A Population Genomic Study of Mutton Snapper (Lutjanus analis) Throughout Florida and the Caribbean

<p>The mutton snapper (<em>Lutjanus analis</em>) is a reef fish commonly found in tropical waters of the Western Atlantic Ocean. This species is sedentary at the juvenile and adult stages when spatial movements are limited to short migrations to join spawning aggregations. Dispersal, mediated by oceanic currents, may occur during the 27-37 days pelagic larval phase. Information on genetic stock structure is critical to design management units for mutton snapper fisheries. Previous genetic studies did not detect significant structuring, but the surveys only included 8-16 genetic markers and limited geographic sampling. In this study, a chromosome-level reference genome with a BUSCO completeness score of 93.3% was developed using Illumina and PACBio sequencing combined with Hi-C scaffolding and applied in population genomic analysis. Mutton snapper (total sample size 724) were collected between 2021 and 2025 from coastal waters off Belize, Puerto Rico, St. Thomas, Martinique, and three areas around the Florida peninsula. Samples were assayed using dd-RAD sequencing, revealing 7,748 SNP markers. Mantel tests showed a weak isolation-by-distance pattern across the sampled range. Significant spatial autocorrelation of genotypes sampled within a 300 km window along the Florida coast was also detected. Principal component analyses and Bayesian clustering revealed two weakly differentiated groups, one containing Belize and Florida mutton snapper, and the other containing the three Eastern Caribbean populations (F_ST = 0.001). Outlier analysis revealed an outlier genomic region on chromosome 10 (42 loci, F_ST up to 0.24) differentiating the two groups, suggesting selection is associated with the divergence of the two units.</p>

Name thesis:degree_name

Master of Science (MS)

Level thesis:degree_level

Masters Thesis

Year dc:date.available

2025

Author dc:creator

• Holman, Lora G

Contributors dc:contributor

• Dr. Eric Saillant
• Dr. Chet Rakocinski
• Dr. Dave Wells

• population genomics
• mutton snapper
• genome assembly
• lutjanus analis
• outlier loci
• RAD sequencing
• Genetics
• Genomics
• Marine Biology
• Population Biology

Repository record dc:identifier

https://aquila.usm.edu/masters_theses/1167

OAI identifier oai:identifier

oai:aquila.usm.edu:masters_theses-2249