Date of Award

Fall 12-7-2023

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

School

Ocean Science and Engineering

Committee Chair

Dr. Eric Saillant

Committee Chair School

Ocean Science and Engineering

Committee Member 2

Dr. Zachary Darnell

Committee Member 2 School

Ocean Science and Engineering

Committee Member 3

Mr. Jim Franks

Committee Member 3 School

Ocean Science and Engineering

Committee Member 4

Dr. Frank Hernandez

Committee Member 5

Dr. Chet Rakocinski

Committee Member 5 School

Ocean Science and Engineering

Abstract

The gray snapper (Lutjanus griseus) is a reef fish distributed in tropical and subtropical coastal waters of the Western Atlantic Ocean. The species is sedentary at the juvenile and adult stages but embryos and larvae are dispersed via pelagic transport for up to 40 days. These life history features are expected to promote connectivity and isolation by distance. However, gray snapper juveniles experience variable environments in their coastal and estuarine habitats. The relative roles of genetic adaptation and of phenotypic plasticity in responding to these variations are currently unknown. In this work, a draft reference genome was developed to support genomic studies of gray snapper. It was then applied to study population structure, local adaptation, and phenotypic plasticity in geographic populations.

A hybrid de novo assembly was generated using PACBIO and Illumina sequencing. The assembly was anchored by a linkage map generated by genotyping 256 full-sib larvae and their parents through the double digest Restriction Associated DNA (ddRAD) protocol. The anchored assembly spans 962,844,722bp (N50=41,865,368bp, L50=11 scaffolds) in 24 pseudo chromosomes and yielded a BUSCO score of 95.2%.

A total of 1,096 gray snapper, primarily juveniles, collected in coastal waters from South Texas to Jacksonville, Florida and reference populations from the Southern Gulf of Mexico (Merida, Mexico) and the Northwestern and Northeastern Caribbean Sea (Belize and Puerto Rico) between 2018 and 2022 were assayed at 12,916 SNPs using the ddRAD protocol. Mantel tests indicated a weak isolation by distance pattern (r =0.039, P = 0.022) and a significant positive spatial autocorrelation of samples collected within 1,400 km of one another was detected. There was no evidence for genetic discontinuities or divergent selection within the sampled range.

Reduced Representation Bisulfite Sequencing (RRBS) was applied to detect methylation of genes in DNA extracted from muscle tissue in 71 young of the year gray snapper collected in 2018 and 2019 from estuaries around the Florida peninsula. Analysis of genome-wide methylation profiles differentiated Indian River Lagoon specimens from the other nursery areas. Annotations suggested the differentially methylated genes were associated with epigenetic responses to anthropogenic contaminants (antibiotics, bacteria, chemicals) in the Indian River region.

Available for download on Monday, December 31, 2063

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