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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Liu L, He M, Yang Z, Wang H, Zhang X, He J, Buttino I, Qi P, Yan X, Liao Z. Myticofensin, a novel antimicrobial peptide family identified from Mytilus coruscus. FISH & SHELLFISH IMMUNOLOGY 2022; 131:817-826. [PMID: 36349653 DOI: 10.1016/j.fsi.2022.10.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In this study, seven transcripts representing a novel antimicrobial peptide (AMP) family with structural features similar to those of arthropod defensins were identified from Mytilus coruscus. These novel defensins from the Mytilus AMP family were named myticofensins. To explore the possible immune-related functions of these myticofensins, we examined their expression profiles in different tissues and larval stages, as well as in three immune-related tissues under the threat of different microbes. Our data revealed that the seven myticofensins had relatively high expression levels in immune-related tissues. Most myticofensins were undetectable, or had low expression levels, in different larval mussel stages. Additionally, in vivo microbial challenges significantly increased the expression levels of myticofensins in M. coruscus hemocytes, gills, and digestive glands, showing different immune response patterns under challenges from different microbes. Our data indicates that different myticofensins may have different immune functions in different tissues. Furthermore, peptide sequences corresponding to the beta-hairpin, alpha-helix, and N-terminal loop of myticofensin were synthesized and the antimicrobial activities of these peptide fragments were tested. Our data confirms the diversity of defensins in Mytilus and reports the complex regulation of these defensins in the mussel immune response to different microbes in immune-related tissues. The immune system of Mytilus has been studied for years as they are a species with strong environmental adaptations. Our data can be regarded as a step forward in the study of the adaptation of Mytilus spp. to an evolving microbial world.
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Affiliation(s)
- Lu Liu
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Menglan He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Zongxin Yang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Haodong Wang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Jianyu He
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China; Donghai Laboratory, Zhoushan City, 316022, Zhejiang, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research ISPRA, Via Vitaliano Brancati 48, 00144, Rome, Italy
| | - Pengzhi Qi
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Xiaojun Yan
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China.
| | - Zhi Liao
- Laboratory of Marine Biology Protein Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China.
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Le Bloa S, Boidin-Wichlacz C, Cueff-Gauchard V, Rosa RD, Cuvillier-Hot V, Durand L, Methou P, Pradillon F, Cambon-Bonavita MA, Tasiemski A. Antimicrobial Peptides and Ectosymbiotic Relationships: Involvement of a Novel Type IIa Crustin in the Life Cycle of a Deep-Sea Vent Shrimp. Front Immunol 2020; 11:1511. [PMID: 32765521 PMCID: PMC7381244 DOI: 10.3389/fimmu.2020.01511] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/09/2020] [Indexed: 01/04/2023] Open
Abstract
The symbiotic shrimp Rimicaris exoculata dominates the macrofauna inhabiting the active smokers of the deep-sea mid Atlantic ridge vent fields. We investigated the nature of the host mechanisms controlling the vital and highly specialized ectosymbiotic community confined into its cephalothoracic cavity. R. exoculata belongs to the Pleocyemata, crustacean brooding eggs, usually producing Type I crustins. Unexpectedly, a novel anti-Gram-positive type II crustin was molecularly identified in R. exoculata. Re-crustin is mainly produced by the appendages and the inner surfaces of the cephalothoracic cavity, embedding target epibionts. Symbiosis acquisition and regulating mechanisms are still poorly understood. Yet, symbiotic communities were identified at different steps of the life cycle such as brooding stage, juvenile recruitment and molt cycle, all of which may be crucial for symbiotic acquisition and control. Here, we show a spatio-temporal correlation between the production of Re-crustin and the main ectosymbiosis-related life-cycle events. Overall, our results highlight (i) a novel and unusual AMP sequence from an extremophile organism and (ii) the potential role of AMPs in the establishment of vital ectosymbiosis along the life cycle of deep-sea invertebrates.
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Affiliation(s)
- Simon Le Bloa
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Valérie Cueff-Gauchard
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Rafael Diego Rosa
- Laboratory of Immunology Applied to Aquaculture, Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Lucile Durand
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Pierre Methou
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Florence Pradillon
- Ifremer, Laboratoire Environnement Profond (REM/EEP/LEP), Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Univ. Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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4
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Lazzaro BP, Zasloff M, Rolff J. Antimicrobial peptides: Application informed by evolution. Science 2020; 368:368/6490/eaau5480. [PMID: 32355003 DOI: 10.1126/science.aau5480] [Citation(s) in RCA: 461] [Impact Index Per Article: 115.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/25/2019] [Accepted: 03/09/2020] [Indexed: 12/13/2022]
Abstract
Antimicrobial peptides (AMPs) are essential components of immune defenses of multicellular organisms and are currently in development as anti-infective drugs. AMPs have been classically assumed to have broad-spectrum activity and simple kinetics, but recent evidence suggests an unexpected degree of specificity and a high capacity for synergies. Deeper evaluation of the molecular evolution and population genetics of AMP genes reveals more evidence for adaptive maintenance of polymorphism in AMP genes than has previously been appreciated, as well as adaptive loss of AMP activity. AMPs exhibit pharmacodynamic properties that reduce the evolution of resistance in target microbes, and AMPs may synergize with one another and with conventional antibiotics. Both of these properties make AMPs attractive for translational applications. However, if AMPs are to be used clinically, it is crucial to understand their natural biology in order to lessen the risk of collateral harm and avoid the crisis of resistance now facing conventional antibiotics.
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Affiliation(s)
- Brian P Lazzaro
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Michael Zasloff
- MedStar Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, USA
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Institut für Biologie, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany. .,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
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5
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Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, Richter-Boix A, Laurila A, Höglund J. Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans. BMC Genet 2020; 21:38. [PMID: 32228443 PMCID: PMC7106915 DOI: 10.1186/s12863-020-00839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. RESULTS We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. CONCLUSION Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
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Affiliation(s)
- Maria Cortázar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
| | - Yvonne Meyer-Lucht
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.,Centre for Paleogenetics Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Tom Van der Valk
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Alex Richter-Boix
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
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6
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Chapman JR, Hill T, Unckless RL. Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides. Genome Biol Evol 2019; 11:2691-2701. [PMID: 31504505 PMCID: PMC6764478 DOI: 10.1093/gbe/evz191] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Genes involved in immune defense against pathogens provide some of the most well-known examples of both directional and balancing selection. Antimicrobial peptides (AMPs) are innate immune effector genes, playing a key role in pathogen clearance in many species, including Drosophila. Conflicting lines of evidence have suggested that AMPs may be under directional, balancing, or purifying selection. Here, we use both a linear model and control-gene-based approach to show that balancing selection is an important force shaping AMP diversity in Drosophila. In Drosophila melanogaster, this is most clearly observed in ancestral African populations. Furthermore, the signature of balancing selection is even more striking once background selection has been accounted for. Balancing selection also acts on AMPs in Drosophila mauritiana, an isolated island endemic separated from D. melanogaster by about 4 Myr of evolution. This suggests that balancing selection may be broadly acting to maintain adaptive diversity in Drosophila AMPs, as has been found in other taxa.
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Affiliation(s)
| | - Tom Hill
- Department of Molecular Biosciences, University of Kansas
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7
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Qiao M, Tu M, Chen H, Mao F, Yu C, Du M. Identification and In Silico Prediction of Anticoagulant Peptides from the Enzymatic Hydrolysates of Mytilus edulis Proteins. Int J Mol Sci 2018; 19:ijms19072100. [PMID: 30029529 PMCID: PMC6073223 DOI: 10.3390/ijms19072100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/13/2023] Open
Abstract
Mytilus edulis is a typical marine bivalve mollusk. Many kinds of bioactive components with nutritional and pharmaceutical activities in Mytilus edulis were reported. In this study, eight different parts of Mytilus edulis tissues, i.e., the foot, byssus, pedal retractor muscle, mantle, gill, adductor muscle, viscera, and other parts, were separated and the proteins from these tissues were prepared. A total of 277 unique peptides from the hydrolysates of different proteins were identified by UPLC-Q-TOF-MS/MS, and the molecular weight distribution of the peptides in different tissues was investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The bioactivity of the peptides was predicted through the Peptide Ranker database and molecular docking. Moreover, the peptides from the adductor muscle were chosen to do the active validation of anticoagulant activity. The active mechanism of three peptides from the adductor muscle, VQQELEDAEERADSAEGSLQK, RMEADIAAMQSDLDDALNGQR, and AAFLLGVNSNDLLK, were analyzed by Discovery Studio 2017, which also explained the anticoagulant activity of the hydrolysates of proteins from adductor muscle. This study optimized a screening and identification method of bioactive peptides from enzymatic hydrolysates of different tissues in Mytilus edulis.
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Affiliation(s)
- Meiling Qiao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Hui Chen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Fengjiao Mao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Cuiping Yu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Ming Du
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
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8
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Rolff J, Schmid-Hempel P. Perspectives on the evolutionary ecology of arthropod antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0297. [PMID: 27160599 DOI: 10.1098/rstb.2015.0297] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2016] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial peptides (AMPs) are important elements of the innate immune defence in multicellular organisms that target and kill microbes. Here, we reflect on the various points that are raised by the authors of the 11 contributions to a special issue of Philosophical Transactions on the 'evolutionary ecology of arthropod antimicrobial peptides'. We see five interesting topics emerging. (i) AMP genes in insects, and perhaps in arthropods more generally, evolve much slower than most other immune genes. One explanation refers to the constraints set by AMPs being part of a finely tuned defence system. A new view argues that AMPs are under strong stabilizing selection. Regardless, this striking observation still invites many more questions than have been answered so far. (ii) AMPs almost always are expressed in combinations and sometimes show expression patterns that are dependent on the infectious agent. While it is often assumed that this can be explained by synergistic interactions, such interactions have rarely been demonstrated and need to be studied further. Moreover, how to define synergy in the first place remains difficult and needs to be addressed. (iii) AMPs play a very important role in mediating the interaction between a host and its mutualistic or commensal microbes. This has only been studied in a very small number of (insect) species. It has become clear that the very same AMPs play different roles in different situations and hence are under concurrent selection. (iv) Different environments shape the physiology of organisms; especially the host-associated microbial communities should impact on the evolution host AMPs. Studies in social insects and some organisms from extreme environments seem to support this notion, but, overall, the evidence for adaptation of AMPs to a given environment is scant. (v) AMPs are considered or already developed as new drugs in medicine. However, bacteria can evolve resistance to AMPs. Therefore, in the light of our limited understanding of AMP evolution in the natural context, and also the very limited understanding of the evolution of resistance against AMPs in bacteria in particular, caution is recommended. What is clear though is that study of the ecology and evolution of AMPs in natural systems could inform many of these outstanding questions, including those related to medical applications and pathogen control.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
- Jens Rolff
- Evolutionary Biology, Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Paul Schmid-Hempel
- ETH Zürich, Institute of Integrative Biology (IBZ), ETH-Zentrum CHN, Universitätsstrasse 16, 8092 Zürich, Switzerland
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9
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Papot C, Massol F, Jollivet D, Tasiemski A. Antagonistic evolution of an antibiotic and its molecular chaperone: how to maintain a vital ectosymbiosis in a highly fluctuating habitat. Sci Rep 2017; 7:1454. [PMID: 28469247 PMCID: PMC5431198 DOI: 10.1038/s41598-017-01626-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/30/2017] [Indexed: 12/25/2022] Open
Abstract
Evolution of antimicrobial peptides (AMPs) has been shown to be driven by recurrent duplications and balancing/positive selection in response to new or altered bacterial pathogens. We use Alvinella pompejana, the most eurythermal animal known on Earth, to decipher the selection patterns acting on AMP in an ecological rather than controlled infection approach. The preproalvinellacin multigenic family presents the uniqueness to encode a molecular chaperone (BRICHOS) together with an AMP (alvinellacin) that controls the vital ectosymbiosis of Alvinella. In stark contrast to what is observed in the context of the Red queen paradigm, we demonstrate that exhibiting a vital and highly conserved ecto-symbiosis in the face of thermal fluctuations has led to a peculiar selective trend promoting the adaptive diversification of the molecular chaperone of the AMP, but not of the AMP itself. Because BRICHOS stabilizes beta-stranded peptides, this polymorphism likely represents an eurythermal adaptation to stabilize the structure of alvinellacin, thus hinting at its efficiency to select and control the epibiosis across the range of temperatures experienced by the worm; Our results fill some knowledge gaps concerning the function of BRICHOS in invertebrates and offer perspectives for studying immune genes in an evolutionary ecological framework.
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Affiliation(s)
- Claire Papot
- University Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, SPICI group, F-59000, Lille, France
| | - François Massol
- University Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, SPICI group, F-59000, Lille, France
| | - Didier Jollivet
- AD2M, ABICE team, Université Pierre et Marie Curie-CNRS, UMR7144, Station Biologique de Roscoff, 29682, Roscoff, France
| | - Aurélie Tasiemski
- University Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, SPICI group, F-59000, Lille, France.
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10
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Macke E, Tasiemski A, Massol F, Callens M, Decaestecker E. Life history and eco-evolutionary dynamics in light of the gut microbiota. OIKOS 2017. [DOI: 10.1111/oik.03900] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emilie Macke
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | | | - François Massol
- Univ. Lille; CNRS UMR 8198 Evo-Eco-Paleo SPICI group Lille France
| | - Martijn Callens
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | - Ellen Decaestecker
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
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11
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Hanson MA, Hamilton PT, Perlman SJ. Immune genes and divergent antimicrobial peptides in flies of the subgenus Drosophila. BMC Evol Biol 2016; 16:228. [PMID: 27776480 PMCID: PMC5078906 DOI: 10.1186/s12862-016-0805-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/14/2016] [Indexed: 11/14/2022] Open
Abstract
Background Drosophila is an important model for studying the evolution of animal immunity, due to the powerful genetic tools developed for D. melanogaster. However, Drosophila is an incredibly speciose lineage with a wide range of ecologies, natural histories, and diverse natural enemies. Surprisingly little functional work has been done on immune systems of species other than D. melanogaster. In this study, we examine the evolution of immune genes in the speciose subgenus Drosophila, which diverged from the subgenus Sophophora (that includes D. melanogaster) approximately 25–40 Mya. We focus on D. neotestacea, a woodland species used to study interactions between insects and parasitic nematodes, and combine recent transcriptomic data with infection experiments to elucidate aspects of host immunity. Results We found that the vast majority of genes involved in the D. melanogaster immune response are conserved in D. neotestacea, with a few interesting exceptions, particularly in antimicrobial peptides (AMPs); until recently, AMPs were not thought to evolve rapidly in Drosophila. Unexpectedly, we found a distinct diptericin in subgenus Drosophila flies that appears to have evolved under diversifying (positive) selection. We also describe the presence of the AMP drosocin, which was previously thought to be restricted to the subgenus Sophophora, in the subgenus Drosophila. We challenged two subgenus Drosophila species, D. neotestacea and D. virilis with bacterial and fungal pathogens and quantified AMP expression. Conclusions While diptericin in D. virilis was induced by exposure to gram-negative bacteria, it was not induced in D. neotestacea, showing that conservation of immune genes does not necessarily imply conservation of the realized immune response. Our study lends support to the idea that invertebrate AMPs evolve rapidly, and that Drosophila harbor a diverse repertoire of AMPs with potentially important functional consequences. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0805-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark A Hanson
- Department of Biology, University of Victoria, Victoria, BC, Canada.
| | | | - Steve J Perlman
- Department of Biology, University of Victoria, Victoria, BC, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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De Wit P, Dupont S, Thor P. Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepod Pseudocalanus acuspes. Evol Appl 2016; 9:1112-1123. [PMID: 27695519 PMCID: PMC5039324 DOI: 10.1111/eva.12335] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/21/2015] [Indexed: 01/06/2023] Open
Abstract
Ocean acidification is expected to have dramatic impacts on oceanic ecosystems, yet surprisingly few studies currently examine long-term adaptive and plastic responses of marine invertebrates to pCO 2 stress. Here, we exposed populations of the common copepod Pseudocalanus acuspes to three pCO 2 regimes (400, 900, and 1550 μatm) for two generations, after which we conducted a reciprocal transplant experiment. A de novo transcriptome was assembled, annotated, and gene expression data revealed that genes involved in RNA transcription were strongly down-regulated in populations with long-term exposure to a high pCO 2 environment, even after transplantation back to control levels. In addition, 747 000 SNPs were identified, out of which 1513 showed consistent changes in nucleotide frequency between replicates of control and high pCO 2 populations. Functions involving RNA transcription and ribosomal function, as well as ion transport and oxidative phosphorylation, were highly overrepresented. We thus conclude that pCO 2 stress appears to impose selection in copepods on RNA synthesis and translation, possibly modulated by helicase expression. Using a physiological hypothesis-testing strategy to mine gene expression data, we herein increase the power to detect cellular targets of ocean acidification. This novel approach seems promising for future studies of effects of environmental changes in ecologically important nonmodel organisms.
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Affiliation(s)
- Pierre De Wit
- Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Sam Dupont
- Department of Biological and Environmental SciencesUniversity of GothenburgFiskebäckskilSweden
| | - Peter Thor
- FramcentreNorwegian Polar InstituteTromsøNorway
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Unckless RL, Lazzaro BP. The potential for adaptive maintenance of diversity in insect antimicrobial peptides. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150291. [PMID: 27160594 PMCID: PMC4874389 DOI: 10.1098/rstb.2015.0291] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 02/07/2023] Open
Abstract
Genes involved in immune defence are among the fastest evolving in the genomes of many species. Interestingly, however, genes encoding antimicrobial peptides (AMPs) have shown little evidence for adaptive divergence in arthropods, despite the centrality of these peptides in direct killing of microbial pathogens. This observation, coupled with a failure to detect phenotypic consequence of genetic variation in AMPs, has led to the hypothesis that individual AMPs make minor contributions to overall immune defence and that AMPs instead act as a collective cocktail. Recent data, however, have suggested an alternative explanation for the apparent lack of adaptive divergence in AMP genes. Molecular evolutionary and phenotypic data have begun to suggest that variant AMP alleles may be maintained through balancing selection in invertebrates, a pattern similar to that observed in several vertebrate AMPs. Signatures of balancing selection include high rates of non-synonymous polymorphism, trans-species amino acid polymorphisms, and convergence of amino acid states across the phylogeny. In this review, we revisit published literature on insect AMP genes and analyse newly available population genomic datasets in Drosophila, finding enrichment for patterns consistent with adaptive maintenance of polymorphism.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'.
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Affiliation(s)
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
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Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene. Genetics 2016; 203:525-41. [PMID: 27017626 PMCID: PMC4858797 DOI: 10.1534/genetics.115.183285] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
Abstract
A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects.
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Unckless RL, Howick VM, Lazzaro BP. Convergent Balancing Selection on an Antimicrobial Peptide in Drosophila. Curr Biol 2016; 26:257-262. [PMID: 26776733 DOI: 10.1016/j.cub.2015.11.063] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/12/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
Abstract
Genes of the immune system often evolve rapidly and adaptively, presumably driven by antagonistic interactions with pathogens [1-4]. Those genes encoding secreted antimicrobial peptides (AMPs), however, have failed to exhibit conventional signatures of strong adaptive evolution, especially in arthropods (e.g., [5, 6]) and often segregate for null alleles and gene deletions [3, 4, 7, 8]. Furthermore, quantitative genetic studies have failed to associate naturally occurring polymorphism in AMP genes with variation in resistance to infection [9-11]. Both the lack of signatures of positive selection in AMPs and lack of association between genotype and immune phenotypes have yielded an interpretation that AMP genes evolve under relaxed evolutionary constraint, with enough functional redundancy that variation in, or even loss of, any particular peptide would have little effect on overall resistance [12, 13]. In stark contrast to the current paradigm, we identified a naturally occurring amino acid polymorphism in the AMP Diptericin that is highly predictive of resistance to bacterial infection in Drosophila melanogaster [13]. The identical amino acid polymorphism arose in parallel in the sister species D. simulans, by independent mutation with equivalent phenotypic effect. Convergent substitutions at the same amino acid residue have evolved at least five times across the Drosophila genus. We hypothesize that the alternative alleles are maintained by balancing selection through context-dependent or fluctuating selection. This pattern of evolution appears to be common in AMPs but is invisible to conventional screens for adaptive evolution that are predicated on elevated rates of amino acid divergence.
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Affiliation(s)
- Robert L Unckless
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA.
| | | | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
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Fraïsse C, Belkhir K, Welch JJ, Bierne N. Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Mol Ecol 2015; 25:269-86. [DOI: 10.1111/mec.13299] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Christelle Fraïsse
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
| | - John J. Welch
- Department of Genetics; University of Cambridge; Downing Street CB2 3EH Cambridge UK
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution (UMR 5554); CNRS - Université Montpellier; Place Eugène Bataillon 34095 Montpellier France
- Station Marine; Université Montpellier; 2 rue des Chantiers 34200 Sète France
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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