Deepwater snappers of Puerto Rico
Project Leader: Stuart Willis
Silk snapper (Lutjanus vivanus), blackfin snapper (Lutjanus buccanella), and vermillion snapper (Rhomboplites aurorubrens) represent part of a major fishery along the west coast of Puerto Rico; this fishery is overexploited and at risk of collapse. Key questions about whether recruitment patterns are predictable and whether some areas serve to supplement the fishery more than others remain unanswered. In particular, marine protected areas (MPAs), where fishing is prohibited, may provide refuges for spawning adults that supplement exploited sites with planktonic larvae (dependent on currents), and/or may provide settling sites for recruits that later emigrate to exploited sites. We are using a genetic approach to assess whether regional recruitment is random across sampled sites, constrained by geographic distance, or mediated by current patterns. Further, for silk snapper, we are determining whether recruitment is predictable across years, whether cohorts at some sites are more related to each other genetically than would be expected at random, and whether recruits collected at each site are most similar to the adults also collected there, indicating self-recruitment. Settling larvae also may experience habitat-specific selective regimes that produce non-random, predictable patterns of recruitment. We are comparing cohorts of young-of-the-year and adult silk snapper to assess whether loci experiencing repeatable patterns of divergence in allele frequencies can be identified. The project utilizes double-digest RAD sequencing (ddRAD) and the dDocent analysis pipeline to genotype thousands of single nucleotide polymorphisms (SNPs) in each individual assayed.
Project Leader: Jon Puritz
The red snapper (Lutjanus campechanus) is a prized demersal reef fish that supports economically valuable fisheries for the U.S. and Mexico. Currently, the MGL is working to sequence the red snapper genome. We are also surveying genomic variation among red snapper populations in the northern and southern Gulf of Mexico (GOM), and in U.S. waters of the western Atlantic, focusing on two central questions:
1.) What is the spatial variation in recruitment of red snapper across the GOM and the U.S. Atlantic?
2.) How much mixing of red snapper occurs between Mexico (Veracruz-Tamaulipas shelf and the Campeche Banks) and the U.S. (SW Texas and SW Florida)?
Both projects utilize double-digest RAD sequencing (ddRAD) and the dDocent analysis pipeline to genotype thousands of single nucleotide polymorphisms (SNPs) in different populations. Sampling the entire genome allows for the examination of both neutral loci and adaptive loci. Neutral variation is useful for estimating migration (population connectivity) and effective population size while adaptive variation is useful for identifying how habitat and environment are affecting populations of red snapper. Information about neutral and adaptive processes affecting red snapper is critical for successful management of this critical fishery.
Project Leader: Stuart Willis
The king mackerel (Scomberomorus cavalla) is a migratory, coastal pelagic fish native to warm waters of the western Atlantic. In the summer months, king mackerel are popular with U.S. anglers in the northern Gulf of Mexico and along the U.S. Atlantic coast. During this period, spawning adults produce fast-growing larvae, which ride surface currents along the coast. In the Atlantic, young king mackerel appear to grow more rapidly than individuals in the Gulf, and this disparity has implications for population maintenance and sustainable exploitation. As the water cools in the fall, adults and young-of-year move south to warmer environs. In southern Florida and in the Bay of Campeche in Mexico, these fish, especially yearlings (>50cm), become targets of the commercial and recreational fisheries. The following year, as warm weather returns, the fish move north again. It is unclear whether migratory groups that move between seasons along each coast (Atlantic, eastern Gulf, western Gulf) represent separate populations or stocks, and to what extent different stocks may contribute to southern winter fisheries. We are addressing this question by using double-digest RAD sequencing to generate thousands of SNPs and asking whether discrete genetic groupings exist, and if so, how much mixing occurs in the winter fisheries.
Building a genetic linkage map of red drum
Project Leader: Chris Hollenbeck
Red drum, Sciaenops ocellatus, are extremely popular sport fish in U.S. waters of the Gulf of Mexico and the southeastern Atlantic coast. Red drum are cultured for use in both restoration enhancement and commercial aquaculture. We are using double-digest RAD sequencing (ddRAD) and the dDocent analysis pipeline to genotype thousands of polymorphic single nucleotide polymorphisms (SNPs) and map each SNP to individual red drum chromosomes. This SNP map will complement a prior map developed in our laboratory, which contains map positions of nearly 500 nuclear-encoded microsatellites, and will have two immediate applications. The first will be to enhance genetic selection for performance traits (e.g., growth rate, fillet yield) or to remove impediments (e.g., thermal sensitivity, disease resistance) that currently constrain red drum aquaculture. The second will be to identify polymorphic SNPs that are linked to each chromosome for use in estimating genetic effective population size (Ne) via linkage disequilibrium and documenting declines or increases in prior generations. This approach has tremendous potential for application to conservation and management of threatened or endangered biota.
Population structure, connectivity, and genetic demographics of red drum in U.S. waters
Project Leader: Chris Hollenbeck
This project involves the use of polymorphic, single nucleotide polymorphisms derived from double-digest RAD sequencing (ddRAD) to assess genetic population structure, connectivity, and demographics of red drum (Sciaenops ocellatus) in U.S. waters of the Gulf of Mexico and western Atlantic Ocean. To date, we have sampled red drum from estuaries near the Mexican border, through the central part of the Gulf and along the west coast of Florida, and from the southeastern coast of Florida as far north as North Carolina. The goal of this work is to identify geographic units (stocks) based on genetic differences representing both restricted gene flow (inferred from genetic markers presumed to be selectively neutral) and local adaptations (inferred from genetic markers
presumed to be selectively neutral or influenced by selection). Estimates of genetic effective population size (Ne) for each spatial unit will provide critical data on continued sustainability of each identified unit. The work will have immediate impact on conservation and management of red drum resources.
Building genomic maps of southern flounder it ID genes or chromosomal regions that are involved in sustainability (adaptation) and resilience to future environmental/anthropogenic insult
Project Leader: Shannon O'Leary
The goal for this project is the construction of a genetic map (linkage map) to be used in restoration and commercial aquaculture and to improve management of southern flounder. We will use DNA extracted from two hatchery-reared families (two sets of parents and approximately 200 offspring) and restriction-site-associated DNA sequencing (RADseq) to identify thousands of single-nucleotide polymorphisms (SNPs) and to map their locations in the genome to specific chromosomes. We will then screen individuals sampled from wild populations for these mapped markers. This will allow us to identify markers and chromosomal regions that vary spatially and to determine how and if they are associated with environmental factors (for example, salinity). As a result, we will identify genomic regions potentially affecting fitness traits resulting in local adaptations and will be able to quantify the allele frequencies of these mapped markers across geographic space. This will further our understanding of chromosomal regions involved in local adaptation to a specific set of environmental factors and the potential of southern flounder’s resilience to future changes in environmental conditions of local habitats.
MARINE GENOMICS LABORATORY • TEXAS A&M UNIVERSITY - CORPUS CHRISTI • 6300 OCEAN DRIVE • CORPUS CHRISTI, TX 78412 - 5869