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Kumar S, Tao Q, Lamarca AP, Tamura K. Computational Reproducibility of Molecular Phylogenies. Mol Biol Evol 2023; 40:msad165. [PMID: 37467477 PMCID: PMC10370456 DOI: 10.1093/molbev/msad165] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
Repeated runs of the same program can generate different molecular phylogenies from identical data sets under the same analytical conditions. This lack of reproducibility of inferred phylogenies casts a long shadow on downstream research employing these phylogenies in areas such as comparative genomics, systematics, and functional biology. We have assessed the relative accuracies and log-likelihoods of alternative phylogenies generated for computer-simulated and empirical data sets. Our findings indicate that these alternative phylogenies reconstruct evolutionary relationships with comparable accuracy. They also have similar log-likelihoods that are not inferior to the log-likelihoods of the true tree. We determined that the direct relationship between irreproducibility and inaccuracy is due to their common dependence on the amount of phylogenetic information in the data. While computational reproducibility can be enhanced through more extensive heuristic searches for the maximum likelihood tree, this does not lead to higher accuracy. We conclude that computational irreproducibility plays a minor role in molecular phylogenetics.
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Affiliation(s)
- Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Alessandra P Lamarca
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Koichiro Tamura
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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Lamarca AP, Souza UJBD, Moreira FRR, Almeida LGPD, Menezes MTD, Souza ABD, Ferreira ACDS, Gerber AL, Lima ABD, Guimarães APDC, Cavalcanti AC, Silva ABPE, Lima BI, Lobato C, Silva CGD, Mendonça CPTB, Queiroz DC, Zauli DAG, Menezes D, Possebon FS, Cardoso FDP, Malta FSV, Braga-Paz I, Silva JDP, Ferreira JGG, Galvão JD, Souza LMD, Ferreira L, Possuelo LG, Cavalcante LTDF, Alvim LB, Souza LFAD, Santos LCGDAE, Dias RC, Souza RB, Castro TRY, Valim ARDM, Campos FS, Araujo JP, Trindade PDA, Aguiar RS, Michael Delai R, Vasconcelos ATRD. The Omicron Lineages BA.1 and BA.2 ( Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub. Viruses 2023; 15:888. [PMID: 37112869 PMCID: PMC10146814 DOI: 10.3390/v15040888] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.
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Affiliation(s)
- Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Ueric José Borges de Souza
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins, Campus de Gurupi, Palmas 77410-570, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Mariane Talon de Menezes
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | | | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | - Aline B de Lima
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-075, Brazil
| | | | - Aryel B Paz E Silva
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Bruna Israel Lima
- Laboratório de Biologia Molecular, Parque Científico e Tecnológico Regional, Universidade de Santa Cruz do Sul, Santa Cruz do Sul 96815-900, Brazil
| | - Cirley Lobato
- Centro de Ciências de Saúde e do Desporto, Universidade Federal do Acre, Rio Branco 69920-900, Brazil
| | | | - Cristiane P T B Mendonça
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Daniel Costa Queiroz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Diego Menezes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Fábio Sossai Possebon
- Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu 18618-689, Brazil
| | | | | | - Isabela Braga-Paz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Joice do Prado Silva
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Jorge Gomes Goulart Ferreira
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | | | - Leonardo Ferreira
- Centro de Medicina Tropical da Tríplice Fronteira, Foz do Iguaçu 85866-010, Brazil
| | - Lia Gonçalves Possuelo
- Departmento de Ciências da Vida, Universidade de Santa Cruz do Sul, Santa Cruz do Sul 96815-900, Brazil
| | | | - Luige B Alvim
- Departamento de Pesquisa & Desenvolvimento, Instituto Hermes Pardini, Belo Horizonte 30140-070, Brazil
| | - Luiz Fellype Alves de Souza
- Centro de Infectologia Charles Mérieux and Laboratório Rodolphe Mérieux, Hospital das Clínicas do Acre, Rio Branco 69920-223, Brazil
| | - Luiza C G de Araújo E Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rillery Calixto Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Rutilene Barbosa Souza
- Centro de Infectologia Charles Mérieux and Laboratório Rodolphe Mérieux, Hospital das Clínicas do Acre, Rio Branco 69920-223, Brazil
| | - Thaís Regina Y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | | | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, Brazil
| | - João Pessoa Araujo
- Instituto de Biotecnologia, Universidade Estadual Paulista, Botucatu 18618-689, Brazil
| | - Priscila de Arruda Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Robson Michael Delai
- Centro de Medicina Tropical da Tríplice Fronteira, Foz do Iguaçu 85866-010, Brazil
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3
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Nour D, Rafei R, Lamarca AP, de Almeida LGP, Osman M, Ismail MB, Mallat H, Berry A, Burfin G, Semanas Q, Josset L, Hassan H, Dabboussi F, Lina B, Colson P, Vasconcelos ATR, Hamze M. The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example. Viruses 2022; 14:1640. [PMID: 36016262 PMCID: PMC9412248 DOI: 10.3390/v14081640] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 02/03/2023] Open
Abstract
In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese-Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants.
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Affiliation(s)
- Dalal Nour
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
| | - Alessandra P. Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brazil; (A.P.L.); (L.G.P.d.A.)
| | - Luiz G. P. de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brazil; (A.P.L.); (L.G.P.d.A.)
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mohamad Bachar Ismail
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
- Faculty of Sciences, Lebanese University, Tripoli 1300, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
| | - Atika Berry
- Head of the Preventive Medicine Department, Ministry of Public Health, Beirut 1001, Lebanon;
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, F-69004 Lyon, France; (G.B.); (Q.S.); (L.J.); (B.L.)
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ. Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Quentin Semanas
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, F-69004 Lyon, France; (G.B.); (Q.S.); (L.J.); (B.L.)
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ. Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, F-69004 Lyon, France; (G.B.); (Q.S.); (L.J.); (B.L.)
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ. Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut 1001, Lebanon;
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, F-69004 Lyon, France; (G.B.); (Q.S.); (L.J.); (B.L.)
- GenEPII Sequencing Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004 Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ. Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France;
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Ana Tereza R. Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brazil; (A.P.L.); (L.G.P.d.A.)
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School for Science & Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon; (D.N.); (R.R.); (M.O.); (M.B.I.); (H.M.); (F.D.)
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Francisco Junior RDS, de Almeida LGP, Lamarca AP, Cavalcante L, Martins Y, Gerber AL, Guimarães APDC, Salviano RB, Dos Santos FL, de Oliveira TH, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, da Silva FD, Garcia MHDO, de Souza LM, da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Tanuri A, Vasconcelos ATR. Emergence of Within-Host SARS-CoV-2 Recombinant Genome After Coinfection by Gamma and Delta Variants: A Case Report. Front Public Health 2022; 10:849978. [PMID: 35273945 PMCID: PMC8902039 DOI: 10.3389/fpubh.2022.849978] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, we report the first case of intra-host SARS-CoV-2 recombination during a coinfection by the variants of concern (VOC) AY.33 (Delta) and P.1 (Gamma) supported by sequencing reads harboring a mosaic of lineage-defining mutations. By using next-generation sequencing reads intersecting regions that simultaneously overlap lineage-defining mutations from Gamma and Delta, we were able to identify a total of six recombinant regions across the SARS-CoV-2 genome within a sample. Four of them mapped in the spike gene and two in the nucleocapsid gene. We detected mosaic reads harboring a combination of lineage-defining mutations from each VOC. To our knowledge, this is the first report of intra-host RNA-RNA recombination between two lineages of SARS-CoV-2, which can represent a threat to public health management during the COVID-19 pandemic due to the possibility of the emergence of viruses with recombinant phenotypes.
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Affiliation(s)
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Yasmmin Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Ricardo Barbosa Salviano
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Leitão Dos Santos
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago Henrique de Oliveira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
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Lamarca AP, Mello B, Schrago CG. The performance of outgroup-free rooting under evolutionary radiations. Mol Phylogenet Evol 2022; 169:107434. [PMID: 35143961 DOI: 10.1016/j.ympev.2022.107434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 11/18/2022]
Abstract
Tree rooting implies a temporal dimension to phylogenies. Only after defining the position of the root node is that the ancestral-descendant relationship between branches can be fully deduced. Rooting has been usually carried out by employing evolutionarily close outgroup lineages, which is a drawback when these lineages are unavailable or unknown. Alternatively, outgroup-free rooting methods were proposed, which rely on the constancy of evolutionary rates to varying degrees. In this work we analyzed the performance of two of these methods, the midpoint rooting (MPR) and the minimal ancestor deviation (MAD), in rooting topologies evolved under challenging scenarios of fast evolutionary radiations derived from empirical data, characterized by short internal branches near the crown node. Considering all branch length combinations investigated, both methods exhibited average success rates below 50%, although MAD slightly outperformed MPR. Moreover, tree balance significantly impacted the relative performance of the methods. We found that, in four-taxa unrooted trees, the outcome of whether both methodologies will correctly root the tree can be roughly predicted by two simple dimensionless metrics: the coefficient of variation of the external branch lengths, and the ratio between the internal branch length to the total sum of branch lengths, which were employed to devise a general linear model that allowed calculating the probability of correct placing the root node for any four-taxa tree. We predicted that the performance of both outgroup-free rooting methods on loci representing the placental mammal radiation ranged between 50% and 75%.
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Affiliation(s)
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, RJ, Brazil.
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6
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da Silva Francisco Junior R, Lamarca AP, de Almeida LGP, Cavalcante L, Machado DT, Martins Y, Brustolini O, Gerber AL, de C Guimarães AP, Gonçalves RB, Alves C, Mariani D, Cruz TF, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, da Silva FD, de Oliveira Garcia MH, de Souza LM, da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Struchiner CJ, Tanuri A, Vasconcelos ATR. Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil. Viruses 2021; 13:2013. [PMID: 34696443 PMCID: PMC8537965 DOI: 10.3390/v13102013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023] Open
Abstract
In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.
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Affiliation(s)
- Ronaldo da Silva Francisco Junior
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Douglas Terra Machado
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Yasmmin Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Otávio Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Reinaldo Bellini Gonçalves
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Cassia Alves
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Diana Mariani
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Thais Felix Cruz
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | | | - Erika Martins de Carvalho
- Unidades de Apoio ao Diagnóstico da COVID-19, Rio de Janeiro 21040-900, Brazil; (I.V.d.S.); (E.M.d.C.)
| | - Mario Sergio Ribeiro
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Flávio Dias da Silva
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | | | - Leandro Magalhães de Souza
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Cristiane Gomes da Silva
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Caio Luiz Pereira Ribeiro
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | - Andréa Cony Cavalcanti
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Claudia Maria Braga de Mello
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
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7
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Lamarca AP, de Almeida LGP, Francisco RDS, Lima LFA, Scortecci KC, Perez VP, Brustolini OJ, Sousa ESS, Secco DA, Santos AMG, Albuquerque GR, Mariano APM, Maciel BM, Gerber AL, Guimarães APDC, Nascimento PR, Neto FPF, Gadelha SR, Porto LC, Campana EH, Jeronimo SMB, Vasconcelos ATR. Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. PLoS Negl Trop Dis 2021; 15:e0009835. [PMID: 34644287 PMCID: PMC8544873 DOI: 10.1371/journal.pntd.0009835] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/25/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.
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Affiliation(s)
- Alessandra P. Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz G. P. de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | | | - Kátia Castanho Scortecci
- Laboratório de Biologia Molecular e Genômica, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Vinícius Pietta Perez
- Laboratório de Endemias, Núcleo de Medicina Tropical, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Otavio J. Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Eduardo Sérgio Soares Sousa
- Laboratório de Biologia Molecular, Centro de Ciências Médicas, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Danielle Angst Secco
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Angela Maria Guimarães Santos
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - George Rego Albuquerque
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Ana Paula Melo Mariano
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Bianca Mendes Maciel
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Alexandra L. Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Paulo Ricardo Nascimento
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Francisco Paulo Freire Neto
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Sandra Rocha Gadelha
- Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Luís Cristóvão Porto
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eloiza Helena Campana
- Laboratório de Biologia Molecular, Centro de Ciências Médicas, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Selma Maria Bezerra Jeronimo
- Instituto de Medicina Tropical do Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Brazil
- Departamento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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8
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Francisco RDS, Benites LF, Lamarca AP, de Almeida LGP, Hansen AW, Gularte JS, Demoliner M, Gerber AL, de C Guimarães AP, Antunes AKE, Heldt FH, Mallmann L, Hermann B, Ziulkoski AL, Goes V, Schallenberger K, Fillipi M, Pereira F, Weber MN, de Almeida PR, Fleck JD, Vasconcelos ATR, Spilki FR. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Virus Res 2021; 296:198345. [PMID: 33631222 PMCID: PMC7898980 DOI: 10.1016/j.virusres.2021.198345] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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: 01/13/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/24/2022]
Abstract
Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13 L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.
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Affiliation(s)
| | - L Felipe Benites
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Meriane Demoliner
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Fagner Henrique Heldt
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Larissa Mallmann
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Bruna Hermann
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Ana Luiza Ziulkoski
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Vyctoria Goes
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Micheli Fillipi
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Francini Pereira
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | | | - Juliane Deise Fleck
- Laboratório de Microbiologia Molecular,Universidade Feevale, Rio Grande do Sul, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
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9
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Moreira DA, Lamarca AP, Soares RF, Coelho AMA, Furtado C, Scherer NM, Moreira MAM, Seuánez HN, Boroni M. Transcriptome of the Southern Muriqui Brachyteles arachnoides (Primates:Platyrrhini), a Critically Endangered New World Monkey: Evidence of Adaptive Evolution. Front Genet 2020; 11:831. [PMID: 32849820 PMCID: PMC7412869 DOI: 10.3389/fgene.2020.00831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/16/2020] [Accepted: 07/09/2020] [Indexed: 12/03/2022] Open
Abstract
The southern muriqui (Brachyteles arachnoides) is the largest neotropical primate. This species is endemic to Brazil and is currently critically endangered due to its habitat destruction. The genetic basis underlying adaptive traits of New World monkeys has been a subject of interest to several investigators, with significant concern about genes related to the immune system. In the absence of a reference genome, RNA-seq and de novo transcriptome assembly have proved to be valuable genetic procedures for accessing gene sequences and testing evolutionary hypotheses. We present here a first report on the sequencing, assembly, annotation and adaptive selection analysis for thousands of transcripts of B. arachnoides from two different samples, corresponding to 13 different blood cells and fibroblasts. We assembled 284,283 transcripts with N50 of 2,940 bp, with a high rate of complete transcripts, with a median high scoring pair coverage of 88.2%, including low expressed transcripts, accounting for 72.3% of complete BUSCOs. We could predict and extract 81,400 coding sequences with 79.8% of significant BLAST hit against the Euarchontoglires SwissProt dataset. Of these 64,929 sequences, 34,084 were considered homologous to Supraprimate proteins, and of the remaining sequences (30,845), 94% were associated with a protein domain or a KEGG Orthology group, indicating potentially novel or specific protein-coding genes of B. arachnoides. We use the predicted protein sequences to perform a comparative analysis with 10 other primates. This analysis revealed, for the first time in an Atelid species, an expansion of APOBEC3G, extending this knowledge to all NWM families. Using a branch-site model, we searched for evidence of positive selection in 4,533 orthologous sets. This evolutionary analysis revealed 132 amino acid sites in 30 genes potentially evolving under positive selection, shedding light on primate genome evolution. These genes belonged to a wide variety of categories, including those encoding the innate immune system proteins (APOBEC3G, OAS2, and CEACAM1) among others related to the immune response. This work generated a set of thousands of complete sequences that can be used in other studies on molecular evolution and may help to unveil the evolution of primate genes. Still, further functional studies are required to provide an understanding of the underlying evolutionary forces modeling the primate genome.
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Affiliation(s)
- Daniel A Moreira
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Alessandra P Lamarca
- Laboratory of Bioinformatics and Molecular Evolution, Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rafael Ferreira Soares
- Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ana M A Coelho
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carolina Furtado
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Nicole M Scherer
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Miguel A M Moreira
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Hector N Seuánez
- Genetics Program, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
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10
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Abstract
Abstract
Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root.
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Affiliation(s)
- Alessandra P Lamarca
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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