Geology Reports⌕ Search

Geology topics

Scott A. Bonar

Publications and source records attributed to Scott A. Bonar.

At least 37 records · Page 2Linked to original sources
USGS2018

Effectiveness of ultrasonic imaging for evaluating presence and maturity of eggs in fishes in remote field locations

Ultrasonic imaging is an effective, nonlethal method used to determine sex and maturity in a variety of fishes. However, many previous studies of this technique have been performed in laboratory environments. Using Common Carp Cyprinus carpio , we developed a standardized method for ultrasonically scanning cyprinids, and we accurately sexed 78% ( N = 58) of those individuals. We then applied this method to endangered Humpback Chub Gila cypha and obtained 751 scans of Humpback Chub in remote field locations within the Grand Canyon, Arizona. Ultrasonic scanning took less than 1 min per fish to perform, and we identified females containing eggs based on two jpeg images and one 10-s video clip. Using ImageJ software to evaluate ultrasonic scans of ovulatory, captive Humpback Chub, we determined that female fish were potentially ovulatory when scanned eggs exhibited an ImageJ brightness value within the range of 32–44. Although we could successfully evaluate egg maturity, we were unable to estimate egg mass. Fisheries managers can use this noninvasive scanning method or a similar technique in remote field locations to collect ultrasonic scans from cyprinids to determine their reproductive status.

North American Journal of Fisheries Management↗
USGS2018

Propagation of endangered moapa dace

We report successful captive spawning and rearing of the highly endangered Moapa Dace, Moapa coriacea (approximately 650 individual fish in existence at time of this study). We simulated conditions under which this stream-dwelling southern Nevada cyprinid and similar species spawned and reared in the wild by varying temperature, photoperiod, flow, and substrate in 14 different spawning and rearing treatments in a propagation facility. Successful spawning occurred in artificial streams with the following characteristics: water flow directed both across the bottom gravel substrate into a cobble bed and across the upper water column; 12–14 fish/stream (0.016–0.026 fish/L depending on water level); static water temperature of 30–32°C; photoperiod of 12 h light and 12 h dark; gradual replacement of water from their natal stream with on-site well water; a combination of pelleted, frozen and live food; and minimal disturbance of fish. Nevada Department of Wildlife now uses these techniques successfully to produce fish in a culture setting. Identification of the effective combination of factors to trigger spawning in exceptionally rare fishes can be difficult and time consuming, and limiting factors can be subtle. Sufficient numbers of available test fish, close study and replication of wild spawning conditions, careful documentation, and patience to identify subtle limiting factors are often required to effectively rear and spawn fishes not previously propagated.

Nevada↗
USGS2017

Comparison of American Fisheries Society (AFS) standard fish sampling techniques and environmental DNA for characterizing fish communities in a large reservoir

Recently, methods involving examination of environmental DNA (eDNA) have shown promise for characterizing fish species presence and distribution in waterbodies. We evaluated the use of eDNA for standard fish monitoring surveys in a large reservoir. Specifically, we compared the presence, relative abundance, biomass, and relative percent composition of Largemouth Bass Micropterus salmoides and Gizzard Shad Dorosoma cepedianum measured through eDNA methods and established American Fisheries Society standard sampling methods for Theodore Roosevelt Lake, Arizona. Catches at electrofishing and gillnetting sites were compared with eDNA water samples at sites, within spatial strata, and over the entire reservoir. Gizzard Shad were detected at a higher percentage of sites with eDNA methods than with boat electrofishing in both spring and fall. In contrast, spring and fall gillnetting detected Gizzard Shad at more sites than eDNA. Boat electrofishing and gillnetting detected Largemouth Bass at more sites than eDNA; the exception was fall gillnetting, for which the number of sites of Largemouth Bass detection was equal to that for eDNA. We observed no relationship between relative abundance and biomass of Largemouth Bass and Gizzard Shad measured by established methods and eDNA copies at individual sites or lake sections. Reservoirwide catch composition for Largemouth Bass and Gizzard Shad (numbers and total weight [g] of fish) as determined through a combination of gear types (boat electrofishing plus gillnetting) was similar to the proportion of total eDNA copies from each species in spring and fall field sampling. However, no similarity existed between proportions of fish caught via spring and fall boat electrofishing and the proportion of total eDNA copies from each species. Our study suggests that eDNA field sampling protocols, filtration, DNA extraction, primer design, and DNA sequencing methods need further refinement and testing before incorporation into standard fish sampling surveys.

Arizona↗
USGS2017

Comparing efficiency of American Fisheries Society standard snorkeling techniques to environmental DNA sampling techniques

Analysis of environmental DNA (eDNA) is an emerging technique used to detect aquatic species through water sampling and the extraction of biological material for amplification. Our study compared the efficacy of eDNA methodology to American Fisheries Society (AFS) standard snorkeling surveys with regard to detecting the presence of rare fish species. Knowing which method is more efficient at detecting target species will help managers to determine the best way to sample when both traditional sampling methods and eDNA sampling are available. Our study site included three Navajo Nation streams that contained Navajo Nation Genetic Subunit Bluehead Suckers Catostomus discobolus and Zuni Bluehead Suckers C. discobolus yarrowi . We first divided the entire wetted area of streams into consecutive 100-m reaches and then systematically selected 10 reaches/stream for snorkel and eDNA surveys. Surface water samples were taken in 10-m sections within each 100-m reach, while fish presence was noted via snorkeling in each 10-m section. Quantitative PCR was run on each individual water sample in quadruplicate to test for the presence or absence of the target species. With eDNA sampling techniques, we were able to positively detect both species in two out of the three streams. Snorkeling resulted in positive detection of both species in all three streams. In streams where the target species were detected with eDNA sampling, snorkeling detected fish at 11–29 sites/stream, whereas eDNA detected fish at 3–12 sites/stream. Our results suggest that AFS standard snorkeling is more effective than eDNA for detecting target fish species. To improve our eDNA procedures, the amount of water collected and tested should be increased. Additionally, filtering water on-site may improve eDNA techniques for detecting fish. Future research should focus on standardization of eDNA sampling to provide a widely operational sampling tool.

Arizona, New Mexico↗
USGS2016

Enhancing hatch rate and survival in laboratory-reared hybrid Devils Hole Pupfish through application of antibiotics to eggs and larvae

We evaluated the effectiveness of four antibiotics in enhancing the hatch rate, larval survival, and adult survival of hybrid Devils Hole Pupfish Cyprinodon diabolis (hybridized with Ash Meadows Amargosa Pupfish C. nevadensis mionectes ). Cephalexin (CEX; concentration = 6.6 mg/L of water), chloramphenicol (CAM; 50 mg/L), erythromycin (ERY; 12.5 mg/L), and trimethoprim sulfamethoxazole (TMP-SMX; 25 mg/L) were applied as a constant bath either to incubating eggs or to larvae that hatched from untreated eggs. Hatch rate was roughly doubled by incubation in the presence of CAM (68% hatch) and TMP-SMX (66%) relative to the control (28%). Cephalexin and ERY conferred no benefit upon the hatch rate. Among fry that hatched from treated eggs, there was no increase in 15-d larval survival. However, fish that hatched from eggs treated with CAM, ERY, and TMP-SMX demonstrated enhanced survival at 360 d (51.2, 38.4, and 43.6%, respectively) and at 540 d (22.6, 6.8, and 20.2%, respectively); the untreated control had no survivors to those time points. All groups of eggs treated with antibiotics showed reductions in bacterial colony-forming units (CFUs) at 24 h posttreatment. At 120 h posttreatment, CEX-treated eggs had CFU counts similar to those of the control, whereas the TMP-SMX-treated eggs had the lowest CFU counts. Eggs treated with CAM and ERY had similar CFU counts, which were significantly reduced from the control counts. Larvae that were treated with CAM and TMP-SMX within 12 h posthatch showed enhanced 15-d survival (74% and 72%, respectively) in comparison with the control (56%). For pupfish rearing efforts in which antibiotic use is appropriate, CAM and TMP-SMX appear to provide the greatest benefit, particularly when applied to incubating eggs rather than to hatched larvae.

North American Journal of Aquaculture↗
USGS2016

Determination of habitat requirements for Apache Trout

The Apache Trout Oncorhynchus apache , a salmonid endemic to east-central Arizona, is currently listed as threatened under the U.S. Endangered Species Act. Establishing and maintaining recovery streams for Apache Trout and other endemic species requires determination of their specific habitat requirements. We built upon previous studies of Apache Trout habitat by defining both stream-specific and generalized optimal and suitable ranges of habitat criteria in three streams located in the White Mountains of Arizona. Habitat criteria were measured at the time thought to be most limiting to juvenile and adult life stages, the summer base flow period. Based on the combined results from three streams, we found that Apache Trout use relatively deep (optimal range = 0.15–0.32 m; suitable range = 0.032–0.470 m) pools with slow stream velocities (suitable range = 0.00–0.22 m/s), gravel or smaller substrate (suitable range = 0.13–2.0 [Wentworth scale]), overhead cover (suitable range = 26–88%), and instream cover (large woody debris and undercut banks were occupied at higher rates than other instream cover types). Fish were captured at cool to moderate temperatures (suitable range = 10.4–21.1°C) in streams with relatively low maximum seasonal temperatures (optimal range = 20.1–22.9°C; suitable range = 17.1–25.9°C). Multiple logistic regression generally confirmed the importance of these variables for predicting the presence of Apache Trout. All measured variables except mean velocity were significant predictors in our model. Understanding habitat needs is necessary in managing for persistence, recolonization, and recruitment of Apache Trout. Management strategies such as fencing areas to restrict ungulate use and grazing and planting native riparian vegetation might favor Apache Trout persistence and recolonization by providing overhead cover and large woody debris to form pools and instream cover, shading streams and lowering temperatures.

Arizona↗
USGS2016

Design and testing of a mesocosm-scale habitat for culturing the endangered Devils Hole Pupfish

aptive propagation of desert spring fishes, whether for conservation or research, is often difficult, given the unique and often challenging environments these fish utilize in nature. High temperatures, low dissolved oxygen, minimal water flow, and highly variable lighting are some conditions a researcher might need to recreate to simulate their natural environments. Here we describe a mesocosm-scale habitat created to maintain hybrid Devils Hole × Ash Meadows Amargosa Pupfish ( Cyprinodon diabolis × C. nevadensis mionectes ) under conditions similar to those found in Devils Hole, Nevada. This 13,000-L system utilized flow control and natural processes to maintain these conditions rather than utilizing complex and expensive automation. We designed a rotating solar collector to control natural sunlight, a biological reactor to consume oxygen while buffering water quality, and a reverse-daylight photosynthesis sump system to stabilize nighttime pH and swings in dissolved oxygen levels. This system successfully controlled many desired parameters and helped inform development of a larger, more permanent desert fish conservation facility at the U.S. Fish and Wildlife Service’s Ash Meadows National Wildlife Refuge, Nevada. For others who need to raise fish from unique habitats, many components of the scalable and modular design of this system can be adapted at reasonable cost.

North American Journal of Aquaculture↗
USGS2016

Stock assessment in inland fisheries: a foundation for sustainable use and conservation

Fisheries stock assessments are essential for science-based fisheries management. Inland fisheries pose challenges, but also provide opportunities for biological assessments that differ from those encountered in large marine fisheries for which many of our assessment methods have been developed. These include the number and diversity of fisheries, high levels of ecological and environmental variation, and relative lack of institutional capacity for assessment. In addition, anthropogenic impacts on habitats, widespread presence of non-native species and the frequent use of enhancement and restoration measures such as stocking affect stock dynamics. This paper outlines various stock assessment and data collection approaches that can be adapted to a wide range of different inland fisheries and management challenges. Although this paper identifies challenges in assessment, it focuses on solutions that are practical, scalable and transferrable. A path forward is suggested in which biological assessment generates some of the critical information needed by fisheries managers to make effective decisions that benefit the resource and stakeholders.

Reviews in Fish Biology and Fisheries↗
USGS2016

How well are you teaching one of the most important biological concepts for humankind? A call to action

We represent several generations of biology educators – with teaching experiences beginning in the 1940s and continuing to the present, from elementary school to graduate-level programs. We find the vast array of subjects that biology teachers can now cover both thrilling and mind-boggling. Depending on the grade level, units exist that focus on neurobiology, forensics, DNA analysis, biotechnology, marine biology, and a host of other topics. Although science teachers cover a potpourri of advanced topics, we must ask ourselves – no matter our biology-teaching responsibilities – how well we are teaching carrying capacity , one of the most fundamental biological concepts for our society, knowledge of which becomes more important every day. As biology teachers, most of you know that carrying capacity is defined as the maximum population an environment can sustain, given the amounts of food, habitat, and other resources available. Every environment – from your goldfish bowl to the local forest to planet Earth – can only sustain a set number (weight) of a particular species, based on available resources and space. Currently, most science classes teach …

The American Biology Teacher↗
USGS2015

A simple web-based tool to compare freshwater fish data collected using AFS standard methods

The American Fisheries Society (AFS) recently published Standard Methods for Sampling North American Freshwater Fishes. Enlisting the expertise of 284 scientists from 107 organizations throughout Canada, Mexico, and the United States, this text was developed to facilitate comparisons of fish data across regions or time. Here we describe a user-friendly web tool that automates among-sample comparisons in individual fish condition, population length-frequency distributions, and catch per unit effort (CPUE) data collected using AFS standard methods. Currently, the web tool (1) provides instantaneous summaries of almost 4,000 data sets of condition, length frequency, and CPUE of common freshwater fishes collected using standard gears in 43 states and provinces; (2) is easily appended with new standardized field data to update subsequent queries and summaries; (3) compares fish data from a particular water body with continent, ecoregion, and state data summaries; and (4) provides additional information about AFS standard fish sampling including benefits, ongoing validation studies, and opportunities to comment on specific methods. The web tool—programmed in a PHP-based Drupal framework—was supported by several AFS Sections, agencies, and universities and is freely available from the AFS website and fisheriesstandardsampling.org . With widespread use, the online tool could become an important resource for fisheries biologists.

Fisheries↗
USGS2015

Underwater videography outperforms above-water videography and in-person surveys for monitoring the spawning of Devils Hole Pupfish

The monitoring of threatened and endangered fishes in remote environments continues to challenge fisheries biologists. The endangered Devils Hole Pupfish Cyprinodon diabolis , which is confined to a single warm spring in Death Valley National Park, California–Nevada, has recently experienced record declines, spurring renewed conservation and recovery efforts. In February–December 2010, we investigated the timing and frequency of spawning in the species' native habitat by using three survey methods: underwater videography, above-water videography, and in-person surveys. Videography methods incorporated fixed-position, solar-powered cameras to record continuous footage of a shallow rock shelf that Devils Hole Pupfish use for spawning. In-person surveys were conducted from a platform placed above the water's surface. The underwater camera recorded more overall spawning throughout the year (mean ± SE = 0.35 ± 0.06 events/sample) than the above-water camera (0.11 ± 0.03 events/sample). Underwater videography also recorded more peak-season spawning (March: 0.83 ± 0.18 events/sample; April: 2.39 ± 0.47 events/sample) than above-water videography (March: 0.21 ± 0.10 events/sample; April: 0.9 ± 0.32 events/sample). Although the overall number of spawning events per sample did not differ significantly between underwater videography and in-person surveys, underwater videography provided a larger data set with much less variability than data from in-person surveys. Fixed videography was more cost efficient than in-person surveys (\$1.31 versus \$605 per collected data-hour), and underwater videography provided more usable data than above-water videography. Furthermore, video data collection was possible even under adverse conditions, such as the extreme temperatures of the region, and could be maintained successfully with few study site visits. Our results suggest that self-contained underwater cameras can be efficient tools for monitoring remote and sensitive aquatic ecosystems.

Nevada↗
USGS2015

Propagation of hybrid Devils Hole Pupfish × Ash Meadows Amargosa Pupfish

Recent censuses of Devils Hole Pupfish Cyprinodon diabolis revealed that fewer than 100 individuals currently remain in the wild. Captive propagation is among actions being considered to prevent their extinction, but no pure-strain Devils Hole Pupfish were available for broodstock. To help provide emergency information, we investigated techniques to propagate their most closely related relative, hybrid Devils Hole Pupfish C. diabolis × Ash Meadows Amargosa Pupfish C. nevadensis mionectes. We tested various temperatures and larval feeds with respect to egg production, larval survival, and growth. Larval survival and growth were similar from 24°C to 32°C and egg production peaked at static 28°C; however, reducing water temperatures to 23°C and then raising them to 28°C resulted in even higher production. Larvae fed infusoria, Rio Grande Silvery Minnow Chow (RGSM), or Zeigler larval diet (ZLD) had the highest survival (79.4, 71.6, and 73.4%, respectively), and those fed Otohime (OTO) had the lowest survival (60.8%), although OTO provided greatest (14 mm) 30-d growth. Supplementation of RGSM or ZLD with Artemia nauplii increased growth but decreased survival. Larval production was maximized by placing six spawning mops, constructed of yarn and tile, in each of four 437-L parental aquaria, stocked with 24 adult fish each (1:1 sex ratio) for 3 d, to attract adults and provide spawning substrate. A 30% water change conducted on the same day of mop placement lowered water temperature from 28°C to 23°C. Water temperature was raised back to 28°C over 48 h. After 3 d, mops were transferred to hatching aquaria that were held at 28°C and aerated until larval hatch. Although some differences likely exist in effective propagation techniques for hybrid and pure-strain Devils Hole Pupfish, these data help provide initial recommendations to aid recovery.

North American Journal of Aquaculture↗
USGS2015

Effectiveness of two commercial rotenone formulations in the eradication of virile crayfish Orconectes virillis

The virile or northern crayfish Orconectes virilis is an invasive species throughout much of the USA, damaging aquatic communities where it is introduced. Therefore, identification of effective methods for its eradication from areas in which it is unwanted is important. We studied the effectiveness of two commercial formulations of rotenone, Chem Fish Regular and CFT Legumine, for virile crayfish control. Although both formulations were effective for fish eradication, earlier observations by fisheries managers suggested that the relative effectiveness of the two formulations differs for crayfish. The only noteworthy difference between the formulations is that the former contains a synergist. In our first experiment, we tested each toxicant at the maximum labeled dosage (5 ppm) and found CFT Legumine to be 100% ineffective (0% mortality), while the Chem Fish Regular treatment resulted in 12.5% mortality. After we deemed Chem Fish Regular to be the only toxicant with any effectiveness against virile crayfish, we tested concentrations from 5 to 50 ppm and found 10 times the maximum labeled dosage (50 ppm rotenone) was needed to kill all virile crayfish. Because crayfish burrow and can leave water, and because 100% eradication is usually desired, rotenone applied at the labeled rates will not be effective for crayfish control. However, treating a body of water with CFT Legumine to eradicate invasive fish while leaving desirable crayfish unharmed is possible.

North American Journal of Fisheries Management↗
USGS2015

Effects of effects of suspended sediment on early-life stage survival of Yaqui chub, an endangered USA–Mexico borderlands cyprinid

High levels of total suspended sediment (TSS) can have negative consequences on fishes, such as altering food supply, lowering food acquisition, clogging gills, and disrupting reproduction. While effects of TSS on salmonids and estuarine fish are well studied, less is known about possible negative impacts of suspended sediment on desert fishes. Several imperiled desert fishes inhabit streams and springs near the U.S.–Mexico border and are potentially threatened by increased sediment loads from borderlands activity such as livestock grazing, road building, illegal traffic, and law enforcement patrols. One such species is the Yaqui Chub Gila purpurea, a federally listed endangered cyprinid. We exposed Yaqui Chub embryos and fry (mean TL = 12.6 mm; SE = 0.42) to a range of TSS levels commonly found in one of the only streams they inhabit, Black Draw, which crosses the Arizona–Mexico border. We tested effects of 0; 300; 500; 1,000; 5,000; and 10,000 mg/L TSS loads on fry and embryos over a 5-d period in three replicate containers for each treatment. Fifty percent hatch rate (i.e., median lethal concentration, LC50) was 3,977 mg/L for embryos. The LC50 for fry (concentration at which half died) was 8,372 mg/L after 12 h of exposure; however, after 5-d exposure, LC50 leveled at 1,197 mg/L. The TL of fry did not change significantly in any treatment over the 5-d period. Suspended sediment in Black Draw reached concentrations lethal to Yaqui Chub embryo and fry during four floods in 2012. Although some desert fishes have evolved in rivers and streams subject to elevated TSS and are tolerant to high TSS concentrations, other fish species are less tolerant and may be impacted by land practices which increase erosion into stream systems. Management of critically endangered desert fishes should include considerations of the effects of increased suspended sediment.

Transactions of the American Fisheries Society↗
USGS2014

Book review: Ecology of North American freshwater fishes

This book will be important in courses for upper undergraduates studying fish ecology or for graduate students. However, it will also be an excellent reference for the fishery manager who asks ‘Why does this fish do that?’. With the wealth of great information contained in Ross’ book, chances are an answer will be found. Review info: Ecology of North American freshwater fishes. Edited by Stephen T. Ross, 2013. ISBN: 978-0520249455, 408 pp.

Journal of Fish Biology↗