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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [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: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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2
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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, Slate J. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 2024; 24:e13969. [PMID: 38747336 DOI: 10.1111/1755-0998.13969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Adriaensen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tamer Albayrak
- Department of Biology, Science and art Faculty, Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
- Biology Education, Buca Faculty of Education, Mathematics and Science Education, Dokuz Eylül University, İzmir, Turkey
| | | | - Eduardo Belda
- Institut d'Investigació per a la Gestió Integrada de Zones Costaneres, Campus de Gandia, Universitat Politècnica de València, València, Spain
| | - Andrey Bushuev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | | | - Mariusz Cichon
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU München, Planegg-Martinsried, Germany
| | - Blandine Doligez
- UMR CNRS 5558-LBBE, Biométrie et Biologie Évolutive, Villeurbanne, France
- Department of Ecology and Evolution, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku, Finland
| | - Kjell Einar Erikstad
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, Tromsø, Norway
| | | | - Matteo Griggio
- Department of Biology, University of Padova, Padova, Italy
| | - Dieter Heylen
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Sabine Hille
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, Vienna, Austria
| | - Camilla A Hinde
- Behavioural Ecology Group, Department of Life Sciences, Anglia Ruskin University, Cambridgeshire, UK
| | - Elena Ivankina
- Faculty of Biology, Zvenigorod Biological Station, Lomonosov Moscow State University, Moscow, Russia
| | - Bart Kempenaers
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Anvar Kerimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Milos Krist
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Raivo Mänd
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ruedi Nager
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Boris P Nikolov
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ana Claudia Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Markku Orell
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | | | - Gergana Petrova-Dinkova
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università Degli Studi di Milano, Milan, Italy
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vallo Tilgar
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Csongor I Vágási
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Teru Yuta
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Ben C Sheldon
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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3
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Martin CA, Sheppard EC, Ali HAA, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci? Mol Ecol 2024; 33:e17365. [PMID: 38733214 DOI: 10.1111/mec.17365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/01/2024] [Indexed: 05/13/2024]
Abstract
When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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4
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Ślesak I, Ślesak H. From cyanobacteria and cyanophages to chloroplasts: the fate of the genomes of oxyphototrophs and the genes encoding photosystem II proteins. THE NEW PHYTOLOGIST 2024; 242:1055-1067. [PMID: 38439684 DOI: 10.1111/nph.19633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024]
Abstract
Chloroplasts are the result of endosymbiosis of cyanobacterial organisms with proto-eukaryotes. The psbA, psbD and psbO genes are present in all oxyphototrophs and encode the D1/D2 proteins of photosystem II (PSII) and PsbO, respectively. PsbO is a peripheral protein that stabilizes the O2-evolving complex in PSII. Of these genes, psbA and psbD remained in the chloroplastic genome, while psbO was transferred to the nucleus. The genomes of selected cyanobacteria, chloroplasts and cyanophages carrying psbA and psbD, respectively, were analysed. The highest density of genes and coding sequences (CDSs) was estimated for the genomes of cyanophages, cyanobacteria and chloroplasts. The synonymous mutation rate (rS) of psbA and psbD in chloroplasts remained almost unchanged and is lower than that of psbO. The results indicate that the decreasing genome size in chloroplasts is more similar to the genome reduction observed in contemporary endosymbiotic organisms than in streamlined genomes of free-living cyanobacteria. The rS of atpA, which encodes the α-subunit of ATP synthase in chloroplasts, suggests that psbA and psbD, and to a lesser extent psbO, are ancient and conservative and arose early in the evolution of oxygenic photosynthesis. The role of cyanophages in the evolution of oxyphototrophs and chloroplastic genomes is discussed.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Halina Ślesak
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
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5
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de Jong MJ, van Oosterhout C, Hoelzel AR, Janke A. Moderating the neutralist-selectionist debate: exactly which propositions are we debating, and which arguments are valid? Biol Rev Camb Philos Soc 2024; 99:23-55. [PMID: 37621151 DOI: 10.1111/brv.13010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
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Affiliation(s)
- Menno J de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
| | - Cock van Oosterhout
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse 9, Frankfurt am Main, 60438, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, 60325, Germany
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6
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Zhang H, Hellweger FL, Luo H. Genome reduction occurred in early Prochlorococcus with an unusually low effective population size. THE ISME JOURNAL 2024; 18:wrad035. [PMID: 38365237 PMCID: PMC10837832 DOI: 10.1093/ismejo/wrad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
In the oligotrophic sunlit ocean, the most abundant free-living planktonic bacterial lineages evolve convergently through genome reduction. The cyanobacterium Prochlorococcus responsible for 10% global oxygen production is a prominent example. The dominant theory known as "genome streamlining" posits that they have extremely large effective population sizes (Ne) such that selection for metabolic efficiency acts to drive genome reduction. Because genome reduction largely took place anciently, this theory builds on the assumption that their ancestors' Ne was similarly large. Constraining Ne for ancient ancestors is challenging because experimental measurements of extinct organisms are impossible and alternatively reconstructing ancestral Ne with phylogenetic models gives large uncertainties. Here, we develop a new strategy that leverages agent-based modeling to simulate the changes in the genome-wide ratio of radical to conservative nonsynonymous nucleotide substitution rate (dR/dC) in a possible range of Ne in ancestral populations. This proxy shows expected increases with decreases of Ne only when Ne falls to about 10 k - 100 k or lower, magnitudes characteristic of Ne of obligate endosymbiont species where drift drives genome reduction. Our simulations therefore strongly support a scenario where the primary force of Prochlorococcus genome reduction is drift rather than selection.
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Affiliation(s)
- Hao Zhang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong SAR
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, 10623, Germany
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong SAR
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, 999077, Hong Kong SAR
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7
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Duan L, Wang F, Shen H, Xie S, Chen X, Xie Q, Li R, Cao A, Li H. Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis. BMC Genomics 2023; 24:795. [PMID: 38129780 PMCID: PMC10734139 DOI: 10.1186/s12864-023-09717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism. RESULTS A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner. CONCLUSIONS Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.
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Affiliation(s)
- Lisheng Duan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Shuangquan Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xifeng Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Aiping Cao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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8
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Forsythe D, Hsu JL. Neutral theory and beyond: A systematic review of molecular evolution education. Ecol Evol 2023; 13:e10365. [PMID: 37529584 PMCID: PMC10375367 DOI: 10.1002/ece3.10365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023] Open
Abstract
Molecular evolution-including the neutral theory of molecular evolution-is a major sub-discipline of evolution and is widely taught in undergraduate evolution courses. However, despite its ubiquity, there have not been any previous attempts to compile and review the molecular evolution education literature. Here, we draw upon the framework proposed in a past literature review examining the broader evolution education landscape to conduct a literature review of papers related to molecular evolution education, classifying the contributions of such papers to evolution pedagogy as well as evolution education research. We find that there remains very limited coverage of molecular evolution in the education literature, with existing papers focusing primarily on providing new instructional modules and strategies for teaching molecular evolution. Our work suggests several areas of critical need as well as opportunities to advance evolution education and evolution education research, including compiling instructional goals for the sub-discipline, developing validated assessments, and investigating student thinking related to molecular evolution. We conclude by providing general strategies, advice, and a novel curricular activity for teaching molecular evolution and the neutral theory of molecular evolution.
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Affiliation(s)
- Desiree Forsythe
- Grand Challenges Initiative, Schmid College of Science and TechnologyChapman UniversityOrangeCaliforniaUSA
- Schmid College of Science and TechnologyChapman UniversityOrangeCaliforniaUSA
| | - Jeremy L. Hsu
- Schmid College of Science and TechnologyChapman UniversityOrangeCaliforniaUSA
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9
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Howden BP, Giulieri SG, Wong Fok Lung T, Baines SL, Sharkey LK, Lee JYH, Hachani A, Monk IR, Stinear TP. Staphylococcus aureus host interactions and adaptation. Nat Rev Microbiol 2023; 21:380-395. [PMID: 36707725 PMCID: PMC9882747 DOI: 10.1038/s41579-023-00852-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to develop drug resistance. S. aureus is an excellent case study of the potential for a bacterium to be commensal, colonizing, latent or disease-causing; these states defined by the interplay between S. aureus and host. This interplay is multidimensional and evolving, exemplified by the spread of S. aureus between humans and other animal reservoirs and the lack of success in vaccine development. In this Review, we examine recent advances in understanding the S. aureus-host interactions that lead to infections. We revisit the primary role of neutrophils in controlling infection, summarizing the discovery of new immune evasion molecules and the discovery of new functions ascribed to well-known virulence factors. We explore the intriguing intersection of bacterial and host metabolism, where crosstalk in both directions can influence immune responses and infection outcomes. This Review also assesses the surprising genomic plasticity of S. aureus, its dualism as a multi-mammalian species commensal and opportunistic pathogen and our developing understanding of the roles of other bacteria in shaping S. aureus colonization.
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Affiliation(s)
- Benjamin P. Howden
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.410678.c0000 0000 9374 3516Department of Infectious Diseases, Austin Health, Heidelberg, Victoria Australia ,grid.416153.40000 0004 0624 1200Microbiology Department, Royal Melbourne Hospital, Melbourne, Victoria Australia
| | - Stefano G. Giulieri
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.416153.40000 0004 0624 1200Victorian Infectious Diseases Service, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Tania Wong Fok Lung
- grid.21729.3f0000000419368729Department of Paediatrics, Columbia University, New York, NY USA
| | - Sarah L. Baines
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Liam K. Sharkey
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Jean Y. H. Lee
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.419789.a0000 0000 9295 3933Department of Infectious Diseases, Monash Health, Clayton, Victoria Australia
| | - Abderrahman Hachani
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Ian R. Monk
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
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10
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Guo S, Zeng M, Gao W, Li F, Wei X, Shi Q, Wen Z, Song Z. Toll-like Receptor 3 in the Hybrid Yellow Catfish ( Pelteobagrus fulvidraco ♀ × P. vachelli ♂): Protein Structure, Evolution and Immune Response to Exogenous Aeromonas hydrophila and Poly (I:C) Stimuli. Animals (Basel) 2023; 13:ani13020288. [PMID: 36670828 PMCID: PMC9854889 DOI: 10.3390/ani13020288] [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: 11/12/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
As a major mediator of cellular response to viral infection in mammals, Toll-like receptor 3 (TLR3) was proved to respond to double-stranded RNA (dsRNA). However, the molecular mechanism by which TLR3 functions in the viral infection response in teleosts remains to be investigated. In this study, the Toll-like receptor 3 gene of the hybrid yellow catfish was identified and characterized by comparative genomics. Furthermore, multiple sequence alignment, genomic synteny and phylogenetic analysis suggested that the homologous TLR3 genes were unique to teleosts. Gene structure analysis showed that five exons and four introns were common components of TLR3s in the 12 examined species, and interestingly the third exon in teleosts was the same length of 194 bp. Genomic synteny analysis indicated that TLR3s were highly conserved in various teleosts, with similar organizations of gene arrangement. De novo predictions showed that TLR3s were horseshoe-shaped in multiple taxa except for avian (with a round-shaped structure). Phylogenetic topology showed that the evolution of TLR3 was consistent with the evolution of the studied species. Selection analysis showed that the evolution rates of TLR3 proteins were usually higher than those of TLR3-TIR domains, indicating that the latter were more conserved. Tissue distribution analysis showed that TLR3s were widely distributed in the 12 tested tissues, with the highest transcriptions in liver and intestine. In addition, the transcription levels of TLR3 were significantly increased in immune-related tissues after infection of exogenous Aeromonas hydrophila and poly (I:C). Molecular docking showed that TLR3 in teleosts forms a complex with poly (I:C). In summary, our present results suggest that TLR3 is a pattern recognition receptor (PRR) gene in the immune response to pathogen infections in hybrid yellow catfish.
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Affiliation(s)
- Shengtao Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Mengsha Zeng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenxue Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Fan Li
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641100, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiuying Wei
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641100, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Zhengyong Wen
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641100, China
- Correspondence: (Z.W.); (Z.S.)
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Correspondence: (Z.W.); (Z.S.)
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11
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Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration. Genes (Basel) 2022; 13:genes13091615. [PMID: 36140782 PMCID: PMC9498720 DOI: 10.3390/genes13091615] [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: 07/22/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes of Exostoma tibetanum and Exostoma tenuicaudatum—two sympatric congeners from the lower Yarlung Tsangpo River, Tibet, China. The mitogenomes of both species contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one light-strand origin of replication, and one control region, with lengths of 16,528 bp and 16,533 bp, respectively. The mitogenome architecture, nucleotide composition, and codon usage of protein-coding genes were almost identical between the two Exostoma species, although some estimated parameters varied. Phylogenetic analysis strongly supported the monophyly of Exostoma in the subfamily Glyptosternae, and Exostoma tibetanum had the closest relationship to Exostoma tenuicaudatum. The divergence time estimation demonstrated that these two species diverged approximately 1.51 Ma during the early Pleistocene, which was speculated to be triggered by the river system changes caused by the uplift of the southeastern Tibetan Plateau. Selection pressure analyses indicated that all protein-coding genes of Exostoma species underwent a strong purifying selection, while minority positive sites from NADH dehydrogenase complex genes were detected. These findings are expected to promote our understanding of the molecular phylogeny of the genus Exostoma and provide valuable mitogenomic resources for the subfamily Glyptosternae
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12
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Bräutigam C, Smerlak M. Diffusion approximations in population genetics and the rate of Muller's ratchet. J Theor Biol 2022; 550:111236. [PMID: 35926567 DOI: 10.1016/j.jtbi.2022.111236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 07/13/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
Abstract
The Wright-Fisher binomial model of allele frequency change is often approximated by a scaling limit in which selection, mutation and drift all decrease at the same 1/N rate. This construction restricts the applicability of the resulting 'Wright-Fisher diffusion equation' to the weak selection, weak mutation regime of evolution. We argue that diffusion approximations of the Wright-Fisher model can be used more generally, for instance in cases where genetic drift is much weaker than selection. One important example of this regime is Muller's ratchet phenomenon, whereby deleterious mutations slowly but irreversibly accumulate through rare stochastic fluctuations. Using a modified diffusion equation we derive improved analytical estimates for the mean click time of the ratchet.
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Affiliation(s)
- Camila Bräutigam
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
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13
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Wang Y, Xiong F, Song Z. Molecular Phylogeny and Adaptive Mitochondrial DNA Evolution of Salmonids (Pisces: Salmonidae). Front Genet 2022; 13:903240. [PMID: 35783273 PMCID: PMC9249015 DOI: 10.3389/fgene.2022.903240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Salmonids are composed of anadromous and freshwater fishes, which is an important model for studying adaptive evolution. Herein, 49 salmonid complete mitochondrial genomes and those of two outgroups were used to infer a robust phylogeny for the family Salmonidae. The BI and RAxML phylogenetic trees based on 13 concatenated mitochondrial protein-coding genes showed well-supported nodes, and topologies were highly congruent. The concatenated 13 mitochondrial protein-coding genes, ND2, ND3, and ND5 genes were shown to have significantly larger dN/dS ratios in anadromous species than in freshwater species of Salmonidae, but the CYTB gene had significantly smaller dN/dS in anadromous species. The FEL analysis identified positively selected sites and negatively selected sites in each mitochondrial protein-coding gene separately. The RELAX program revealed that the ATP8 and CYTB genes supported intensified selection of the anadromous lineages. Our results demonstrated the phylogeny of Salmonidae and explored the mitochondrial DNA evolution pattern between anadromous and freshwater salmonids.
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Affiliation(s)
- Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
- *Correspondence: Fei Xiong, ; Zhaobin Song,
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Fei Xiong, ; Zhaobin Song,
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14
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The Roles of Mutation and Selection Acting on Mitochondrial Genomes Inferred from Intraspecific Variation in Seed Plants. Genes (Basel) 2022; 13:genes13061036. [PMID: 35741799 PMCID: PMC9222611 DOI: 10.3390/genes13061036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
There is a paradox in the plant mitochondrial genome, that is, the genic region evolves slowly while the intergenic region evolves rapidly. Thus, the intergenic regions of the plant mitochondrial genome are difficult to align across different species, even in closely related species. Here, to character the mechanism of this paradox, we identified interspecific variations in the Ginkgo biloba, Oryza sativa, and Arabidopsis thaliana mitochondrial and plastid genome at a genome-wide level. The substitution rate of synonymous sites in genic regions was similar to the substitution rate of intergenic regions, while the substitution rate of nonsynonymous sites in genic regions was lower than that in intergenic regions, suggesting the mutation inputs were the same among different categories within the organelle genome, but the selection pressure varied. The substitution rate of single-copy regions was higher than that of IR (inverted repeats) in the plastid genome at an intraspecific level. The substitution rate of single-copy regions was higher than that of repeats in the G. biloba and A. thaliana mitochondrial genomes, but lower in that of O. sativa. This difference may be related to the length and distribution of repeats. Copy number variations that existed in the G. biloba and O. sativa mitochondrial genomes were confirmed. This study reveals the intraspecific variation pattern of organelle genomes at a genome-wide level, and that copy number variations were common in plant mitochondrial genomes.
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15
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Hsu TK, Asmussen J, Koire A, Choi BK, Gadhikar MA, Huh E, Lin CH, Konecki DM, Kim YW, Pickering CR, Kimmel M, Donehower LA, Frederick MJ, Myers JN, Katsonis P, Lichtarge O. A general calculus of fitness landscapes finds genes under selection in cancers. Genome Res 2022; 32:916-929. [PMID: 35301263 PMCID: PMC9104707 DOI: 10.1101/gr.275811.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Genetic variants drive the evolution of traits and diseases. We previously modeled these variants as small displacements in fitness landscapes and estimated their functional impact by differentiating the evolutionary relationship between genotype and phenotype. Conversely, here we integrate these derivatives to identify genes steering specific traits. Over cancer cohorts, integration identified 460 likely tumor-driving genes. Many have literature and experimental support but had eluded prior genomic searches for positive selection in tumors. Beyond providing cancer insights, these results introduce a general calculus of evolution to quantify the genotype-phenotype relationship and discover genes associated with complex traits and diseases.
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Affiliation(s)
- Teng-Kuei Hsu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer Asmussen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Koire
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Byung-Kwon Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mayur A Gadhikar
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eunna Huh
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chih-Hsu Lin
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Daniel M Konecki
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Young Won Kim
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Marek Kimmel
- Departments of Statistics and Bioengineering, Rice University, Houston, Texas 77005, USA
- Department of Systems Engineering and Biology, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Lawrence A Donehower
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mitchell J Frederick
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Olivier Lichtarge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
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16
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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Abstract
Modern evolutionary theory gives a detailed quantitative description of microevolutionary processes that occur within evolving populations of organisms, but evolutionary transitions and emergence of multiple levels of complexity remain poorly understood. Here, we establish the correspondence among the key features of evolution, learning dynamics, and renormalizability of physical theories to outline a theory of evolution that strives to incorporate all evolutionary processes within a unified mathematical framework of the theory of learning. According to this theory, for example, replication of genetic material and natural selection readily emerge from the learning dynamics, and in sufficiently complex systems, the same learning phenomena occur on multiple levels or on different scales, similar to the case of renormalizable physical theories. We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].
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18
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Borges R, Boussau B, Szöllősi GJ, Kosiol C. Nucleotide Usage Biases Distort Inferences of the Species Tree. Genome Biol Evol 2022; 14:6496956. [PMID: 34983052 PMCID: PMC8829901 DOI: 10.1093/gbe/evab290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the importance of natural selection in species’ evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to compromise phylogenetic inferences significantly. However, genome-wide processes like GC-bias and some variation segregating at the coding regions are known to evolve in the nearly neutral range. As we are now using genome-wide data to estimate species trees, it is natural to ask whether weak but pervasive selection is likely to blur species tree inferences. We developed a polymorphism-aware phylogenetic model tailored for measuring signatures of nucleotide usage biases to test the impact of selection in the species tree. Our analyses indicate that although the inferred relationships among species are not significantly compromised, the genetic distances are systematically underestimated in a node-height-dependent manner: that is, the deeper nodes tend to be more underestimated than the shallow ones. Such biases have implications for molecular dating. We dated the evolutionary history of 30 worldwide fruit fly populations, and we found signatures of GC-bias considerably affecting the estimated divergence times (up to 23%) in the neutral model. Our findings call for the need to account for selection when quantifying divergence or dating species evolution.
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Affiliation(s)
- Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Bastien Boussau
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, LBBE, Villeurbanne, France
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös University, Budapest , Hungary.,MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Budapest, Hungary.,Evolutionary Systems Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
| | - Carolin Kosiol
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.,Centre for Biological Diversity, University of St Andrews, St Andrews, United Kingdom
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19
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Beatty J. The Synthesis and the Two Scenarios. Evolution 2021; 76:6-14. [PMID: 34951705 DOI: 10.1111/evo.14423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/23/2021] [Accepted: 12/22/2021] [Indexed: 11/28/2022]
Abstract
On the occasion of the 75th anniversary of the Society for the Study of Evolution, I look back at the so-called "evolutionary synthesis," to which many of the Society's founders and prominent founding members were committed. An important plank in the synthesis platform had to do with the importance of selection relative to mutation. Of course, there is no evolutionary change without mutation, and no adaptive evolutionary change without selection. So how could selection be more important than mutation, or vice-versa? At issue was whether adaptive evolutionary change is initiated and directed by selection, or by the appearance of new advantageous variation. Proponents of the synthesis took the position that Darwin himself had defended, namely that adaptive evolutionary change is initiated and directed by natural selection on standing variation, no new variation, no mutation, required. Natural selection is, in this sense, not just "creative," but is the creative agent of evolutionary change. In taking this extreme position, proponents of the synthesis were reacting to the equally extreme position of Mendelian-mutationists, who held that adaptive evolutionary change always commences with, and is directed by, the appearance of new advantageous mutations, and for whom mutation is the creative agent of evolutionary change. I conclude with some comments on "relative significance" issues and controversies, and respects in which the relative significance issues at the heart of the synthesis persist. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- John Beatty
- Department of Philosophy, University of British Columbia, Vancouver, V6T 1Z1, Canada
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20
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Young A, Anderson RO, Naimo A, Alton LA, Goulet CT, Chapple DG. How do the physiological traits of a lizard change during its invasion of an oceanic island? Oecologia 2021; 198:567-578. [PMID: 34725729 DOI: 10.1007/s00442-021-05054-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/28/2021] [Indexed: 11/30/2022]
Abstract
Physiology is crucial for the survival of invasive species in new environments. Yet, new climatic conditions and the limited genetic variation found within many invasive populations may influence physiological responses to new environmental conditions. Here, we studied the case of the delicate skinks (Lampropholis delicata) invading Lord Howe Island (LHI), Australia. On LHI, the climate is different from the mainland source of the skinks, and independent introduction events generated invasive populations with distinct genetic backgrounds. To understand how climate and genetic background may shape physiological responses along biological invasions, we compared the physiological traits of a source and two invasive (single-haplotype and multi-haplotype) populations of the delicate skink. For each population, we quantified physiological traits related to metabolism, sprint speed, and thermal physiology. We found that, for most physiological traits analysed, population history did not influence the ecophysiology of delicate skinks. However, invasive populations showed higher maximum speed than the source population, which indicates that locomotor performance might be a trait under selection during biological invasions. As well, the invasive population with a single haplotype was less cold-tolerant than the multi-haplotype and source populations. Our results suggest that limited genetic variability and climate may influence physiological responses of invasive organisms in novel environments. Incorporating the interplay between genetic and physiological responses into models predicting species invasions can result in more accurate understanding of the potential habitats those species can occupy.
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Affiliation(s)
- Alyse Young
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Rodolfo O Anderson
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - Annalise Naimo
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Lesley A Alton
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Celine T Goulet
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David G Chapple
- Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
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21
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Zhang X, Sun A, Ge J. Origin and Spread of the ALDH2 Glu504Lys Allele. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:222-228. [PMID: 36939783 PMCID: PMC9590465 DOI: 10.1007/s43657-021-00017-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 01/14/2023]
Abstract
Gene polymorphism of acetaldehyde dehydrogenase 2 (ALDH2), a key enzyme for alcohol metabolism in humans, can affect catalytic activity. The ALDH2 Glu504Lys mutant allele has a high-frequency distribution in East Asian populations and has been demonstrated to be associated with an increased risk of cardiovascular disease, stroke, and tumors. Available evidence suggests that the evolution of the ALDH2 gene has been influenced by multiple factors. Random mutations produce Glu504Lys, and genetic drift alters the frequency of this allele; additionally, environmental factors such as hepatitis B virus infection and high-elevation hypoxia affect its frequency through selective effects, ultimately resulting in a high frequency of this allele in East Asian populations. Here, the origin, selection, and spread of the ALDH2 Glu504Lys allele are discussed, and an outlook for further research is proposed to realize a precision medical strategy based on the genetic and environmental variations in ALDH2.
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Affiliation(s)
- Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Aijun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
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22
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Flowers EM, Neely HR, Guo J, Almeida T, Ohta Y, Castro CD, Flajnik MF. Identification of the Fc-alpha/mu receptor in Xenopus provides insight into the emergence of the poly-Ig receptor (pIgR) and mucosal Ig transport. Eur J Immunol 2021; 51:2590-2606. [PMID: 34411303 DOI: 10.1002/eji.202149383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Indexed: 01/17/2023]
Abstract
The polyimmunoglobulin receptor (pIgR) transcytoses J chain-containing antibodies through mucosal epithelia. In mammals, two cis-duplicates of PIGR, FCMR, and FCAMR, flank the PIGR gene. A PIGR duplication is first found in amphibians, previously annotated as PIGR2 (herein xlFCAMR), and is expressed by APCs. We demonstrate that xlFcamR is the equivalent of mammalian FcamR. It has been assumed that pIgR is the oldest member of this family, yet our data could not distinguish whether PIGR or FCAMR emerged first; however, FCMR was the last family member to emerge. Interestingly, bony fish "pIgR" is not an orthologue of tetrapod pIgR, and possibly acquired its function via convergent evolution. PIGR/FCAMR/FCMR are members of a larger superfamily, including TREM, CD300, and NKp44, which we name the "double-disulfide Ig superfamily" (ddIgSF). Domains related to each ddIgSF family were identified in cartilaginous fish (sharks, chimeras) and encoded in a single gene cluster syntenic to the human pIgR locus. Thus, the ddIgSF families date back to the earliest antibody-based adaptive immunity, but apparently not before. Finally, our data strongly suggest that the J chain arose in evolution only for Ig multimerization. This study provides a framework for further studies of pIgR and the ddIgSF in vertebrates.
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Affiliation(s)
- Emily M Flowers
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Harold R Neely
- Department of Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Guo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tereza Almeida
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Caitlin D Castro
- Committee on Immunology and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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23
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Lahr DJ. An emerging paradigm for the origin and evolution of shelled amoebae, integrating advances from molecular phylogenetics, morphology and paleontology. Mem Inst Oswaldo Cruz 2021; 116:e200620. [PMID: 34406221 PMCID: PMC8370470 DOI: 10.1590/0074-02760200620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/05/2021] [Indexed: 11/22/2022] Open
Abstract
The phylogenetic paradigm of eukaryotic evolution has changed dramatically over the past two decades, with profound reflections on the understanding of life on earth. Arcellinida testate (shelled) amoebae lineages represent some of the oldest fossils of eukaryotes, and the elucidation of their phylogenetic relationships opened a window to the distant past, with important implications for understanding the evolution of life on earth. This four-part essay summarises advances made in the past 20 years regarding: (i) the phylogenetic relationships among amoebae with shells evolving in concert with the advances made in the phylogeny of eukaryotes; (ii) paleobiological studies unraveling the biological affinities of Neoproterozoic vase-shaped microfossils (VSMs); (iii) the interwoven interpretation of these different sets of data concluding that the Neoproterozoic contains a surprising diversity of organisms, in turn demanding a reinterpretation of the most profound events we know in the history of eukaryotes, and; (iv) a synthesis of the current knowledge about the evolution of Arcellinida, together with the possibilities and pitfalls of their interpretation.
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Affiliation(s)
- Daniel Jg Lahr
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brasil
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24
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Podder S, Ghosh A, Ghosh T. Mutations in membrane-fusion subunit of spike glycoprotein play crucial role in the recent outbreak of COVID-19. J Med Virol 2021; 93:2790-2798. [PMID: 33090493 PMCID: PMC7675664 DOI: 10.1002/jmv.26598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/14/2020] [Accepted: 10/11/2020] [Indexed: 01/06/2023]
Abstract
Coronavirus disease‐2019 (COVID‐19), the ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a major threat to the entire human race. It is reported that SARS‐CoV‐2 seems to have relatively low pathogenicity and higher transmissibility than previously outbroke SARS‐CoV. To explore the reason of the increased transmissibility of SARS‐CoV‐2 compared with SARS‐CoV, we have performed a comparative analysis on the structural proteins (spike, envelope, membrane, and nucleoprotein) of two viruses. Our analysis revealed that extensive substitutions of hydrophobic to polar and charged amino acids in spike glycoproteins of SARS‐CoV2 creates an intrinsically disordered region (IDR) at the beginning of membrane‐fusion subunit and intrinsically disordered residues in fusion peptide. IDR provides a potential site for proteolysis by furin and enriched disordered residues facilitate prompt fusion of the SARS‐CoV2 with host membrane by recruiting molecular recognition features. Here, we have hypothesized that mutation‐driven accumulation of intrinsically disordered residues in spike glycoproteins play dual role in enhancing viral transmissibility than previous SARS‐coronavirus. These analyses may help in epidemic surveillance and preventive measures against COVID‐19. Spike glycoprotein of SARS‐CoV2 experiences higher synonymous and non‐synonymous substitution rates than other three structural (E, M, N) proteins. Extensive hydrophobic to polar and charged amino acid substitutions in S proteins during evolution from SARS‐CoV generate intrinsically disordered residues in the membrane fusion subunit (S2) of S protein. Intrinsically disordered region at the beginning of S2 offers cleavage site of furin protease and by virtue of their flexible nature, they provide sensitive site for efficient proteolysis to activate the fusion peptide. Enrichment of intrinsically disordered residues in fusion peptide prompts rapid fusion of viral envelop with host membrane by recruiting several MoRFs. Intrinsic disorderness in spike glycoproteins in SARS‐CoV2 play dual role in enhancing their transmissibility than previous SARS‐corona virus.
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Affiliation(s)
- Soumita Podder
- Department of Microbiology, Raiganj University, Uttar Dinajpur, West Bengal, India
| | - Avishek Ghosh
- Department of Microbiology, Maulana Azad College, Kolkata, West Bengal, India
| | - Tapash Ghosh
- Department of Microbiology, Raiganj University, Uttar Dinajpur, West Bengal, India.,Department of Bioinformatics, Bose Institute, Kolkata, West Bengal, India
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25
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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26
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Lv W, Jiang H, Bo J, Wang C, Yang L, He S. Comparative mitochondrial genome analysis of Neodontobutis hainanensis and Perccottus glenii reveals conserved genome organization and phylogeny. Genomics 2020; 112:3862-3870. [DOI: 10.1016/j.ygeno.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022]
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27
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Abstract
We present selected topics of population genetics and molecular phylogeny. As several excellent review articles have been published and generally focus on European and American scientists, here, we emphasize contributions by Japanese researchers. Our review may also be seen as a belated 50-year celebration of Motoo Kimura's early seminal paper on the molecular clock, published in 1968.
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28
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Xia B, Yan Y, Baron M, Wagner F, Barkley D, Chiodin M, Kim SY, Keefe DL, Alukal JP, Boeke JD, Yanai I. Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates. Cell 2020; 180:248-262.e21. [PMID: 31978344 DOI: 10.1016/j.cell.2019.12.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023]
Abstract
The testis expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Our single-cell transcriptomic data of human and mouse spermatogenesis provide evidence that this widespread transcription maintains DNA sequence integrity in the male germline by correcting DNA damage through a mechanism we term transcriptional scanning. We find that genes expressed during spermatogenesis display lower mutation rates on the transcribed strand and have low diversity in the population. Moreover, this effect is fine-tuned by the level of gene expression during spermatogenesis. The unexpressed genes, which in our model do not benefit from transcriptional scanning, diverge faster over evolutionary timescales and are enriched for sensory and immune-defense functions. Collectively, we propose that transcriptional scanning shapes germline mutation signatures and modulates mutation rates in a gene-specific manner, maintaining DNA sequence integrity for the bulk of genes but allowing for faster evolution in a specific subset.
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Affiliation(s)
- Bo Xia
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Yun Yan
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Maayan Baron
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Florian Wagner
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Dalia Barkley
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Marta Chiodin
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Sang Y Kim
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, NYU Langone Health, New York, NY 10016, USA
| | - Joseph P Alukal
- Department of Obstetrics and Gynecology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
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29
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Exploration of space to achieve scientific breakthroughs. Biotechnol Adv 2020; 43:107572. [PMID: 32540473 DOI: 10.1016/j.biotechadv.2020.107572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/05/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.
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30
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Begum Y, Mondal SK. Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species. J Biomol Struct Dyn 2020; 39:2387-2414. [PMID: 32292132 DOI: 10.1080/07391102.2020.1748717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chlorophyll (Chl) biosynthesis is one of the most important cellular processes essential for plant photosynthesis. Chl degradation pathway is also important catabolic process occurs during leaf senescence, fruit ripening and under biotic or abiotic stress conditions. Here we have systematically investigated the molecular evolution, gene structure, compositional analysis along with ENc plot, correspondence analysis and codon usage bias of the proteins and encoded genes involved in Chl metabolism from monocots and dicots. The gene and species specific phylogenetic trees using amino acid sequences showed clear clustering formation of the selected species based on monocots and dicots but not supported by 18S rRNA. Nucleotide composition of the encoding genes showed that average GC%, GC1%, GC2% and GC3% were higher in monocots. RSCU analysis depicts that genes from monocots for both pathways and genes for synthesis pathway from dicots only biased to G/C-ending synonymous codons but in degradation pathway most optimal codons (except UUG) in dicots biased to A/U-ending synonymous codons. We found strong evidence of episodic diversifying selection at several amino acid sites in all genes investigated. Conserved domain and gene structures were observed for the genes with varying lengths of introns and exons, involved in Chl metabolism along with some intronless genes within synthesis pathway. ENc and correspondence analyses suggested the mutational or selection constraint on the genes to shape the codon usage. These comprehensive studies may be helpful in further research in molecular phylogenetics and genomics and to better understand the evolutionary dynamics of Chl metabolic pathway.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, West Bengal, India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
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31
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Chen B, Shi Z, Chen Q, Shen X, Shibata D, Wen H, Wu CI. Tumorigenesis as the Paradigm of Quasi-neutral Molecular Evolution. Mol Biol Evol 2020; 36:1430-1441. [PMID: 30912799 DOI: 10.1093/molbev/msz075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the absence of both positive and negative selections, coding sequences evolve at a neutral rate (R = 1). Such a high genomic rate is generally not achievable due to the prevalence of negative selection against codon substitutions. Remarkably, somatic evolution exhibits the seemingly neutral rate R ∼ 1 across normal and cancerous tissues. Nevertheless, R ∼ 1 may also mean that positive and negative selections are both strong, but equal in intensity. We refer to this regime as quasi-neutral. Indeed, individual genes in cancer cells often evolve at a much higher, or lower, rate than R ∼ 1. Here, we show that 1) quasi-neutrality is much more likely when populations are small (N < 50); 2) stem-cell populations in single normal tissue niches, from which tumors likely emerge, have a small N (usually <50) but selection at this stage is measurable and strong; 3) when N dips below 50, selection efficacy decreases precipitously; and 4) notably, N is smaller in the stem-cell niche of the small intestine than in the colon. Hence, the ∼70-fold higher rate of phenotypic evolution (observed as cancer risk) in the latter can be explained by the greater efficacy of selection, which then leads to the fixation of more advantageous and fewer deleterious mutations in colon cancers. In conclusion, quasi-neutral evolution sheds a new light on a general evolutionary principle that helps to explain aspects of cancer evolution.
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Affiliation(s)
- Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zongkun Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingjian Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xu Shen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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32
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Beatty J. The Creativity of Natural Selection? Part II: The Synthesis and Since. JOURNAL OF THE HISTORY OF BIOLOGY 2019; 52:705-731. [PMID: 31571023 DOI: 10.1007/s10739-019-09583-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This is the second of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. In the first part, I focussed on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled "mutationists." The second part focuses on the evolutionary synthesis and some of its critics, especially the "neutralists" and "neo-mutationists." Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as "Darwinism." I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection directing evolutionary change, for example by creating the variation that it subsequently acts upon. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.
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Affiliation(s)
- John Beatty
- Department of Philosophy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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33
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Zhang J, Li S, Deng F, Baikeli B, Yu W, Liu G. Distribution of aquaporins and sodium transporters in the gastrointestinal tract of a desert hare, Lepus yarkandensis. Sci Rep 2019; 9:16639. [PMID: 31719660 PMCID: PMC6851143 DOI: 10.1038/s41598-019-53291-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/30/2019] [Indexed: 01/16/2023] Open
Abstract
Lepus yarkandensis is a desert hare of the Tarim Basin in western China, and it has strong adaptability to arid environments. Aquaporins (AQPs) are a family of water channel proteins that facilitate transmembrane water transport. Gastrointestinal tract AQPs are involved in fluid absorption in the small intestine and colon. This study aimed to determine the distribution of AQPs and sodium transporters in the gastrointestinal tract of L. yarkandensis and to compare the expression of these proteins with that in Oryctolagus cuniculus. Immunohistochemistry was performed to analyse the cellular distribution of these proteins, and the acquired images were analysed with IpWin32 software. Our results revealed that AQP1 was located in the colonic epithelium, central lacteal cells, fundic gland parietal cells, and capillary endothelial cells; AQP3 was located in the colonic epithelium, small intestinal villus epithelium, gastric pit and fundic gland; AQP4 was located in the fundic gland, small intestinal gland and colonic epithelium; and epithelial sodium channel (ENaC) and Na+-K+-ATPase were located in the epithelial cells, respectively. The higher expression levels of AQP1, AQP3, ENaC and Na+-K+-ATPase in the colon of L. yarkandensis compared to those in O. cuniculus suggested that L. yarkandensis has a higher capacity for faecal dehydration.
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Affiliation(s)
- Jianping Zhang
- College of Life Science, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China.
- Key Laboratory of Biological Resources Protection and Utilization in Tarim Basin, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China.
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Translational Cancer Research Bengbu Medical College Bengbu, Anhui Province, 233030, People's Republic of China.
| | - Shuwei Li
- College of Life Science, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China
- Key Laboratory of Biological Resources Protection and Utilization in Tarim Basin, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China
| | - Fang Deng
- College of Life Science, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China
| | - Buheliqihan Baikeli
- College of Life Science, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China
| | - Weijiang Yu
- College of Life Science, Tarim University Alar, Xinjiang Province, 843300, People's Republic of China
| | - Guoquan Liu
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, and Anhui Province Key Laboratory of Translational Cancer Research Bengbu Medical College Bengbu, Anhui Province, 233030, People's Republic of China.
- Department of Basic Veterinary Medicine, and Key Lab of Swine Genetics and Breeding and Agricultural Animal Breeding and Reproduction, College of Animal Science and Veterinary Medicine Huazhong Agricultural University Wuhan, Hubei Province, 430070, People's Republic of China.
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34
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Zhang J, Li S, Deng F, Baikeli B, Huang S, Wang B, Liu G. Higher Expression Levels of Aquaporin Family of Proteins in the Kidneys of Arid-Desert Living Lepus yarkandensis. Front Physiol 2019; 10:1172. [PMID: 31572217 PMCID: PMC6751383 DOI: 10.3389/fphys.2019.01172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Lepus yarkandensis specifically lives in arid climate with rare precipitation of Tarim Basin in western China. Aquaporins (AQPs) are a family of channel proteins that facilitate water transportation across cell membranes. Kidney AQPs play vital roles in renal tubule water permeability and maintenance of body water homeostasis. This study aimed to investigate whether kidney AQPs exhibit higher expression in arid-desert living animals. Immunohistochemistry results revealed localization of AQP1 to the capillary endothelial cells in glomerulus and epithelial cells in proximal tubule and descending thin limbs, AQP2 to the apical plasma membrane of principal cells in the cortical collecting duct (CCD), outer medullary collecting duct (OMCD), and IMCD cells in the initial inner medullary collecting duct (IMCD1) and middle IMCD (IMCD2), and AQP3 and AQP4 to the basolateral plasma membrane of principal cells and IMCD cells in CCD, OMCD, IMCD1, and IMCD2 in L. yarkandensis kidneys. Quantitative real-time PCR analysis showed higher mRNA levels of AQP1, AQP2, AQP3, and AQP4 in L. yarkandensis kidneys compared with Oryctolagus cuniculus. Similar results were obtained by western blotting. Our results suggested that higher expression levels of AQP1, AQP2, AQP3, and AQP4 in L. yarkandensis kidneys favored for drawing more water from the tubular fluid.
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Affiliation(s)
- Jianping Zhang
- College of Life Science, Tarim University, Alar, China.,Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, China
| | - Shuwei Li
- College of Life Science, Tarim University, Alar, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar, China
| | - Fang Deng
- College of Life Science, Tarim University, Alar, China
| | | | - Shuguang Huang
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Binyu Wang
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Guoquan Liu
- Department of Basic Veterinary Medicine, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Anhui Province Key Laboratory of Translational Cancer Research, Department of Biochemistry, College of Laboratory Medicine, Bengbu Medical College, Bengbu, China
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35
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Striedter GF. Variation across Species and Levels: Implications for Model Species Research. BRAIN, BEHAVIOR AND EVOLUTION 2019; 93:57-69. [PMID: 31416083 DOI: 10.1159/000499664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/08/2019] [Indexed: 11/19/2022]
Abstract
The selection of model species tends to involve two typically unstated assumptions, namely: (1) that the similarity between species decreases steadily with phylogenetic distance, and (2) that similarities are greater at lower levels of biological organization. The first assumption holds on average, but species similarities tend to decrease with the square root of divergence time, rather than linearly, and lineages with short generation times (which includes most model species) tend to diverge faster than average, making the decrease in similarity non-monotonic. The second assumption is more difficult to test. Comparative molecular research has traditionally emphasized species similarities over differences, whereas comparative research at higher levels of organization frequently highlights the species differences. However, advances in comparative genomics have brought to light a great variety of species differences, not just in gene regulation but also in protein coding genes. Particularly relevant are cases in which homologous high-level characters are based on non-homologous genes. This phenomenon of non-orthologous gene displacement, or "deep non-homology," indicates that species differences at the molecular level can be surprisingly large. Given these observations, it is not surprising that some findings obtained in model species do not generalize across species as well as researchers had hoped, even if the research is molecular.
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Affiliation(s)
- Georg F Striedter
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA,
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36
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Čertnerová D, Čertner M, Škaloud P. Molecular phylogeny and evolution of phenotype in silica-scaled chrysophyte genus Mallomonas. JOURNAL OF PHYCOLOGY 2019; 55:912-923. [PMID: 31055831 DOI: 10.1111/jpy.12882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
The evolution of phenotypes is highly understudied in protists, due to the dearth of morphological characters, missing fossil record, and/or unresolved phylogeny in the majority of taxa. The chrysophyte genus Mallomonas (Stramenopiles) forms species-specific silica scales with extraordinary diversity of their ornamentation. In this paper, we molecularly characterized three additional species to provide an updated phylogeny of 43 species, and combined this with evaluations of 24 morphological traits. Using phylogenetic comparative methods, we evaluated phylogenetic signal in traits, reconstructed the trait evolution, and compared the overall phylogenetic and morphological diversity. The majority of traits showed strong phylogenetic signal and mostly dynamic evolution. Phylogenetic relatedness was often reflected by the phenotypic similarity. Both V-rib and dome are very conservative structures that are presumably involved in precise scale overlap and bristle attachment, respectively. Based on modern species, it seems the dome firstly appeared on apical and/or caudal scales, and only later emerged on body scales. Bristle was presumably present in the common ancestor and gradually elongated ever since. However, most other morphological traits readily changed during the evolution of Mallomonas.
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Affiliation(s)
- Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Prague, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-25243, Průhonice, Czech Republic
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Prague, Czech Republic
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37
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Bolívar P, Mugal CF, Rossi M, Nater A, Wang M, Dutoit L, Ellegren H. Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It. Mol Biol Evol 2019; 35:2475-2486. [PMID: 30085180 PMCID: PMC6188562 DOI: 10.1093/molbev/msy149] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories (“strong”-to-“weak,” “weak-to-strong,” and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22–33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein–protein interactions, but not Hill–Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.
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Affiliation(s)
- Paulina Bolívar
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Matteo Rossi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Alexander Nater
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mi Wang
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ludovic Dutoit
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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38
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Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nat Microbiol 2019; 4:1221-1230. [PMID: 30936490 DOI: 10.1038/s41564-019-0412-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments-from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost-across all the environments and conditions that we tested, the wild type was the fittest allele.
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Affiliation(s)
- Lianet Noda-García
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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39
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Luquet E, Rödin Mörch P, Cortázar‐Chinarro M, Meyer‐Lucht Y, Höglund J, Laurila A. Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient. J Evol Biol 2019; 32:356-368. [DOI: 10.1111/jeb.13419] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Emilien Luquet
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA Villeurbanne France
| | - Patrik Rödin Mörch
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Maria Cortázar‐Chinarro
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
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40
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Ellis GFR, Kopel J. The Dynamical Emergence of Biology From Physics: Branching Causation via Biomolecules. Front Physiol 2019; 9:1966. [PMID: 30740063 PMCID: PMC6355675 DOI: 10.3389/fphys.2018.01966] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/31/2018] [Indexed: 01/30/2023] Open
Abstract
Biology differs fundamentally from the physics that underlies it. This paper proposes that the essential difference is that while physics at its fundamental level is Hamiltonian, in biology, once life has come into existence, causation of a contextual branching nature occurs at every level of the hierarchy of emergence at each time. The key feature allowing this to happen is the way biomolecules such as voltage-gated ion channels can act to enable branching logic to arise from the underlying physics, despite that physics per se being of a deterministic nature. Much randomness occurs at the molecular level, which enables higher level functions to select lower level outcomes according to higher level needs. Intelligent causation occurs when organisms engage in deduction, enabling prediction and planning. This is possible because ion channels enable action potentials to propagate in axons. The further key feature is that such branching biological behavior acts down to cause the underlying physical interactions to also exhibit a contextual branching behavior.
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Affiliation(s)
- George F. R. Ellis
- Mathematics Department, University of Cape Town, Cape Town, South Africa
| | - Jonathan Kopel
- Texas Tech University Health Sciences Center (TTUHSC), Lubbock, TX, United States
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41
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Vasylenko L, Feldman MW, Papadimitriou C, Livnat A. Sex: The power of randomization. Theor Popul Biol 2019; 129:41-53. [PMID: 30638926 DOI: 10.1016/j.tpb.2018.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 10/11/2018] [Accepted: 11/01/2018] [Indexed: 10/27/2022]
Abstract
In evolutionary biology, randomness has been perceived as a force that, in and of itself, is capable of inventing: mutation creates new genetic information at random across the genome which leads to phenotypic change, which is then subject to selection. However, in science in general and in computer science in particular, the widespread use of randomness takes a different form. Here, randomization allows for the breaking of pattern, as seen for example in its removal of biases (patterns) by random sampling or random assignment to conditions. Combined with various forms of evaluation, this breaking of pattern becomes an extraordinarily powerful tool, as also seen in many randomized algorithms in computer science. Here we show that this power of randomness is harnessed in nature by sex and recombination. In a finite population, and under the assumption of interactions between genetic variants, sex and recombination allow selection to test how well an allele will perform in a sample of combinations of interacting genetic partners drawn at random from all possible such combinations; consequently, even a small number of tests of genotypes such as takes place in a finite population favors alleles that will most likely perform well in a vast number of yet unrealized genetic combinations. This power of randomization is not manifest in asexual populations.
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Affiliation(s)
- Liudmyla Vasylenko
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, 3498838, Israel
| | | | | | - Adi Livnat
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, 3498838, Israel.
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42
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Massey SE. Genetic Code Error Minimization as a Non-Adaptive But Beneficial Trait. J Mol Evol 2019; 87:4-6. [PMID: 30604016 DOI: 10.1007/s00239-018-9880-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
In a recent Letter, Di Giulio questions the use of the term 'neutral' when describing the process by which error minimization may have arisen as a side-product of genetic code expansion, resulting from the addition of similar amino acids to similar codons (Di Giulio, in J Mol Evol 86(9):593-597, 2018). However, I point out that in this scenario error minimization is non-adaptive, and so 'neutral' is an appropriate term to describe its imperviousness to direct selection. Error minimization is a form of mutational robustness, and so commonly viewed as beneficial. This in turn implies that not all beneficial traits may be adaptations generated by direct selection for that trait.
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Affiliation(s)
- Steven E Massey
- Biology Department, University of Puerto Rico - Rio Piedras, San Juan, PR, 00931, USA.
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43
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McAvoy A, Adlam B, Allen B, Nowak MA. Stationary frequencies and mixing times for neutral drift processes with spatial structure. Proc Math Phys Eng Sci 2018; 474:20180238. [PMCID: PMC6237506 DOI: 10.1098/rspa.2018.0238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/25/2018] [Indexed: 09/03/2023] Open
Abstract
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types (traits), which can be discrete or continuous. Under minimal assumptions, we show that the marginal trait distributions of the evolutionary process, which specify the probability that any given individual has a certain trait, all converge to the stationary distribution of the mutation process. In particular, the stationary frequencies of traits in the population are independent of its size, spatial structure and evolutionary update rule, and these frequencies can be calculated by evaluating a simple stochastic process describing a population of size one (i.e. the mutation process itself). We conclude by analysing mixing times, which characterize rates of convergence of the mutation process along the lineages, in terms of demographic variables of the evolutionary process.
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Affiliation(s)
- Alex McAvoy
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | - Ben Adlam
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Allen
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Department of Mathematics, Emmanuel College, Boston, MA 02115, USA
| | - Martin A. Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
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44
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Allendorf FW. Zen and deep evolution: The optical delusion of separation. Evol Appl 2018; 11:1212-1218. [PMID: 30151034 PMCID: PMC6099813 DOI: 10.1111/eva.12620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/15/2018] [Indexed: 12/01/2022] Open
Abstract
The Buddha taught that everything is connected and constantly changing. These fundamental observations of the world are shared by ecology and evolution. We are living in a time of unprecedented rates of extinction. Science provides us with the information that we need to address this extinction crisis. However, the problems underlying extinction generally do not result from a lack of scientific understanding, but they rather result from an unwillingness to take the needed action. I present mindfulness and meditative aspects of Zen practice that provide the deeper “knowing,” or awareness that we need to inspire action on these problems.
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Affiliation(s)
- Fred W. Allendorf
- Division of Biological Sciences; University of Montana; Missoula MT USA
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45
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Sverdlov ED. Unsolvable Problems of Biology: It Is Impossible to Create Two Identical Organisms, to Defeat Cancer, or to Map Organisms onto Their Genomes. BIOCHEMISTRY (MOSCOW) 2018; 83:370-380. [PMID: 29626924 DOI: 10.1134/s0006297918040089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The review is devoted to unsolvable problems of biology. 1) Problems unsolvable due to stochastic mutations occurring during DNA replication that make it impossible to create two identical organisms or even two identical complex cells (Sverdlov, E. D. (2009) Biochemistry (Moscow), 74, 939-944) and to "defeat" cancer. 2) Problems unsolvable due to multiple interactions in complex systems leading to the appearance of unpredictable emergent properties that prevent establishment of unambiguous relationships between the genetic architecture and phenotypic manifestation of the genome and make impossible to predict with certainty responses of the organism, its parts, or pathological processes to external factors. 3) Problems unsolvable because of the uncertainty principle and observer effect in biology, due to which it is impossible to obtain adequate information about cells in their tissue microenvironment by isolating and analyzing individual cells. In particular, we cannot draw conclusions on the properties of stem cells in their niches based on the properties of stem cell cultures. A strategy is proposed for constructing the pattern most closely approximated to the relationship of genotypes with their phenotypes by designing networks of intermediate phenotypes (endophenotypes).
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Affiliation(s)
- E D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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46
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Danino M, Shnerb NM. Fixation and absorption in a fluctuating environment. J Theor Biol 2018; 441:84-92. [DOI: 10.1016/j.jtbi.2018.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
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47
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Mans BJ, Featherston J, de Castro MH, Pienaar R. Gene Duplication and Protein Evolution in Tick-Host Interactions. Front Cell Infect Microbiol 2017; 7:413. [PMID: 28993800 PMCID: PMC5622192 DOI: 10.3389/fcimb.2017.00413] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 09/06/2017] [Indexed: 01/01/2023] Open
Abstract
Ticks modulate their hosts' defense responses by secreting a biopharmacopiea of hundreds to thousands of proteins and bioactive chemicals into the feeding site (tick-host interface). These molecules and their functions evolved over millions of years as ticks adapted to blood-feeding, tick lineages diverged, and host-shifts occurred. The evolution of new proteins with new functions is mainly dependent on gene duplication events. Central questions around this are the rates of gene duplication, when they occurred and how new functions evolve after gene duplication. The current review investigates these questions in the light of tick biology and considers the possibilities of ancient genome duplication, lineage specific expansion events, and the role that positive selection played in the evolution of tick protein function. It contrasts current views in tick biology regarding adaptive evolution with the more general view that neutral evolution may account for the majority of biological innovations observed in ticks.
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Affiliation(s)
- Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary ResearchOnderstepoort, South Africa.,Department of Veterinary Tropical Diseases, University of PretoriaPretoria, South Africa.,Department of Life and Consumer Sciences, University of South AfricaPretoria, South Africa
| | - Jonathan Featherston
- Agricultural Research Council-The Biotechnology PlatformOnderstepoort, South Africa
| | - Minique H de Castro
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary ResearchOnderstepoort, South Africa.,Department of Life and Consumer Sciences, University of South AfricaPretoria, South Africa.,Agricultural Research Council-The Biotechnology PlatformOnderstepoort, South Africa
| | - Ronel Pienaar
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary ResearchOnderstepoort, South Africa
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48
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Martin J, Ponstingl H, Lefranc MP, Archer J, Sargan D, Bradley A. Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci. Immunogenetics 2017; 70:223-236. [PMID: 28924718 PMCID: PMC5871656 DOI: 10.1007/s00251-017-1028-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/12/2017] [Indexed: 12/11/2022]
Abstract
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.
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Affiliation(s)
- Jolyon Martin
- Wellcome Trust Sanger Institute, Hinxton, UK.
- University of Cambridge, Cambridge, UK.
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49
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Houchmandzadeh B, Vallade M. Fisher waves: An individual-based stochastic model. Phys Rev E 2017; 96:012414. [PMID: 29347142 DOI: 10.1103/physreve.96.012414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 11/07/2022]
Abstract
The propagation of a beneficial mutation in a spatially extended population is usually studied using the phenomenological stochastic Fisher-Kolmogorov-Petrovsky-Piscounov (SFKPP) equation. We derive here an individual-based, stochastic model founded on the spatial Moran process where fluctuations are treated exactly. The mean-field approximation of this model leads to an equation that is different from the phenomenological FKPP equation. At small selection pressure, the front behavior can be mapped into a Brownian motion with drift, the properties of which can be derived from the microscopic parameters of the Moran model. Finally, we generalize the model to take into account dispersal kernels beyond migration to nearest neighbors. We show how the effective population size (which controls the noise amplitude) and the diffusion coefficient can both be computed from the dispersal kernel.
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Affiliation(s)
- B Houchmandzadeh
- CNRS, LIPHY, F-38000 Grenoble, France and Université Grenoble Alpes, LIPHY, F-38000 Grenoble, France
| | - M Vallade
- CNRS, LIPHY, F-38000 Grenoble, France and Université Grenoble Alpes, LIPHY, F-38000 Grenoble, France
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Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol 2017; 1:1160-1167. [PMID: 29046583 DOI: 10.1038/s41559-017-0237-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 06/14/2017] [Indexed: 02/02/2023]
Abstract
Endosymbiosis plays an important role in ecology and evolution, but fundamental aspects of the origin of intracellular symbionts remain unclear. The extreme age of many symbiotic relationships, lack of data on free-living ancestors and uniqueness of each event hinder investigations. Here, we describe multiple strains of the bacterium Polynucleobacter that evolved independently and under similar conditions from closely related, free-living ancestors to become obligate endosymbionts of closely related ciliate hosts. As these genomes reduced in parallel from similar starting states, they provide unique glimpses into the mechanisms underlying genome reduction in symbionts. We found that gene loss is contingently lineage-specific, with no evidence for ordered streamlining. However, some genes in otherwise disrupted pathways are retained, possibly reflecting cryptic genetic network complexity. We also measured substitution rates between many endosymbiotic and free-living pairs for hundreds of genes, which showed that genetic drift, and not mutation pressure, is the main non-selective factor driving molecular evolution in endosymbionts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Biology, University of Pisa, Pisa, 56126, Italy
| | - Martin Kolisko
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Prague, 370 05, Czech Republic
| | - Michele Felletti
- Department of Chemistry, University of Konstanz, Konstanz, 78464, Germany
| | - Claudia Vannini
- Department of Biology, University of Pisa, Pisa, 56126, Italy
| | - Denis H Lynn
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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