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opencc-zeroDec 2020View details →

Data from: Identifying 'useful' fitness models: balancing the benefits of added complexity with realistic data requirements in models of individual plant fitness

Direct species interactions are commonly included in individual fitness models used for coexistence and local-diversity modeling. Though widely considered important for such models, direct interactions alone are often insufficient for accurately predicting fitness, coexistence or diversity outcomes. Incorporating higher-order interactions (HOIs) can lead to more accurate individual fitness models, but also adds many model terms, which can quickly result in model over-fitting. We explore approaches for balancing the trade-off between tractability and model accuracy that occurs when HOIs are added to individual fitness models. To do this, we compare models parameterized with data from annual plant communities in Australia and Spain, varying in the extent of information included about the focal and neighbor species. The best performing models for both datasets were those that grouped neighbors based on origin status and life form, a grouping approach that reduced the number of model parameters substantially while retaining important ecological information about direct interactions and HOIs. Results suggest that specific focal- or neighbor-species identity is not necessary for building well-performing fitness models that include HOIs. In fact, grouping neighbors by even basic functional information seems sufficient to maximize model accuracy, an important outcome for the practical use of HOI-inclusive fitness models.

opencc-zeroDec 2010View details →

Data from: Are pollination "syndromes" predictive? Asian dalechampia fit neotropical models

Using pollination-syndrome parameters and pollinator correlations with floral phenotype from the neotropics, we predicted that Dalechampia bidentata Blume (Euphorbiaceae) in southern China would be pollinated by female resin-collecting bees between 12 and 20 mm in length. Observations in southwestern Yunnan Province, China, revealed pollination by resin-collecting, female Megachile (Callomegachile) nr. faceta Bingham (Hymenoptera: Megachilidae). These bees, at 14 mm in length, were in the predicted size range, confirming the utility of syndromes and models developed in distant regions. Phenotypic-selection analyses and estimation of adaptive surfaces and adaptive accuracies together suggest that the blossoms of D. bidentata are well adapted to pollination by their most common floral visitors.

opencc-zeroDec 2017View details →

Data from: Estimating the relative fitness of escaped farmed salmon offspring in the wild and modeling the consequences of invasion for wild populations

Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in lab and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically-based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1%, 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively), and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modeling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.

opencc-zeroDec 2011View details →

Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.

opencc-zeroDec 2014View details →

Data from: Successful by chance? the power of mixed models and neutral simulations for the detection of individual fixed heterogeneity in fitness components

Heterogeneity in fitness components consists of fixed heterogeneity due to latent differences fixed throughout life (e.g. genetic variation), and dynamic heterogeneity generated by stochastic variation. Their relative magnitude is crucial for evolutionary processes, as only the former may allow for adaptation. However, the importance of fixed heterogeneity in small populations has recently been questioned. Using neutral simulations (NS), several studies failed to detect fixed heterogeneity, thus challenging previous results from mixed models (MM). To understand the causes of this discrepancy, we estimate the statistical power and false positive rate of both methods, and apply them to empirical data from a wild rodent population. While MM show high false positive rates if confounding factors are not accounted for, they have high statistical power to detect real fixed heterogeneity. In contrast, NS are also subject to high false positive rates, but have always low power. Indeed, MM analyses of the rodent population data show significant fixed heterogeneity in reproductive success, whereas NS analyses do not. We suggest that fixed heterogeneity may be more common than is suggested by NS, and that NS are useful only if more powerful methods are not applicable and if they are complemented by a power analysis.

opencc-by-4.0Dec 2021View details →

Relative traveltimes and amplitude ratios of seismic triplications for the four earthquakes in the southwestern Siberia and resulting best-fit LVL velocity models

For details about the data,  please see the published paper titled "A partial molten low-velocity layer atop the mantle transition zone beneath the western Junggar: implication for the formation of subduction-induced sub-slab mantle plume" in the journal G-Cubed.

opencc-by-4.0Jul 2022View details →

Pre-fitted Bayesian models for "Gene panel selection for targeted spatial transcriptomics"

simulation_parameters_DARTFISH_slim.rds: Bayesian model fitted on the Zhang dataset. simulation_parameters_MERFISH_slim.rds: Bayesian model fitted on the Moffit dataset. simulation_parameters_osmFISH_slim.rds: Bayesian model fitted on the Codeluppi dataset.

opencc-by-4.0Jun 2024View details →

Outputs from fitted models across the cross-validation scenarios for 'Space-time species distribution modeling with opportunistic presence-only data: a case study of passerines in a protected area'

Three Zenodo repositories are linked to the preprint Space-time Species Distribution Modeling for Opportunistic Presence-Only Data: A Case Study of Passerines in a Protected Area  (Lasgorceux et al., unpublished, <a href="https://hal.science/hal-04616332">https://hal.science/hal-04616332</a>): <ul> <li>Data, scripts and, code (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052</a>)</li> <li>Outputs from fitted models across the cross-validation scenarios (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12544212">https://doi.org/10.5281/zenodo.12544212</a>)</li> <li>Supplementary information at (Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12541412">https://doi.org/10.5281/zenodo.12541412</a>)</li> </ul> This repository contains the outputs from fitted models across the cross-validation scenarios. In the folder Ouputs_cross_validation, each species is represented by a .RData file, numbered from 1 to 77 (excluding 7, which corresponds to Bombycilla garrulus; see the preprint for details). This dataset is specifically used to generate Figure 1, which shows the AUC of various cross-validation scenarios. To reproduce this figure in R, place all the files in the Results/Fitted_models folder and run the Models_Outputs.R script located in the Results folder of Lasgorceux et al., Zenodo, <a href="https://doi.org/10.5281/zenodo.12545052">https://doi.org/10.5281/zenodo.12545052.</a> Note: These data have been separated due to memory requirements (23.14GB).

opencc-by-4.0Jul 2024View details →

Pylake example: Data to fit the Twistable Worm-Like Chain Model

Open the record for dataset details and reuse information.

opencc-by-4.0Oct 2018View details →

Model fits (MCMC samples) for two papers on perceptual confidence

These are model fits for two papers on perceptual confidence. See <a href="https://github.com/wtadler/confidence/">github.com/wtadler/confidence</a> for more info.

opennotspecifiedSep 2011View details →

Fig. 8 Fitness landscape for models 7 and 8 in Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs

Fig. 8 Fitness landscape for models 7 and 8. Relative fitness is a function of trait T1 and trait T2. Epistasis is modelled as follows:

opencc-by-4.0Aug 2024View details →

Best-fit Abundances, Observed Spectra and Spectral Models for the New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization

Dataset associated with Fisher et al. 2024 in RNAAS <a href="https://iopscience.iop.org/article/10.3847/2515-5172/ad79f0">[link to publication]</a> <code>summary.mrt</code> is a table of identifiers, photometry, fundamental stellar parameters and detailed chemical compositions for 13 candidate wide binary systems with FGK Main Sequence primaries (5100 K < Teff < 6300 K) and ultracool dwarf companions (2500 K < Teff < 3100 K). Refer to the file header for detailed description of columns and units. <code>stars.zip</code> contains the high-resolution spectra of primaries observed with the Automated Planet Finder (APF, program <code>2021B_A010</code>), as well as the corresponding best-fit spectral models. Each FITS file in the archive represents an individual exposure of the primary. The files are arranged in directories by identifiers of the primaries. The total number of exposures varies from source to source. FITS files are composed of a primary HDU and 6 extensions. <ul> <li>The primary HDU contains the unmodified sky-subtracted spectrum of the object as produced by the APF pipeline and published on <a href="https://jump.caltech.edu/">Jump</a>. The spectrum is stored as a 2D array organized by Echelle orders.</li> <li>The first extension contains the corresponding air wavelengths [in A] transformed to the rest frame of the source.</li> <li>The second extension is the boolean mask of pixels included in model fitting.</li> <li>The third extension is the adopted statistical weights of each pixel, estimated as inverse variances under the assumption of Poisson noise.</li> <li>The fourth extension contains the best-fit synthetic spectrum in CGS units of surface intensity per wavelength in A.</li> <li>The fifth extension is the best-fit spline continuum correction between the model and the data.</li> <li>The final extension contains the adopted FWHM of the line spread function in each pixel, estimated by combining in quadrature a wavelength-dependent component with λ/Δλ=120,000 and a best-fit wavelength independent component (the <code>quickblur</code> parameter of the <a href="https://github.com/Roman-UCSD/chemfit">chemfit</a> package)</li> </ul> This repository is for the research note "New Sample of Ultracool Dwarf Benchmarks with Detailed Chemical Characterization" by Fisher et al. It is associated with manuscript number AAS58102.

Figure 4 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models

Figure 4. Scaling relationship between log pronotum width and log horn length in Bledius tricornis (Herbst, 1784). The slope is 1.166 (SE = 0.093) and the linear model has an R2 of 0.78.

Figure 3 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models

Figure 3. Scaling relationship between log pronotum width and log horn length in Bledius frisius Lohse, 1978. The slope is 1.816 (SE = 0.136) and the linear model has an R2 of 0.78.

Figure 1 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models

Figure 1. (a) Bledius spectabilis Kraatz, 1857 schematic diagram of pronotal measurements taken and habitus. (b) Bledius spectabilis at Chesil Fleet, Dorset, UK (photograph by Steve Trewhella). HL = horn length; PW = pronotum width.

Figure 2 in Horn scaling relationships in three species of Bledius Leach 1819 (Insecta: Coleoptera: Staphylinidae) show no indication of fitting non-linear allometric models

Figure 2. Scaling relationship between log pronotum width and log horn length in Bledius spectabilis Kraatz, 1857. The slope is 1.447 (SE = 0.096) and the linear model has an R2 of 0.68.

opencc-zeroFeb 2023View details →

Fitting and evaluating univariate and multivariate models of within-lineage evolution

The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time-series of ancestor-descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. Using uni- and multivariate models of trait evolution that make different assumptions regarding the dynamics of the adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian Eucyrtidium calvertense and armor in the stickleback Gaserosteus doryssus. Body size evolution in E. calvertense is best explained by a model where the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (Gasterosteus doryssus) shows evidence of adaptation towards independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in an R package evoTS, which builds on the commonly used paleoTS framework.

opencc-zeroApr 2023View details →

Data from: Integrated species distribution models fitted in INLA are sensitive to mesh parameterisation

The ever-growing popularity of citizen science, as well as recent technological and digital developments, have allowed the collection of data on species' distributions at an extraordinary rate. In order to take advantage of these data, information of varying quantity and quality needs to be integrated. Point process models have been proposed as an elegant way to achieve this for estimates of species distributions. These models can be fitted efficiently using Bayesian methods based on integrated nested Laplace approximations (INLA) with stochastic partial differential equations (SPDE). This approach uses an efficient way to model spatial autocorrelation using a Gaussian random field and a triangular mesh over the spatial domain. The mesh is constructed by user-defined variables, so effectively represents a free parameter in the model. However, there is a lack of understanding about how to set these mesh parameters, and their effect on model performance. Here, we assess how mesh parameters affect predictions and model fit to estimate the distribution of the serotine bat, Eptesicus serotinus, in Great Britain. A Bayesian INLA model was fitted using five meshes of varying densities to a dataset comprising both structured observations from a national monitoring programme and opportunistic records. We demonstrate that mesh density impacted spatial predictions with a general loss of accuracy with increasing mesh coarseness. However, we also show that the finest mesh was unable to overcome spatial biases in the data. In addition, the magnitude of the covariate effects differed markedly between meshes. This confirms that mesh parameterisation is an important and delicate process with implications for model inference. We discuss how species distribution modellers might adapt their use of INLA in light of these findings.

opennotspecifiedOct 2021View details →

FIG. 4. Individual growth model fits for 36 in Hoplodactylus duvaucelii

FIG. 4. Individual growth model fits for 36 male Diamondback Terrapins. Blue lines represent the individual von Bertalanffy model fits for the corresponding plastron-at-age observations, which are represented with black dots. The 95% credible regions are show in the pink-shaded region.