Balancing selection maintains intraspecific diversity in a deep-sea fish

Segregating alleles in natural populations can be driven to fixation or loss by genetic drift or directional selection, or may be maintained in a polymorphic state by balancing selection. Balancing selection in a panmictic population is theoretically well established, but not widely understood at the molecular level. In this study, we focus on the evolutionary processes affecting non-synonymous variants at eight functionally relevant loci (based on candidate SNP genotyping) in a deep-sea fish species (Coryphaenoides rupestris) that lives across habitat zones ranging from ~200 m to ~2000 m depth. At each of these loci, one allele is predominant in the deeper water. Across a shallower depth range, we find that minor allele frequencies show a highly significant increase or decline progressively across five defined age categories. At single depths below a threshold depth, the deep-water allele declines in frequency with age. Together, these data indicate segregatio n to different depths, ei..., , # Balancing selection maintains intraspecific diversity in a deep-sea fish

Dataset DOI: [10.5061/dryad.34tmpg4xx](https://doi.org/10.5061/dryad.34tmpg4xx)

## Description of the data and file structure

Specimens of 290 *Coryphaenoides rupestris* were collected from eight depths ranging from 750m to 1900m and run on a MiSeq (Illumina Inc.) with a 2 x 75 bp paired-end sequencing protocol. Raw reads were automatically de-multiplexed by the MiSeq (Illumina Inc.) Analysis Software using the individual-specific index barcodes. Paired-end reads were combined using FLASH (min overlap of 4 and max overlap of 50; Magoč and Salzberg 2011). Merged reads were then mapped to the compiled consensus sequences for the target loci using BWA-MEM v0.7.17-r1188 (Li and Durbin 2009). Mapped reads were converted from Sequence Alignment/Map (SAM) files to BAM files with SAMtools v1.13 (Li et al., 2009). Variable sites were identified using FreeBayes v1.3.6 (--haplotype-length 0 -kwVa –no-mnps –no-complex; Ga...,