Predicting hybrid fitness: the effects of ploidy and complex ancestry

# Predicting hybrid fitness: the effects of ploidy and complex ancestryHybridization between divergent populations places alleles in novel genomic contexts. This can inject adaptive variation -- which is useful for breeders and conservationists -- or reduce fitness, leading to reproductive isolation. Most theoretical work on hybrids involves haploid or diploid hybrids between two parental lineages, but real-world hybridization is often more complex. We introduce a simple fitness landscape model to predict hybrid fitness with arbitrary ploidy and an arbitrary number of hybridizing lineages. We test our model on published data from maize (<i>Zea mays</i>) and rye (<i>Secale cereale</i>), including hybrids between multiple inbred lines, both as diploids and synthetic tetraploids. Quantitative predictions for the effects of inbreeding, and the strength of progressive heterosis, are well supported. Results suggest that the model captures the important properties of dosage and genetic interactions, and may help to unify theories of heterosis and reproductive isolation.<br>## Description of the data and file structure<br>The three folders contain the scripts and data files required to produce the figures in the article<br>"Predicting hybrid fitness: the effects of ploidy and complex ancestry" by Hilde Schneemann ([[e-mail]](mailto:[e-mail])) and John Welch.<br>The data in the '.csv' files was extracted from the following sources (filtered and reformatted to facilitate our analysis):<br>rye data: Lundqvist, A. (1966). Heterosis and inbreeding depression in autotetraploid rye. Hereditas, 56(2-3):317–366.<br>maize data: Yao, H., Srivastava, S., Swyers, N., Han, F., Doerge, R. W., and Birchler, J. A. (2020). Inbreeding depression in genotypically matched diploid and tetraploid maize. Frontiers in Genetics,11:564928<br>You can run the scripts ending in '.R' files in R, setting the working directory to that in which the file is found.<br>The 'maize' folder contains script to produce the figures with maize data (Figure 1 and S1).<br>The 'rye' folder contains the script to produce the figures with rye data (Figure 2, S2, S3 and S4).<br>The 'FigS5' folder contains the script to produce the conceptual Figure S5.<br>### Files and variables<br>#### File: code.zip<br>**Description:** This compressed archive contains three folders ('maize', 'rye' and 'FigS5'). Each of these contains a single R script and the PDF figures created by this script. The 'maize' and 'rye' folder also contain CSV files with the data required by the scripts.<br>## Access information<br>Data was derived from the following sources:<br>* Lundqvist, A. (1966). Heterosis and inbreeding depression in autotetraploid rye. Hereditas, 56(2-3):317–366.* Yao, H., Srivastava, S., Swyers, N., Han, F., Doerge, R. W., and Birchler, J. A. (2020). Inbreeding depression in genotypically matched diploid and tetraploid maize. Frontiers in Genetics,11:564928<br><br>