Quantitative PCR assays for detection of five Alaskan fish species: Lota lota, Salvelinus alpinus, Salvelinus malma, Thymallus arcticus, and Cottus cognatus from environmental DNA

The North Slope of Alaska contains arctic fish populations that are important for subsistence of local human populations, and under threat from natural resource extraction and climate change. We designed and evaluated four quantitative PCR assays for detection of environmental DNA from five Alaskan fish species present on the North Slope of Alaska: burbot (Lota lota), arctic char (Salvelinus alpinus), Dolly Varden (Salvelinus malma), arctic grayling (Thymallus arcticus), and slimy sculpin (Cottus cognatus). All assays were designed and tested for species specificity and sensitivity, and all assays detected target species from filtered water samples collected from the field. These assays will enable efficient and economical detection of the above species from lakes and rivers. This in turn will provide managers with improved knowledge of current distributions and future range shifts associated with climate and development threats, enabling more timely management

Quantitative PCR Assays for Detection of Five Arctic Fish Species: \u3ci\u3eLota lota\u3c/i\u3e, \u3ci\u3eCottus cognatus\u3c/i\u3e, \u3ci\u3eSalvelinus alpinus\u3c/i\u3e, \u3ci\u3eSalvelinus malma\u3c/i\u3e, and \u3ci\u3eThymallus arcticus\u3c/i\u3e from Environmental DNA

The North Slope of Alaska contains arctic fish populations that are important for subsistence of local human populations, and are under threat from natural resource extraction and climate change. We designed and evaluated four quantitative PCR assays for the detection of environmental DNA from five Alaskan fish species present on the North Slope of Alaska: burbot (Lota lota), arctic char (Salvelinus alpinus), Dolly Varden (Salvelinus malma), arctic grayling (Thymallus arcticus), and slimy sculpin (Cottus cognatus). All assays were designed and tested for species specificity and sensitivity, and all assays detected target species from filtered water samples collected from the field. These assays will enable efficient and economical detection and monitoring of these species in lakes and rivers. This in turn will provide managers with improved knowledge of current distributions and future range shifts associated with climate and development threats, enabling more timely management

Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high-profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection methods for many aquatic species. A second and perhaps underappreciated benefit of eDNA sampling is that a sample originally collected to determine the presence of one species can be re-analyzed to detect additional taxa without additional field effort. We developed an eDNA assay for the western pearlshell mussel (Margaritifera falcata) and evaluated its effectiveness by analyzing previously collected eDNA samples that were annotated with information including sample location and deposited in a central repository. The eDNA samples were initially collected to determine habitat occupancy by nonbenthic fish species at sites that were in the vicinity of locations recently occupied by western pearlshell. These repurposed eDNA samples produced results congruent with historical western pearlshell surveys and permitted a more precise delineation of the extent of local populations. That a sampling protocol designed to detect fish was also successful for detecting a freshwater mussel suggests that rapidly accumulating collections of eDNA samples can be repurposed to enhance the efficiency and cost-effectiveness of aquatic biodiversity monitoring

Connecting Earth Observation to High-Throughput Biodiversity Data

There is much interest in using Earth Observation (EO) technology to track biodiversity, ecosystem functions, and ecosystem services, understandable given the fast pace of biodiversity loss. However, because most biodiversity is invisible to EO, EO-based indicators could be misleading, which can reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing, and modern ecological modelling to extract much more of the information available in EO data. This approach is achievable now, 62 offering efficient and near-real time monitoring of management impacts on biodiversity and its functions and services

Connecting Earth observation to high-throughput biodiversity data

Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services

At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations

Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes, and additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates (〖"R " 〗_"adj" ^"2" = 0.78) and exponentially correlated with char densities (〖"R " 〗_"adj" ^"2" = 0.96 by area; 0.82 by volume). Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Comparison of noninvasive genetics and camera trapping for estimating population density of ocelots (Leopardus pardalis) on Barro Colorado Island, Panama

Estimates of population density are essential for the effective conservation and management of any threatened species. Accurately estimating density of elusive carnivores can be a challenge, however. One approach to this challenge is integration of DNA collected noninvasively from feces with capture-recapture modeling. To date, the bias and precision of this technique have seldom been evaluated in the field. We compared density estimates of ocelots (Leopardus pardalis) derived from fecal noninvasive genetic techniques to density estimates from camera trapping in the same population, during the same study period. Density estimates from the two techniques were comparable, especially when using spatially explicit capture-recapture models. Population density estimated using the program DENSITY was 1.74/km2 (SE = 0.584) from noninvasive genetics and 1.59/km2 (SE = 0.464) from camera trapping. These estimates also represent the highest reported ocelot population density within the species range

Kvalitetssäkring av ASF-EU genom analys och optimering av testrutiner

Detta examensarbete visar hur man har gått till väga för att planera samt tillverka testskåp som underlättar testningen av maskinmoduler i produktionen av en maskin vid företaget LKI Käldman. Företaget tillverkar olika plåthanteringsmaskiner till metallindustrin runtom i världen. Uppgiften har varit att analysera vilka maskinfunktioner som bör testas med testskåp, hur funktionerna bör testas, planering och val av komponenter till testskåpen samt tillverkning av skåpen. Att programmera PLC och manöverpanel har inte ingått i arbetet, men instruktioner har utformats till den som utför programmeringen. Examensarbetets slutresultat blev ett testskåp som är redo att tas i bruk inom produktionen. Med hjälp av detta skåp kan testningen av maskinmodulen LST underlättas och gå snabbare. Därtill har det även planerats och dokumenterats ett gemensamt testskåp för tre andra maskinmoduler. Dokumentationen är klar så långt att en tillverkning är möjlig.This thesis describes how the planning and manufacture of test cabinets have been done. The test cabinets will facilitate the testing of machine modules in the production of a machine at the company LKI Käldman. The company manufactures various sheet metal handling machines for the metal industry worldwide. The task included an analysis of the machine functions that should be tested with the test cabinets and an analysis of how the functions should be tested. Planning and component selection for the test cabinets, and also the manufacture of the cabinets were included. The programming of the PLC and the control panel has not been part of the thesis, only document guidelines for the person that will program have been made. The end result of the thesis is a test cabinet that is ready for use in the production. The test cabinet facilitates and speeds up the testing of the machine module LST. Also, another test cabinet which can be used for three other machine modules has been planned and documented. The documentation has been done so far that the manufacture of the test cabinet is possible

mammal16S_OTU

Fasta file containing all mammal 16S OTU sequence