Mexican blindcat, Prietella phreatophila, was described in 1954 from a single locality in Northern Coahuila, México. Long listed as endangered by the Mexican federal government, it was listed by the U.S. Fish and Wildlife Service as a foreign endangered species in 1970, and the most recent (1996) update of its assessment for the IUCN Red List considers it endangered as well. Explorations in the late 1990s discovered many new localities extending nearly to the international border, and a captive population established provided insights into the species’ basic biology and behavior. In 2016 the species was discovered in a cave in the Amistad National Recreation Area (ANRA), just north of the Río Grande in Texas. The 1970 listing instantly gave the TX population full protection under the U.S. Endangered Species Act. The species’ subterranean and mostly inaccessible habitat endows it with extremely low detectability and its actual range is likely broader than physical sampling of specimens has revealed. We review all prior and new knowledge of the species and its habitat to provide an updated international reassessment of its overall conservation status and threats, which most notably include aquifer depletion and contamination in both the Mexican and U.S. portions of its known range. A live captive population of two specimens collected in 1997 in Coahuila and one Texas specimen is now at the San Antonio Zoo, we are working with NPS to further explore ANRA caves and hope eventually to return to Coahuila to more fully update the species’ conservation status.

Assessments of growth can provide information needed to understand how fish populations respond to changing environmental conditions and management actions, including ecosystem experimentation. We estimated growth rates and parameter uncertainty from otoliths of endangered Humpback Chub Gila cypha from the Colorado River in Grand Canyon, Arizona. We then compared growth of Humpback Chub \textless age 2 that were 1) occupying the mainstem Colorado River during a period of variable discharge and cooler water temperatures (1980–1998; epoch 1), 2) occupying the Colorado River during a period of moderate discharge variability and warmer water (2001–2011; epoch 2), and 3) occupying the unregulated Little Colorado River. Because growth rates of juvenile Humpback Chub (\textless age 2) may be more sensitive to changes in environmental conditions than adult fish, we used analysis of covariance and linear models to compare growth of juvenile fish (slopes) between epochs and capture sites (mainstem Colorado River vs. Little Colorado River). Our analysis of covariance results were ambiguous (age × epoch × site interaction; P = 0.06). However, individual linear regressions of size and age by epoch and site suggest biologically important differences in growth, as evidenced by slower growth in the Colorado River in epoch 1 than in epoch 2, and slower growth in the Colorado River compared with the Little Colorado River for all time periods. Overall our results 1) provide information on growth and growth variability useful for parameterizing models to assess population viability and 2) provide empirical information on how growth of juvenile and adult Humpback Chub growth may respond to changing environmental conditions.

Desert ecosystems are particularly susceptible to anthropogenic influences. This is especially true for desert aquatic systems where limited water resources can be easily impaired by excessive water mining depleting the underlying aquifers. We discuss the decline of these aquatic environments throughout the Chihuahuan Desert region of Texas and present observations on the relationship between declining aquifer levels and the status of native fishes. Examples from the Big Bend region, the Balmorhea Springs Complex, the Pecos River region, and the Devils River region reveal a decline in distribution and abundance of native species (including extirpations and extinctions) resulting from declining water supplies. Ongoing and impending land use and water consumption patterns point to even further reductions in the near future. However, there are activities underway that offer some optimism in the region. Native Fish Conservation Areas are being developed to enhance management of these desert ecosystems in a way that provides functional watersheds with self-sustaining populations of native species. Increased awareness by landowners of the value of cooperative conservation of aquatic resources and mechanisms to include them in management decisions are critically important, particularly in Texas where the vast majority of land is privately owned. Ultimately, archaic Texas water laws need to be revisited and reformulated if the desert aquatic systems are to be truly conserved for more than the immediate future.

Compilation of basic occurrence records of American Eel in Texas revealed not only a general paucity of data, but also biases of different sources, and overall, inaccessibility of many different sources of useful records. Methodical searching, mining, normailization and basic data cleaning across a diversity of resources provided a much better picture of temporal and spatial occurrences of the species than had readily available sources. Similar data mining and sharing by all researchers and managers could greatly improve overall understanding of the species in the GoM and its tributaries, and help focus monitoring and research efforts.

On a recent afternoon at the University of Texas’ J.J. Pickle Research Campus, researcher Adam Cohen reached elbow deep into a bright blue barrel

A natural population of the Mexican blindcat, Prietella phreatophila Carranza 1954, previously known only from México, was documented in 2016 from a cave in the Amistad National Recreation Area in Texas. Occurrence of the species in Texas is consistent with other indicators of international interconnections of aquifers in this region under the Río Grande. Long listed as Endangered by the Mexican government, it was also listed by the U.S. Fish and Wildlife Service as Endangered in 1970, and so the Texas population is fully protected under the Endangered Species Act as Endangered. As a result of the extremely low detectability of the species and very limited access to its habitat to sample, it is likely that the range of the species in both countries is broader than physical sampling of specimens has revealed. Here we review all previous knowledge of the species and its habitat and provide a reassessment of its overall conservation status and threats, most notably including aquifer depletion and contamination in both the Mexican and U.S. portions of its known range.

The American eel, Anguilla rostrata, is an amazing catadromous (living in fresh water and spawning in the ocean) fish with a remarkable life history involving huge migrations. Immature adults, a.k.a. “yellow eel,” live in freshwater rivers, lakes, and estuaries, feeding on fishes and invertebrates for 5 to 20 years before making a remarkable, long-distance journey to the Atlantic Ocean to spawn in the depths of the Sargasso Sea (by the Bermuda Triangle).

Substantive progress was made on all major Project Activities in this first year: Activity 1. Coordinate and Facilitate Science and Conservation Actions for Conserving Texas Biodiversity - We expanded and strengthened UT-TPWD coordination, transitioning the relationship between these partners into a much more collaborative one than was previously realized. The flow of data between TPWD and the Fishes of Texas Project (supported in part by this project) has become much more bi-directional. Many newly collected TPWD specimens, agency databases, legacy data products and reports, and feedback from resource managers are now beginning to contribute substantively to growth and diversity (now including non-specimen-vouchered records) of data served through the FoTX Project’s websites. Work on cleaning and normalizing of FoTX’s online specimen-vouchered database continued, and the updated FoTX occurrence and distribution data are being actively used. Most recently they were used by this project, together with expert (TPWD, UT and others’) opinions, to develop recommendations on conservation status of native fishes of Texas’ Species of Greatest Conservation Need for TPWD’s consideration in anticipated updates to the Texas Conservation Action Plan. Within two months of this report, a new and substantially larger and improved version of the FoTX website/database and related collection of images, field notes, and ancillary datasets, will be formally announced. Activity 2. Identify Priority Geographic Management Units for Conserving Fishes of Greatest Conservation Need - We used FoTX data in a systematic conservation area prioritization analysis to identify Native Fish Conservation Areas (NFCAs) for large portions of Texas where such comprehensive planning had not been previously carried out. Updated and new FoTX data for all Texas fish Species of Greatest Conservation Need (SGCN) were used in production of newly improved Species Distribution Models for input into this planning process, and the results of the planning exercise have already been integrated by TPWD into management prioritizations of both those species and the resultant NFCAs. Activity 3. Develop Monitoring and Conservation Plans for Native Fish Conservation Areas - Monitoring and conservation plans were delivered to TPWD for all NFCAs identified in Activity 2. Activity 4. Conduct Field-Based Surveys Detailed Biodiversity Assessments (i.e. Bioblitzing), and Citizen-Based Monitoring - Field surveys with detailed biodiversity assessments (“bioblitzes”) and citizen-based monitoring were conducted in three areas selected collaboratively by TPWD and FoTX Project staff from within the identified NFCAs: Nueces River headwaters, Big Cypress Bayou basin, and Village Creek basin. Along with this field effort, FoTX Project staff developed and circulated guidelines and best practices, and provided training for citizen-based monitoring that leverages iNaturalist for capture and reporting of photo-vouchered occurrence records in ways that will help assure scientifically useful data are obtained. All specimens acquired during these field efforts, and from many other routine specimen acquisitions from across the state (1845 total records/jars of specimens), were cataloged in the UT Fish Collection database. From there, these new records will soon be fed into GBIF, VertNet, FishNet2 and other major online data aggregators, including the online Fishes of Texas database.

American Eel is undoubtedly one of the most studied freshwater fishes of North America. Many recent discoveries have added new insights that re-write important aspects of the “text book” knowledge of the species’ complex life history in ways that could have significant impacts on management. Despite all of this new information, debate about the species’ conservation status continues, and new threats, such as continued habitat loss and major clandestine fisheries driven by extremely high value in the global market, have further complicated management. Though USFWS recently decided that the species does not merit listing as “Endangered,” in 2012 Canada changed that country’s assessment of the species’ status from “Special Concern” (since 2006) to “Threatened” and IUCN upped its classification in 2013 to “Endangered.” Ontario has considered it “Endangered” since 2007. All U.S. Atlantic states vowed to work together to produce, in 1999, the American Eel Benchmark Stock Assessment, which mandated each state conduct standardized monitoring of recruitment and later, mandatory catch and effort monitoring. Given all that activity and data generation, it is remarkable that still so little is known about the populations of the Gulf of Mexico (GOM) and its tributary rivers that making any management decisions in that large, neglected part of the species’ range is virtually impossible. The Fishes of Texas Project team has been collating and improving the limited and scattered data on occurrences of the species in the region and concludes it important to promote a broad scale (Gulf of Mexico) collaborative community effort to acquire and share data and carefully curated specimens and, hopefully, develop a GOM-wide collaborative research and management plan like that implemented by Atlantic states. Here we’ll review the literature and state of knowledge about the species in Texas and GOM, and suggest ways to begin work toward such an effort.

We examined allelic variation at nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA in 10 geographic samples representing 6 nominal species of the cyprinid genus Dionda. Species of Dionda are found in springs and spring-fed headwaters in the southwestern United States and Mexico and are of particular interest to conservation and management, in part because of their limited distribution and habitat specificity, and in part as indicator species of habitat quality. All 10 samples examined appear to be discrete, demographically independent populations, with greater observed FST values between or among samples within species (0.123–0.280) than threshold values above which demographic independence is indicated. All 10 exhibited microsatellite and mtDNA variation comparable to or lower than that found in other cyprinids considered to be threatened or endangered; across microsatellites, average number of alleles across populations ranged from of 2.09 to 9.76, allelic richness from 2.24 to 8.45, and gene diversity from 0.0211 to 0.606; for mtDNA, the number of haplotypes across populations ranged from 1 to 14. Estimates of historical and present-day genetic demography indicated that all 10 populations have experienced order-of-magnitude declines in effective population size, with lower bounds of time intervals for the declines in 9 of the populations ranging from 6 to 65 years. Estimates of average long-term effective population size (536 in Dionda argentosa from San Felipe Creek to 2335 in D. texensis) and effective number of breeders (22 in D. flavipinnis from Fessenden Spring to 555 in D. diaboli from Devils River) also indicated recent declines in effective size, and at least 5 of the populations appear to have undergone recent, severe bottlenecks (mean Mc range 0.806–0.848, P value range 0.000–0.0350). The observation that all 10 populations are demographically independent indicates that local extirpations likely would not be replaced by new migrants and that loss of any of the populations would represent loss of a unique genetic entity. Conservation recommendations for each of the populations are briefly discussed.

Attempts to infer mating systems in wild fish populations can be limited by the logistics of locating nests and thoroughly sampling offspring and potential participants. Captive populations are more easily evaluated but may exhibit modified behavior. We used microsatellites (17 loci) to determine parentage among production offspring and infer the mating system of raceway spawning Guadalupe Bass Micropterus treculii, which are part of a supplemental stocking program. Offspring were collected over the course of two production seasons (n = 303 and 492). Spawning activity was nonrandom, with respect to location and time in most compartments, and individuals that spawned were significantly larger, by length and weight, than individuals that did not. During the first year of captivity, significantly fewer males (21 of 60) than females (49 of 61) spawned. Inequalities between the number of nest locations used and the numbers of spawning males and females suggest that males recruited females to spawning sites. While most spawning females (61%) participated with a single mate, most spawning males (90%) participated with multiple females and only 3% of mating pairs were monogamous. This predominantly polygynous mating system contrasts with the primarily monogamous systems of wild congeners and resulted in an effective number of breeders (Nb) less than 30% of the number of penned broodfish. Quarantining particularly prolific males to separate pens during the second year of captivity had little effect on mating behavior, as other males filled their roles. This represents the first documentation of mate choice and fidelity in Guadalupe Bass and provides a template for expected reproductive behavior in a standard hatchery setting. Understanding mating systems, including the effects of captivity on behavior, should enhance restoration efforts, particularly when supplemental stocking programs are involved.

Interspecific hybridization among micropterids was once thought to be rare but has been documented in several cases of North American endemics. Introduction of the nonnative Smallmouth Bass Micropterus dolomieu across Texas has threatened to eliminate the Guadalupe Bass M. treculii genome throughout its native range via introgression between the species. In 1992, the Texas Parks and Wildlife Department began a stocking program in the Guadalupe River watershed to restore the genetic integrity of the local population. More than 600,000 hatchery-reared Guadalupe Bass fingerlings (\textasciitilde30 mm total length) were stocked in Johnson Creek over a 19-year period, and 360,000 fish were released in the North Fork, South Fork, and main-stem Guadalupe River over a 5-year period. Annual genetic monitoring indicated that hybridization significantly declined in all stream segments (P \textless 0.001) during the period of time when stocking occurred. Initially high hybridization rates (range, 20–100%; mean = 43.4%) were reduced to 0–24.2% (mean = 11.4%) at the termination of stocking. Linear regression indicated that hybridization in the North Fork and main-stem stream segments declined faster (9.0% per year) than all other test stream segments, whereas the South Fork Guadalupe River and upper Johnson Creek declined at 0.9% per year and lower Johnson Creek declined at 1.9% per year. Our data show that supplemental stocking is an effective approach to genetic restoration of compromised populations and should be considered as a viable management and conservation tool.

The Fishes of Texas Project (www.fishesoftexas.org) compiled Texas fish species occurrence records from 42 museum collections and applied rigorous quality control and data normalization/standardization to result in 124,415 specimen-based records collected between 1851 and 2010 by 5,924 collectors. Though Gulf of Mexico and estuarine records are included, manual georeferencing of localities focused primarily on inland (freshwater) Texas records, resulting in 88,348 records from 7,868 unique Texas inland localities, all with estimates of placement error. Though not all georeferenced, 8,460 marine (Gulf of Mexico) and 18,923 inland records from neighboring Mexican and U.S. states have been partially processed. All georeferenced records were plotted and 4,107 geographic outliers flagged as potential identification or location errors. Most flagged specimens, and often related original documentation, were examined and identifications corrected or confirmed. Data curation methodology is thoroughly documented in the website, where the dataset can be queried in diverse ways, mapped, and data downloaded. Also online are a large set of high quality fish images, collectors' field notes, specimen photos, species distribution models derived from the data, accounts of species' biology and ecology, and digital identification keys. Users can comment on any record and upload images, field notes and other documentation.

The Fishes of Texas Project (www.fishesoftexas.org) compiled Texas fish species occurrence records from 42 museum collections and applied rigorous quality control and data normalization/standardization to result in 124,415 specimen-based records collected between 1851 and 2010 by 5,924 collectors. Though Gulf of Mexico and estuarine records are included, manual georeferencing of localities focused primarily on inland (freshwater) Texas records, resulting in 88,348 records from 7,868 unique Texas inland localities, all with estimates of placement error. Though not all georeferenced, 8,460 marine (Gulf of Mexico) and 18,923 inland records from neighboring Mexican and U.S. states have been partially processed. All georeferenced records were plotted and 4,107 geographic outliers flagged as potential identification or location errors. Most flagged specimens, and often related original documentation, were examined and identifications corrected or confirmed. Data curation methodology is thoroughly documented in the website, where the dataset can be queried in diverse ways, mapped, and data downloaded. Also online are a large set of high quality fish images, collectors' field notes, specimen photos, species distribution models derived from the data, accounts of species' biology and ecology, and digital identification keys. Users can comment on any record and upload images, field notes and other documentation.

Largemouth Bass Micropterus salmoides ranges naturally in Mexico from the binational Rio Grande basin, including Cuatro Cienegas valley in the state of Coahuila, southward and eastward through two adjacent Gulf Coast drainages, the Rio San Fernando and Rio Soto La Marina in Nuevo Leon and Tamaulipas. Within this range, Florida Bass M. floridanus has been introduced into reservoirs in at least the Rio Grande and Soto La Marina basins. To assess the conservation status of native Mexican bass, we study genetic variability within and among Largemouth Bass populations and the degree of genetic introgression by Florida Bass within them. We sampled numerous localities in Cuatro Cienegas, the San Fernando and Rio Soto La Marina basins, and Vicente Guerrero Reservoir, where Florida Bass was introduced. We examined restriction-fragment polymorphisms within the 12S and 16S ribosomal RNA mitochondrial DNA genes and genotypes at two allozyme and five microsatellite DNA loci. Levels of introgression were quantified by Bayesian assignment testing using the nuclear data. Largemouth Bass specimens possessed generally lower nuclear diversity, but higher mitochondrial diversity, than those of Florida Bass. Populations from Cuatro Cienegas differed from those in the San Fernando and Soto La Marina basins. Nuclear analyses revealed three genetically pure populations in Cuatro Cienegas (Charcos Prietos, Las Playitas, and Canal del Tio Julio), but hybrids in Rio Garabatal and Mojarral Este. Another presumably pure Largemouth Bass population was found in Rio El Tigre of the Soto La Marina drainage. Our results could be explained by geographic barriers, sex-biased dispersion, hybrid disadvantage, or selection for coadapted gene complexes. More extensive surveys are needed to fully assess the conservation status of native Largemouth Bass populations in Mexico. We anticipate that these will reveal additional native diversity. Meanwhile, the remnant native populations delineated herein are important to protect and we advocate that their ranges be managed as genetic conservation areas.

Read this work by Hendrickson D, at F1000Research.

Phylogenetic trees have historically been used to determine evolutionary relatedness between organisms. In the past few decades, as we've developed increasingly powerful computational algorithms and toolsets for performing analyses using phylogenetic methods, the use of these trees has expanded into other areas, including biodiversity informatics and geoinformatics. This report proposes using phylogenetic methods to create "fluviagenies" - trees that represent the effects of river fragmentation over time caused by damming. Faculty at the Center for Research in Water Resources at the University of Texas worked to develop tools and documentation for automating the creation of river segment codes (a.k.a., "fluvcodes") based on spatiotemporal data. Python was used to generate fluviageny trees from lists of these codes. The resulting trees can be exported into the appropriate data format for use with various phylogenetics programs. The Fishes of Texas Database (fshesoftexas.org), a comprehensive geospatial database of Texas fish occurrences aggregated and normalized from 42 museum collections around the world, was employed to create an example of how this tool might be used to analyze and hypothesize changes in fish populations as a consequence of river fragmentation. Additionally, this paper serves to theorize and analyze past and future potential uses for phylogenetic trees in various other fields of informatics.