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829 results for “Evolvability”
Viral protein instability enhances host-range evolvability
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Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV
<p>SARS-CoV-2, the causative agent of COVID-19, is widespread in several countries around the world following its late 2019 emergence in humans. We determined the SARS-CoV-2 selectome by calculating rates of pervasive and episodic diversifying selection for every amino acid coding position in the SARS-CoV-2 genome. To provide context for evolutionary dynamics of a highly pathogenic betacoronavirus following a zoonotic spillover into human hosts, we also determined the selectomes of SARS-CoV and MERS-CoV, and performed evolvability calculations for SARS-CoV-2 based on SARS-CoV. These findings provide a comprehensive view of zoonotic, highly pathogenic betacoronavirus evolutionary dynamics that can be directly applied to diagnostic assay and vaccine design for SARS-CoV-2.</p>
Data from: Cross-sex genetic covariances limit the evolvability of wing-shape within and among species of Drosophila
The independent evolution of males and females is potentially constrained by both sexes inheriting the same alleles from their parents. This genetic constraint can limit the evolvability of complex traits; however, there are few studies of multivariate evolution that incorporate cross-sex genetic covariances in their predictions. Drosophila wing-shape has emerged as a model high-dimensional phenotype; wing-shape is highly evolvable in contemporary populations, and yet perplexingly stable across phylogenetic timescales. Here we show that cross-sex covariances in D. melanogaster, given by the B-matrix, may considerably bias wing-shape evolution. Using random skewers, we show that B would constrain the response to antagonistic selection by 90%, but would double the response to concordant selection. Both cross-sex within-trait and cross-sex cross-trait covariances determined the response to antagonistic selection, but only cross-sex within-trait covariances facilitated the response to concordant selection. Similar patterns were observed when selection was applied in the direction of extant sexual dimorphism in D. melanogaster, and in directions of most and least dimorphic variation across the Drosophila phylogeny. Our results highlight the importance of considering between-sex genetic covariances when making predictions about evolution on both macro- and micro- evolutionary timescales, and may provide one more explanatory piece in the puzzle of stasis.
Dataset for: Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves
<p>Data generated with VirtualMicrobes (<a href="https://bitbucket.org/thocu/virtual-microbes">https://bitbucket.org/thocu/virtual-microbes</a>) supporting: </p> <p>J.Meijer, B. van Dijk, P. Hogeweg. Contingent evolution of alternative metabolic network topologies determines whether cross-feeding evolves. Nature Communication Biology (2020)</p>
IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria
<p>The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with <em>Escherichia coli</em>. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017) in light with the IS dynamics and their correlation with fitness improvements described in the present work. </p>
Divergence of responses to variable socio-sexual environments in laboratory populations of Drosophila melanogaster evolving under altered operational sex-ratios
<p class="BodyA">Post-copulatory sexual selection (PSS) is an important selective force that determines fitness in polyandrous species. PSS can be intense in some cases and can drive the evolution of remarkable ejaculate properties. In males, investment in ejaculate plays an important role in the outcome of PSS. Thus, males are expected to adaptively tailor their ejaculate according to the perceived competition in their vicinity. Plastic responses in ejaculate investment to variation in intra-sexual competition are disparate and widespread in males.</p> <p class="BodyA"><span>We investigated the evolution of plasticity in reproductive traits using <i>Drosophila melanogaster</i> populations evolving for more than 150 generations under male- or female-biased sex ratios.</span> <span>When exposed to different numbers of competitors early in their life, males from these two regimes responded differently in terms of their copulation duration and sperm competitive ability. In addition, the effect of this early life experience wore off at different rates in males of male-biased and female-biased regimes with increasing time from the removal of competitive cues. Furthermore, our study finds that males change their reproductive strategies depending upon the identity of rival males. Together, our results provide evidence of the evolution of male reproductive investment that depends on socio-sexual cues experienced early in life. </span></p>
Evolutionary divergences mirror Pleistocene paleodrainages in a rapidly-evolving complex of oasis-dwelling jumping spiders (Salticidae, Habronattus tarsalis)
<p>We aimed to understand the diversification history of jumping spiders in the <i>Habronattus tarsalis</i> species complex, with particular emphasis on how history in this system might illuminate biogeographic patterns and processes in deserts of the western United States. Desert populations of <i>H. tarsalis</i> are now confined to highly discontinuous oasis-like habitats, but these habitats would have been periodically more connected during multiple pluvial periods of the Pleistocene. We estimated divergence times using relaxed molecular clock analyses of published transcriptome datasets. Geographic patterns of diversification history were assessed using phylogenetic and cluster analyses of original sequence capture, RADSeq and morphological data. Clock analyses of multiple replicate transcriptome datasets indicate mid- to late-Pleistocene divergence dates within the <i>H. tarsalis</i> group complex. Coalescent and concatenated phylogenetic analyses <span><span>indicate</span></span><span> </span>four early-diverging lineages (<i>H. mustaciata</i>, <i>H. ophrys</i>, and <i>H. tarsalis</i> from the Lahontan and Owens drainage basins), with remaining samples separated into larger clades from the Mojave desert, and western populations from the California Floristic Province of California and northern Baja California. Focusing on desert populations, there is a strong correspondence between RAD lineages and modern and/or paleodrainages, mirrored more finely in STRUCTURE and machine learning results. Non-metric multidimensional scaling analysis reveals a strong congruence between morphological clusters and genetic lineages, whether the latter represent previously described species or <i>H.tarsalis </i>RAD lineages. Here we have uncovered a system that adds to our regional biogeographic knowledge in unique ways, using multiple types of evidence in a broadly-distributed terrestrial taxon. At the same time, we have discovered rapid evolution of both novel morphological forms and diverging genetic lineages. The hierarchical nature of variation in the <i>H. tarsalis</i> complex, the minute range sizes of many forms, the high likelihood that geographic distributions have shrunk and expanded through time, and signs of introgression all align with an ephemeral speciation model.</p>
Data from: Testicular melanization has evolved in birds with high mtDNA mutation rates
Melanin is mainly found in the integument of animals, but it also appears in several extracutaneous tissues. The presence of melanin in testes has been anecdotally reported in all vertebrate groups, but the causes and functions of this melanin remain unknown. Similar to other extracutaneous melanins, testicular melanin may protect male germ cells from oxidative stress. Given the high respiratory activity of spermatozoa, oxidative stress generated by mitochondrial dysfunction as a consequence of mtDNA mutations directly affects sperm viability. Thus, natural selection may favour testicular melanization in males of species with high historical mutation rates in the mitochondrial genome. Here, we tested this hypothesis using information on occurrence of testicular melanization and mutation accumulation as reflected by cytochrome b mtDNA base pair substitution rates in a large set of 134 species of birds, controlling for the confounding effects of body mass, reproductive activity and phylogeny. We found that testicular melanization has evolved in species with high rates of accumulated mitochondrial mutations and propose that this is an adaptive response related to the protective capacity of melanin against oxidative stress. In support of this hypothesis, testicular melanization was more frequently observed during the breeding season of birds (i.e. when spermatogenesis is likely to occur) than during reproductive inactivity. In contrast to other extracutaneous melanins whose abundance seems to reflect skin and coat colour, we did not find a correlation between the proportion of plumage coloured by melanins and occurrence of testicular melanization. Whereas future experimental studies should test these hypotheses, our study highlights for the first time that melanization patterns in animals may evolve as a response to historical mutation rates.
Data from: Sexually selected traits evolve positive allometry when some matings occur irrespective of the trait
Positive allometry of secondary sexual traits (whereby larger individuals have disproportionally larger traits than smaller individuals) has been called one of the most pervasive and poorly understood regularities in the study of animal form and function. Its widespread occurrence is in contrast with theoretical predictions that it should evolve only under rather special circumstances.
Data from: Experimental evolution demonstrates evolvability of preferential nutrient allocation to competing traits, in response to chronic malnutrition.
Investigating the evolutionary origins of disease vulnerability is an important aspect of evolutionary medicine that strongly complements our current understanding on proximate causes of disease. Life history trade-offs mediated through evolutionary changes in resource allocation strategies could be one possible explanation to why suboptimal traits that leave bodies vulnerable to disease exist. For example, Drosophila melanogaster populations experimentally evolved to tolerate chronic larval malnutrition succumb to intestinal infection despite eliciting a competent immune response, owing to the loss of their intestinal integrity. Here, I test if evolved changes in resource allocation underlies this trade-off, by assaying preferential allocation of dietary protein towards growth and tissue repair in the same populations. Using two phenotypic traits: regeneration of intestinal epithelium post-pathogenic infection and body weight, I show that in accordance to the dynamic energy budget theory (DEB) dietary protein acquired during the larval phase is allocated to both growth and adult tissue repair. Furthermore, by altering the ratio of protein and carbohydrates in the larval diets I demonstrate that in comparison to the control populations, the evolved (selected) populations differ in their protein allocation strategy towards these two traits. While the control populations stored away excess protein for tissue repair, the selected populations invested it towards immediate increase in body weight rather than towards an unanticipated tissue damage. Thus, I show how macronutrient availability and their allocation between traits can alter resistance, and provide empirical evidence that supports the 'mismatch hypothesis', wherein vulnerability to disease is proposed to stem from the differences between ancestral and current environment.
Data from: Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity
Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. Here we measure quantitative genetic variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, we found that Spatial populations tend to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. We discuss the patterns for quantitative genetic (QG) variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs whereas the QG patterns for some other traits resembled that of neutral SNPs.
Data from: Evolutionary stability of jointly evolving traits in subdivided populations
The evolutionary stability of quantitative traits depends on whether a population can resist invasion by any mutant. While uninvadability is well understood in well-mixed populations, it is much less so in subdivided populations when multiple traits evolve jointly. Here, we investigate whether a spatially subdivided population at a monomorphic equilibrium for multiple traits can withstand invasion by any mutant or is subject to diversifying selection. Our model also explores the correlations among traits arising from diversifying selection and how they depend on relatedness due to limited dispersal. We find that selection tends to favor a positive (negative) correlation between two traits when the selective effects of one trait on relatedness is positively (negatively) correlated to the indirect fitness effects of the other trait. We study the evolution of traits for which this matters: dispersal that decreases relatedness and helping that has positive indirect fitness effects. We find that when dispersal cost is low and the benefits of helping accelerate faster than its costs, selection leads to the coexistence of mobile defectors and sessile helpers. Otherwise, the population evolves to a monomorphic state with intermediate helping and dispersal. Overall, our results highlight the effects of population subdivision for evolutionary stability and correlations among traits.
Data from: Evolvability meets biogeography: evolutionary potential decreases at high and low environmental favourability
Understanding and forecasting the effects of environmental change on wild populations requires knowledge on a critical question: do populations have the ability to evolve in response to that change? However, our knowledge on how evolution works in wild conditions under different environmental circumstances is extremely limited. We investigated how environmental variation influences the evolutionary potential of phenotypic traits. We used published data to collect or calculate 135 estimates of evolvability of morphological traits of European wild bird populations. We characterized the environmental favourability of each population throughout the species' breeding distribution. Our results suggest that the evolutionary potential of morphological traits decreases as environmental favourability becomes high or low. Strong environmental selection pressures and high intra-specific competition may reduce species' evolutionary potential in low- and high- favourability areas, respectively. This suggests that species may be least able to adapt to new climate conditions at their range margins and at the centre. Our results underscore the need to consider the evolutionary potential of populations when studying the drivers of species distributions, particularly when predicting the effects of environmental change. We discuss the utility of integrating evolutionary dynamics into a biogeographical perspective to understand how environmental variation shapes evolutionary patterns. This approach would also produce more reliable predictions about the effect of environmental change on population persistence and therefore on biodiversity.
Data from: The SOS response increases bacterial fitness, but not evolvability, under a sublethal dose of antibiotic
Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.
Data from: Increased survival of experimentally evolved antimicrobial peptide-resistant Staphylococcus aureus in an animal host
Antimicrobial peptides (AMPs) have been proposed as new class of antimicrobial drugs, following the increasing prevalence of bacteria resistant to antibiotics. Synthetic AMPs are functional analogues of highly evolutionarily conserved immune effectors in animals and plants, produced in response to microbial infection. Therefore, the proposed therapeutic use of AMPs bears the risk of 'arming the enemy': bacteria that evolve resistance to AMPs may be cross-resistant to immune effectors (AMPs) in their hosts. We used a panel of populations of Staphylococcus aureus that were experimentally selected for resistance to a suite of individual AMPs and antibiotics to investigate the 'arming the enemy' hypothesis. We tested whether the selected strains showed higher survival in an insect model (Tenebrio molitor) and cross-resistance against other antimicrobials in vitro. A population selected for resistance to the antimicrobial peptide iseganan showed increased in vivo survival, but was not more virulent. We suggest that increased survival of AMP-resistant bacteria almost certainly poses problems to immune-compromised hosts.
Data from: Functional C-terminally encoded peptide (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis
Sedentary plant-parasitic nematodes (PPNs) induce and maintain an intimate relationship with their host, stimulating cells adjacent to root vascular tissue to re-differentiate into unique and metabolically active 'feeding sites'. The interaction between PPNs and their host is mediated by nematode effectors. We describe the discovery of a large and diverse family of effector genes, encoding C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone mimics (RrCEPs), in the syncytia-forming plant parasite Rotylenchulus reniformis. The particular attributes of RrCEPs distinguish them from all other CEPs, regardless of origin. Together with the distant phylogenetic relationship of R. reniformis to the only other CEP-encoding nematode genus identified to date (Meloidogyne), this suggests that CEPs probably evolved de novo in R. reniformis. We have characterized the first member of this large gene family (RrCEP1), demonstrating its significant up-regulation during the plant–nematode interaction and expression in the effector-producing pharyngeal gland cell. All internal CEP domains of multi-domain RrCEPs are followed by di-basic residues, suggesting a mechanism for cleavage. A synthetic peptide corresponding to RrCEP1 domain 1 is biologically active and capable of up-regulating plant nitrate transporter (AtNRT2.1) expression, whilst simultaneously reducing primary root elongation. When a non-CEP-containing, syncytia-forming PPN species (Heterodera schachtii) infects Arabidopsis in a CEP-rich environment, a smaller feeding site is produced. We hypothesize that CEPs of R. reniformis represent a two-fold adaptation to sustained biotrophy in this species: (i) increasing host nitrate uptake, whilst (ii) limiting the size of the syncytial feeding site produced.
Data from: Phenotypic variation and covariation indicate high evolvability of acoustic communication in crickets
Studying the genetic architecture of sexual traits provides insight into the rate and direction at which traits can respond to selection. Traits associated with few loci and limited genetic and phenotypic constraints tend to evolve at high rates typically observed for secondary sexual characters. Here, we examined the genetic architecture of song traits and female song preferences in the field crickets Gryllus rubens and G. texensis. Song and preference data were collected from both species and interspecific F1 and F2 hybrids. We first analysed phenotypic variation to examine interspecific differentiation and trait distributions in parental and hybrid generations. Then, the relative contribution of additive and additive-dominance variation was estimated. Finally, phenotypic variance-covariance (P) matrices were estimated to evaluate the multivariate phenotype available for selection. Song traits and preferences had unimodal trait distributions and hybrid offspring were intermediate with respect to the parents. We uncovered additive and dominance variation in song traits and preferences. For two song traits we found evidence for X-linked inheritance. On one hand, the observed genetic architecture does not suggest rapid divergence, although sex-linkage may have allowed for somewhat higher evolutionary rates. On the other hand, P matrices revealed that multivariate variation in song traits aligned with major dimensions in song preferences, suggesting a strong selection response. We also found strong covariance between the main traits that are sexually selected and traits that are not directly selected by females, providing an explanation for the striking multivariate divergence in male calling songs despite limited divergence in female preferences.
Data from: Virus resistance is not costly in a marine alga evolving under multiple environmental stressors
Viruses are important evolutionary drivers of host ecology and evolution. The marine picoplankton Ostreococcus tauri has three known resistance types that arise in response to infection with the Phycodnavirus OtV5: susceptible cells (S) that lyse following viral entry and replication; resistant cells (R) that are refractory to viral entry; and resistant producers (RP) that do not all lyse but maintain some viruses within the population. To test for evolutionary costs of maintaining antiviral resistance, we examined whether O. tauri populations composed of each resistance type differed in their evolutionary responses to several environmental drivers (lower light, lower salt, lower phosphate and a changing environment) in the absence of viruses for approximately 200 generations. We did not detect a cost of resistance as measured by life-history traits (population growth rate, cell size and cell chlorophyll content) and competitive ability. Specifically, all R and RP populations remained resistant to OtV5 lysis for the entire 200-generation experiment, whereas lysis occurred in all S populations, suggesting that resistance is not costly to maintain even when direct selection for resistance was removed, or that there could be a genetic constraint preventing return to a susceptible resistance type. Following evolution, all S population densities dropped when inoculated with OtV5, but not to zero, indicating that lysis was incomplete, and that some cells may have gained a resistance mutation over the evolution experiment. These findings suggest that maintaining resistance in the absence of viruses was not costly.
Data from: Here's to the losers: evolvable residents accelerate the evolution of high fitness invaders
Recent work has shown that evolvability plays a key role in determining the long-term population dynamics of asexual clones. However, simple considerations suggest that the evolvability of a focal lineage of bacteria should also be influenced by the evolvability of its competitors. First, evolvable competitors should accelerate evolution by impeding the fixation of the focal lineage through a clonal interference–like mechanism. Second, evolvable competitors should increase the strength of selection by rapidly degrading the environment, increasing selection for adaptive mutations. Here we tested these ideas by allowing a high-fitness clone of the bacterium Pseudomonas aeruginosa to invade populations of two low-fitness resident clones that differ in their evolvability. Both competition from mutations in the resident lineage and environmental degradation lead to faster adaptation in the invader through fixing single mutations with a greater fitness advantage. The results suggest that competition from mutations in both the successful invader and the unsuccessful resident shapes the adaptive trajectory of the invader through both direct competition and indirect environmental effects. Therefore, to predict evolutionary outcomes, it will be necessary to consider the evolvability of all members of the community and the effects of adaptation on the quality of the environment. This is particularly relevant to mixed microbial communities where lineages differ in their adaptive potential, a common feature of chronic infections.
Data from: Neural modularity helps organisms evolve to learn new skills without forgetting old
A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks are organized critically affects their learning dynamics. In this paper, we test whether catastrophic forgetting can be reduced by evolving modular neural networks. Modularity intuitively should reduce learning interference between tasks by separating functionality into physically distinct modules in which learning can be selectively turned on or off. Modularity can further improve learning by having a reinforcement learning module separate from sensory processing modules, allowing learning to happen only in response to a positive or negative reward. In this paper, learning takes place via neuromodulation, which allows agents to selectively change the rate of learning for each neural connection based on environmental stimuli (e.g. to alter learning in specific locations based on the task at hand). To produce modularity, we evolve neural networks with a cost for neural connections. We show that this connection cost technique causes modularity, confirming a previous result, and that such sparsely connected, modular networks have higher overall performance because they learn new skills faster while retaining old skills more and because they have a separate reinforcement learning module. Our results suggest (1) that encouraging modularity in neural networks may help us overcome the long-standing barrier of networks that cannot learn new skills without forgetting old ones, and (2) that one benefit of the modularity ubiquitous in the brains of natural animals might be to alleviate the problem of catastrophic forgetting.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.