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.

Rivers and streams of the southern United States contain more than 1,800 aquatic species, 500 of which are regionally endemic. At present, 34% of the fish species and 90% of the mussel species in peril nationwide are found in these systems. Declines in these imperiled species are due to many factors, including hydrologic alteration, degraded water quality, loss of instream and watershed connectivity, physical habitat degradation, and the negative effects of nonindigenous species (e.g., predation on, competition with, and hybridization with native forms). In addition, this situation is exacerbated through human population growth, competing water demands, land-use changes, and other interrelated issues. If unchecked, these issues will likely continue to contribute to the imperilment and loss of native species in the region. Of the nine described species and subspecies of black bass, six are endemic to the southern United States: Guadalupe Bass Micropterus treculii, Shoal Bass M cataractae, Redeye Bass M. coosae, Florida Bass M floridanus, Alabama Bass M henshalli, and Suwannee Bass M notius. In addition, undescribed species and subspecies also exist and all are in need of conservation measures to prevent them from becoming imperiled. In an effort to focus and coordinate actions to support the long-term persistence of endemic black bass populations, local, state, and federal agencies, universities, nongovernmental organizations, and corporations from across the region joined with the National Fish and Wildlife Foundation to form the Native Black Bass Initiative (NBBI). The NBBI provides regional conservation strategies, objectives, and targets to restore and preserve functional processes in those watersheds that support natural habitat conditions and sustainable populations of endemic black bass and other native fishes of the region. Initial actions implemented through the NBBI focus on addressing the conservation needs of Guadalupe Bass in streams of the Edwards Plateau ecoregion of Texas, Redeye Bass in the Savannah River watershed of Georgia and South Carolina, and Shoal Bass populations in the Apalachicola River watershed of Alabama, Florida, and Georgia.

Recent literature reviews of bioassessment methods raise questions about use of least-impacted reference sites to characterize natural conditions that no longer exist within contemporary landscapes. We explore an alternate approach for bioassessment that uses species site occupancy data from museum archives as input for species distribution models (SDMs) stacked to predict species assemblages of freshwater fishes in Texas. When data for estimating reference conditions are lacking, deviation between richness of contemporary versus modeled species assemblages could provide a means to infer relative biological integrity at appropriate spatial scales. We constructed SDMs for 100 freshwater fish species to compare predicted species assemblages to data on contemporary assemblages acquired by 4 independent surveys that sampled 269 sites. We then compared site-specific observed/predicted ratios of the number of species at sites to scores from a multimetric index of biotic integrity (IBI). Predicted numbers of species were moderately to strongly correlate with the numbers observed by the four surveys. We found significant, though weak, relationships between observed/predicted ratios and IBI scores. SDM-based assessments identified patterns of local assemblage change that were congruent with IBI inferences, however, modeling artifacts that likely contributed to over-prediction of species presence may restrict the stand-alone use of SDM-derived patterns for bioassessment and therefore warrant examination. Our results suggest that when extensive standardized survey data that includes reference sites are lacking, as is commonly the case, SDMs derived from generally much more readily available species site occupancy data could be used to provide a complementary tool for bioassessment.

Sharpnose shiner, Notropis oxyrhynchus, was recently listed as federally endangered  Known from the Brazos and Colorado Rivers, but Colorado population believed to be introduced and now extinct  Our species distribution models indicate sufficient habitat for the species to occur in the Colorado (Fig. 3).  Our previous work (Fig. 1) to verify cyprinid museum specimens in the Colorado indicate 5 records of N. oxyrhynchus collected from 1884 to 1955 strongly suggesting nativity of the species (or a morphologically similar form) Visual examination of specimens from the Colorado suggest distinctive morphological (shape) differences compared to Brazos specimens  We hypothesized Colorado population might be a separate or incipient species

Behavioral studies have often examined parental care by measuring phenotypic plasticity of behavior within a species. Phylogenetic studies have compared parental care among species, but only at broad categories (e.g., care vs. no care). Here we provide a detailed account that integrates phylogenetic analysis with quantitative behavioral data to better understand parental care behavior in the Cuatro Ciénegas cichlid, Herichthys minckleyi. We found that H. minckleyi occurs in a clade of sexually monochromatic or weakly dichromatic monogamous species, but that male and female H. minckleyi have dramatically different reproductive coloration patterns, likely as a result of sexual selection. Furthermore, we found that males are polygynous; large males guard large territories, and smaller males may attempt alternative mating tactics (sneaking). Finally, compared to the closely related monogamous Rio Grande cichlid, H. cyanoguttatus, males of H. minckleyi were present at their nests less often and performed lower rates of aggressive offspring defense, and females compensated for the absence of their mates by performing higher levels of offspring defense. Body color, mating system, and parental care in H. minckleyi appear to have evolved after it colonized Cuatro Ciénegas, and are likely a result of evolution in an isolated, stable environment.