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203 results for “phenotypic evolution”
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype
<p>Source codes and data sets for arXiv:2012.03030. For details, see readme.txt file.</p>
Data from: In vivo functional phenotypes from a computational epistatic model of evolution
<p><span>Computational models of evolution are valuable for understanding the dynamics of sequence variation, to infer phylogenetic relationships or potential evolutionary pathways, and for biomedical and industrial applications. Despite these benefits, few have validated their propensities to generate outputs with <em>in vivo </em>functionality, which would enhance their value as accurate and interpretable evolutionary algorithms. Utilizing the Hamiltonian of the joint probability of sequences in the family as fitness metric, we sampled and experimentally tested for <em>in vivo</em> beta-lactamase activity in E. coli TEM-1 variants. These variants retain family-like functionality while being more active than their WT predecessor. We found that depending on the inference method used to generate the epistatic constraints, different parameters simulate diverse selection strengths. Under weaker selection, local Hamiltonian fluctuations reliably predict relative changes to variant fitness, recapitulating neutral evolution. In this dataset, we include input datasets, simulation trajectories as well as experimental data to support the publication: "In vivo functional phenotypes from a computationa epistatic model of evolution".</span></p>
Data from: Evolution of fungal phenotypic disparity
<p><span>Organismal grade multicellularity has been achieved only in animals, plants, and fungi. All three kingdoms manifest phenotypically disparate body plans, but their evolution has only been considered in detail for animals. Here we seek to test the general relevance of hypotheses on the evolution of animal body plans by characterising the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated, zygomycetous, sac-bearing, and club-bearing. The discontinuity between morphotypes is a consequence of the extinction of phylogenetic intermediates, indicating that a complete record of fungal disparity would present a much more homogeneous distribution of form. Fungal phenotypic variety gradually expands through time for the most part but sharply increases with the emergence of multicellular body plans. Simulations show these temporal trends to be decidedly non-random, and at least partially shaped by hierarchical contingency. Fungal phenotypic distance is decoupled from changes in gene number, genome size, and taxonomic diversity. Only differences in organismal complexity, the number of traits that constitute an organism, at the cellular and multicellular levels present a meaningful relationship with fungal disparity. Both animals and fungi exhibit a gradual increase in disparity through time, resulting in distributions of form made discontinuous by the extinction of phylogenetic intermediates. These congruences hint at a common mode of multicellular body plan evolution.</span></p>
Building behaviour does not drive rates of phenotypic evolution in spiders
<p>This data set contains raw data tables, scripts and supplemental figures supporting the article Wolff et al. (2021, PNAS 118: e2102693118). In our study we assembled morphometric and ecological trait data of spiders from literature and de novo measurements and observations and used this data to infer the rates of morphological change over deep time in relation to web building behaviour.</p>
Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
<p>Quantifying the relative contribution of functional and developmental constraints on phenotypic variation is a longstanding goal of macroevolution, but it is often difficult to distinguish different types of constraints. Alternatively, selection can limit phenotypic (co)variation if some trait combinations are generally maladaptive. The anatomy of leaves with stomata on both surfaces (amphistomatous) presents a unique opportunity to test the importance of functional and developmental constraints on phenotypyic evolution. The key insight is that stomata on each leaf surface encounter the same functional and developmental constraints, but potentially different selective pressures because of leaf asymmetry in light capture, gas exchange, and other features. Independent evolution of stomatal traits on each surface implies that functional and developmental constraints alone likely do not explain trait covariance. Packing limits on how many stomata can fit into a finite epidermis and cell-size-mediated developmental integration are hypothesized to constrain variation in stomatal anatomy. The simple geometry of the planar leaf surface and knowledge of stomatal development makes it possible to derive equations for phenotypic (co)variance caused by these constraints and compare them with data. We analyzed evolutionary covariance between stomatal density and length in amphistomatous leaves from 236 phylogenetically independent contrasts using a robust Bayesian model. Stomatal anatomy on each surface diverges partially independently, meaning that packing limits and developmental integration are not sufficient to explain phenotypic (co)variation. Hence, (co)variation in ecologically important traits like stomata arises in part because there is a limited range of evolutionary optima. We show how it is possible to evaluate the contribution of different constraints by deriving expected patterns of (co)variance and testing them using similar but separate tissues, organs, or sexes.</p>
Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants
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Data from: The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family
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Data from: In vivo functional phenotypes from a computational epistatic model of evolution
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Building behaviour does not drive rates of phenotypic evolution in spiders
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Data from: Evolution of fungal phenotypic disparity
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Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes
<p>Intraspecific competition has long been considered a key driver of evolutionary diversification, but whether it can also promote evolutionary innovation is less clear. We examined the interplay between competition and phenotypic plasticity in fueling the origins of a novel, complex phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles (genus <i>Spea</i>) that specializes on fairy shrimp. We specifically sought to explore the possible origins of this phenotype by providing shrimp to <i>Scaphiopus holbrookii</i> tadpoles (the sister genus to <i>Spea </i>that does not produce carnivores) while subjecting them to competition for their standard diet of detritus. Previous research had shown that this species will eat shrimp when detritus is limited, and that these shrimp-fed individuals produce features that are redolent of a rudimentary <i>Spea </i>carnivore. In this study, we found that: 1) behavioral and morphological plasticity enabled some individuals to expand their diet to include shrimp; 2) there was heritable variation in this plasticity; and 3) individuals received a growth and development benefit by eating shrimp. Thus, novel resource use can arise via plasticity as an adaptive response to intraspecific competition. More generally, our results show how competition and plasticity may interact to pave the way for the evolution of complex, novel phenotypes, such as the distinctive carnivore morph in present-day <i>Spea</i>.</p>
Trait-fitness associations do not predict within-species phenotypic evolution over 2 million years
Long-term patterns of phenotypic change are the cumulative results of tens of thousands to millions of years of evolution. Yet, empirical and theoretical studies of phenotypic selection are largely based on contemporary populations. The challenges in studying phenotypic evolution, in particular trait-fitness associations in the deep past, are barriers to linking micro- and macroevolution. Here, we capitalize on the unique opportunity offered by a marine colonial organism commonly preserved in the fossil record to investigate trait-fitness associations over 2 million years. We use the density of female polymorphs in colonies of <em>Antartothoa tongima</em> as a proxy for fecundity, a fitness component, and investigate multivariate signals of trait-fitness associations in six time intervals on the backdrop of Pleistocene climatic shifts. We detect negative trait-fitness associations for feeding polymorph (autozooid) sizes, positive associations for autozooid shape but no particular relationship between fitness and brood chamber size. In addition, we demonstrate that long-term trait patterns are explained by palaeoclimate and to a lesser extent by ecological interactions. Our analyses show that macroevolutionary outcomes of trait evolution are not a simple scaling-up from the trait-fitness associations.
A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
<p>Detecting the signature of selection in coding sequences and associating it with shifts in phenotypic states can unveil genes underlying complex traits. Of the various signatures of selection exhibited at the molecular level, changes in the pattern of selection at protein coding genes have been of main interest. To this end, phylogenetic branch-site codon models are routinely applied to detect changes in selective patterns along specific branches of the phylogeny. Many of these methods rely on a pre-specified partition of the phylogeny to branch categories, thus treating the course of trait evolution as fully resolved and assuming that phenotypic transitions have occurred only at speciation events. Here we present TraitRELAX, a new phylogenetic model that alleviates these strong assumptions by explicitly accounting for the uncertainty in the evolution of both trait and coding sequences. This joint statistical framework enables the detection of changes in selection intensity upon repeated trait transitions. We evaluated the performance of TraitRELAX using simulations and then applied it to two case studies. Using TraitRELAX, we found an intensification of selection in the primate SEMG2 gene in polygynandrous species compared to species of other mating forms, as well as changes in the intensity of purifying selection operating on sixteen bacterial genes upon transitioning from a free-living to an endosymbiotic lifestyle.</p>
Data from: Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies
Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this since amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype - the duration of bioluminescent courtship pulses - is shaped by biochemical function. First, by measuring light production from induced bioluminescence in 38 species, we discovered differences between species in their biochemical reactions. Then, for 16 species of which biochemical, phylogenetic, and behavioral data are all available, we used phylogenetic comparative models to show that differences in biochemical reaction are nonlinearly correlated with the duration of courtship pulses. This relationship indicates that changes to both enzyme (c-luciferase) function and usage have shaped the evolution of courtship displays, but that they differentially contribute to these phenotypic changes. This nonlinear dynamic may have consequences for the disparity of signaling phenotypes observed across species, and demonstrates how unappreciated diversity at the biochemical level can lead to inferences about behavioural evolution.
Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)
<p class="Normal1">Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro-computed tomographic (µCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology.</p>
Data from: Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque-headed lizards
Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque-headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus) while in others, both sexes are monomorphic. To characterize these patterns, we define phenotypic integration at the interspecific level as a pattern or network of traits evidenced by phylogenetically adjusted correlations that persist among species. At this level, modularity is an increased connectedness (e.g., higher correlation) among sections of these networks that persist in a lineage during the evolution of complex phenotypes. To test both concepts, we used phylogenetic geomorphometrics to characterize the head structure of corytophanid lizards, based on a time-calibrated phylogeny that includes candidate fossil ancestors. We found evidence of an older diversification of corytophanids than previously reported (~67 vs. ~23.5 MYA) and show that this clade includes two morphological head architectures: (1) Sexually dimorphic crests present in males that are evolving independently from the rest of the head structure, and (2) full integration of the head morphology in monomorphic species. We propose that both architectures are optimal evolutionary trajectories of the parietal crest bones in the head of these lizards. In sexually dimorphic species, these bones are elongated and thinner, and gave rise to the extended crest used in male courtship displays. In monomorphic species, the parietal crest grew thicker in both sexes to allow for a better insertion of muscles associated with a stronger bite.
Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
<p class="Standard">The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: <i>Berndtia</i> and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.</p> <p class="Standard"> </p> <p class="Standard"><i>Key words: </i>adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny</p>
Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism
<p>Locusts exhibit one of nature's most spectacular examples of complex phenotypic plasticity, in which changes in density cause solitary and cryptic individuals to transform into gregarious and conspicuous locusts forming large migrating swarms. We investigated how these coordinated alternative phenotypes might have evolved by studying the Central American locust and three closely related non-swarming grasshoppers in a comparative framework. By experimentally isolating and crowding during nymphal development, we induced density-dependent phenotypic plasticity and quantified the resulting behavioural, morphological, and molecular reaction norms. All four species exhibited clear plasticity, but the individual reaction norms varied among species and showed different magnitudes. Transcriptomic responses were species-specific, but density-responsive genes were functionally similar across species. There were modules of co-expressed genes that were highly correlated with plastic reaction norms, revealing a potential molecular basis of density-dependent phenotypic plasticity. These findings collectively highlight the importance of studying multiple reaction norms from a comparative perspective.</p>
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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.
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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.
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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
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