It’s complicated…Environmental DNA as a predictor of trout and char abundance in streams

2020 ◽  
Author(s):  
Adam J. Sepulveda ◽  
Robert Al-Chokhachy ◽  
Matthew B Laramie ◽  
Kyle Crapster ◽  
W Ladd Knotek ◽  
...  
Keyword(s):  
Cutthroat Trout ◽  
Environmental Dna ◽  
Fish Abundance ◽  
Bull Trout ◽  
Intermountain West ◽  
Salvelinus Confluentus ◽  
Oncorhynchus Clarkii ◽  
Habitat Monitoring ◽  
Abundance Estimates ◽  
Random Site

The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dynamics. We therefore evaluated the relationships between eDNA concentration and abundance of bull trout (Salvelinus confluentus), westslope cutthroat trout (Oncorhynchus clarkii lewisi) and rainbow trout (O. mykiss) at 42 stream sites in the Intermountain West (USA and CAN) and tested if accounting for site-specific habitat attributes improved the accuracy of fish abundance estimates. eDNA concentrations were positively associated with fish abundance but these relationships varied by species and site and there was considerable variation unaccounted for. Random site-level differences explained much of this variation, but specific habitat attributes of those sites explained relatively small amounts of this variation. Our results underscore that either eDNA sampling or environmental characterization will require further refinement before eDNA can be used reliably to estimate fish abundance in streams.

scholarly journals Using forensic geochemistry via fish otoliths to investigate an illegal fish introduction

2018 ◽  
Vol 75 (11) ◽  
pp. 1778-1783 ◽  
Author(s):  
Samuel L. Bourret ◽  
Niall G. Clancy
Keyword(s):  
Cutthroat Trout ◽  
Bull Trout ◽  
Introduced Fish ◽  
Fish Introduction ◽  
Oncorhynchus Clarkii ◽  
Ecosystem Impacts ◽  
Swan Lake ◽  
Resource Managers ◽  
Species Of Conservation Concern ◽  
Fish Otoliths

Illegal fish introductions create some of the most challenging problems for resource managers because of their potential to harm existing recreational fisheries and their impact on species of conservation concern. Determining the origin of a suspected illegal fish introduction can aid managers in preventing the colonization and subsequent ecosystem impacts of introduced species. In this study, we used forensic geochemistry via fish otoliths to investigate an illegal walleye (Sander vitreus) introduction in Swan Lake, Montana, which provides critical habitat for threatened bull trout (Salvelinus confluentus) and native westslope cutthroat trout (Oncorhynchus clarkii). Core to edge geochemical profiles of 87Sr/86Sr and Sr/Ca ratios in the walleye otoliths revealed that these fish had been introduced to Swan Lake within the past growing season, and their geochemical signature matched that of walleye sampled from Lake Helena, Montana, located 309 road kilometres away. This research highlights application of a tool fisheries managers can use to identify the natal waterbody source of illegally introduced fish.

A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)

2014 ◽  
Vol 6 (2) ◽  
pp. 283-284 ◽  
Author(s):  
Taylor M. Wilcox ◽  
Michael K. Schwartz ◽  
Kevin S. McKelvey ◽  
Michael K. Young ◽  
Winsor H. Lowe
Keyword(s):  
Dna Detection ◽  
Environmental Dna ◽  
Bull Trout ◽  
Salvelinus Confluentus ◽  
Blocking Primer

scholarly journals An improved environmental DNA assay for bull trout (Salvelinus confluentus) based on the ribosomal internal transcribed spacer I

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0206851 ◽  
Author(s):  
Joseph C. Dysthe ◽  
Thomas W. Franklin ◽  
Kevin S. McKelvey ◽  
Michael K. Young ◽  
Michael K. Schwartz
Keyword(s):  
Internal Transcribed Spacer ◽  
Environmental Dna ◽  
Bull Trout ◽  
Salvelinus Confluentus ◽  
Dna Assay

Influence of water temperature and biotic interactions on the distribution of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) in a population stronghold under climate change

2020 ◽  
Author(s):  
Kadie B. Heinle ◽  
Lisa A. Eby ◽  
Clint C. Muhlfeld ◽  
Amber C. Steed ◽  
Leslie A. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Climate Adaptation ◽  
Cutthroat Trout ◽  
Stream Temperature ◽  
High Elevation ◽  
Suitable Habitat ◽  
Bull Trout ◽  
Westslope Cutthroat Trout ◽  
Oncorhynchus Clarkii ◽  
Species Response

Climate warming is expected to have substantial impacts on native trout across the Rocky Mountains, but there is little understanding of how these changes affect future distributions of co-occurring native fishes within population strongholds. We used mixed-effects logistic regression to investigate the role of abiotic (e.g., temperature) and biotic factors (Bull Trout presence, Salvelinus confluentus) on distributions of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi; WCT) in the North Fork Flathead River, USA and Canada. The probability of WCT presence increased with stream temperature and decreased with channel gradient and Bull Trout presence, yet the effect of Bull Trout was reduced with increasing pool densities. Combining this model with spatially-explicit stream temperature projections, we predict a 29% increase in suitable habitat under high emissions through 2075, with gains at mid-elevation sites predicted to exceed Bull Trout thermal tolerances and high-elevation sites expected to become more thermally suitable for WCT. Our study illustrates the importance of considering abiotic and biotic drivers to assess species response to climate change, helping to guide local scale climate adaptation and management.

Potential future climate effects on mountain hydrology, stream temperature, and native salmonid life history

2014 ◽  
Vol 71 (2) ◽  
pp. 189-202 ◽  
Author(s):  
Ryan J. MacDonald ◽  
Sarah Boon ◽  
James M. Byrne ◽  
Mike D. Robinson ◽  
Joseph B. Rasmussen
Keyword(s):  
Cutthroat Trout ◽  
Stream Temperature ◽  
Climate Impacts ◽  
Future Climate ◽  
Bull Trout ◽  
Westslope Cutthroat Trout ◽  
Environmental Pressures ◽  
Oncorhynchus Clarkii ◽  
Thermal Regimes ◽  
Native Salmonids

Native salmonids of western North America are subject to many environmental pressures, most notably the effects of introduced species and environmental degradation. To better understand how native salmonids on the eastern slopes of the Canadian Rocky Mountains may respond to future changes in climate, we applied a process-based approach to hydrologic and stream temperature modelling. This study demonstrates that stream thermal regimes in western Alberta, Canada, may only warm during the summer period, while colder thermal regimes during spring, fall, and winter could result from response to earlier onset of spring freshet. Model results of future climate impacts on hydrology and stream temperature are corroborated by an intercatchment comparison of stream temperature, air temperature, and hydrological conditions. Earlier fry emergence as a result of altered hydrological and thermal regimes may favour native westslope cutthroat trout (Oncorhynchus clarkii lewisii) in isolated headwater streams. Colder winter stream temperatures could result in longer incubation periods for native bull trout (Salvelinus confluentus) and limit threatened westslope cutthroat trout habitat.

scholarly journals Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

2020 ◽  
Author(s):  
C. Di Muri ◽  
L.L. Handley ◽  
C.W. Bean ◽  
J. Li ◽  
G. Peirson ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Quantitative Information ◽  
Fish Abundance ◽  
Fish Diversity ◽  
Natural Systems ◽  
Abundance Estimates ◽  
Dna Metabarcoding ◽  
Dna Capture ◽  
Cost Efficient ◽  
Number Of Individuals

AbstractThe sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed.Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals.eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used.This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.

Seasonal and diel changes in habitat use by juvenile bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in a mountain stream

1998 ◽  
Vol 76 (5) ◽  
pp. 783-790 ◽  
Author(s):  
Joseph L Bonneau ◽  
Dennis L Scarnecchia
Keyword(s):  
Habitat Use ◽  
Cutthroat Trout ◽  
Mountain Stream ◽  
Oncorhynchus Clarki ◽  
Bull Trout ◽  
Salvelinus Confluentus ◽  
Lower Velocity ◽  
Wide Range ◽  
Bed Stability ◽  
Velocity Water

Habitat use by juvenile bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in Trestle Creek, Idaho, changed seasonally and dielly. Both cutthroat and bull trout selected pools over riffles in both summer and winter. Both species used a wide range of depths at night but were absent from shallow water (<15 cm) during the day in summer and winter. During summer, juveniles of both species occupied areas of lower velocity water at night than during the day. Both species also occupied lower velocity water during winter days than summer days. During winter days, juvenile bull trout were located below or directly on cobble substrate, whereas cutthroat trout often formed aggregations suspended in the water column of large pools. Both species were more closely associated with cover during the day, and made the greatest use of cover during winter days. Land management activities resulting in decreased pool habitat, instream cover, and stream-bed stability may be especially detrimental to bull trout and cutthroat trout in winter.

Predicting cutthroat trout (Oncorhynchus clarkii) abundance in high-elevation streams: revisiting a model of translocation success

2005 ◽  
Vol 62 (10) ◽  
pp. 2399-2408 ◽  
Author(s):  
Michael K Young ◽  
Paula M Guenther-Gloss ◽  
Ashley D Ficke
Keyword(s):  
Population Size ◽  
Habitat Complexity ◽  
Cutthroat Trout ◽  
High Elevation ◽  
Stream Length ◽  
Oncorhynchus Clarkii ◽  
Abundance Estimates ◽  
Population Sizes ◽  
Bankfull Width ◽  
Habitat Variables

Assessing viability of stream populations of cutthroat trout (Oncorhynchus clarkii) and identifying streams suitable for establishing populations are priorities in the western United States, and a model was recently developed to predict translocation success (as defined by an index of population size) of two subspecies based on mean July water temperature, pool bankfull width, and deep pools counts. To determine whether the translocation model applied to streams elsewhere with more precise abundance estimates, we examined the relation between electrofishing-based estimates of cutthroat trout abundance and these habitat variables plus occupied stream length. The preferred model was (population size)1/2 = 0.00508(stream length (m)) + 5.148 (N = 31). In contrast, a model based on data from the original translocation model included stream temperature and deep pool counts as variables. Differences in models appear to largely have a methodological rather than biological basis. Additional habitat coupled with increased habitat complexity may account for the form of the abundance – stream length relation in the electrofishing-based model. Model-derived estimates imply that many cutthroat trout populations are below thresholds associated with reduced risk of extinction. We believe that this model can reduce uncertainty about projected population sizes when selecting streams for reintroductions or evaluating unsampled streams.

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