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Nyakio M, Were M, Wekesa C, Lungayia H, Okoth P, Were H. Molecular Footprints of Potato Virus Y Isolate Infecting Potatoes ( Solanum tuberosum) in Kenya. Adv Virol 2024; 2024:2197725. [PMID: 39139708 PMCID: PMC11321891 DOI: 10.1155/2024/2197725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/06/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Potato virus Y (PVY) is a highly diverse and genetically variable virus with various strains. Differential evolutionary routes have been reported in the genus Potyvirus, caused by natural selection pressure, mutation, and recombination, with their virulence being dependent on different environmental conditions. Despite its significance and economic impact on Solanaceous species, the understanding of PVY's phylogeography in Kenya remains limited and inadequately documented. The study centers on the molecular characterization of a Kenyan PVY isolate, GenBank accession number PP069009. In-depth phylogenetic analysis unveiled a strong evolutionary association between the Kenyan isolate and isolate [JQ924287] from the United States of America, supported by a robust 92% probability. Recombinant analyses exposed a mosaic-like genetic architecture within the Kenyan isolate, indicating multiple gene recombination events. Selection pressure scrutiny identified specific sites under selective pressure, with evidence of positive/diversifying and negative/purifying selection. Population genetics analysis revealed a calculated nucleotide diversity (π) of 0.00354881, while analysis of molecular variance (AMOVA) unveiled a structured genetic landscape with an øST value of 0.45224. The extensive haplotype network depicted the possibility of diverse PVY strains occurring across continents. This analysis provides valuable insights into the genetic diversity and distribution of PVY globally, highlighting the importance of understanding evolutionary dynamics for effective management and control strategies of PVY on a global scale.
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Affiliation(s)
- Maryrose Nyakio
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Mariam Were
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Clabe Wekesa
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Henry Lungayia
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Patrick Okoth
- Department of Biological SciencesSchool of Natural SciencesMasinde Muliro University of Science & Technology, P.O. Box 190, Kakamega 50100, Kenya
| | - Hassan Were
- Department of Agriculture and Land Use ManagementSchool of AgricultureVeterinary Sciences and TechnologyMasinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya
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Gaballa A, Wiedmann M, Carroll LM. More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases. Front Cell Infect Microbiol 2023; 13:1060519. [PMID: 37360531 PMCID: PMC10285318 DOI: 10.3389/fcimb.2023.1060519] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Laura M. Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
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Álvarez-Carretero S, Kapli P, Yang Z. Beginner's Guide on the Use of PAML to Detect Positive Selection. Mol Biol Evol 2023; 40:7140562. [PMID: 37096789 PMCID: PMC10127084 DOI: 10.1093/molbev/msad041] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
The CODEML program in the PAML package has been widely used to analyze protein-coding gene sequences to estimate the synonymous and nonsynonymous rates (dS and dN) and to detect positive Darwinian selection driving protein evolution. For users not familiar with molecular evolutionary analysis, the program is known to have a steep learning curve. Here, we provide a step-by-step protocol to illustrate the commonly used tests available in the program, including the branch models, the site models, and the branch-site models, which can be used to detect positive selection driving adaptive protein evolution affecting particular lineages of the species phylogeny, affecting a subset of amino acid residues in the protein, and affecting a subset of sites along prespecified lineages, respectively. A data set of the myxovirus (Mx) genes from ten mammal and two bird species is used as an example. We discuss a new feature in CODEML that allows users to perform positive selection tests for multiple genes for the same set of taxa, as is common in modern genome-sequencing projects. The PAML package is distributed at https://github.com/abacus-gene/paml under the GNU license, with support provided at its discussion site (https://groups.google.com/g/pamlsoftware). Data files used in this protocol are available at https://github.com/abacus-gene/paml-tutorial.
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Affiliation(s)
- Sandra Álvarez-Carretero
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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Chen WT, Li M, Hu SY, Wang SH, Yuan ML. Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation. Front Genet 2023; 14:1137588. [PMID: 37144132 PMCID: PMC10151513 DOI: 10.3389/fgene.2023.1137588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.
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Affiliation(s)
- Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
| | - Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Ming-Long Yuan,
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Almeida de Jesus D, Batista DM, Monteiro EF, Salzman S, Carvalho LM, Santana K, André T. Structural changes and adaptative evolutionary constraints in FLOWERING LOCUS T and TERMINAL FLOWER1-like genes of flowering plants. Front Genet 2022; 13:954015. [PMID: 36246591 PMCID: PMC9556947 DOI: 10.3389/fgene.2022.954015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures through in silico modeling to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure are under positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.
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Affiliation(s)
- Deivid Almeida de Jesus
- Institute of Biology Genetics Graduate Program, Federal University of Rio de Janeiro Rio de Janeiro, Rio de Janeiro, Brazil
| | - Darlisson Mesquista Batista
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal do Oeste do Pará Santarém, Pará, Santarém, Brazil
| | - Elton Figueira Monteiro
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal do Oeste do Pará Santarém, Pará, Santarém, Brazil
| | - Shayla Salzman
- School of Integrative Plant Sciences. Section of Plant Biology. Cornell University Ithaca, New York, NY, United States
| | - Lucas Miguel Carvalho
- Center for Computing in Engineering and Sciences, State University of Campinas. Campinas, São Paulo, Brazil
| | - Kauê Santana
- Institute of Biodiversity, Federal University of Western Pará Santarém Pará, Santarém, Brazil
- *Correspondence: Kauê Santana, ; Thiago André,
| | - Thiago André
- Botany Department, University of Brasília, Brasília, Brazil
- *Correspondence: Kauê Santana, ; Thiago André,
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7
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Bondareva O, Genelt-Yanovskiy E, Petrova T, Bodrov S, Smorkatcheva A, Abramson N. Signatures of Adaptation in Mitochondrial Genomes of Palearctic Subterranean Voles (Arvicolinae, Rodentia). Genes (Basel) 2021; 12:1945. [PMID: 34946894 PMCID: PMC8701191 DOI: 10.3390/genes12121945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
This study evaluates signatures of selection in the evolution of the mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: Ellobius talpinus, Ellobius fuscocapillus and Ellobius lutescens, two species of the genus Terricola: Terricola subterraneus and Terricola daghestanicus, Lasiopodomys mandarinus, and Hyperacrius fertilis) and their closest aboveground relatives was applied using codon-substitution models. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mitochondrial DNA protein-coding genes for subterranean species. The largest amount of relaxed genes is discovered in mole voles (genus Ellobius). The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptation in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.
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Affiliation(s)
- Olga Bondareva
- Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, 199034 Saint-Petersburg, Russia; (E.G.-Y.); (T.P.); (S.B.)
| | - Evgeny Genelt-Yanovskiy
- Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, 199034 Saint-Petersburg, Russia; (E.G.-Y.); (T.P.); (S.B.)
| | - Tatyana Petrova
- Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, 199034 Saint-Petersburg, Russia; (E.G.-Y.); (T.P.); (S.B.)
| | - Semen Bodrov
- Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, 199034 Saint-Petersburg, Russia; (E.G.-Y.); (T.P.); (S.B.)
| | - Antonina Smorkatcheva
- Department of Vertebrate Zoology, Biology Faculty, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia;
| | - Natalia Abramson
- Laboratory of Evolutionary Genomics and Paleogenomics, Zoological Institute RAS, 199034 Saint-Petersburg, Russia; (E.G.-Y.); (T.P.); (S.B.)
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Gonzalez-Ibeas D, Ibanez V, Perez-Roman E, Borredá C, Terol J, Talon M. Shaping the biology of citrus: I. Genomic determinants of evolution. THE PLANT GENOME 2021; 14:e20104. [PMID: 34275210 DOI: 10.1002/tpg2.20104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
We performed genomic analyses on wild species of the genus Citrus to identify major determinants of evolution. The most notable effect occurred on the pathogen-defense genes, as observed in many other plant genera. The gene space was also characterized by changes in gene families intimately related to relevant biochemical properties of citrus fruit, such as pectin modifying enzymes, HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, and O-methyltransferases. Citrus fruits are highly abundant on pectins and secondary metabolites such as terpenoids and flavonoids, the targets of these families. Other gene types under positive selection, expanded through tandem duplications and retained as triplets from whole genome duplications, codified for purple acid phosphatases and MATE-efflux proteins. Although speciation has not been especially rapid in the genus, analyses of selective pressure at the codon level revealed that the extant species evolved from the ancestral citrus radiation show signatures of pervasive adaptive evolution and is therefore potentially responsible for the vast phenotypic differences observed among current species.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Victoria Ibanez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Estela Perez-Roman
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Carles Borredá
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Javier Terol
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Manuel Talon
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
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Xu Y, Pan X, Lu J, Wang J, Shan Q, Stout J, Chen G. Evolutionary and biochemical characterization of a Chromochloris zofingiensis MBOAT with wax synthase and diacylglycerol acyltransferase activity. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5584-5598. [PMID: 34037747 DOI: 10.1093/jxb/erab236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Wax synthase (WS) catalyzes the last step in wax ester biosynthesis in green plants. Two unrelated sub-families of WS, including the bifunctional acyltransferase and plant-like WS have been reported, but the latter is largely uncharacterized in microalgae. Here, we functionally characterized a putative plant-like WS (CzWS1) from the emerging model green microalga Chromochloris zofingiensis. Our results showed that plant-like WS evolved under different selection constraints in plants and microalgae, with positive selection likely contributing to functional divergence. Unlike jojoba with high amounts of wax ester in seeds and a highly active WS enzyme, C. zofingiensis has no detectable wax ester but a high abundance of WS transcripts. Co-expression analysis showed that C. zofingiensis WS has different expression correlation with lipid biosynthetic genes from jojoba, and may have a divergent function. In vitro characterization indicated that CzWS1 had diacylglycerol acyltransferase activity along with WS activity, and overexpression of CzWS1 in yeast and Chlamydomonas reinhardtii affected triacylglycerol accumulation. Moreover, biochemical and bioinformatic analyses revealed the relevance of the C-terminal region of CzWS1 in enzyme function. Taken together, our results indicated a functional divergence of plant-like WS in plants and microalgae, and the importance of its C-terminal region in specialization of enzyme function.
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Affiliation(s)
- Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Xue Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Junhao Lu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Juli Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Qiyuan Shan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jake Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Escalera-Zamudio M, Golden M, Gutiérrez B, Thézé J, Keown JR, Carrique L, Bowden TA, Pybus OG. Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nat Commun 2020; 11:5511. [PMID: 33139731 PMCID: PMC7608645 DOI: 10.1038/s41467-020-19364-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/12/2020] [Indexed: 01/30/2023] Open
Abstract
Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. We combine phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein structure. Our resulting mutational panel may help to reveal new links between virulence evolution and other traits, and raises the possibility of predicting aspects of AIV evolution.
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Affiliation(s)
| | - Michael Golden
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | | | - Julien Thézé
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | - Jeremy Russell Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
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Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes. Genes (Basel) 2020; 11:genes11111271. [PMID: 33126655 PMCID: PMC7692064 DOI: 10.3390/genes11111271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.
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12
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Seoighe C, Kiniry SJ, Peters A, Baranov PV, Yang H. Selection Shapes Synonymous Stop Codon Use in Mammals. J Mol Evol 2020; 88:549-561. [PMID: 32617614 DOI: 10.1007/s00239-020-09957-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
Abstract
Phylogenetic models of the evolution of protein-coding sequences can provide insights into the selection pressures that have shaped them. In the application of these models synonymous nucleotide substitutions, which do not alter the encoded amino acid, are often assumed to have limited functional consequences and used as a proxy for the neutral rate of evolution. The ratio of nonsynonymous to synonymous substitution rates is then used to categorize the selective regime that applies to the protein (e.g., purifying selection, neutral evolution, diversifying selection). Here, we extend the Muse and Gaut model of codon evolution to explore the extent of purifying selection acting on substitutions between synonymous stop codons. Using a large collection of coding sequence alignments, we estimate that a high proportion (approximately 57%) of mammalian genes are affected by selection acting on stop codon preference. This proportion varies substantially by codon, with UGA stop codons far more likely to be conserved. Genes with evidence of selection acting on synonymous stop codons have distinctive characteristics, compared to unconserved genes with the same stop codon, including longer [Formula: see text] untranslated regions (UTRs) and shorter mRNA half-life. The coding regions of these genes are also much more likely to be under strong purifying selection pressure. Our results suggest that the preference for UGA stop codons found in many multicellular eukaryotes is selective rather than mutational in origin.
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Affiliation(s)
- Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland.
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew Peters
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Haixuan Yang
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
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13
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Elbassiouny AA, Lovejoy NR, Chang BSW. Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190179. [PMID: 31787042 PMCID: PMC6939368 DOI: 10.1098/rstb.2019.0179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2019] [Indexed: 12/26/2022] Open
Abstract
The ability to generate and detect electric fields has evolved in several groups of fishes as a means of communication, navigation and, occasionally, predation. The energetic burden required can account for up to 20% of electric fishes' daily energy expenditure. Despite this, molecular adaptations that enable electric fishes to meet the metabolic demands of bioelectrogenesis remain unknown. Here, we investigate the molecular evolution of the mitochondrial oxidative phosphorylation (OXPHOS) complexes in the two most diverse clades of weakly electric fishes-South American Gymnotiformes and African Mormyroidea, using codon-based likelihood approaches. Our analyses reveal that although mitochondrial OXPHOS genes are generally subject to strong purifying selection, this constraint is significantly reduced in electric compared to non-electric fishes, particularly for complexes IV and V. Moreover, analyses of concatenated mitochondrial genes show strong evidence for positive selection in complex I genes on the two branches associated with the independent evolutionary origins of electrogenesis. These results suggest that adaptive evolution of proton translocation in the OXPHOS cellular machinery may be associated with the evolution of bioelectrogenesis. Overall, we find striking evidence for remarkably similar effects of electrogenesis on the molecular evolution of mitochondrial OXPHOS genes in two independently derived clades of electrogenic fishes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Ahmed A. Elbassiouny
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Nathan R. Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - Belinda S. W. Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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14
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Yuan M, Zhang L, Zhang Q, Zhang L, Li M, Wang X, Feng R, Tang P. Mitogenome evolution in ladybirds: Potential association with dietary adaptation. Ecol Evol 2020; 10:1042-1053. [PMID: 32015863 PMCID: PMC6988538 DOI: 10.1002/ece3.5971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein-coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits.
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Affiliation(s)
- Ming‐Long Yuan
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Li‐Jun Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi‐Lin Zhang
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunmingChina
| | - Li Zhang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Min Li
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Xiao‐Tong Wang
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Run‐Qiu Feng
- State Key Laboratory of Grassland Agro‐EcosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pei‐An Tang
- Collaborative Innovation Center for Modern Grain Circulation and SafetyCollege of Food Science and EngineeringNanjing University of Finance and EconomicsNanjingChina
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15
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Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data. Methods Mol Biol 2019; 1910:399-426. [PMID: 31278672 DOI: 10.1007/978-1-4939-9074-0_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Codon substitution models (CSMs) are commonly used to infer the history of natural section for a set of protein-coding sequences, often with the explicit goal of detecting the signature of positive Darwinian selection. However, the validity and success of CSMs used in conjunction with the maximum likelihood (ML) framework is sometimes challenged with claims that the approach might too often support false conclusions. In this chapter, we use a case study approach to identify four legitimate statistical difficulties associated with inference of evolutionary events using CSMs. These include: (1) model misspecification, (2) low information content, (3) the confounding of processes, and (4) phenomenological load, or PL. While past criticisms of CSMs can be connected to these issues, the historical critiques were often misdirected, or overstated, because they failed to recognize that the success of any model-based approach depends on the relationship between model and data. Here, we explore this relationship and provide a candid assessment of the limitations of CSMs to extract historical information from extant sequences. To aid in this assessment, we provide a brief overview of: (1) a more realistic way of thinking about the process of codon evolution framed in terms of population genetic parameters, and (2) a novel presentation of the ML statistical framework. We then divide the development of CSMs into two broad phases of scientific activity and show that the latter phase is characterized by increases in model complexity that can sometimes negatively impact inference of evolutionary mechanisms. Such problems are not yet widely appreciated by the users of CSMs. These problems can be avoided by using a model that is appropriate for the data; but, understanding the relationship between the data and a fitted model is a difficult task. We argue that the only way to properly understand that relationship is to perform in silico experiments using a generating process that can mimic the data as closely as possible. The mutation-selection modeling framework (MutSel) is presented as the basis of such a generating process. We contend that if complex CSMs continue to be developed for testing explicit mechanistic hypotheses, then additional analyses such as those described in here (e.g., penalized LRTs and estimation of PL) will need to be applied alongside the more traditional inferential methods.
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16
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Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces. Methods Mol Biol 2019; 1910:427-468. [PMID: 31278673 DOI: 10.1007/978-1-4939-9074-0_14] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural selection is a fundamental force shaping organismal evolution, as it both maintains function and enables adaptation and innovation. Viruses, with their typically short and largely coding genomes, experience strong and diverse selective forces, sometimes acting on timescales that can be directly measured. These selection pressures emerge from an antagonistic interplay between rapidly changing fitness requirements (immune and antiviral responses from hosts, transmission between hosts, or colonization of new host species) and functional imperatives (the ability to infect hosts or host cells and replicate within hosts). Indeed, computational methods to quantify these evolutionary forces using molecular sequence data were initially, dating back to the 1980s, applied to the study of viral pathogens. This preference largely emerged because the strong selective forces are easiest to detect in viruses, and, of course, viruses have clear biomedical relevance. Recent commoditization of affordable high-throughput sequencing has made it possible to generate truly massive genomic data sets, on which powerful and accurate methods can yield a very detailed depiction of when, where, and (sometimes) how viral pathogens respond to various selective forces.Here, we present recent statistical developments and state-of-the-art methods to identify and characterize these selection pressures from protein-coding sequence alignments and phylogenies. Methods described here can reveal critical information about various evolutionary regimes, including whole-gene selection, lineage-specific selection, and site-specific selection acting upon viral genomes, while accounting for confounding biological processes, such as recombination and variation in mutation rates.
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Affiliation(s)
- Stephanie J Spielman
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Brittany Rife Magalis
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Michael Li
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
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17
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Mattle-Greminger MP, Bilgin Sonay T, Nater A, Pybus M, Desai T, de Valles G, Casals F, Scally A, Bertranpetit J, Marques-Bonet T, van Schaik CP, Anisimova M, Krützen M. Genomes reveal marked differences in the adaptive evolution between orangutan species. Genome Biol 2018; 19:193. [PMID: 30428903 PMCID: PMC6237011 DOI: 10.1186/s13059-018-1562-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives, in particular if and to what extent adaptions to environmental differences have occurred. Here, we used whole-genome sequencing data from critically endangered orangutans from North Sumatra (Pongo abelii) and Borneo (P. pygmaeus) to investigate adaptive responses of each species to environmental differences during the Pleistocene. RESULTS Taking into account the markedly disparate demographic histories of each species after their split ~ 1 Ma ago, we show that persistent environmental differences on each island had a strong impact on the adaptive evolution of the genus Pongo. Across a range of tests for positive selection, we find a consistent pattern of between-island and species differences. In the more productive Sumatran environment, the most notable signals of positive selection involve genes linked to brain and neuronal development, learning, and glucose metabolism. On Borneo, however, positive selection comprised genes involved in lipid metabolism, as well as cardiac and muscle activities. CONCLUSIONS We find strikingly different sets of genes appearing to have evolved under strong positive selection in each species. In Sumatran orangutans, selection patterns were congruent with well-documented cognitive and behavioral differences between the species, such as a larger and more complex cultural repertoire and higher degrees of sociality. However, in Bornean orangutans, selective responses to fluctuating environmental conditions appear to have produced physiological adaptations to generally lower and temporally more unpredictable food supplies.
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Affiliation(s)
- Maja P. Mattle-Greminger
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tugce Bilgin Sonay
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
| | - Alexander Nater
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Marc Pybus
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Guillem de Valles
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona, Spain
| | - Carel P. van Schaik
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maria Anisimova
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences ZHAW, Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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18
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Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ. The Influence of HIV on the Evolution of Mycobacterium tuberculosis. Mol Biol Evol 2017; 34:1654-1668. [PMID: 28369607 PMCID: PMC5455964 DOI: 10.1093/molbev/msx107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates.
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Affiliation(s)
- Anastasia S Koch
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Joanna C Evans
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ronnett Seldon
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- University of Cape Town, and National Health Laboratory Service, Cape Town, South Africa
| | - Tolu Oni
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.,The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Darren P Martin
- Division of Computational Biology, Department of Integrated Biology Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,Francis Crick Institute, London, United Kingdom
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19
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Meireles JE, Beulke A, Borkowski DS, Romero-Severson J, Cavender-Bares J. Balancing selection maintains diversity in a cold tolerance gene in broadly distributed live oaks. Genome 2017; 60:762-769. [DOI: 10.1139/gen-2016-0208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cold poses major physiological challenges to plants, especially long-lived trees. In trees occurring along variable temperature clines, the expected direction and consequences of selection on cold acclimation ability and freezing tolerance are not straightforward. Here we estimated selection in cold acclimation genes at two evolutionary timescales in all seven species of the American live oaks (Quercus subsection Virentes). Two cold response candidate genes were chosen: ICE1, a key gene in the cold acclimation pathway, and HOS1, which modulates cold response by negatively regulating ICE1. Two housekeeping genes, GAPDB and CHR11, were also analyzed. At the shallow evolutionary timescale, we demonstrate that HOS1 experienced recent balancing selection in the two most broadly distributed species, Q. virginiana and Q. oleoides. At a deeper evolutionary scale, a codon-based model of evolution revealed the signature of negative selection in ICE1. In contrast, three positively selected codons have been identified in HOS1, possibly a signature of the diversification of Virentes into warmer climates from a freezing adapted lineage of oaks. Our findings indicate that evolution has favored diversity in cold tolerance modulation through balancing selection in HOS1 while maintaining core cold acclimation ability, as evidenced by purifying selection in ICE1.
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Affiliation(s)
- Jose Eduardo Meireles
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Anne Beulke
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel S. Borkowski
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
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20
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de Carvalho DB, Congrains C, Chahad-Ehlers S, Pinotti H, de Brito RA, da Rosa JA. Differential transcriptome analysis supports Rhodnius montenegrensis and Rhodnius robustus (Hemiptera, Reduviidae, Triatominae) as distinct species. PLoS One 2017; 12:e0174997. [PMID: 28406967 PMCID: PMC5390988 DOI: 10.1371/journal.pone.0174997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/17/2017] [Indexed: 11/18/2022] Open
Abstract
Chagas disease is one of the main parasitic diseases found in Latin America and it is estimated that between six and seven million people are infected worldwide. Its etiologic agent, the protozoan Trypanosoma cruzi, is transmitted by triatomines, some of which from the genus Rhodnius. Twenty species are currently recognized in this genus, including some closely related species with low levels of morphological differentiation, such as Rhodnius montenegrensis and Rhodnius robustus. In order to investigate genetic differences between these two species, we generated large-scale RNA-sequencing data (consisting of four RNA-seq libraries) from the heads and salivary glands of males of R. montenegrensis and R. robustus. Transcriptome assemblies produced for each species resulted in 64,952 contigs for R. montenegrensis and 70,894 contigs for R. robustus, with N50 of approximately 2,100 for both species. SNP calling based on the more complete R. robustus assembly revealed 3,055 fixed interspecific differences and 216 transcripts with high levels of divergence which contained only fixed differences between the two species. A gene ontology enrichment analysis revealed that these highly differentiated transcripts were enriched for eight GO terms related to AP-2 adaptor complex, as well as other interesting genes that could be involved in their differentiation. The results show that R. montenegrensis and R. robustus have a substantial quantity of fixed interspecific polymorphisms, which suggests a high degree of genetic divergence between the two species and likely corroborates the species status of R. montenegrensis.
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Affiliation(s)
- Danila Blanco de Carvalho
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Carlos Congrains
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - Samira Chahad-Ehlers
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - Heloisa Pinotti
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Reinaldo Alves de Brito
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Paulo, Brazil
| | - João Aristeu da Rosa
- Department of Parasitology, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
- * E-mail:
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21
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Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V, Antunes A. LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics 2016; 17:354. [PMID: 27597435 PMCID: PMC5011788 DOI: 10.1186/s12859-016-1204-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 08/24/2016] [Indexed: 12/22/2022] Open
Abstract
Background Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the efficiency to pinpoint genes involved in the adaptive evolution of phenotypes. Reliability of such findings is most often examined with statistical and computational methods using Maximum Likelihood codon-based models (i.e., site, branch, branch-site and clade models), such as those available in codeml from the Phylogenetic Analysis by Maximum Likelihood (PAML) package. While these models represent a well-defined workflow for documenting adaptive evolution, in practice they can be challenging for researchers having a vast amount of data, as multiple types of relevant codon-based datasets are generated, making the overall process hard and tedious to handle, error-prone and time-consuming. Results We introduce LMAP (Lightweight Multigene Analyses in PAML), a user-friendly command-line and interactive package, designed to handle the codeml workflow, namely: directory organization, execution, results gathering and organization for Likelihood Ratio Test estimations with minimal manual user intervention. LMAP was developed for the workstation multi-core environment and provides a unique advantage for processing one, or more, if not all codeml codon-based models for multiple datasets at a time. Our software, proved efficiency throughout the codeml workflow, including, but not limited, to simultaneously handling more than 20 datasets. Conclusions We have developed a simple and versatile LMAP package, with outstanding performance, enabling researchers to analyze multiple different codon-based datasets in a high-throughput fashion. At minimum, two file types are required within a single input directory: one for the multiple sequence alignment and another for the phylogenetic tree. To our knowledge, no other software combines all codeml codon substitution models of adaptive evolution. LMAP has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP package is released under GPLv3 license and is freely available at http://lmapaml.sourceforge.net/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1204-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuel Maldonado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Daniela Almeida
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tibisay Escalona
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Imran Khan
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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22
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Görnerup O, Gillblad D, Vasiloudis T. Domain-agnostic discovery of similarities and concepts at scale. Knowl Inf Syst 2016. [DOI: 10.1007/s10115-016-0984-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Mingrone J, Susko E, Bielawski J. Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites. Mol Biol Evol 2016; 33:2976-2989. [PMID: 27486222 DOI: 10.1093/molbev/msw160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To detect positive selection at individual amino acid sites, most methods use an empirical Bayes approach. After parameters of a Markov process of codon evolution are estimated via maximum likelihood, they are passed to Bayes formula to compute the posterior probability that a site evolved under positive selection. A difficulty with this approach is that parameter estimates with large errors can negatively impact Bayesian classification. By assigning priors to some parameters, Bayes Empirical Bayes (BEB) mitigates this problem. However, as implemented, it imposes uniform priors, which causes it to be overly conservative in some cases. When standard regularity conditions are not met and parameter estimates are unstable, inference, even under BEB, can be negatively impacted. We present an alternative to BEB called smoothed bootstrap aggregation (SBA), which bootstraps site patterns from an alignment of protein coding DNA sequences to accommodate the uncertainty in the parameter estimates. We show that deriving the correction for parameter uncertainty from the data in hand, in combination with kernel smoothing techniques, improves site specific inference of positive selection. We compare BEB to SBA by simulation and real data analysis. Simulation results show that SBA balances accuracy and power at least as well as BEB, and when parameter estimates are unstable, the performance gap between BEB and SBA can widen in favor of SBA. SBA is applicable to a wide variety of other inference problems in molecular evolution.
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Affiliation(s)
- Joseph Mingrone
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Joseph Bielawski
- Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada Department of Biology, Dalhousie University, Halifax, NS, Canada
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24
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Van Nynatten A, Bloom D, Chang BSW, Lovejoy NR. Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion. Biol Lett 2016. [PMID: 26224386 DOI: 10.1098/rsbl.2015.0349] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.
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Affiliation(s)
- Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Devin Bloom
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA Environmental and Sustainability Studies Program, Western Michigan University, Kalamazoo, MI, USA
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Nathan R Lovejoy
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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25
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Balakirev ES, Anisimova M, Pavlyuchkov VA, Ayala FJ. DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea). BMC Genet 2016; 17:66. [PMID: 27176219 PMCID: PMC4866015 DOI: 10.1186/s12863-016-0374-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The sperm gene bindin encodes a gamete recognition protein, which plays an important role in conspecific fertilization and reproductive isolation of sea urchins. Molecular evolution of the gene has been extensively investigated with the attention focused on the protein coding regions. Intron evolution has been investigated to a much lesser extent. We have studied nucleotide variability in the complete bindin locus, including two exons and one intron, in the sea urchin Strongylocentrotus intermedius represented by two morphological forms. We have also analyzed all available bindin sequences for two other sea urchin species, S. pallidus and S. droebachiensis. RESULTS The results show that the bindin sequences from the two forms of S. intermedius are intermingled with no evidence of genetic divergence; however, the forms exhibit slightly different patterns in bindin variability. The level of the bindin nucleotide diversity is close for S. intermedius and S. droebachiensis, but noticeably higher for S. pallidus. The distribution of variability is non-uniform along the gene; however there are striking similarities among the species, indicating similar evolutionary trends in this gene engaged in reproductive function. The patterns of nucleotide variability and divergence are radically different in the bindin coding and intron regions. Positive selection is detected in the bindin coding region. The neutrality tests as well as the maximum likelihood approaches suggest the action of diversifying selection in the bindin intron. CONCLUSIONS Significant deviation from neutrality has been detected in the bindin coding region and suggested in the intron, indicating the possible functional importance of the bindin intron variability. To clarify the question concerning possible involvement of diversifying selection in the bindin intron evolution more data combining population genetic and functional approaches are necessary.
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Affiliation(s)
- Evgeniy S Balakirev
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Science, Vladivostok, 690041, Russia.
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA.
- Far Eastern Federal University, Vladivostok, 690950, Russia.
| | - Maria Anisimova
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Wädenswil, 8820, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | | | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
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Wang K, Remigi P, Anisimova M, Lonjon F, Kars I, Kajava A, Li CH, Cheng CP, Vailleau F, Genin S, Peeters N. Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2016; 17:553-64. [PMID: 26300048 PMCID: PMC6638336 DOI: 10.1111/mpp.12302] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R. solanacearum are the type III secretion system (T3SS) and its associated type III effectors (T3Es), translocated into the host cells. Of the conserved T3Es among R. solanacearum strains, the Fbox protein RipG7 is required for R. solanacearum pathogenesis on Medicago truncatula. In this work, we describe the natural ripG7 variability existing in the R. solanacearum species complex. We show that eight representative ripG7 orthologues have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M. truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely a result of the variability in the leucine-rich repeat (LRR) domain of RipG7. We identified 11 sites under positive selection in the LRR domains of RipG7. By studying the functional impact of these 11 sites, we show the contribution of five positively selected sites for the function of RipG7CMR15 in M. truncatula colonization. This work reveals the genetic and functional variation of the essential core T3E RipG7 from R. solanacearum. This analysis is the first of its kind on an essential disease-controlling T3E, and sheds light on the co-evolutionary arms race between the bacterium and its hosts.
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Affiliation(s)
- Keke Wang
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Philippe Remigi
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Gruenalstrasse 14, 8820, Wädesnwil, Switzerland
| | - Fabien Lonjon
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Ilona Kars
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Andrey Kajava
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, UMR5237, 1919 Route de Mende, 34000, Montpellier, France
| | - Chien-Hui Li
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Chiu-Ping Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Fabienne Vailleau
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, 18 Chemin de Borde Rouge, Castanet-Tolosan, 31326, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Nemo Peeters
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
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Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae). Mol Phylogenet Evol 2016; 100:31-40. [PMID: 27015897 DOI: 10.1016/j.ympev.2016.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 01/07/2023]
Abstract
Positive selection is known to drive the evolution of genes involved in evolutionary arms races, but what role does it play in the evolution of genes involved in developmental processes? We used the single-celled epidermal trichomes of Brassicaceae as a model to uncover the molecular evolutionary processes that contributed to the transition from dendritic trichomes, as seen in most species of Brassicaceae, to the distinctive stellate trichomes of the genus Physaria. We explored the role of positive selection on the evolution of BRANCHLESS TRICHOME (BLT), a candidate gene for changes in trichome branching pattern. Maximum likelihood models of codon evolution point to a shift in selective pressure affecting the evolution of BLT across the entire Physaria clade, and we found strong evidence that positive selection has acted on a subset of Physaria BLT codons. Almost all of the 10 codon sites with the highest probability of having evolved under positive selection are clustered in a predicted coiled-coil domain, pointing to changes in protein-protein interactions. Thus, our findings suggest that selection acted on BLT to modify its interactions with other proteins. The fact that positive selection occurred throughout the radiation of Physaria could reflect selection to stabilize development in response to an abrupt switch from the dendritic form to the stellate form, divergent selection for diversification of the stellate form, or both. These results point to the need for evolutionary developmental studies of BLT and its interacting proteins in Physaria.
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Moon S, Lee JW, Shin D, Shin KY, Kim J, Choi IY, Kim J, Kim H. A Genome-wide Scan for Selective Sweeps in Racing Horses. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1525-31. [PMID: 26333666 PMCID: PMC4647090 DOI: 10.5713/ajas.14.0696] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/09/2014] [Accepted: 02/22/2015] [Indexed: 11/27/2022]
Abstract
Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.
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Affiliation(s)
- Sunjin Moon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jin Woo Lee
- Horse Registry, Korea Racing Authority (KRA), Gwacheon 427-711, Korea
| | - Donghyun Shin
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Korea
| | | | - Jun Kim
- Institute for Livestock Promotion, Jeju 690-802, Korea
| | - Ik-Young Choi
- Genome analysis center, National Instrumentation and Environmental Management (NICEM), Seoul National University, Seoul 151-921, Korea
| | - Jaemin Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Korea ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea ; C&K Genomics, Seoul 151-742, Korea
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Gutiérrez V, Rego N, Naya H, García G. First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes. BMC Genomics 2015; 16:879. [PMID: 26511223 PMCID: PMC4625726 DOI: 10.1186/s12864-015-2090-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background Among teleosts, the South American genus Austrolebias (Cyprinodontiformes: Rivulidae) includes 42 taxa of annual fishes divided into five different species groups. It is a monophyletic genus, but morphological and molecular data do not resolve the relationship among intrageneric clades and high rates of substitution have been previously described in some mitochondrial genes. In this work, the complete mitogenome of a species of the genus was determined for the first time. We determined its structure, gene order and evolutionary peculiar features, which will allow us to evaluate the performance of mitochondrial genes in the phylogenetic resolution at different taxonomic levels. Results Regarding gene content and order, the circular mitogenome of A. charrua (17,271 pb) presents the typical pattern of vertebrate mitogenomes. It contains the full complement of 13 proteins-coding genes, 22 tRNA, 2 rRNA and one non-coding control region. Notably, the tRNA-Cys was only 57 bp in length and lacks the D-loop arm. In three full sibling individuals, heteroplasmatic condition was detected due to a total of 12 variable sites in seven protein-coding genes. Among cyprinodontiforms, the mitogenome of A. charrua exhibits the lowest G+C content (37 %) and GCskew, as well as the highest strand asymmetry with a net difference of T over A at 1st and 3rd codon positions. Considering the 12 coding-genes of the H strand, correspondence analyses of nucleotide composition and codon usage show that A and T at 1st and 3rd codon positions have the highest weight in the first axis, and segregate annual species from the other cyprinodontiforms analyzed. Given the annual life-style, their mitogenomes could be under different selective pressures. All 13 protein-coding genes are under strong purifying selection and we did not find any significant evidence of nucleotide sites showing episodic selection (dN >dS) at annual lineages. When fast evolving third codon positions were removed from alignments, the “supergene” tree recovers our reference species phylogeny as well as the Cytb, ND4L and ND6 genes. Therefore, third codon positions seem to be saturated in the aforementioned coding regions at intergeneric Cyprinodontiformes comparisons. Conclusions The complete mitogenome obtained in present work, offers relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomic controversial endemic genus of annual fishes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2090-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Verónica Gutiérrez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225 (CP.11400), Montevideo, Uruguay.
| | - Natalia Rego
- Institut Pasteur de Montevideo, Unidad de Bioinformática, Montevideo, Uruguay.
| | - Hugo Naya
- Institut Pasteur de Montevideo, Unidad de Bioinformática, Montevideo, Uruguay. .,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Paysandú, Uruguay.
| | - Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225 (CP.11400), Montevideo, Uruguay.
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Arenas M. Trends in substitution models of molecular evolution. Front Genet 2015; 6:319. [PMID: 26579193 PMCID: PMC4620419 DOI: 10.3389/fgene.2015.00319] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/09/2015] [Indexed: 11/13/2022] Open
Abstract
Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.
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Affiliation(s)
- Miguel Arenas
- Institute of Molecular Pathology and Immunology of the University of Porto Porto, Portugal
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31
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Dungan SZ, Kosyakov A, Chang BS. Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment. Mol Biol Evol 2015; 33:323-36. [DOI: 10.1093/molbev/msv217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Tubiana L, Božič AL, Micheletti C, Podgornik R. Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses. Biophys J 2015; 108:194-202. [PMID: 25564866 DOI: 10.1016/j.bpj.2014.10.070] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/08/2014] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison, it has been suggested that wild-type viral RNA may have evolved to be atypically compact so as to aid its encapsidation and assist the viral assembly process. To further explore the compactness selection hypothesis, we systematically compare the predicted sizes of >100 wild-type viral sequences with those of their mutants, which are evolved in silico and subject to a number of known evolutionary constraints. In particular, we enforce mutation synonynimity, preserve the codon-bias, and leave untranslated regions intact. It is found that progressive accumulation of these restricted mutations still suffices to completely erase the characteristic compactness imprint of the viral RNA genomes, making them in this respect physically indistinguishable from randomly shuffled RNAs. This shows that maintaining the physical compactness of the genome is indeed a primary factor among ssRNA viruses' evolutionary constraints, contributing also to the evidence that synonymous mutations in viral ssRNA genomes are not strictly neutral.
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Affiliation(s)
- Luca Tubiana
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia.
| | - Anže Lošdorfer Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia; Department of Physics, University of Massachusetts, Amherst, Massachusetts
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Benard E, Lèbre S, Michel CJ. Genome evolution by transformation, expansion and contraction (GETEC). Biosystems 2015; 135:15-34. [PMID: 26135206 DOI: 10.1016/j.biosystems.2015.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 05/04/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
We propose here the GETEC (Genome Evolution by Transformation, Expansion and Contraction) model of gene evolution based on substitution, insertion and deletion of genetic motifs. The GETEC model unifies two classes of evolution models: models of substitution, insertion and deletion of nucleotides as function of time (Lèbre and Michel, 2010) and sequence length (Lèbre and Michel, 2012), and models of symmetric substitution of genetic motifs as function of time (Benard and Michel, 2011). Evolution of genetic motifs based on substitution, insertion and deletion is modeled by a differential equation whose analytical solutions give an expression of the genetic motif occurrence probabilities as a function of time or sequence length, as well as in direct time direction (past-present) or inverse time direction (present-past). Evolution models with "substitution only", i.e. without insertion and deletion, and with "insertion and deletion only", i.e. without substitution, are particular cases of the GETEC model. We have also developed a research software for computing the analytical solutions of the GETEC model. It is freely accessible at http://icube-bioinfo.u-strasbg.fr/webMathematica/GETEC/ or via the web site http://dpt-info.u-strasbg.fr/∼michel/.
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Affiliation(s)
- Emmanuel Benard
- Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
| | - Sophie Lèbre
- Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
| | - Christian J Michel
- Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.
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Zoller S, Boskova V, Anisimova M. Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions. Mol Biol Evol 2015; 32:2208-16. [PMID: 25911229 DOI: 10.1093/molbev/msv097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many protein sequences have distinct domains that evolve with different rates, different selective pressures, or may differ in codon bias. Instead of modeling these differences by more and more complex models of molecular evolution, we present a multipartition approach that allows maximum-likelihood phylogeny inference using different codon models at predefined partitions in the data. Partition models can, but do not have to, share free parameters in the estimation process. We test this approach with simulated data as well as in a phylogenetic study of the origin of the leucin-rich repeat regions in the type III effector proteins of the pythopathogenic bacteria Ralstonia solanacearum. Our study does not only show that a simple two-partition model resolves the phylogeny better than a one-partition model but also gives more evidence supporting the hypothesis of lateral gene transfer events between the bacterial pathogens and its eukaryotic hosts.
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Affiliation(s)
- Stefan Zoller
- Computational Biochemistry Research Group, ETH Zürich, Zürich, Switzerland Swiss Institute of Bioinformatics, Switzerland
| | - Veronika Boskova
- Computational Biochemistry Research Group, ETH Zürich, Zürich, Switzerland
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
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35
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Abstract
Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct methods relate to one another remains largely unknown. Here, we elucidate the relationship between two widely used phylogenetic modeling frameworks: dN/dS models and mutation-selection (MutSel) models. We derive a mathematical relationship between dN/dS and scaled selection coefficients, the focal parameters of MutSel models, and use this relationship to gain deeper insight into the behaviors, limitations, and applicabilities of these two modeling frameworks. We prove that, if all synonymous changes are neutral, standard MutSel models correspond to dN/dS ≤ 1. However, if synonymous codons differ in fitness, dN/dS can take on arbitrarily high values even if all selection is purifying. Thus, the MutSel modeling framework cannot necessarily accommodate positive, diversifying selection, while dN/dS cannot distinguish between purifying selection on synonymous codons and positive selection on amino acids. We further propose a new benchmarking strategy of dN/dS inferences against MutSel simulations and demonstrate that the widely used Goldman-Yang-style dN/dS models yield substantially biased dN/dS estimates on realistic sequence data. In contrast, the less frequently used Muse-Gaut-style models display much less bias. Strikingly, the least-biased and most precise dN/dS estimates are never found in the models with the best fit to the data, measured through both AIC and BIC scores. Thus, selecting models based on goodness-of-fit criteria can yield poor parameter estimates if the models considered do not precisely correspond to the underlying mechanism that generated the data. In conclusion, establishing mathematical links among modeling frameworks represents a novel, powerful strategy to pinpoint previously unrecognized model limitations and strengths.
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Affiliation(s)
- Stephanie J Spielman
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute of Cellular and Molecular Biology, The University of Texas at Austin
| | - Claus O Wilke
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute of Cellular and Molecular Biology, The University of Texas at Austin
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36
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Pan X, Peng FY, Weselake RJ. Genome-wide analysis of PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) genes in plants reveals the eudicot-wide PDAT gene expansion and altered selective pressures acting on the core eudicot PDAT paralogs. PLANT PHYSIOLOGY 2015; 167:887-904. [PMID: 25585619 PMCID: PMC4348769 DOI: 10.1104/pp.114.253658] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE (PDAT) is an enzyme that catalyzes the transfer of a fatty acyl moiety from the sn-2 position of a phospholipid to the sn-3-position of sn-1,2-diacylglyerol, thus forming triacylglycerol and a lysophospholipid. Although the importance of PDAT in triacylglycerol biosynthesis has been illustrated in some previous studies, the evolutionary relationship of plant PDATs has not been studied in detail. In this study, we investigated the evolutionary relationship of the PDAT gene family across the green plants using a comparative phylogenetic framework. We found that the PDAT candidate genes are present in all examined green plants, including algae, lowland plants (a moss and a lycophyte), monocots, and eudicots. Phylogenetic analysis revealed the evolutionary division of the PDAT gene family into seven major clades. The separation is supported by the conservation and variation in the gene structure, protein properties, motif patterns, and/or selection constraints. We further demonstrated that there is a eudicot-wide PDAT gene expansion, which appears to have been mainly caused by the eudicot-shared ancient gene duplication and subsequent species-specific segmental duplications. In addition, selection pressure analyses showed that different selection constraints have acted on three core eudicot clades, which might enable paleoduplicated PDAT paralogs to either become nonfunctionalized or develop divergent expression patterns during evolution. Overall, our study provides important insights into the evolution of the plant PDAT gene family and explores the evolutionary mechanism underlying the functional diversification among the core eudicot PDAT paralogs.
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Affiliation(s)
- Xue Pan
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Fred Y Peng
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Randall J Weselake
- Agricultural Lipid Biotechnology Program, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
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37
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Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 2015; 32:1342-53. [PMID: 25697341 DOI: 10.1093/molbev/msv022] [Citation(s) in RCA: 450] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Over the past two decades, comparative sequence analysis using codon-substitution models has been honed into a powerful and popular approach for detecting signatures of natural selection from molecular data. A substantial body of work has focused on developing a class of "branch-site" models which permit selective pressures on sequences, quantified by the ω ratio, to vary among both codon sites and individual branches in the phylogeny. We develop and present a method in this class, adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion. By applying models of different complexity to different branches in the phylogeny, aBSREL delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster. Based on simulated data analysis, we offer guidelines for what extent and strength of diversifying positive selection can be detected reliably and suggest that there is a natural limit on the optimal parametric complexity for "branch-site" models. An aBSREL analysis of 8,893 Euteleostomes gene alignments demonstrates that over 80% of branches in typical gene phylogenies can be adequately modeled with a single ω ratio model, that is, current models are unnecessarily complicated. However, there are a relatively small number of key branches, whose identities are derived from the data using a model selection procedure, for which it is essential to accurately model evolutionary complexity.
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Affiliation(s)
- Martin D Smith
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego
| | | | - Steven Weaver
- Department of Medicine, University of California San Diego
| | - Ben Murrell
- Department of Medicine, University of California San Diego
| | - Konrad Scheffler
- Department of Medicine, University of California San Diego Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
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Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Gene-wide identification of episodic selection. Mol Biol Evol 2015; 32:1365-71. [PMID: 25701167 DOI: 10.1093/molbev/msv035] [Citation(s) in RCA: 354] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites subject to episodic positive selection on any foreground branches. We compare BUSTED with existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted, with a widget allowing the interactive specification of foreground branches.
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Affiliation(s)
- Ben Murrell
- Department of Medicine, University of California San Diego
| | - Steven Weaver
- Department of Medicine, University of California San Diego
| | - Martin D Smith
- Graduate program in Bioinformatics and Systems Biology, University of California San Diego
| | | | - Sasha Murrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Anthony Aylward
- Graduate program in Bioinformatics and Systems Biology, University of California San Diego
| | - Kemal Eren
- Graduate program in Bioinformatics and Systems Biology, University of California San Diego Graduate program in Biomedical Informatics, University of California San Diego
| | | | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Davey M Smith
- Department of Medicine, University of California San Diego Veterans Affairs San Diego Healthcare System, San Diego, CA
| | - Konrad Scheffler
- Department of Medicine, University of California San Diego Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
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39
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Arenas M, Lopes JS, Beaumont MA, Posada D. CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation. Mol Biol Evol 2015; 32:1109-12. [PMID: 25577191 PMCID: PMC4379410 DOI: 10.1093/molbev/msu411] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.
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Affiliation(s)
- Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
| | - Joao S Lopes
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
| | - Mark A Beaumont
- School of Mathematical Sciences and School of Biological Sciences, University of Bristol, University Walk, Bristol, United Kingdom
| | - David Posada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
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40
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Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol 2014; 32:820-32. [PMID: 25540451 DOI: 10.1093/molbev/msu400] [Citation(s) in RCA: 405] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of natural selection, can drive evolutionary innovation and presage lineage extinction or loss of function. Mechanisms through which selection can be relaxed range from the removal of an existing selective constraint to a reduction in effective population size. Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection, because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection. Here, we present a general hypothesis testing framework (RELAX) for detecting relaxed selection in a codon-based phylogenetic framework. Given two subsets of branches in a phylogeny, RELAX can determine whether selective strength was relaxed or intensified in one of these subsets relative to the other. We establish the validity of our test via simulations and show that it can distinguish between increased positive selection and a relaxation of selective strength. We also demonstrate the power of RELAX in a variety of biological scenarios where relaxation of selection has been hypothesized or demonstrated previously. We find that obligate and facultative γ-proteobacteria endosymbionts of insects are under relaxed selection compared with their free-living relatives and obligate endosymbionts are under relaxed selection compared with facultative endosymbionts. Selective strength is also relaxed in asexual Daphnia pulex lineages, compared with sexual lineages. Endogenous, nonfunctional, bornavirus-like elements are found to be under relaxed selection compared with exogenous Borna viruses. Finally, selection on the short-wavelength sensitive, SWS1, opsin genes in echolocating and nonecholocating bats is relaxed only in lineages in which this gene underwent pseudogenization; however, selection on the functional medium/long-wavelength sensitive opsin, M/LWS1, is found to be relaxed in all echolocating bats compared with nonecholocating bats.
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Affiliation(s)
| | - Ben Murrell
- Department of Medicine, University of California, San Diego
| | - Martin D Smith
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego
| | | | - Konrad Scheffler
- Department of Medicine, University of California, San Diego Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
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41
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Garvin MR, Bielawski JP, Sazanov LA, Gharrett AJ. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12079] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael R. Garvin
- Fisheries Division; School of Fisheries and Ocean Sciences; University of Alaska Fairbanks; Juneau AK USA
| | - Joseph P. Bielawski
- Department of Biology; Dalhousie University; Halifax NS Canada
- Department of Mathematics & Statistics; Dalhousie University; Halifax NS Canada
| | | | - Anthony J. Gharrett
- Fisheries Division; School of Fisheries and Ocean Sciences; University of Alaska Fairbanks; Juneau AK USA
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42
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Abstract
Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models.
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Affiliation(s)
- Maryam Zaheri
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Linda Dib
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandSwiss Institute of Bioinformatics, Genopode, Quartier Sorge, 1015 Lausanne, Switzerland
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43
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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44
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Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol 2014; 31:1149-65. [PMID: 24509690 DOI: 10.1093/molbev/msu064] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.
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Affiliation(s)
- Ryan K Schott
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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45
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Vera-Ruiz VA, Lau KW, Robinson J, Jermiin LS. Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics. BMC Bioinformatics 2014; 15 Suppl 2:S8. [PMID: 24564837 PMCID: PMC4015178 DOI: 10.1186/1471-2105-15-s2-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Under a Markov model of evolution, recoding, or lumping, of the four nucleotides into fewer groups may permit analysis under simpler conditions but may unfortunately yield misleading results unless the evolutionary process of the recoded groups remains Markovian. If a Markov process is lumpable, then the evolutionary process of the recoded groups is Markovian. Results We consider stationary, reversible, and homogeneous Markov processes on two taxa and compare three tests for lumpability: one using an ad hoc test statistic, which is based on an index that is evaluated using a bootstrap approximation of its distribution; one that is based on a test proposed specifically for Markov chains; and one using a likelihood-ratio test. We show that the likelihood-ratio test is more powerful than the index test, which is more powerful than that based on the Markov chain test statistic. We also show that for stationary processes on binary trees with more than two taxa, the tests can be applied to all pairs. Finally, we show that if the process is lumpable, then estimates obtained under the recoded model agree with estimates obtained under the original model, whereas, if the process is not lumpable, then these estimates can differ substantially. We apply the new likelihood-ratio test for lumpability to two primate data sets, one with a mitochondrial origin and one with a nuclear origin. Conclusions Recoding may result in biased phylogenetic estimates because the original evolutionary process is not lumpable. Accordingly, testing for lumpability should be done prior to phylogenetic analysis of recoded data.
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46
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Valle M, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N. Optimization strategies for fast detection of positive selection on phylogenetic trees. ACTA ACUST UNITED AC 2014; 30:1129-1137. [PMID: 24389654 PMCID: PMC3982156 DOI: 10.1093/bioinformatics/btt760] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 12/23/2013] [Indexed: 12/20/2022]
Abstract
Motivation: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. Results: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total). Availability and implementation:ftp://ftp.vital-it.ch/tools/FastCodeML/. Contact:selectome@unil.ch or nicolas.salamin@unil.ch
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Affiliation(s)
- Mario Valle
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Hannes Schabauer
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Christoph Pacher
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Heinz Stockinger
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Alexandros Stamatakis
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Marc Robinson-Rechavi
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
| | - Nicolas Salamin
- Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany Swiss National Supercomputing Centre, Scientific Computing Group, Lugano, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, AIT Austrian Institute of Technology, Safety & Security Department, Vienna, Austria, Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland, Heidelberg Institute for Theoretical Studies, Scientific Computing Group and Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
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Tomasco IH, Lessa EP. Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents. Gene 2014; 534:371-8. [DOI: 10.1016/j.gene.2013.09.097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/28/2013] [Accepted: 09/26/2013] [Indexed: 11/27/2022]
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Datta S, Prado R, Rodríguez A. Bayesian factor models in characterizing molecular adaptation. J Appl Stat 2013; 40:1402-1424. [DOI: 10.1080/02664763.2013.785652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bielawski JP. Detecting the signatures of adaptive evolution in protein-coding genes. ACTA ACUST UNITED AC 2013; Chapter 19:Unit 19.1.. [PMID: 23288462 DOI: 10.1002/0471142727.mb1901s101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation. Many DNA changes are believed to have little to no functional effect, and a neutral process will best explain their evolution. Thus, a central task is to discover which changes had positive fitness consequences and were subject to Darwinian natural selection during the course of evolution. Due the size and complexity of modern molecular datasets, the field has come to rely extensively on statistical modeling techniques to meet this analytical challenge. For DNA sequences that encode proteins, one of the most powerful approaches is to employ a statistical model of codon evolution. This unit provides a general introduction to the practice of modeling codon evolution using the statistical framework of maximum likelihood. Four real-data analysis activities are used to illustrate the principles of parameter estimation, robustness, hypothesis testing, and site classification. Each activity includes an explicit analytical protocol based on programs provided by the Phylogenetic Analysis by Maximum Likelihood (PAML) package.
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Affiliation(s)
- Joseph P Bielawski
- Department of Biology, Department of Mathematics & Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
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Vinogradov AE. Density peaks of paralog pairs in human and mouse genomes. Gene 2013; 527:55-61. [PMID: 23751307 DOI: 10.1016/j.gene.2013.05.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/10/2013] [Accepted: 05/12/2013] [Indexed: 11/30/2022]
Abstract
Paralog gene trees, which reflect the increase of genomic complexity in the evolution, can be complicated and ambiguous. A simpler complementary approach is analysis of density distribution of paralog pairs. It can reveal general features of genome evolution, which may be hidden in the forest of gene trees. It is known that distribution of human paralog pairs along the axis of protein divergence between pair members forms two main peaks. Here I show that there are three main peaks in the mouse genome. Thus, the multimodality of paralog pair distribution seems to be a fundamental feature of mammalian genomes. Despite the great diversity of domains presented in small amounts or in multidomain architectures with a few predominant domains, both in human and mouse the first peak consists mostly of gene pairs with zinc finger domains or olfactory receptor domain. In the mouse the olfactory receptor predominates, which stipulates the three-peak distribution (since in the olfactory receptors the second peak is closer to the first peak than in other genes). The mammalian-wide zinc finger orthologs are biased towards the second peak. Thus, the marsupial orthologs are nearly absent in the first peak of human and mouse. The gene pairs in the first peak show a lower ratio of nonsynonymous to synonymous substitutions, which suggests that their evolution is more constrained. The plausible explanation is that they are in subfunctionalization state (partition of initial function of ancestral gene), whereas the second peak contains gene pairs that are already in neofunctionalization state (acquiring of novel functions). These data suggest that the adaptive radiation of mammals was accompanied by a burst of duplication of zinc finger genes, which are located in the first (most recent) peak of paralog pairs.
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