| 1. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 2. |
- Bowes, Rachel E., et al.
(författare)
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Cobble substrate in a surface bypass reduces bypass acceptance by common roach Rutilus rutilus
- 2021
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Ingår i: Ecological Engineering. - : Elsevier. - 0925-8574 .- 1872-6992. ; 172
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Tidskriftsartikel (refereegranskat)abstract
- Historically, ecological engineered solutions for fish passage across anthropogenic barriers in rivers has mainly focused on facilitating upstream passage for long-migrating diadromous fish, such as salmonids. More recently, passage solutions have shifted their focus to a more holistic ecological perspective, allowing passage for species with different swimming capacity, both upstream and downstream. This experiment investigated whether the addition of cobble in the passageway of a surface bypass could facilitate downstream movement of a cyprinid fish, the common roach Rutilus rutilus. Surface bypasses were constructed in large experimental flumes and roach were released into the flumes and monitored for bypass passage using PIT-telemetry through 11-h night-trials. Behavior was scored using four continuously-recording video cameras at the bypass construction. There was a negative effect of substrate-treatment on the passage rate through the bypass. The majority of the fish in the No substrate treatment had successfully passed within 4 h, while a lesser proportion of the fish in the Substrate treatment had done so (additional fish in the latter treatment passed later in the trials). Fish exposed to cobble substrate in the bypass passageway showed more avoidance-like behaviors at the ramp section of the bypass and tended to return back upstream more often than the fish in the no-substrate control trials. When reaching the passageway, the substrate-exposed fish expressed no behaviors that could be indicative of reduced passage success, as compared to controls. We conclude that passage was not hindered by the presence of cobble substrate, but passage was delayed due to avoidance behavior at the bypass ramp when cobble substrate was present. Based on these results, the addition of cobble substrate in a surface bypass cannot be recommended as a measure to facilitate the downstream passage performance of the common roach through surface bypasses.
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| 3. |
- Bowes, Rachel E., et al.
(författare)
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Consequences of employing amino acid vs. bulk-tissue, stable isotope analysis : a laboratory trophic position experiment
- 2015
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Ingår i: Ecosphere. - : John Wiley & Sons. - 2150-8925 .- 2150-8925. ; 6:1, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- An important metric of environmental health is food web structure because it reflects species richness, natural history diversity, and resource availability. While bulk-tissue stable isotope analysis has proven valuable for food web studies, field conditions may severely restrict its use and data can be quite variable. Amino acid stable isotope analysis potentially reduces this variability, in part by eliminating the need for signatures near the trophic base because a single top consumer contains both the primary producer signature (constant phenylalanine signature) and information reflecting number of trophic transfers (a progressively increasing d15N signature of glutamic acid). To evaluate the ecological sensitivity and cost/benefits of the techniques, we conducted a laboratory food chain experiment with four trophic levels. Water fleas (Daphnia magna) were cultured on a diet of powdered algae and then fed daily to guppies (Poecilia reticulata) for three months. These invertivorous fishes were then consumed by piscivororus bluegill sunfishes (Lepomis macrochirus) for a subsequent three months. All members of the food web were analyzed for 15N values and degree of fractionation using both bulk-tissue and amino acid stable isotope techniques. Our experiment demonstrated that the amino acid technique more accurately identified the true trophic position (TP) and food chain length (FCL ¼ maximum TP) with significantly less variability around mean values for each consumer trophic level. Moreover, use of amino acids requires significantly fewer replicates to identify TP. We discuss here the relative advantages and disadvantages of both approaches for determining TP and FCL and recommend that investigators switch as soon as possible to the amino acid isotope technique for determining FCL.
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| 4. |
- Bowes, Rachel E., et al.
(författare)
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Landscape features control river's confluences water quality and tributary fish composition
- 2023
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Ingår i: Rivers Research and Applications. - : John Wiley & Sons. - 1535-1459 .- 1535-1467. ; 39:6, s. 1025-1036
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Tidskriftsartikel (refereegranskat)abstract
- Rivers networks represent hierarchical dendritic habitats within terrestrial landscapes and differences in connectivity and land use influence dispersal, and consequently biodiversity patterns. We, therefore, measured variation in water chemistry and fish abundance and related these to a number of landscape characteristics (e.g., wetland, urban, wooded, and agricultural) in the River Klaralven and its 30 permanently flowing tributaries. We hypothesized that these environmental attributes would differ between tributary and main stem habitat and that these differences would be driven by landscape attributes including land use. We found considerable intertributary variation in temperature and nutrient levels, and between the tributaries and the main stem. Generally, water temperature was lower in the tributaries, whereas nutrient levels were higher in the tributaries. The lower water temperature has implications for coldwater fishes, and we found two fishes, burbot and lamprey, associated with coldwater tributaries. We also found an inverse relationship between water quality and anthropogenic land use. Protecting tributaries with low anthropogenic impact will likely become increasingly important with ongoing global warming as they can function as thermal refugia for coldwater fishes. Hence, this study underscores the need to evaluate water courses at regional scales to identify spatial refuges and ensure connectivity.
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| 5. |
- Bowes, Rachel E., et al.
(författare)
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Less means more : nutrient stress leads to higher delta N-15 ratios in fish
- 2014
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Ingår i: Freshwater Biology. - : Wiley-Blackwell. - 0046-5070 .- 1365-2427. ; 59:9, s. 1926-1931
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Tidskriftsartikel (refereegranskat)abstract
- 1. Isotopic ratios of nitrogen are often used in food-web studies to determine trophic position (including food chain length) and food sources, with greater ratios of 15N/14N (d15N) usually considered indicative of higher trophic position. However, fasting and starving animals may also show a progressive increase in d15N over time as they catabolise their own tissues.2. To determine the importance of starvation, we conducted a 4-month laboratory experiment testing effects of starvation on body condition and isotope ratios in the muscle tissue of freshwater guppies (Poecilia reticulata). We also compared laboratory results and conclusions with analyses of body condition and isotope ratios in various small species of fish collected in four seasons from the Kansas River in north-eastern Kansas, U.S.A.3. Fish starved in our laboratory experiment had significantly higher 15N values and poorer body condition than those fed more regularly. The diverse group of fish species collected in summer (July) from the Kansas River had higher weight-to-length ratios and lower 15N values than those retrieved in other seasons. Overall body condition resulting from reduced food consumption explained 44 and 53% of the variability in 15N for field and laboratory fish, respectively.4. These results are applicable to a wide variety of food-web research but are especially pertinent to studies of organisms that undergo large changes in life history, dormancy, extended fasts or periods of significant nutritional allocation to young.
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| 6. |
- Bowes, Rachel E., et al.
(författare)
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Multidimensional metrics of niche space for use with diverse analytical techniques
- 2017
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Ingår i: Scientific Reports. - : Springer. - 2045-2322. ; 7, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Multidimensional data are integral to many community-ecological studies and come in various forms, such as stable isotopes, compound specific analyses (e.g., amino acids and fatty acids), and both biodiversity and life history traits. Scientists employing such data often lack standardized metrics to evaluate communities in niche space where more than 2 dimensions are involved. To alleviate this problem, we developed a graphing and analytical approach for use with more than two variables, based on previously established stable isotope bi-plot metrics. We introduce here our community metrics as R scripts. By extending the original metrics to multiple dimensions, we created n-dimensional plots and metrics to characterize any set of quantitative measurements of a community. We demonstrate the utility of these metrics using stable isotope data; however, the approaches are applicable to many types of data. The resulting metrics provide more and better information compared to traditional analytic frameworks. The approach can be applied in many branches of community ecology, and it offers accessible metrics to quantitatively analyze the structure of communities across ecosystems and through time.
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| 7. |
- Bowes, Rachel E., et al.
(författare)
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Reweaving river food webs through time
- 2020
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Ingår i: Freshwater Biology. - : Wiley-Blackwell. - 0046-5070 .- 1365-2427. ; 65:3, s. 390-402
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Tidskriftsartikel (refereegranskat)abstract
- Our project sought to determine ecological effects of adding low-head dams and levees to large rivers by examining potential changes to aquatic food webs over a 70-year period in the Lower Ohio River (LOR) and Upper Mississippi River (UMR). We employed museum collections of fish and compound specific stable isotope analysis of amino acids to evaluate long-term changes in primary food sources for multiple species of fish in each river. Fishes in both rivers depended more on autochthonous than allochthonous carbon sources throughout the 70-year period (based on measurements of isotopic signatures of algae, C-3 plants, C-4 plants, cyanobacteria, and fungi), but the relative use of different carbon sources differed between the UMR and LOR. Significant but opposite shifts in trophic positions (TP) between rivers over time (higher TP in the UMR; lower in the LOR) were correlated with major anthropogenic changes to habitat structure (e.g. slight decrease in abundance of side channels in the UMR; increase in pool water depth in the LOR) resulting from low-head dam construction. They may also have been influenced by likely increased primary productivity in the UMR from agricultural nitrogen inputs and by possible shifts in the importance of phytoplankton versus benthic algae in the LOR from changes in water depth. Shifts in trophic position and reliance on various food sources were not correlated with variation in discharge, gage height, or temperature. Although these two rivers have contrasting hydrogeomorphic complexity (UMR is an anastomosing river, while the LOR is a constricted channel river) and different discharge patterns (seasonal versus yearly operation in some cases), both differ substantially from rivers having hydrogeomorphic changes resulting from construction of high dams (>15 m). It is not surprising, therefore, that factors controlling trophic position and reliance on different carbon sources vary among different types of dams and river structures.
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| 8. |
- Marker, Jeffery
(författare)
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Forests, Functions, and Food Webs : Riparian processes through an ecological and molecular lens
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Riparian systems are critical ecological interfaces that have a significant impact on the surrounding aquatic and terrestrial ecosystems. The riparian and surrounding systems have significant roles in regulating energy flow, providing essential nutrients, and supporting unique species, making them important for ecosystem function. Both the aquatic and terrestrial ecosystems are reliant on the reciprocal exchange of energy subsides to maintain productive and stable food webs. Retention of forested buffers along streams during tree felling operations is a common management technique used to protect aquatic resources and conserve the surrounding ecosystem processes. Measuring the effects of forestry practices on the function and food webs of riparian predators is vital to making forest management decisions that strengthen and protect these fundamental services. Insight into predator function and predator-prey interactions using powerful molecular techniques can further the understanding of these complex systems and help to mitigate the effects of forestry practices.This thesis explores the functional diversity, food webs, and predator-prey interactions in riparian systems impacted by forestry felling practices. I have studied the effects of clear-cutting and forested buffer zones on riparian functional diversity through the assessment of functional richness and redundancy of spider and plant communities. In addition, I have both validated and used stable isotope analysis and DNA metabarcoding to investigate the primary food sources and prey choices of riparian predators. Riparian buffer size had no direct effect on the functional richness or redundancy of riparian spiders and vascular plants. However, riparian buffer variables such as canopy closure, buffer density, and vegetation coverage did have direct impacts on both spider and plant function. Most riparian spiders and brown trout received a significant majority of their food source from the terrestrial environment and the presence or absence of a riparian buffer did not effect this outcome. However, web-weaving spiders in unbuffered systems were more likely to exploit aquatic resources as a primary food source. Overall, the responses of predator function and food webs to forestry practice are site-specific.
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| 9. |
- Marker, Jeffery, et al.
(författare)
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Greater than the sum of your parts : Nonlethal stable isotope sampling methods in spiders
- 2022
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Ingår i: Ecosphere. - : John Wiley & Sons. - 2150-8925 .- 2150-8925. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- As top consumers and generalist predators, spiders are ideal organisms to study food webs and complex ecological functions using stable isotopes. Most researchers use whole-body samples to analyze stable isotope ratios in spiders. Spiders can regrow lost legs and produce multiple molts during a life cycle, and nonlethal sampling utilizing legs and molts may provide a useful alternative to whole-body sampling especially in larger bodied or threatened species. Furthermore, removing spider abdomens and thus leftover prey in the gut contents may provide a more accurate isotopic value. We tested the hypothesis that the delta N-15, delta C-13, or delta H-2 isotopic values in spider legs are reliable proxies for spider prosomas, abdomens, or whole bodies. We used laboratory-reared large-bodied spiders (Pterinochilus murinus) and field-collected Lycosidae to compare lethal and nonlethal tissue isotopic values. We found that nonlethal samples of spider legs and molts are acceptable alternatives to lethal whole-body samples to determine delta C-13 and delta N-15 stable isotope signatures. Nonlethal samples are not suitable proxies for whole-body samples to determine delta H-2 isotopic values. Using nonlethal leg or molts samples in stable isotope investigations of spiders will allow researchers to promote conservation efforts and study threatened species while ensuring accurate and repeatable results.
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| 10. |
- Marker, Jeffery, et al.
(författare)
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Small stream predators rely heavily on terrestrial matter energy input in the fall, regardless of riparian buffer size
- 2023
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Ingår i: Food Webs. - : Elsevier. - 2352-2496. ; 36
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Tidskriftsartikel (refereegranskat)abstract
- Stream ecosystems are reliant on the reciprocal exchange of terrestrial and aquatic energy subsides to maintain a productive and stable food web. Land use around streams can have strong effects on the size and availability of resource subsidies for stream and riparian predators such as fish and spiders. A common forestry technique around streams is the establishment of forested buffers to protect aquatic and riparian ecosystems from upland disturbances. Buffer size may determine prey abundance, richness, and spatial extent of prey reach into both the aquatic and terrestrial systems. To test the effects of forested buffers subsidy direction, we explored the carbon and nitrogen stable isotope signatures of brown trout (Salmo trutta), Tetragnathidae and Lycosidae spiders, and their aquatic and terrestrial prey sources around twelve streams in southern Sweden. For both predator groups, buffer presence showed no effect on resource subsidy source. We found that both brown trout and spiders are significantly reliant on terrestrial sources of prey for their diets in the fall. To support the terrestrial subsidy into small streams it is vital to maintain ecologically functional riparian zones by conserving complex surrounding habitats that optimize habitat and both terrestrial and aquatic prey diversity.
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