Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany

SIMPLE SUMMARY: Roughly two-thirds of the insect species described from Germany belong to the orders Diptera (flies) or Hymenoptera (wasps, bees, ants and sawflies). However, both orders contain several species-rich families that have received little taxonomic attention until now. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae and Sciaridae). The estimates given in this paper are based on the sequencing results of over 48,000 fly specimens that have been collected in southern Germany via Malaise traps that were operated for one season each. We evaluated the fraction of species in our samples belonging to well-known fly families in order to estimate the species richness of the challenging “dark taxa” (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery and description in Germany in these four families. ABSTRACT: Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these “dark taxa” families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four “dark taxa” families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800–2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.