An official website of the United States government
Abstract Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of thehwepR package on the Comprehensive R Archive Networkhttps://cran.r‐project.org/package=hwep.
more »
« less
This content will become publicly available on May 1, 2025
‘rtry’: An R package to support plant trait data preprocessing
Abstract Plant trait data are used to quantify how plants respond to environmental factors and can act as indicators of ecosystem function. Measured trait values are influenced by genetics, trade‐offs, competition, environmental conditions, and phenology. These interacting effects on traits are poorly characterized across taxa, and for many traits, measurement protocols are not standardized. As a result, ancillary information about growth and measurement conditions can be highly variable, requiring a flexible data structure. In 2007, the TRY initiative was founded as an integrated database of plant trait data, including ancillary attributes relevant to understanding and interpreting the trait values. The TRY database now integrates around 700 original and collective datasets and has become a central resource of plant trait data. These data are provided in a generic long‐table format, where a unique identifier links different trait records and ancillary data measured on the same entity. Due to the high number of trait records, plant taxa, and types of traits and ancillary data released from the TRY database, data preprocessing is necessary but not straightforward. Here, we present the ‘rtry’ R package, specifically designed to support plant trait data exploration and filtering. By integrating a subset of existing R functions essential for preprocessing, ‘rtry’ avoids the need for users to navigate the extensive R ecosystem and provides the functions under a consistent syntax. ‘rtry’ is therefore easy to use even for beginners in R. Notably, ‘rtry’ does not support data retrieval or analysis; rather, it focuses on the preprocessing tasks to optimize data quality. While ‘rtry’ primarily targets TRY data, its utility extends to data from other sources, such as the National Ecological Observatory Network (NEON). The ‘rtry’ package is available on the Comprehensive R Archive Network (CRAN;https://cran.r‐project.org/package=rtry) and the GitHub Wiki (https://github.com/MPI‐BGC‐Functional‐Biogeography/rtry/wiki) along with comprehensive documentation and vignettes describing detailed data preprocessing workflows.
more »
« less
- PAR ID:
- 10518015
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 14
- Issue:
- 5
- ISSN:
- 2045-7758
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract BackgroundPlant architecture can influence crop yield and quality. Manual extraction of architectural traits is, however, time-consuming, tedious, and error prone. The trait estimation from 3D data addresses occlusion issues with the availability of depth information while deep learning approaches enable learning features without manual design. The goal of this study was to develop a data processing workflow by leveraging 3D deep learning models and a novel 3D data annotation tool to segment cotton plant parts and derive important architectural traits. ResultsThe Point Voxel Convolutional Neural Network (PVCNN) combining both point- and voxel-based representations of 3D data shows less time consumption and better segmentation performance than point-based networks. Results indicate that the best mIoU (89.12%) and accuracy (96.19%) with average inference time of 0.88 s were achieved through PVCNN, compared to Pointnet and Pointnet++. On the seven derived architectural traits from segmented parts, an R2value of more than 0.8 and mean absolute percentage error of less than 10% were attained. ConclusionThis plant part segmentation method based on 3D deep learning enables effective and efficient architectural trait measurement from point clouds, which could be useful to advance plant breeding programs and characterization of in-season developmental traits. The plant part segmentation code is available athttps://github.com/UGA-BSAIL/plant_3d_deep_learning.more » « less
-
dadi-cli: Automated and distributed population genetic model inference from allele frequency spectraAbstract Summarydadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. Availability and Implementationdadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/.more » « less
-
Abstract BackgroundEstimating and accounting for hidden variables is widely practiced as an important step in molecular quantitative trait locus (molecular QTL, henceforth “QTL”) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for this purpose. ResultsHere we benchmark popular hidden variable inference methods including surrogate variable analysis (SVA), probabilistic estimation of expression residuals (PEER), and hidden covariates with prior (HCP) against principal component analysis (PCA)—a well-established dimension reduction and factor discovery method—via 362 synthetic and 110 real data sets. We show that PCA not only underlies the statistical methodology behind the popular methods but is also orders of magnitude faster, better-performing, and much easier to interpret and use. ConclusionsTo help researchers use PCA in their QTL analysis, we provide an R package along with a detailed guide, both of which are freely available athttps://github.com/heatherjzhou/PCAForQTL. We believe that using PCA rather than SVA, PEER, or HCP will substantially improve and simplify hidden variable inference in QTL mapping as well as increase the transparency and reproducibility of QTL research.more » « less
-
Abstract Conjoint analysis is a popular experimental design used to measure multidimensional preferences. Many researchers focus on estimating the average marginal effects of each factor while averaging over the other factors. Although this allows for straightforward design-based estimation, the results critically depend on the ways in which factors interact with one another. An alternative model-based approach can compute various quantities of interest, but requires correct model specifications, a challenging task for conjoint analysis with many factors. We propose a new hypothesis testing approach based on the conditional randomization test (CRT) to answer the most fundamental question of conjoint analysis: Does a factor of interest matterin any waygiven the other factors? Although it only provides a formal test of these binary questions, the CRT is solely based on the randomization of factors, and hence requires no modeling assumption. This means that the CRT can provide a powerful and assumption-free statistical test by enabling the use of any test statistic, including those based on complex machine learning algorithms. We also show how to test commonly used regularity assumptions. Finally, we apply the proposed methodology to conjoint analysis of immigration preferences. An open-source software package is available for implementing the proposed methodology. The proposed methodology is implemented via an open-source software R packageCRTConjoint, available through the Comprehensive R Archive Networkhttps://cran.r-project.org/web/packages/CRTConjoint/index.html.more » « less
