Supplementary Materials

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S7
  • Tables S1 to S7
  • Legends for Databases S1 to S5
  • Full Reference List
Database S1
Regions inferred to have been targeted by directional selection using: 1) a FST-H outlier approach contrasting genetic diversity between wild and domestic rabbits, 2) allele frequency spectra (SweepFinder), and 3) an explicit demographic model contrasting genetic diversity between wild and domestic rabbits (capture arrays data).
Database S2
P-values obtained using coalescent simulations of the demographic scenario inferred in this study for the SweepFinder and targeted capture analyses. The obtained value for the magnitude of the domestication bottleneck in this study (kdom = 1.3) was lower than a previous estimate (kdom = 2.8). Under the model used to infer directional selection in the domesticated lineage using the targeted capture dataset, the estimation from this study describes a stronger bottleneck and thus renders our selection tests conservative. However, this is not the case for the SweepFinder analysis and P-values using both bottlenecks estimates are provided.
Database S3
Full results of overrepresentation analysis using SNPs at conserved non-coding sited with ΔAF>0.80 performed using the GREAT tool.
Database S4
Missense SNPs showing a delta allele frequency difference of 0.90 or higher between wild and domestic rabbits.
Database S5
Duplications and deletions showing allele frequency differences between wild and domestic rabbits according to an ANOVA analysis.