@cedricfeschotte.bsky.social , @james-gagnon.bsky.social, @naltemose.bsky.social, @dparichy.bsky.social, and others not on here! We’d love to hear any thoughts or feedback.

A huge thank you to many people for help & feedback: Most of the lab, past and present, contributed to this project and since we are so new to TE and ERV biology we benefited enormously from input of colleagues including @fueyoraquel.bsky.social , @psudmant.bsky.social, @emiliapsantos.bsky.social,

Nadia found that sparkle fish often produce this “flash” during preexisting predator evasion behaviors shared across phenotypes. In addition to a whole new world (for me!) of TEs in gene regulation, we have a lot to do to better understand this trait – stay tuned for future work on this!

From videos of these fish from their natural habitats, we found that they often appear to “flash” as they change direction in the water. We are now curious about whether the trait might impact predator evasion, particularly of the avian predators that frequently make a meal of swordtails.

This recent insertion is remarkable because the trait is already at high frequency (~30%) in the population. @nadiahaghani.bsky.social and others in the lab were very interested in how this trait might impact survival or mating success in the natural environment.

This, together with evidence of expression of the ERV and high sequence identity ERV elements in the genome suggested that the retrovirus was active. Using SLiM, we estimated the age of the insertion on chromosome 15 and found that it was consistent with an insertion in the last 15-20k generations.

Guanzhu mined our phased genome assemblies and available genomes for the larger group to better understand the evolution of this element. He found dozens of complete insertions of this ERV-foamy retrovirus in our phased assemblies, most at low frequency.

At this point we knew we were out of our depth & connected with Guanzhu Han who has now schooled us in many elements of TEs and ERV biology. Guanzhu & co helped us characterize this as an ERV-foamy retrovirus and found that this TE contains all protein coding domains needed for transposition.

ERVs are often coopted for host regulatory functions over evolutionary time, particularly the LTR regions which act as promoters and enhancers for the element. We were excited to find that the LTR regions had evidence of higher chromatin accessibility and drove high reporter activity in vitro.

Based on this, we found that all sparkle fish had a 17 kb insertion in at least one haplotype & PCR to confirmed this pattern in a large sample. A simple blast suggested that this insert was an endogenous retrovirus (ERV), a TE that enters the host as a retrovirus and becomes vertically transmitted.

This is where the project expanded and has led to so many new directions. We realized early on there was something odd about the peak. With help from @tododge.bsky.social and @gpreising.bsky.social , Nadia generated phased haplotypes with PacBio HiFi for several individuals of each phenotype.

She found the type of genetic signal that one only finds with pigmentation traits: a single, whopping peak on chromosome 15. This region contained 16 genes, and @nadiahaghani.bsky.social found that only one of these genes, alkal2a, is strongly upregulated in sparkle scales.

Nadia had just joined the lab and was excited to characterize this phenotype. She also dubbed the phenotype “sparkle” which instantly stuck. She did some lovely imaging of the phenotype at the cellular level and beyond (see Figure 1!) and then moved on to tackling its genetic basis with GWAS.