DNA barcoding of invertebrates inhabiting olive orchards and vineyards accelerates understudied Mediterranean biodiversity assessment
Description
The DNA barcoding results consisting of sequences for 269 specimens were used for species identification and species richness assessment through the comparison of our data with the data available in BOLD and NCBI databases, and/or by applying species delimitation methods. The files provided are alignment used for species delimiatation of Collembola and Oligochaeta specimens. Methods applied are the following: Sequencing of purified DNA amplicons was performed by Macrogen Inc. (Amsterdam, Netherlands) using the same amplification primer (LCO1490). Sequences were edited using BIOEDIT v.7.2. (Gene Codes Corporation, Ann Arbor, MI USA) [Hall 1999]. Chromatograms were manually checked for ambiguous nucleotides, stop codons and indels in BIOEDIT v.7.2. Sequences of specimens, including sequences from BOLD, were grouped and aligned in MEGA X [Kumar et al. 2018] using MUSCLE [Edgar 2004]. After, alignment sequences were collapsed to unique haplotypes (haploid genotype) using FaBox (1.5) [Villesen 2007]. The DNA sequence alignments were checked for stop codons using Mesquite ver. 3.5 [Maddison & Maddison 2019].