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Tetramethylammonium–acetate solution molecular dynamics simulations

Simulation data used for the publication: "Ion pairing in aqueous tetramethylammonium–acetate solutions by neutron scattering and molecular dynamics simulations". GROMACS FFMD simulations: <ul> <li> SI-charmm-full </li> <li> SI-charmm-ecc85 </li> <li> SI-charmm-ecc75 </li> <li> SI-charmm-lowCH </li> <li> SI-charmm-lowCO </li> <li> SI-charmm-highCO </li> <li> SI-amber-full </li> <li> SI-amber-ecc85 </li> <li> SI-amber-ecc75 </li> <li> SI-FFMD-for-AIMD-1tma-1acet </li> </ul> CP2K AIMD simulation:  <ul> <li> SI-AIMD </li> </ul>

Project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model"

<pre>README file to the project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model" October 8, 2024 Authors: Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Lorenzo Rovigatti, Luca Tubiana, Samuela Pasquali, Raffaello Potestio</pre> ================================== Trajectories and obsvervables relative to the scientific paper entitled: "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with oxRNA" Authors: Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Luca Tubiana, Samuela Pasquali, Raffaello Potestio Brief description of the content of this folder: |_ oxDNA-CCMV_force.zip: the modified version of the oxDNA software we used to make the simulations with the CCMV-like spherical potential described in the paper | |_ CCMV_RNA2_oxRNA_simulations    |_ FOLDING (files of the "freely-folding" simulations)    |   |_ FIRST_LAST_FRAMES (frames generated by oxDNA software)    |   |   |_ 0.15M (first and last frames of the runs at 0.15M)    |   |   |   |_ REP1 (files relative to REP1 / REPI)    |   |   |   |   |_ first.dat    |   |   |   |   |_ last.dat     |   |   |   |    |   |   |   |_ REP2 (files relative to REP2 / REPII)    |   |   |   |   |_ first.dat    |   |   |   |   |_ last.dat     |   |   |   |    |   |   |   |_ REP3 (files relative to REP3 / REPIII)    |   |   |       |_ first.dat    |   |   |       |_ last.dat     |   |   |    |   |   |_ 0.50M (first and last frames of the runs at 0.50M)    |   |   |  |_ [same structure as for 0.15M]    |   |   |    |   |   |_ 0.50M (first and last frames of the runs at 0.50M, T293K)    |   |   |  |_ [same structure as for 0.15M]    |   |   |    |   |   |_ 0.50M (first and last frames of the runs at 0.50M, T293K, harmonic constraint to the ends)    |   |      |_ [same structure as for 0.15M]    |   |    |   |    |   |_ HB_FILES (base pairs files generated by oxDNA software)    |   |   |_ hb_015M_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.15M salt concentration)    |   |   |_ hb_015M_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.15M salt concentration)    |   |   |_ hb_015M_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.15M salt concentration)    |   |   |_ hb_050M_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration)    |   |   |_ hb_050M_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration)    |   |   |_ hb_050M_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration)    |   |   |_ hb_050M_293K_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K)    |   |   |_ hb_050M_293K_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K)    |   |   |_ hb_050M_293K_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K)    |   |   |_ hb_050M_293K_harm_I.dat    (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)    |   |   |_ hb_050M_293K_harm_II.dat    (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)    |   |   |_ hb_050M_293K_harm_III.dat    (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)    |   |    |   |_ example_input.ox (example of oxDNA input file used to launch simulations and dump observables and trajectories)    |   |    |   |_ example_input_harm.ox (example of oxDNA input file used to launch simulations with harmonic constraint to the ends and dump observables and trajectories)    |   |    |   |_ harmonic_ends.dat (constraint force file used to run simulations with harmonic constraint to the ends)    |    |_ PACKED        |_ SIM_VTHEO (files of the simulations with the analytic-based external potential, as described in the paper...)        |   |_ 0.15M (... with a salt concentration of 0.15M)        |   |   |_ REP1 (Replica with id 1, or I)        |   |   |   |_ MD_scripts (files required by oxDNA software to launch the simulation for this replica)        |   |   |   |   |_ input_0.15M_REP1.ox (input file of oxDNA software to launch the simulation)        |   |   |   |   |_ force_0.15M_REP1.dat (additional file required for the application of an external force in the simulation, containing the relative parameters)        |   |   |   |        |   |   |   |_ input_structure (structure files in oxDNA format, one of which is used as starting configuration for the specific replica)        |   |   |   |   |_ PackingRNA2_0.15M_REP1.dat (last structure of simulation with time-dependent external packaging force)        |   |   |   |   |_ PackingRNA2_0.15M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)        |   |   |   |   |_ PackingRNA2_0.15M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)        |   |   |   |   |_ PackingRNA2_0.5M_REP1.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)        |   |   |   |   |_ PackingRNA2_0.5M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)        |   |   |   |   |_ PackingRNA2_0.5M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)        |   |   |   |        |   |   |   |_ data (output data generated by the simulation)        |   |   |       |_ 1.E (files of the observables dumped during simulation)        |   |   |       |   |_ E_RNA2_0.15M_REP1.dat  (energies of the system per each time frame: time frame, potential energy U, kinetic energy, total energy)        |   |   |       |   |_ P_RNA2_0.15M_REP1.dat  (internal pressure of the system: time frame, total pressure, stress tensor components xx, yy, zz, xy, xz, yz)        |   |   |       |   |_ F_RNA2_0.15M_REP1.dat  (components of the external force acting on each nucleotide, ordered according to the topology, per each frame)        |   |   |       |   |_ HB_RNA2_0.15M_REP1.dat (base pairs annotated, per each time frame dumped)        |   |   |       |        |   |   |       |_ 3.restart (restart/last configuration file dumped during simulation)        |   |   |           |_ last_conf_RNA2_0.15M_Yukawa_REP1.dat (last frame dumped in the simulation, in oxDNA format)        |   |   |        |   |   |        |   |   |_ REP2 (Replica with id 2, or II)        |   |   |   |_ [same content as REP1, but relative to replica 2 or II]        |   |   |        |   |   |_ REP3 (Replica with id 3, or III)        |   |       |_ [same content as REP1, but relative to replica 3 or III]        |   |        |   |_ 0.5M  (... with a salt concentration of 0.5M)        |   |   |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]        |   |        |   |_ 0.5M_293K_harm  (... with a salt concentration of 0.5M, Temperature 293K and harmonic constraint to the ends)        |       |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]        |        |_ SIM_VCCMV (files of the simulations with the structure-based external potential, as described in the paper)            |_ [same content as SIM_VTHEO, but for simulations done with the structure-based external potential] For any additional file or data not present here, that was used to produce results in the paper, please ask to: giovanni.mattiotti@inserm.fr, manuel.micheloni@unitn.it, lorenzo.petrolli@unitn.it

All-atom molecular dynamics simulations for Targeting Human Prostaglandin Reductase 1 with Licochalcone A: Insights from Molecular Dynamics and Covalent Docking Studies

The dataset comprises simulations of the PTGR1 protein under four different conditions: in its apo (unbound) form, bound to the cofactor NADH, and in complex with both covalently and non-covalently bound licochalcone A. Each simulation was conducted using the ff19SB force field and the OPC water model, with water molecules excluded from the trajectories. For the apo form, NADH-bound, and non-covalently bound licochalcone A conditions, each trajectory consists of 5000 snapshots, representing a total of 500 nanoseconds of simulation. However, the trajectory for the no covalently bound licochalcone A condition includes only 1000 frames, corresponding to 150 nanoseconds. This discrepancy in frame count and simulation length across conditions is important to consider when comparing dynamics and structural behavior within the dataset. PTGR1-NADPH.tar.xz - PTGR1 dimer in complex with NADPH PTGR1-apo.tar.xz - PTGR1 apo dimer PTGR1-monomer_NADPH.tar.xz - PTGR1 monomer in complex with NADPH PTGR1-LicA_covalent.tar.xz - PTGR1 dimer with covalently bound licochalcone A PTGR1-LicA_NO_covalent.tar.xz - PTGR1 dimer with covalently bound licochalcone A   All folders contain: *.parm7 - dry topology in amber format *.nc - dry trajectories in netcdf format   Plain molecular dynamics simulations. Two structures of human PTGR1 have been deposited in the PDB: one bound to NADPH and the raloxifene inhibitor (PDB ID 2Y05, 2.2 Å resolution), and another in apo form (PDB ID 1ZSV, 2.3 Å resolution). In the first structure, it is reported as a monomer, whereas in the second as a dimer. However, the protomers exhibit highly similar conformations in both structures (backbone RMSD ~0.5 Å). Experimental evidence, akin to PTGR1 orthologs and many other MDR enzymes, indicates that the functional form of human PTGR1 is a homodimer (Mesa et al., 2015). Thus, to construct the dimeric form of the coenzyme complex, we duplicated the NADPH-bound protomer from 2Y05 and aligned the two subunits with the dimer from 1ZSV, deleting the raloxifene molecule. In the resulting structure, no steric clashes between the protomers were observed. This structure was used as the starting point for the simulations. Additionally, the apo dimer was generated by removing the NADPH from both subunits, and the monomeric form in complex with NADPH was derived from the initial structure.   The pmemd.cuda module of AMBER 22 was used to perform the MD simulations, employing the force field FF19SB and the OPC water model (Case et al., 2022; Izadi, Anandakrishnan, & Onufriev, 2014; Salomon-Ferrer, Götz, Poole Duncan and Le Grand, & Walker, 2013; Tian et al., 2020). NADPH parameters were taken from (Cummins, Ramnarayan, Singh, & Gready, 1991). The system was protonated at pH 7.4 with PDBfixer (Eastman et al., 2017a) and placed in a truncated octahedral box, initially spanning 12 Å further from the solute in each direction using the AMBER tLeap module. The overall charge of the system was neutralized by the addition of four sodium ions. ParmEd (Eastman et al., 2017b) was used to implement the hydrogen mass repartitioning scheme (Hopkins, Le Grand, Walker, & Roitberg, 2015). Local clashes and solvent orientation were corrected using the steepest descent algorithm for 5,000 cycles. During the initial NVT equilibration, the velocities gradually increased through five steps of 200 ps each. The temperature progression started at 150 K and was raised to 200 K, 250 K, 300 K, and finally, 310 K. Position restraints were applied to heavy atoms of the protein, with the restraining forces progressively decreasing at each step. The spring constants were set at 4, 5, 3, and 1 kcal/mol Å2, respectively, to allow for the gradual relaxation of the protein. The system was further equilibrated for 1 ns in the NPT ensemble with no restraints. For treating long-range electrostatic interactions, periodic boundary conditions and Ewald sums were used with a 9 Å cutoff for direct interactions (Darden, York, & Pedersen, 1993; Simmonett & Brooks, 2021). The same cutoff was used for Lennard-Jones interactions. The Langevin thermostat (Sindhikara, Kim, Voter, & Roitberg, 2009) with a collision frequency of 4 ps-1 and the Monte Carlo barostat(Åqvist, Wennerström, Nervall, Bjelic, & Brandsdal, 2004) with a pressure relaxation time of 2 ps were used to control temperatures and pressures, respectively. The SHAKE algorithm was used to fix any bond involving hydrogen atoms (Ryckaert, Ciccotti, & Berendsen, 1977), and a 4-fs time step integration was used. This protocol was taken from (Cofas-Vargas et al., 2022; Medrano‐Cerano et al., 2024) Unless otherwise stated, no other constraints were used. Five replicas of 500 ns each per system were produced. The topology and parameter files for a LicA molecule and for this inhibitor covalently bound to the sulfur atom of a cysteine residue were generated with Antechamber suite (J. Wang, Wang, Kollman, & Case, 2006), using the general Amber force field (GAFF2) for organic molecules (He, Man, Yang, Lee, & Wang, 2020). Atomic charges were derived using the AM1-BB method (Jakalian, Jack, & Bayly, 2002). The parameters are documented in Supplementary Tables SI-1 and SI-2. Trajectories for PTGR1 covalently and noncovalently bound to LicA were run using the same conditions as described above. All molecular structure representations were created using UCSF ChimeraX v1.8 (Meng et al., 2023; Pettersen et al., 2021).   Solvent-site identification and guided docking. Determination of solvent sites (SS) for ethanol and water molecules was conducted by employing the MDmix method. After removing both NADPH molecules from the enzyme dimer, the system was protonated at pH 7.4 with PDBfixer (Eastman et al., 2017a) and placed in a truncated octahedral box of water/ethanol 80/20% v/v, extending12 Å beyond the solute in each direction using the AMBER tLeap module. Five 20 ns replicas were run, using the same conditions described above, but applying Cartesian restrictions of 0.01 kcal/mol A2 over all heavy atoms. After the alignment of trajectories, density maps for probe atoms were generated by constructing a static mesh with cubic grids (0.5 Å edge length) over the entire simulation box. The occurrence of probe atoms within each grid were tracked across the trajectories. These density distributions were then converted into binding free energy using the Boltzmann relationship, comparing observed probe atom distributions against the expected bulk solvent distribution at 1.0 M. Solvent sites were then filtered by applying an energy threshold of 1 kcal/mol, as previously described (Alvarez-Garcia & Barril, 2014; Avila-Barrientos et al., 2022). LicA docking. For covalent docking, LicA, bound through its Cb atom to the sulfur atom of C239, was docked onto the NADPH-binding site of human PTGR1 employing the covalent docking module of AutoDock4 v4.2.6 (Bianco, Forli, Goodsell, & Olson, 2016; Morris et al., 2009). The flexible side-chain methodology was used. In a subsequent non-covalent docking, solvent sites previously identified for ethanol and water were used as pharmacophoric element for rDock (Ruiz-Carmona et al., 2014). This docking involved defining the receptor system and generating a binding cavity using the NADPH as a reference molecule. During the non-covalent docking, a penalty score proportional to the square of the distance from each ligand conformation to a solvent site (SS) was applied when the separation exceeded 2 Å. The docking run included 100 simulations, generating a set of potential binding modes for LicA within the NADPH site.

Data for "Dynamics of Energetic Heliospheric Ions in Pluto's Induced Magnetosphere"

Dataproducts for manuscript titled "Dynamics of Energetic Heliospheric Ions in Pluto's Induced Magnetosphere". Includes files used to generate figures 4-9. Accompanied by a readme.txt file for further description of the file structure and content.

Experimental investigation on dynamics and flow resistance of granular-fluid flows

Dataset related to the manuscript “Experimental investigation on dynamics and flow resistance of granular-fluid flows”, submitted to the Journal of Geophysical Research: Earth Surface.

Adaptive Rational Interpolation and Higher-order SVD for Low-rank Tensor Approximation in Structural Dynamics Simulations

<h1>Vibroacoustic Data Compression and Interpolation</h1> This is the code that accompanies the paper <blockquote> Adaptive Rational Interpolation and Higher-order SVD for Low-rank Tensor Approximation in Structural Dynamics Simulations </blockquote> which we (Jan Heiland, Victor Gosea, Ulrich Römer, Davide Pradovera, Harikrishnan Sreekumar, Sabine Langer) submitted for presentation at the ECC-2025. See the <code>README.md</code> for information and instruction to reproduce the results of the paper.

Artifact for "Modular criticality analysis for dynamic fault trees"

This artifact contains the fault trees and log files of the experimental evaluation from the paper "Modular criticality analysis for dynamic fault trees". The implementation is available in the <a href="https://www.safest.dgbtek.com/">SAFEST tool</a>.

Data and code for "Assessing the spatial scale of synchrony in forest tree population dynamics"

The data sets and code provided here facilitate reproduction of our results from this paper on synchrony of forest tree population dynamics.  <h3>Description of the data and file structure</h3> The analyses in the paper were conducted at three scales, and each involves its own data files: <ul> <li>Local scale: The relevant data files are named, e.g., "BCI1-7,L=250m,dbh=100mm.Rdata", where "BCI1-7" indicates the ForestGEO site name  ("BCI") and census intervals (1 to 7 for BCI), "L=250m" indicates the quadrat size, and "dbh=100mm" indicates the diameter-at-breast height (DBH) threshold used. There are 12 such files (two ForestGEO plots--BCI and Pasoh--times three quadrat sizes times two DBH thresholds).  Each file contains a single list "N_all", whose length is equal to the number of quadrats at the given grain. Each element in the list is a data frame containing mean census times (in days), tree species' population sizes and number of survivors across the two censuses for the corresponding quadrat.</li> <li>Regional scale: The relevant data files are "Marena_data,dbh=100mm,spp_anonymised.Rdata" and "Marena_data,dbh=100mm,spp_anonymised.Rdata". Each file contains three objects: "dists" is a matrix giving the distances between all pairs of sites; "N_all1" is a list with one element for each plot, and each element being a data frame with (anonymised) species ids in the first column and abundances in the remaining columns (column names give mean census dates in days); "S_all1" has a similar structure to "N_all1" except that the data give numbers of survivors from any given census to any subsequent census (column headings indicate the two census numbers).</li> <li>Global scale: The relevant data files are "global_data,dbh=10mm,spp_anonymised.Rdata" and "global_data,dbh=100mm,spp_anonymised.Rdata". The data in the files have the same structure as in the regional-scale files.</li> </ul>

opencc-zeroDec 2013View details →

Data from: Migration and stress during reproduction govern telomere dynamics in a seabird

Changes in telomere length are believed to reflect changes in physiological state and life expectancy in animals. However, much remains unknown about the determinants of telomere dynamics in wild populations, and specifically the influence of conditions during highly mobile life-history stages, for example migration. We tested whether telomere dynamics were associated with migratory behaviour and/or with stress during reproduction in free-living seabirds. We induced short-term stress during reproduction in chick-rearing, black-legged kittiwakes (Rissa tridactyla), tracked winter migration with geolocators and measured telomere length before and after winter migration. We found that time spent at wintering grounds correlated with reduced telomere loss, while stress during reproduction accelerated telomere shortening. Our results suggest that different life-history stages interact to influence telomere length, and that migratory patterns may be important determinants of variation in an individual's telomere dynamics.

opencc-zeroDec 2019View details →

Forest microclimate dynamics drive plant responses to warming

Climate warming is causing a shift in biological communities in favor of warm-affinity species (i.e., thermophilisation). However, species responses often lag behind climate warming and local microclimates modulated by vegetation and topography are usually ignored. Here we analyze multidecadal understorey microclimate dynamics in European forests and show that thermophilisation and the climatic lag in forest plant communities are primarily controlled by microclimate. Increasing tree canopy cover reduces warming rates inside forests, but loss of canopy cover leads to increased microclimatic heat that exacerbates the disequilibrium between community responses and climate change. Reciprocal effects between plants and microclimates are key to understanding the response of forest biodiversity and functioning to climate and land-use changes.

opencc-zeroDec 2015View details →

Data from: Early and dynamic colonization of Central America drives speciation in Neotropical army ants

The emergence of the Isthmus of Panama is one of the most important events in recent geological history, yet its timing and role in fundamental evolutionary processes remain controversial. While the formation of the isthmus was complete around 3 million years ago (Ma), recent studies have suggested prior intercontinental biotic exchange. In particular, the possibility of early intermittent land bridges facilitating colonization constitutes a potential mechanism for speciation and colonization before full closure of the isthmus. To test this hypothesis, we employed genomic methods to study the biogeography of the army ant genus Eciton, a group of keystone arthropod predators in Neotropical rainforests. Army ant colonies are unable to disperse across water and are therefore ideally suited to study the biogeographic impact of land bridge formation. Using a reduced representation genome sequencing approach, we show that all strictly Central American lineages of Eciton diverged from their respective South American sister lineage between 4 and 7 Ma, significantly prior to the complete closure of the isthmus. Furthermore, three of the lineage pairs form extensive and coincident secondary contact zones in Costa Rica and Nicaragua, with no evidence of gene flow. Such a discrete and repeated biogeographic pattern indicates at least two waves of army ant dispersal into Central America that were separated by significant genetic divergence times. Thus, by integrating phylogenomic, population genomic and geographic evidence, we show that early colonization of Central America across the emerging Isthmus of Panamá drove parallel speciation in Eciton army ants.

opencc-zeroOct 2019View details →

A practical method for estimating coupling functions in complex dynamical systems

A foremost challenge in modern network science is the inverse problem of reconstruction (inference) of coupling equations and network topology from the measurements of the network's dynamics. Of particular interest are the methods that can operate on real (empirical) data without interfering with the system. One of such earlier attempts (Tokuda et al. 2007 Phys. Rev. Lett. 99, 064101) was a method suited for general limit-cycle oscillators, yielding both oscillators' natural frequencies and coupling functions between them (phase equations) from empirically measured time series. The present paper reviews the above method in a way comprehensive to domain-scientists other than physics. It also presents applications of the method to (i) detection of the network connectivity, (ii) inference of the phase sensitivity function, (iii) approximation of the interaction among phase-coherent chaotic oscillators, and (iv) experimental data from a forced Van der Pol electric circuit. This reaffirms the range of applicability of the method for reconstructing coupling functions and makes it accessible to a much wider scientific community.

opencc-zeroDec 2014View details →

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.

opencc-zeroDec 2017View details →

Data from: Microenvironment and functional-trait context dependence predict alpine plant community dynamics

Predicting the structure and dynamics of communities is difficult. Approaches linking functional traits to niche boundaries, species co‐occurrence and demography are promising, but have so far had limited success. We hypothesized that predictability in community ecology could be improved by incorporating more accurate measures of fine‐scale environmental heterogeneity and the context‐dependent function of traits. We tested these hypotheses using long term whole‐community demography data from an alpine plant community in Colorado. Species distributions along microenvironmental gradients covaried with traits important for below‐ground processes. Positive associations between species distributions across life stages could not be explained by abiotic microenvironment alone, consistent with facilitative processes. Rates of growth, survival, fecundity and recruitment were predicted by the direct and interactive effects of trait, microenvironment, macroenvironment and neighbourhood axes. Synthesis. Context‐dependent interactions between multiple traits and microenvironmental axes are needed to predict fine‐scale community structure and dynamics.

opencc-zeroDec 2013View details →

Data from: Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome

Seasonal patterns in pathogen transmission can influence the impact of disease on populations and the speed of spatial spread. Increases in host contact rates or births drive seasonal epidemics in some systems, but other factors may occasionally override these influences. White-nose syndrome, caused by the emerging fungal pathogen Pseudogymnoascus destructans, is spreading across North America and threatens several bat species with extinction. We examined patterns and drivers of seasonal transmission of P. destructans by measuring infection prevalence and pathogen loads in six bat species at 30 sites across the eastern United States. Bats became transiently infected in autumn, and transmission spiked in early winter when bats began hibernating. Nearly all bats in six species became infected by late winter when infection intensity peaked. In summer, despite high contact rates and a birth pulse, most bats cleared infections and prevalence dropped to zero. These data suggest the dominant driver of seasonal transmission dynamics was a change in host physiology, specifically hibernation. Our study is the first, to the best of our knowledge, to describe the seasonality of transmission in this emerging wildlife disease. The timing of infection and fungal growth resulted in maximal population impacts, but only moderate rates of spatial spread.

opencc-zeroDec 2013View details →

Data from: Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb

Variation of DNA-methylation is thought to play an important role for rapid adjustments of plant populations to dynamic environmental conditions, thus compensating for the relatively slow response time of genetic adaptations. However, genetic and epigenetic variation of wild plant populations has not yet been directly compared in fast changing environments. Here we surveyed populations of Viola elatior from two adjacent habitat types along a successional gradient characterized by strong differences in light availability. Using AFLP and MSAP analyses we found relatively low levels of genetic (H'gen=0.19) and epigenetic (H'epi=0.23) diversity and high genetic (ϕST=0.72) and epigenetic (ϕST=0.51) population differentiation. Diversity and, respectively, differentiation were significantly correlated, suggesting that epigenetic variation partly depends on the same driving forces as genetic variation. Correlation based genome scans detected comparable levels of genetic (17.0%) and epigenetic (14.2%) outlier markers associated with site specific light availability. However, as revealed by separate differentiation based genome scans for AFLP, only few genetic markers seemed to be actually under positive selection (0-4.5%). Moreover, PCoA and Mantel tests showed that overall epigenetic variation was more closely related to habitat conditions, indicating that environmentally-induced methylation changes may lead to convergence of populations experiencing similar habitat conditions and may thus play a major role for the transient and/or heritable adjustment to changing environments. Additionally, using a new MSAP scoring approach, we found that mainly the unmethylated (ϕST=0.60) and CG-methylated states (ϕST=0.46) of epiloci contributed to population differentiation and putative habitat related adaptation, whereas CHG-hemimethylated states (ϕST=0.21) only played a marginal role.

opencc-zeroDec 2012View details →

Data from: Niche opportunities and invasion dynamics in a desert annual community

Although many factors influence the ability of exotics to invade successfully, most studies focus on only a few variables to explain invasion; attempts at theoretical synthesis are largely untested. The niche opportunities framework proposes that the demographic success of an invader is largely affected by the availability of resources and the abundance of its enemies. Here, we use a 31-year study from a desert ecosystem to examine the niche opportunities framework via the invasion of the annual plant Erodium cicutarium. While the invader remained rare for two decades, a decline in granivory combined with an ideal climate window created an opportunity for E. cicutarium to escape control and become the dominant annual plant in the community. We show that fluctuations in consumption and resources can create niche opportunities for invaders and highlight the need for additional long-term studies to track the influence of changing climate and community dynamics on invasions.

opencc-zeroDec 2009View details →

Data from: Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China

Understanding population history and genetic structure are key drivers of ecological research. Here we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 fecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K=2). We estimate that a major divergence took place between these populations 26 000 YBP, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise FS on mtDNA and nuclear DNA) so that in effect, four smaller sub-populations now exist. Promisingly, we identified two possible first generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.

opencc-zeroDec 2016View details →

Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America

Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen with lineages that pose health risks for domestic birds, wild birds, and humans. One mechanism of intercontinental HPAIV spread is through wild bird reservoirs and wild birds were the likely sources of a Eurasian (EA) lineage HPAIV into North America in 2014. The introduction resulted in several reassortment events with North American (NA) lineage low pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on to cause one of the largest HPAIV poultry outbreaks in North America. We evaluated three hypotheses about novel HPAIV introduced into wild and domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was restricted by mechanisms associated with highly-pathogenic phenotypes; (ii) the HPAIV poultry outbreak was not self-sustaining and required viral input from wild birds; (iii) reassortment of the EA H5N8 generated reassortant EA/NA AIVs with a fitness advantage over fully Eurasian lineages in North American wild birds. We used a time-rooted phylodynamic model that explicitly incorporated viral population dynamics with evolutionary dynamics to estimate the basic reproductive number (R0) and viral migration among host types in domestic and wild birds, as well as between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence to support hypothesis (i) or (ii) as our estimates of the transmission parameters suggested that the HPAIV outbreak met or exceeded the threshold for persistence in wild birds (R0 > 1) and poultry (R0 ≈ 1) with minimal estimated transmission among host types. There was also no evidence to support hypothesis (iii) because R0 values were similar among EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel HPAIV and reassortments did not encounter any transmission barriers sufficient to prevent persistence when introduced to wild or domestic birds.