Adding value to monitoring efforts with environmental DNA
No abstract available.
Idaho, Montana, Wyoming↗
Geology topics
Adam J. Sepulveda
Publications and source records attributed to Adam J. Sepulveda.
A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae , which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.
Conservation Genetics Resources↗
Evaluating species-specific changes in hydrologic regimes: an iterative approach for salmonids in the Greater Yellowstone Area (USA)
Despite the importance of hydrologic regimes to the phenology, demography, and abundance of fishes such as salmonids, there have been surprisingly few syntheses that holistically assess regional, species-specific trends in hydrologic regimes within a framework of climate change. Here, we consider hydrologic regimes within the Greater Yellowstone Area in the Rocky Mountains of western North America to evaluate changes in hydrologic metrics anticipated to affect salmonids, a group of fishes with high regional ecological and socioeconomic value. Our analyses assessed trends across different sites and time periods (1930–, 1950–, and 1970–2015) as means to evaluate spatial and temporal shifts. Consistent patterns emerged from our analyses indicating substantial shifts to (1) earlier peak discharge events; (2) reductions of summer minimum streamflows; (3) declines in the duration of river ice; and (4) decreases in total volume of water. We found accelerated trends in hydrologic change for the 1970–2015 period, with an average peak discharge 7.5 days earlier, 27.5% decline in summer minimum streamflows, and a 15.6% decline in the annual total volume of water (1 October–September 30) across sites. We did observe considerable variability in magnitude of change across sites, suggesting different levels of vulnerability to a changing climate. Our analyses provide an iterative means for assessing climate predictions and an important step in identifying the climate resilience of landscapes.
Greater Yellowstone Area↗
Terrestrial–aquatic linkages in spring-fed and snowmelt-dominated streams
The importance of trophic linkages between aquatic and terrestrial ecosystems is predicted to vary as a function of subsidy quantity and quality relative to in situ resources. To test this prediction, I used multi-year diet data from Bonneville cutthroat trout Oncorhynchus clarki Utah in spring-fed and snowmelt-driven streams in the high desert of western North America. I documented that trout in spring-fed streams consumed more (number and weight) aquatic than terrestrial invertebrates, while trout in snowmelt-driven streams consumed a similar number of both prey types but consumed more terrestrial than aquatic invertebrates by weight. Trout in spring-fed streams consumed more aquatic invertebrates than trout in snowmelt streams and trout consumed more terrestrial invertebrates in snowmelt than in spring-fed streams. Up to 93% of trout production in spring-fed streams and 60% in snowmelt streams was fueled by aquatic invertebrates, while the remainder of trout production in each stream type was from terrestrial production. I found that the biomass and occurrence of consumed terrestrial invertebrates were not related to our measures of in situ resource quality or quantity in either stream type. These empirical data highlight the importance of autotrophic-derived production to trout in xeric regions.
Idaho↗
Guest editorial: Aquatic science in the Northwest
In recent years, Northwest Science has seen a significant increase in the number of submissions representing aquatic science. Our region is punctuated by aquatic systems. The current issue in particular, presents a number of new aquatic science contributions. Accordingly, Northwest Science invited the authors of this guest editorial to address the question, why is aquatic science so important in the Northwest?
Northwest Science↗
Introduced American Bullfrog distribution and diets in Grand Teton National Park
Introduced American Bullfrogs (Lithobates catesbeianus) have been present in Grand Teton National Park since approximately the 1950s, but little is known about their distribution and potential impacts. In this study, we surveyed the current bullfrog distribution and spatial overlap with sympatric native amphibians in the park, and characterized post-metamorphic bullfrog diets from July – September 2015. Despite surveys in multiple large rivers and floodplain habitats, we only documented bullfrogs in a geothermal pond and 5 km of stream channel immediately downstream of this pond. In these waters, bullfrogs overlapped with native amphibians at the downstream end of their distribution, and we did not document native amphibians in bullfrog stomach contents. Larger bullfrogs (SVL ≥ 96 mm) primarily consumed native rodents (especially meadow voles, Microtus pennsylvanicus ), while smaller bullfrogs frequently consumed native invertebrates and less frequently consumed non-native invertebrates and fish. Taken together, these data indicate that the distribution and implications of the bullfrog invasion in Grand Teton National Park are currently localized to a small area, so these bullfrogs should therefore be vulnerable to eradication.
Wyoming↗
Potential of environmental DNA to evaluate Northern pike ( Esox lucius ) eradication efforts: An experimental test and case study
Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike ( Esox lucius ) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water.
PLoS ONE↗
Influence of climate drivers on colonization and extinction dynamics of wetland-dependent species
Freshwater wetlands are particularly vulnerable to climate change. Specifically, changes in temperature, precipitation, and evapotranspiration (i.e., climate drivers) are likely to alter flooding regimes of wetlands and affect the vital rates, abundance, and distributions of wetland-dependent species. Amphibians may be among the most climate-sensitive wetland-dependent groups, as many species rely on shallow or intermittently flooded wetland habitats for breeding. Here, we integrated multiple years of high-resolution gridded climate and amphibian monitoring data from Grand Teton and Yellowstone National Parks to explicitly model how variations in climate drivers and habitat conditions affect the occurrence and breeding dynamics (i.e., annual extinction and colonization rates) of amphibians. Our results showed that models incorporating climate drivers outperformed models of amphibian breeding dynamics that were exclusively habitat based. Moreover, climate-driven variation in extinction rates, but not colonization rates, disproportionately influenced amphibian occupancy in monitored wetlands. Long-term monitoring from national parks coupled with high-resolution climate data sets will be crucial to describing population dynamics and characterizing the sensitivity of amphibians and other wetland-dependent species to climate change. Further, long-term monitoring of wetlands in national parks will help reduce uncertainty surrounding wetland resources and strengthen opportunities to make informed, science-based decisions that have far-reaching benefits.
Grand Teton National Park, Yellowstone National Pa↗
Genetic reconstruction of a bullfrog invasion to elucidate vectors of introduction and secondary spread
Reconstructing historical colonization pathways of an invasive species is critical for uncovering factors that determine invasion success and for designing management strategies. The American bullfrog ( Lithobates catesbeianus ) is endemic to eastern North America, but now has a global distribution and is considered to be one of the worst invaders in the world. In Montana, several introduced populations have been reported, but little is known of their sources and vectors of introduction and secondary spread. We evaluated the genetic composition of introduced populations at local (Yellowstone River floodplain) and regional (Montana and Wyoming) scales in contrast to native range populations. Our objectives were to (1) estimate the number of introductions, (2) identify probable native sources, (3) evaluate genetic variation relative to sources, and (4) characterize properties of local- and regional-scale spread. We sequenced 937 bp of the mitochondrial cytochrome b locus in 395 tadpoles collected along 100 km of the Yellowstone River, from three additional sites in MT and a proximate site in WY. Pairwise Φ ST revealed high divergence among nonnative populations, suggesting at least four independent introductions into MT from diverse sources. Three cyt b haplotypes were identical to native haplotypes distributed across the Midwest and Great Lakes regions, and AMOVA confirmed the western native region as a likely source. While haplotype ( H d = 0.69) and nucleotide diversity ( π = 0.005) were low in introduced bullfrogs, the levels of diversity did not differ significantly from source populations. In the Yellowstone, two identified haplotypes implied few introduction vectors and a significant relationship between genetic and river distance was found. Evidence for multiple invasions and lack of subsequent regional spread emphasizes the importance of enforcing legislation prohibiting bullfrog importation and the need for continuing public education to prevent transport of bullfrogs in MT. More broadly, this study demonstrates how genetic approaches can reveal key properties of a biological invasion to inform management strategies.
Montana↗
Does water chemistry limit the distribution of New Zealand mud snails in Redwood National Park?
New Zealand mud snails (NZMS) are exotic mollusks present in many waterways of the western United States. In 2009, NZMS were detected in Redwood Creek in Redwood National Park, CA. Although NZMS are noted for their ability to rapidly increase in abundance and colonize new areas, after more than 5 years in Redwood Creek, their distribution remains limited to a ca. 300 m reach. Recent literature suggests that low specific conductivity and environmental calcium can limit NZMS distribution. We conducted laboratory experiments, exposing NZMS collected from Redwood Creek to both natural waters and artificial treatment solutions, to determine if low conductivity and calcium concentration limit the distribution of NZMS in Redwood National Park. For natural water exposures, we held NZMS in water from their source location (conductivity 135 μS/cm, calcium 13 mg/L) or water from four other locations in the Redwood Creek watershed encompassing a range of conductivity (77–158 μS/cm) and calcium concentration (<5–13 mg/L). For exposures in treatment solutions, we manipulated both conductivity (range 20–200 μS/cm) and calcium concentration (range <5–17.5 mg/L) in a factorial design. Response variables measured included mortality and reproductive output. Adult NZMS survived for long periods (>4 months) in the lowest conductivity waters from Redwood Creek and all but the lowest-conductivity treatment solutions, regardless of calcium concentration. However, reproductive output was very low in all natural waters and all low-calcium treatment solutions. Our results suggest that water chemistry may inhibit the spread of NZMS in Redwood National Park by reducing their reproductive output.
California↗
Effect of electric barrier on passage and physical condition of juvenile and adult rainbow trout
Electric barriers can inhibit passage and injure fish. Few data exist on electric barrier parameters that minimize these impacts and on how body size affects susceptibility, especially to nontarget fish species. The goal of this study was to determine electric barrier voltage and pulse-width settings that inhibit passage of larger bodied rainbow trout Oncorhynchus mykiss (215–410 mm fork length) while allowing passage of smaller bodied juvenile rainbow trout (52–126 mm) in a static laboratory setting. We exposed rainbow trout to 30-Hz pulsed-direct current voltage gradients (0.00–0.45 V cm −1 ) and pulse widths (0.0–0.7 ms) and recorded their movement, injury incidence, and mortality. No settings tested allowed all juveniles to pass while impeding all adult passage. Juvenile and adult rainbow trout avoided the barrier at higher pulse widths, and fewer rainbow trout passed the barrier at 0.7-ms pulse width compared to 0.1 ms and when the barrier was turned off. We found no effect of voltage gradient on fish passage. No mortality occurred, and we observed external bruising in 5 (7%) juvenile rainbow trout and 15 (21%) adult rainbow trout. This study may aid managers in selecting barrier settings that allow for increased juvenile passage.
Journal of Fish and Wildlife Management↗
Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout ( Salvelinus fontinalis ) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.
Montana↗
Ecological relevance of current water quality assessment unit designations in impaired rivers
Managers often nest sections of water bodies together into assessment units (AUs) to monitor and assess water quality criteria. Ideally, AUs represent an extent of waters with similar ecological, watershed, habitat and land-use conditions and no overlapping characteristics with other waters. In the United States, AUs are typically based on political or hydrologic boundaries rather than on ecologically relevant features, so it can be difficult to detect changes in impairment status. Our goals were to evaluate if current AU designation criteria of an impaired water body in southeastern Idaho, USA that, like many U.S. waters, has three-quarters of its mainstem length divided into two AUs. We focused our evaluation in southeastern Idaho's Portneuf River, an impaired river and three-quarters of the river is divided into two AUs. We described biological and environmental conditions at multiple reaches within each AU. We used these data to (1) test if variability at the reach-scale is greater within or among AUs and, (2) to evaluate alternate AU boundaries based on multivariate analyses of reach-scale data. We found that some biological conditions had greater variability within an AU than between AUs. Multivariate analyses identified alternative, 2- and 3-group, AUs that reduced this variability. Our results suggest that the current AU designations in the mainstem Portneuf River contain ecologically distinct sections of river and that the existing AU boundaries should be reconsidered in light of the ecological conditions measured at the reach scale. Variation in biological integrity within designated AUs may complicate water quality and biological assessments, influence management decisions or affect where monitoring or mitigation resources are directed.
Idaho↗
Potential utility of environmental DNA for early detection of Eurasian watermilfoil ( Myriophyllum spicatum )
Considering the harmful and irreversible consequences of many biological invasions, early detection of an invasive species is an important step toward protecting ecosystems (Sepulveda et al. 2012). Early detection increases the probability that suppression or eradication efforts will be successful because invasive populations are small and localized (Vander Zanden et al. 2010). However, most invasive species are not detected early because current tools have low detection probabilities when target species are rare and the sampling effort required to achieve acceptable detection capabilities with current tools is seldom tractable (Jerde et al. 2011). As a result, many invasive species go undetected until they are abundant and suppression efforts become costly. Novel DNA-based surveillance tools have recently revolutionized early detection abilities using environmental DNA (eDNA) present in the water (Darling and Mahon 2011, Bohmann et al. 2014). In brief, eDNA monitoring enables the identification of organisms from DNA present and collected in water samples. Aquatic and semiaquatic organisms release DNA contained in sloughed, damaged, or partially decomposed tissue and waste products into the water and molecular techniques allow this eDNA in the water column to be identified from simple and easy-tocollect water samples (Darling and Mahon 2011). Despite limited understanding of the production, persistence, and spread of DNA in water (Barnes et al. 2014), eDNA monitoring has been applied not only to invasive species (Jerde et al. 2011), but also to species that are rare, endangered, or highly elusive (Spear et al. 2014). However, most eDNA research and monitoring has focused on detection of invertebrates and vertebrates and less attentionhas been given to developing eDNA techniques for detecting aquatic invasive plants. Eurasian watermilfoil (EWM; Myriophyllum spicatum L.) is an invasive species for which improved early detection would be particularly helpful. Advanced EWM invasions have negative impacts on native biodiversity, recreational boating, fishing, and other types of aquatic tourism (e.g., Eiswerth et al. 2000). On a broader scale, EWM can also be harmful to man-made aquatic infrastructure, such as hydroelectric dams. If an EWM invasion can be detected in an early stage where eradication is still a possibility, many of these negative consequences can be limited or prevented altogether (e.g., Madsen et al. 2002). The purpose of this research was to develop and validate a traditional polymerase chain reaction (PCR) assay for the detection of pure and hybridized EWM DNA using both laboratory and field experiments. We performed a pilot experiment in outdoor tanks to determine the basic functionality and sensitivity of the assay. Following this initial test, we collected field samples from Michigan and Montana lakes with and without known EWM populations. Taken together, our findings suggest that eDNA techniques have potential to be a useful strategy for the early detection of EWM.
Journal of Aquatic Plant Management↗
The shifting climate portfolio of the Greater Yellowstone Area
Knowledge of climatic variability at small spatial extents (< 50 km) is needed to assess vulnerabilities of biological reserves to climate change. We used empirical and modeled weather station data to test if climate change has increased the synchrony of surface air temperatures among 50 sites within the Greater Yellowstone Area (GYA) of the interior western United States. This important biological reserve is the largest protected area in the Lower 48 states and provides critical habitat for some of the world’s most iconic wildlife. We focused our analyses on temporal shifts and shape changes in the annual distributions of seasonal minimum and maximum air temperatures among valley-bottom and higher elevation sites from 1948–2012. We documented consistent patterns of warming since 1948 at all 50 sites, with the most pronounced changes occurring during the Winter and Summer when minimum and maximum temperature distributions increased. These shifts indicate more hot temperatures and less cold temperatures would be expected across the GYA. Though the shifting statistical distributions indicate warming, little change in the shape of the temperature distributions across sites since 1948 suggest the GYA has maintained a diverse portfolio of temperatures within a year. Spatial heterogeneity in temperatures is likely maintained by the GYA’s physiographic complexity and its large size, which encompasses multiple climate zones that respond differently to synoptic drivers. Having a diverse portfolio of temperatures may help biological reserves spread the extinction risk posed by climate change.
Montana, Wyoming↗
Evaluation of a fine sediment removal tool in spring-fed and snowmelt driven streams
The accumulation of fine-grained sediments impairs the structure and function of streams, so removing fine sediments may be required to achieve restoration objectives. There has been little work on methods of removing excess sediment or on the efficacy of the methods. We used a 4-year before-after-control-impact design in southeastern Idaho streams to test a fine sediment removal system (FSRS) manufactured by Streamside Environmental LLC. The FSRS agitates fine sediment in the substrate with clean pump water and then vacuums the sediment out of the stream with a second pump. Our objectives were: 1) to test if the FSRS can selectively remove fine sediment; 2) to monitor the bio-physical responses in FSRS treated and downstream waters; and 3) to compare the bio-physical responses to the FSRS in spring-fed and snowmelt driven stream reaches. The FSRS removed ~ 14 metric tons of sediment from the two treated reaches. More than 90% of this sediment was < 2 mm, indicating that the FSRS selected for fine sediment in both stream types. Sustained effects of removing this sediment were confined to substrate improvements in treated reaches. Embeddedness in the spring-fed reach decreased and subsurface grain size in spring-fed and snowmelt driven reaches increased. We did not detect any sustained invertebrate or fish responses in treated reaches or any detrimental bio-physical responses in downstream waters. These results indicate that the FSRS reduced fine sediment levels but sediment removal did not reverse the impacts of sediment accumulation to stream biota within our monitoring time frame.
Ecological Restoration↗
Invasion of American bullfrogs along the Yellowstone River
The American bullfrog ( Lithobates catesbeianus ) is a globally distributed invasive species that was introduced to the Yellowstone River floodplain of Montana. Knowledge about floodplain habitat features that allow for bullfrog persistence and spread will help identify effective control strategies. We used field surveys in 2010, 2012 and 2013 to describe bullfrog spread in the Yellowstone River floodplain and the habitat features that are associated with bullfrog occupancy and colonization. Bullfrogs in our study area expanded from ~ 60 km in 2010 to 106 km in 2013, and are spreading to up- and downstream habitats. The number of breeding sites (i.e., presence of bullfrog eggs or larvae) increased from 12 sites in 2010 to 45 sites in 2013. We found that bullfrogs were associated with deeper waters, emergent vegetation and public-access sites, which are habitat features that characterize permanent waters and describe human-mediated introductions. Control strategies that reduce the hydroperiod of breeding sites may help to limit bullfrog persistence and spread, while an increase in public outreach and education may help prevent further bullfrog introductions at public-access sites.
Montana↗
Fall and winter movements and habitat use of the introduced American bullfrog ( Lithobates catesbeiana ) in a Montana pond
American Bullfrogs (Lithobates catesbeianus) have been introduced across the globe, including in many northern latitude habitats where wetlands are ice-covered for part of the year. Because bullfrogs are less mobile at low temperatures, greater knowledge about their overwintering habitat may provide additional opportunities for control. Here, we described fall and early-winter movements and habitat associations for introduced juvenile bullfrogs in a pond within the Yellowstone River corridor near Billings, Montana, USA. We attached radio-transmitters to 13 juvenile bullfrogs and located individuals from 28 August to 10 December 2014. Bullfrogs moved greater distances in late summer and early autumn, and later during brief warming periods. Collectively, all bullfrog locations were distributed across a 15,384 m2 area during the active season, but contracted to a 130 m2 area in the east cove of the pond by the time the study site froze over. Our research provides evidence that managers in northern latitude regions like Montana may be able to use the long, cold winters to their advantage because the site-specific distributions of introduced bullfrogs contracted as temperatures decreased.
Montana↗