Population Genetics Research Program

Current Research and Future Directions

The function of the population genetics laboratory at Perry R. Bass Marine Fisheries Research Station (PRBMFRS) is to apply genetic techniques to answer questions raised by fishery managers of the Coastal Fishery Division of Texas Parks and Wildlife Department. The goal of this interaction is to avoid the mistakes committed in the past by individuals and agencies charged with managing the world’s fisheries. Examples of such mistakes are failures to recognize genetic subdivision in the face of differential harvest (Ricker 1958; Hartman and Raleigh 1964; Todd and Larkin 1971), failures to take genetic subdivision into account in stocking strategies (Ryman 1981; Allendorf et al. 1987), failures to match genetic diversity in hatchery stocks with that occurring in natural populations (Calaprice 1969; Millenbach 1973; Hershberger and Iwamoto 1981), and failure to prevent introgression of exotic genes into native populations (Philipp et al. 1983; Ward et al. 1995). The factor each of these mistakes has in common is a failure to recognize and conserve the genetic integrity of the species being managed. Genetic conservation is now recognized as crucial to the scientific management of biotic resources. Inter- and intrapopulation genetic variation represents a resource critical to the adaptation of organisms to spatially diverse and temporally dynamic environmental conditions. It is in the best interests of conservation agencies and fishery managers to understand and protect this valuable resource.

Past and present research:

Long-term studies at PRBMFRS have focused on three broad areas: 1) application of genetic markers for species identification; 2) utilization of genetic tags in the evaluation of stocking success and strategy; and 3) examination of population structure (genetic subdivision) prior to management interventions.

Species identification

Species, subspecies, and hybrids can be identified using a variety of molecular techniques including both DNA and protein examinations. At PRBMFRS isoelectric focusing (IEF) of sarcoplasmic proteins was the primary technique for species ID. IEF has the necessary qualities of relatively limited intraspecific variation and consistent interspecific differences. The genetics laboratory at PRBMFRS used this tool to verify release of exotic organisms into Texas waters (see King et al. 1992), identify closely related or morphologically similar species (King et al. 1988; King et al. 1991; Ward et al. 1994), and investigate hybridization events (Ward et al. 1995). The strength of the technique was that identification can usually be made from filleted, headless, or otherwise processed individuals. As an aid to IEF identification, an extensive library of muscle samples from known individuals was accumulated, allowing screening of unknown and known samples on the same gel. Currently, DNA sequencing of specific DNA fragments and comparison to known samples is the most powerful means of identifying species.

An automated DNA sequencer has been purchased by the Coastal Fisheries Division to enhance our capabilities to recognize and distinguish fine-scale genetic variation and PRBMFRS genetics personnel are in the process of building a library of known sequences for species identification comparisons.

Genetic tagging:

A variety of techniques have been employed by Coastal Fisheries Division personnel in efforts to determine the efficacy of red drum and spotted seatrout stockings in Texas waters (McEachron et al. 1998). One of these efforts involves genetic tagging of stocked fingerlings. Unlike artificial and chemical tags, genetic tags are not lost over time, require no special handling, and can be passed across generations (King et al. 1993; King et al. 1995). Each of our genetic-marking studies involves collecting broodfish with a specific uncommon allele (genetic variant), testing the offspring of those broodfish for allele-frequency stability, growth, and survival differences, and finally stocking those fingerlings into a bay. The frequency of the marker-allele is then monitored in fish encountered in resource and harvest surveys in the years following stocking. An increase in the frequency of the marker-allele over base-line levels will infer stocking success. Failure to find an increase in marker-allele frequency will suggest stocking failure. Marker-allele frequency in red drum did not increase in a bay system stocked at variable densities over three years, while marker allele-frequency in spotted seatrout did increase for one year in an area local to one stocking site, but not on a bay-wide or multi-year basis.

Population structure:

Genetic structuring is a common component of animal and plant species. Structuring may be influenced by historical factors (such as past isolating events), stochastic processes (changes in genetic characteristics of a population related to small effective population size), gene-flow or the lack thereof, or natural selection. Any or all of these factors may have played a role in determining the genetic structure of a species. Regardless of the source of genetic structure, the function of the variation within and among populations is to act as a reservoir allowing adaptation to future environmental changes. Surveys of the genetic variation within a species can provide estimates of the overall genetic diversity and insight into the general well-being of the population. On a more applied level, genetic studies offer the most precise means of identifying fishery stocks or management units and accurate recognition of these management units is essential for effective fishery management. Investigations of population structure are also particularly important prior to implementation of stocking programs. Stocking programs which fail to take genetic structure into account may introduce foreign alleles into natural populations, change the frequencies of naturally occurring alleles, reduce adaptation to local environments, and reduce isolation between contiguous populations. Both of the current coastal stocking programs have been influenced by findings of genetic surveys.

Red Drum

Studies of population structure in red drum by the genetics laboratory of Dr. John Gold at Texas A&M University, working closely with PRBMFRS genetics personnel, initially found few biologically significant differences within the Gulf of Mexico (Gold et al. 1993a; Gold et al 1994), and fingerlings spawned from broodfish collected anywhere along the Texas coast were stocked into all the Texas bays. Subsequent studies, utilizing more powerful molecular analyses, have since indicated that biological meaningful differences do exist among red drum along the Texas coast (Gold and Richardson 1999; Gold et al. 1999). These differences indicate a significant isolation-by-distance effect in red drum, possibly indicative of some degree of female natal fidelity, and have prompted the Coastal Fisheries Division to modify their red drum stocking schemes resulting in upper coast and lower coast broodfish being utilized to stock, respectively, upper and lower coast bays.

Spotted Seatrout

Spotted seatrout stock structure was found to differ from that exhibited by red drum. Examination of variation in nuclear genes (allozymes) found statistically significant clines in allele frequencies and in heterozygosity across the northern Gulf of Mexico, suggesting a more localized adaptation was present (King and Pate 1992; King and Zimmerman (1993).

Similar clines have been suggested to be associated with adaptation to environmental gradients (Koehn 1969; Merritt 1972). As a result of this knowledge, the Coastal Fisheries Division determined that spotted seatrout fingerlings would be stocked only into those bays, or bays adjacent to those from which their parents were captured.

Black drum

Black drum were investigated using protein electrophoresis (allozymes) and were found to exhibit levels of genetic variability slightly higher than that exhibited by other Texas sciaenids. Although no significant stock structuring was noted, some degree of population subdivision based upon distance was evident.

Atlantic Croaker

Allozymes and mitochondrial DNA were examined and indicated that Atlantic croaker exhibited a high level of genetic diversity and limited population subdivision on at least a regional basis.

Sand Seatrout

Sand seatrout were shown to exhibit at least regional population subdivision along the Texas coast and furthermore, demonstrated some degree of differentiation between inshore and offshore populations.


Sequencing of chloroplast DNA fragments found Halodule wrightii populations on the upper coast of Texas to be genetically differentiated from populations on the middle and lower coast. The biological significance of the differences is unknown but it must be noted prior to the implementation of any sort of transplant/rehabilitation strategy.


Investigation of blacktip and bonnethead sharks utilizing microsatellite analysis and sequencing of mitochondrial DNA fragments has revealed some degree of regional differences but no localized differences.

Southern Flounder

Southern flounder were examined using allozymes and were seen to exhibit regional differences between the upper/middle coast of Texas and the lower coast. In addition, some degree of clinal variation was demonstrated, suggesting the population structure of southern flounder may also be influenced by isolation-by-distance effects.


Restoration of the Texas tarpon fishery by stocking hatchery-reared fish has been proposed recently. Examination of the genetic variation within this species has indicated that while differentiation between most populations is minimal, there are differences between the eastern and western Gulf of Mexico and extensive variability within the group as a whole exists. We propose that, should stocking efforts proceed, broodstock be retained from only the northwestern Gulf and that there be high frequency of turnover within the broodstock to keep levels of genetic variability high.

Current Surveys:

We are currently conducting DNA surveys on a variety of marine organisms including spotted seatrout, gulf menhaden and sheepshead. For each of these species we will provide biologically pertinent information which will better allow our agency to manage the resource. We are also developing techniques to allow species identification from single eggs in order to better characterize spawning habitats.

Future research directions:

There is still much to be understood concerning the population structure of Texas’ recreationally and commercially important marine species. We will use mtDNA RFLP analyses, DNA sequencing and DNA fragment analysis to address questions about the genetic structure and character of species such as snook, gray snapper, tripletail and marshgrass which are still poorly understood. For each of these species we will provide biologically pertinent information which will better allow our agency to manage the resource and, should supplemental stocking be deemed necessary, allow artificial enhancement efforts which are not open to criticisms of poor planning and lack of concern for the genetic integrity of our managed species. We will also use DNA analysis to better understand species such as spotted seatrout, black drum, southern flounder and shrimp which we previously investigated using allozyme techniques. There are still many questions about the genetic structuring of our managed populations which need study, however it is important to recognize that this may be an opportune time to begin applying our genetic techniques to a new set of questions and some additional management applications of genetic markers may include forensic identification, determining parentage and relatedness among individuals or groups, inferring migration rates, and most importantly, estimating the overall genetic diversity and health of a population.


Perry R. Bass Marine Fisheries Research Station

Palacios Texas

(361) 972-5483

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