sbresnahan / igc-retinue

Beyond conflict: intragenomic conflict predicts individual variation in altruistic behaviour.

Beyond conflict: kinship theory of intragenomic conflict predicts individual variation in altrustic behaviour

Bresnahan, S. T., Galbraith, D., Ma, R., Anton, K., Rangel, J., & Grozinger, C. M. (2023). Beyond conflict: Kinship theory of intragenomic conflict predicts individual variation in altruistic behaviour. Molecular Ecology. https://doi.org/10.1111/mec.17145

Using a reciprocal cross design, we tested for parent-of-origin effects on the workers’ 1) responsiveness to QMP, 2) ovary activation, and 3) brain transcriptome. We hypothesized that QMP-responsive workers have smaller and less active ovaries, influenced by the workers’ parent-of-origin. We tested whether QMP-responsive workers show enriched maternal allele-biased gene expression compared to QMP-unresponsive workers. Finally, we explored how parent-of-origin gene expression patterns are associated with overall gene expression patterns and gene regulatory networks.

Bioinformatics

Allele-specific read counts

https://github.com/sbresnahan/IGC-retinue/blob/main/retinue_ASReadCounts.md

Statistics

Behavior assay analysis

https://github.com/sbresnahan/IGC-retinue/blob/main/Retinue_behavior.R

Ovary physiology analysis

https://github.com/sbresnahan/IGC-retinue/blob/main/Retinue_ovaries.R

Parent-specific gene expression analysis

https://seantbresnahan.com/IGC-retinue/

DEG and WGCNA analyses

https://github.com/sbresnahan/IGC-retinue/blob/main/Retinue_DEGandWGCNA.R

SVM analysis

https://github.com/sbresnahan/IGC-retinue/blob/main/Retinue_SVM.R

TRN analysis

https://github.com/sbresnahan/IGC-retinue/blob/main/Retinue_analyzeTRN.R