Sensitivity analysis script for: Why so many polyploids?
Data files
Jan 26, 2024 version files 111.96 KB
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README.md
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UG_data.xlsx
Abstract
While polyploids are common in nature, existing models suggest that polyploid establishment should be difficult and rare. We explore this apparent paradox by focusing on the role of unreduced gametes, as their union is the main route for formation of neopolyploids. Production of such gametes is affected by genetic and environmental factors, resulting in variation in the formation rate of unreduced gametes (u). Once formed, neopolyploids face minority cytotype exclusion (MCE) due to a lack of viable mating opportunities. More than a dozen theoretical models have explored factors that could permit neopolyploids to overcome minority cytotype exclusion and become established. Until now, however, none have explored variability in u and its consequences for the rate of polyploid establishment. Here, we determine the distribution that best fits available empirical data on u. We perform a global sensitivity analysis exploring the consequences of using empirical distributions of u to investigate effects on polyploid establishment. We determined in many cases u is best fit by a log-normal distribution. We found environmental stochasticity in u dramatically impacts model predictions when compared to a static u. Our results help reconcile previous modeling results suggesting high barriers to polyploid establishment with the observation that polyploids are common in nature.
README: Sensitivity Analysis Script from Why so many polyploids?
https://doi.org/10.5061/dryad.66t1g1k80
Description of the data and file structure
There are two files included for the global sensitivity analysis of a model for overcoming minority cytotype exclusion, through including environmental stochasticity in the rate of unreduced gametes.
- Sobol_MCE.R
- UG_data.csv
The input file (FinalUGdataset.csv) for the Sobol_MCE.R analysis script can be found at osf.io/y784s, where it has been published by the original author.
From the input file the CorX column was used for the corrected measurement of unreduced gametes per sample. The analysis script puts out a table of the Sobol indices for the model parameterized from the original data.
UG_data.xlsx
A workbook that has three tabs; UG_data, Species and Location.
UG_data
- Sample = a string of characters identifying each individual sample. The values come from Pop and then an individual sample.
- Species = the species epithet for the sample. See second tab for complete list.
- Pop = a string of characters identifying the Species and Location. The values come from Species and Location.
- LH = Life History; overall life history of species as annual, biennial or perennial.
- Ploidy = Assigned ploidy level for the sample.
- Cx = Chromosome number of the sample.
- DNA = The measured amount of DNA per sample.
- Sexual = Primary mode of reproduction for the species; selfing, mixed, outcrossing and apomictic.
- Location = The collection location for the sample. See Location tab for Longitude and Latitude (also see Kriener 2017 Table S1).
- CorX = The corrected value for the occurrence of unreduced gametes in that sample.
Species list
All species names are listed.
Location
Each location has a general site name and then the longitude and latitude provided.
Sharing/Access information
Data was derived from the following sources:
- Kreiner, Julia M., Paul Kron, and Brian C. Husband. 2017. “Frequency and Maintenance of Unreduced Gametes in Natural Plant Populations: Associations with Reproductive Mode, Life History and Genome Size.” New Phytologist 214 (2): 879–89. https://doi.org/10.1111/nph.14423.
- Kreiner, J. (2021, December 1). Frequency and maintenance of unreduced gametes. Retrieved from osf.io/y784s
Code/Software
The script file is commented throughout and explains how to adapt the code/what is occurring each step of the way.