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Missaggia BO, Reales G, Cybis GB, Hünemeier T, Bortolini MC. Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans. Am J Med Genet C Semin Med Genet 2020; 184:1060-1077. [PMID: 33325159 DOI: 10.1002/ajmg.c.31873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/06/2022]
Abstract
We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.
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Affiliation(s)
- Bruna Oliveira Missaggia
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela B Cybis
- Statistics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Reales G, Paixão-Côrtes VR, Cybis GB, Gonçalves GL, Pissinatti A, Salzano FM, Bortolini MC. Serotonin, behavior, and natural selection in New World monkeys. J Evol Biol 2018; 31:1180-1192. [DOI: 10.1111/jeb.13295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 05/16/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Guillermo Reales
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | | | - Gabriela B. Cybis
- Departamento de Estatística; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Gislene L. Gonçalves
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | | | - Francisco M. Salzano
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética; Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
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Cybis GB, Sinsheimer JS, Bedford T, Rambaut A, Lemey P, Suchard MA. Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza. Stat Med 2018; 37:195-206. [PMID: 28098392 DOI: 10.1002/sim.7196] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022]
Abstract
Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Gabriela B Cybis
- Department of Statistics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Janet S Sinsheimer
- Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.,Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California, U.S.A
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, U.K.,Fogarty International Center, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.,Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California, U.S.A
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Affiliation(s)
- Gabriela B. Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcio Valk
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sílvia R. C. Lopes
- Institute of Mathematics and Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P, Suchard MA. ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. Ann Appl Stat 2015; 9:969-991. [PMID: 27053974 PMCID: PMC4820077 DOI: 10.1214/15-aoas821] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the correlation between multiple types of data, while simultaneously controlling for their unknown shared evolutionary history informed through molecular sequences. The latent formulation enables us to consider in a single model combinations of continuous traits, discrete binary traits, and discrete traits with multiple ordered and unordered states. Previous approaches have entertained a single data type generally along a fixed history, precluding estimation of correlation between traits and ignoring uncertainty in the history. We implement our model in a Bayesian phylogenetic framework, and discuss inference techniques for hypothesis testing. Finally, we showcase the method through applications to columbine flower morphology, antibiotic resistance in Salmonella, and epitope evolution in influenza.
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Ramos-Fregonezi AMC, Fregonezi JN, Cybis GB, Fagundes NJR, Bonatto SL, Freitas LB. Were sea level changes during the Pleistocene in the South Atlantic Coastal Plain a driver of speciation in Petunia (Solanaceae)? BMC Evol Biol 2015; 15:92. [PMID: 25989835 PMCID: PMC4438590 DOI: 10.1186/s12862-015-0363-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/27/2015] [Indexed: 11/26/2022] Open
Abstract
Background Quaternary climatic changes led to variations in sea level and these variations played a significant role in the generation of marine terrace deposits in the South Atlantic Coastal Plain. The main consequence of the increase in sea level was local extinction or population displacement, such that coastal species would be found around the new coastline. Our main goal was to investigate the effects of sea level changes on the geographical structure and variability of genetic lineages from a Petunia species endemic to the South Atlantic Coastal Plain. We employed a phylogeographic approach based on plastid sequences obtained from individuals collected from the complete geographic distribution of Petunia integrifolia ssp. depauperata and its sister group. We used population genetics tests to evaluate the degree of genetic variation and structure among and within populations, and we used haplotype network analysis and Bayesian phylogenetic methods to estimate divergence times and population growth. Results We observed three major genetic lineages whose geographical distribution may be related to different transgression/regression events that occurred in this region during the Pleistocene. The divergence time between the monophyletic group P. integrifolia ssp. depauperata and its sister group (P. integrifolia ssp. integrifolia) was compatible with geological estimates of the availability of the coastal plain. Similarly, the origin of each genetic lineage is congruent with geological estimates of habitat availability. Conclusions Diversification of P. integrifolia ssp. depauperata possibly occurred as a consequence of the marine transgression/regression cycles during the Pleistocene. In periods of high sea level, plants were most likely restricted to a refuge area corresponding to fossil dunes and granitic hills, from which they colonized the coast once the sea level came down. The modern pattern of lineage geographical distribution and population variation was established by a range expansion with serial founder effects conditioned on soil availability. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0363-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aline M C Ramos-Fregonezi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, Brazil.
| | - Jeferson N Fregonezi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, Brazil.
| | - Gabriela B Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, P.O. Box 15080, Porto Alegre, Brazil.
| | - Nelson J R Fagundes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, Brazil.
| | - Sandro L Bonatto
- Genomic and Molecular Biology Laboratory, Pontifícia Universidade Católica do Rio Grande do Sul, Ipiranga 6681, 90610 001, Porto Alegre, RS, Brazil.
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Porto Alegre, Brazil.
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Abstract
Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. Consider N exchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients.
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Affiliation(s)
- Gabriela B Cybis
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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