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8 results for “variance partitioning”
Data from: Partitioning variance in population growth for models with environmental and demographic stochasticity
<ol> <li>How demographic factors lead to variation or change in growth rates can be investigated using life table response experiments (LTRE) based on structured population models. Traditionally, LTREs focused on decomposing the asymptotic growth rate, but more recently decompositions of annual 'realized' growth rates have gained in popularity.</li> <li>Realized LTREs have been used particularly to understand how variation in vital rates translates into variation in growth for populations under long-term study. For these, complete population models may be constructed by combining data in an integrated population model (IPM). IPMs are also used to investigate how temporal variation in environmental drivers affect vital rates. Such investigations have usually come down to estimating covariate coefficients for the effects of environmental variables on vital rates, but formal ways of assessing how they lead to variation in growth rates have been lacking. </li> <li>We extend realized LTREs in two ways. First, we further partition the contributions from vital rates into contributions from temporally varying factors that affect them. The decomposition allows us to compare the resultant effect on the growth rate of different environmental factors that may each act via multiple vital rates. Second, we show how realized growth rates can be decomposed into separate components from environmental and demographic stochasticity. The latter is typically omitted in LTRE analyses.</li> <li>We illustrate how to use the approach in an IPM for data from a 26-year study on northern wheatears (Oenanthe oenanthe), a migratory passerine bird breeding in an agricultural landscape. For this population, consisting of around 50–120 breeding pairs per year, we partition variation in realized growth rates into environmental contributions from temperature, rainfall, population density, and unexplained random variation via multiple vital rates, and from demographic stochasticity.</li> <li>The case study suggests that variation in first-year survival via the random component, and adult survival via temperature are two main factors behind environmental variation in growth rates. More than half of the variation in growth rates is suggested to come from demographic stochasticity, demonstrating the importance of this factor for populations of moderate size.</li> </ol>
Data from: Partitioning variance in population growth for models with environmental and demographic stochasticity
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Challenges and limitations of applying the flux variance similarity (FVS) method to partition evapotranspiration in a montane cloud forest
<p>Dataset</p> <table> <tbody> <tr> <td>Name</td> <td>Description</td> </tr> <tr> <td>FVS_ori.zip</td> <td>the output from FVS method</td> </tr> <tr> <td>ModFVS.zip</td> <td>the output from ModFVS method</td> </tr> <tr> <td>CLM.zip</td> <td>the output from CLM </td> </tr> <tr> <td>Chilan_30min_sap_velocity_20200601_20211120_QC.csv</td> <td>the sap flow data in Chi-Lan</td> </tr> <tr> <td>*_clim.csv</td> <td>the observation data in Chi-Lan and Lien-Hua-Chih</td> </tr> </tbody> </table> <p> </p> <p>Codes for Analysis</p> <table> <tbody> <tr> <td>Name</td> <td>Description</td> </tr> <tr> <td>*.ipynb</td> <td>the python code used for analyzing output</td> </tr> <tr> <td>*_FVS_process.py</td> <td>the python code used for process ModFVS method</td> </tr> </tbody> </table> <p> </p> <p>ModFVS method (fluxpart-0.2.10+rhtest-py3-none-any.whl)</p> <ul> <li>use "pip install fluxpart-0.2.10+rhtest-py3-none-any.whl" to install the package</li> <li> <p>To specify a maximum allowable relative humidity when calculating WUE, set a value for "max_rh" in "wue_options". For example, to set the max RH to 95%, you would change your example code to this:</p> <p>wue_options = {"meas_ht": 23.7,"canopy_ht":10, "ppath": "C3","ci_mod":ci_mod, "max_rh":95}</p> </li> <li> <p>Note that this code is a fork of (https://github.com/usda-ars-ussl/fluxpart)</p> </li> </ul> <p> </p> <p> </p>
Variance partitioning of nest provisioning rates in blue tits: individual repeatability, heritability and partner interactions
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Data and code for: Partitioning variance in a signaling trade-off under sexual selection reveals among-individual covariance in trait allocation
<p>Understanding the evolution of traits subject to trade-offs is challenging because phenotypes can (co)vary at both the among- and within-individual levels. Among-individual covariation indicates consistent, possibly genetic, differences in how individuals resolve the trade-off, while within-individual covariation indicates trait plasticity. There is also the potential for consistent among-individual differences in behavioral plasticity, although this has rarely been investigated. We studied the sources of (co)variance in two characteristics of an acoustic advertisement signal that trade off with one another and are under sexual selection in the gray treefrog, <em>Hyla chrysoscelis</em>: call duration and call rate. We recorded males on multiple nights calling spontaneously and in response to playbacks simulating different competition levels. Call duration, call rate, and their product, call effort, were all repeatable both within and across social contexts. Call duration and call rate covaried negatively, and the largest covariance was at the among-individual level. There was extensive plasticity in calling with changes in social competition, and we found some evidence for among-individual variance in call rate plasticity. The significant negative among-individual covariance in trait values is perpendicular to the primary direction of sexual selection in this species, indicating potential limits on the response to selection.</p>
Data and code from: Partitioning variance in a signaling trade-off under sexual selection reveals among-individual covariance in trait allocation
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Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement
Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted of adaptations that involve sets of high dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining by high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.
Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement
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International Brain Laboratory public data
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OpenNeuro
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