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173 results for “evolutionary dynamics”
Synthetic eco-evolutionary dynamics in simple molecular environment
<p>The understanding of eco-evolutionary dynamics, and in particular the mechanism of emergence of species, is still fragmentary and in need of test bench model systems. To this aim, we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10^15 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼ 10^12 DNA oligomers of fixed sequence ('resources') over which they compete. At each cycle ('generation'), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences ('species') drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource binding dominates the selection in the first generations, while inter and intra-individual interactions becomes important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.</p>
Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History
<p>This repository contains the supplementary files associated with the study 'Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History'.</p>
Exo-Metabolomics Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Exo-Metabolomics Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Illumina Sequencing Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity
Global change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to diversity loss and how this affects their responses to global change. Here, we performed a common garden experiment testing whether plant responses to global change are influenced by their selection history and the conditioning history of soil at different plant diversity levels. Using seeds of four grass species and soil samples from a 14-year-old biodiversity experiment, we grew the offspring of the plants either in their own soil or in soil of a different community, and exposed them either to drought, increased nitrogen input, or a combination of both. Under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, soil history, and to a lesser extent plant history, had species-specific effects on trait expression. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which in turn affects plant eco-evolutionary pathways. How this change affects species' response to global change and whether this can cause a feedback loop should be investigated in more detail in future studies.
Summary data for plots in: Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations
<p>Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting in local extinction and recolonization through evolving dispersal, facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favour increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.</p>
Viral diversity and co-evolutionary dynamics across the ant phylogeny
<p>This repository contains the alignment file and phylogeny of every viral clade assessed in this study. The viral phylogenies are in Newick format as well as a pdf and contain bootstrap values greater than 50. The alignment files are in PHYLIP format. Additionally, this repository contains nucleotide sequences of every viral sequence identified in this study and it is entitled: "final_viruses_contigs.fasta" in fasta format. </p>
lingpy/sign-language-evolution-paper: Evolutionary Dynamics in the Dispersal of Sign Languages
<p>Supplement for study on Manual Alphabet evolution.</p>
Data and Code for: An Experimental Test of Eco-evolutionary Dynamics on Rocky Shores
<p><span>Abstract: </span></p> <p><span>Despite a growing body of theoretical studies and laboratory experiments that have brought attention to the reciprocal impacts that ecological and evolutionary processes can have on one another, few studies have tested the importance of eco-evolutionary feedbacks in natural communities. We examined whether selection on natural phenotypic variation in a population of drilling dogwhelks (<em>Nucella canaliculata</em>) could impact rocky shore community dynamics. We performed a selection experiment raising newly-hatched dogwhelks on four diet treatments, reflecting natural variation in the abundance and shell thickness of prey species. Adult dogwhelks were tested in the laboratory on their ability to drill thick-shelled mussels. In addition, snails were outplanted to field cages to track the effects of dogwhelk phenotype on mussel bed succession. Despite our laboratory experiments suggesting that prey can impose selection and result in divergent consumer traits, successional patterns differed minimally based on the early-life diet of the dogwhelks.</span></p>
Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
<p><span><span><span><span><span><span><span><span><span><span><span>The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which likely played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
<p><strong>Background</strong></p> <p>During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. Here we examine how several <em>Sgs</em> genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in <em>Drosophila</em> species.</p> <p><strong>Results</strong></p> <p>We examined high-quality genome assemblies of 24 <em>Drosophila</em> species to study the evolutionary dynamics of four glue genes that are present in <em>D. melanogaster</em> and are part of the same gene family <em>–</em> <em>Sgs1, Sgs3, Sgs7 and Sgs8 –</em> across approximately 30 millions of years. We annotated a total of 102 <em>Sgs</em> genes and grouped them into 4 subfamilies. We present here a new nomenclature for these <em>Sgs</em> genes based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (<em>Sgs1, Sgs3x, Sgs3e</em>) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (<em>Sgs3b, Sgs7, Sgs8</em>) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. Our data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics.</p> <p><strong>Conclusions</strong></p> <p>Our comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. Our molecular, phylogenetic and comparative analysis of the four glue genes <em>Sgs1, Sgs3, Sgs7</em> and <em>Sgs8 </em>provides the foundation for investigating the role of the various glue genes during <em>Drosophila</em> life.</p>
Data for: Morphological covariance and onset of foot prehensility as indicators of integrated evolutionary dynamics in the herons (Ardeidae)
<p>The ultimate form an organism attains is based, in part, on the rate and timing of developmental trajectories and on compensatory relationships between morphological traits. For example, there is often an inverse correlation between the relative size of an organism's head and the length of its legs. Avian examples with disproportionately small heads and long legs include ostriches (Struthionidae), flamingos (Phoenicopteridae), cranes (Gruidae), stilts (Recurvirostridae), and storks (Ciconiidae). To determine whether a possible compensatory relationship exists between relative head size and hind-limb length in a typically long-legged family of birds—the Ardeidae—we measured skull dimensions (length, width, and height of cranium, and total skull length, including culmen) and skeletal hind-limb dimensions (femur, tibiotarsus, and tarsometatarsus) of the 12 North American species (north of Mexico) and of 12 additional taxa, including the morphologically divergent Agamia and Cochlearius. Our analyses reveal a negative allometric relationship between head size and leg length. For example, <em>Ardea</em> species exhibit the smallest relative head sizes and the longest legs, while <em>Butorides</em>, <em>Nycticorax</em>, <em>Nyctanassa</em>, and <em>Cochlearius</em> have among the largest heads relative to hind-limb length. Furthermore, both positive and negative allometries occur in paired comparisons between the three hind-limb bones, resulting in tall morphotypes having disproportionately short femurs while small morphotypes exhibit long femurs; this relationship has implications for foraging behavior. Moreover, long legs of <em>Ardea</em> apparently derive from an extended growth period, or hypermorphosis, while relatively short legs of <em>Butorides</em> result from growth truncation. The latter are thus morphologically paedomorphic features that, paradoxically, permit a functional precociality of the hind limbs: early onset of prehensile ability of the feet for grasping branches, which nestlings retain into adulthood, later expressed in foraging mode. This developmentally accelerated prehensile function in small species may be attributed, in part, to selection for predator avoidance in the early nestling stage.</p>
Data from: Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents
<p><span>Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species </span><span>(<em>Ashinkailepas kermadecensis</em>,<em> Imbricaverruca yamaguchii</em>) </span><span>from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481.5 to 1054.6 Mb, with repetitive sequence contents of 21.2 to 50.7%. Concordance rates of orthologs and heterozygosity ratios were between 82.4 and 91.7% and between 1.1 and 2.6, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, <em>CP100A</em>, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesized to be essential for thoracican settlement. Duplicated genes, <em>CP100B</em> and <em>CP100C</em>, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of <em>CP52 </em>genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no <em>CP52</em> genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.</span></p>
Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography
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Data from: Unraveling the web of life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species
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Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
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Synthetic eco-evolutionary dynamics in simple molecular environment
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Data from: Eco-evolutionary dynamics in the wild: clonal turnover and stability in Daphnia populations
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The evolutionary dynamics and fitness landscape of clonal hematopoiesis
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Molecular Dynamics Simulations and associated data for: Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases
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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.