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Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023; 46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.
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Affiliation(s)
- Anieli Guirro Pereira
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| | - Tiana Kohlsdorf
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
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Wheeler LC, Walker JF, Ng J, Deanna R, Dunbar-Wallis A, Backes A, Pezzi PH, Palchetti MV, Robertson HM, Monaghan A, Brandão de Freitas L, Barboza GE, Moyroud E, Smith SD. Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway. Mol Biol Evol 2022; 39:6536971. [PMID: 35212724 PMCID: PMC8911815 DOI: 10.1093/molbev/msac044] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.
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Affiliation(s)
- Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Joseph F Walker
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Rocío Deanna
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334.,Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Amy Dunbar-Wallis
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Pedro H Pezzi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - M Virginia Palchetti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Holly M Robertson
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Andrew Monaghan
- Research Computing,University of Colorado, 3100 Marine Street, 597 UCB Boulder, CO 80303
| | - Loreta Brandão de Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina.,Facultad de Ciencias Químicas, Universidad Nacional de Córdoba,Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - Edwige Moyroud
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
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