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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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Lenser T, Theißen G. Molecular mechanisms involved in convergent crop domestication. TRENDS IN PLANT SCIENCE 2013; 18:704-14. [PMID: 24035234 DOI: 10.1016/j.tplants.2013.08.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/21/2013] [Indexed: 05/21/2023]
Abstract
Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions.
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Affiliation(s)
- Teresa Lenser
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
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Roda F, Liu H, Wilkinson MJ, Walter GM, James ME, Bernal DM, Melo MC, Lowe A, Rieseberg LH, Prentis P, Ortiz-Barrientos D. CONVERGENCE AND DIVERGENCE DURING THE ADAPTATION TO SIMILAR ENVIRONMENTS BY AN AUSTRALIAN GROUNDSEL. Evolution 2013; 67:2515-29. [DOI: 10.1111/evo.12136] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/03/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Federico Roda
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Huanle Liu
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Melanie J. Wilkinson
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Gregory M. Walter
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maddie E. James
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Diana M. Bernal
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | - Maria C. Melo
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
| | | | | | - Peter Prentis
- Queensland Institute of Technology; Biogeosciences; Brisbane; QLD; 4001; Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences; The University of Queensland; St. Lucia; QLD; 4072; Australia
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Mühlhausen A, Lenser T, Mummenhoff K, Theißen G. Evidence that an evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) was caused by a change in the control of valve margin identity genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:824-35. [PMID: 23173897 DOI: 10.1111/tpj.12079] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 05/08/2023]
Abstract
In the Brassicaceae, indehiscent fruits evolved from dehiscent fruits several times independently. Here we use closely related wild species of the genus Lepidium as a model system to analyse the underlying developmental genetic mechanisms in a candidate gene approach. ALCATRAZ (ALC), INDEHISCENT (IND), SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2) are known fruit developmental genes of Arabidopsis thaliana that are expressed in the fruit valve margin governing dehiscence zone formation. Comparative expression analysis by quantitative RT-PCR, Northern blot and in situ hybridization show that their orthologues from Lepidium campestre (dehiscent fruits) are similarly expressed at valve margins. In sharp contrast, expression of the respective orthologues is abolished in the corresponding tissue of indehiscent Lepidium appelianum fruits, indicating that changes in the genetic pathway identified in A. thaliana caused the transition from dehiscent to indehiscent fruits in the investigated species. As parallel mutations in different genes are quite unlikely, we conclude that the changes in gene expression patterns are probably caused by changes in upstream regulators of ALC, IND and SHP1/2, possible candidates from A. thaliana being FRUITFULL (FUL), REPLUMLESS (RPL) and APETALA2 (AP2). However, neither expression analyses nor functional tests in transgenic plants provided any evidence that the FUL or RPL orthologues of Lepidium were involved in evolution of fruit indehiscence in Lepidium. In contrast, stronger expression of AP2 in indehiscent compared to dehiscent fruits identifies AP2 as a candidate gene that deserves further investigation.
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Affiliation(s)
- Andreas Mühlhausen
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
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