture-derived adaptive radiation potential
Kagawa Kotaro, Seehausen Ole (2020), The propagation of admixture-derived adaptive radiation potential, in Proceedings of the Royal Society B: Biological Sciences, 287(1934), 20200941-20200941.
Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids
Feller Anna F., Selz Oliver M., McGee Matthew D., Meier Joana I., Mwaiko Salome, Seehausen Ole (2020), Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids, in Ecology and Evolution, 10(14), 7445-7462.
Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids
Feller Anna F., Haesler Marcel P., Peichel Catherine L., Seehausen Ole (2020), Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids, in Proceedings of the Royal Society B: Biological Sciences, 287(1924), 20200270-20200270.
Comparing Adaptive Radiations Across Space, Time, and Taxa
Gillespie Rosemary G, Bennett Gordon M, De Meester Luc, Feder Jeffrey L, Fleischer Robert C, Harmon Luke J, Hendry Andrew P, Knope Matthew L, Mallet James, Martin Christopher, Parent Christine E, Patton Austin H, Pfennig Karin S, Rubinoff Daniel, Schluter Dolph, Seehausen Ole, Shaw Kerry L, Stacy Elizabeth, Stervander Martin, Stroud James T, Wagner Catherine, Wogan Guinevere O U (2020), Comparing Adaptive Radiations Across Space, Time, and Taxa, in Journal of Heredity, 111(1), 1-20.
Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback
Marques David A., Lucek Kay, Sousa Vitor C., Excoffier Laurent, Seehausen Ole (2019), Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback, in Nature Communications, 10(1), 4240-4240.
The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes
Meier Joana I., Stelkens Rike B., Joyce Domino A., Mwaiko Salome, Phiri Numel, Schliewen Ulrich K., Selz Oliver M., Wagner Catherine E., Katongo Cyprian, Seehausen Ole (2019), The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes, in Nature Communications, 10(1), 5391-5391.
Interspecific hybridization can generate functional novelty in cichlid fish
Selz O. M., Seehausen O. (2019), Interspecific hybridization can generate functional novelty in cichlid fish, in Proceedings of the Royal Society B: Biological Sciences, 286(1913), 20191621-20191621.
A Combinatorial View on Speciation and Adaptive Radiation
Marques David A., Meier Joana I., Seehausen Ole (2019), A Combinatorial View on Speciation and Adaptive Radiation, in Trends in Ecology & Evolution, 34(6), 531-544.
A key metabolic gene for recurrent freshwater colonization and radiation in fishes
Ishikawa Asano, Kabeya Naoki, Ikeya Koki, Kakioka Ryo, Cech Jennifer N., Osada Naoki, Leal Miguel C., Inoue Jun, Kume Manabu, Toyoda Atsushi, Tezuka Ayumi, Nagano Atsushi J., Yamasaki Yo Y., Suzuki Yuto, Kokita Tomoyuki, Takahashi Hiroshi, Lucek Kay, Marques David, Takehana Yusuke, Naruse Kiyoshi, Mori Seiichi, Monroig Oscar, Ladd Nemiah, Schubert Carsten J., et al. (2019), A key metabolic gene for recurrent freshwater colonization and radiation in fishes, in Science, 364(6443), 886-889.
Detecting the macroevolutionary signal of species interactions
Harmon Luke J., Andreazzi Cecilia S., Débarre Florence, Drury Jonathan, Goldberg Emma E., Martins Ayana B., Melián Carlos J., Narwani Anita, Nuismer Scott L., Pennell Matthew W., Rudman Seth M., Seehausen Ole, Silvestro Daniele, Weber Marjorie, Matthews Blake (2019), Detecting the macroevolutionary signal of species interactions, in Journal of Evolutionary Biology, 32(8), 769-782.
Recent sympatric speciation involving habitat-associated nuptial colour polymorphism in a crater lake cichlid
Lemoine Melissa, Barluenga Marta, Lucek Kay, Mwaiko Salome, Haesler Marcel, Chapman Lauren J., Chapman Colin A., Seehausen Ole (2019), Recent sympatric speciation involving habitat-associated nuptial colour polymorphism in a crater lake cichlid, in Hydrobiologia, 832(1), 297-315.
A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination
Feulner Philine G D, Schwarzer Julia, Haesler Marcel P, Meier Joana I, Seehausen Ole (2018), A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination, in G3 Genes|Genomes|Genetics, 8(7), 2411-2420.
Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids
Meier Joana Isabel, Marques David Alexander, Wagner Catherine Elise, Excoffier Laurent, Seehausen Ole (2018), Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids, in Molecular Biology and Evolution, 35(6), 1489-1506.

Datasets

Data from: The ecological and genomic basis of explosive adaptive radiation

Author McGee, Matt
Publication date 21.09.2020
Persistent Identifier (PID) https://doi.org/10.5061/dryad.fn2z34tr0
Repository Dryad
Abstract
Rates of speciation vary tremendously among evolutionary lineages, with our understanding of what fuels the rapid succession of speciation events within young adaptive radiations remaining particularly incomplete. The cichlid fish family provides the most notable example of such variation among extant metazoans. It includes many slowly speciating lineages as well as the several exceptionally large and rapid adaptive radiations. By reconstructing a large phylogeny of all described cichlid species, we show that explosive speciation is solely concentrated in several large yet young lake species flocks. Across the family, speciation rate increases are associated with absence of top predators, and speciation rate decreases are associated with arid climate, but these factors are not nearly sufficient to explain explosive speciation in lake radiations, in particular the Lake Victoria adaptive radiation. Across lake radiations we observe a positive relationship between speciation rate and enrichment with large indel polymorphisms. Assembly of one hundred Victorian cichlid genomes comprising all extant ecological guilds and taxonomic genera reveals this radiation contains exceptional ‘genomic potential’ - hundreds of ancient haplotypes bearing indel polymorphisms, many of which are strongly associated with specific ecologies and are shared with ecologically similar species from other older lake radiations elsewhere in Africa. Network analysis reveals fundamentally non-treelike evolution through recombining old haplotypes, with origins of ecological guilds concentrated early in the Victoria radiation. Our results suggest that the combination of ecological opportunity, sexual selection and exceptional genomic potential is the key to understanding explosive adaptive radiation.

Haplochromine cichlids: Lake Victoria cichlid ecological diversity

Author McGee, Matt
Publication date 19.04.2020
Persistent Identifier (PID) PRJNA626405 ID: 626405
Repository NCBI
Abstract
This project contains short-read sequencing data from 100 species of cichlid from Lake Victoria and the nearby Kyoga Basin that together comprise the full range of extant ecological diversity for this classic example of adaptive radiation.

Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids

Author Meier, Joana
Publication date 19.03.2019
Persistent Identifier (PID) https://doi.org/10.5061/dryad.8p6m07g
Repository Dryad
Abstract
The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case are blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through “hybrid parallel speciation”. Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new “nyererei-like” and “pundamilia-like” species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.

The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlids

Author Meier, Joana
Publication date 17.09.2019
Persistent Identifier (PID) https://zenodo.org/record/3435419#.YKbI66gzZPY
Repository Zenodo
Abstract
This dataset contains all the underlying data and scripts used for the publication by Meier et al., 2019, in Nature Communications on "The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlids".This package contains the R scripts and all input files to produce Figures 2-4, Supplementary Figures 3, 6-8, and Supplementary Data 1. It contains the morphology data, the D statistics used for plotting, the genomic data files used for generating PCA plots, the fineRADstructure output files, the BEAST trees with all calibration sets, the RAD variant calls, the mitochondrial D-loop alignment, and the mitochondrial and RAD RAxML trees. For more information, see Meier et al., 2019, Nature Communications.

Haplochromine cichlid fishes from Lake Mweru, Lake Bangweulu and adjacent rivers Raw sequence reads

Author Meier, Joana
Publication date 10.07.2019
Persistent Identifier (PID) PRJNA553794 ID: 553794
Repository NCBI
Abstract
RAD tag reads of haplochromine cichlids from Lakes Mweru and Bangweulu and adjacent rivers associated with the study "The coincidence of ecological opportunity with hybridization explains the prevalence of rapid adaptive radiation"

Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids

Author Feller, Anna
Publication date 25.03.2020
Persistent Identifier (PID) https://doi.org/10.5061/dryad.5tb2rbp1n
Repository Dryad
Abstract
One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum vs blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest vs blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant QTLs with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum x blue cross, whereas we find no significant QTLs in the non-sympatric red-chest x blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.

Data from: Rapid generation of ecologically relevant behavioural novelty in experimental cichlid hybrids

Author Feller, Anna
Publication date 13.08.2020
Persistent Identifier (PID) https://doi.org/10.5061/dryad.280gb5mn7
Repository Dryad
Abstract
The East African cichlid radiations are characterised by repeated and rapid diversification into many distinct species with different ecological specialisations and by a history of hybridization events between non-sister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialised on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialised on sand sifting. We combined experimental behavioural and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behaviour related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioural traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behaviour in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behaviour, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

Data from: Interspecific hybridization can generate functional novelty in cichlid fish

Author Selz, Oliver
Publication date 14.10.2019
Persistent Identifier (PID) https://doi.org/10.5061/dryad.m25t886
Repository Dryad
Abstract
The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has on the one hand been suggested to facilitate the evolution of ecological novelty and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether additional ecological opportunities do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental types when feeding on food either parental species are adapted to, and if the same hybrids perform better compared to their parents when feeding on food none of the species are adapted to. We generated two first-generation experimental hybrid crosses between species of African cichlids. In feeding efficiency experiments we measure the performance of hybrids and parental species on food types representing both parental species niches and additional ‘novel’ niches, not utilized by part of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the ‘novel’ food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.

Collaboration

Group / person Country
Types of collaboration
Dr. Catherine Wagner/University of Wyoming United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Sam Borstein/Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Philine Feulner/Eawag Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Maria Kishe/Tanzania Fisheries Research Institute Tanzania (Africa)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Anthony Taabu/National Fisheries Resources Research Institute, Jinja, Uganda Uganda (Africa)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Journal Club Natural History Museum Bern Individual talk Whole genomes retell the origin of species 17.05.2021 Bern, Switzerland Marques David;
Seminar Evolutinary Biology group, University of Konstanz, Germany Individual talk Old genetic variation: key to rapid adaptation, speciation and adaptive radiation? 10.05.2021 Konstanz, Germany Marques David;
Interfaculty Bioinformatics group meeting Individual talk Whole genomes retell the origin of species 23.03.2021 Bern, Switzerland Marques David;
Department of Biology seminar, Lund University Individual talk Admixture and the gain and loss of biodiversity 03.03.2021 Lund, Sweden Marques David;
MEEGene seminar, Leipniz Institut Individual talk Rapid speciation facilitated by hybridisation 19.01.2021 Bonn, Germany Meier Joana;
Departmental seminar UMass-Dartmouth Individual talk The role of hybridisation in rapid speciation 13.11.2020 Darthmouth, United States of America Meier Joana;
Genetic Diversity Center (GDC) Symposium, ETHZ Talk given at a conference The multifaceted effects of admixture on biodiversity: lessons from African cichlid genomics 10.09.2020 Zürich, Switzerland Marques David;
Departmental seminar in Zoology and Environmental Sciences, U Punjabi Individual talk How hybridisation facilitates adaptive radiation in cichlid fishes and Heliconius butterflies 04.09.2020 Punjab, India Meier Joana;
Seminario de Investigacion, Universidad del Rosario Individual talk Introgression & Adaptive Radiation in cichlid & Heliconius  24.08.2020 Bogota, Colombia Meier Joana;
Speciation and Introgression Discussion, U Berkeley Individual talk Introgression & Adaptive Radiation in cichlid & Heliconius  23.06.2020 Berkeley, United States of America Meier Joana;
Aquatic Ecology and Evolution seminar, Eawag Individual talk Adaptive radiation genomics and the repeatability of evolution 25.03.2020 Kastanienbaum, LU, Switzerland Marques David;
Biology20, Swiss conference of organismic biology Talk given at a conference Demographic test of alternative modes of speciation in a large adaptive radiation 06.02.2020 Fribourg, Switzerland Marques David;
The Temporal Dynamics of Evolution Talk given at a conference The ecological and genomic basis of explosive adaptive radiation in sympatry 10.09.2019 Fribourg, Switzerland Seehausen Ole;
Departmental Seminar at McGill U Individual talk Hybridization fuels rapid adaptive radiation in cichlid fishes 30.08.2019 Montreal, Canada Meier Joana;
IBS 2019 Humboldt Meeting Talk given at a conference Hybridization fuels adaptive radiation of cichlid fishes 06.08.2019 Quito, Ecuador Meier Joana;
Departmental Seminar at U Edinburgh Individual talk Hybridization fuels adaptive radiation of cichlid fishes 05.06.2019 Edinburgh, Great Britain and Northern Ireland Meier Joana;
PhD defense symposium Shane Wright Talk given at a conference Genetic architecture of a mate choice trait differs between allopatric and sympatric sister species of cichlid fish 29.03.2019 Groningen, Netherlands Seehausen Ole;
PhD defense symposium Shane Wright Talk given at a conference Eco-genomic insights into the explosive species radiation of cichlid fish in the Lake Victoria region 28.03.2019 Groningen, Netherlands Seehausen Ole;
Gordon Research Seminar and Congress on Speciation Talk given at a conference Ancient hybridization fuels cichlid adaptive radiations 10.03.2019 Ventura, United States of America Meier Joana;
Gordon research conference and seminar on speciation Talk given at a conference A combinatorial view on speciation and adaptive radiation 10.03.2019 Ventura, United States of America Marques David;
MVZ Lunch Seminar, U Berkeley Talk given at a conference Hybridization fuels chichlid fish adaptive radiations 06.03.2019 Berkeley, United States of America Meier Joana;
SMILE seminar at Collège de France Individual talk Hybridization fuels repeated adaptive radiations in cichlid fishes 20.02.2019 Paris, France Meier Joana;
Biology19, Swiss conference of organismic biology Talk given at a conference Reassembly of old variants into novel combinations facilitated adaptive radiations in fish 07.02.2019 Zürich, Switzerland Marques David;
Departmental seminar, CNRS Individual talk Evolutionary novelty through hybridisation 13.01.2019 Paris, France Meier Joana;
PopGroup52 Talk given at a conference Hybridization fuels repeated bouts of adaptive radiation in Lake Victoria Region cichlid fishes 03.01.2019 Oxford, Great Britain and Northern Ireland Meier Joana;
Speciation Meeting, IST Talk given at a conference The reticulate evolutionary history of Lake Victoria cichlids 26.11.2018 Wien, Austria Meier Joana;
Evolution 2018 Talk given at a conference Admixture between divergent lineages facilitated fast ecological speciation in Lake Constance stickleback 19.08.2018 Montpellier, France Marques David;
Evolution2018 Talk given at a conference Tracing back the evolutionary history of adaptive radiation genes through the tangled web of cichlids 18.08.2018 Montpellier, France Meier Joana;
The American Genetic Association President’s Symposium Talk given at a conference Ecology and genomics of quantum speciation in Lake Victoria cichlid fish 22.07.2018 Hawaii, United States of America Seehausen Ole;
STICKLEBACK 2018 9th International Conference on Stickleback Behavior and Evolution Talk given at a conference The genomic basis of quantum speciation in Lake Victoria cichlids 07.07.2018 Kyoto, Japan Seehausen Ole;
Evolutionary Ecology and Population Genetics group seminar, Uni Zürich Individual talk Merging divergent gene pools: the key to rapid adaptation and speciation? 18.05.2018 Zürich, Switzerland Marques David;
Evolutionary Genetics and Genomics symposium 2018 Talk given at a conference Replaying the tape: repeatability of adaptation at genome level in stickleback and cichlids adaptive radiations 03.05.2018 Cambridge, Great Britain and Northern Ireland Marques David;
Current Topics in Zoology and Evolution Individual talk The reticulate evolution of Lake Victoria cichlids 30.04.2018 Basel, Switzerland Meier Joana;
Speciation Genomics Meeting Talk given at a conference Reshuffling of old variation facilitates rapid adaptive radiation in Lake Victoria 18.03.2018 Cambridge, Great Britain and Northern Ireland Meier Joana;
Lecture series in Ecology and Evolution Individual talk The reticulate evolution of Lake Victoria cichlid fishes 27.02.2018 Bern, Switzerland Meier Joana;
Biology18, Swiss conference of organismic biology Talk given at a conference Genomic structure in Lake Victoria cichlids 21.02.2018 Neuchatel, Switzerland Seehausen Ole; Meier Joana;
Biology18, Swiss conference of organismic biology Talk given at a conference Repeatability of genomic evolution across multiple adaptive radiations 21.02.2018 Neuchatel, Switzerland Marques David;
Evolutionary Genetics and Ecology group seminar, Centre d’Ecologie Fonctionelle et Evolutive, CNRS Montpellier Individual talk Merging divergent gene pools: the key to rapid adaptation and speciation? 18.12.2017 Montpellier, France Marques David;
Hybridization - causes and consequences for speciation Talk given at a conference Hybridization fuels adaptive radiation of cichlid fishes 14.12.2017 Oslo, Norway Meier Joana;
Annual meeting of Population Ecology Talk given at a conference Adaptive radiation fueled by hybridization - Genomic insights from Lake Victoria cichlid fishes 13.10.2017 Fukuoka, Japan Meier Joana;
Cambridge Speciation Genomics Meeting Talk given at a conference Panel discussion 19.09.2017 Cambridge, Great Britain and Northern Ireland Seehausen Ole;
Symposium of the Genetic Diversity Center at ETH Zürich Talk given at a conference Hybridization facilitates rapid adaptive radiation of cichlid fishes 05.09.2017 Zürich, Switzerland Meier Joana;
Cichlid Science 2017 Talk given at a conference Towards explaining how the impossible became true – the origin of 500 different species in 15’000 years 05.09.2017 Prague, Czech Republic Seehausen Ole;
Departmental highlight talk at the EAWAG symposium Talk given at a conference Ancient hybridization fuels rapid cichlid fish adaptive radiations 01.09.2017 Zürich, Switzerland Meier Joana;
European Society for Evolutionary Biology (ESEB) conference Talk given at a conference Tracing back the evolutionary history of trophic guilds through the tangled web of cichlids 21.08.2017 Groningen, Netherlands Seehausen Ole; Meier Joana;
European Society for Evolutionary Biology (ESEB) Talk given at a conference Unravelling the genomic structure and the importance of hybridization in Lake Victoria cichlid fishes 20.08.2017 Groningen, Netherlands Meier Joana;
AFRICAN GREAT LAKES CONFERENCE Talk given at a conference Session convener on ECOSYSTEM SERVICES AND BIODIVERSITY BENEFITS 01.05.2017 Jinja, Uganda Seehausen Ole;
Gordon Research Conference on Speciation Talk given at a conference Genomic structure in Lake Victoria cichlids 21.02.2017 Lucca, Italy Meier Joana; Seehausen Ole;
Gordon Research Conference on Speciation Talk given at a conference Diversity of Lake Victoria cichlids evolved within the modern lake through rapid reshuffling of ancient variation 19.02.2017 Lucca, Italy Meier Joana;
department seminar Individual talk Many questions and some answers about the origins of unusually large species richness in very little time 24.01.2017 Earlham Institute, Norwich, Great Britain and Northern Ireland Seehausen Ole;
"Biology of biodiversity” Commemorative Symposium for the 32nd International Prize for Biology Talk given at a conference On the origins of unusual species richness in cichlid fish 22.11.2016 Tokyo, Japan Seehausen Ole;


Self-organised

Title Date Place
Evolutionary implications of hybridization 24.08.2017 Groningen, Netherlands

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Hybrid Animals Are Not Nature’s Mis The Scientist International 2021
Media relations: radio, television The Zedonk Problem BBC Radio 4 International 2020
Media relations: print media, online media New Hybrid Species Remix Old Genes Creatively Quanta Magazine International 2019
Media relations: print media, online media Hybrids spawned Lake Victoria’s rich fish diversity Science International 2018
Media relations: print media, online media Buntbarsche im Viktoriasee Kreuzung liess Artenvielfalt explodieren Neue Zürcher Zeitung German-speaking Switzerland 2017
Video/Film Discovery Channel International 2017
Talks/events/exhibitions Explosive Artenbildung bei Buntbarschen Italian-speaking Switzerland German-speaking Switzerland Western Switzerland 2017
Media relations: print media, online media Number of species depends how you count them Science News International 2017

Awards

Title Year
Top Cited Article Journal of Evolutionary Biology 2019-2020 2021
Branco Weiss Fellowship 2020
Clarivate/Web of Science 2020 Highly Cited Researcher 2020
Marie Curie Individual Fellowship Origin and maintenance of biodiversity: An ecological, evolutionary and developmental theory of organisms’ interactions 2020
Clarivate/Web of Science 2019 Highly Cited Researcher 2019
Faculty award for the best PhD thesis of the Department of Biology, University of Bern 2018
St John's College research fellowship at University of Cambridge 2018
Wilhelmine Key Distinguished Lecture 2018 of the American Genetic Association 2018
Best poster award at the annual poster competition of the Centre for Ecology, Evolution and Biogeochemistry (CEEB) of EAWAG 2017

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
134657 Population genomics of adaptive radiation 01.02.2012 ProDoc
144046 Measuring ecological and genetic constraints to speciation 01.07.2013 Project funding (Div. I-III)
144046 Measuring ecological and genetic constraints to speciation 01.07.2013 Project funding (Div. I-III)

Abstract

Large and rapid adaptive radiations are iconic textbook examples of evolution in action. When analyzed in an appropriate comparative context, they become powerful systems to investigate and identify causes of variation in rates and patterns of diversification among evolutionary lineages. When cichlid fishes colonized a newly refilled Lake Victoria 15,000 years ago, they diversified into more than 500 species. This is one of the fastest rates of speciation ever documented in animals. Learning how the genomes of these cichlids interacted with environmental and intrinsic drivers of evolution during this radiation will shed light on the evolution of species diversity in general. When compared to other taxa in similar environmental situations, it will also elucidate how constraints to diversification can be overcome. Together with colleagues, we have recently generated five fully annotated reference genomes of African cichlid fish, including one from Lake Victoria. We have also generated extensive population genomic data for several Lake Victoria cichlid species using reduced representation library sequencing methods, and most recently we have sequenced whole genomes of eight further species. In order to more fully understand both the evolutionary processes of species diversification and the genomic mechanisms underlying these processes, we now need whole genome sequence information from many species across the radiation. In this project we propose to reconstruct the evolutionary history of the Lake Victoria radiation by sequencing more than 120 of the 500 known species of Lake Victoria cichlids. We will also use genomic sequence data to reconstruct relationships for several small radiations in isolated lakes that were colonized either by populations descending from the same admixed ancestry as the Victoria radiation, or that descended from one of the lineages that admixed in the history of the Lake Victoria region superflock. Reconstructing the phylogenetic history of radiations in Lake Victoria and those in the smaller lakes will allow us to test important hypotheses about the dynamics of adaptive radiation, such as the temporal sequence in the origination of major ecotypic groups (the “stages of radiation” hypothesis), the extent of parallel speciation at different geographical and time scales, and will allow us, for the first time in a large recent cichlid radiation, to test for a slowdown in speciation and phenotypic evolution rates as would be predicted by ecological limits to evolving species richness. The comparison of radiations with different ancestries will then allow us to understand how a history of admixture has affected these dynamics and shaped the outcomes of cichlid radiation.Using population genomic analyses to infer species and clade-level demographic histories, we will infer demographic parameters for key phases in the radiations and for individual speciation events. We will use these inferences to test predictions made by alternative evolutionary models for speciation and adaptive radiation (speciation in sympatry versus intralacustrine allopatry, speciation in small populations with founder effects versus speciation in large populations, divergent selection, gene flow, hybrid speciation). We shall seek to characterize the genomic elements involved in speciation and post-speciation adaptive radiation in terms of genetic incompatibilities, adaptation-related and sexually selected genes. We will examine if the same elements are repeatedly involved in species differentiation, and at which level such parallelism occurs (SNP, gene, pathway). Finally, we will infer the sources of genetic variants from standing variation within one ancestral population, ancestral admixture between species, and de novo mutation within the radiation. We will use this data to test components of the hybrid swarm origin and syngameon hypotheses of adaptive radiation.
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