David S. Portnoy

Objective: Eastern oysters Crassostrea virginica have been harvested commercially for well over 200 years in the United States, but worldwide declines in oyster populations have led to an increased focus on conservation of oyster species in general. Among the risks to extant oyster populations, genetic containment associated with human-mediated mariculture and stock enhancement is an important consideration due to the risk posed by introducing potentially exotic or invasive genotypes to wild populations. Knowledge of wild population structure can improve strategies for ensuring genetic compatibility of cultured and wild stocks. Methods: Here, we examined genetic diversity and divergence among eastern oyster populations sampled from 386 individuals in 14 major bay systems throughout the Gulf of Mexico (Gulf), from southern Texas to southern Florida. We used a reduced representation genomic library consisting of 3,173 single nucleotide polymorphisms to make inferences about population structure and connectivity throughout the sampled range. Results: The major findings of this work were (1) deep genomic divergence among four population clusters principally centered around the western Gulf, northern Gulf, northern Florida, and southern Florida, (2) a zone of admixture between highly diverged clusters in north and south Texas, and (3) high rates of intermediate genotypes observed in oysters sampled from northern Florida compared with the northern Gulf and southern Florida. Regarding this last finding, inbreeding coefficients (FIS) in the northern Florida population were sufficiently high and heterozygosity sufficiently low that contemporary admixture seemed an unlikely explanation for the observed pattern. Conclusions: Taken as a whole, these results imply the presence of multiple discrete populations of eastern oysters in the Gulf of Mexico, and the geographic boundaries that separate them are roughly consistent with previously described studies. The presence of structured populations has implications for the selection of broodstock, and the knowledge of population boundaries will allow for more accurate assessment of risk when cultured stocks might harbor germplasm that is genomically inconsistent with wild populations in the area of culture.

The Pecos pupfish, Cyprinodon pecosensis , is an imperilled freshwater fish found in arid regions of Texas and New Mexico (USA). The species faces multiple challenges to persistence including reductions in suitable habitat, water shortages, as well as hybridization and competition with an introduced congener (sheepshead minnow, C. variegatus ). As part of the current management strategy, refuge populations, seeded with non‐introgressed individuals collected from Texas, are maintained at the Fort Worth Zoo and on private property in West Texas. Therefore, assessments of standing genetic variation within and among wild and refuge populations and levels of admixture in the wild are critical for future conservation and management planning. Fin clips were acquired in 10 locations in the wild, five in Texas, five in New Mexico and from two refuge populations in Texas (one maintained by Fort Worth Zoo and another on a private property in West Texas). In Texas, non‐introgressed C. pecosensis were found in the wild at only one location Upper Salt Creek (USC); all other locations were composed of admixed individuals or non‐introgressed C. variegatus . No admixed individuals were found in New Mexico. Significant genetic heterogeneity was detected between all locations of non‐introgressed C. pecosensis , including the refuge populations, and estimates of divergence between Texas locations (USC and refuge populations) and New Mexico locations were relatively large ( F _ST : 0.23–0.32). Estimates of contemporary effective population size for USC and the two refuge populations were less than 50, but greater than 500 for all New Mexico populations. In summation, while New Mexico populations look secure, the data suggest that C. pecosensis in Texas is currently imperilled by the threat of hybridization, as well as potential loss of genetic diversity on contemporary time scales. Deep divergence between Texas (including refuge populations) and New Mexico suggests that further study would be needed prior to any management plans that would involve assisted gene flow between the regions.

In the United States Atlantic snapper-grouper fishery, no single species has garnered more attention than red snapper (Lutjanus campechanus). The earliest assessments of this stock (i.e. 1998, 2009, 2010) showed a population that was being overexploited (biomass severely depleted) and undergoing overfishing (fishing mortality rate too high). Since then, scientific understanding of the stock and fishery has advanced, and more recent assessments have shown substantial progress towards recovery. In this Story from the Front Lines, we document some broad lessons learned during this period of recovery, including the criticality of fishery-independent surveys for understanding population dynamics, the benefits of stakeholder involvement, the challenges of regulating a multispecies fishery, and the utility of economic considerations in fishery management. Throughout, we describe specific research studies that have benefited the scientific enterprise, culminating in a large-scale undertaking referred to as the South Atlantic Red Snapper Research Program that is estimating red snapper absolute abundance. The lessons learned during the evolution of science and management for red snapper have broad implications, documented here in the hope of benefitting other fisheries around the globe.

The Leon Springs pupfish, Cyprinodon bovinus , is federally listed as endangered and currently confined to spring-fed pools on the Diamond Y Spring Preserve in Pecos County, Texas, USA. A refuge population is maintained by U.S. Fish and Wildlife Service in Dexter, New Mexico, USA because of ongoing threats from hybridization with the introduced congener, the sheepshead minnow, C. variegatus. To inform continued conservation and management planning for this species, a comprehensive conservation genomics study using double digest restriction-site associated DNA sequencing was performed. No evidence of contemporary hybridization or recent introgression between C. bovinus and C. variegatus was found. The refuge population was significantly differentiated from wild samples collected at two locations, and the two wild populations (less than 1 km apart) also exhibited significant heterogeneity in allele frequencies. Estimates of within population diversity were smaller for wild locations than the refuge population. Correspondingly, the wild populations’ contemporary effective population size estimates were smaller than the refuge’s effective population size estimates (145–262 versus 679). Temporal analyses, involving genetic data collected from samples obtained in 2013, suggest an increased magnitude of drift acting on the wild populations relative to the reserve population. Based on the results of this study, it appears that steps taken in the early 2000s to eradicate genetically admixed individuals from the wild populations were successful. However, habitat fragmentation and small effective population sizes of the wild populations have led to accelerated drift and decreasing levels of within population genetic diversity. This may jeopardize the long-term persistence of C. bovinus .

Gambusia nobilis is a federally endangered species found across a fragmented distribution within the Pecos River Drainage of Texas and New Mexico, USA. Drought, human water usage, and potential hybridization and competition with introduced congeners threaten species persistence. Therefore, a population genomics study was conducted to provide critical information for conservation planning. Unsupervised clustering suggested hierarchical structure, with a primary K = 3, and deep divergences were detected among samples grouped into the Leon Creek watershed, the Toyah Creek watershed, and water bodies within the Bitter Lake National Wildlife Refuge ( F’ _ST = 0.55–0.76 for putatively neutral data). Phylogenetic analyses showed three distinct clades corresponding to these groups, with divergence times estimated to be in the last 50 000 years. Complimentary morphological analyses detected differences among the three groups, including features of male colour pattern, and the number of caudal-fin rays in both sexes. Taken as a whole, the results indicate that the endangered G. nobilis comprises three species (two of which are named herein as G. pyrros n. sp. and G. echelleorum n. sp.), rather than one, and the study highlights the daunting yet critical task of documenting species diversity during a period of unprecedented diversity loss.

Black basses ( Micropterus spp.) are the most popular freshwater sportfishes in North America, with high recreational, societal, and economic value. The conservation and management of black bass fisheries rely on the generation of age data to estimate population dynamics. Age data are typically produced via counts of opaque zones in otolith sections, a necessarily lethal process. The development of an accurate, nonlethal age estimation method would expand opportunities for collecting age‐related information in cases where sacrificing fish is either not an option (e.g., tournaments) or undesirable (e.g., trophy‐sized fish). An epigenetic clock was developed for Florida bass ( Micropterus salmoides ) using DNA extracted from fin clips and enzymatically converted restriction site‐associated DNA sequencing (EC‐RADseq). CpG sites exhibiting age‐correlated DNA methylation were identified using Bayesian generalized linear models in individuals ( n = 176; age range: 0.84–13.21 years) captured from six different water bodies across Florida, USA, and potential environmentally influenced, age‐predictive sites were identified and removed. The epigenetic clock developed using elastic net regression was highly accurate (mean absolute error, MAE = 0.28 years) and precise ( R ² = 0.98). Overall, results demonstrate an accurate, nonlethal alternative to otolith‐based age determination of Florida bass and could likely be applied to other black basses. In addition, when compared to traditional age estimation via hard structures, epigenetic age estimation is relatively rapid and cost‐effective, with important implications for black bass assessment, management, and conservation.

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co‐occur in spring‐fed tributaries of the Rio Grande in Texas and Mexico. Both N. megalops and N. amabilis are listed as Species of Greatest Conservation Need by the Texas Parks and Wildlife Department. Notropis amabilis is widespread and listed as apparently secure by Texas Parks and Wildlife Department whereas N. megalops has a very limited distribution and has not been ranked by Texas Parks and Wildlife Department because of data deficiency. Morphological differences between these species have been described; however, proper identification in situ remains problematic. Furthermore, given their range of overlap there is potential for hybridization, and limited genetic data have been collected comparing the species. Therefore, reduced representation genomic and mitochondrial sequencing data were used to reassess the distinctness of the species, screen for hybridization, and characterize their relative frequencies throughout their range of overlap. Genomic analyses recovered two distinct genetic groups corresponding to the species (F'_CT = 0.89) with no evidence of admixture or introgression. The species were found to co‐occur at three sampling locations, two in the Devils River and one in the Pecos, but not in equal frequencies. Overall, these results provide data and tools for further research on N. megalops needed for accurate conservation policies and management practices.

The Leuciscidae (minnows, shiners and relatives) is a diverse family of freshwater fishes with many species endangered due to anthropogenic stressors. Notropis oxyrhynchus and Notropis buccula are two shiners found only in the upper Brazos River basin in Texas, USA and listed as endangered due to contracted habitat. The complete mitochondrial genome was sequenced for two vouchered specimens for each species; Notropis oxyrhynchus having a total mitogenome length of 16,711 bp and N. buccula having a total mitogenome length 16685-16686 bp, with both including 13 protein-coding genes, 22 transfer RNAs genes, and 2 ribosomal RNA genes. Phylogenetic analysis supports previous hypotheses regarding placement of these species.

Age data are essential for estimating life history parameters and are thus critical for population assessment, management, and conservation. Traditional vertebrae-based age estimation in elasmobranchs can be costly, time intensive, of low accuracy, and is by necessity lethal. Herein, epigenetic clocks were developed for an elasmobranch, the cownose ray (Rhinoptera bonasus), using aquarium-born individuals (n = 42) with known dates of birth (age range: 7−7,878 days or 0−21 years) and two tissue types (fin clips and whole blood) that can be sampled in a relatively non-invasive manner. Enzymatically-converted restriction site-associated DNA sequencing (ECrad-seq) was used to identify CpG sites that exhibited age-correlated DNA methylation. The epigenetic clocks developed were highly accurate (mean absolute error, MAE, < 0.75 years) and precise (R² > 0.98). Age-associated CpG sites were identified across tissues, and a multi-tissue clock was also highly accurate (MAE < 1 year) and precise (R² = 0.97). Using the developed fin clip clock, three wild-caught individuals of unknown age but managed in aquariums for > 22 years were predicted to be 22.10−23.49 years old. Overall, the results have important implications for future epigenetic clock development and noninvasive age estimation in elasmobranchs.