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1,548 results for “Trajectories”
Data from: Age-dependent trajectories differ between within-pair and extra-pair paternity success
Reproductive success is associated with age in many taxa, increasing in early life followed by reproductive senescence. In socially monogamous, but genetically polygamous species, this generates the interesting possibility of differential trajectories of within-pair and extra-pair siring success with age in males. We investigate these relationships simultaneously using within-individual analyses with 13 years of data from an insular house sparrow (Passer domesticus) population. As expected, we found that both within- and extra-pair paternity success increased with age, followed by a senescence-like decline. However, the age trajectories of within- and extra-pair paternity successes differed significantly, with the extra-pair paternity success increasing faster, albeit non-significantly so, in early life, and showing a delayed decline by 1.5 years on average later in life compared to within-pair paternity success. These different trajectories indicate that the two alternative mating tactics should have age-dependent payoffs. Males may partition their reproductive effort between within- and extra-pair matings depending on their current age in order to reap the maximal combined benefit from both strategies. The interplay between these mating strategies and age-specific mortality may explain the variation in rates of extra-pair paternity observed within and between-species.
Data from: Paleo-trajectories of forest savannization in the southern Congo
Tropical savanna and forest are thought to represent alternative stable states in ecosystem structure in some climates. The implication is that biomes are maintained by positive feedbacks, e.g., with fire, and that historical distributions could play a role in determining modern ones. In this context, climate alone does not govern transitions between biomes, and understanding the causes and pathways of such transitions becomes crucial. Here, we use a multi-proxy analysis of a 2000-year core to evaluate modes of transition in vegetation structure and fire regimes. We demonstrate a first transition c.1540 BP, when a cyclic fire regime entered a forested landscape, eventually resulting, by c.1060 BP, in a transition to a more open savanna-like or mosaicked structure. This pattern may parallel currently accelerating fire regimes in tropical forests suggesting that fires can savannize forests, but perhaps more slowly than feared. Finally, c.540 BP, a drought combined with anthropogenic influences resulted in a conclusive transition to savanna, probably resembling the modern landscape in the region. We show here that fire interacted with drought to transition forest to savanna, suggesting that disturbance by fire can be a major driver of biome change.
Data from: Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories
Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal (n = 127) and offshore (n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites FST = 0.385, p < .001; mtDNA FST = 0.183, p < .001; ΦST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.
Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus, we show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, neither diet composition nor neutral population structure explain venom variation. Instead, venom divergence is strongly correlated with environmental conditions. Individual toxin genes correlate with distinct environmental factors, suggesting that different selective pressures can act on individual loci independently of their co-expression patterns or genomic proximity. Our results challenge common assumptions about diet composition as the key selective driver of snake venom evolution and emphasise how the interplay between genomic architecture and local-scale spatial heterogeneity in selective pressures may facilitate the retention of adaptive functional polymorphisms across a continuous space.
Data from: Senescence or selective disappearance? Age trajectories of body mass in wild and captive populations of a small-bodied primate
Classic theories of ageing consider extrinsic mortality (EM) a major factor in shaping longevity and ageing, yet most studies of functional ageing focus on species with low EM. This bias may cause overestimation of the influence of senescent declines in performance over condition-dependent mortality on demographic processes across taxa. To simultaneously investigate the roles of functional senescence (FS) and intrinsic, extrinsic and condition-dependent mortality in a species with a high predation risk in nature, we compared age trajectories of body mass (BM) in wild and captive grey mouse lemurs (Microcebus murinus) using longitudinal data (853 individuals followed through adulthood). We found evidence of non-random mortality in both settings. In captivity, the oldest animals showed senescence in their ability to regain lost BM, whereas no evidence of FS was found in the wild. Overall, captive animals lived longer, but a reversed sex bias in lifespan was observed between wild and captive populations. We suggest that even moderately condition-dependent EM may lead to negligible FS in the wild. While high EM may act to reduce the average lifespan, this evolutionary process may be counteracted by the increased fitness of the long-lived, high-quality individuals.
Data from: Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana)
Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2S) and compared two population pairs of sulphide-adapted and ancestral fish by sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of Jcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genes therein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 2242 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for POPC bilayer in low hydration (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, CHARMM36 force field in low hydration (dx.doi.org/10.1021/jp101759q), 20ns, T=303K, 72 POPC molecules, 504 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1021/jp101759q).</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory for POPC/50% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/50%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 80 POPC/80 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for n-octyl-b-D-maltoside (C8G2) simulation in lamellar phase (Gromacs 4.5.)
<p>Simulation trajectory and related files used in:</p> <p>Signal intensities in 1H–13C CP and INEPT MAS NMR of liquid crystals</p> <p>A. Nowacka, N.A. Bongartz, O.H.S. Ollila, T. Nylander and D. Topgaard</p> <p>Journal of Magnetic Resonance 230 (2013) 165–175</p> <p>http://dx.doi.org/10.1016/j.jmr.2013.02.016</p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, Reaction Field, traj 2)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using Reaction Field for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p> <p> </p>
MD simulation trajectory and related files for DPPC bilayer in full hydration (Poger GROMOS 53A6_L, Gromacs 4.0.7, PME, traj 1)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.0.7 using PME (Particle Mesh Ewald) for computing electrostatics, Poger GROMOS 53A6_L force field in full hydration (dx.doi.org/10.1002/jcc.21396), 100ns, T=323K, 128 DPPC molecules, 5841 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters (dx.doi.org/10.1002/jcc.21396).</p>
MD simulation trajectory and related files for POPC bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 128 POPC at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory for POPC/20% Chol bilayer (CHARMM36, Gromacs 4.5)
<p>Equilibrated POPC/20%CHL lipid bilayer ran with Gromacs 4.5 with CHARMM36 lipid forcefield.<br /> The simulation is composed of 100 POPC/24 Cholesterol at full hydratation and ran for 200ns at 303K, data saved every 20ps.<br /> All input parameters can be find on the github repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD simulation trajectory and related files for DPPC bilayer (GAFFlipid, Gromacs 4.5)
<p>Equilibrated DPPC lipid bilayer simulation ran with Gromacs 4.5, GAFFlipid force field (http://dx.doi.org/10.1039/C2SM26007G), 50ns, T=323K, 72 DPPC molecules, 2197 water molecules. This data is ran for the nmrlipids.blospot.fi project. More details from nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi. If data is used, please cite nmrlipids.blogspot.fi project and the original publication of the parameters: Dickson et al. Soft Matter, 2012,8, 9617-9627 http://dx.doi.org/10.1039/C2SM26007G.</p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=4 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=4 water/lipid. This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=28 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=28 water/lipid.</p>
MD trajectory for DLPC bilayer (Berger, Gromacs 4.5.4), nw=12 w/l
<p>Equilibrated DLPC lipid bilayer ran with Gromacs 4.5.4 with Berger force field, 80ns, T=300K, 72 DLPC molecules, hydration level nw=12 water/lipid.</p> <p>This data is used in the project "Matching lipid force fields with NMR data". More information at : http://nmrlipids.blogspot.fi/</p> <p> </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.