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61 results for “Long-term Evolution”
Dataset: The role of long-term hydrodynamic evolution in the accumulation and preservation of organic carbon-rich deposits in the shelf seas
<p>Output files from harmonic analysis of regional tidal model, glacial isostatic adjustment model input and output (relative sea level and ice sheet extent datasets), and scripts for figure generation.</p> <p>If using these data, please cite: </p> <p><strong>Ward, S.L., Bradley, S.L., Roseby, Z.A., Wilmes, S.B., Vosper, D.F., Roberts, C.M. and Scourse, J.D., 2025. The role of long‐term hydrodynamic evolution in the accumulation and preservation of organic carbon‐rich shelf sea deposits. <em>Journal of Geophysical Research: Oceans</em>, <em>130</em>(4), p.e2024JC022092. <a href="https://doi.org/10.1029/2024JC022092">https://doi.org/10.1029/2024JC022092</a></strong></p> <p> </p>
Data and code for Rowan et al. "Long-term biotic homogenization in the East African Rift System over the last 6 Myr of hominin evolution"
<p>Data and code for Rowan et al. "Long-term biotic homogenization in the East African Rift System over the last 6 Myr of hominin evolution" published in <em>Nature Ecology and Evolution</em>.</p>
D3.10 - Users document for methods and models of the long-term coastline evolution.
<p>The D3.10, related to Task 3.5 and entitled "User Document for Methods and Models of the Long-term Coastline Evolution," is a WP3 deliverable, specifically a report describing the methods and models used to study long-term morpho-dynamic processes in a climate-change scenario. </p>
Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction
Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 Mya) to long-term stasis during the post-Paleozoic (250 Mya to present). Thus, a dramatic shift in the evolutionary mode coincides with the most severe biotic catastrophe of the Phanerozoic (543 Mya to present). Paleozoic tracking of pO2 was confined to Order Fusulinida, whereas Paleozoic lagenides, miliolids, and textulariids were best described by the stasis model. Stasis continued to best describe miliolids and textulariids during post-Paleozoic time, while random walk was the best supported mode for the other diverse orders. The shift in evolutionary dynamics thus appears to have resulted primarily from the selective elimination of fusulinids at the end of the Permian Period. These findings illustrate the potential for mass extinction to alter macroevolutionary dynamics for hundreds of millions of years.
Data from: Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon.
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother to offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated in two different diets: a regular one (Chow diet, CD) and high-fat high-sugar one (Western diet, WD). Genome sequences revealed an early and rapid selection during the breast-feeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD, however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
Long-term Clinico-radiological Evolution of Patients With Brain Lesions During Infectious Endocarditis
ClinicalTrials.gov study NCT02252900. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Thermal evolution ameliorates the long-term plastic effects of warming, temperature fluctuations and heat waves on predator-prey interaction strength
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Data from: The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels
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Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
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Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction
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Data from: Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon.
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Data from: Developmental constraints do not influence long-term phenotypic evolution of marsupial forelimbs as revealed by interspecific disparity and integration patterns
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Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
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Data from: Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli
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Data from: Experimental test of plant defense evolution in four species using long-term rabbit exclosures
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Female and male song exhibit both parallel and divergent patterns of cultural evolution: a long-term study of song structure and diversity in tropical wrens
<p>Animal culture changes over time through processes that include drift, immigration, selection, and innovation. Cultural change has been particularly well-studied for animal vocalizations, especially for the vocalizations of male animals in the temperate zone. Here we examine cultural change in the vocalizations of tropical Rufous-and-white Wrens (<i>Thryophilus rufalbus</i>), quantifying temporal variation in song structure, song type diversity, and population-level distribution of song types in both males and females. We use data from 10 microsatellite loci to quantify patterns of immigration and neutral genetic differentiation over time, to investigate whether cultural diversity changes with rates of immigration. Based on 11 years of data, we show that the spectro-temporal features of several widely-used persistent song types maintain a relatively high level of consistency for both males and females, whereas the distribution and frequency of particular song types change over time for both sexes. Males and females exhibit comparable levels of cultural diversity (i.e. the diversity of song types across the population), although females exhibit greater rates of cultural change over time. We found that female changes in cultural diversity increased when immigration is high, whereas male cultural diversity did not change with immigration. Our study is the first long-term study to explore cultural evolution for both male and female birds and suggests that cultural patterns exhibit notable differences between the sexes.</p>
Data from: Long-term nitrogen addition causes the evolution of less cooperative mutualists
Human activities have altered the global nitrogen (N) cycle, and as a result, elevated N inputs are causing profound ecological changes in diverse ecosystems. The evolutionary consequences of this global change have been largely ignored even though elevated N inputs are predicted to cause mutualism breakdown and the evolution of decreased cooperation between resource mutualists. Using a long-term (22 year) N addition experiment, we find that elevated N inputs have altered the legume-rhizobium mutualism (where rhizobial bacteria trade N in exchange for photosynthates from legumes), causing the evolution of less mutualistic rhizobia. Plants inoculated with rhizobium strains isolated from N-fertilized treatments produced 17–30% less biomass and had reduced chlorophyll content compared to plants inoculated with strains from unfertilized control plots. Because the legume-rhizobium mutualism is the major contributor of naturally-fixed N to terrestrial ecosystems, the evolution of less cooperative rhizobia may have important environmental consequences.
Data from: Evolution of long-term coloration trends with biochemically unstable ingredients
The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins. Here, we examine evolutionary lability and transitions between the two strategies across 126 species of birds. We report that species that express mostly unmodified, fast-degrading, carotenoids have pre-breeding moults, and a particularly short time between carotenoid deposition and the subsequent breeding season. Species that expressed mostly slow-degrading carotenoids in their plumage accomplished this through increased metabolic modification of dietary carotenoids, and the selective expression of these slow-degrading compounds. In these species, the timing of moult was not associated with carotenoid composition of plumage displays. Using repeated samples from individuals of one species, we found that metabolic modification of dietary carotenoids significantly slowed their degradation between moult and breeding season. Thus, the most complex and colourful ornamentation is likely the most biochemically stable in birds, and depends less on ecological factors, such as moult timing and migration tendency. We suggest that coevolution of metabolic modification, selective expression and biochemical stability of plumage carotenoids enables the use of unstable pigments in long-term evolutionary trends in plumage coloration.
Data from: Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli
Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment.
Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement events were detected, including 82 deletions, 19 inversions, and 9 duplications, with lineages having between 5 and 20 events. In three populations, successive rearrangements impacted particular regions. In five populations, rearrangements affected over a third of the chromosome. Most rearrangements involved recombination between insertion sequence (IS) elements, illustrating their importance in mediating genome plasticity. Two lines of evidence suggest that at least some of these rearrangements conferred higher fitness. First, parallel changes were observed across the independent populations, with ~65% of the rearrangements affecting the same loci in at least two populations. For example, the ribose-utilization operon and the manB-cpsG region were deleted in 12 and 10 populations, respectively, suggesting positive selection, and this inference was previously confirmed for the former case. Second, optical maps from clones sampled over time from one population showed that most rearrangements occurred early in the experiment, when fitness was increasing most rapidly. However, some rearrangements likely occur at high frequency and may have simply hitchhiked to fixation. In any case, large-scale rearrangements clearly influenced genomic evolution in these populations.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.