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Saulsbury JG, Parins-Fukuchi CT, Wilson CJ, Reitan T, Liow LH. Age-dependent extinction and the neutral theory of biodiversity. Proc Natl Acad Sci U S A 2024; 121:e2307629121. [PMID: 38150497 PMCID: PMC10769858 DOI: 10.1073/pnas.2307629121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023] Open
Abstract
Red Queen (RQ) theory states that adaptation does not protect species from extinction because their competitors are continually adapting alongside them. RQ was founded on the apparent independence of extinction risk and fossil taxon age, but analytical developments have since demonstrated that age-dependent extinction is widespread, usually most intense among young species. Here, we develop ecological neutral theory as a general framework for modeling fossil species survivorship under incomplete sampling. We show that it provides an excellent fit to a high-resolution dataset of species durations for Paleozoic zooplankton and more broadly can account for age-dependent extinction seen throughout the fossil record. Unlike widely used alternative models, the neutral model has parameters with biological meaning, thereby generating testable hypotheses on changes in ancient ecosystems. The success of this approach suggests reinterpretations of mass extinctions and of scaling in eco-evolutionary systems. Intense extinction among young species does not necessarily refute RQ or require a special explanation but can instead be parsimoniously explained by neutral dynamics operating across species regardless of age.
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Affiliation(s)
- James G. Saulsbury
- Natural History Museum, University of Oslo, Oslo0187, Norway
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS66045
| | - C. Tomomi Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 3B2, Canada
| | - Connor J. Wilson
- Natural History Museum, University of Oslo, Oslo0187, Norway
- School of Geography and the Environment, University of Oxford, OxfordOX1 3QY, United Kingdom
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ85721
| | - Trond Reitan
- Natural History Museum, University of Oslo, Oslo0187, Norway
- Center for Planetary Habitability, Department of Geosciences, University of Oslo, Oslo0371, Norway
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo0187, Norway
- Center for Planetary Habitability, Department of Geosciences, University of Oslo, Oslo0371, Norway
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2
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Debray R, De Luna N, Koskella B. Historical contingency drives compensatory evolution and rare reversal of phage resistance. Mol Biol Evol 2022; 39:6673247. [PMID: 35994371 PMCID: PMC9447851 DOI: 10.1093/molbev/msac182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
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Affiliation(s)
- Reena Debray
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nina De Luna
- Department of Immunology, Pennsylvania State University, State College, PA, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg BioHub, San Francisco, CA, USA
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3
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Gregor Johann Mendel and the development of modern evolutionary biology. Proc Natl Acad Sci U S A 2022; 119:e2201327119. [PMID: 35858454 PMCID: PMC9335310 DOI: 10.1073/pnas.2201327119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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4
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Polymicrobial infections can select against Pseudomonas aeruginosa mutators because of quorum-sensing trade-offs. Nat Ecol Evol 2022; 6:979-988. [PMID: 35618819 DOI: 10.1038/s41559-022-01768-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022]
Abstract
Bacteria with increased mutation rates (mutators) are common in chronic infections and are associated with poorer clinical outcomes, especially in the case of Pseudomonas aeruginosa infecting cystic fibrosis (CF) patients. There is, however, considerable between-patient variation in both P. aeruginosa mutator frequency and the composition of co-infecting pathogen communities. We investigated whether community context might affect selection of mutators. Using an in vitro CF model community, we show that P. aeruginosa mutators were favoured in the absence of other species but not in their presence. This was because there were trade-offs between adaptation to the biotic and abiotic environments (for example, loss of quorum sensing and associated toxin production was beneficial in the latter but not the former in our in vitro model community) limiting the evolvability advantage of an elevated mutation rate. Consistent with a role of co-infecting pathogens selecting against P. aeruginosa mutators in vivo, we show that the mutation frequency of P. aeruginosa population was negatively correlated with the frequency and diversity of co-infecting bacteria in CF infections. Our results suggest that co-infecting taxa can select against P. aeruginosa mutators, which may have potentially beneficial clinical consequences.
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5
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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6
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Engen S, Grøtan V, Sæther BE, Coste CFD. An Evolutionary and Ecological Community Model for Distribution of Phenotypes and Abundances among Competing Species. Am Nat 2021; 198:13-32. [PMID: 34143723 DOI: 10.1086/714529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractHere, we propose a theory for the structure of communities of competing species. We include ecologically realistic assumptions, such as density dependence and stochastic fluctuations in the environment, and analyze how evolution caused by r- and K-selection will affect the packing of species in the phenotypic space as well as the species abundance distribution. Species-specific traits have the same matrix G of additive genetic variances and covariances, and evolution of mean traits is affected by fluctuations in population size of all species. In general, the model produces a shape of the distributions of log abundances that is skewed to the left, which is typical of most natural communities. Mean phenotypes of the species in the community are distributed approximately uniformly on the surface of a multidimensional sphere. However, environmental stochasticity generates selection that deviates species slightly from this surface; nonetheless, phenotypic distribution will be different from a random packing of species. This model of community evolution provides a theoretical framework that predicts a relationship between the structure of the phenotypic space and the form of species abundance distributions that can be compared against time series of variation in community structure.
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7
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Searle CL, Christie MR. Evolutionary rescue in host-pathogen systems. Evolution 2021; 75:2948-2958. [PMID: 34018610 DOI: 10.1111/evo.14269] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022]
Abstract
Natural populations encounter a variety of threats that can increase their risk of extinction. Populations can avoid extinction through evolutionary rescue (ER), which occurs when an adaptive, genetic response to selection allows a population to recover from an environmental change that would otherwise cause extinction. While the traditional framework for ER was developed with abiotic risk factors in mind, ER may also occur in response to a biotic source of demographic change, such as the introduction of a novel pathogen. We first describe how ER in response to a pathogen differs from the traditional ER framework; density-dependent transmission, pathogen evolution, and pathogen extinction can change the strength of selection imposed by a pathogen and make host population persistence more likely. We also discuss several variables that affect traditional ER (abundance, genetic diversity, population connectivity, and community composition) that also directly affect disease risk resulting in diverse outcomes for ER in host-pathogen systems. Thus, generalizations developed in studies of traditional ER may not be relevant for ER in response to the introduction of a pathogen. Incorporating pathogens into the framework of ER will lead to a better understanding of how and when populations can avoid extinction in response to novel pathogens.
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Affiliation(s)
- Catherine L Searle
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, 47907
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8
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Castledine M, Padfield D, Buckling A. Experimental (co)evolution in a multi-species microbial community results in local maladaptation. Ecol Lett 2020; 23:1673-1681. [PMID: 32893477 DOI: 10.1111/ele.13599] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/19/2020] [Accepted: 08/13/2020] [Indexed: 01/01/2023]
Abstract
Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species' populations to (1) the presence of the other four species in general and (2) sympatric vs. allopatric communities. We found that species did not show an increase in net biotic adaptation:ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates within communities. However, 4/5 species' growth rates were significantly lower within the community they evolved in relative to an allopatric community. 'Local maladaptation' suggests that species evolved increased competitive interactions to sympatric species' populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.
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Affiliation(s)
- Meaghan Castledine
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Daniel Padfield
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Angus Buckling
- College of Life and Environmental Sciences, Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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9
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Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, Faust K, Knight R, Jansson JK, Cardona C, Röttjers L, Xu J. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. MICROBIOME 2020; 8:82. [PMID: 32498714 PMCID: PMC7273686 DOI: 10.1186/s40168-020-00857-2] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. RESULTS This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.
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Affiliation(s)
- Bin Ma
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Yiling Wang
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Shudi Ye
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Shan Liu
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Erinne Stirling
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, and BioEngineering, University of California San Diego, La Jolla, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, 99352, WA, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, 60637, IL, USA
| | - Lisa Röttjers
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Jianming Xu
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
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10
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Luo TT, Zhu JL, Reitan T, Yedid G. Alteration of (Frequency-Dependent) Fitness in Time-Shift Experiments Reveals Cryptic Coevolution and Uncoordinated Stasis in a Virtual Jurassic Park. ARTIFICIAL LIFE 2020; 26:196-216. [PMID: 32271633 DOI: 10.1162/artl_a_00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Among the major unresolved questions in ecosystem evolution are whether coevolving multispecies communities are dominated more by biotic or by abiotic factors, and whether evolutionary stasis affects performance as well as ecological profile; these issues remain difficult to address experimentally. Digital evolution, a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve, is an excellent platform for investigating such topics in a rigorous experimental manner. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths (Strong and Weak), along with unperturbed Control experiments. We performed several kinds of competition experiments using simplified versions of these communities to see whether long-term stability that was implied previously by ecological and phylogenetic metrics was also reflected in performance, namely, whether fitness was static over long periods of time. Results from Control and Weak treatment communities revealed almost completely transitive evolution, while Strong treatment communities showed higher incidences of temporal intransitivity, with pre-treatment ecotypes often able to displace some of their post-recovery successors. However, pre-treatment carryovers more often had lower fitness in mixed communities than in their own fully native conditions. Replacement and invasion experiments pitting single ecotypes against pre-treatment reference communities showed that many of the invading ecotypes could measurably alter the fitnesses of one or more residents, usually with depressive effects, and that the strength of these effects increased over time even in the most stable communities. However, invaders taken from Strong treatment communities often had little or no effect on resident performance. While we detected periods of time when the fitness of a particular evolving ecotype remained static, this stasis was not permanent and never affected an entire community at once. Our results lend support to the fitness-deterioration interpretation of the Red Queen hypothesis, and highlight community context dependence in determining fitness, the shaping of communities by both biotic factors and abiotic forcing, and the illusory nature of evolutionary stasis. Our results also demonstrate the potential of digital evolution studies to illuminate many aspects of evolution in interacting multispecies communities.
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Affiliation(s)
- Tian-Tong Luo
- Nanjing Agricultural University, Department of Zoology, College of Life Sciences
| | - Jian-Long Zhu
- Nanjing Agricultural University, Department of Zoology, College of Life Sciences
| | - Trond Reitan
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biology.
| | - Gabriel Yedid
- Nanjing Agricultural University, Department of Zoology, College of Life Sciences.
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11
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Abstract
Continual evolution describes the unceasing evolution of at least one trait involving at least one organism. The Red Queen Hypothesis is a specific case in which continual evolution results from coevolution of at least two species. While microevolutionary studies have described examples in which evolution does not cease, understanding which general conditions lead to continual evolution or to stasis remains a major challenge. In many cases, it is unclear which experimental features or model assumptions are necessary for the observed continual evolution to emerge, and whether the described behavior is robust to variations in the given setup. Here, we aim to find the minimal set of conditions under which continual evolution occurs. To this end, we present a theoretical framework that does not assume any specific functional form and, therefore, can be applied to a wide variety of systems. Our framework is also general enough to make predictions about both monomorphic and polymorphic populations. We show that the combination of a fast positive and a slow negative feedback between environment, population, and evolving traits causes continual evolution to emerge even from the evolution of a single evolving trait, provided that the ecological timescale is sufficiently faster than the timescales of mutation and the negative feedback. Our approach and results thus contribute to a deeper understanding of the evolutionary dynamics resulting from biotic interactions.
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12
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Abstract
How biodiversity is maintained in ecosystems is a central issue in ecology. According to the evolutionary theory, heritable variations between individuals are important for the generation of species diversity, linking both intra and interspecific variations. The present food web model shows that intraspecific variations via natural selection also play crucial roles in maintaining the stability of large communities with diverse species. In particular, our computations indicate that larger communities need more intraspecific variation to be maintained and are powerfully stabilized when multiple traits are variable. Consequently, these variations are likely to be maintained in larger communities. Hence, intra and interspecific diversities may support each other during evolution.
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Affiliation(s)
- Akihiko Mougi
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
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13
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Snyder BF. The genetic and cultural evolution of unsustainability. SUSTAINABILITY SCIENCE 2020; 15:1087-1099. [PMID: 32292525 PMCID: PMC7133775 DOI: 10.1007/s11625-020-00803-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 03/25/2020] [Indexed: 05/11/2023]
Abstract
Anthropogenic changes are accelerating and threaten the future of life on earth. While the proximate mechanisms of these anthropogenic changes are well studied (e.g., climate change, biodiversity loss, population growth), the evolutionary causality of these anthropogenic changes have been largely ignored. Anthroecological theory (AET) proposes that the ultimate cause of anthropogenic environmental change is multi-level selection for niche construction and ecosystem engineering. Here, we integrate this theory with Lotka's Maximum Power Principle and propose a model linking energy extraction from the environment with genetic, technological and cultural evolution to increase human ecosystem carrying capacity. Carrying capacity is partially determined by energetic factors such as the net energy a population can acquire from its environment and the efficiency of conversion from energy input to offspring output. These factors are under Darwinian genetic selection in all species, but in humans, they are also determined by technology and culture. If there is genetic or non-genetic heritable variation in the ability of an individual or social group to increase its carrying capacity, then we hypothesize that selection or cultural evolution will act to increase carrying capacity. Furthermore, if this evolution of carrying capacity occurs faster than the biotic components of the ecological system can respond via their own evolution, then we hypothesize that unsustainable ecological changes will result.
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Affiliation(s)
- Brian F. Snyder
- Department of Environmental Science, Louisiana State University, Baton Rouge, USA
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14
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Dyachkova MS, Chekalin EV, Danilenko VN. Positive Selection in Bifidobacterium Genes Drives Species-Specific Host-Bacteria Communication. Front Microbiol 2019; 10:2374. [PMID: 31681231 PMCID: PMC6803598 DOI: 10.3389/fmicb.2019.02374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022] Open
Abstract
Bifidobacteria are commensal microorganisms that inhabit a wide range of hosts, including insects, birds and mammals. The mechanisms responsible for the adaptation of bifidobacteria to various hosts during the evolutionary process remain poorly understood. Previously, we reported that the species-specific PFNA gene cluster is present in the genomes of various species of the Bifidobacterium genus. The cluster contains signal transduction and adhesion genes that are presumably involved in the communication between bifidobacteria and their hosts. The genes in the PFNA cluster show high sequence divergence between bifidobacterial species, which may be indicative of rapid evolution that drives species-specific adaptation to the host organism. We used the maximum likelihood approach to detect positive selection in the PFNA genes. We tested for both pervasive and episodic positive selection to identify codons that experienced adaptive evolution in all and individual branches of the Bifidobacterium phylogenetic tree, respectively. Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial species. Moreover, we found the signatures of pervasive positive selection in the molecular evolution of the tgm gene in all branches of the Bifidobacterium phylogenetic tree. These results are consistent with the suggested role of PFNA gene cluster in the process of specific adaptation of bifidobacterial species to various hosts.
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Affiliation(s)
- Marina S Dyachkova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny V Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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15
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Horgan FG, Srinivasan TS, Crisol‐Martínez E, Almazan MLP, Ramal AF, Oliva R, Quibod IL, Bernal CC. Microbiome responses during virulence adaptation by a phloem-feeding insect to resistant near-isogenic rice lines. Ecol Evol 2019; 9:11911-11929. [PMID: 31695897 PMCID: PMC6822046 DOI: 10.1002/ece3.5699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 08/09/2019] [Accepted: 09/03/2019] [Indexed: 01/21/2023] Open
Abstract
The microbiomes of phloem-feeding insects include functional bacteria and yeasts essential for herbivore survival and development. Changes in microbiome composition are implicated in virulence adaptation by herbivores to host plant species or host populations (including crop varieties). We examined patterns in adaptation by the green leafhopper, Nephotettix virescens, to near-isogenic rice lines (NILs) with one or two resistance genes and the recurrent parent T65, without resistance genes. Only the line with two resistance genes was effective in reducing leafhopper fitness. After 20 generations on the resistant line, selected leafhoppers attained similar survival, weight gain, and egg laying to leafhoppers that were continually reared on the susceptible recurrent parent, indicating that they had adapted to the resistant host. By sequencing the 16s rRNA gene, we described the microbiome of leafhoppers from colonies associated with five collection sites, and continually reared or switched between NILs. The microbiomes included 69-119 OTUs of which 44 occurred in ≥90% of samples. Of these, 14 OTUs were assigned to the obligate symbiont Candidatus sulcia clade. After 20 generations of selection, collection site had a greater effect than host plant on microbiome composition. Six bacteria genera, including C. sulcia, were associated with leafhopper virulence. However, there was significant within-treatment, site-related variability in the prevalence of these taxa such that the mechanisms underlying their association with virulence remain to be determined. Our results imply that these taxa are associated with leafhopper nutrition. Ours is the first study to describe microbiome diversity and composition in rice leafhoppers. We discuss our results in light of the multiple functions of herbivore microbiomes during virulence adaptation in insect herbivores.
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Affiliation(s)
- Finbarr G. Horgan
- EcoLaVerna Integral Restoration EcologyKildinanIreland
- University of Technology SydneySydneyNSWAustralia
| | - Thanga Suja Srinivasan
- Centre for Plant Molecular Biology and BiotechnologyTamil Nadu Agricultural UniversityCoimbatoreIndia
- International Rice Research InstituteMetro ManilaPhilippines
- Centre for Climate Change StudiesSathyabama Institute of Science and TechnologyChennaiIndia
| | - Eduardo Crisol‐Martínez
- EcoLaVerna Integral Restoration EcologyKildinanIreland
- COEXPHAL (Association of Vegetable and Fruit Growers of Almeria)AlmeriaSpain
| | | | - Angelee Fame Ramal
- School of Environmental Science and ManagementUniversity of the PhilippinesLos BañosPhilippines
| | - Ricardo Oliva
- International Rice Research InstituteMetro ManilaPhilippines
| | - Ian L. Quibod
- International Rice Research InstituteMetro ManilaPhilippines
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16
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Nair RR, Vasse M, Wielgoss S, Sun L, Yu YTN, Velicer GJ. Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences. Nat Commun 2019; 10:4301. [PMID: 31541093 PMCID: PMC6754418 DOI: 10.1038/s41467-019-12140-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/22/2019] [Indexed: 01/08/2023] Open
Abstract
Generalist bacterial predators are likely to strongly shape many important ecological and evolutionary features of microbial communities, for example by altering the character and pace of molecular evolution, but investigations of such effects are scarce. Here we report how predator-prey interactions alter the evolution of fitness, genomes and phenotypic diversity in coevolving bacterial communities composed of Myxococcus xanthus as predator and Escherichia coli as prey, relative to single-species controls. We show evidence of reciprocal adaptation and demonstrate accelerated genomic evolution specific to coevolving communities, including the rapid appearance of mutator genotypes. Strong parallel evolution unique to the predator-prey communities occurs in both parties, with predators driving adaptation at two prey traits associated with virulence in bacterial pathogens-mucoidy and the outer-membrane protease OmpT. Our results suggest that generalist predatory bacteria are important determinants of how complex microbial communities and their interaction networks evolve in natural habitats.
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Affiliation(s)
- Ramith R Nair
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland.
| | - Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland.
| | - Sébastien Wielgoss
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
| | - Lei Sun
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
- Department of Systems Biology, Harvard Medical School, 02115, Boston, MA, USA
| | - Yuen-Tsu N Yu
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
| | - Gregory J Velicer
- Institute for Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
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17
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Strotz LC, Simões M, Girard MG, Breitkreuz L, Kimmig J, Lieberman BS. Getting somewhere with the Red Queen: chasing a biologically modern definition of the hypothesis. Biol Lett 2019; 14:rsbl.2017.0734. [PMID: 29720444 DOI: 10.1098/rsbl.2017.0734] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/13/2018] [Indexed: 01/24/2023] Open
Abstract
The Red Queen hypothesis (RQH) is both familiar and murky, with a scope and range that has broadened beyond its original focus. Although originally developed in the palaeontological arena, it now encompasses many evolutionary theories that champion biotic interactions as significant mechanisms for evolutionary change. As such it de-emphasizes the important role of abiotic drivers in evolution, even though such a role is frequently posited to be pivotal. Concomitant with this shift in focus, several studies challenged the validity of the RQH and downplayed its propriety. Herein, we examine in detail the assumptions that underpin the RQH in the hopes of furthering conceptual understanding and promoting appropriate application of the hypothesis. We identify issues and inconsistencies with the assumptions of the RQH, and propose a redefinition where the Red Queen's reign is restricted to certain types of biotic interactions and evolutionary patterns occurring at the population level.
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Affiliation(s)
- Luke C Strotz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA .,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Marianna Simões
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew G Girard
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Laura Breitkreuz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Julien Kimmig
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Bruce S Lieberman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
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18
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Edwards KF, Kremer CT, Miller ET, Osmond MM, Litchman E, Klausmeier CA. Evolutionarily stable communities: a framework for understanding the role of trait evolution in the maintenance of diversity. Ecol Lett 2018; 21:1853-1868. [PMID: 30272831 DOI: 10.1111/ele.13142] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/16/2018] [Accepted: 07/23/2018] [Indexed: 01/15/2023]
Abstract
Biological diversity depends on the interplay between evolutionary diversification and ecological mechanisms allowing species to coexist. Current research increasingly integrates ecology and evolution over a range of timescales, but our common conceptual framework for understanding species coexistence requires better incorporation of evolutionary processes. Here, we focus on the idea of evolutionarily stable communities (ESCs), which are theoretical endpoints of evolution in a community context. We use ESCs as a unifying framework to highlight some important but under-appreciated theoretical results, and we review empirical research relevant to these theoretical predictions. We explain how, in addition to generating diversity, evolution can also limit diversity by reducing the effectiveness of coexistence mechanisms. The coevolving traits of competing species may either diverge or converge, depending on whether the number of species in the community is low (undersaturated) or high (oversaturated) relative to the ESC. Competition in oversaturated communities can lead to extinction or neutrally coexisting, ecologically equivalent species. It is critical to consider trait evolution when investigating fundamental ecological questions like the strength of different coexistence mechanisms, the feasibility of ecologically equivalent species, and the interpretation of different patterns of trait dispersion.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Colin T Kremer
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.,Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Elizabeth T Miller
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Matthew M Osmond
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, USA
| | - Elena Litchman
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA.,Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Christopher A Klausmeier
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA.,Program in Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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19
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Kopp M, Nassar E, Pardoux E. Phenotypic lag and population extinction in the moving-optimum model: insights from a small-jumps limit. J Math Biol 2018; 77:1431-1458. [PMID: 29980824 DOI: 10.1007/s00285-018-1258-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/22/2018] [Indexed: 11/24/2022]
Abstract
Continuous environmental change-such as slowly rising temperatures-may create permanent maladaptation of natural populations: Even if a population adapts evolutionarily, its mean phenotype will usually lag behind the phenotype favored in the current environment, and if the resulting phenotypic lag becomes too large, the population risks extinction. We analyze this scenario using a moving-optimum model, in which one or more quantitative traits are under stabilizing selection towards an optimal value that increases at a constant rate. We have recently shown that, in the limit of infinitely small mutations and high mutation rate, the evolution of the phenotypic lag converges to an Ornstein-Uhlenbeck process around a long-term equilibrium value. Both the mean and the variance of this equilibrium lag have simple analytical formulas. Here, we study the properties of this limit and compare it to simulations of an evolving population with finite mutational effects. We find that the "small-jumps limit" provides a reasonable approximation, provided the mean lag is so large that the optimum cannot be reached by a single mutation. This is the case for fast environmental change and/or weak selection. Our analysis also provides insights into population extinction: Even if the mean lag is small enough to allow a positive growth rate, stochastic fluctuations of the lag will eventually cause extinction. We show that the time until this event follows an exponential distribution, whose mean depends strongly on a composite parameter that relates the speed of environmental change to the adaptive potential of the population.
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Affiliation(s)
- Michael Kopp
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, 3 Place Victor Hugo, 13331, Marseille Cedex 3, France.
| | - Elma Nassar
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, 3 Place Victor Hugo, 13331, Marseille Cedex 3, France.,Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran Beirut, 1102 2801, Lebanon
| | - Etienne Pardoux
- Aix Marseille Université, CNRS, Centrale Marseille, I2M, 3 Place Victor Hugo, 13331, Marseille Cedex 3, France
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20
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Is evolution always “egolution” : Discussion of evolutionary efficiency of altruistic energy exchange. ECOLOGICAL COMPLEXITY 2018. [DOI: 10.1016/j.ecocom.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics 2018; 208:1585-1599. [PMID: 29437826 PMCID: PMC5887150 DOI: 10.1534/genetics.117.300567] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races.
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22
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Bonachela JA, Wortel MT, Stenseth NC. Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system. Sci Rep 2017; 7:17655. [PMID: 29247226 PMCID: PMC5732168 DOI: 10.1038/s41598-017-17774-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/29/2017] [Indexed: 01/18/2023] Open
Abstract
The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.
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Affiliation(s)
- Juan A Bonachela
- Marine Population Modeling Group, Department of Mathematics and Statistics, University of Strathclyde, Glasgow, G1 1XH, Scotland, UK.
- Department of Ecology, Evolution, and Natural Resources, 14 College Farm Rd, New Brunswick, NJ 08901, USA.
| | - Meike T Wortel
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo, 0316, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo, 0316, Norway
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23
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Žliobaitė I, Fortelius M, Stenseth NC. Reconciling taxon senescence with the Red Queen’s hypothesis. Nature 2017; 552:92-95. [DOI: 10.1038/nature24656] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 10/27/2017] [Indexed: 11/09/2022]
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24
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Schenk H, Traulsen A, Gokhale CS. Chaotic provinces in the kingdom of the Red Queen. J Theor Biol 2017; 431:1-10. [PMID: 28757073 DOI: 10.1016/j.jtbi.2017.07.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/11/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Abstract
The interplay between parasites and their hosts is found in all kinds of species and plays an important role in understanding the principles of evolution and coevolution. Usually, the different genotypes of hosts and parasites oscillate in their abundances. The well-established theory of oscillatory Red Queen dynamics proposes an ongoing change in frequencies of the different types within each species. So far, it is unclear under what conditions Red Queen dynamics persists, especially when the number of types per species increases. Some models show that with many types of hosts and parasites or more species chaotic dynamics occur. In our analysis, an arbitrary number of types within two species are examined in a deterministic framework with constant or changing population size and very simple interactions. This general framework allows for analytical solutions for internal fixed points and their stability. The numerical analysis shows that for two species, once more than two types are considered per species, irregular dynamics in their frequencies can be observed in the long run. The nature of the dynamics depends strongly on the initial configuration of the system; the usual regular Red Queen oscillations are only observed when all types initially have similar abundance.
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Affiliation(s)
- Hanna Schenk
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany
| | - Chaitanya S Gokhale
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, August-Thienemann Str-2, Plön, 24306, Germany; New Zealand Institute for Advanced Study, Massey University, Albany, Private Bag 102904, North Shore Mail Centre, Auckland, 0745, New Zealand.
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25
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Abstract
Arms races between predators and prey may be driven by two related processes—escalation and coevolution. Escalation is enemy-driven evolution. In this top-down view of an arms race, the role of prey (with the exception of dangerous prey) is downplayed. In coevolution, two or more species change reciprocally in response to one another; prey are thought to drive the evolution of their predator, and vice versa. In the fossil record, the two processes are most reliably distinguished when the predator-prey system is viewed within the context of the other species that may influence the interaction, thus allowing for a relative ranking of the importance of selective agents. Detailed documentation of the natural history of living predator-prey systems is recommended in order to distinguish the processes in some fossil systems. A geographic view of species interactions and the processes driving their evolution may lead to a more diverse array of testable hypotheses on how predator-prey systems evolve and what constraints interactions impose on the evolution of organisms. Scale is important in evaluating the role of escalation and coevolution in the evolution of species interactions. If short-term reciprocal adaptation (via phenotypic plasticity or selection mosaics among populations) between predator and prey is a common process, then prey are likely to exert some selective pressure over their predators over the short term (on ecological time scales), but in the long run predators may still exert primary “top-down” control in directing evolution. On the scale of evolutionary time, predators of large effect likely control the overall directionality of evolution due to the inequalities of predator and prey in control of resources.
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26
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Correlates and catalysts of hominin evolution in Africa. Theory Biosci 2017; 136:123-140. [PMID: 28597395 DOI: 10.1007/s12064-017-0250-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/28/2017] [Indexed: 10/19/2022]
Abstract
Hominin evolution in the African Pliocene and Pleistocene was accompanied and mediated by changes in the abiotic and biotic spheres. It has been hypothesized that such environmental changes were catalysts of hominin morphological evolution and speciations. Whereas there is little doubt that ecological changes were relevant to shaping the trajectories of mammalian evolution, testing specific hypotheses with data from the fossil record has yielded ambiguous results regarding environmental disruption as a primary catalyst. Proposed mechanisms for abiotic and biotic causes of evolution are not always consistent with the timing and trends exhibited by the African fossil record of hominins and other mammals. Analyses of fossil and genetic data suggest that much of hominin evolution, and by extension mammalian evolution, was autocatalytic, driven by feedback loops within a species or lineage, irrespective of changes in the external environment.
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27
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Abrams PA, Harada Y, Matsuda H. ON THE RELATIONSHIP BETWEEN QUANTITATIVE GENETIC AND ESS MODELS. Evolution 2017; 47:982-985. [PMID: 28567889 DOI: 10.1111/j.1558-5646.1993.tb01254.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/1992] [Accepted: 01/29/1993] [Indexed: 11/27/2022]
Affiliation(s)
- Peter A Abrams
- Department of Ecology Evolution and Behavior, University of Minnesota, 1987 Upper Buford Circle, St. Paul, Minnesota, 55108
| | - Yasushi Harada
- Department of Fisheries Resource Management, Tokyo University of Fisheries, Konan, Minato-ku, Tokyo, 108, Japan
| | - Hiroyuki Matsuda
- National Institute of Fisheries Science, 5-5-1 Kachidoki, Chuo-ku, Tokyo, 104, Japan
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28
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Abrams PA. ADAPTIVE RESPONSES OF PREDATORS TO PREY AND PREY TO PREDATORS: THE FAILURE OF THE ARMS-RACE ANALOGY. Evolution 2017; 40:1229-1247. [PMID: 28563514 DOI: 10.1111/j.1558-5646.1986.tb05747.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/1985] [Accepted: 07/07/1986] [Indexed: 11/30/2022]
Abstract
This paper analyzes a number of relatively general models of predator-prey adaptation and coadaptation. The motivation behind this work is, in part, to evaluate the "race analogy" that has been applied in analyzing predator-prey coevolution. The models are based on the assumption that increased investment in predation-related adaptations must be paid for by decreased adaptation to some other factor. Increased investment in predation-related adaptations by the prey lowers the predator's functional response, and increased investment by the predator increases the functional response. The models are used to determine how each species should respond to an increase in the predation-related investment of the other species. Several broad classes of population-dynamics models and several alternatives for the cost of predation-related adaptation are investigated. The results do not support the general applicability of the race analogy. In the type of model analyzed in greatest detail here, predator and prey adaptations combine multiplicatively in determining the predator's capture-rate constant. In such models, prey usually increase investment in predator avoidance or escape when predators increase their investment in capture. However, predators often do not change or decrease their investment in response to an increase in the prey's investment. The direction of the predator's response depends on the particular parameter that pays the cost of increased predation investment, the shape of the cost-benefit functions, and the assumptions about the population dynamics of the predator-prey system. Similar models are used to determine whether increased investment by one species should increase the rate of incorporation of mutations that improve the predation-related adaptations of the other species. The arms-race analogy also fails for this case. The results cast doubt on the usefulness of Dawkins and Krebs (1979) "life-dinner" principle.
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Affiliation(s)
- Peter A Abrams
- Department of Ecology and Behavioral Biology, University of Minnesota, Minneapolis, MN, 55455
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29
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de Vladar HP, Santos M, Szathmáry E. Grand Views of Evolution. Trends Ecol Evol 2017; 32:324-334. [DOI: 10.1016/j.tree.2017.01.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 01/25/2023]
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30
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Zhao XF, Hao YQ, Zhang QG. Stability of A Coevolving Host-parasite System Peaks at Intermediate Productivity. PLoS One 2017; 12:e0168560. [PMID: 28076419 PMCID: PMC5226335 DOI: 10.1371/journal.pone.0168560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/02/2016] [Indexed: 11/18/2022] Open
Abstract
Habitat productivity may affect the stability of consumer-resource systems, through both ecological and evolutionary mechanisms. We hypothesize that coevolving consumer-resource systems show more stable dynamics at intermediate resource availability, while very low-level resource supply cannot support sufficiently large populations of resource and consumer species to avoid stochastic extinction, and extremely resource-rich environments may promote escalatory arms-race-like coevolution that can cause strong fluctuations in species abundance and even extinction of one or both trophic levels. We tested these ideas by carrying out an experimental evolution study with a model bacterium-phage system (Pseudomonas fluorescens SBW25 and its phage SBW25Φ2). Consistent with our hypothesis, this system was most stable at intermediate resource supply (fewer extinction events and smaller magnitude of population fluctuation). In our experiment, the rate of coevolution between bacterial resistance and phage infectivity was correlated with the magnitude of population fluctuation, which may explain the different in stability between levels of resource supply. Crucially, our results are consistent with a suggestion that, among the two major modes of antagonistic coevolution, arms race is more likely than fluctuation selection dynamics to cause extinction events in consumer-resource systems. This study suggests an important role of environment-dependent coevolutionary dynamics for the stability of consumer-resource species systems, therefore highlights the importance to consider contemporaneous evolutionary dynamics when studying the stability of ecosystems, particularly those under environmental changes.
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Affiliation(s)
- Xin-Feng Zhao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
| | - Yi-Qi Hao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University, Beijing, China
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31
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Fenton IS, Pearson PN, Dunkley Jones T, Purvis A. Environmental Predictors of Diversity in Recent Planktonic Foraminifera as Recorded in Marine Sediments. PLoS One 2016; 11:e0165522. [PMID: 27851751 PMCID: PMC5112986 DOI: 10.1371/journal.pone.0165522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/13/2016] [Indexed: 11/18/2022] Open
Abstract
Global diversity patterns are thought to result from a combination of environmental and historical factors. This study tests the set of ecological and evolutionary hypotheses proposed to explain the global variation in present-day coretop diversity in the macroperforate planktonic foraminifera, a clade with an exceptional fossil record. Within this group, marine surface sediment assemblages are thought to represent an accurate, although centennial to millennial time-averaged, representation of recent diversity patterns. Environmental variables chosen to capture ocean temperature, structure, productivity and seasonality were used to model a range of diversity measures across the world's oceans. Spatial autoregressive models showed that the same broad suite of environmental variables were important in shaping each of the four largely independent diversity measures (rarefied species richness, Simpson's evenness, functional richness and mean evolutionary age). Sea-surface temperature explains the largest portion of diversity in all four diversity measures, but not in the way predicted by the metabolic theory of ecology. Vertical structure could be linked to increased diversity through the strength of stratification, but not through the depth of the mixed layer. There is limited evidence that seasonal turnover explains diversity patterns. There is evidence for functional redundancy in the low-latitude sites. The evolutionary mechanism of deep-time stability finds mixed support whilst there is relatively little evidence for an out-of-the-tropics model. These results suggest the diversity patterns of planktonic foraminifera cannot be explained by any one environmental variable or proposed mechanism, but instead reflect multiple processes acting in concert.
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Affiliation(s)
- Isabel S. Fenton
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
| | - Paul N. Pearson
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Tom Dunkley Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom
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32
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Pieczynska MD, Wloch-Salamon D, Korona R, de Visser JAGM. Rapid multiple-level coevolution in experimental populations of yeast killer and nonkiller strains. Evolution 2016; 70:1342-53. [PMID: 27168531 DOI: 10.1111/evo.12945] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/26/2016] [Accepted: 04/28/2016] [Indexed: 01/09/2023]
Abstract
Coevolution between different biological entities is considered an important evolutionary mechanism at all levels of biological organization. Here, we provide evidence for coevolution of a yeast killer strain (K) carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and an isogenic toxin-sensitive strain (S) during 500 generations of laboratory propagation. Signatures of coevolution developed at two levels. One of them was coadaptation of K and S. Killing ability of K first increased quickly and was followed by the rapid invasion of toxin-resistant mutants derived from S, after which killing ability declined. High killing ability was shown to be advantageous when sensitive cells were present but costly when they were absent. Toxin resistance evolved via a two-step process, presumably involving the fitness-enhancing loss of one chromosome followed by selection of a recessive resistant mutation on the haploid chromosome. The other level of coevolution occurred between cell and killer virus. By swapping the killer viruses between ancestral and evolved strains, we could demonstrate that changes observed in both host and virus were beneficial only when combined, suggesting that they involved reciprocal changes. Together, our results show that the yeast killer system shows a remarkable potential for rapid multiple-level coevolution.
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Affiliation(s)
- Magdalena D Pieczynska
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands.,Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland.,Current address: Kavli Institute of NanoScience, Delft University of Technology, 2600 GD Delft, The Netherlands
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
| | - Ryszard Korona
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Krakow, Poland
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Ezard THG, Quental TB, Benton MJ. The challenges to inferring the regulators of biodiversity in deep time. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150216. [PMID: 26977058 PMCID: PMC4810811 DOI: 10.1098/rstb.2015.0216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 11/12/2022] Open
Abstract
Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas.
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Affiliation(s)
- Thomas H G Ezard
- Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
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Tran LAP. Interaction between Digestive Strategy and Niche Specialization Predicts Speciation Rates across Herbivorous Mammals. Am Nat 2016; 187:468-80. [PMID: 27028075 DOI: 10.1086/685094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biotic and abiotic factors often are treated as mutually exclusive drivers of diversification processes. In this framework, ecological specialists are expected to have higher speciation rates than generalists if abiotic factors are the primary controls on species diversity but lower rates if biotic interactions are more important. Speciation rate is therefore predicted to positively correlate with ecological specialization in the purely abiotic model but negatively correlate in the biotic model. In this study, I show that the positive relationship between ecological specialization and speciation expected from the purely abiotic model is recovered only when a species-specific trait, digestive strategy, is modeled in the terrestrial, herbivorous mammals (Mammalia). This result suggests a more nuanced model in which the response of specialized lineages to abiotic factors is dependent on a biological trait. I also demonstrate that the effect of digestive strategy on the ecological specialization-speciation rate relationship is not due to a difference in either the degree of ecological specialization or the speciation rate between foregut- and hindgut-fermenting mammals. Together, these findings suggest that a biological trait, alongside historical abiotic events, played an important role in shaping mammal speciation at long temporal and large geographic scales.
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Asymmetric ecological conditions favor Red-Queen type of continued evolution over stasis. Proc Natl Acad Sci U S A 2016; 113:1847-52. [PMID: 26831108 DOI: 10.1073/pnas.1525395113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Four decades ago, Leigh Van Valen presented the Red Queen's hypothesis to account for evolution of species within a multispecies ecological community [Van Valen L (1973) Evol Theory 1(1):1-30]. The overall conclusion of Van Valen's analysis was that evolution would continue even in the absence of abiotic perturbations. Stenseth and Maynard Smith presented in 1984 [Stenseth NC, Maynard Smith J (1984) Evolution 38(4):870-880] a model for the Red Queen's hypothesis showing that both Red-Queen type of continuous evolution and stasis could result from a model with biotically driven evolution. However, although that contribution demonstrated that both evolutionary outcomes were possible, it did not identify which ecological conditions would lead to each of these evolutionary outcomes. Here, we provide, using a simple, yet general population-biologically founded eco-evolutionary model, such analytically derived conditions: Stasis will predominantly emerge whenever the ecological system contains only symmetric ecological interactions, whereas both Red-Queen and stasis type of evolution may result if the ecological interactions are asymmetrical, and more likely so with increasing degree of asymmetry in the ecological system (i.e., the more trophic interactions, host-pathogen interactions, and the like there are [i.e., +/- type of ecological interactions as well as asymmetric competitive (-/-) and mutualistic (+/+) ecological interactions]). In the special case of no between-generational genetic variance, our results also predict dynamics within these types of purely ecological systems.
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Agarwal R, Tiwana A. Editorial—Evolvable Systems: Through the Looking Glass of IS. INFORMATION SYSTEMS RESEARCH 2015. [DOI: 10.1287/isre.2015.0595] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Abstract
Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.
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Voje KL, Holen ØH, Liow LH, Stenseth NC. The role of biotic forces in driving macroevolution: beyond the Red Queen. Proc Biol Sci 2015; 282:20150186. [PMID: 25948685 PMCID: PMC4455800 DOI: 10.1098/rspb.2015.0186] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/14/2015] [Indexed: 11/12/2022] Open
Abstract
A multitude of hypotheses claim that abiotic factors are the main drivers of macroevolutionary change. By contrast, Van Valen's Red Queen hypothesis is often put forward as the sole representative of the view that biotic forcing is the main evolutionary driver. This imbalance of hypotheses does not reflect our current knowledge: theoretical work demonstrates the plausibility of biotically driven long-term evolution, whereas empirical work suggests a central role for biotic forcing in macroevolution. We call for a more pluralistic view of how biotic forces may drive long-term evolution that is compatible with both phenotypic stasis in the fossil record and with non-constant extinction rates. Promising avenues of research include contrasting predictions from relevant theories within ecology and macroevolution, as well as embracing both abiotic and biotic proxies while modelling long-term evolutionary data. By fitting models describing hypotheses of biotically driven macroevolution to data, we could dissect their predictions and transcend beyond pattern description, possibly narrowing the divide between our current understanding of micro- and macroevolution.
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Affiliation(s)
- Kjetil L Voje
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Øistein H Holen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Lee Hsiang Liow
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
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Leger EA, Espeland EK. Coevolution between native and invasive plant competitors: implications for invasive species management. Evol Appl 2015; 3:169-78. [PMID: 25567917 PMCID: PMC3352482 DOI: 10.1111/j.1752-4571.2009.00105.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 10/22/2009] [Indexed: 11/30/2022] Open
Abstract
Invasive species may establish in communities because they are better competitors than natives, but in order to remain community dominants, the competitive advantage of invasive species must be persistent. Native species that are not extirpated when highly invasive species are introduced are likely to compete with invaders. When population sizes and genetic diversity of native species are large enough, natives may be able to evolve traits that allow them to co-occur with invasive species. Native species may also evolve to become significant competitors with invasive species, and thus affect the fitness of invaders. Invasive species may respond in turn, creating either transient or continuing coevolution between competing species. In addition to demographic factors such as population size and growth rates, a number of factors including gene flow, genetic drift, the number of selection agents, encounter rates, and genetic diversity may affect the ability of native and invasive species to evolve competitive ability against one another. We discuss how these factors may differ between populations of native and invasive plants, and how this might affect their ability to respond to selection. Management actions that maintain genetic diversity in native species while reducing population sizes and genetic diversity in invasive species could promote the ability of natives to evolve improved competitive ability.
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Affiliation(s)
- Elizabeth A Leger
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, NV, USA
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Networks and Hierarchies: Approaching Complexity in Evolutionary Theory. INTERDISCIPLINARY EVOLUTION RESEARCH 2015. [DOI: 10.1007/978-3-319-15045-1_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lindholm M. Morphologically Conservative but Physiologically Diverse: The Mode of Stasis in Anostraca (Crustacea: Branchiopoda). Evol Biol 2014; 41:503-507. [PMID: 25152547 PMCID: PMC4129224 DOI: 10.1007/s11692-014-9283-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/12/2014] [Indexed: 11/18/2022]
Abstract
The essay discusses whether biotic and abiotic environments differ in their ability to speed up or slow down morphological change and the generation of new lineages. Examples from the class Branchiopoda show that morphological conservatism is associated with enemy free space in species-poor habitats dominated by abiotic factors, while Red Queen mechanisms are predominant in larger systems with complex biotic interactions. Splitting of Branchiopod main lineages is associated with increased fish predation during the Devonian. The order Cladocera adapted and remained in larger aquatic systems, and subsequently generated a variety of new families, genera and species. The order Anostraca, on the other hand, maintained its ancestral morphology and survived only as "living fossils" in isolated ponds of harsh habitats. Despite their archaic morphology, however, they possess highly sophisticated adaptations to local physicochemical properties of their extreme environment. Hence, although morphologically conservative and possessing traits typical for "living fossils", anostracan physiological abilities are closely adapted to the challenging and variable physicochemical conditions of ponds and ephemeral pools.
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Affiliation(s)
- Markus Lindholm
- Norwegian Institute for Water Research/NIVA, Gaustadalleen 23, 0349 Oslo, Norway
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Sanchez S, Schoch RR. Bone Histology Reveals a High Environmental and Metabolic Plasticity as a Successful Evolutionary Strategy in a Long-Lived Homeostatic Triassic Temnospondyl. Evol Biol 2013; 40:627-647. [PMID: 24293739 PMCID: PMC3832766 DOI: 10.1007/s11692-013-9238-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/06/2013] [Indexed: 11/29/2022]
Abstract
Evolutionary stasis (long-term stability of morphology in an evolving lineage) is a pattern for which explanations are usually elusive. The Triassic tetrapod Gerrothorax pulcherrimus, a gill-bearing temnospondyl, survived for 35 million years in the Germanic Basin of Central Europe persisting throughout the dinosaur-dominated Late Triassic period. This evolutionary stasis coincides with the occurrence of this species in a wide range of habitats and environmental conditions. By the combination of palaeoecological and palaeohistological analyses, we found great ecological flexibility in G. pulcherrimus and present substantial evidence of developmental and metabolic plasticity despite the morphological stasis. We conclude that G. pulcherrimus could show the capacity to settle in water bodies too harsh or unpredictable for most other tetrapods. This would have been made possible by a unique life history strategy that involved a wide reaction norm, permitting adjustment to fluctuating conditions such as salinity and level of nutrients. Growth rate, duration of juvenile period, age at maturity, and life span were all subject to broad variation within specimens of G. pulcherrimus in one single lake and in between different lakes. In addition to providing a better understanding of fossil ecosystems, this study shows the potential of such a methodology to encourage palaeobiologists and evolutionary biologists to consider the mechanisms of variation in extant and fossil organisms by using a similar time-scope reference.
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Affiliation(s)
- S. Sanchez
- Subdepartment of Evolutionary Organismal Biology, Department of Physiology and Developmental Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, 752 36 Uppsala, Sweden
| | - R. R. Schoch
- Staatliches Museum für Naturkunde, Rosenstein 1, 70191 Stuttgart, Germany
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Morvan C, Malard F, Paradis E, Lefébure T, Konecny-Dupré L, Douady CJ. Timetree of Aselloidea Reveals Species Diversification Dynamics in Groundwater. Syst Biol 2013; 62:512-22. [DOI: 10.1093/sysbio/syt015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Claire Morvan
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
| | - Florian Malard
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
| | - Emmanuel Paradis
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
| | - Tristan Lefébure
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
| | - Lara Konecny-Dupré
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
| | - Christophe J. Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
- Université de Lyon; UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France; 2 Institut de Recherche pour le Développement, ISEM UMR 226/5554 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia; 3 Institut Universitaire de France, Paris F-75005, France
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The evolutionary ecology of biotic association in a megadiverse bivalve superfamily: sponsorship required for permanent residency in sediment. PLoS One 2012; 7:e42121. [PMID: 22905116 PMCID: PMC3414514 DOI: 10.1371/journal.pone.0042121] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Marine lineage diversification is shaped by the interaction of biotic and abiotic factors but our understanding of their relative roles is underdeveloped. The megadiverse bivalve superfamily Galeommatoidea represents a promising study system to address this issue. It is composed of small-bodied clams that are either free-living or have commensal associations with invertebrate hosts. To test if the evolution of this lifestyle dichotomy is correlated with specific ecologies, we have performed a statistical analysis on the lifestyle and habitat preference of 121 species based on 90 source documents. METHODOLOGY/PRINCIPAL FINDINGS Galeommatoidea has significant diversity in the two primary benthic habitats: hard- and soft-bottoms. Hard-bottom dwellers are overwhelmingly free-living, typically hidden within crevices of rocks/coral heads/encrusting epifauna. In contrast, species in soft-bottom habitats are almost exclusively infaunal commensals. These infaunal biotic associations may involve direct attachment to a host, or clustering around its tube/burrow, but all commensals locate within the oxygenated sediment envelope produced by the host's bioturbation. CONCLUSIONS/SIGNIFICANCE the formation of commensal associations by Galeommatoidean clams is robustly correlated with an abiotic environmental setting: living in sediments (P < 0.001). Sediment-dwelling bivalves are exposed to intense predation pressure that drops markedly with depth of burial. Commensal galeommatoideans routinely attain depth refuges many times their body lengths, independent of siphonal investment, by virtue of their host's burrowing and bioturbation. In effect, they use their much larger hosts as giant auto-irrigating siphon substitutes. The evolution of biotic associations with infaunal bioturbating hosts may have been a prerequisite for the diversification of Galeommatoidea in sediments and has likely been a key factor in the success of this exceptionally diverse bivalve superfamily.
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Ferrada E, Wagner A. Evolutionary innovations and the organization of protein functions in genotype space. PLoS One 2010; 5:e14172. [PMID: 21152394 PMCID: PMC2994758 DOI: 10.1371/journal.pone.0014172] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 10/28/2010] [Indexed: 11/18/2022] Open
Abstract
The organization of protein structures in protein genotype space is well studied. The same does not hold for protein functions, whose organization is important to understand how novel protein functions can arise through blind evolutionary searches of sequence space. In systems other than proteins, two organizational features of genotype space facilitate phenotypic innovation. The first is that genotypes with the same phenotype form vast and connected genotype networks. The second is that different neighborhoods in this space contain different novel phenotypes. We here characterize the organization of enzymatic functions in protein genotype space, using a data set of more than 30,000 proteins with known structure and function. We show that different neighborhoods of genotype space contain proteins with very different functions. This property both facilitates evolutionary innovation through exploration of a genotype network, and it constrains the evolution of novel phenotypes. The phenotypic diversity of different neighborhoods is caused by the fact that some functions can be carried out by multiple structures. We show that the space of protein functions is not homogeneous, and different genotype neighborhoods tend to contain a different spectrum of functions, whose diversity increases with increasing distance of these neighborhoods in sequence space. Whether a protein with a given function can evolve specific new functions is thus determined by the protein's location in sequence space.
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Affiliation(s)
- Evandro Ferrada
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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Calcagno V, Dubosclard M, de Mazancourt C. Rapid exploiter-victim coevolution: the race is not always to the swift. Am Nat 2010; 176:198-211. [PMID: 20565235 DOI: 10.1086/653665] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The modeling of coevolutionary races has traditionally been dominated by methods invoking a timescale separation between ecological and evolutionary dynamics, the latter assumed to be much slower than the former. Yet it is becoming increasingly clear that in many cases the two processes occur on similar timescales and that such "rapid" evolution can have profound implications for the dynamics of communities and ecosystems. After briefly reviewing the timescale separations most common in coevolution theory, we use a general model of exploiter-victim coevolution to confront predictions from slow-evolution analysis with Monte Carlo simulations. We show how rapid evolution radically alters the dynamics and outcome of coevolutionary arms races. In particular, a fast-evolving exploiter can enable victim diversification and thereby lose a race it is expected to win. We explain simulation results, using mathematical analysis with relaxed timescale separations. Unusual mutation parameters are not required, since rapid evolution naturally emerges from slow competitive exclusion. Our results point to interesting consequences of exploiter rapid evolution and experimentally testable patterns, while indicating that more attention should be paid to rapid evolution in evolutionary theory.
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Affiliation(s)
- Vincent Calcagno
- Redpath Museum, McGill University, Montreal, Quebec H3A 2K6, Canada.
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Dercole F, Ferriere R, Rinaldi S. Chaotic Red Queen coevolution in three-species food chains. Proc Biol Sci 2010; 277:2321-30. [PMID: 20356888 DOI: 10.1098/rspb.2010.0209] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coevolution between two antagonistic species follows the so-called 'Red Queen dynamics' when reciprocal selection results in an endless series of adaptation by one species and counteradaptation by the other. Red Queen dynamics are 'genetically driven' when selective sweeps involving new beneficial mutations result in perpetual oscillations of the coevolving traits on the slow evolutionary time scale. Mathematical models have shown that a prey and a predator can coevolve along a genetically driven Red Queen cycle. We found that embedding the prey-predator interaction into a three-species food chain that includes a coevolving superpredator often turns the genetically driven Red Queen cycle into chaos. A key condition is that the prey evolves fast enough. Red Queen chaos implies that the direction and strength of selection are intrinsically unpredictable beyond a short evolutionary time, with greatest evolutionary unpredictability in the superpredator. We hypothesize that genetically driven Red Queen chaos could explain why many natural populations are poised at the edge of ecological chaos. Over space, genetically driven chaos is expected to cause the evolutionary divergence of local populations, even under homogenizing environmental fluctuations, and thus to promote genetic diversity among ecological communities over long evolutionary time.
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Affiliation(s)
- Fabio Dercole
- DEI, Politecnico di Milano, Via Ponzio 34/5, 20133 Milan, Italy
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48
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Antagonistic coevolution accelerates molecular evolution. Nature 2010; 464:275-8. [PMID: 20182425 DOI: 10.1038/nature08798] [Citation(s) in RCA: 370] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/23/2009] [Indexed: 12/14/2022]
Abstract
The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation. Although the divergence observed at some host-resistance and parasite-infectivity genes is consistent with this, the long time periods typically required to study coevolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Phi2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species.
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