The northern red snapper (Lutjanus campechanus) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 markers distributed across 24 linkage groups and was used to anchor genome contigs obtained during assembly of P-454 and Illumina sequencing reads. Genetic variation among four geographic populations of northern red snapper and one population of southern red snapper (Lutjanus purpureus) was studied using 6,890 SNPs generated by RAD sequencing. Northern and southern red snapper diverged significantly (average FST estimate 0.188) and Bayesian clustering suggested a complete lack of current gene flow between the two taxa. These results, coupled with the finding of divergent selection impacting several genomic regions during sliding window analysis, suggests that northern and southern red snapper should, at minimum, be managed as distinct population segments. Little evidence of population subdivision was found among northern red snapper populations, consistent with previous genetic studies. Further work is needed to improve the draft reference genome and estimate dispersal parameters in order to design management units for U.S. populations.
","abstract_html":"<p>The northern red snapper (<em>Lutjanus campechanus</em>) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 markers distributed across 24 linkage groups and was used to anchor genome contigs obtained during assembly of P-454 and Illumina sequencing reads. Genetic variation among four geographic populations of northern red snapper and one population of southern red snapper (<em>Lutjanus purpureus</em>) was studied using 6,890 SNPs generated by RAD sequencing. Northern and southern red snapper diverged significantly (average <em>F<sub>ST</sub></em> estimate 0.188) and Bayesian clustering suggested a complete lack of current gene flow between the two taxa. These results, coupled with the finding of divergent selection impacting several genomic regions during sliding window analysis, suggests that northern and southern red snapper should, at minimum, be managed as distinct population segments. Little evidence of population subdivision was found among northern red snapper populations, consistent with previous genetic studies. Further work is needed to improve the draft reference genome and estimate dispersal parameters in order to design management units for U.S. populations.</p>","abstract_has_math":false,"creators":["Norrell, Adrienne Elise"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":"Coastal Sciences, Gulf Coast Research Laboratory","degree_department":null,"school":null,"contributors":["Eric Saillant","Kenneth Jones","Jeffrey Lotz"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-08-01T07:00:00Z","date_published":"2016-08-01T07:00:00Z","updated_at":"2026-07-24T05:44:34Z","subjects":["red snapper","Lutjanus campechanus","population genomics","linkage map","draft reference genome","SNPs","Aquaculture and Fisheries","Genetics","Genomics","Population Biology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/197","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Eric Saillant","Kenneth Jones","Jeffrey Lotz"]},{"key":"dc:creator","label":"Author","values":["Norrell, Adrienne Elise"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2016-06-29T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Coastal Sciences, Gulf Coast Research Laboratory"]},{"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":["red snapper","Lutjanus campechanus","population genomics","linkage map","draft reference genome","SNPs","Aquaculture and Fisheries","Genetics","Genomics","Population Biology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/197"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The northern red snapper (Lutjanus campechanus) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 markers distributed across 24 linkage groups and was used to anchor genome contigs obtained during assembly of P-454 and Illumina sequencing reads. Genetic variation among four geographic populations of northern red snapper and one population of southern red snapper (Lutjanus purpureus) was studied using 6,890 SNPs generated by RAD sequencing. Northern and southern red snapper diverged significantly (average FST estimate 0.188) and Bayesian clustering suggested a complete lack of current gene flow between the two taxa. These results, coupled with the finding of divergent selection impacting several genomic regions during sliding window analysis, suggests that northern and southern red snapper should, at minimum, be managed as distinct population segments. Little evidence of population subdivision was found among northern red snapper populations, consistent with previous genetic studies. Further work is needed to improve the draft reference genome and estimate dispersal parameters in order to design management units for U.S. populations.
"]},{"key":"dc:title","label":"Title","values":["Development of Genomic Resources for the Evaluation of Red Snapper, an Emerging Species Candidate for Marine Aquaculture and Stock Enhancement"]}]}],"canonical_facts":{"dc:contributor":["Eric Saillant","Kenneth Jones","Jeffrey Lotz"],"dc:creator":["Norrell, Adrienne Elise"],"dc:date.available":["2016-06-29T07:00:00Z"],"dc:description.abstract":["The northern red snapper (Lutjanus campechanus) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 markers distributed across 24 linkage groups and was used to anchor genome contigs obtained during assembly of P-454 and Illumina sequencing reads. Genetic variation among four geographic populations of northern red snapper and one population of southern red snapper (Lutjanus purpureus) was studied using 6,890 SNPs generated by RAD sequencing. Northern and southern red snapper diverged significantly (average FST estimate 0.188) and Bayesian clustering suggested a complete lack of current gene flow between the two taxa. These results, coupled with the finding of divergent selection impacting several genomic regions during sliding window analysis, suggests that northern and southern red snapper should, at minimum, be managed as distinct population segments. Little evidence of population subdivision was found among northern red snapper populations, consistent with previous genetic studies. Further work is needed to improve the draft reference genome and estimate dispersal parameters in order to design management units for U.S. populations.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/197"],"dc:subject":["red snapper","Lutjanus campechanus","population genomics","linkage map","draft reference genome","SNPs","Aquaculture and Fisheries","Genetics","Genomics","Population Biology"],"dc:title":["Development of Genomic Resources for the Evaluation of Red Snapper, an Emerging Species Candidate for Marine Aquaculture and Stock Enhancement"],"thesis:degree_discipline":["Coastal Sciences, Gulf Coast Research Laboratory"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:44:34Z"}