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Oud MD, Mahoney SM, Pageau C, de Menezes MA, Smith N, Briskie JV, Reudink MW. Global patterns of plumage color evolution in island-living passeriform birds. PLoS One 2023; 18:e0294338. [PMID: 38100474 PMCID: PMC10723677 DOI: 10.1371/journal.pone.0294338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Island environments have the potential to change evolutionary trajectories of morphological traits in species relative to their mainland counterparts due to habitat and resource differences, or by reductions in the intensity of social or sexual selection. Latitude, island size, and isolation may further influence trait evolution through biases in colonization rates. We used a global dataset of passerine plumage color as a model group to identify selective pressures driving morphological evolution of island animals using phylogenetically-controlled analyses. We calculated chromaticity values from red and blue scores extracted from images of the majority of Passeriformes and tested these against the factors hypothesized to influence color evolution. In contrast to predictions based on sexual and social selection theory, we found consistent changes in island female color (lower red and higher blue chromaticity), but no change in males. Instead, island size and distance from mainland and other islands influenced color in both sexes, reinforcing the importance of island physiognomy in shaping evolutionary processes. Interactions between ecological factors and latitude also consistently influenced color for both sexes, supporting a latitudinal gradient hypothesis. Finally, patterns of color evolution varied among families, indicating taxon-specific microevolutionary processes in driving color evolution. Our results show island residency influences color evolution differently between sexes, but the patterns in both sexes are tempered by ecological, island characteristics, and phylogenetic effects that further vary in their importance among families. The key role of environmental factors in shaping bird plumage on islands further suggests a reduced importance of sexual and social factors in driving color evolution.
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Affiliation(s)
- Madison D. Oud
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Sean M. Mahoney
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
- School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ, United States of America
| | - Claudie Pageau
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Marcio Argollo de Menezes
- Physics Institute, Fluminense Federal University, Niteroi, Brazil
- National Institute of Science and Technology on Complex Systems, Rio de Janeiro, Brazil
| | - Nathan Smith
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - James V. Briskie
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Matthew W. Reudink
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
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Chagas MDS, Trindade dos Santos M, Argollo de Menezes M, da Silva FAB. Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851. Front Microbiol 2023; 14:1274740. [PMID: 38152377 PMCID: PMC10752298 DOI: 10.3389/fmicb.2023.1274740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/31/2023] [Indexed: 12/29/2023] Open
Abstract
Introduction Pseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil. Methods One way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems. Results and discussion Therefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies.
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Chagas MDS, Medeiros F, dos Santos MT, de Menezes MA, Carvalho-Assef APD, da Silva FAB. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Mem Inst Oswaldo Cruz 2022; 117:e220111. [PMID: 36259790 PMCID: PMC9565603 DOI: 10.1590/0074-02760220111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/09/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.
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Affiliation(s)
- Márcia da Silva Chagas
- Fundação Oswaldo Cruz-Fiocruz, Programa de Computação Científica, Rio de Janeiro, RJ, Brasil,+ Corresponding authors: /
| | - Fernando Medeiros
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia, Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Rio de Janeiro, RJ, Brasil
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Medeiros Filho F, do Nascimento APB, Costa MDOCE, Merigueti TC, de Menezes MA, Nicolás MF, Dos Santos MT, Carvalho-Assef APD, da Silva FAB. A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Models. Front Mol Biosci 2021; 8:728129. [PMID: 34616771 PMCID: PMC8488468 DOI: 10.3389/fmolb.2021.728129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that has been a constant global health problem due to its ability to cause infection at different body sites and its resistance to a broad spectrum of clinically available antibiotics. The World Health Organization classified multidrug-resistant Pseudomonas aeruginosa among the top-ranked organisms that require urgent research and development of effective therapeutic options. Several approaches have been taken to achieve these goals, but they all depend on discovering potential drug targets. The large amount of data obtained from sequencing technologies has been used to create computational models of organisms, which provide a powerful tool for better understanding their biological behavior. In the present work, we applied a method to integrate transcriptome data with genome-scale metabolic networks of Pseudomonas aeruginosa. We submitted both metabolic and integrated models to dynamic simulations and compared their performance with published in vitro growth curves. In addition, we used these models to identify potential therapeutic targets and compared the results to analyze the assumption that computational models enriched with biological measurements can provide more selective and (or) specific predictions. Our results demonstrate that dynamic simulations from integrated models result in more accurate growth curves and flux distribution more coherent with biological observations. Moreover, identifying drug targets from integrated models is more selective as the predicted genes were a subset of those found in the metabolic models. Our analysis resulted in the identification of 26 non-host homologous targets. Among them, we highlighted five top-ranked genes based on lesser conservation with the human microbiome. Overall, some of the genes identified in this work have already been proposed by different approaches and (or) are already investigated as targets to antimicrobial compounds, reinforcing the benefit of using integrated models as a starting point to selecting biologically relevant therapeutic targets.
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Vale MM, Berenguer E, Argollo de Menezes M, Viveiros de Castro EB, Pugliese de Siqueira L, Portela RDCQ. The COVID-19 pandemic as an opportunity to weaken environmental protection in Brazil. Biol Conserv 2021; 255:108994. [PMID: 33568834 PMCID: PMC7862926 DOI: 10.1016/j.biocon.2021.108994] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 05/25/2023]
Abstract
This paper examines the effects of the COVID-19 pandemic on environmental protection and legislation in Brazil. We evaluate major legislative actions, environmental fines and deforestation since January 2019. We show that 57 legislative acts aimed at weakening environmental protection in Brazil during the current administration, almost half of which in the seven-month period of the pandemic in Brazil, with September 2020 as the month with the most legislative acts (n = 16). These acts either deregulated or weakened current environmental legislation, with a number of them aimed at dismantling the main federal institutions in charge of environmental protection. We also found a 72% reduction in environmental fines during the pandemic, despite an increase in Amazonian deforestation during this period. We conclude that the current administration is taking advantage of the COVID-19 pandemic to intensify a pattern of weakening environmental protection in Brazil. This has the potential to intensify ongoing loss of biodiversity, greenhouse gas emissions, and the likelihood of other zoonotic disease outbreaks, and inflict substantial harm to traditional and indigenous peoples. We highlight the key role of the scientific community, media and civil society, national and international levels, in order to reverse these harmful actions.
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Affiliation(s)
- Mariana M Vale
- Ecology Department, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
- National Institute of Science and Technology on Ecology, Evolution and Biodiversity Conservation, Goiania, GO 74690-900, Brazil
- Board of Trustees, Tijuca National Park, Rio de Janeiro, RJ 22241-330, Brazil
| | - Erika Berenguer
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, OX1 3QY Oxford, UK
- Lancaster Environment Centre, Lancaster University, LA1 4YQ Lancaster, UK
| | | | | | | | - Rita de Cássia Q Portela
- Ecology Department, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
- Board of Trustees, Poço das Antas Biological Reserve, Silva Jardim, RJ 28820-000, Brazil
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Pageau C, Vale MM, de Menezes MA, Barçante L, Shaikh M, S. Alves MA, Reudink MW. Evolution of altitudinal migration in passerines is linked to diet. Ecol Evol 2020; 10:3338-3345. [PMID: 32273991 PMCID: PMC7141039 DOI: 10.1002/ece3.6126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 11/22/2022] Open
Abstract
Bird migration is typically associated with a latitudinal movement from north to south and vice versa. However, many bird species migrate seasonally with an upslope or downslope movement in a process termed altitudinal migration. Globally, 830 of the 6,579 Passeriformes species are considered altitudinal migrants and this pattern has emerged multiple times across 77 families of this order. Recent work has indicated an association between altitudinal migration and diet, but none have looked at diet as a potential evolutionary driver. Here, we investigated potential evolutionary drivers of altitudinal migration in passerines around the world by using phylogenetic comparative methods. We tested for evolutionary associations between altitudinal migration and foraging guild and primary habitat preference in passerines species worldwide. Our results indicate that foraging guild is evolutionarily associated with altitudinal migration, but this relationship varies across zoogeographical regions. In the Nearctic, herbivorous and omnivorous species are associated with altitudinal migration, while only omnivorous species are associated with altitudinal migration in the Palearctic. Habitat was not strongly linked to the evolution of altitudinal migration. While our results point to diet as a potentially important driver of altitudinal migration, the evolution of this behavior is complex and certainly driven by multiple factors. Altitudinal migration varies in its use (for breeding or molting), within a species, population, and even at the individual level. As such, the evolution of altitudinal migration is likely driven by an ensemble of factors, but this study provides a beginning framework for understanding the evolution of this complex behavior.
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Affiliation(s)
- Claudie Pageau
- Department of Biological SciencesThompson Rivers UniversityKamloopsBCCanada
| | - Mariana M. Vale
- Ecology DepartmentFederal University of Rio de JaneiroRio de JaneiroBrazil
- National Institutes for Science and Technology in Ecology, Evolution and Biodiversity ConservationGoiásBrazil
| | - Marcio Argollo de Menezes
- Physics InstituteFluminense Federal UniversityNiteroiBrazil
- National Institute of Science and Technology on Complex SystemsRio de JaneiroBrazil
| | - Luciana Barçante
- Programa de Pós‐graduação em Ecologia e EvoluçãoUniversidade do Estado do Rio de JaneiroRio de JaneiroBrazil
| | - Mateen Shaikh
- Department of Mathematics & StatisticsThompson Rivers UniversityKamloopsBCCanada
| | - Maria Alice S. Alves
- Departamento de EcologiaUniversidade do Estado do Rio de JaneiroRio de JaneiroBrazil
| | - Matthew W. Reudink
- Department of Biological SciencesThompson Rivers UniversityKamloopsBCCanada
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