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      Airborne eDNA Reflects Human Activity and Seasonal Changes on a Landscape Scale

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      Frontiers in Environmental Science

      Frontiers Media SA

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          Abstract

          Recent research on environmental DNA (eDNA), genetic material shed by organisms into their environment that can be used for sensitive and species-specific detection, has focused on the ability to collect airborne eDNA released by plants and carried by the wind for use in terrestrial plant populations, including detection of invasive and endangered species. Another possible application of airborne eDNA is to detect changes in plant communities in response to activity or changes on a landscape-scale. Therefore, the goal of this study was to demonstrate how honey mesquite, blue grama, and general plant airborne eDNA changes in response to human activity on a landscape-scale. We monitored airborne eDNA before, during, and after a rangeland restoration effort that included honey mesquite removal. As expected, restoration activity resulted in a massive increase in airborne honey mesquite eDNA. However, we also observed changes in abundance of airborne eDNA from the grass genus Bouteloua, which was not directly associated with the restoration project, and we attribute these changes to both human activity and seasonal trends. Overall, we demonstrate for the first time that activity and changes on a landscape-scale can be tracked using airborne eDNA collection, and we suggest that airborne eDNA has the potential to help monitor and assess ecological restoration projects, track changes due to global warming, or investigate community changes in response to encroachment by invasive species or extirpation of threatened and endangered species.

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          Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

          Background Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the number and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such analysis usually makes this a time-consuming and very difficult task for users, especially when the primers have a large number of hits. Furthermore, although the BLAST program has been widely used for primer target detection, it is in fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necessarily return complete match information over the entire primer range. Results We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers. This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant number of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers. Conclusions We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the specificity threshold and other primer properties. This tool is publicly available at http://www.ncbi.nlm.nih.gov/tools/primer-blast.
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            Viewing invasive species removal in a whole-ecosystem context

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              Extinction risk from climate change.

              Climate change over the past approximately 30 years has produced numerous shifts in the distributions and abundances of species and has been implicated in one species-level extinction. Using projections of species' distributions for future climate scenarios, we assess extinction risks for sample regions that cover some 20% of the Earth's terrestrial surface. Exploring three approaches in which the estimated probability of extinction shows a power-law relationship with geographical range size, we predict, on the basis of mid-range climate-warming scenarios for 2050, that 15-37% of species in our sample of regions and taxa will be 'committed to extinction'. When the average of the three methods and two dispersal scenarios is taken, minimal climate-warming scenarios produce lower projections of species committed to extinction ( approximately 18%) than mid-range ( approximately 24%) and maximum-change ( approximately 35%) scenarios. These estimates show the importance of rapid implementation of technologies to decrease greenhouse gas emissions and strategies for carbon sequestration.
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                Author and article information

                Journal
                Frontiers in Environmental Science
                Front. Environ. Sci.
                Frontiers Media SA
                2296-665X
                January 25 2021
                January 25 2021
                : 8
                Article
                10.3389/fenvs.2020.563431
                2ad763f2-1628-4670-90da-b1ee75375628
                © 2021

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