title: The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands.
abstract: To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe. New DNA sequences were obtained from 325 individuals and 64 species (58 genera, 34 families). By adding 28S D3-sequences from GenBank we altogether analysed 385 sequences from 89 German species, 32 of them restricted to peatlands and further 42 occurring in peatlands occasionally, representing 46 and 33% of the oribatids in German peatlands, respectively. P-distances were measured between species within families as well as for intraspecific divergence. 28S D3 showed low intraspecific genetic p-distances between 0 and 0.5%, interspecific distances within families varied between 0 and 9.7%. Most species pairs within families were further separated by one to four indels in addition to substitutions. Altogether, 93% of all analysed species are clearly delineated by 28S D3. Our study emphasises that 28S D3 rDNA is a useful barcode for the identification of oribatid mite specimens and represents an important step in building-up a comprehensive barcode library to allow metabarcoding analyses of environmental peatland samples for Oribatida in Germany as well as in Central Europe.
authors.affiliation: Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826, Görlitz, Germany. ricarda.lehmitz@senckenberg.de.
authors.forename: Ricarda
authors.identifier: http://orcid.org/0000-0003-3122-5002
authors.initials: R
authors.lastname: Lehmitz
authors.affiliation: Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826, Görlitz, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Decker
mesh_terms: D000818:Animals; D001483:Base Sequence; D004275:DNA, Ribosomal / Q000737:chemistry* / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D005819:Genetic Markers; D005858:Germany; D008925:Mites / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010312:Parthenogenesis / Q000235:genetics; D010802:Phylogeny; D012339:RNA, Ribosomal, 28S / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity
chemical_list: D004275:DNA, Ribosomal; D005819:Genetic Markers; D012339:RNA, Ribosomal, 28S
keywords: 28S D3; Barcode; Germany; Indels; Mites; Peatlands