Tiaroga Research Articles

Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow Ptychocheilus lucius.

Advancements in genome sequencing technology have brought unprecedented accessibility of high-throughput sequencing to species of conservation interest. The potential knowledge gained from application of these techniques is maximized by availability of high-quality, annotated reference genomes for endangered species. However, these vital resources are often lacking for endangered minnows of North America (Cypriniformes: Leuciscidae). One such endangered species, Colorado pikeminnow (Ptychocheilus lucius) is the largest North American minnow and the top-level native aquatic predator in the Colorado River Basin of the southwestern United States and northwestern Mexico. Over the past century Colorado pikeminnow has suffered habitat loss and population declines due to anthropogenic habitat modifications and invasive species introductions. The lack of genetic resources for Colorado pikeminnow has hindered conservation genomic study of this unique organism. This study seeks to remedy this issue by presenting a high-quality reference genome for Colorado pikeminnow developed from Pacific Biosciences HiFi sequencing and Hi-C scaffolding. The final assembly was a 1.1 Gb genome comprised of 305 contigs including 25 chromosome-sized scaffolds. Measures of quality, contiguity, and completeness met or exceeded those observed for Danio rerio (Danionidae) and two other Colorado River Basin leuciscids (Meda fulgida and Tiaroga cobitis). Comparative genomic analyses identified enrichment of gene families for growth, development, immune activity, and gene transcription; all of which are important for a large-bodied piscivorous fish living in a dynamic environment. This reference genome will provide a basis for important conservation genomic study of Colorado pikeminnow and help efforts to better understand the evolution of desert fishes.

Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis).

North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.

Assessing Conservation Potential of Streams for Spikedace and Loach Minnow Using Species Distribution Modeling

Abstract Identifying, evaluating, and prioritizing freshwater systems for conservation is a persistent challenge for managers tasked with conservation and recovery of native fishes. We used historical records from the Gila River basin, the national hydrography data set, and Random Forest modeling to predict probability of Spikedace Meda fulgida and Loach Minnow Rhinichthys cobitis occurrence throughout their range in the Gila River basin. Models for both species performed moderately well, with relatively high predicted probability of occurrence at streams with historical records. Predicted probability of occurrence was also relatively high in several streams without historical records of focal species, suggesting that there are unoccupied reaches throughout the Gila River basin with similar environmental conditions to historically occupied reaches for both species. Unoccupied reaches with the highest predicted probability of occurrence may have a greater chance of supporting translocated populations of focal species. Our results can be used as a first step for locating reaches most likely to support translocated populations of Spikedace and Loach Minnow within their respective historical ranges. Our approach may be applicable to other species of conservation concern with available historic records in need of population restoration.

How fast is too fast? Water velocity differentially affects growth of four Gila River, native cyprinids

AbstractUnderstanding trade‐offs associated with occupying various aquatic habitats provides a mechanistic understanding of habitat needs that can be used to evaluate the consequences of habitat loss or alteration. We used instream enclosures and field observations to identify how velocity affects the growth rates of four native species in the upper Gila River basin: longfin dace (Agosia chrysogaster) and speckled dace (Rhinichthys osculus), two species of no conservation concern, and loach minnow (Tiaroga cobitis) and spikedace (Meda fulgida), two federally endangered species. Elevated velocity was predicted to increase food delivery through drift or stimulation of benthic primary production. Energetic costs of high‐velocity habitat were predicted to vary with morphology and behaviour and be lowest for speckled dace and loach minnow because they are adapted to occupy interstitial spaces of the substrate in riffles. Spikedace and longfin dace should perform best in moderate velocities, where the trade‐off between exposure to drifting macroinvertebrates outweighs the energetic costs of maintaining position in the water column. Growth rates of loach minnow and speckled dace increased in higher velocities, but contrary to our initial predictions, spikedace growth rates also increased in high‐velocity habitats while longfin dace grew fastest in low‐velocity habitats; similar to the locations these species occupied based on field observations. These results indicate that for spikedace, the increased abundance of drifting macroinvetebrates in high‐velocity habitats outweighs the energy expenditure, but for longfin dace the energetic costs of occupying moderate to high‐velocity habitats outweigh the benefit to increased food availability. Our experiment provides a mechanistic understanding of habitat requirements across species and may inform predictions on how modifications or restoration of riverine ecosystems influence native fish diversity.

Successful Restoration of a Native Fish Assemblage in the Blue River, Arizona

AbstractTranslocation is one of the most commonly proposed management actions for securing and recovering native fish species. However, the success of native fish translocations has varied widely due to several limiting factors, including the presence of nonnative fishes. The Blue River Native Fish Restoration Project involved construction of a fish passage barrier, removal of nonnative fish, translocation of three native fish species (Spikedace Meda fulgida, Loach Minnow Rhinichthys cobitis, and Roundtail Chub Gila robusta), and monitoring to determine the success of these actions. After construction of a physical fish passage barrier, the three focal species were stocked several times upstream of the barrier. Nonnative fish were removed annually using multiple gear types, including spearfishing, backpack electrofishing, and trapping. Monitoring data demonstrated a significant shift in the fish assemblage from one with a substantial component of nonnative fishes to one that was exclusively native fishes. Persistence, reproduction, increased abundance, and dispersal were documented for all three focal species within the study area, meeting criteria for establishment success. All nonnative fishes, including the primary targets of removal efforts—Channel Catfish Ictalurus punctatus and Green Sunfish Lepomis cyanellus—were successfully suppressed, if not eradicated entirely, during the study period. Our results illustrate the importance of long‐term monitoring to track and successfully achieve native fish recovery goals. In addition, our results demonstrate that nonnative fish can be mechanically removed from warmwater streams if initial abundance is low, distribution is restricted, and fish passage barriers are in place. Results from this study may be informative for managers hoping to improve the conservation status of warmwater stream fishes through creation of a fish passage barrier, nonnative species removal, and native fish translocation efforts.

The complete mitochondrial genomes of three imperiled cyprinid fishes Bonytail (Gila elegans), Rio Grande Silvery Minnow (Hybognathus amarus) and Loach Minnow (Tiaroga cobitis)

Gila elegans, Hybognathus amarus, and Tiaroga cobitis (Family Cyprinidae, Order Cypriniformes) are endemic and endangered fishes in the southwestern United States. We present complete mitochondrial genomes for each species. Each mitochondrion consisted of 13 protein-coding genes, 2 ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and a single control region (D-loop), and gene order was consistent with other cyprinid fishes. Total genome lengths were 16,593 base pairs (bp) for G. elegans, 16,705 bp for H. amarus, and 16,802 for T. cobitis. The GC content in G. elegans and H. amarus was 44%, but higher in T. cobitis at 48%. Phylogenetic trees were generated to confirm relationships inferred via novel mitogenomes, and best-supported trees were consistent with previous research.

Environmental DNA Sampling of Small‐Bodied Minnows: Performance Relative to Location, Species, and Traditional Sampling

AbstractWe performed experiments in southwestern USA streams to evaluate the efficacy of environmental DNA (eDNA) sampling for two rare small‐bodied minnows: Spikedace Meda fulgida and Loach Minnow Rhinichthys cobitis. We collected eDNA by filtering 5‐L samples and compared detection sensitivity of eDNA assays to traditional sampling methods (electrofishing and seining) by using both techniques at 33 sites in seven streams. We used caged‐fish experiments to estimate eDNA production rates, persistence, and travel distances and to estimate relationships between fish density, biomass, and eDNA quantity. Loach Minnows were detected at 22 sites by both eDNA and traditional sampling, were not detected by either technique at 7 sites, and were detected only by eDNA at 4 sites. Spikedace were detected with both techniques at 15 sites, were not detected by either technique at 8 sites, and were detected only by eDNA at 7 sites. In the Verde River and Wet Beaver Creek, both species’ eDNA was detected downstream of caged fish out to our maximum sampling distance of 500 m. Estimated eDNA production rates were greater for Spikedace than for Loach Minnows, although more Spikedace were used. Production rates for both species were greater in the Verde River than in Wet Beaver Creek. Persistence of eDNA did not differ among species but was greater in Wet Beaver Creek than in the Verde River. In density experiments, the amount of Spikedace eDNA was positively related to the density and biomass of caged Spikedace, but the relationship differed between streams. We conclude that eDNA surveys are more sensitive than traditional methods for detecting rare minnows in southwestern streams. With the sensitivity to detect even a single fish in a 100‐m reach, managers will be able to more effectively identify reaches occupied by threatened or endangered fish, even if a population is in decline.

Predicted Native Fish Response, Potential Rewards and Risks from Flow Alteration in a New Mexico Arid Mountain Stream

AbstractWater and natural resource managers are concerned with evaluating how fish habitat and populations may respond to water diversions and small‐scale flow augmentations. We used two‐dimensional hydraulic models, habitat suitability curves and an individual‐based population viability model to assess whether flow augmentations of about 0.28–0.57 m3/s would create suitable habitat for federally listed native fish loach minnow Rhinichthys cobitis and spikedace Meda fulgida in a reach of the Gila River, New Mexico, and then examined how fish population viability may change under a variety of colonization and extinction scenarios. These simulations help to inform water management decisions in a reach of the Gila River where river diversions currently exist and new diversions and augmentations are being proposed. Our results suggest that the flow augmentations evaluated will result in small changes (on average across life stages, −0.22% to 4.06%) in suitable habitat for loach minnow and spikedace depending on augmentation scenario and fish life stage. While these percent changes are small, they would result in a reduction in the dewatering of the river channel in a river reach where native fish abundance is thought to be low. Actual native fish responses to these habitat changes are unknown; however, these flow augmentations could potentially allow these native species to re‐colonize this river segment from upstream or downstream sources increasing species distribution and likely population viability. Maintaining viable populations of native fish in this river reach is dependent on complex factors including persistence of suitable habitat for multiple life stages, connectivity with other populations and minimizing risk of invasion from non‐native species. We recommend that these predictions from the habitat and population models be tested and verified in an adaptive management framework linking modelling, experimental management, monitoring and reassessment to inform water management decisions in the Gila River. Copyright © 2017 John Wiley & Sons, Ltd.

Quantitative PCR Assays for Detecting Loach Minnow (Rhinichthys cobitis) and Spikedace (Meda fulgida) in the Southwestern United States.

Loach minnow (Rhinichthys cobitis) and spikedace (Meda fulgida) are legally protected with the status of Endangered under the U.S. Endangered Species Act and are endemic to the Gila River basin of Arizona and New Mexico. Efficient and sensitive methods for monitoring these species’ distributions are critical for prioritizing conservation efforts. We developed quantitative PCR assays for detecting loach minnow and spikedace DNA in environmental samples. Each assay reliably detected low concentrations of target DNA without detection of non-target species, including other cyprinid fishes with which they co-occur.

Comparison of Upper Thermal Tolerances of Native and Nonnative Fish Species in Arizona

AbstractWe used a lethal thermal method to estimate the upper thermal tolerances of 11 native and 7 nonnative fish species found throughout southern Arizona. Fish were acclimated to 25°C and 30°C. For all species tested, an increase in acclimation temperature resulted in a higher thermal tolerance value. Among the species acclimated to 25°C, desert pupfish Cyprinodon macularius, western mosquitofish Gambusia affinis, and Gila topminnow Poeciliopsis occidentalis were most tolerant to high temperature. Speckled dace Rhinichthys osculus, spikedace Meda fulgida, and loach minnow R. cobitis were least tolerant. Many native species demonstrated a limited ability to extend their upper temperature tolerances via acclimation. Our data suggest that several native species may be sensitive to increasing annual and large daily temperature fluctuations in Arizona's streams and rivers. Although southwestern native fishes were previously believed to be tolerant to high temperature due to their evolution in desert environments, this study suggests that many of these fishes are less tolerant than previously thought. In addition, many fishes introduced from the eastern United States had higher temperature tolerances than some of the native desert species tested. Increases in stream temperatures in Arizona could reduce the habitat available for native fishes and therefore may favor those nonnative species with higher thermal tolerances.

Upper Temperature Tolerance of Loach Minnow under Acute, Chronic, and Fluctuating Thermal Regimes

AbstractWe used four methods to estimate the upper lethal temperature of loach minnow Rhinichthys cobitis: The lethal thermal method (LTM), chronic lethal method (CLM), acclimated chronic exposure (ACE) method with static temperatures, and ACE method with diel temperature fluctuations. The upper lethal temperature of this species ranged between 32°C and 38°C, depending on the method and exposure time; however, temperatures as low as 28°C resulted in slowed growth compared with the control groups. In LTM trials, we increased temperatures 0.3°C/min and death occurred at 36.8 ± 0.2°C (mean ± SE) for fish (37–49 mm total length) acclimated to 30°C and at 36.4 ± 0.07°C for fish acclimated to 25°C. In CLM trials, temperatures were increased more slowly (1°C/d), allowing fish to acclimate. Mean temperature at death was 33.4 ± 0.1°C for fish 25–35 mm and 32.9 ± 0.4°C for fish 45–50 mm. In the ACE experiment with static temperatures, we exposed fish for 30 d to four constant temperatures. No fish (20–40 mm) survived beyond 30 d at 32°C and the 30‐d temperature lethal to 50% of the test animals was 30.6°C. Growth at static 28°C and 30°C was slower than growth at 25°C, suggesting that fish were stressed at sublethal temperatures. In ACE trials with diel temperature fluctuations of 4, 6, and 10°C and a 32°C peak temperature, over 80% of fish (20–40 mm) survived 30 d. Although brief exposures to 32°C were not lethal, the growth of fish in the three fluctuating‐temperature treatments was significantly less than the growth at the ambient temperature (25–29°C). To minimize thermal stress and buffer against temperature spikes, we recommend that loach minnow habitat be managed to avoid water temperatures above 28°C.

NEW AND REDISCOVERED POPULATIONS OF LOACH MINNOW, TIAROGA COBITIS (CY PRINIDAE), IN ARIZONA

Abstract We report collections of threatened loach minnow, Tiaroga cobitis, from 2 Gila River basin (Arizona) streams, one representing a rediscovery and the other a new record. The species had been taken in 1950 from Eagle Creek, but it was not seen again until 1994–1997 and, despite repeated attempts, has not been detected since. It likely persists in adjacent, unsampled areas. A new distribution record is reported for loach minnow captured in 1996 from North Fork of East Fork Black River. This last population has been resampled repeatedly and seems stable. Genetic analysis confirms the uniqueness of these and most other known populations, and we recommend protection and conservation of loach minnow in these 2 streams.

EFFECTS OF INTRINSIC AND EXTRINSIC FACTORS ON POPULATION FRAGMENTATION IN THREE SPECIES OF NORTH AMERICAN MINNOWS (TELEOSTEI: CYPRINIDAE)

Geographic patterns of genetic variation (mitochondrial DNA [mtDNA] and allozymes) were used to examine effects of intrinsic characteristics (e.g., vagility, habitat specificity, and reproductive behaviors) and extrinsic factors (e.g., climatic and geological history) on population fragmentation. The three species of cyprinid fishes examined (Tiaroga cobitis, Meda fulgida, and Agosia chrysogaster) occupied similar historical ranges within the lower Colorado River drainage, but differ in intrinsic characteristics conducive to population fragmentation. Relationships among populations were similar across species, reflecting common historical influences, but results indicate the distribution of variation among species is strongly affected by intrinsic characteristics. Variation within two species (T. cobitis and M. fulgida) is subdivided among populations, suggesting little gene flow among rivers. In contrast, similarity of A. chrysogaster populations throughout the Gila River drainage supports the hypothesis that levels of gene flow are high for this species. Levels of mtDNA divergence were much higher than expected for both T. cobitis and A. chrysogaster suggesting long-term isolation of geographic regions. These results indicate that both long-term and short-term extrinsic factors have shaped basic patterns of variation within these fishes; however, the intrinsic characteristics of each species have strongly affected the population genetic structure of these fishes.

Physical habitat utilization of fish in a Sonoran Desert stream, Arizona, southwestern United States

Abstract– The physical habitat utilization of 7 species of native fishes in a Sonoran Desert stream, Aravaipa Creek, Arizona is described. The species occupied significantly different depths and velocities of water. Longfin dace (Agosia chrysogaster), speckled dace (Rhinichthys osculus) and loach minnow (Tiaroga cobitis) used similar depths and velocities. Two of the three larger species (Sonora sucker [Catostomus insignis] and roundtail chub [Gila robusta]) used areas of greater depth and reduced velocity. Desert sucker (Catostomus clarki) grouped with loach minnow and speckled dace in the velocity of water occupied, but utilized deeper waters. The spikedace (Meda fulgida) aligned very closely with desert sucker in use of all 3 physical habitat variables.

Habitat and Biology of the Loach Minnow, Tiaroga cobitis, in New Mexico

The eggs of the loach minnow, Tiaroga cobitis, were deposited on the undersides of cobble in moderate-velocity riffles. Nearshore larval nursery areas were characterized by slower velocities and smaller substrate particles. Larger individuals occupied higher velocity microhabitats with cobble substrates. Geographic differences in microhabitat distributions of juveniles and adults were minor and were probably related to habitat availability. Male and female T. cobitis in their second summer (Age I) comprised the bulk (60%+) of the spawning population. Spawning in the Cliff-Gila Valley reach of the Gila River in New Mexico occurred for a brief period in April 1984 when daytime water temperatures were 16-20 C. Larval growth was rapid, and by autumn, Age-0 fish were 30-35 mm SL. Thereafter, growth was slower and few individuals exceeded 60 mm SL or Age II. Tiaroga cobitis fed mainly upon ephemeropteran naiads and chironomid larvae. Destruction and modification of riffle habitat and establishment of non-

Autumn Spawning and Other Reproductive Notes on Loach Minnow, a Threatened Cyprinid Fish of the American Southwest

The loach minnow (Tiaroga cobitis Girard) is a small (<70 mm SL), darter-like, rare cyprinid fish endemic to the Gila River basin of Arizona and New Mexico and of Sonora, Mexico (Minckley, 1973, 1980). It is listed as threatened by the United States Fish and Wildlife Service (1986) and endangered by the states of Arizona and New Mexico. Reasons for its decline are cited as habitat alteration and establishment of non-native

Physical Habitat Use by Loach Minnow, Tiaroga cobitis (Pisces: Cyprinidae), in Southwestern Desert Streams

Physical Habitat Use by Loach Minnow, Tiaroga cobitis (Pisces: Cyprinidae), in Southwestern Desert Streams

Fishes of Aravaipa Creek, Graham and Pinal Counties, Arizona

-Aravaipa Creek in Graham and Pinal counties, Arizona, is a nowisolated, spring-fed tributary of the San Pedro River. This stream acts as a refugium for 7 of the 12 known native fish species of the San Pedro drainage (Gila robusta, Rhinichthys osculus, Agosia chrysogaster, Tiaroga cobitis, Meda fulgida, Catostomus insignis, and Pantosteus clarki). Only two introduced fishes are present (Ictalurus melas and Lepomis cyanellus), and these are restricted to a pond lateral to the creek. Increasing demands on water in the American Southwest, along with changes in land use, possibly climate, and other factors, have had adverse effects on the native aquatic fauna (Miller, 1961, et seq.). A substantial percentage of natural marshes, springs, and streams already are modified beyond reclamation; only a few enjoy relative immunity. In addition, animals in the West have been increasingly subject to competition from a myriad of exotic animals (Miller, 1961; Deacon, et al., 1964; Hubbs and Deacon, 1964; and others). All this contributes to marked modification of the distribution and abundance of native fishes, and to their decline and extinction in some instances. One of the few aquatic habitats that has maintained relative virginity is Aravaipa Creek, Graham and Pinal counties, Arizona. In this paper we record some collections of fishes from that stream, including results of our intensive survey of the fishes between 6 November 1964 and 1 May 1965. Charles H. Lowe and Wallace G. Heath, University of Arizona (the latter now at Western Washington State College), studied Aravaipa Creek in the 1950's, with special reference to thermal ecology of the fishes. Results of their studies are soon to be published elsewhere. TOPOGRAPHY AND GEOLOGY OF THE AREA. Aravaipa Creek drains the northwest end of a structural trough that to the south holds the Willcox Playa (a remnant of Pluvial Lake Cochise; Cole, 1963), and the extreme headwaters of the south-flowing Rio Yaqui of Mexico. It originates at a low divide about 1,310 meters (m.) above mean sea level, passes northwest for 75 linear kilometers (km.) (ca. 140 km. by actual stream channel), to enter the now-dry San Pedro River at an elevation of 660 m., 16.8 km. south-southeast of Winckleman, Arizona (Fig. 1). Only about 50 creek-km. of the channel holds permanent surface water.