Influence of killing method on Lepidoptera DNA barcode recovery

Molecular identification of the potentially forensically relevant cluster flies Pollenia rudis (Fabricius) and Pollenia vagabunda (Meigen) (Diptera: Polleniidae) — non-recorded species in Algeria

Cluster flies are represented by the genus Pollenia Robineau-Desvoidy, 1830 of the family Polleniidae Brauer and Bergenstamm, 1889. Their larvae are known to be internal parasites or predators of earthworms. Herein, we report for the first time the occurrence of the cluster flies Pollenia rudis Fabricius, 1794 and Pollenia vagabunda (Meigen, 1826) (Diptera: Polleniidae) on carcasses in Algeria and identify them through DNA barcoding. A region of the mitochondrial cytochrome c oxidase I gene (COI) was amplified and sequenced. Genetic distances were determined. A phylogenetic tree was constructed with the maximum parsimony method using 10 000 bootstrap replicates. A total number of 157 adults of P. rudis were collected together with 325 adults of Pollenia vagabunda. The occurrence of Pollenia on animal carcasses does not seem to be correlated with a particular stage of decomposition. All the sequences were correctly identified using the BLASTn tool from the GenBank database and the BOLD identification engine. Intra- and interspecific sequence divergence values were less than 1% and greater than 3%, respectively. COI barcodes obtained from this study were robust enough to identify and distinguish unambiguously between P. rudis and P. vagabunda. In the tree-based analysis, the cluster flies were all assigned to their respective species separately from each other confirming the morphological identification. These results provide DNA barcodes that contribute to the growth of reference databases and allow fast and accurate identification.

A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys)

Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).

Preserving and vouchering butterflies and moths for large-scale museum-based molecular research

Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world.

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota

Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways.