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GENADAP Résumé de rapport

Project ID: 293700
Financé au titre de: FP7-IDEAS-ERC
Pays: Germany

Mid-Term Report Summary - GENADAP (Comparative genomics of parallel evolution in repeated adaptive radiations)

ERC advanced grant GenAdap aims to study the comparative genomics of parallel evolution in repeated adaptive radiations. Biological diversity arises through the formation of new species. Adaptive radiation by ecological speciation is seen as a particularly powerful and fast mechanism for the orgin of biodiversity. We aimed in this project to understand the role of natural selection in adaptation and speciation through the study of parallel evolved phenotypes, since they are one of the most informative biological contexts in which to investigate how adaptive traits and new species evolve both at the phenotypic/ecological as well at the genomic/genetic level. The genetics of adaptation is still poorly understood and we aimed to contribute to the knowledge of how many and what portions of the genome are involved in adaptive speciation, what kind of genes, and what kind of genetic changes result in (parallel) adaptations.

In the crater lakes of Nicaragua of a unique natural experiment. Several adaptive radiations of cichlid fishes formed independently within only a few thousand years after colonization from a large ancestral lake. These extremely young adaptive radiations consist of a set of species that arose in sympatry and evolved parallel adaptations (such as limnetic and benthic body forms, hypertrophied lips and molariform dentition) repeatedly in their new habitats.

Bridging the genotype-phenotype gap is now becoming possible through recent advances in next-generation DNA sequencing technologies. Using these we investigated the role and mechanisms of natural selection at the level of the entire genome. We already published 18 publications that resulted from this grant. We established the evolutionary history of the radiations, uncovered hybridization between species through highly sensitive genetic markers (such as thousands of ddRNA markers). This permitted us not only to use these markers to reconstruct the evolutionary history of these repeated adaptive radiations, but also to separate the effects of demography from selection.

Through comparative genomic and population genomic analyses (including establishing a reference genome), genome re-sequencing, and linkage, quantitative trait and association mapping, we have already identified genomic regions (QTLs) that are responsible for phenotypic differences between species and adaptation. We have identified QTLs with major phenotypic effects and suspected pleiotropy that affects correlated phenotypic traits. In the second half of this grant we aim to identify candidate genes, and aim to understand how and which mutations in these genes contribute to the adaptive phenotypic differences (and similarities) between extremely young species. We have established a set of genomic tools (BAC library, linkage maps, reference genome and now 150 re-sequenced genomes) to identify next structural variants, genes, types of mutations, differentiate between the effects of standing genetic variation vs. de-novo-mutations and lastly we will soon be in position to conduct functional assays using CRISPER-Cas technology.

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