‘Who’s Your Daddy?’: Ddradseq Parentage In Broodstock-Offspring Pairs Of Diadema Antillarum In A Population Restoration Initiative

In the early 1980s Diadema antillarum, or the long-spined urchin, was hit by a catastrophic mass mortality event across the western Atlantic and Gulf of Mexico, inclusive of the Florida Keys. The cause of this die-off event was likely triggered by a pathogen or environmental stressor that decimated native populations by up to 98%. The species has not yet fully recovered and is struggling with recruitment success which is why it may benefit from an ex-situ recovery program. In this study, I used single nucleotide polymorphisms (SNPs) to identify genetic variation and analyze parentage in a captive population of D. antillarum. Harnessing these methods as an identification tool is incredibly useful in understanding populations and head-starting conservation and restoration projects for at-risk species through captive breeding programs. Sea urchins collected for this study were all housed at the Florida Aquarium and included urchins that fell into three categories: unique broodstock (n=15), larvae (n=80), and juveniles (n=50). I extracted DNA and conducted double digest restriction-site associated sequencing (ddRADseq) to generate SNPs for parentage analysis. Following alignment and filtering procedures, I generated a final set of 2426 high-quality SNPs from 14 unique broodstock samples and 24 juveniles. To infer pairwise relationships between all pairs of individuals sequenced, I used the R package CKMRsim using the likelihood ratio method. I was able to assign dual parentage to 9 juveniles, and for the remaining 15 juveniles I identified a single parent. Additionally, I found that 7 broodstock adults participated in offspring generation and 7 broodstock adults failed to generate offspring. Moreover, since this was a closed system, my data suggests that the one missing adult successfully participated in the breeding event. Variation in adult participation ranged from 1 offspring assigned (for two broodstock) to 9 assigned (for 1 broodstock). Interestingly, given the numbers, the missing broodstock sample would have parented 15 offspring. These results demonstrate that ddRADseq enables accurate identification of breeders and their offspring in D. antillarum, providing insight into reproductive dynamics and offering a powerful tool for optimizing genetic diversity and enhancing the effectiveness of long-term conservation and restoration strategies.