Barcoding Texas Fishes
Traditionally, species identification has been based on external morphology alone, but this can be problematic because of cryptic similarity among taxa, and the need for trained experts. This has led to the adoption of DNA-based identification techniques (often referred to as DNA-barcoding) that offer many advantages over traditional methods. DNA-based identification can be used to accurately identify species using small pieces of tissue and confirm species presence using DNA passively shed into the environment (eDNA), which facilitates estimates of diversity as well as species monitoring.
Conservation Genomics of the Comanche Springs Pupfish (Cyprinodon elegans)
The entire geographic range of the Comanche Springs pupfish falls within the Chihuahuan Desert Ecoregion of Texas, with contemporary populations restricted to fragmented, spring-associated habitats in Reeves and Jeff Davis counties, Texas. Comanche Springs pupfish have undergone population/range contraction within recent years in response to human activities, including water extraction, pollution, and are also imperiled by the introduction of the sheepshead minnow, Cyprinodon variegatus. Previous research highlighted reduced genetic variation in Comanche Springs pupfish from several wild populations and concluded that there was a need for more genetic resources to be developed. Conservation genomic work using next-generation sequencing techniques will allow for a robust assessment of standing genetic diversity within and among wild populations, as well as an assessment of the potential for current and/or historical hybridization with C. variegatus. In addition, diversity in wild populations will be compared to that in captive (reserve) populations to assess whether reserve populations adequately represent standing diversity in the wild.
Using genetics to differentiate between morphologically conserved congeners – scamp, Mycteroperca phenax, and yellowmouth grouper, Mycteroperca interstitialis
Yellowmouth grouper, Mycteroperca interstitialis, and scamp, Mycteroperca phenax, are similar in physical appearance, leading to high rates of misidentification. Without proper species identification, understanding species-specific landings and life history becomes a challenge. To improve species identification, next generation sequencing techniques are being employed to resolve genetic differences between the species. These data will be used to design a diagnostic molecular panel to differentiate between scamp and yellowmouth grouper utilizing tissue samples collected by “fisheries dependent” and "fisheries-independent” sampling. In additional to finding species specific genetic markers, these data will provide tools for assessments of genetic population structure for both species throughout the western North Atlantic.
Conservation of Pecos Pupfish
The Pecos pupfish, Cyprinodon pecosensis¸ is an imperiled freshwater fish, endemic to the Rio Grande drainage of the southern United States in New Mexico and Texas. This species is of conservation concern due to potential habitat loss and degradation, low population numbers, and potential interactions with the introduced sheepshead minnow, Cyprinodon variegatus. Due to the extreme vulnerability of narrowly distributed species of Cyprinodon, assessing levels of genetic diversity is essential for guiding population conservation and management decisions. Information for this assessment will be used by Texas Parks and Wildlife in coordination with the Fort Worth Zoo and the U.S. Fish and Wildlife Service to develop genetically informed management plans for the species. A genetic assessment of the Pecos Pupfish population in Texas will also be critical for informing the upcoming Pecos Pupfish Conservation Agreement and species status assessment.
Conservation Genomic Assessment of imperiled freshwater fishes endemic to the Pecos and Devils Rivers
Many freshwater fishes endemic to the major and minor spring-fed tributaries of the lower Rio Grande within Texas exhibit small, highly fragmented distributions and are a priority for conservation by Texas Parks and Wildlife Department or the U.S. Fish and Wildlife Service. Several of these species (e.g., Etheostoma grahami, Dionda argentosa, D. diaboli, Cyprinella proserpina, and Notropis megalops) have distributions that fall almost entirely within two Texan native fish conservations areas (NFCAs), the Devils and Pecos River NFCAs. The small geographic ranges of each of the five species are highly fragmented and have undergone contraction within recent years in response to human activities, including (but not limited to) water extraction and the introduction of non-natives. Conservation genomics will involve next-generation sequencing techniques allowing for a robust assessment of standing genetic diversity and geneflow for each species, providing crucial information for future management and conservation planning.
Estimating Atlantic red snapper population size with genetic close-kin mark-recapture
Red snapper, Lutjanus campechanus, is an ecologically and economically significant reef fish in US Atlantic waters between North Carolina and south Florida, where it has been estimated to be overfished since the early 1970s. Restrictive management of the fishery has caused vocal dissent among various user groups driving a need for a more in-depth population assessment. Using two methods to estimate the population size independent of the stock assessment we hope to benefit future fisheries management decisions. The first method (carried out by colleagues at UF and NC State) will use a hierarchical Bayesian integrated abundance model to produce an estimate of age-2+ red snapper population size in the study region based on SERFS trap-camera and ROV survey data. For the second method we are developing a genotyping in thousands by sequencing (GT-seq) panel of 400 loci to genotype individuals for close-kin mark-recapture (CKMR). Genotyping will be carried out on over 6,000 individuals each year to identify half-siblings and population size will be estimated from this number using a red snapper specific CKMR model. From this data set we can also assess fine-scale resolution of within and between group genetic diversity (i.e., genetic stock structure) and estimate the effective number of breeders in the population.
Multiscale assessment of the distribution of imperiled fish assemblages in the upper Red River watershed with emphasis in long-term trends, life history approaches, and population genetics
The upper Red River basin in the Central lowlands of Oklahoma and Texas, is a unique and dynamic ecosystem within the semiarid Great Plain ecoregion. Streams within this ecoregion are characterized by extreme flood and seasonal drought events, and native fish assemblages are mostly composed of small-bodied, salt-tolerant species, includinge true minnows (family Leuciscidae) and pupfish. During the past five decades, however, flow regime alteration and fragmentation, and land cover modification in the region has resulted in significant changes to the physicochemical conditions of aquatic ecosystems, making native fish species more vulnerable to decline and extirpation. Greater information on the status and changes in fish assemblages within the upper Red River stream will benefit conservation planning and management decisions within the basin. This study is focused on the state threatened Red River pupfish (Cyprinodon rubrofluviatilis), prairie chub (Macrybopsis australis), and the imperiled Red River Shiner (Notropis bairdi). Using next-generation sequencing techniques, this project will be the first conservation genomic survey of these species to assess current standing levels of genetic diversity and whether hybridization between Red River pupfish and sheepshead minnow is occurring and/or has occurred within the Red River basin in Texas.