Find research datasets worth reusing

opencc-zeroJul 2019View details →

Data from: Faster speciation of fig-wasps than their host figs leads to decoupled speciation dynamics

The genus Ficus (Moraceae) is best known for its obligate mutualism with pollinating fig-wasps (Agaonidae), where species are thought to reciprocally trigger genetic differentiation resulting in tight co-speciation. Here, we used nextRAD DNA sequencing to study the population structure of multiple fig species and their corresponding fig-wasps along an elevational gradient in Papua New Guinea. Contrary to the expected one-to-one species specificity in this mutualism we find evidence of multiple pollinating wasp species, which through limited dispersal abilities along the gradient, likely limit pollen flow and influence fig population structure along these slopes. In two cases, where the fig species studied have wide distribution along the mountain, we found between three and four wasp species pollinating closely related populations of fig species. In the case of one fig subspecies complex, we identified two fig-wasp species according to the distribution of their host subspecies. Finally, in a parapatric, three sister species complex, we identified three individual wasp species, each corresponding to its host fig species. Fig-wasps appear to speciate more rapidly through faster generation times, faster rates of local adaptation and/or weak dispersal abilities compared to figs. This in turn restricts pollen movement between fig ecotypes, strengthening reproductive barriers and so facilitating their speciation. Fig speciation along the gradient and wasp lineage extinction may eventually restore the one-to-one rule in this mutualism through split and sort speciation dynamics.

opencc-zeroDec 2013View details →

Data from: Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. X. Age-specific dynamics of adult epicuticular hyrdocarbon expression in response to different host plants

Analysis of sexual selection and sexual isolation in Drosophila mojavensis and its relatives has revealed a pervasive role of rearing substrates on adult courtship behavior when flies were reared on fermenting cactus in preadult stages. Here, we assessed expression of contact pheromones comprised of epicuticular hydrocarbons (CHCs) from eclosion to 28 days of age in adults from two populations reared on fermenting tissues of two host cacti over the entire life cycle. Flies were never exposed to laboratory food and showed significant reductions in average CHC amounts consistent with CHCs of wild-caught flies. Overall, total hydrocarbon amounts increased from eclosion to 14–18 days, well past age at sexual maturity, and then declined in older flies. Most flies did not survive past 4 weeks. Baja California and mainland populations showed significantly different age-specific CHC profiles where Baja adults showed far less age-specific changes in CHC expression. Adults from populations reared on the host cactus typically used in nature expressed more CHCs than on the alternate host. MANCOVA with age as the covariate for the first six CHC principal components showed extensive differences in CHC composition due to age, population, cactus, sex, and age × population, age × sex, and age × cactus interactions. Thus, understanding variation in CHC composition as adult D. mojavensis age requires information about population and host plant differences, with potential influences on patterns of mate choice, sexual selection, and sexual isolation, and ultimately how these pheromones are expressed in natural populations. Studies of drosophilid aging in the wild are badly needed.

opencc-zeroDec 2015View details →

Data from: The role of inhibitory dynamics in the loss and re-emergence of macropodoid tooth traits

The reversibility of phenotypic evolution is likely to be strongly influenced by the ability of underlying developmental systems to generate ancestral traits. However, few studies have quantitatively linked these developmental dynamics to traits which re-evolve. In this study we assess how changes in the inhibitory cascade, a developmental system that regulates relative tooth size in mammals, influenced the loss and reversals of the posthypocristid, a molar tooth crest, in the kangaroo superfamily Macropodoidea. We find that posthypocristid loss is linked with reduced levels of posterior molar inhibition, potentially driven by selection for lophodont, higher-crowned molar teeth. There is strong support for two posthypocristid reversals, each occurring after more than 15 million years of absence, in large-bodied species of Macropus, and two giant extinct species of short-faced sthenurine kangaroo (Procoptodon). We find that whereas primitive posthypocristid expression is linked to higher levels of posterior molar inhibition, re-emergence is tied to a relative increase in third molar size associated with increasing body mass, producing molar phenotypes similar to those in mouse where the ectodysplasin pathway is up-regulated. We argue that although shifts in the inhibitory cascade may enable re-emergence, dietary ecology may limit the frequency of phylogenetic reversal.

opencc-zeroDec 2016View details →

Data from: Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins

Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-microsecond resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates—many separated by as few as two or three amino acids—exhibited complex dynamics, including frequent refolding and state occupancies of <10 μs. Equilibrium measurements between such states enabled the folding free-energy landscape to be deduced. These results sharpen the picture of the mechanical unfolding of membrane proteins and, more broadly, enable experimental access to previously obscured protein dynamics.

opencc-zeroDec 2017View details →

Data from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Elucidating the dynamic distribution of organismal lineages has been central to biology since the nineteenth century, yet the difficulty of combining biogeographic methods with shifts in habitat suitability remains a limitation. This integration, however, is critical to understanding geographic distributions, present and past, as well as the time-extended trajectories of lineages. Here, we link previous advances in phyloclimatic modeling to develop a framework that overcomes existing methodological gaps by predicting potential ecological and geographic overlap directly from estimated ancestral trait distributions. We show the utility of this framework by focusing on a clade in the montane angiosperm genus Heuchera, which is noteworthy in that it experienced ancient introgression from circumboreally distributed species of Mitella, lineages now ~1,300 km disjunct. Using this system, we demonstrate an application of ancestral state reconstruction to assess geographic range dynamics in a lineage lacking a fossil record. We test hypotheses regarding inferred past geographic distributions and examine the potential for ancient geographic contact. Application of this multifaceted approach suggests potential past contact between species of Heuchera and Mitella in western North America during cooler periods of the Pleistocene. Integration of niche models and phylogenetic estimates suggests that climatic cooling may have promoted range contact and gene flow between currently highly disjunct species. Our approach has wide applicability for testing hypotheses concerning organismal co-occurrences in deep time.

Pyrene fluorescence data obtained by nonadiabatic dynamics calculations

The dataset includes all trajectories of the nonadiabatic molecular dynamics simulations of pyrene. Each tar.gz directory contains two directories: INPUT and RESULTS. In the INPUT directory, one has the input files for the Newton-X dynamics calculations and the subdirectory JOB_AD with the inputs for the ADC(2) calculations with TURBOMOLE. One also has the files "final_output.1.2" and "final_output.1.3" with the data used to obtain the emission spectrum. In the RESULTS directory, one has the 20 trajectories for the S2 state and 52 trajectories initiated in S7-S8. For the latter, the trajectories numbered 1-32 started in S7, and those numbered 33-52 started in S8. One also has a directory called TRAJ1_uncorrected that corresponds to the data for TRAJ1 without the kinetic energy correction. The RESULTS directory contains all the output files from the Newton-X dynamics calculation, including the file dyn.out with the atomic coordinates, velocities, and energies for each time step. There is also a file called "get_points.py," a python script used to extract the data (from the dyn.out files) for the emission spectrum.

The appendix for dynamic model of respiratory infectious disease transmission by population mobility based on city network

First, a scale-free city network was established, and the shortest path between any two nodes was determined. Second, the movement path of tourists was designed based on the shortest path. Subsequently, every infected person's information, such as the city, infection time, onset, and hospitalisation, was confirmed based on their movement path. Third, the features of the transmission path and time distribution of the epidemic were characterised after summarising the information. Finally, the reliability of the model was verified.

Spatiotemporal connectivity dynamics in spatially structured populations

Connectivity is a fundamental concept linking dispersal to the emergent dynamics and persistence of spatially structured populations. Functional measures of connectivity typically seek to integrate aspects of landscape structure and animal movement to describe ecologically meaningful connectedness at the landscape and population scale. Despite this focus on function, traditional measures of landscape connectivity assume it is a static property of the landscape, hence abstracting out the underlying spatiotemporal population dynamics. Connectivity is, arguably, a dynamic property of landscapes, and is inherently related to the spatial distribution of individuals and populations across the landscape. Static representations of connectivity potentially overlook this variation and therefore adopting a dynamic approach should offer improved insights about connectivity and associated ecological processes. Using a large scale, long-term time-series of occupancy data from a metapopulation of water voles (Arvicola amphibius), we tested competing hypotheses about how considering the dynamic nature of connectivity improves the ability of spatially-explicit occupancy models to recover population dynamics. Iteratively relaxing standing assumptions of connectivity metrics, these models ranged from spatially and temporally fixed connectivity metrics that are widely applied, to the more flexible, but lesser used model that allowed temporally-varying connectivity measures that incorporate spatiotemporally dynamic patch occupancy states. Our results provide empirical evidence that demographic-weighting using patch occupancy dynamics and temporal variability in connectivity measures are important for describing metapopulation dynamics. We highlight the implications of commonly held assumption in connectivity modeling and demonstrate how they result in different and highly variable predictions of metapopulation capacity. Thus, we argue that the concept of connectivity and its potential applications would benefit from recognizing inherent spatiotemporal variation in connectivity that is explicitly linked to underlying ecological state variables.

opengpl-2.0-or-laterJul 2022View details →

Dynamical Variational Autoencoders (DVAE) pretrained models

The Variational Autoencoder (VAE) is a powerful deep generative model that is now extensively used to represent high-dimensional complex data via a low-dimensional latent space learned in an unsupervised manner. In the original VAE model, input data vectors are processed independently. In recent years, a series of papers have presented different extensions of the VAE to process sequential data, that not only model the latent space, but also model the temporal dependencies within a sequence of data vectors and corresponding latent vectors, relying on recurrent neural networks or state space models. In this paper we perform an extensive literature review of these models. Importantly, we introduce and discuss a general class of models called Dynamical Variational Autoencoders (DVAEs) that encompasses a large subset of these temporal VAE extensions. Then we present in detail seven different instances of DVAE that were recently proposed in the literature, with an effort to homogenize the notations and presentation lines, as well as to relate these models with existing classical temporal models. We reimplemented those seven DVAE models and we present the results of an experimental benchmark conducted on the speech analysis-resynthesis task (the PyTorch code is made publicly available). The paper is concluded with an extensive discussion on important issues concerning the DVAE class of models and future research guidelines.

u-track 3D: measuring and interrogating dense particle dynamics in three dimensions

This datasets is set up to help users test the u-track 3D software. The tutorial scripts automatically download and process the following images: Endocytosis dataset: Breast cancer cells expressing eGFP-labelled alpha subunit of the AP-2 complex imaged with diaSLM by K. Dean (Dean et. al. 2016). The raw data has been cropped and limited to 50 time point (540MB). Mitosis dataset: HeLa cells undergoing mitosis and expressing eGFP-labeled EB3 and mCherry-labeled CENPA imaged in dual-channel lattice light-sheet microscopy by W. Legant (David et. al. 2019). The raw data has been cropped, the entire sequence has been made available.

opencc-by-4.0May 2022View details →

Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - V142G mutant

Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.

opencc-by-4.0Mar 2022View details →

Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - A55G and V135G mutants

Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.

Arms-race and fluctuating-selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1

Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms-race dynamics (ARD) and fluctuating-selection dynamics (FSD). Here, we tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory; whether ARD versus FSD coevolution occurred; and how coevolution affected a predicted phenotypic trade-off between phage resistance and antibiotic sensitivity. We used a unique "deep" sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage attack, and resistance against antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD while the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade-off. Whole genome sequencing revealed that treatment populations of bacteria accrued more de novo mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type-IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade-off in the ARD-coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria-phage system, and that occurrence of predicted phage-driven evolutionary trade-offs may depend on the genetics underlying evolution of phage-resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics.

Characterizing the Dynamics of Wildland-Urban Interface and the Potential Impacts on Fire Activities in Alaska from 2000 to 2010

The material contains the shapefiles of wildland-urban interface in Alaska in 2000 and 2010, which are derived from census data and National Land Cover Database.

Spatio-temporal dynamics of genetic variation at the quantitative and molecular levels within a natural Arabidopsis thaliana population

Evolutionary change begins at the population scale. Therefore, understanding adaptive variation requires the identification of the factors maintaining and shaping standing genetic variation at the within-population level. Spatial and temporal environmental heterogeneity represent ecological drivers of within-population genetic variation, determining the evolutionary trajectory of populations along with random processes. Here, we focused on the effects of spatio-temporal heterogeneity on quantitative and molecular variation in a natural population of the annual plant Arabidopsis thaliana. We sampled 1,093 individuals from a Spanish A. thaliana population across an area of 7.4 ha for 10 years (2012-2021). Based on a sample of 279 maternal lines, we estimated spatio-temporal variation in life-history traits and fitness from a common garden experiment. We genotyped 884 individuals with nuclear microsatellites to estimate spatio-temporal variation in genetic diversity. We assessed spatial patterns by estimating spatial autocorrelation of traits and fine-scale genetic structure. We analyzed the relationships between phenotypic variation, geographic location and genetic relatedness, as well as the effects of environmental suitability and genetic rarity on phenotypic variation. The common garden experiment indicated that there was more temporal than spatial variation in life-history traits and fitness. Despite the differences among years, genetic distance in ecologically relevant traits (e.g. flowering time) tended to be positively correlated to genetic distance among maternal lines, whilst isolation by distance was less important. Genetic diversity exhibited significant spatial structure at short distances, which were consistent among years. Finally, genetic rarity, and not environmental suitability, accounted for genetic variation in life-history traits. Synthesis. Our study highlighted the importance of repeated sampling to detect the large amount of genetic diversity at the quantitative and molecular levels that a single A. thaliana population can harbor. Overall, population genetic attributes estimated from our long-term monitoring scheme (genetic relatedness and genetic rarity), rather than biological (dispersal) or ecological (vegetation types and environmental suitability) factors, emerged as the most important drivers of within-population structure of phenotypic variation in A. thaliana.

Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

Capsella is a model plant genus of the Brassicaceae, closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognised Capsella species were genotyped, using a restriction digest-based next generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern clade consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridisation of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within Capsella orientalis postdated any extensive glacial events. Ecological niche modelling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridisation events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.

opencc-by-4.0Apr 2022View details →

CG molecular dynamics simulations. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".

<pre>Coarse-grained molecular dynamics simulations with Martini 3 with varying rescaling of protein-water interactions. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".</pre>

opencc-by-4.0Aug 2022View details →

Estimation of the hypocenter location and rupture extent of the 1850 Xichang, Sichuan, China, earthquake by dynamic rupture simulations on a multi-segment stepover structure

These datasets accompany the Zemuhe fault surface coordinates that were used for construction of the fault geometry model, the observational fault surface slip of the 1850 Xichang M 7.5 earthquake and the intensity distribution in Estimation of the hypocenter location and rupture extent of the 1850 Xichang, Sichuan, China, earthquake by dynamic rupture simulations on a multi-segment stepover structure submitted to Journal of Geophysical Research: Solid Earth by Yu et al. (2022). The data is structured as follows:   Once unzipped the data within the archive are six txt files: fault_surface_slip_Feng.txt, which is from Feng et al. (2000); fault_surface_slip_Ren.txt, which is from Ren and Lin (2010), fault_surface_slip_Yu.txt, which is from Yu et al., (2001); intensity.txt, which is from Feng et al. (2000); landslides.txt, which is from Guo et al. (2014) and Cao (2015); zemuhe_fault_surface_coordinates.txt, which is from Working group for geologic mapping on Zemuhe fault (2000).

opencc-by-4.0Jun 2022View details →

Parametrically enhanced interactions and non-reciprocal bath dynamics in a photon-pressure Kerr amplifier

Data and measurements scripts for the paper "Parametrically enhanced interactions and non-reciprocal bath dynamics in a photon-pressure Kerr amplifier"