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Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, Alberto FJ, Servin B, Biscarini F, Alberti A, Engelen S, Stella A, Colli L, Coissac E, Bruford MW, Ajmone-Marsan P, Negrini R, Clarke L, Flicek P, Chikhi A, Joost S, Taberlet P, Pompanon F. Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints. Mol Ecol 2023:e17257. [PMID: 38149334 DOI: 10.1111/mec.17257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/18/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
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Affiliation(s)
- Badr Benjelloun
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Florian J Alberto
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Castanet-Tolosan, France
| | - Filippo Biscarini
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, Evry, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Wales, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, Piacenza, Italy
- AIA Associazione Italiana Allevatori, Roma, Italy
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Abdelkader Chikhi
- Livestock Genomics Laboratory, Regional Center of Agricultural Research Tadla, National Institute of Agricultural Research INRA, Rabat, Morocco
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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