Creating, curating, and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA|生物多样性监测数据集|基因组学数据集

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous, and estuarine fishes representing 24 families, 55 genera, and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) ..., Voucher Specimen and Tissue Collection
The study area initially encompassed the state of Oregon—the region of interest for our eDNA monitoring program—and expanded to a few sites in northern California and Washington State (Fig 3). To strategize sample collection, we examined historical location records in fish collections such as the Oregon State Ichthyology Collection and conferred with local biologists to identify current distributions. For cases where we knew or suspected that deeply divergent evolutionary lineages existed in the present concept of a species, we aimed to include representatives of all lineages. We ultimately identified 146 native and nonnative freshwater fish species and lineages that are currently found in Oregon and strategized collections to span watersheds throughout the state (Appendix S1). 
To facilitate consistent sampling, we provided sampling kits (Appendix S2, Box S1) to collectors that contained a 500-mL Nalgene bottle filled with 10% formalin, a 2.0 mL c..., Microsoft Excel, LibreOffice, or Microsoft's free XLS Viewer can be used to open the Excel files and an unzip utility such as 7-Zip or WinZip can be used to unzip zipped fastas. For pdfs, use Adobe Acrobat Reader. Open Microsoft Word documents using Microsoft Word, OpenOffice Writer or Google Docs.,