Czech Butterfly Barcoding

Czech Butterfly Barcoding DatasetsThis dataset consists of separate nexus files of COI sequences for each butterfly species covered in the Czech Republic Butterfly barcoding scheme.Nexus files include newly generated sequences from the Czech Republic, and database data from BOLD (https://v3.boldsystems.org/) (Ratnasingham &amp; Hebert 2007) (downloaded on 12 October 2022) for each species across its range, which were georeferenced and sequenced from the 5' end. We manually aligned samples with different length than 658 bp.We used an R script CZbar.R for data handling. It is a script for quick extracting of already downloaded data from BOLD. The data should be in a table containing all data and also sequences, saved as combined TSV file. Save the script, open under R, install the dependencies and run following the instructions directly in the script.We further used the script BAPS analyses (via rhierbaps R package, Tonkin-Hill et al. 2018), and for generating Nexus inputs for POPART (Leigh &amp; Bryant 2015; available from https://popart.maths.otago.ac.nz/). Both results of rhierbaps and POPART were checked visually and the dataset was cleaned to omit database samples which were either shorter than 500 bp, or potentially misidentified (dissimilarity of sequences represented by long branches in haplotype networks was evaluated using the BLAST algorithm, Altschul et al. 1990, in the NCBI database). After such cleaning, the final dataset (samplelist_metadata2.xlxs) and final nexus files, presented here, were produced.<br>Altschul, S.F., Gish, W., Miller, W., Myers, E.W. &amp; Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403–410.Leigh, J.W. &amp; Bryant, D. (2015). popart: full-feature software for haplotype network construction. Methods Ecol. Evol., 6, 1110–1116.Ratnasingham, S. &amp; Hebert, P.D.N. (2007). bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol. Notes, 7, 355–364.Tonkin-Hill, G., Lees, J.A., Bentley, S.D., Frost, S.D.W. &amp; Corander, J. (2018). RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res., 3, 93.