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150 results for “evolutionary models”
Eco‐evolutionary dynamics driven by fishing: from single species models to dynamic evolution within complex food webs
<p>Evidence of contemporary evolution across ecological time scales stimulated research on the eco-evolutionary dynamics of natural populations. Aquatic systems provide a good setting to study eco-evolutionary dynamics owing to a wealth of long-term monitoring data and the detected trends in fish life-history traits across intensively harvested marine and freshwater systems. In the present study, we focus on modelling approaches to simulate eco-evolutionary dynamics of fishes and their ecosystems. Firstly, we review the development of modelling from single-species to multispecies approaches. Secondly, we advance the current state-of-the-art methodology by implementing evolution of life-history traits of a top predator into the context of complex food web dynamics as described by the allometric trophic network (ATN) framework. The functioning of our newly developed eco-evolutionary ATNE framework is illustrated using a well-studied lake food web. Our simulations show how both natural selection arising from feeding interactions and size-selective fishing cause evolutionary changes in the top predator and how those feed back to its prey species and further cascade down to lower trophic levels. Finally, we discuss future directions, particularly the need to integrate genomic discoveries into eco-evolutionary projections.</p>
Individual variability and versatility in an eco-evolutionary model of avian migration
<p>Seasonal migration is a complex and variable behavior with the potential to promote reproductive isolation. In Eurasian blackcaps (<em>Sylvia atricapilla</em>), a migratory divide in central Europe separating populations with southwest and southeast autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies. Blackcaps to the west and east of the divide used predominantly SW and SE directions, respectively, but close to the contact zone many individuals took intermediate (S) routes. At 14.0ºE, we documented a sharp transition from SW to SE migratory directions across only 27 (10–86) km, implying a strong selection gradient across the divide. Blackcaps wintering in Britain took northwesterly migration routes from continental European breeding grounds. They originated from a surprisingly extensive area, spanning 2000 km of the breeding range. British winterers bred in sympatry with SW-bound migrants but arrived 9.8 days earlier on the breeding grounds, suggesting some potential for assortative mating by timing. Overall, our data reveal complex variation in songbird migration and suggest that selection can maintain variation in migration direction across short distances while enabling the spread of a novel strategy across a wide range.</p>
The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model
<p>Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population-genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- vs higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant non-zero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of non-zero recombination formulated by classical models.</p>
Supporting data: Structure-based Markov random field model for representing evolutionary constraints on functional sites
<p>Supporting data for the paper:</p> <p>Chan-Seok Jeong, Dongsup Kim. Structure-based Markov random field model for representing evolutionary constraints on functional sites. Submitted. (2015)</p> <p>See 'README' for a description of the contents.</p>
Supplemental 3D Model Data - New insights into the evolutionary history of Fungi from a 407 million year old blastocladiomycota-like fossil showing multiple sporangia and an extensive hyphal network (SPIERSView and VAXML format)
<p>Three-dimensional reconstruction models of Fungi from a 407 million year old blastocladiomycota-like fossil showing multiple sporangia and an extensive hyphal network in SPIERSView and VAXML format. 2D and 3D (Red/Cyan) images also provided as a PDF.</p> <p>Notes:</p> <ol> <li>SPIERSView file (.SPV) models can conveniently be viewed using the SPIERSView software, freely available in both Windows and Mac versions from http://www.spiers‐software.org. However, note that low-performance computers may not possess a sufficiently powerful graphics card to render and rotate the model.</li> <li>VAXML file format models are saved as a ZIP-compressed VAXML datasets. VAXML uses one or more .STL files to define the geometry of objects that comprise the dataset, together with one .VAXML file that provides metadata on the dataset as a whole, and specifies how the .STL files should be put together. We recommend using the free SPIERS software to view this model format (http://spiers-software.org/). However, .STL files can be opened independently in several freely available software programs (e.g. MeshLab, Blender). Additional information on the VAXML format can be found here: http://spiers-software.org/VAXML.htm.</li> </ol>
Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
<p>Midfacial morphology varies between hominoids, in particular between great apes and humans for which the face is small and retracted. The underlying developmental processes for these morphological differences are still largely unknown. Here we investigate the cellular mechanism of maxillary development (bone modelling), and how potential changes in this process may have shaped facial evolution. We analysed cross-sectional developmental series of gibbons, orangutans, gorillas, chimpanzees and present-day humans (N=183). Individuals were organized into five age groups according to their dental development. To visualize each species' bone modelling pattern and corresponding morphology during ontogeny, maps based on microscopic data were mapped onto species-specific age group average shapes obtained using geometric morphometrics. The amount of bone resorption was quantified and compared between species. Great apes share a highly similar bone modelling pattern, whereas gibbons have a distinctive resorption pattern. This suggests a change in cellular activity on the hominid branch. Humans possess most of the great ape pattern, but bone resorption is high in the canine area from birth on, suggesting a key role of canine reduction in facial evolution. We also observed that humans have high levels of bone resorption during childhood, a feature not shared with other apes.</p>
Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
<p>Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method which allows the mapping of evolutionary rate variation directly on three-dimensional phenotypes, informing on the direction and magnitude of trait change automatically.</p> <p>This new method, implemented by the function rate.map embedded in the R package 'RRphylo', is based on phylogenetic ridge regression rate estimates. Since the latter represent ridge regression slopes, they possess sign and magnitude. In 'RRphylo', different rates are calculated for different districts of the phenotype, which can then be visualized directly onto the phenotype itself. We present the application of rate.map to the evolution of facial skeleton in Hominoidea (the clade including living and fossil apes), the primate clade inclusive of Homo and the greater apes. We found that the highly derived, unique shape of the face in modern humans evolved through rapid phenotypic changes affecting the nasal bones, the brow ridge and the maxillary region. The canine fossa, a facial feature unique to Homo sapiens, did not belong to a region of rapid phenotypic change, and could be seen as the by-product of midface evolution as suggested by previous studies.</p>
Models of evolutionary rescue with plasticity and nonlinear environmental change: code and data
<p>Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here we present the simulation code and data from a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change. </p>
The role of spatial structure in multi-deme models of evolutionary rescue
<p>Genetic variation and population sizes are critical factors for successful adaptation to novel environmental conditions. Gene flow between sub-populations is a potent mechanism to provide such variation and can hence facilitate adaptation, for instance by increasing genetic variation or via the introduction of beneficial variants. On the other hand, if gene flow between different habitats is too strong, locally beneficial alleles may not be able to establish permanently. In the context of evolutionary rescue, intermediate levels of gene flow are therefore often optimal for maximizing a species' chance for survival in metapopulations without spatial structure. To which extent and under which conditions gene flow facilitates or hinders evolutionary rescue in spatially structured populations remains unresolved. We address this question by studying the differences between evolutionary rescue in the island model and in the stepping stone model in a gradually deteriorating habitat. We show that evolutionary rescue is modulated by the rate of gene flow between different habitats, which in turn depends strongly on the spatial structure and the pattern of environmental deterioration. We use these insights to show that in many cases spatially structured models can be translated into a simpler island model using an appropriately scaled effective migration rate.</p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Simulation scripts and data for the stochastic modelling of evolutionary rescue in resistance to pesticides
<p>Evolutionary rescue occurs when the genetic evolution of adaptation saves a population from extinction after environmental change. The evolution of resistance to pesticides is a special scenario of abrupt environmental change, where rescue occurs under strong selection for one or a few <em>de novo</em> resistance mutations of large effect. Here, we develop continuous-time approximations that accurately predict classic discrete-time dynamics in population genetics and population ecology in an integrated eco-evolutionary model of adaptive rescue through pesticide resistance. We derive analytical approximations for the key distributions and statistics that characterise the results, including the probability density function for the time to resistance and the probability of population extinction. The time to resistance shows a lag period, a narrow peak and a long tail, which implies that it can be difficult to predict when resistance will arise. The probability of population extinction shows a sharp transition, in that when extinction is possible, it is also highly likely, which can make eradication a theoretically achievable goal. Alongside these results contributing to the theory of evolutionary rescue, the methods have produced powerful approximations that lay the foundations of a flexible modelling framework for the applied study of eco-evolutionary dynamics to improve scientific resistance management.</p>
Applications of the k-ω Model in Stellar Evolutionary Models
<p>MESA inlists and run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017ApJ...841...10L">Li (2017)</a>. MESA version 9793.</p> <p>Publication DOI: <a href="https://doi.org/10.3847/1538-4357/aa6d4e">10.3847/1538-4357/aa6d4e</a></p>
Data for "Evolutionary velocity with protein languge models"
<p>Data tar ball for "Evolutionary velocity with protein language models"; more information can be found here: https://github.com/brianhie/evolocity#data.</p>
Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation
<p>The group Anguimorpha represents one of the most unified squamate clades in terms of body plan, ecomorphology, ecophysiology and evolution. On the other hand, the anguimorphs vary between different habitats and ecological niches. Therefore, we focused on the group Anguimorpha to test a possible correlation between heart morphology and ecological niche with respect to phylogenetic position in Squamata with <em>Sphenodon</em>, <em>Salvator</em>, and <em>Pogona</em> as the outgroups. The chosen lepidosaurian species were investigated by microCT. Generally, all lepidosaurs had two well-developed atria with complete interatrial septum and one ventricle divided by ventricular septa to three different areas. The ventricles of all lepidosaurians had a compact layer and abundant trabeculae. The compact layer and trabeculae were developed in accordance with the particular ecological niche of the species; the trabeculae in nocturnal animals with low metabolism, such as <em>Sphenodon, Heloderma</em> or <em>Lanthanotus</em>, were more massive. On the other hand, athletic animals, such as varanids or <em>Salvator</em>, had ventricle compartmentalization divided by three incomplete septa. A difference between varanids and <em>Salvator</em> was found in compact layer thickness: thicker in monitor lizards and possibly linked to their mammalian-like high blood pressure, and the level of ventricular septation. In summary: heart morphology varied among clades in connection with the ecological niche of particular species and it reflects the phylogenetic position in the model clade Anguimorpha. In the absence of fossil evidence, this is the closest approach to understanding heart evolution and septation in clades with different cardiac compartmentalization levels. </p>
Codes for: A numerical model supports the evolutionary advantage of recombination plasticity in shifting environments
<p><span>Numerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions.</span> <span>Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario – when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination </span><span>in individuals developing in a different environment than their parents and optionally, also in offspring of such individuals. </span><span>We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may appear beneficial also when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared to the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms such as chromatin epigenetics remodeling.</span></p>
Data from: A shared pattern of midfacial bone modelling in hominids suggests deep evolutionary roots for human facial morphogenesis
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Development of a homeolog-specific gene editing system in an evolutionary model for the study of polyploidy in nature
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Individual variability and versatility in an eco-evolutionary model of avian migration
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Codes for: A numerical model supports the evolutionary advantage of recombination plasticity in shifting environments
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Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
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Allen Brain Atlas
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.