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.

Red snapper

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.

King mackerel/kingfish

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.

Epigenetic response of oil-exposed fishes

Project Leader: Andrew Fields

In 2010, the Deepwater Horizon oil spill released approximately 5 million barrels of crude oil into the northern Gulf of Mexico. While exposure to this crude oil had immediate lethal effects on fishes, the sublethal effects were not as apparent. Using reduced-representation bisulfite sequencing (RRBS) of fishes exposed to oil in the laboratory (carried out by Dr. Dana Wetzel's Lab, the Environmental Laboratory of Forensics, at Mote Marine Laboratory and the Mote Aquaculture Park) and the wild, we are exploring whether exposure alters the methylation state of the DNA of fishes and their offspring. Using multiple species of fishes and multiple generations, we are looking to explore what effects are species specific and what are generalizable across many fishes.

Assessment of levels of population structure and connectivity of golden tilefish throughout their range

Project Leader: Shannon O'Leary

Golden tilefish, Lopholatilus chamaeleonticeps, are a demersal, sedentary, deepwater-burrowing fish found along the entire U.S. East coast and Gulf of Mexico. They favor a habitat characterized by a narrow range of depth, temperature and sediment type. As adults, they burrow in the clay substrates of the shelf-slope and exhibit high site-fidelity; potentially resulting in patterns of isolation by distance, or strong population structure. By contrast, their larvae have high dispersal potential which could result in high levels of connectivity throughout their range. In this study we are using restriction-site associated DNA sequencing to generate a data set consisting of several thousand genetic markers distributed throughout coding and non-coding parts of the genome. We are then going to assess genomic variation within- and between-groups of golden tilefish sampled throughout their range to identify the relative importance of microevolutionary processes (gene flow, genetic drift, selection) and historical demography in shaping current patterns of diversity.

Assessment of population-level effects of oil exposure on the genetic diversity of golden tilefish

Project Leader: Shannon O'Leary

As adults, golden tilefish, Lopholatilus chamaeleonticeps, burrow in clay substrates of the shelf-slope break and exhibit sedentary behavior resulting in an intimate association with the sediment. Subsequent to the Deepwater Horizon Oil Spill, tilefish sampled from oil-impacted areas have shown high concentrations of biomarkers consistent with oil exposure. We are using restriction-site associated DNA to characterize adaptive and neutral genomic variation and test for (1) genome-wide effects, by comparing spatial (impacted/non-impacted areas) and temporal (pre/post-oil spill) patterns of genomic variation to identify demographic changes, (2) locus-specific responses to the oil spill, by identifying FST-outlier loci potentially under divergent selection, and temporal shifts at specific loci. Finally, we will look for correlations between genomic data and Gulf-wide data sets of biological and environmental variables including levels of oil-exposure biomarkers in fish assemblages, sediment composition, and PAHs in liver and bile of sampled fishes, to identify chromosomal regions associated with organismal response to the oil spill.

Mixed stock analysis of bull sharks in Texas bays and estuaries

Project Leader: Shannon O'Leary

We are using next-generation sequencing techniques to genotype young-of-the-year bull sharks, Carcharhinus leucas, caught in Texas bays and estuaries for several thousand markers throughout the genome. We will use this data set to determine if nursery of origin can be distinguished using genetic markers. If this is the case, we will identify a panel of markers that are indicative of specific estuaries and use these data sets to assign adult bull sharks caught in Texas waters back to their nursery of origin.  This will allow for an assessment of the relative contributions of major Texas bays to the adult population of bull sharks. This study is being conducted in concert with vertebral chemistry research at the laboratory of Dr. R.J. David Wells at Texas A&M University – Galveston (

Impacts of sewage effluent on genomic diversity and connectivity of marine intertidal communities

Project Leader: Jon Puritz

The MGL is about to begin a project focused on understanding the consequences of an abundant and pervasive anthropogenic stressor, sewage effluent, on genetic diversity and connectivity of intertidal communities.  Mudflat fiddler crabs (Uca rapax) will be sampled near three different wastewater outfalls in the City of Corpus Christi, and at two control sites unlikely to be influenced by sewage effluent.  Next-generating sequencing will be employed to assess neutral genetic diversity, genetic connectivity, and potential genes under selection in these populations. Results from this project will have implications for the placement and design of marine reserves and for ecological sustainability in coastal urban areas.  

Figure 1.  Map of sampling area.  Wastewater outfalls are marked by red circles.  Sampling localities, marked by blue and yellow diamonds, represent spatially explicit sites around the Whitecap outfall.  White diamonds mark sites near large wastewater outfalls to be used as positive controls.  Green diamonds mark sites near open ocean exchanges, to be used as negative control sites.

Red drum stock enhancement

Project Leader:  Shannon O'Leary

Prior to the mid-1980s, when red drum (Sciaenops ocellatus) was designated as a game fish in Texas and other Gulf coast states, red drum supported an important commercial fishery.  Reported landings in the Gulf totaled >13 million pounds. Since the closure of the commercial fishery, red drum have been cultured in several states, principally Texas, for stock restoration enhancement. However, there is potential for negative genetic impacts of cultured fish on wild populations through escapement from commercial facilities or improper matching of released hatchery-derived individuals to wild stocks during restoration enhancement. One strategy for mitigating the risk of these negative impacts is to closely match brood fish genetically with wild individuals in geographic proximity to the commercial facility or stock. We are using polymorphic SNPs to match genomic profiles of hatchery brood stock and ‘wild’ fish in Texas bays and estuaries where active red drum restoration is ongoing.  This work will provide information useful for conservation and management of red drum resources in Texas, and elsewhere, and will contribute to future discussion and decisions regarding restoration enhancement.

Restoration and enhancement of southern flounder in Texas bays and estuaries

Project Leader: Shannon O'Leary

The southern flounder (Paralichthys lethostigma) is an extremely popular food fish in the Gulf of Mexico and has historically supported a multi-million dollar fishery along the Texas coast. Currently, southern flounder are seriously overfished in Texas waters, and concerns regarding the spawning stocks in several Gulf locations have arisen due to recent low year-class strength. Because life-history, fishing mortality and both demographic and genetic characteristics may differ among subpopulations, stock structure assessment is essential to rebuild and manage overfished stocks. Failure to integrate underlying population structure into management plans can result to depletion of localized stocks and associated loss of unique genetic resources, i.e. the adaptive potential harbored by that subpopulation.  Thus, the target of this project is to

provide critical information for the effective management of southern flounder resources in Texas bays and estuaries through a spatial assessment of the genetic diversity, population connectivity and potential local adaptation of wild populations.


The Texas Parks and Wildlife Department plans to rear millions of juvenile southern flounder in hatcheries, to stock Texas bays and estuaries. For this restoration-enhancement program to be successful, assessments of the productivity of individual brood fish, the long-term survival of hatchery-released fish, and the potentially negative genetic impacts of hatchery-bred fish on wild populations are crucial. By building reduced-representation libraries consisting of thousands of RADseq-derived SNPs distributed throughout the selectively neutral and adaptive regions of the genome, we will be able to identify geographic differences in genomic regions and determine if genetic profiles of hatchery offspring match the wild stocks in various areas where they are to be released. This information will result in the capability of brood-selection based on inherent genetic variation within the species, which in turn will enhance the yield of commercial aquaculture facilities and stocking efforts. Stock enhancement efficiency will be further increased by aiding in the site selection for release based on matching genetic profiles of hatchery-released and wild fish. Further, we will be able to address genetic risks and problems associated with escapees from hatcheries.

Composition of the Sphyrna lewini/gilberti complex in the eastern and southern coastal U.S.

Project Leader: Amanda Barker

The scalloped hammerhead (Sphyrna lewini) and the recently discovered Carolina hammerhead (Sphyrna gilberti) are cryptic species that are sympatrically distributed in the southeastern United States. Differing only in the number of precaudal vertebrae, scalloped and Carolina hammerheads are morphologically conserved, and a way to distinguish them in situ has yet to be determined. Four of the six scalloped hammerhead distinct population segments (DPS) have been listed as threatened or endangered under the U.S. Endangered Species Act, however listing for the Northwest Atlantic and Gulf of Mexico DPS was not warranted. Due to its recent discovery and lack of morphological differentiation Carolina hammerheads have likely been included in previous stock assessments for scalloped hammerheads, leading to an overestimation of scalloped hammerhead abundance, particularly in the Northwest Atlantic where Carolina hammerheads are known to occur. Double digest restriction-site associated DNA (ddRAD) sequencing will be used to genotype individuals at thousands of single nucleotide polymorphisms (SNPs), and a panel of SNPs will be identified that can be used to reliably identify each species. Genetic and ecological data will be used to estimate relative abundance and habitat utilization of each species within known nurseries off the east coast of the United States. Because nursery utilization may not be equivalent between the species, one or more nurseries may be critical to one or both individual species persistence. Patterns of nursery habitat usage by both species will be investigated to determine the extent of resource partitioning and identify potential drivers of ecological speciation.

Philopatry, genetic monitoring and stock structure of blacktip and scalloped hammerhead sharks, using high throughput next-generation sequencing

Project Leaders: Amanda Barker & Dominic Swift

Blacktip sharks (Carcharhinus limbatus) and scalloped hammerheads (Sphyrna lewini) are large coastal sharks found off the eastern coast of the U.S. and throughout the Gulf of Mexico. Across these regions, blacktips and scalloped hammerheads give birth in nurseries which are vital for juvenile survival. Scalloped hammerheads are considered globally endangered by the IUCN, and are currently the only shark species protected under the U.S. Endangered Species Act. Blacktip sharks are one of the dominant species landed by commercial and recreational fisheries in the U.S. Atlantic and Gulf of Mexico. Although blacktips are not currently considered overfished in U.S. waters, increased and/or localized fishing, combined with habitat exploitation could cause declines similar to those experienced by other shark species. Therefore it is essential that management and conservation strategies are continually improved. This project will sample hundreds of blacktip and scalloped hammerhead sharks across the U.S. Atlantic and Gulf of Mexico and will use double digest restriction-site associated DNA (ddRAD) sequencing to (i) establish baseline genetic monitoring data; (ii) provide high-resolution genetic data for stock assessment; (iii) develop replicable methods for genetic monitoring and stock structure assessment of other shark species. We will also investigate the potential for localized adaptation associated with nurseries and develop fine-scale genetic tags to use in future mark-and-recapture studies. By characterizing the stock structure of these fisheries we aim to increase sustainability by reducing localized overfishing and loss of genetic variation.