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Melepat B, Li T, Vinkler M. Natural selection directing molecular evolution in vertebrate viral sensors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105147. [PMID: 38325501 DOI: 10.1016/j.dci.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/30/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.
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Affiliation(s)
- Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Tao Li
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic.
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2
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Bralet T, Risco-Castillo V, Valsecchi I, Laidebeure S, Sailler A, Lécu A, Botterel F, Guillot J, Arné P, Jouvion G. Aspergillosis in a colony of Humboldt penguins (Spheniscus humboldti) in a french zoological park: evaluation of environmental exposure. Vet Res Commun 2024; 48:437-448. [PMID: 37819485 DOI: 10.1007/s11259-023-10220-z] [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: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Aspergillosis is a major health problem in captive penguins due to the inhalation and the development of airborne spores of opportunistic environmental molds of the genus Aspergillus. Diagnosis is often delayed and treatments, based on the use of azole antifungals, are not fully effective. This study assesses the risk of exposure to Aspergillus sp. and determines the environmental reservoirs in the direct environment of a colony of Humboldt penguins (Spheniscus humboldti) in a zoological park in Paris, and the risk of contamination with resistant isolates. Every 15 days between February and May 2022, environmental samples (air and subtract from the nests, pond water, pigeon and penguin droppings) were carried out in the penguin enclosure as well as clinical samples (one-time non-invasive sampling on chicks), and screened for Aspergillus sp. conidia. From 191 environmental samples, 264 strains of Aspergillus including 221 strains of A. fumigatus were isolated, mostly from ambient air, in the nests, and pond water. No "at risk" areas in the penguin environment have been highlighted, nor an increased risk because of the proximity with urban wild birds. However, the load of airborne Aspergillus in the nests increased significantly with outdoor temperature. Of the 221 strains isolated, we identified only one azole-resistant strain, displaying the TR34/L98H mutation in the cyp51A gene. This low prevalence of resistant strains may probably be partly explained by the urban location of the zoological park, surrounded by kilometers of urban areas without agricultural activities.
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Affiliation(s)
- Tristan Bralet
- Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC ANSES, Dynamyc research team, Créteil, F-94000, France
- French Food Safety Agency, Bacterial Zoonosis unit, Maisons-Alfort, F-94700, France
| | - Veronica Risco-Castillo
- Anses, INRAE, Laboratoire de Santé Animale, Ecole nationale vétérinaire d'Alfort, BIPAR, Maisons- Alfort, F-94700, France
- Ecole nationale vétérinaire d'Alfort, Centre Hospitalo-Universitaire de la Faune Sauvage, Maisons-Alfort, F-94700, France
| | - Isabel Valsecchi
- Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC ANSES, Dynamyc research team, Créteil, F-94000, France
| | - Sylvie Laidebeure
- Parc Zoologique de Paris, Museum national d'Histoire naturelle, Paris, F-75012, France
| | - Anaïs Sailler
- Parc Zoologique de Paris, Museum national d'Histoire naturelle, Paris, F-75012, France
| | - Alexis Lécu
- Parc Zoologique de Paris, Museum national d'Histoire naturelle, Paris, F-75012, France
| | - Françoise Botterel
- Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC ANSES, Dynamyc research team, Créteil, F-94000, France
| | - Jacques Guillot
- Dermatology, Parasitology and Mycology department, ONIRIS, Nantes, F-44300, France
- Université d'Angers, Université de Brest, IRF, SFR ICAT, Angers, F-49000, France
| | - Pascal Arné
- Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC ANSES, Dynamyc research team, Créteil, F-94000, France
- Ecole nationale vétérinaire d'Alfort, Centre Hospitalo-Universitaire de la Faune Sauvage, Maisons-Alfort, F-94700, France
| | - Grégory Jouvion
- Université Paris-Est Créteil, Ecole nationale vétérinaire d'Alfort, USC ANSES, Dynamyc research team, Créteil, F-94000, France.
- Histology and pathology unit, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, F-94700, France.
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3
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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4
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Vlček J, Miláček M, Vinkler M, Štefka J. Effect of population size and selection on Toll-like receptor diversity in populations of Galápagos mockingbirds. J Evol Biol 2023; 36:109-120. [PMID: 36398499 DOI: 10.1111/jeb.14121] [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: 12/09/2021] [Revised: 08/25/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022]
Abstract
The interactions of evolutionary forces are difficult to analyse in free-living populations. However, when properly understood, they provide valuable insights into evolutionary biology and conservation genetics. This is particularly important for the interplay of genetic drift and natural selection in immune genes that confer resistance to disease. The Galápagos Islands are inhabited by four closely related species of mockingbirds (Mimus spp.). We used 12 different-sized populations of Galápagos mockingbirds and one population of their continental relative northern mockingbird (Mimus polyglottos) to study the effects of genetic drift on the molecular evolution of immune genes, the Toll-like receptors (TLRs: TLR1B, TLR4 and TLR15). We found that neutral genetic diversity was positively correlated with island size, indicating an important effect of genetic drift. However, for TLR1B and TLR4, there was little correlation between functional (e.g., protein) diversity and island size, and protein structural properties were largely conserved, indicating only a limited effect of genetic drift on molecular phenotype. By contrast, TLR15 was less conserved and even its putative functional polymorphism correlated with island size. The patterns observed for the three genes suggest that genetic drift does not necessarily dominate selection even in relatively small populations, but that the final outcome depends on the degree of selection constraint that is specific for each TLR locus.
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Affiliation(s)
- Jakub Vlček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic.,Department of Botany, Charles University Faculty of Science, Prague, Czech Republic
| | - Matěj Miláček
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Charles University Faculty of Science, Prague, Czech Republic
| | - Jan Štefka
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.,Department of Zoology, University of South Bohemia in České Budějovice Faculty of Science, České Budějovice, Czech Republic
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5
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Neves F, Muñoz-Mérida A, Machado AM, Almeida T, Gaigher A, Esteves PJ, Castro LFC, Veríssimo A. Uncovering a 500 million year old history and evidence of pseudogenization for TLR15. Front Immunol 2022; 13:1020601. [PMID: 36605191 PMCID: PMC9808068 DOI: 10.3389/fimmu.2022.1020601] [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: 08/16/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Toll like receptors (TLRs) are at the front line of pathogen recognition and host immune response. Many TLR genes have been described to date with some being found across metazoans while others are restricted to specific lineages. A cryptic member of the TLR gene family, TLR15, has a unique phylogenetic distribution. Initially described in extant species of birds and reptiles, an ortholog has been reported for cartilaginous fish. Methods Here, we significantly expanded the evolutionary analysis of TLR15 gene evolution, taking advantage of large genomic and transcriptomic resources available from different lineages of vertebrates. Additionally, we objectively search for TLR15 in lobe-finned and ray-finned fish, as well as in cartilaginous fish and jawless vertebrates. Results and discussion We confirm the presence of TLR15 in early branching jawed vertebrates - the cartilaginous fish, as well as in basal Sarcopterygii - in lungfish. However, within cartilaginous fish, the gene is present in Holocephalans (all three families) but not in Elasmobranchs (its sister-lineage). Holocephalans have long TLR15 protein sequences that disrupt the typical TLR structure, and some species display a pseudogene sequence due to the presence of frameshift mutations and early stop codons. Additionally, TLR15 has low expression levels in holocephalans when compared with other TLR genes. In turn, lungfish also have long TLR15 protein sequences but the protein structure is not compromised. Finally, TLR15 presents several sites under negative selection. Overall, these results suggest that TLR15 is an ancient TLR gene and is experiencing ongoing pseudogenization in early-branching vertebrates.
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Affiliation(s)
- Fabiana Neves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,*Correspondence: Fabiana Neves,
| | - Antonio Muñoz-Mérida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - André M. Machado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Tereza Almeida
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany,Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Pedro J. Esteves
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CITS - Center of Investigation in Health Technologies, CESPU, Gandra, Portugal
| | - L. Filipe C. Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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6
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Krchlíková V, Hron T, Těšický M, Li T, Ungrová L, Hejnar J, Vinkler M, Elleder D. Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET. Viruses 2022; 15:3. [PMID: 36680044 PMCID: PMC9861763 DOI: 10.3390/v15010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are key RNA virus sensors belonging to the RIG-I-like receptor (RLR) family. The activation of the RLR inflammasome leads to the establishment of antiviral state, mainly through interferon-mediated signaling. The evolutionary dynamics of RLRs has been studied mainly in mammals, where rare cases of RLR gene losses were described. By in silico screening of avian genomes, we previously described two independent disruptions of MDA5 in two bird orders. Here, we extend this analysis to approximately 150 avian genomes and report 16 independent evolutionary events of RIG-I inactivation. Interestingly, in almost all cases, these inactivations are coupled with genetic disruptions of RIPLET/RNF135, an ubiquitin ligase RIG-I regulator. Complete absence of any detectable RIG-I sequences is unique to several galliform species, including the domestic chicken (Gallus gallus). We further aimed to determine compensatory evolution of MDA5 in RIG-I-deficient species. While we were unable to show any specific global pattern of adaptive evolution in RIG-I-deficient species, in galliforms, the analyses of positive selection and surface charge distribution support the hypothesis of some compensatory evolution in MDA5 after RIG-I loss. This work highlights the dynamic nature of evolution in bird RNA virus sensors.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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7
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Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
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Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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8
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Genomic insights into the secondary aquatic transition of penguins. Nat Commun 2022; 13:3912. [PMID: 35853876 PMCID: PMC9296559 DOI: 10.1038/s41467-022-31508-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth. This study examines the tempo and drivers of penguin diversification by combining genomes from all extant and recently extinct penguin lineages, stratigraphic data from fossil penguins and morphological and biogeographic data from all extant and extinct species. Together, these datasets provide new insights into the genetic basis and evolution of adaptations in penguins.
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9
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Minias P, Vinkler M. Selection balancing at innate immune genes: adaptive polymorphism maintenance in Toll-like receptors. Mol Biol Evol 2022; 39:6586215. [PMID: 35574644 PMCID: PMC9132207 DOI: 10.1093/molbev/msac102] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Balancing selection is a classic mechanism for maintaining variability in immune genes involved in host–pathogen interactions. However, it remains unclear how widespread the mechanism is across immune genes other than the major histocompatibility complex (MHC). Although occasional reports suggest that balancing selection (heterozygote advantage, negative frequency-dependent selection, and fluctuating selection) may act on other immune genes, the current understanding of the phenomenon in non-MHC immune genes is far from solid. In this review, we focus on Toll-like receptors (TLRs), innate immune genes directly involved in pathogen recognition and immune response activation, as there is a growing body of research testing the assumptions of balancing selection in these genes. After reviewing infection- and fitness-based evidence, along with evidence based on population allelic frequencies and heterozygosity levels, we conclude that balancing selection maintains variation in TLRs, though it tends to occur under specific conditions in certain evolutionary lineages rather than being universal and ubiquitous. Our review also identifies key gaps in current knowledge and proposes promising areas for future research. Improving our understanding of host–pathogen interactions and balancing selection in innate immune genes are increasingly important, particularly regarding threats from emerging zoonotic diseases.
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