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, either shallow or deep, and balancing selection to
retain variants needed for each depth range. This is supported by signals
for long-term balancing selection at these loci (based on published
genomic data). We discuss alternative interpretations and conclude that
balancing selection, maintaining ecotype diversity, is the best supported
mechanism.