scholarly journals Reining in the Red Queen: the dynamics of adaptation and extinction reexamined

Paleobiology ◽  
10.1666/13009 ◽  
2013 ◽  
Vol 39 (4) ◽  
pp. 560-575 ◽  
Author(s):  
Geerat J. Vermeij ◽  
Peter D. Roopnarine
Keyword(s):  
Evolutionary Game ◽  
Single Species ◽  
Ecosystem Productivity ◽  
Red Queen ◽  
Interacting Species ◽  
Living Things ◽  
Zero Sum ◽  
Selective Regime ◽  
The Red Queen

One of the most enduring evolutionary metaphors is Van Valen's (1973) Red Queen. According to this metaphor, as one species in a community adapts by becoming better able to acquire and defend resources, species with which it interacts are adversely affected. If those other species do not continuously adapt to compensate for this biotically caused deterioration, they will be driven to extinction. Continuous adaptation of all species in a community prevents any single species from gaining a long-term advantage; this amounts to the Red Queen running in place. We have critically examined the assumptions on which the Red Queen metaphor was founded. We argue that the Red Queen embodies three demonstrably false assumptions: (1) evolutionary adaptation is continuous; (2) organisms are important agents of extinction; and (3) evolution is a zero-sum process in which living things divide up an unchanging quantity of resources. Changes in the selective regime need not always elicit adaptation, because most organisms function adequately under many “suboptimal” conditions and often compensate by demonstrating adaptive flexibility. Likewise, ecosystems are organized in such a way that they tend to be robust and capable of absorbing invasions and extinctions, at least up to a point. With a simple evolutionary game involving three species, we show that Red Queen dynamics (continuous adaptation by all interacting species) apply in only a very small minority of possible outcomes. Importantly, cooperation and facilitation among species enable competitors to increase ecosystem productivity and therefore to enlarge the pool and turnover of resources. The Red Queen reigns only under a few unusual circumstances.

scholarly journals Mechanisms of gene death in the Red Queen race revealed by the analysis ofde novomicroRNAs

2018 ◽  
Author(s):  
Guang-An Lu ◽  
Yixin Zhao ◽  
Ao Lan ◽  
Zhongqi Liufu ◽  
Haijun Wen ◽  
...  
Keyword(s):  
De Novo ◽  
Mirna Gene ◽  
Red Queen ◽  
Fitness Effects ◽  
New Genes ◽  
Knockout Mutants ◽  
Laboratory Populations ◽  
The Many ◽  
The Red Queen

AbstractThe prevalence ofde novocoding genes is controversial due to the length and coding constraints. Non-coding genes, especially small ones, are freer to evolvede novoby comparison. The best examples are microRNAs (miRNAs), a large class of regulatory molecules ~22 nt in length. Here, we study 6de novomiRNAs inDrosophilawhich, like most new genes, are testis-specific. We ask how and whyde novogenes die because gene death must be sufficiently frequent to balance the many new births. By knocking out each miRNA gene, we could analyze their contributions to each of the 9 components of male fitness (sperm production, length, competitiveness etc.). To our surprise, the knockout mutants often perform better in some components, and slightly worse in others, than the wildtype. When two of the younger miRNAs are assayed in long-term laboratory populations, their total fitness contributions are found to be essentially zero. These results collectively suggest that adaptivede novogenes die regularly, not due to the loss of functionality, but due to the canceling-out of positive and negative fitness effects, which may be characterized as “quasi-neutrality”. Sincede novogenes often emerge adaptively and become lost later, they reveal ongoing period-specific adaptations, reminiscent of the “Red-Queen” metaphor for long term evolution.

The evolutionary significance of mass extinctions

2004 ◽  
Author(s):  
Tony Hallam
Keyword(s):  
Biotic Interactions ◽  
Evolutionary Significance ◽  
Red Queen Hypothesis ◽  
Mass Extinctions ◽  
Red Queen ◽  
Physical Conditions ◽  
The Face ◽  
Competition For Food ◽  
Zero Sum ◽  
The Red Queen

Darwin was firmly of the opinion that biotic interactions, such as competition for food and space – the ‘struggle for existence’ – were of considerably greater importance in promoting evolution and extinction than changes in the physical environment. This is clearly brought out by this quotation from The Origin of Species: . . . Species are produced and exterminated by slowly acting causes . . . and the most important of all causes of organic change is one that is almost independent of altered . . . physical conditions, namely the mutual relation of organism to organism – the improvement of one organism entailing the improvement or extermination of others. . . . The driving force of competition in a crowded world is also stressed in another quotation presenting Darwin’s famous wedge metaphor: . . . In looking at Nature, it is most necessary . . . never to forget that every single organic being around us may be said to be striving to the utmost to increase in numbers; that each lives by a struggle at some period of its life; that heavy destruction inevitably falls either on the young or the old, during each generation . . . The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force. . . . The implication of the Darwinian view concerning the dominance of biotic competition is that for each winner there is a loser – a kind of zero-sum game. It has been accepted more or less uncritically by generations of evolutionary biologists, but not until the 1970s did it become graced with a name – the Red Queen hypothesis. The story behind the emergence of this name is an interesting one. At the beginning of the 1970s the rather eccentric University of Chicago palaeobiologist Leigh Van Valen did some interesting research concerning the analysis of survivors of Phanerozoic taxa which suggested that the probability of a fossil group becoming extinct was more or less constant in time. To account for this, Van Valen put forward his Red Queen hypothesis.

scholarly journals The Red Queen and King in finite populations

2017 ◽  
Vol 114 (27) ◽  
pp. E5396-E5405 ◽  
Author(s):  
Carl Veller ◽  
Laura K. Hayward ◽  
Christian Hilbe ◽  
Martin A. Nowak
Keyword(s):  
Red Queen ◽  
Rates Of Evolution ◽  
Generation Times ◽  
Host Parasite ◽  
Red Queen Effect ◽  
Two Populations ◽  
The Red Queen ◽  
Demographic Evolution ◽  
Insight Into

In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts.

scholarly journals The Red Queen in the Repository

2020 ◽  
Vol 15 (1) ◽  
pp. 16
Author(s):  
Joakim Philipson
Keyword(s):  
General Purpose ◽  
Research Data ◽  
Data Repository ◽  
Red Queen ◽  
Changing Environment ◽  
Data Repositories ◽  
Metadata Standards ◽  
And Migration ◽  
The Red Queen

One of the grand curation challenges is to secure metadata quality in the ever-changing environment of metadata standards and file formats. As the Red Queen tells Alice in Through the Looking-Glass: “Now, here, you see, it takes all the running you can do, to keep in the same place.” That is, there is some “running” needed to keep metadata records in a research data repository fit for long-term use and put in place. One of the main tools of adaptation and keeping pace with the evolution of new standards, formats – and versions of standards in this ever-changing environment are validation schemas. Validation schemas are mainly seen as methods of checking data quality and fitness for use, but are also important for long-term preservation. We might like to think that our present (meta)data standards and formats are made for eternity, but in reality we know that standards evolve, formats change (some even become obsolete with time), and so do our needs for storage, searching and future dissemination for re-use. Eventually, we come to a point where transformation of our archival records and migration to other formats will be necessary. This could also mean that even if the AIPs, the Archival Information Packages stay the same in storage, the DIPs, the Dissemination Information Packages that we want to extract from the archive are subject to change of format. Further, in order for archival information packages to be self-sustainable, as required in the OAIS model, it is important to take interdependencies between individual files in the information packages into account. This should be done already by the time of ingest and validation of the SIPs, the Submission Information Packages, and along the line at different points of necessary transformation/migration (from SIP to AIP, from AIP to DIP etc.), in order to counter obsolescence. This paper investigates possible validation errors and missing elements in metadata records from three general purpose, multidisciplinary research data repositories – Figshare, Harvard’s Dataverse and Zenodo, and explores the potential effects of these errors on future transformation to AIPs and migration to other formats within a digital archive.  

scholarly journals Ecological and Evolutionary Oscillations in Host-Parasite Population Dynamics, and The Red Queen

2014 ◽  
Author(s):  
Jomar Fajardo Rabajante
Keyword(s):  
Population Size ◽  
Carrying Capacity ◽  
Quantitative Traits ◽  
Oscillatory Behavior ◽  
Red Queen ◽  
Trade Off ◽  
Oscillatory Dynamics ◽  
Host Parasite ◽  
The Red Queen

In a host-parasite system, the constitutive interaction among the species, regulated by the growth rates and functional response, may induce populations to approach equilibrium or sometimes to exhibit simple cycles or peculiar oscillations, such as chaos. A large carrying capacity coupled with appropriate parasitism effectiveness frequently drives long-term apparent oscillatory dynamics in population size. We name these oscillations due to the structure of the constitutive interaction among species as ecological. On the other hand, there are also exceptional cases when the evolving quantitative traits of the hosts and parasites induce oscillating population size, which we call as evolutionary. This oscillatory behavior is dependent on the speed of evolutionary adaptation and degree of evolutionary trade-off. A moderate level of negative trade-off is essential for the existence of oscillations. Evolutionary oscillations due to the host-parasite coevolution (known as the Red Queen) can be observed beyond the ecological oscillations, especially when there are more than two competing species involved.

Effects of GMO agricultural products on living things

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
ERCAN ÇATAK ◽  
Ali ATALAY
Keyword(s):  
Genetically Modified Organisms ◽  
World Population ◽  
Negative Effects ◽  
Qualitative And Quantitative ◽  
Living Things ◽  
Late Twentieth ◽  
Agricultural Use ◽  
Late Twentieth Century ◽  
Living Creature

By obtaining changes on gene sequences of living things with the applied biotechnological methods; The idea of "Genetically Modified Organisms (GMO)", which aims to bring the living creature in question the original gene combinations with the desired characteristics, came to life in the late twentieth century. Despite the high probability that hunger problems may increase with the increasing world population; It is thought that plant breeding with classical farming methods will be insufficient in solving these problems. With various GMO applications developed all over the world, it aims to produce solutions to these problems. With the presence of GMO, it was possible to increase the shelf life of qualitative and quantitative values of the existing foods. In addition, decreases in agricultural use of pesticides used in agricultural struggle and threatening human health with GMO production are noteworthy. However, some concerns about anomalies that may occur in living things fed GMO products remain on the agenda. Because, in the long term, there is no clear and precise information that GMO will not have negative effects on living things; There are many recorded incidents showing their negative effects.

scholarly journals Modeling cesium migration through Opalinus clay: a benchmark for single- and multi-species sorption-diffusion models

2021 ◽  
Author(s):  
Jesús F. Águila ◽  
Vanessa Montoya ◽  
Javier Samper ◽  
Luis Montenegro ◽  
Georg Kosakowski ◽  
...  
Keyword(s):  
Time Discretization ◽  
Single Species ◽  
Opalinus Clay ◽  
Sorption Behavior ◽  
Diffusion Experiment ◽  
Modeling Tools ◽  
Cesium Sorption ◽  
Code Performance ◽  
Good Agreement

AbstractSophisticated modeling of the migration of sorbing radionuclides in compacted claystones is needed for supporting the safety analysis of deep geological repositories for radioactive waste, which requires robust modeling tools/codes. Here, a benchmark related to a long term laboratory scale diffusion experiment of cesium, a moderately sorbing radionuclide, through Opalinus clay is presented. The benchmark was performed with the following codes: CORE2DV5, Flotran, COMSOL Multiphysics, OpenGeoSys-GEM, MCOTAC and PHREEQC v.3. The migration setup was solved with two different conceptual models, i) a single-species model by using a look-up table for a cesium sorption isotherm and ii) a multi-species diffusion model including a complex mechanistic cesium sorption model. The calculations were performed for three different cesium boundary concentrations (10−3, 10−5, 10−7 mol / L) to investigate the models/codes capabilities taking into account the nonlinear sorption behavior of cesium. Generally, good agreement for both single- and multi-species benchmark concepts could be achieved, however, some discrepancies have been identified, especially near the boundaries, where code specific spatial (and time) discretization had to be improved to achieve better agreement at the expense of longer computation times. In addition, the benchmark exercise yielded useful information on code performance, setup options, input and output data management, and post processing options. Finally, the comparison of single-species and multi-species model concepts showed that the single-species approach yielded generally earlier breakthrough, because this approach accounts neither for cation exchange of Cs+ with K+ and Na+, nor K+ and Na+ diffusion in the pore water.

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