Epigenetic signatures of social status in wild spotted hyenas (Crocuta crocuta)

In mammalian societies, dominance hierarchies translate into inequalities in health, reproductive performance and survival. DNA methylation is thought to mediate the effects of social status on gene expression and phenotypic outcomes, yet, a study of social status-specific DNA methylation profiles in different age classes in a wild social mammal is missing. We tested for social status signatures in DNA methylation profiles in wild female spotted hyenas (Crocuta crocuta) in cubs and adults using non-invasively collected gut epithelium samples. In spotted hyena clans, female social status influences access to resources, foraging behaviour, health, reproductive performance and survival. We identified 149 differentially methylated regions between 42 high- and low-ranking spotted hyena females (cubs and adults). Differentially methylated genes were associated with energy conversion, immune function and glutamate receptor signalling. Our results provide evidence that socio-environmental inequ..., In the Serengeti National Park in Tanzania, we collected gut epithelium cells from faecal samples of 42 free-ranging female hyenas (24 cubs and 18 adults) of either low (15 cubs, 9 adults) or high (9 cubs, 9 adults) social status. In spotted hyenas, social status is determined by the animals’ interactions within their social group (clan). We extracted DNA and RNA from each sample. Epithelium cells contain mainly one cell-type, reducing the effect of cell-type specific methylation. We first performed whole genome bisulfite sequencing (WGBS), but mapping yielded in up to 99% bacterial data and parasitic DNA and the analysis with MACAU did not give coherent and in trustworthy results (Supplementary Table 7). Using methylation capture targeting CpG-methylation (with MBD2, MethylMiner, Invitrogen), we enriched methylated DNA fragments of hyenas. After Illumina sequencing (HiSeqX 150 bp PE, Macrogen), we mapped the quality-filtered reads to the novel spotted hyena reference sequence50 with th..., , # Data from: Epigenetic signatures of social status in free-ranging spotted hyenas (Crocuta crocuta)

The MBD-Seq data are uploaded to NCBI BioProject ID PRJNA1036526, including reference genome \"crocuta.fasta\". The statistical analysis is available as a R-package “Weyrich23” at [https://github.com/vullioud/Weyrich23](https://github.com/vullioud/Weyrich23). Dryad data contain the novel annotation file and read count tables for our study DOI xxx.

## Description of the data and file structure

**Annotation file \"crocuta_liftoff_Hhy_ASM300989v1_addPromoter.gtf\":**
We performed the custom annotation file in which we incorporated relevant positions for epigenetic regulation (i.e. gene annotations, Transcription Start Sites (TSS), promoters). In a first step, we mapped the annotation of the recently published striped hyena (*Hyena hyena)* annotation (RefSeq Assembly ID: GCF_003009895.1) to the spotted hyena genome as closest relative using the Liftoff software (v1.6.1). This provided the ann...