Date of Award

Summer 8-2016

Degree Type

Masters Thesis

Degree Name

Master of Science (MS)


Coastal Sciences, Gulf Coast Research Laboratory

Committee Chair

Eric Saillant

Committee Chair Department

Coastal Sciences, Gulf Coast Research Laboratory

Committee Member 2

Kenneth Jones

Committee Member 3

Jeffrey Lotz

Committee Member 3 Department

Coastal Sciences, Gulf Coast Research Laboratory


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.


Adrienne Norrell - additional, large table.pdf (4265 kB)
Table A4. Detailed Red Snapper Linkage Map