FACEPAI: a script for fast and consistent environmental DNA processing and identification.

BACKGROUND: The use of environmental DNA (eDNA) has become an increasing important tool in environmental surveys and taxonomic research. High throughput sequencing of samples from soil, water, sediment, trap alcohol or bulk samples generate large amount of barcode sequences that can be assigned to a known taxon with a reference sequence. This process can however be bioinformatic cumbersome and time consuming, especially for researchers without specialised bioinformatic training. A number of different software packages and pipelines are available, but require training in preparation of data, running of analysis and formatting results. Comparison of results produced by different packages are often difficult. RESULTS: FACEPIE is an open source script dependant on a few open source applications that provides a pipeline for rapid analysis and taxonomic assignment of environmental DNA samples. It requires an initial formatting of a reference database, using the script CaPReSe, and a configuration file and can thereafter be run to process any number of samples in succession using the same settings and references. Both configuration and executing are designed to demand as little hands on work as possible, while assuring repeatable results. CONCLUSION: The demonstration using example data from real environmental samples provides results in a time span ranging from less than 3 min to just above 15 min depending on the numbers of sequences to process. The memory usage is below 2 GB on a desktop PC. FACEPAI and CaPReSe provides a pipeline for analysing a large number of eDNA samples on common equipment, with little bioinformatic skills necessary, for subsequent ecological and taxonomical studies.

The age, ancestral distribution and radiation of Chimarra (Trichoptera: Philopotamidae) using molecular methods.

The phylogeny of Chimarra has previously been examined using morphological characters for a smaller subset of taxa and geographical representativeness. Here molecular data from three genes (COI, CAD and POL-II) are used to reconstruct the phylogeny of the genus. The results show Chimarra to be monophyletic, and that some of the sister groups are paraphyletic. Previous hypotheses regarding the relationships of subgenera within the genus are corroborated but incongruences are also found compared to morphological characters that have been used in keys. The origin of the genus is explored using three different hypotheses of biogeographical region. The biogeography analyses reveal an origin in the Neotropical region and a subsequent rapid radiation, with dispersal into the Oriental, Palaearctic and Australasian regions and secondarily to the Nearctic region. The Afrotropical region has been colonized in several independent events. The molecular dating using a relaxed clock and calibration with four fossil species indicates that Chimarra is about 138million years old, and that the radiation out of the Neotropical region occurred approximately 124million years ago.

Seven new species of Chimarra (Trichoptera: Philopotamidae) from Malawi.

For the first time species of caddisflies in the genus Chimarra Stephens 1829 are reported from Malawi. The following new species are described: Chimarra zombaensis, C. flaviseta, C. chichewa, C. circumverta, C. mulanjae, C. psittacus and C. calidopectoris. The descriptions add to the knowledge of Afrotropical diversity in the order Trichoptera.

Identification key to and checklist of the Swedish Phlaeothripidae (Thysanoptera).

The Swedish fauna of thrips (Thysanoptera) in the family Phlaeothripidae consists of 49 species. A key to the species of Phlaeothripidae found in Sweden is provided. One species is recorded as new for the country, and 10 new regional records are presented. A checklist of all Swedish tubuliferan species with regional distributions is also given.

The Century Old Taxonomic Confusion Surrounding Wiedemannia zetterstedti Fallén and Related Species Is Resolved (Diptera: Empididae): Revision of the W. zetterstedti Group.

The Wiedemannia zetterstedti species group is revised after examination of all available type specimens and includes one new species (W. ulrichi Ivkovic & Sinclair sp. nov.) and four redescribed species (W. czernyi (Bezzi), W. longipennis (Mik) stat. rev., W. rufipes (Oldenberg) stat. rev. and W. zetterstedti (Fallén)). The following new synonyms are proposed: W. (Roederella) ouedorum Vaillant, 1952 = W. czernyi (Bezzi, 1905); Paramesia riparia Robert, 1836 = W. zetterstedti (Fallén, 1826). Lectotypes are designated for the following species/subspecies: Atalanta hirtiloba Speiser, Brachystoma escheri Zetterstedt, Clinocera czernyi Bezzi, Clinocera longipennis Mik, Paramesia riparia Robert, and Roederia czernyi rufipes Oldenberg. In addition to morphological evidence, molecular species concepts were investigated using a molecular phylogenetic divergence-based species delimitation (bPTP) and results confirmed the morphological conclusions. A key to species is presented and geographic distributions are mapped.

Ancistrocerus waldenii waldenii (Viereck 1906) (Hymenoptera: Vespidae, Eumeninae), a new addition to the fauna of Greenland.

Ancistrocerus waldenii waldenii (Viereck 1906) is newly recorded from West Greenland. This is a new northern limit for the species.