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Lähteenaro M, Benda D, Straka J, Nylander JAA, Bergsten J. Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees. Mol Phylogenet Evol 2024; 195:108068. [PMID: 38554985 DOI: 10.1016/j.ympev.2024.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.
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Affiliation(s)
- Meri Lähteenaro
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Daniel Benda
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic; Department of Entomology, National Museum of the Czech Republic, Cirkusová 1740, CZ-19300 Prague 9, Czech Republic.
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44, Prague 2, Czech Republic.
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-106 91 Stockholm, Sweden.
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, P. O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Faculty of Science, Stockholm University, SE-106 91 Stockholm, Sweden.
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2
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024:fiae052. [PMID: 38678007 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Tiwary BK. A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2. Gene 2024; 915:148427. [PMID: 38575097 DOI: 10.1016/j.gene.2024.148427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage. The positive selection has operated on the spike gene of B lineages and its sub-lineages. The B.1 lineage has undergone positive selection on site 501 of the receptor binding domain ultimately reflected in a key substitution N501Y in its three descendant lineages namely B.1.1.7, B.1.351 and P.1. The intensity of purifying selection on the multiple sites of the spike gene has increased substantially in the sub-lineages of B.1 in a timescale. The binding site 501 on the spike protein in B lineage is found to coevolve with other amino acid sites. This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.
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Affiliation(s)
- Basant K Tiwary
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605 014, India.
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Rebeaud ME, Tiwari S, Fauvet B, Mohr A, Goloubinoff P, De Los Rios P. Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains. Cell Stress Chaperones 2024; 29:338-348. [PMID: 38521349 PMCID: PMC10999819 DOI: 10.1016/j.cstres.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in need to be structurally modified by the chaperone. Here, we measured the protein disaggregation and refolding activities of the main yeast cytosolic Hsp70, Ssa1, in the presence of its most abundant JDPs, Sis1 and Ydj1, and two swap mutants, in which the J-domains have been interchanged. The observed differences by which the four constructs differently cooperate with Ssa1 and cooperate with each other, as well as their observed intrinsic ability to bind misfolded substrates and trigger Ssa1's ATPase, indicate the presence of yet uncharacterized intramolecular dynamic interactions between the J-domains and the remaining C-terminal segments of these proteins. Taken together, the data suggest an autoregulatory role to these intramolecular interactions within both type A and B JDPs, which might have evolved to reduce energy-costly ATPase cycles by the Ssa1-4 chaperones that are the most abundant Hsp70s in the yeast cytosol.
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Affiliation(s)
- Mathieu E Rebeaud
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland; Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Satyam Tiwari
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Bruno Fauvet
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Adelaïde Mohr
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland.
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland; Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland.
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Porter LL, Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins and how to find them. Curr Opin Struct Biol 2024; 86:102807. [PMID: 38537533 DOI: 10.1016/j.sbi.2024.102807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which reversibly interconvert between multiple, sometimes highly dissimilar, native states. As the number of known metamorphic proteins increases, several computational and experimental strategies have emerged for gaining insights about their refolding processes and identifying unknown metamorphic proteins amongst the known proteome. In this review, we describe the current advances in biophysically and functionally ascertaining the structural interconversions of metamorphic proteins and how coevolution can be harnessed to identify novel metamorphic proteins from sequence information. We also discuss the challenges and ongoing efforts in using artificial intelligence-based protein structure prediction methods to discover metamorphic proteins and predict their corresponding three-dimensional structures.
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Affiliation(s)
- Lauren L Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago 833150, Chile.
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6
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Fu SJ, Zhang N, Fan J. Personality and cognition: shoal size discrimination performance is related to boldness and sociability among ten freshwater fish species. Anim Cogn 2024; 27:6. [PMID: 38429558 PMCID: PMC10907435 DOI: 10.1007/s10071-024-01837-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 03/03/2024]
Abstract
Several studies have reported that animals' personalities are often correlated with individual differences in cognition. Here, we tested whether personality is related to cognition across species, focusing on 10 freshwater fishes and a task relevant for fitness, the ability to discriminate shoal size. Bolder species exhibited more 'shuttle' behavior for information sampling during shoal selection and showed high performance (HP) in the numerical discrimination than shyer species, i.e., low performance (LP) species. Species at both the high and low ends of sociability showed LP, possibly due to loosened selection pressure because of either no need to perform shoal size discrimination tasks frequently in nature for very high sociability species or decreased willingness and motivation to join and stay within shoals for very low sociability species. Notably, the numerical discrimination was sensitive to the numerical contrast ratio in LP species but not in HP species, suggesting that the numerical system used for size discrimination also varied between species. Overall, we demonstrated the interspecies relationship between personality and shoal size discrimination across fish species, suggesting an evolutionary link between numerical abilities and behavior.
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Affiliation(s)
- Shi-Jian Fu
- Laboratory of Evolutionary Physiology and Behavior, Chongqing Key Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 401331, China.
| | - Na Zhang
- Laboratory of Evolutionary Physiology and Behavior, Chongqing Key Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Jie Fan
- Laboratory of Evolutionary Physiology and Behavior, Chongqing Key Laboratory of Animal Biology, Chongqing Normal University, Chongqing, 401331, China
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Balchan NR, Smith CF, Mackessy SP. A plethora of rodents: Rattlesnake predators generate unanticipated patterns of venom resistance in a grassland ecosystem. Toxicon X 2024; 21:100179. [PMID: 38144228 PMCID: PMC10746501 DOI: 10.1016/j.toxcx.2023.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Predation has the potential to impart strong selective pressures on organisms within their environments, resulting in adaptive changes in prey that minimize risk of predation. Pressures from venomous snakes present an exceptional challenge to prey, as venom represents a unique chemical arsenal evolutionarily tailored to incapacitate prey. In response, venom resistance has been detected in various snake prey species, and to varying degrees. This study analyzes venom resistance in an eastern Colorado grassland habitat, where the Prairie Rattlesnake (Crotalus viridis) and Desert Massasauga Rattlesnake (Sistrurus tergeminus edwardsii) co-occur with a suite of grassland rodents. We test for venom resistance across rodent and snake pairings using two geographically distant field sites to determine the role of 1) predation pressure and trophic ecology, and 2) sympatric and allopatric patterns of venom resistance. Resistance was measured using serum-based metalloproteinase inhibition assays to determine potential inhibition of proteolytic activity, augmented by median lethal dose (LD50) assays on rodent species to assess toxicity of crude venoms. Resistance is present in several rodent species, with strong resistance present in populations of Eastern Woodrat (Neotoma floridana), Ord's Kangaroo Rat (Dipodomys ordii), and Northern Grasshopper Mouse (Onychomys leucogaster). Resistance is less developed in other species, including the House Mouse (Mus musculus) and Plains Pocket Mouse (Perognathus flavescens). An unexpected differential is present, where Lincoln County Kangaroo Rats are highly resistant to venom of co-occurring Prairie Rattlesnakes yet are sensitive to an allopatric population of Prairie Rattlesnakes in Weld County. Lincoln Co. Northern Grasshopper Mice also demonstrate extremely elevated resistance to Weld Co. Prairie Rattlesnake venoms, and they may possess resistance mechanisms for myotoxin a, an abundant component of Weld Co. C. v viridis venoms. This study illustrates the complexity of venom resistance in biological communities that can exist when incorporating multiple species interactions. Future studies aimed at characterizing resistance mechanisms at the molecular level will provide a more detailed physiological context for understanding mechanisms by which resistance to venoms occurs.
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Affiliation(s)
- Neil R. Balchan
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Cara F. Smith
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
- Department of Biochemistry and Molecular Genetics, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Stephen P. Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, 80639, USA
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Buckingham LJ, Ashby B. Separation of evolutionary timescales in coevolving species. J Theor Biol 2024; 579:111688. [PMID: 38096978 DOI: 10.1016/j.jtbi.2023.111688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Many coevolutionary processes, including host-parasite and host-symbiont interactions, involve one species or trait which evolves much faster than the other. Whether or not a coevolutionary trajectory converges depends on the relative rates of evolutionary change in the two species, and so current adaptive dynamics approaches generally either determine convergence stability by considering arbitrary (often comparable) rates of evolutionary change or else rely on necessary or sufficient conditions for convergence stability. We propose a method for determining convergence stability in the case where one species is expected to evolve much faster than the other. This requires a second separation of timescales, which assumes that the faster evolving species will reach its evolutionary equilibrium (if one exists) before a new mutation arises in the more slowly evolving species. This method, which is likely to be a reasonable approximation for many coevolving species, both provides straightforward conditions for convergence stability and is less computationally expensive than traditional analysis of coevolution models, as it reduces the trait space from a two-dimensional plane to a one-dimensional manifold. In this paper, we present the theory underlying this new separation of timescales and provide examples of how it could be used to determine coevolutionary outcomes from models.
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Affiliation(s)
- Lydia J Buckingham
- Department of Mathematical Sciences, University of Bath, Bath, UK; Milner Centre for Evolution, University of Bath, Bath, UK.
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK; Milner Centre for Evolution, University of Bath, Bath, UK; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada; The Pacific Institute on Pathogens, Pandemics and Society (PIPPS), Simon Fraser University, Burnaby, BC, Canada
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9
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Xing W, Gai X, Xue L, Chen G. Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas. Sci Total Environ 2024; 912:169009. [PMID: 38040368 DOI: 10.1016/j.scitotenv.2023.169009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/04/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China; Nanjing Forestry University, Nanjing 210037, China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Liang Xue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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10
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Mallott EK. Disentangling the mechanisms underlying phylosymbiosis in mammals. Mol Ecol 2024; 33:e17193. [PMID: 37921987 DOI: 10.1111/mec.17193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023]
Abstract
Mammalian gut microbial communities are frequently found to be host-specific-microbial community compositions are more similar within than between host species-and some individual microbial taxa consistently associate with a single or small set of host species. The ecoevolutionary dynamics that result in this pattern of phylosymbiosis or host specificity have been proposed, but robust tests of the mechanisms driving these relationships are lacking. In this issue of Molecular Ecology, Mazel et al. (2023) combine large amplicon sequencing data sets with bacterial phenotypic traits to test whether microbial dispersal patterns contribute to the host specificity of the gut microbiome. They find that both transmission mode and oxygen tolerance are predictive of how specialized a microbe is. Horizontally transmitted, oxygen-tolerant microbes are more likely to be generalists, and vertically transmitted anaerobes are more likely to be limited to a few host species. This creative use of publicly available data provides a roadmap for testing hypotheses about the mechanisms underlying phylosymbiosis.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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11
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Ma D, Cheng Z, Han L, Guo J, Peplowski L, Zhou Z. Structure-oriented engineering of nitrile hydratase: Reshaping of substrate access tunnel and binding pocket for efficient synthesis of cinnamamide. Int J Biol Macromol 2024; 254:127800. [PMID: 37918589 DOI: 10.1016/j.ijbiomac.2023.127800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
Cinnamamide and its derivatives are the most common and important building blocks widely present in natural products. Currently, nitrile hydratase (NHase, EC 4.2.1.84) has been widely used in large-scale industrial production of nicotinamide and acrylamide, while its catalytic activity is extremely low or inactive for bulky nitrile substrates such as cinnamonitrile. Therefore, beneficial variant βF37P/L48P/F51N were obtained from PtNHase of Pseudonocardia thermophila JCM3095 by reshaping of substrate access tunnel and binding pocket, which exhibited 14.88-fold improved catalytic efficiency compared to the wild-type PtNHase. Structure analysis, molecular dynamics simulations and dynamical cross-correlation matrix (DCCM) analysis revealed that the introduced mutations enlarged the substrate access tunnel and binding pocket, enhanced overall anti-correlated movements of enzymes, which would promote product release during the dynamic process of catalysis. In a hydration process, the complete conversion of 5 mM cinnamonitrile was achieved by βF37P/L48P/F51N in a 50 mL reaction, with cinnamamide yield of almost 100 % and productivity of 0.736 g L-1 h-1. The study demonstrates the co-evolution of substrate access tunnel and binding pocket is an effective strategy, and provides a valuable reference for future research. Furthermore, NHases have huge potential for catalyzing bulky nitriles to form corresponding amides in large-scale industrial production.
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Affiliation(s)
- Dong Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu, China.
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12
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Rai GP, Shanker A. Coevolution-based computational approach to detect resistance mechanism of epidermal growth factor receptor. Biochim Biophys Acta Mol Cell Res 2024; 1871:119592. [PMID: 37730130 DOI: 10.1016/j.bbamcr.2023.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/24/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023]
Abstract
Tyrosine kinase epidermal growth factor receptor (EGFR) correlates the neoplastic cell metastasis, angiogenesis, neoplastic incursion, and apoptosis. Due to the involvement of EGFR in these biological processes, it becomes a most potent target for treating non-small cell lung cancer (NSCLC). The tyrosine kinase inhibitors (TKI) have endorsed high efficacy and anticipation to patients but unfortunately, within a year of treatment, drug targets develop resistance due to mutations. The present study detected the compensatory mutations in EGFR to know the evolutionary mechanism of drug resistance. The results of this study demonstrate that compensatory mutations enlarge the drug-binding pocket which may lead to the altered orientation of the ligand (gefitinib and erlotinib) causing drug resistance. This indicates that coevolutionary forces play a significant role in fine-tuning the structure of EGFR protein against the drugs. The analysis provides insight into the evolution-induced structural aspects of drug resistance changes in EGFR which in turn be useful in designing drugs with better efficacy.
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Affiliation(s)
- Gyan Prakash Rai
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar 824236, India
| | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar 824236, India.
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13
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Pires-Silva CM, Zilberman B, Eloi I, Rocha MM. A New Termitophilous Rove Beetle from Brazil Suggests an Undersampling Scenario and Cospeciation between Termites and their Termitophiles in the Neotropical region (Coleoptera: Staphylinidae: Aleocharinae). Neotrop Entomol 2023; 52:802-813. [PMID: 37495766 DOI: 10.1007/s13744-023-01063-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/15/2023] [Indexed: 07/28/2023]
Abstract
Numerous staphylinid species can be found in termite nests. While the distributional range of termite hosts has been well studied, the same cannot be said for their associated fauna. There is a lack of comprehensive sampling even in areas where termite fauna has been well-sampled. In recent surveys in Southeastern Brazil, we collected a new species of termitophilous rove beetle from the tribe Termitohospitini (Aleocharinae): Termitosocius boraceiensis sp. nov., is herein described. The new species is the first termitophile found in Boracéia, SP, Brazil, even with decades of termite sampling in the place. Additionally, we discuss the diversity and description rate of neotropical Termitohospitini, and investigate the potential of cospeciation between termites and their termitophilous beetles on the Emerson-Kistner principle. Our findings suggest that the neotropical Termitohospitini may be more diverse than previously believed and that Termitosocius species are present in host species that are geographically separated, implying a cospeciation scenario. Additional sampling is required to fully comprehend the relationships between termitophiles and their termite hosts. The outcomes of this study provide new insights into the undersampling scenario and possibly cospeciation between termites and their termitophiles in the Neotropical region.
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Affiliation(s)
- Carlos M Pires-Silva
- Programa de Pós-Graduação em Sistemática, Taxonomia Animal e Biodiversidade, LaC - Laboratório de Coleoptera, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil.
| | - Bruno Zilberman
- Programa de Pós-Graduação em Sistemática, Taxonomia Animal e Biodiversidade, LaC - Laboratório de Coleoptera, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Igor Eloi
- Programa de Pós-Graduação em Psicobiologia, LBC - Laboratório de Biologia Comportamental, Depto de Fisiologia e Comportamento, Universidade Federal Do Rio Grande Do Norte, Natal, Brazil
| | - Mauricio M Rocha
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
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14
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Sullivan TJ, Roberts H, Bultman TL. Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye. Microb Ecol 2023; 86:1686-1695. [PMID: 36725749 DOI: 10.1007/s00248-022-02166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.
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Affiliation(s)
- T J Sullivan
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA.
| | - Holly Roberts
- School of Sciences, Indiana University Kokomo, 2300 S. Washington St, Kokomo, IN, 46902, USA
| | - Thomas L Bultman
- Department of Biology, Hope College, 35 E. 12th St., Holland, MI, 49423, USA
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15
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Lima MA, Weckstein JD, Batista R, Ribas CC. DO PARASITIC LICE EXHIBIT ENDEMISM IN PARALLEL WITH THEIR AVIAN HOSTS? A COMPARISON ACROSS NORTHERN AMAZONIAN AREAS OF ENDEMISM. J Parasitol 2023; 109:506-513. [PMID: 37821101 DOI: 10.1645/18-135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Areas of endemism are the smallest units in biogeography and can be defined as biologically unique areas comprising taxa with common geographic limits to their distributions. High beta diversity within Amazonia is often related to turnover among these areas. For decades, evolutionary biologists have tried to comprehend the mechanisms generating and maintaining the spatial structure and high diversity of free-living Amazonian organisms, particularly birds. However, few studies have tried to analyze these patterns among their parasites. Host and parasite associations involve shared history that may allow us to better understand the fine-scale evolutionary history of the host. Here we compare the coevolutionary patterns among 2 avian host species with distinct patterns of genetic structure in northern Amazonia, Dendrocincla fuliginosa (Aves: Dendrocolaptidae) and Dixiphia pipra (Aves: Pipridae), and their ectoparasitic lice (Insecta: Phthiraptera), Furnaricola sp. ex Dendrocincla fuliginosa, Myrsidea sp. ex Dixiphia pipra, and Tyranniphilopterus sp. ex Dixiphia pipra. We obtained sequences of the mitochondrial gene cytochrome oxidase subunit I from hosts and parasites collected on opposite banks of the Negro and Japurá rivers, which delimit 3 areas of endemism in northern Amazonia: Napo, Jau, and Guiana. Our results demonstrate that the Negro River is a geographical barrier for both Furnaricola sp. and its avian host, Dendrocincla fuliginosa. Phylogenies of both hosts, Dendrocincla fuliginosa, and the parasites, Furnaricola sp., show monophyletic clades on opposite margins of the river that are not sister taxa. These clades have a mean uncorrected p-distance of 17.8% for Furnaricola sp. and 6.0% for Dendrocincla fuliginosa. Thus, these parasite clades constitute distinct evolutionary lineages and may even be distinct species. In contrast, Dixiphia pipra has no population structure associated with either river. Accordingly, data from their lice Myrsidea sp. indicate weak support for different clades on opposite margins of the Negro River, whereas data from their lice Tyranniphilopterus sp. indicate weak structure across the Japurá. This study is a first step toward understanding the effects of biogeographic history on permanent ectoparasites and suggests that host biogeographic history is to some extent a determinant of the parasite's history. Furthermore, the parasite's evolutionary history is an additional source of information about their hosts' evolution in this highly diverse region of northern Amazonia.
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Affiliation(s)
- Mirna Amoêdo Lima
- Graduate Program in Ecology, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, 69067-375, Manaus, AM, Brazil
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University and Department of Biodiversity, Earth, and Environmental Science, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103
| | - Romina Batista
- Biodiversity Section, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, 69067-375, Manaus, AM, Brazil
| | - Camila Cherem Ribas
- Biodiversity Section, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, 69067-375, Manaus, AM, Brazil
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16
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Mishra SK, Priya P, Rai GP, Haque R, Shanker A. Coevolution based immunoinformatics approach considering variability of epitopes to combat different strains: A case study using spike protein of SARS-CoV-2. Comput Biol Med 2023; 163:107233. [PMID: 37422941 DOI: 10.1016/j.compbiomed.2023.107233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/03/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
In the recent past several vaccines were developed to combat the COVID-19 disease. Unfortunately, the protective efficacy of the current vaccines has been reduced due to the high mutation rate in SARS-CoV-2. Here, we successfully implemented a coevolution based immunoinformatics approach to design an epitope-based peptide vaccine considering variability in spike protein of SARS-CoV-2. The spike glycoprotein was investigated for B- and T-cell epitope prediction. Identified T-cell epitopes were mapped on previously reported coevolving amino acids in the spike protein to introduce mutation. The non-mutated and mutated vaccine components were constructed by selecting epitopes showing overlapping with the predicted B-cell epitopes and highest antigenicity. Selected epitopes were linked with the help of a linker to construct a single vaccine component. Non-mutated and mutated vaccine component sequences were modelled and validated. The in-silico expression level of the vaccine constructs (non-mutated and mutated) in E. coli K12 shows promising results. The molecular docking analysis of vaccine components with toll-like receptor 5 (TLR5) demonstrated strong binding affinity. The time series calculations including root mean square deviation (RMSD), radius of gyration (RGYR), and energy of the system over 100 ns trajectory obtained from all atom molecular dynamics simulation showed stability of the system. The combined coevolutionary and immunoinformatics approach used in this study will certainly help to design an effective peptide vaccine that may work against different strains of SARS-CoV-2. Moreover, the strategy used in this study can be implemented on other pathogens.
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Affiliation(s)
- Saurav Kumar Mishra
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India
| | - Prerna Priya
- Department of Botany, Purnea Mahila College, Purnia, Bihar, India
| | - Gyan Prakash Rai
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India
| | - Rizwanul Haque
- Department of Biotechnology, Central University of South Bihar, Gaya, Bihar, India
| | - Asheesh Shanker
- Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India.
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17
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Noh S, Larson ER, Covitz RM, Chen A, Mazumder PR, Peck RF, Hamilton MC, Dettmann RA. Facultative symbiont virulence determines horizontal transmission rate without host strain specificity. bioRxiv 2023:2023.02.16.528903. [PMID: 36824889 PMCID: PMC9949114 DOI: 10.1101/2023.02.16.528903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In facultative symbioses, only a fraction of hosts are associated with a symbiont. Understanding why specific host and symbiont strains are associated can inform us of the evolutionary forces affecting facultative symbioses. Possibilities include ongoing host-symbiont coevolution driven by reciprocal selection, or priority effects that are neutral in respect to the host-symbiont interaction. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness estimates for naturally co-occurring (native) host and symbiont combinations compared to nonnative combinations. We used the Dictyostelium discoideum - Paraburkholderia bonniea system to test this hypothesis. P. bonniea features a reduced genome size relative to another Paraburkholderia symbiont of D. discoideum, indicating a significant history of coevolution with its host. Facultative symbionts may experience continued genome reduction if coevolution is ongoing, or their genome size may have reached a stable state if the symbiosis has also stabilized. Our work demonstrates that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead represents a stable facultative symbiosis. Specifically associated host and symbiont strains in this system are the result of priority effects, and presently unassociated hosts are simply uncolonized. We find evidence for a virulence-transmission trade-off without host strain specificity, and identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in benevolence.
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Affiliation(s)
- Suegene Noh
- Biology Department, Colby College, Waterville, Maine, USA
| | | | - Rachel M. Covitz
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Anna Chen
- Biology Department, Colby College, Waterville, Maine, USA
| | | | - Ron F. Peck
- Biology Department, Colby College, Waterville, Maine, USA
| | - Marisa C. Hamilton
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Robert A. Dettmann
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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18
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Dexter E, Fields PD, Ebert D. Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites. Mol Biol Evol 2023:msad145. [PMID: 37326294 DOI: 10.1093/molbev/msad145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Understanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.
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Affiliation(s)
- Eric Dexter
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences, The University of Basel; Basel, 4051, Switzerland
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19
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Rivera-Rivera CJ, Grbic D. CastNet: a systems-level sequence evolution simulator. BMC Bioinformatics 2023; 24:247. [PMID: 37308829 DOI: 10.1186/s12859-023-05366-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used to infer phylogenies which, in the simplest form, simulates a single sequence at a time. However, biological systems are multi-genic, and gene products can affect each other's evolutionary paths through coevolution. These crucial evolutionary dynamics still remain to be simulated, and we believe that modelling them can lead to profound insights for comparative genomics. RESULTS Here we present CastNet, a genome evolution simulator that assumes each genome is a collection of genes with constantly evolving regulatory interactions in between them. The regulatory interactions produce a phenotype in the form of gene expression profiles, upon which fitness is calculated. A genetic algorithm is then used to evolve a population of such entities through a user-defined phylogeny. Importantly, the regulatory mutations are a response to sequence mutations, thus making a 1-1 relationship between the rate of evolution of sequences and of regulatory parameters. This is, to our knowledge, the first time the evolution of sequences and regulation have been explicitly linked in a simulation, despite there being a multitude of sequence evolution simulators, and a handful of models to simulate Gene Regulatory Network (GRN) evolution. In our test runs, we see a coevolutionary signal among genes that are active in the GRN, and neutral evolution in genes that are not included in the network, showing that selective pressures imposed on the regulatory output of the genes are reflected in their sequences. CONCLUSION We believe that CastNet represents a substantial step for developing new tools to study genome evolution, and more broadly, coevolutionary webs and complex evolving systems. This simulator also provides a new framework to study molecular evolution where sequence coevolution has a leading role.
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Affiliation(s)
| | - Djordje Grbic
- IT-University of Copenhagen, Rued Langgaards Vej 7, 2300, Copenhagen, Denmark
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20
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Musso AE, Fortier C, Huber DPW, Carroll AL, Evenden ML. Naïve Pine Terpene Response to the Mountain Pine Beetle (Dendroctonus ponderosae) through the Seasons. J Chem Ecol 2023; 49:299-312. [PMID: 36929332 DOI: 10.1007/s10886-023-01418-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023]
Abstract
Insect herbivores must contend with constitutive and induced plant defenses. The mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae, Scolytinae) has expanded its range east of the Rocky Mountains into the western boreal forest and is encountering evolutionarily naïve lodgepole pines (Pinus contorta) and jack pines (Pinus banksiana). Pinus contorta and P. banksiana in the expanded range have different constitutive and induced defenses in response to wounding and inoculation with fungal associates of D. ponderosae. In the historic range, previous studies have examined phloem terpene content prior to and just after D. ponderosae mass attack, but the terpene profile of attacked trees post-overwintering is unknown. We examined the response of mature P. contorta and P. banksiana trees to experimentally-applied mass attack by D. ponderosae and quantified phloem terpenes at three time points, pre-attack, post-attack (same season), and the following spring, post-overwintering. Phloem content of total terpenes as well as many individual terpenes increased after D. ponderosae attack but were only significantly higher than pre-attack levels at the post-overwintering time point in both P. contorta and P. banksiana. The absence of a significant increase in phloem terpenes in the month following attack in naïve pines is a potential cause for increased D. ponderosae offspring production reported in naïve P. contorta. Beetle attack density did not influence the phloem terpene profiles of either species and there was no significant interaction between attack density and sampling time on terpene content. High phloem terpenes in trees that are attacked at low densities could prime these trees for defense against attacks in the following season but it could also make these trees more apparent to early-foraging beetles and facilitate efficient mass attack at low D. ponderosae population densities in the expanded range.
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Affiliation(s)
- A E Musso
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
| | - C Fortier
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - D P W Huber
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, Canada
| | - A L Carroll
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada
| | - M L Evenden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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21
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Nag Chowdhury S, Banerjee J, Perc M, Ghosh D. Eco-evolutionary cyclic dominance among predators, prey, and parasites. J Theor Biol 2023; 564:111446. [PMID: 36868345 DOI: 10.1016/j.jtbi.2023.111446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023]
Abstract
Predator-prey interactions are one of ecology's central research themes, but with many interdisciplinary implications across the social and natural sciences. Here we consider an often-overlooked species in these interactions, namely parasites. We first show that a simple predator-prey-parasite model, inspired by the classical Lotka-Volterra equations, fails to produce a stable coexistence of all three species, thus failing to provide a biologically realistic outcome. To improve this, we introduce free space as a relevant eco-evolutionary component in a new mathematical model that uses a game-theoretical payoff matrix to describe a more realistic setup. We then show that the consideration of free space stabilizes the dynamics by means of cyclic dominance that emerges between the three species. We determine the parameter regions of coexistence as well as the types of bifurcations leading to it by means of analytical derivations as well as by means of numerical simulations. We conclude that the consideration of free space as a finite resource reveals the limits of biodiversity in predator-prey-parasite interactions, and it may also help us in the determination of factors that promote a healthy biota.
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Affiliation(s)
- Sayantan Nag Chowdhury
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Jeet Banerjee
- BYJU'S, Think & Learn Pvt. Ltd., IBC Knowledge Park, 4/1 Bannerghatta Main Road, Bangalore 560029, India
| | - Matjaž Perc
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000 Maribor, Slovenia; Alma Mater Europaea, Slovenska ulica, 17, 2000 Maribor, Slovenia; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan; Complexity Science Hub Vienna, Josefstädterstraße 39, 1080 Vienna, Austria; Department of Physics, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea
| | - Dibakar Ghosh
- Physics and Applied Mathematics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
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22
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Fang F, Ma J, Li Y. The coevolution of the spread of a disease and competing opinions in multiplex networks. Chaos Solitons Fractals 2023; 170:113376. [PMID: 36969948 PMCID: PMC10028538 DOI: 10.1016/j.chaos.2023.113376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
The COVID-19 pandemic has resulted in a proliferation of conflicting opinions on physical distancing across various media platforms, which has had a significant impact on human behavior and the transmission dynamics of the disease. Inspired by this social phenomenon, we present a novel UAP-SIS model to study the interaction between conflicting opinions and epidemic spreading in multiplex networks, in which individual behavior is based on diverse opinions. We distinguish susceptibility and infectivity among individuals who are unaware, pro-physical distancing and anti-physical distancing, and we incorporate three kinds of mechanisms for generating individual awareness. The coupled dynamics are analyzed in terms of a microscopic Markov chain approach that encompasses the aforementioned elements. With this model, we derive the epidemic threshold which is related to the diffusion of competing opinions and their coupling configuration. Our findings demonstrate that the transmission of the disease is shaped in a significant manner by conflicting opinions, due to the complex interaction between such opinions and the disease itself. Furthermore, the implementation of awareness-generating mechanisms can help to mitigate the overall prevalence of the epidemic, and global awareness and self-awareness can be interchangeable in certain instances. To effectively curb the spread of epidemics, policymakers should take steps to regulate social media and promote physical distancing as the mainstream opinion.
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Affiliation(s)
- Fanshu Fang
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, 211101, China
| | - Jing Ma
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, 211101, China
| | - Yanli Li
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, 211101, China
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23
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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24
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Oyejobi GK, Zhang X, Xiong D, Ogolla F, Xue H, Wei H. Phage-bacterial evolutionary interactions: experimental models and complications. Crit Rev Microbiol 2023; 49:283-296. [PMID: 35358006 DOI: 10.1080/1040841x.2022.2052793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Phage treatment of bacterial infections has offered some hope even as the crisis of antimicrobial resistance continues to be on the rise. However, bacterial resistance to phage is another looming challenge capable of undermining the effectiveness of phage therapy. Moreover, the consideration of including phage therapy in modern medicine calls for more careful research around every aspect of phage study. In an attempt to adequately prepare for the events of phage resistance, many studies have attempted to experimentally evolve phage resistance in different bacterial strains, as well as train phages to evolve counter-infectivity of resistant bacterial mutants, in view of answering such questions as coevolutionary dynamics between phage and bacteria, mechanisms of phage resistance, fitness costs of phage resistance on bacteria, etc. In this review, we summarised many such studies and by careful examination, highlighted critical issues to the outcome of phage therapy. We also discuss the insufficiency of many of these in vitro studies to represent actual disease conditions during phage application, alongside other complications that exist in phage-bacterial evolutionary interactions. Conclusively, we present the exploitation of phage-bacterial interactions for successful infection managements, as well as some future perspectives to direct phage research.
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Affiliation(s)
- Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Department of Microbiology, Osun State University, Osogbo, Nigeria.,Organization of African Academic Doctors, Nairobi, Kenya
| | - Xiaoxu Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Dongyan Xiong
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Faith Ogolla
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Organization of African Academic Doctors, Nairobi, Kenya.,Sino-Africa Joint Research Center, Nairobi, Kenya
| | - Heng Xue
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Nairobi, Kenya
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25
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Matthews AE, Boves TJ, Percy KL, Wijeratne AJ. Draft genome sequencing data of a feather mite, Amerodectes protonotaria Hernandes 2018 (Acariformes: Proctophyllodidae). Data Brief 2022; 46:108835. [PMID: 36591378 PMCID: PMC9801072 DOI: 10.1016/j.dib.2022.108835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Feather mites are ubiquitous, permanent, obligate ectosymbionts of avian hosts and are a valuable natural system for studying host-symbiont evolutionary and ecological dynamics at multiple levels of biological organization. However, a lack of a sequenced genome impedes molecular studies using this system. Therefore, we present the first draft genome of a symbiotic feather mite, Amerodectes protonotaria Hernandes 2018. The genome sequence data presented here were derived from an individual female mite that was collected in the field from Protonotaria citrea, its only known host species. Short read sequence data were obtained using an Illumina NovaSeq 6000 platform. From these data, we assembled a 59,665,063 bp draft genome consisting of 2,399 contigs. Raw short reads and the assembled genome sequence are available at the National Center for Biotechnology Information (NCBI)'s Sequence Read Archive (SRA) under BioProject PRJNA884722. The data presented here are beneficial for future research on the biology and evolution of closely related mites and the genomics of host-symbiont interactions.
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Affiliation(s)
- Alix E. Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, Arkansas, United States,Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States,Corresponding author. @matthews_ae
| | - Than J. Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States
| | - Katie L. Percy
- Audubon Delta, National Audubon Society, Baton Rouge, Louisiana, United States,United States Department of Agriculture, Natural Resources Conservation Service, Addis, Louisiana, United States
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States
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26
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Dean CAE, Katz AD, Wu WY, Berenbaum MR. Degree of Dietary Specialization on Furanocoumarin-Containing Hostplants in a Newly Invasive Web Building Caterpillar. J Chem Ecol 2022; 48:850-866. [PMID: 36450872 DOI: 10.1007/s10886-022-01389-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022]
Abstract
The genus Depressaria (Lepidoptera: Depressariidae) mostly comprises specialist herbivores with varying capacity for detoxification of defensive phytochemistry. Depressaria depressana, a Eurasian moth recently introduced into North America, is a family-level specialist of the Apiaceae, whose hosts include more than a dozen species in multiple tribes; Depressaria radiella is a super-specialist of Eurasian origin that feeds exclusively on species in the genera Pastinaca and Heracleum throughout its native and introduced range. In eastern North America, it feeds upon Pastinaca sativa, an invasive European species, and Heracleum maximum, a native species. We determined whether differences in furanocoumarin metabolism exist between D. depressana and two isolated populations of D. radiella, feeding exclusively on either P. sativa or H. maximum. We also compared gravimetric estimates of feeding efficiency to assess D. depressana larval performance on different diets. Both populations of D. radiella metabolized furanocoumarins at a greater rate than D. depressana. Although there was no difference in rates of metabolism of linear furanocoumarins in the two populations of D. radiella, individuals collected from H. maximum metabolized angular furanocoumarins more rapidly. The gravimetric assessments of feeding efficiencies revealed that D. depressana exhibited highest efficiencies consuming Daucus carota; moreover, this species survived to pupation consuming fruits of Zizia aurea, an apiaceous species native to North America. Our preliminary phylogenetic analysis, building on an earlier morphological analysis, incorporates mitochondrial cytochrome oxidase subunit 1 data from the BOLD database and revealed that the presence or absence of furanocoumarins is not a strong predictor of species-level evolution in Depressaria.
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Affiliation(s)
- Charles A E Dean
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Aron D Katz
- Engineer Research and Development Center, Champaign, IL, 61822, USA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, 61820, USA
| | - Wen-Yen Wu
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - May R Berenbaum
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Nevo O, Valenta K, Helman A, Ganzhorn JU, Ayasse M. Fruit scent as an honest signal for fruit quality. BMC Ecol Evol 2022; 22:139. [PMID: 36451093 PMCID: PMC9710009 DOI: 10.1186/s12862-022-02064-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/15/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Fleshy fruits evolved to be attractive to seed dispersers through various signals such as color and scent. Signals can evolve through different trajectories and have various degrees of reliability. The strongest substrate on which reliable signals can evolve is when there is an inherent link between signal and reward, rendering cheating costly or impossible. It was recently proposed that aliphatic esters in fruit scent may be predictive of sugar content due to their synthesis from products of sugar fermentation. We test this hypothesis on a case study of wild fig species (Ficus tiliifolia) from Madagascar, which relies on seed dispersal by lemurs. RESULTS We found a strong positive correlation between signal (esters) and reward (sugar). We also found that non-esters, including direct fermentation products, in fruit scent do not indicate sugar levels, which implies that this relationship is not simply a product of fruit maturation wherein more mature fruits emit more scent and contain more sugar. CONCLUSIONS While based on a single taxon, these results strongly support the hypothesis that a biochemical link between ester synthesis and sugar may render the ester fraction of fruit scent an honest signal for fruit quality, with consequences for animal sensory and feeding ecology, and the evolution of plants in the context of seed dispersal.
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Affiliation(s)
- Omer Nevo
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. .,Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany. .,Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany.
| | - Kim Valenta
- grid.15276.370000 0004 1936 8091Department of Anthropology, University of Florida, Gainesville, FL USA
| | - Annabella Helman
- grid.26009.3d0000 0004 1936 7961Department of Evolutionary Anthropology, Duke University, Durham, NC USA
| | - Jörg U. Ganzhorn
- grid.9026.d0000 0001 2287 2617Animal Ecology and Conservation, University of Hamburg, Hamburg, Germany
| | - Manfred Ayasse
- grid.6582.90000 0004 1936 9748Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
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de Angeli Dutra D, Poulin R, Ferreira FC. Evolutionary consequences of vector-borne transmission: how using vectors shapes host, vector and pathogen evolution. Parasitology 2022; 149:1667-78. [PMID: 36200511 DOI: 10.1017/S0031182022001378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transmission mode is a key factor that influences host–parasite coevolution. Vector-borne pathogens are among the most important disease agents for humans and wildlife due to their broad distribution, high diversity, prevalence and lethality. They comprise some of the most important and widespread human pathogens, such as yellow fever, leishmania and malaria. Vector-borne parasites (in this review, those transmitted by blood-feeding Diptera) follow unique transmission routes towards their vertebrate hosts. Consequently, each part of this tri-partite (i.e. parasite, vector and host) interaction can influence co- and counter-evolutionary pressures among antagonists. This mode of transmission may favour the evolution of greater virulence to the vertebrate host; however, pathogen–vector interactions can also have a broad spectrum of fitness costs to the insect vector. To complete their life cycle, vector-borne pathogens must overcome immune responses from 2 unrelated organisms, since they can activate responses in both vertebrate and invertebrate hosts, possibly creating a trade-off between investments against both types of immunity. Here, we assess how dipteran vector-borne transmission shapes the evolution of hosts, vectors and the pathogens themselves. Hosts, vectors and pathogens co-evolve together in a constant antagonistic arms race with each participant's primary goal being to maximize its performance and fitness.
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29
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 2022; 23:689. [PMID: 36199029 PMCID: PMC9535894 DOI: 10.1186/s12864-022-08909-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08909-7.
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Affiliation(s)
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
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30
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Beaurepaire A, Arredondo D, Genchi-García ML, Castelli L, Reynaldi FJ, Antunez K, Invernizzi C, Mondet F, Le Conte Y, Dalmon A. Genetic diversification of an invasive honey bee ectoparasite across sympatric and allopatric host populations. Infect Genet Evol 2022; 103:105340. [PMID: 35853582 DOI: 10.1016/j.meegid.2022.105340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Invasive parasites are major threats to biodiversity. The honey bee ectoparasite, Varroa destructor, has shifted host and spread almost globally several decades ago. This pest is generally considered to be the main global threat to Western honey bees, Apis mellifera, although the damages it causes are not equivalent in all its new host's populations. Due to the high virulence of this parasite and the viruses it vectors, beekeepers generally rely on acaricide treatments to keep their colonies alive. However, some populations of A. mellifera can survive without anthropogenic mite control, through the expression of diverse resistance and tolerance traits. Such surviving colonies are currently found throughout the globe, with the biggest populations being found in Sub-Saharan Africa and Latin America. Recently, genetic differences between mite populations infesting surviving and treated A. mellifera colonies in Europe were found, suggesting that adaptations of honey bees drive mite evolution. Yet, the prevalence of such co-evolutionary adaptations in other invasive populations of V. destructor remain unknown. Using the previous data from Europe and novel genetic data from V. destructor populations in South America and Africa, we here investigated whether mites display signs of adaptations to different host populations of diverse origins and undergoing differing management. Our results show that, contrary to the differences previously documented in Europe, mites infesting treated and untreated honey bee populations in Africa and South America are genetically similar. However, strong levels of genetic differentiation were found when comparing mites across continents, suggesting ongoing allopatric speciation despite a recent spread from genetically homogenous lineages. This study provides novel insights into the co-evolution of V. destructor and A. mellifera, and confirms that these species are ideal to investigate coevolution in newly established host-parasite systems.
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Affiliation(s)
- Alexis Beaurepaire
- INRAE, UR Abeilles et Environnement, Avignon, France; Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Agroscope, Swiss Bee Research Centre, Bern, Switzerland.
| | - Daniela Arredondo
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - María Laura Genchi-García
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Agroscope, Swiss Bee Research Centre, Bern, Switzerland; Instituto Multidisciplinario de Biología Celular, La Plata, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Loreley Castelli
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Francisco Jose Reynaldi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Karina Antunez
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Ciro Invernizzi
- Facultad de Ciencias, Universidad de la República de Uruguay, Montevideo, Uruguay
| | - Fanny Mondet
- INRAE, UR Abeilles et Environnement, Avignon, France
| | - Yves Le Conte
- INRAE, UR Abeilles et Environnement, Avignon, France
| | - Anne Dalmon
- INRAE, UR Abeilles et Environnement, Avignon, France
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Zhang G, Wei F, Chen Z, Wang Y, Jiao S, Yang J, Chen Y, Liu C, Huang Z, Dong L, Chen S. Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species. Sci Total Environ 2022; 830:154583. [PMID: 35304141 DOI: 10.1016/j.scitotenv.2022.154583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co, Ltd., Wenshan 663000, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling 712100, China.
| | - JiaYing Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Congsheng Liu
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Zhixin Huang
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Hong X, Xue L, Gao J, Jiang Y, Kou X. Epochal coevolution of minor capsid protein in norovirus GII.4 variants with major capsid protein based on their interactions over the last five decades. Virus Res 2022; 319:198860. [PMID: 35817094 DOI: 10.1016/j.virusres.2022.198860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/02/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022]
Abstract
Norovirus is a leading cause of viral gastroenteritis outbreaks worldwide, with GII.4 responsible for the majority of infections. Minor capsid protein VP2 has been found to have functions such as stabilizing virus particles, and VP2 is one of the highly variable proteins of norovirus, similar to major capsid protein VP1. However, whether the variation of VP2 is functionally driven still remains unclear. In this study, VP2 showed a higher evolutionary rate (2.642×10-3 substitutions/site/year) than VP1 (1.587×10-3 substitutions/site/year), and a hypervariable region in VP2 in a serial of norovirus GII.4 over the past 50 years had been observed. Notably, the high variation of VP2 was not haphazard. The evolutionary process of VP2 is similar to that of VP1 with comparable topologies when the phylogenetic trees were constructed. Moreover, VP2 was found to interact with VP1 among epidemic variants of GII.4 using the yeast two-hybrid experiments. The results of interactions were grouped into time-adjacent (e.g. Ancestral-VP1 plus US95-VP2) and non-adjacent (e.g. Ancestral-VP1 plus Sydney-VP2) according to the epochal chronologically based prevalence of GII.4 norovirus. Interestingly, the interaction of the former group was significantly stronger than that of the latter group (P=0.0001). Furthermore, the interaction regions on VP2 (residues 131-160 and 171-180) were mapped to the hypervariable region. And these interaction regions did show an important role in the evolutionary process of VP2, which was consistent with that of VP1. In summary, the minor capsid protein VP2 of GII.4 noroviruses had shown the epochal coevolution with VP1 based on their interactions over the past 50 years. The findings of this study provided valuable information for further understanding and completing the evolutionary mechanism of norovirus.
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Affiliation(s)
- Xiaojing Hong
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Science
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Science.
| | - Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Science
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoxia Kou
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
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Cogni R, Quental TB, Guimarães PR. Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives. Evolution 2022; 76:1108-1123. [PMID: 35262199 DOI: 10.1111/evo.14456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.
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Affiliation(s)
- Rodrigo Cogni
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Paulo R Guimarães
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
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34
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Hugot JP, Feliu C, Ribas A. Human parasites as tracers of the evolution of their hosts. Infect Genet Evol 2022; 100:105262. [PMID: 35245684 DOI: 10.1016/j.meegid.2022.105262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Because parasite data reveal essential information about the behavior and history of their hosts, it is possible to use them as tracers of host evolution. A table built from the analysis of the data contained in the book by Ashford and Crewe "The Parasites of Homo sapiens" allows counting and cross comparing the parasites according to the main descriptors used by the authors: Taxonomic groups, for each group number of parasites species identified in humans; Status, numbers of reported human cases and their dispersion; Geographic distribution, parasite specific richness recorded in biogeographic regions; Habitat, parasite location in or on the human body; Transmission, contamination pathways to man; Hosts, non-human hosts, which have a role in the maintenance of a parasite; Host-specificity status, relative role of man or other hosts in the maintenance of parasite populations. A strong positive correlation is observed between the number of parasites species recorded in humans and the global parasite species richness for each taxonomic group. About 74% of the parasites recorded in humans are rare, sporadic or nowhere common; 10% only are common or abundant worldwide. The Palearctic exhibits the highest parasite species diversity; the Oriental, Nearctic, Neotropical and Aethiopian regions have roughly similar richness values; the Australian Region is the poorest. Earliest domesticated animals, such as dog, cat, cattle or pig, share more parasite species with Humans than tardily domesticated as horse, rabbit or camel. More than one third of our parasites have elected our alimentary canal as a home and about two third are using the digestive tract path for contamination. Time of occupancy of new territories, diversity in feeding habits and commensalism with other animals, widely explain Human particular parasite richness. As suggested by the authors: "There must be few parasitic species which have never had the opportunity to infect a human".
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Affiliation(s)
- Jean-Pierre Hugot
- Muséum National d'Histoire Naturelle, ISYEB, MNHN, CNRS (UMR 7205), UPMC, EPHE, UA, 55, rue Buffon, F-75231 Paris, France.
| | - Carlos Feliu
- IRBio (Institut de Recerca de la Biodiversitat, Universitat de Barcelona), Avda. Diagonal, s/n, 08028 Barcelona, Spain.
| | - Alexis Ribas
- Parasitology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Science, IRBio (Research Institute of Biodiversity), University of Barcelona, Barcelona, Spain.
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De Lisle SP, Bolnick DI, Brodie ED, Moore AJ, McGlothlin JW. Interacting phenotypes and the coevolutionary process: Interspecific indirect genetic effects alter coevolutionary dynamics. Evolution 2022; 76:429-444. [PMID: 34997942 PMCID: PMC9385155 DOI: 10.1111/evo.14427] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/08/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022]
Abstract
Coevolution occurs when species interact to influence one another's fitness, resulting in reciprocal evolutionary change. In many coevolving lineages, trait expression in one species is modified by the genotypes and phenotypes of the other, forming feedback loops reminiscent of models of intraspecific social evolution. Here, we adapt the theory of within-species social evolution, characterized by indirect genetic effects and social selection imposed by interacting individuals, to the case of interspecific interactions. In a trait-based model, we derive general expressions for multivariate evolutionary change in two species and the expected between-species covariance in evolutionary change when selection varies across space. We show that reciprocal interspecific indirect genetic effects can dominate the coevolutionary process and drive patterns of correlated evolution beyond what is expected from direct selection alone. In extreme cases, interspecific indirect genetic effects can lead to coevolution when selection does not covary between species or even when one species lacks genetic variance. Moreover, our model indicates that interspecific indirect genetic effects may interact in complex ways with cross-species selection to determine the course of coevolution. Importantly, our model makes empirically testable predictions for how different forms of reciprocal interactions contribute to the coevolutionary process.
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Affiliation(s)
- Stephen P. De Lisle
- Department of Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut, USA 06269
- Present address: Evolutionary Ecology Unit, Department of Biology, Lund University, Solvegatan 37, Lund, Sweden
| | - Daniel I. Bolnick
- Department of Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Storrs, Connecticut, USA 06269
| | - Edmund D. Brodie
- Department of Biology and Mountain Lake Biological Station, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904 USA
| | - Allen J. Moore
- Department of Entomology, University of Georgia, Athens, GA 30602 USA
| | - Joel W. McGlothlin
- Department of Biological Sciences, Virginia Tech, 2125 Derring Hall, 926 West Campus Drive, Blacksburg, Virginia, USA 24060
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D'Amico F, Skarmoutsou E, Libra M. The S100A7 nuclear interactors in autoimmune diseases: a coevolutionary study in mammals. Immunogenetics 2022. [PMID: 35174412 DOI: 10.1007/s00251-022-01256-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/10/2022] [Indexed: 11/05/2022]
Abstract
S100A7, a member of the S100A family of Ca2+-binding proteins, is considered a key effector in immune response. In particular, S100A7 dysregulation has been associated with several diseases, including autoimmune disorders. At the nuclear level, S100A7 interacts with several protein-binding partners which are involved in transcriptional regulation and DNA repair. By using the BioGRID and GAAD databases, S100A7 nuclear interactors with a putative involvement in autoimmune diseases were retrieved. We selected fatty acid-binding protein 5 (FABP5), autoimmune regulator (AIRE), cystic fibrosis transmembrane conductance regulator (CFTR), chromodomain helicase DNA-binding protein 4 (CHD4), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), histone deacetylase 2 (HDAC2), v-myc avian myelocytomatosis viral oncogene homolog (MYC), protection of telomeres protein 1 (POT1), telomeric repeat-binding factor (NIMA-interacting) 1 (TERF1), telomeric repeat-binding factor 2 (TERF2), and Zic family member 1 (ZIC1). Linear correlation coefficients between interprotein distances were calculated with MirrorTree. Coevolution clusters were also identified with the use of a recent version of the Blocks in Sequences (BIS2) algorithm implemented in the BIS2Analyzer web server. Analysis of pair positions identified interprotein coevolving clusters between S100A7 and the binding partners CFTR and TERF1. Such findings could guide further analysis to better elucidate the function of S100A7 and its binding partners and to design drugs targeting for these molecules in autoimmune diseases.
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Hanifin CT, Kudo Y, Yotsu-Yamashita M. Chemical Ecology of the North American Newt Genera Taricha and Notophthalmus. Prog Chem Org Nat Prod 2022; 118:101-130. [PMID: 35416518 DOI: 10.1007/978-3-030-92030-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The North American newt genera Taricha and Notophthalmus (order Caudata) are well known for the combination of potent toxicity, aposematic coloration, and striking defense postures that protects these animals from predation. This suite of traits is centered around the neurotoxin tetrodotoxin, which causes paralysis and death in metazoans by disrupting the initiation and propagation of electrical signals in the nerves and muscles. Tetrodotoxin defends newts from predation across multiple life history stages and its role in generating arms-race coevolution between Taricha newts and garter snake (genus Thamnophis) predators is well studied. However, understanding the broader picture of chemical defenses in Taricha and Notophthalmus requires an expanded comprehension of the defensive chemical ecology of tetrodotoxin that includes possible coevolutionary interactions with insect egg predators, protection against parasites, as well as mimicry complexes associated with tetrodotoxin and aposematic coloration in both genera. Herein the authors review what is known about the structure, function, and pharmacology of tetrodotoxin to explore its evolution and chemical ecology in the North American newt. Focus is made specifically on the origin and possible biosynthesis of tetrodotoxin in these taxa as well as providing an expanded picture of the web of interactions that contribute to landscape level patterns of toxicity and defense in Taricha and Notophthalmus.
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Affiliation(s)
- Charles T Hanifin
- Department of Biology, Utah State University, 320 N. Aggie Blvd, Vernal, UT, 84078, USA.
| | - Yuta Kudo
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science & Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
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Abstract
The fungal genus Entomophthora consists of highly host-specific pathogens that cause deadly epizootics in their various insect hosts. The most well-known among these is the "zombie fly" fungus E. muscae, which, like other Entomophthora species, elicits a series of dramatic behaviors in infected hosts to promote optimal spore dispersal. Despite having been first described more than 160 years ago, there are still many open questions about Entomophthora biology, including the molecular underpinnings of host behavior manipulation and host specificity. This review provides a comprehensive overview of our current understanding of the biology of Entomophthora fungi and enumerates the most pressing outstanding questions that should be addressed in the field. We briefly review the discovery of Entomophthora and provide a summary of the 21 recognized Entomophthora species, including their type hosts, methods of transmission (ejection of spores after or before host death), and for which molecular data are available. Further, we argue that this genus is globally distributed, based on a compilation of Entomophthora records in the literature and in online naturalist databases, and likely to contain additional species. Evidence for strain-level specificity of hosts is summarized and directly compared to phylogenies of Entomophthora and the class Insecta. A detailed description of Entomophthora's life-cycle and observed manipulated behaviors is provided and used to summarize a consensus for ideal growth conditions. We discuss evidence for Entomophthora's adaptation to growth exclusively inside insects, such as producing wall-less hyphal bodies and a unique set of subtilisin-like proteases to penetrate the insect cuticle. However, we are only starting to understand the functions of unusual molecular and genomic characteristics, such as having large > 1 Gb genomes full of repetitive elements and potential functional diploidy. We argue that the high host-specificity and obligate life-style of most Entomophthora species provides ample scope for having been shaped by close coevolution with insects despite the current general lack of such evidence. Finally, we propose six major directions for future Entomophthora research and in doing so hope to provide a foundation for future studies of these fungi and their interaction with insects.
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Affiliation(s)
- Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Henrik H De Fine Licht
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
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Craig TP, Itami JK. A geographic mosaic of coevolution between Eurosta solidaginis (Fitch) and its host plant tall goldenrod Solidago altissima (L.). Evolution 2021; 75:3056-3070. [PMID: 34726264 DOI: 10.1111/evo.14391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 11/30/2022]
Abstract
A geographic mosaic of coevolution has produced local reciprocal adaptation in tall goldenrod, Solidago altissima (L.), and the goldenrod ball-gall fly, Eurosta solidaginis (Fitch 1855). The fly is selected to induce gall diameters that minimize mortality from natural enemies, and the plant is selected to limit gall growth that reduces plant fitness. We conducted a double reciprocal transplant experiment where S. altissima and E. solidaginis from three sites were grown in gardens at each site to partition the gall morphology variation into fly genotype, plant genotype, and the environment components. The host plant gall diameter induced by each E. solidaginis population was adapted to inhibit local natural enemies from ovipositing on or consuming enclosed larvae. Reciprocally, increasing the gall size induced by the local fly population increased the resistance of the local plant host population to gall growth. Differences among sites in natural enemies produced a mosaic of hotspots of coevolutionary arms races between flies selecting for greater gall diameter and plants for smaller diameters, and coldspots where there is no selection on plant or fly for a change in gall diameter. In contrast, the geographic variations of gall length and gall shape were not due to coevolutionary interactions.
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Affiliation(s)
- Timothy P Craig
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota
| | - Joanne K Itami
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota
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Solórzano-García B, Vázquez-Domínguez E, Pérez-Ponce de León G, Piñero D. Co-structure analysis and genetic associations reveal insights into pinworms (Trypanoxyuris) and primates (Alouatta palliata) microevolutionary dynamics. BMC Ecol Evol 2021; 21:190. [PMID: 34670486 PMCID: PMC8527708 DOI: 10.1186/s12862-021-01924-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In parasitism arm race processes and red queen dynamics between host and parasites reciprocally mold many aspects of their genetics and evolution. We performed a parallel assessment of population genetics and demography of two species of pinworms with different degrees of host specificity (Trypanoxyuris multilabiatus, species-specific; and T. minutus, genus-specific) and their host, the mantled howler monkey (Alouatta palliata), based on mitochondrial DNA sequences and microsatellite loci (these only for the host). Given that pinworms and primates have a close co-evolutionary history, covariation in several genetic aspects of their populations is expected. RESULTS Mitochondrial DNA revealed two genetic clusters (West and East) in both pinworm species and howler monkeys, although population structure and genetic differentiation were stronger in the host, while genetic diversity was higher in pinworms than howler populations. Co-divergence tests showed no congruence between host and parasite phylogenies; nonetheless, a significant correlation was found between both pinworms and A. palliata genetic pairwise distances suggesting that the parasites' gene flow is mediated by the host dispersal. Moreover, the parasite most infective and the host most susceptible haplotypes were also the most frequent, whereas the less divergent haplotypes tended to be either more infective (for pinworms) or more susceptible (for howlers). Finally, a positive correlation was found between pairwise p-distance of host haplotypes and that of their associated pinworm haplotypes. CONCLUSION The genetic configuration of pinworm populations appears to be molded by their own demography and life history traits in conjunction with the biology and evolutionary history of their hosts, including host genetic variation, social interactions, dispersal and biogeography. Similarity in patterns of genetic structure, differentiation and diversity is higher between howler monkeys and T. multilabiatus in comparison with T. minutus, highlighting the role of host-specificity in coevolving processes. Trypanoxyuris minutus exhibits genetic specificity towards the most frequent host haplotype as well as geographic specificity. Results suggest signals of potential local adaptation in pinworms and further support the notion of correlated evolution between pinworms and their primate hosts.
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Affiliation(s)
- Brenda Solórzano-García
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Departamento de Sistemas y Procesos Naturales, Escuela Nacional de Estudios Superiores - Merida, Universidad Nacional Autónoma de México, Yucatán, Mexico
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| | - Gerardo Pérez-Ponce de León
- Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Departamento de Sistemas y Procesos Naturales, Escuela Nacional de Estudios Superiores - Merida, Universidad Nacional Autónoma de México, Yucatán, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
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Varela AA, Cheng S, Werren JH. Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations. PeerJ 2021; 9:e12159. [PMID: 34616619 PMCID: PMC8449537 DOI: 10.7717/peerj.12159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the cell receptor that the coronavirus SARS-CoV-2 binds to and uses to enter and infect human cells. COVID-19, the pandemic disease caused by the coronavirus, involves diverse pathologies beyond those of a respiratory disease, including micro-thrombosis (micro-clotting), cytokine storms, and inflammatory responses affecting many organ systems. Longer-term chronic illness can persist for many months, often well after the pathogen is no longer detected. A better understanding of the proteins that ACE2 interacts with can reveal information relevant to these disease manifestations and possible avenues for treatment. We have undertaken an approach to predict candidate ACE2 interacting proteins which uses evolutionary inference to identify a set of mammalian proteins that “coevolve” with ACE2. The approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. Such proteins are candidates for biological interactions with the ACE2 receptor. The approach has uncovered a number of key ACE2 protein interactions of potential relevance to COVID-19 pathologies. Some proteins have previously been reported to be associated with severe COVID-19, but are not currently known to interact with ACE2, while additional predicted novel ACE2 interactors are of potential relevance to the disease. Using reciprocal rankings of protein ERCs, we have identified strongly interconnected ACE2 associated protein networks relevant to COVID-19 pathologies. ACE2 has clear connections to coagulation pathway proteins, such as Coagulation Factor V and fibrinogen components FGA, FGB, and FGG, the latter possibly mediated through ACE2 connections to Clusterin (which clears misfolded extracellular proteins) and GPR141 (whose functions are relatively unknown). ACE2 also connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR). The ERC prescreening approach has elucidated possible functions for relatively uncharacterized proteins and possible new functions for well-characterized ones. Suggestions are made for the validation of ERC-predicted ACE2 protein interactions. We propose that ACE2 has novel protein interactions that are disrupted during SARS-CoV-2 infection, contributing to the spectrum of COVID-19 pathologies.
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Affiliation(s)
- Austin A Varela
- Department of Biology, University of Rochester, Rochester, New York, United States
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, New York, United States
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, New York, United States
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Gile GH, Taerum SJ, Jasso-Selles DE, Sillam-Dussès D, Ohkuma M, Kitade O, Noda S. Molecular Phylogenetic Position of Microjoenia (Parabasalia: Spirotrichonymphea) from Reticulitermes and Hodotermopsis Termite Hosts. Protist 2021; 172:125836. [PMID: 34757297 DOI: 10.1016/j.protis.2021.125836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
Microjoenia are obligate symbionts of termites. The genus was erected in 1892 for small cells with many flagella that insert near, but not directly from, the cell apex, and an axostyle that can protrude from the cell posterior. Although ultrastructural studies have been carried out on three Microjoenia species to date, no molecular data have been directly attributed to any species. Microjoenia are classified within the parabasalian class Spirotrichonymphea, which is characterized by flagellar bands that emerge near the cell apex and proceed posteriorly in a right-handed helix. In Microjoenia, however, the flagellar bands are very short and proceed longitudinally or with a weakly observable helix. In this study, we have amplified and sequenced the 18S ribosomal RNA gene from individually isolated Microjoenia cells from Reticulitermes and Hodotermopsis hosts as part of an ongoing effort to understand the phylogeny of Spirotrichonymphea and their coevolution with termites. In our 18S rRNA gene phylogeny, Microjoenia forms the sister lineage to Spirotrichonympha, though many other evolutionary relationships within Spirotrichonymphea remain unresolved.
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Affiliation(s)
- Gillian H Gile
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA.
| | - Stephen J Taerum
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Daniel E Jasso-Selles
- School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC) UR4443, University Sorbonne Paris Nord, Villetaneuse, France
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki 305-0074, Japan
| | - Osamu Kitade
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Satoko Noda
- Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
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Wangchuk J, Chatterjee A, Patil S, Madugula SK, Kondabagil K. The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization. Virology 2021; 564:13-25. [PMID: 34598064 DOI: 10.1016/j.virol.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Genome packaging in many dsDNA phages requires a series of precisely coordinated actions of two phage-coded proteins, namely, large terminase (TerL) and small terminase (TerS) with DNA and ATP, and with each other. Despite the strict functional conservation, TerL and TerS homologs exhibit large sequence variations. We investigated the sequence variability across eight phage types and observed a coevolutionary framework wherein the genealogy of TerL homologs mirrored that of the corresponding TerS homologs. Furthermore, a high purifying selection observed (dN/dS«1) indicated strong structural constraints on both TerL and TerS, and identify coevolving residues in TerL and TerS of phage T4 and lambda. Using the highly coevolving (correlation coefficient of 0.99) TerL and TerS of phage N4, we show that their biochemical features are similar to the phylogenetically divergent phage λ terminases. We also demonstrate using the Surface Plasma Resonance (SPR) technique that phage N4 TerL transiently interacts with TerS.
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Affiliation(s)
- Jigme Wangchuk
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Supriya Patil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Santhosh Kumar Madugula
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Kamimura Y, Yoshizawa K, Lienhard C, Ferreira RL, Abe J. Evolution of nuptial gifts and its coevolutionary dynamics with male-like persistence traits of females for multiple mating. BMC Ecol Evol 2021; 21:164. [PMID: 34482815 PMCID: PMC8419916 DOI: 10.1186/s12862-021-01901-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many male animals donate nutritive materials during courtship or mating to their female mates. Donation of large-sized gifts, though costly to prepare, can result in increased sperm transfer during mating and delayed remating of the females, resulting in higher paternity. Nuptial gifting sometimes causes severe female-female competition for obtaining gifts (i.e., sex-role reversal in mate competition) and selection on females to increase their mating rate, changing the intensity of sperm competition and the resultant paternity gains. We built a theoretical model to simulate such coevolutionary feedbacks between nuptial gift size (male trait) and propensity for multiple mating (female trait). Donation of nuptial gifts sometimes causes development of female persistence trait for gift acquisition. We also analyzed the causes and consequences of this type of traits, taking double receptacles for nutritious seminal gifts, which are known to occur in an insect group with a "female penis" (Neotrogla spp.), as an illustrative example. RESULTS Our individual-based simulations demonstrated that female-female competition for male-derived nutrients always occur when the environment is oligotrophic and mating costs are low for females. However, a positive correlation between donated gift size and the resultant paternity gain was a requisite for the co-occurrence of large gifts and females' competitive multiple mating for the gifts. When gift donation satisfied female demands and thus resulted in monandry, exaggeration of nuptial gift size also occurred under the assumption that the last male monopolizes paternity. The evolution of double slots for gift acquisition and digestion (female persistence trait) always occurred when males could not satisfy the demands of females for gifts. However, through coevolutionary reduction in male gift size, fixation of this trait in a population drastically reduced the average female fitness. CONCLUSION Sperm usage patterns, which have rarely been examined for animals with nuptial gifts, can be a critical factor for determining the extent of exaggeration in nuptial gifting. Sex-role reversals in mate competition, as a result of donation of nuptial gifts from males to females, can involve the evolution of male-like, persistent traits in females that reduce population productivity, as is the case with persistence traits in males.
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Affiliation(s)
| | - Kazunori Yoshizawa
- Systematic Entomology, School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Charles Lienhard
- Geneva Natural History Museum, CP 6434, 1211, Geneva 6, Switzerland
| | - Rodrigo L Ferreira
- Biology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Jun Abe
- Faculty of Liberal Arts, Meijigakuin University, Yokohama, Japan
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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and “farmed” organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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Teulière J, Bernard C, Bapteste E. Interspecific interactions that affect ageing: Age-distorters manipulate host ageing to their own evolutionary benefits. Ageing Res Rev 2021; 70:101375. [PMID: 34082078 DOI: 10.1016/j.arr.2021.101375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023]
Abstract
Genetic causes for ageing are traditionally investigated within a species. Yet, the lifecycles of many organisms intersect. Additional evolutionary and genetic causes of ageing, external to a focal species/organism, may thus be overlooked. Here, we introduce the phrase and concept of age-distorters and its evidence. Age-distorters carry ageing interfering genes, used to manipulate the biological age of other entities upon which the reproduction of age-distorters relies, e.g. age-distorters bias the reproduction/maintenance trade-offs of cells/organisms for their own evolutionary interests. Candidate age-distorters include viruses, parasites and symbionts, operating through specific, genetically encoded interferences resulting from co-evolution and arms race between manipulative non-kins and manipulable species. This interference results in organismal ageing when age-distorters prompt manipulated organisms to favor their reproduction at the expense of their maintenance, turning these hosts into expanded disposable soma. By relying on reproduction/maintenance trade-offs affecting disposable entities, which are left ageing to the reproductive benefit of other physically connected lineages with conflicting evolutionary interests, the concept of age-distorters expands the logic of the Disposable Soma theory beyond species with fixed germen/soma distinctions. Moreover, acknowledging age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of the mutation accumulation and of the antagonistic pleiotropy theories.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
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Johnson KP, Weckstein JD, Virrueta Herrera S, Doña J. The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus. Mol Phylogenet Evol 2021; 165:107297. [PMID: 34438049 DOI: 10.1016/j.ympev.2021.107297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022]
Abstract
Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University and Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, USA
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, IL, USA
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Departamento de Biología Animal, Universidad de Granada, Granada, Spain.
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Poulin R. The rise of ecological parasitology: twelve landmark advances that changed its history. Int J Parasitol 2021:S0020-7519(21)00238-1. [PMID: 34390744 DOI: 10.1016/j.ijpara.2021.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
Abstract
In the five decades since the first publication of the International Journal for Parasitology, ecological parasitology has grown from modest beginnings to become a modern discipline with a strong theoretical foundation, a diverse toolkit, and a multidisciplinary approach. In this review, I highlight 12 advances in the field that have spurred its growth over the past 50 years. Where relevant, I identify pivotal contributions that have altered the course of research, as well as the influence of developments in other fields such as mainstream ecology and molecular biology. The 12 key advances discussed are in areas including parasite population dynamics and community assembly, the regulation of host population abundance and food web structure, parasites as agents of natural selection, the impacts of biodiversity and anthropogenic changes on host-parasite interactions, the biogeography of parasite diversity, and the evolutionary genetics of parasites. I conclude by identifying some challenges and opportunities lying ahead, which need to be met for the future growth of ecological research on host-parasite interactions.
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Wicaksono WA, Cernava T, Berg C, Berg G. Bog ecosystems as a playground for plant-microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria. Microbiome 2021; 9:170. [PMID: 34380552 PMCID: PMC8359052 DOI: 10.1186/s40168-021-01117-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/21/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology and plant-microbe co-occurrence in bogs, we selected 12 representative species of bryophytes and vascular plants and subjected them to a shotgun metagenomic sequencing approach. We explored specific plant-microbe associations as well as functional implications of the respective communities on their host plants and the bog ecosystem. RESULTS Microbial communities were shown to be functionally adapted to their plant hosts; a higher colonization specificity was found for vascular plants. Bryophytes that commonly constitute the predominant Sphagnum layer in bogs were characterized by a higher bacterial richness and diversity. Each plant group showed an enrichment of distinct phylogenetic and functional bacterial lineages. Detailed analyses of the metabolic potential of 28 metagenome-assembled genomes (MAGs) supported the observed functional specification of prevalent bacteria. We found that novel lineages of Betaproteobacteria and Actinobacteria in the bog environment harboured genes required for carbon fixation via RuBisCo. Interestingly, several of the highly abundant bacteria in both plant types harboured pathogenicity potential and carried similar virulence factors as found with corresponding human pathogens. CONCLUSIONS The unexpectedly high specificity of the plant microbiota reflects intimate plant-microbe interactions and coevolution in bog environments. We assume that the detected pathogenicity factors might be involved in coevolution processes, but the finding also reinforces the role of the natural plant microbiota as a potential reservoir for human pathogens. Overall, the study demonstrates how plant-microbe assemblages can ensure stability, functioning and ecosystem health in bogs. It also highlights the role of bog ecosystems as a playground for plant-microbe coevolution. Video abstract.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Christian Berg
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, Postdam, Germany
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Liang J, Zhu C, Zhang L. Cospeciation of coronavirus and paramyxovirus with their bat hosts in the same geographical areas. BMC Ecol Evol 2021; 21:148. [PMID: 34325659 PMCID: PMC8319908 DOI: 10.1186/s12862-021-01878-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Bat-borne viruses are relatively host specific. We hypothesize that this host specificity is due to coevolution of the viruses with their hosts. To test this hypothesis, we investigated the coevolution of coronavirus and paramyxovirus with their bat hosts. Published nucleotide sequences of the RNA-dependent RNA polymerase (RdRp) gene of 60 coronavirus strains identified from 37 bat species, the RNA polymerase large (L) gene of 36 paramyxovirus strains from 29 bat species, and the cytochrome B (cytB) gene of 35 bat species were analyzed for coevolution signals. Each coevolution signal detected was tested and verified by global-fit cophylogenic analysis using software ParaFit, PACo, and eMPRess. Results Significant coevolution signals were detected in coronaviruses and paramyxoviruses and their bat hosts, and closely related bat hosts were found to carry closely related viruses. Conclusions Our results suggest that paramyxovirus and coronavirus coevolve with their hosts.
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Affiliation(s)
- Jie Liang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Chunchao Zhu
- Zunyi Medical University, Zhuhai Campus, Zhuhai, 519041, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China.
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