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.

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.

In this study, we document the presence of the monogenean Salsuginus seculus (Mizelle & Arcadi, native to the River Mississippi and Gulf Coast drainages, within its native range in the River North Fork Guadalupe and the River Brazos Basins in Texas, USA. This marks the fourth recorded locality of S. seculus in Texas, expanding its known distribution. Morphometric comparisons show that measurements of S. seculus from Texas largely overlap with previous reports, though some size variation is observed in specimens from the western USA and those associated with G. affinis populations in Japan. Phylogenetic analysis of 28S rDNA sequences places Salsuginus as a sister taxon to a monophyletic group of dactylogyrids, including Gussevia, Sciadicleithrum, and Parasciadicleithrum, all from Neotropical Cichlidae. Given the invasive potential of G. affinis, we highlight the importance of monitoring for potential co-introductions of monogeneans, such as S. seculus, into novel habitats, which may impact native fish communities. The molecular data provided in this study will be essential for tracking and identifying S. seculus in non-native regions, aiding in future invasion assessments.

Common freshwater fish sampling methods (e.g., seining and electrofishing) are inherently invasive and often not appropriate for imperiled species. Visual observation methods provide a noninvasive alternative for population monitoring. Despite increasing popularity, the use of underwater video to monitor imperiled fishes is relatively unexplored. We evaluated the efficacy of underwater video to estimate occurrence and abundance of the imperiled Comanche Springs Pupfish Cyprinodon elegans using both point observations and time intervals (surveys). We deployed camera traps at sites within major habitat types (pool, canal, and cienaga) of Balmorhea State Park, Texas, United States, in March and October 2019 (seasons). We detected Comanche Springs at all occupied sites in both seasons when viewing similar to 30 min of video. The species was detected at 80% of occupied sites when viewing similar to 10 min and similar to 5 min of video in March and October, respectively. Comanche Springs Pupfish detection probability was higher in October, with no variability among habitat types. On average, cumulative species detection probability was >0.9 with 15 60-s surveys. However, species detection probability of a single survey ranged from 0.02 to 0.62 (mean = 0.14). Although there was no variation between seasons or among habitats, variation was high in the detection of the maximum Comanche Springs Pupfish count among sites even with observations every 5 s. Individual capture probability from a repeated-count abundance model was less variable than species detection probability (0.01-0.33) and generally low (mean = 0.06). Site absolute abundance was generally comparable among major habitats but with higher uncertainty with increasing maximum count. Our study provides a comprehensive assessment of underwater video for imperiled fish species population monitoring. The findings show a trade-off between processing effort and information loss and limitations associated with imperfect detection and individual capture common to any fish sampling method.

A parasitological investigation of Cyprinella venusta and Notropis cf. stramineus sampled in Texas, USA, in the Guadalupe River, revealed the presence of Gyrodactylus crysoleucas Mizelle and Kritsky, 1967 on C. venusta, and Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin & Bentzen, 2013 on both fish species. This represents new leuscicid fish hosts and locality records for these two gyrodactylids. Gyrodactylus crysoleucas previously identified from both non-native Californian Notemigonus crysoleucas and from farmed stocks in Minnesota demonstrated intraspecific variability in terms of morphology and genetics as a local adaptation associated with isolation by distance. Results further confirmed G. crysoleucas as alien in the western USA and suggested host-switching involving C. venusta and N. crysoleucas. Conservative morphology and genetics on the part of G. mediotorus from C. venusta and N. cf. stramineus (Guadalupe River) was observed, while higher genetic divergence in the ITS sequences associated with morphological discrepancy was found between the studied G. mediotorus specimens and those of Notropis hudsonius than when considering the parasites of Notropis texanus. The separation of G. mediotorus into geographical subgroups may indicate ongoing speciation linked to the Pleistocene glaciations in North America, and to hydrographic barriers that facilitated separate evolutionary paths leading to speciation. We suggest that deep investigations of Gyrodactylus populations will help to understand the speciation of these parasites and their adaptation to Nearctic fish hosts.

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.

To review the conservation status of Headwater catfish Ictalurus lupus (Girard,1859) in the United States, including quantifying environmental correlates with range contraction and hybridization and introgression with Channel catfish Ictalurus punctatus (Rafinesque, 1818) to inform conservation prioritization.

The Rio Grande drainage of the southwestern United States and Mexico has undergone intense anthropogenic alteration by water diversions, extraction and associated habitat changes. These alterations have disproportionately impacted the pelagic broadcast spawning guild of minnows (pelagophils). Several Rio Grande endemic pelagophils, including the co-occurring Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), have experienced dramatic recent range-wide declines yet have slipped under the radar of conservation efforts. The status of N. jemezanus and M. aestivalis in the Rio Grande and Pecos River was evaluated and standing genetic variation was characterized. Genetic evidence indicates that populations of both species found in the Rio Grande and Pecos River are genetically distinct. Additionally, 159 outlier loci were identified in M. aestivalis suggesting possible local adaptation in the Rio Grande and Pecos River populations. Though range-wide genetic data are limited, N. jemezanus populations in both rivers harbor considerable genetic diversity. Mitochondrial data from both taxa are consistent with a history of secondary contact between formerly isolated populations with deeply divergent haplotypes found within the Rio Grande and Pecos River populations of N. jemezanus and within the Rio Grande population of M. aestivalis. Extensive survey efforts in the lower Rio Grande and its tributaries in Texas document significant range contraction and near extirpation of N. jemezanus from this part of the basin; highlighting the need for immediate action to protect the species.

Freshwater organisms inhabiting arid ecosystems are imperilled by human alterations to water-limited landscapes. This is especially true among desert-dwelling cyprinodontid fishes, 90% of which are imperilled by habitat destruction within limited or shrinking ranges. Constructing habitats that mimic natural habitat form and function may provide a tool for species conservation, especially within freshwater protected areas. However, pupfish population assessments within degraded compared with restored habitats are infrequent, and few comparisons among survey methods exist. Density estimates were developed for Endangered Comanche Springs pupfish Cyprinodon elegans throughout altered and restored habitats in a freshwater protected area by using mark-recapture and N-mixture models fitted to data collected using minnow trap and visual count survey methods. This allowed comparison of habitats, survey methods, and statistical methods commonly used to generate population size estimates for imperilled pupfish. Population estimates varied across major habitat types and were largest among habitats constructed to mimic naturally occurring cienegas. Estimates using visual counts were higher than estimates from minnow traps where water was deeper and where macroalgae cover was highest. N-mixture models generally estimated higher abundances than mark-recapture and were not limited by recapture ability. The results provide strong evidence that restored habitats house greater abundances of pupfish, but survey and statistical methods commonly used to detect these differences have trade-offs in performance according to the habitats surveyed. This work benefits the field of conservation biology by providing guidance for existing and emerging monitoring programmes assessing abundance-based fish responses to habitat improvements.

Texas harbors 191 species of native freshwater fishes, 48% of which are considered imperiled. The primary cause of fish species imperilment in Texas is anthropogenic alteration of freshwater systems, which continues to occur at rates and scales that threaten the long-term resiliency of freshwater habitats, species, and ecosystems. Innovative conservation approaches are needed to restore and maintain functional watershed processes, restore freshwater habitats, and conserve native species while simultaneously supporting human needs, such as flood control, municipal and agricultural water supply, water quality protection, and water-based recreation. The need for an integrated and holistic approach to conservation of freshwater systems has been the impetus for development of the Texas Native Fish Conservation Areas Network (hereafter "Texas NFCAs Network"). The Texas NFCAs Network consists of springs, cienegas, creeks, rivers, and associated watersheds uniquely valued in preservation of Texas freshwater fish diversity. Twenty native fish conservation areas have been designated throughout the state. These were selected based on a spatial prioritization focused on identification of freshwater systems critically important to the long-term persistence of 91 freshwater fishes considered species of greatest conservation need. Through a shared vision of collaborative stewardship, conservation partnerships have formed among nongovernmental organizations, universities, and state and federal agencies to plan and deliver actions within the Texas NFCAs Network to restore and preserve native fishes and their habitats. Furthermore, the Texas NFCAs Network has increased awareness of the ecological, recreational, and economic values of Texas freshwater systems and helped increase interest and capacity of local landowners, communities, and recreational users (e.g., paddlers, anglers) to act as advocates and local stewards of these systems. By facilitating partnership development, coordinating broad-based conservation planning, and leveraging technical and financial resources toward strategic conservation investments, the Texas NFCAs Network has served as a catalyst for collaborative, science-based stewardship of native freshwater fishes and their habitats in Texas. The Texas NFCAs Network offers a successful case study in multispecies and watershed approaches to freshwater fish conservation transferrable to other states in the United States, with particular relevance to those states that, similar to Texas, consist predominately of privately owned landscapes.

The Colorado River of Texas originates in the northwest portion of the state and runs southeasterly across the environmentally sensitive Edwards Plateau ecoregion, eventually emptying into Matagorda Bay on the Gulf of Mexico. The Texas Parks and Wildlife Department (TPWD) and other conservation partners have worked for decades to conserve native fishes in the river and its associated estuary. The river and its tributaries are also the major water source for millions of people, and portions of the watershed are undergoing unprecedented human population growth and a concomitant increased demand for water. Drought, which is a frequent occurrence in Texas, exacerbates these effects. Providing adequate streamflow and water quality to conserve aquatic species while still fulfilling obligations for municipal, industrial, agricultural, hydropower, and recreational water use is increasingly challenging. Since the 1980s, the TPWD has promoted water management policies in the watershed to benefit aquatic life, conducted research to maintain a sound ecological environment for fish and other aquatic taxa, provided technical guidance and financial incentives to private landowners to improve land practices that benefit water quality and quantity, and improved public access to foster increased stewardship of the river. The TPWD has also collaborated with researchers to study the potential impacts of altered hydrology on two endemic, flow-dependent fish species, Guadalupe Bass Micropterus treculii and Blue Sucker Cycleptus elongatus. Two portions of the Colorado River watershed have been identified as native fish conservation areas in part for persistence of populations of these native fishes. Outcomes from these activities are now being leveraged using federally funded research and conservation delivery programs to further advance the conservation of native fish populations and other aquatic life in native fish conservation areas of the Colorado River watershed.

With 95% of the land in Texas privately owned, conservation of the aquatic resources is particularly daunting and is exemplified by the fact that 48% of the 191 native freshwater fishes in Texas are now of conservation concern. Partnerships with private landowners is not only sensible, but often the only way to achieve long-term conservation goals. In the Chihuahuan Desert region of Texas, 55% of the native fishes are of conservation concern or already lost to extirpation or extinction. Although there are numerous contributing factors, habitat degradation and loss are the primary culprits. For decades, research and restoration have focused on some of the more imperiled species and their habitats. From reestablishing ciénegas, to landowner partnerships, to Conservation Agreements, much has been accomplished. Unfortunately, the challenges increase faster than our accomplishments. Our latest, and most promising, approach has been to develop six Native Fish Conservation Areas in the Chihuahuan Desert. These NFCAs represent an ecologically-focused conservation prioritization of watershed segments that serve as native fish “strongholds” and they function as priority areas for conservation investments to promote integrated, holistic conservation strategies that enable the long-term persistence of freshwater biodiversity. Current and future conservation of aquatic resources in Texas emphasizes a landscape-scale approach, working primarily with private landowners to provide conservation best management practices and support on-the-ground projects to maintain or restore habitats to sustain functional ecosystems.

Native fish conservation areas in the Chihuahuan Desert of Texas were identified and designated as part of a statewide network of focal watersheds uniquely valued in preservation of Texas freshwater fish diversity. Native fish conservation areas represent a holistic, multispecies, and habitat-based approach to native fish conservation that encourages and facilitates coordination among landowners, nongovernmental organizations, state and federal agencies, universities, and local governments to achieve landscape scale conservation within focal watersheds. This approach to native fish conservation provides an effective method for addressing the common nature and magnitude of threats facing species and their habitats in freshwater systems. Desert fishes and their habitats are particularly susceptible to habitat alteration, especially anthropogenic land use and water consumption patterns, which continue to create conservation challenges. The strategic and science-based conservation strategies embodied by the native fish conservation areas approach represent an innovative path forward for addressing the conservation needs of native fishes and their habitats in the Chihuahuan Desert of Texas. In this chapter, we describe six native fish conservation areas designated within the Chihuahuan Desert of Texas and profile multiagency conservation planning and delivery that has substantially increased the scope and scale of conservation investments for restoration and protection of native fishes and their habitats in the region.

Efficient conservation can require making strategic decisions across large landscapes. For example, two fish habitat partnerships the Desert Fish Habitat Partnership and the Western Native Trout Initiative (WNTI) fund conservation and restoration projects across the western United States. The Desert Fish Habitat Partnership alone serves 11 states and nearly 180 native fish species, and the Western Native Trout Initiative covers 21 salmonid species across 12 western states. Because of the large landscapes they represent, the partnerships are using multispecies aquatic assessments developed for specific river basins to aid in conservation delivery. These assessments yield a conservation value for every catchment in a basin based on known and modeled native fish distributions (including salmonids), riverine connectivity, and threats to aquatic habitats. The conservation values are scaled between o (low) and 1 (high) and have been used to evaluate the landscape context of conservation projects submitted for funding through the National Fish Habitat Partnership. While assessments are complete for some basins (e.g., upper and lower Colorado basins, upper Rio Grande basin), the partnerships are currently working with additional partners to fund aquatic assessments in new geographies (e.g., Bonneville and Lahontan basins). Multispecies assessments are used in conjunction with the knowledge of field biologists to inform on-the-ground conservation across large landscapes and make conservation delivery more efficient for the many imperiled native fishes in the western United States.

The Texas Parks and Wildlife Department has initiated an innovative approach to fish and wildlife conservation in Texas. By working with alliances of landowners, we provide a holistic approach to technical guidance and help to secure funding for restoration and conservation actions throughout targeted watersheds. Although we have projects in many locations in the state, our most successful utilizes the state fish of Texas as an iconic symbol that provides a positive, high-profile image depicting the need for, and benefits of, watershed conservation. We chose the Llano River Watershed to begin implementation of the Guadalupe Bass Restoration Initiative and, to date, have 17 conservation and restoration initiatives in the watershed that encompass 21,370 ha and 56 km of rivers and streams. Projects focus on actions that restore riparian areas, reduce soil erosion and runoff, increase infiltration and aquifer recharge, improve water quality, and enhance habitat for both aquatic and terrestrial species. Through the initiative, we promote awareness and stewardship of fish and wildlife habitats, share best management practices, organize community involvement in local habitat conservation projects, provide technical guidance and planning assistance, and help leverage available resources. Additionally, in 2011 and 2012, we stocked more than 280,000 genetically pure Guadalupe Bass Micropterus treculii in the South Llano River to reverse the trend of hybridization with the nonnative Smallmouth Bass M. dolomieu. We also supported studies on fish community and habitat analysis in the Llano River Watershed and partnered with private landowners to develop a watershed conservation plan. We are now in the process of developing a habitat conservation demonstration area (CDA) that extends over a 7-km segment of the Llano River, The CDA will provide fishing, paddling and hiking opportunities, promote sustainable public use of the river, and highlight restoration actions through educational kiosks placed along paddling and upland hiking trails.