The mutton snapper (Lutjanus analis) 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 (FST = 0.001). Outlier analysis revealed an outlier genomic region on chromosome 10 (42 loci, FST up to 0.24) differentiating the two groups, suggesting selection is associated with the divergence of the two units.
","abstract_html":"<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<sub>ST</sub> = 0.001). Outlier analysis revealed an outlier genomic region on chromosome 10 (42 loci, F<sub>ST</sub> up to 0.24) differentiating the two groups, suggesting selection is associated with the divergence of the two units.</p>","abstract_has_math":false,"creators":["Holman, Lora G"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Dr. Eric Saillant","Dr. Chet Rakocinski","Dr. Dave Wells"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-12-01T08:00:00Z","date_published":"2025-12-01T08:00:00Z","updated_at":"2026-07-24T05:45:55Z","subjects":["population genomics","mutton snapper","genome assembly","lutjanus analis","outlier loci","RAD sequencing","Genetics","Genomics","Marine Biology","Population Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/1167","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dr. Eric Saillant","Dr. Chet Rakocinski","Dr. Dave Wells"]},{"key":"dc:creator","label":"Author","values":["Holman, Lora G"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2027-01-01T08:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["population genomics","mutton snapper","genome assembly","lutjanus analis","outlier loci","RAD sequencing","Genetics","Genomics","Marine Biology","Population Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/1167"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The mutton snapper (Lutjanus analis) 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 (FST = 0.001). Outlier analysis revealed an outlier genomic region on chromosome 10 (42 loci, FST up to 0.24) differentiating the two groups, suggesting selection is associated with the divergence of the two units.
"]},{"key":"dc:title","label":"Title","values":["A Population Genomic Study of Mutton Snapper (Lutjanus analis) Throughout Florida and the Caribbean"]}]}],"canonical_facts":{"dc:contributor":["Dr. Eric Saillant","Dr. Chet Rakocinski","Dr. Dave Wells"],"dc:creator":["Holman, Lora G"],"dc:date.available":["2027-01-01T08:00:00Z"],"dc:description.abstract":["The mutton snapper (Lutjanus analis) 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 (FST = 0.001). Outlier analysis revealed an outlier genomic region on chromosome 10 (42 loci, FST up to 0.24) differentiating the two groups, suggesting selection is associated with the divergence of the two units.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/1167"],"dc:subject":["population genomics","mutton snapper","genome assembly","lutjanus analis","outlier loci","RAD sequencing","Genetics","Genomics","Marine Biology","Population Biology"],"dc:title":["A Population Genomic Study of Mutton Snapper (Lutjanus analis) Throughout Florida and the Caribbean"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:45:55Z"}