The importance of DNA barcode choice in biogeographic analyses - a case study on marine midges of the genus Clunio.

DNA barcodes are widely used for species identification and biogeographic studies. Here, we compare the use of full mitochondrial genomes versus DNA barcodes and other mitochondrial DNA fragments for biogeographic and ecological analyses. Our dataset comprised 120 mitochondrial genomes from the genus Clunio (Diptera: Chironomidae), comprising five populations from two closely related species (Clunio marinus and Clunio balticus) and three ecotypes. We extracted cytochrome oxidase c subunit I (COI) barcodes and partitioned the mitochondrial genomes into non-overlapping windows of 750 or 1500 bp. Haplotype networks and diversity indices were compared for these windows and full mitochondrial genomes (15.4 kb). Full mitochondrial genomes indicate complete geographic isolation between populations, but do not allow for conclusions on the separation of ecotypes or species. COI barcodes have comparatively few polymorphisms, ideal for species identification, but do not resolve geographic isolation. Many of the similarly sized 750 bp windows have higher nucleotide and haplotype diversity than COI barcodes, but still do not resolve biogeography. Only when increasing the window size to 1500 bp, two windows resolve biogeography reasonably well. Our results suggest that the design and use of DNA barcodes in biogeographic studies must be carefully evaluated for each investigated species.

Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails.

Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.

Integrating multiple criteria for the characterization of Psammotettix populations in European cereal fields.

The wheat dwarf disease is among the most damaging diseases in cereals. Its aetiological agent is the Wheat dwarf virus (WDV), which is exclusively transmitted from plant to plant by leafhoppers from the genus Psammotettix (Hemiptera, Cicadellidae). The parameters linked to the WDV/Psammotettix pathosystem are still poorly understood. We studied Psammotettix individuals collected in wheat and barley fields in France and, as a comparison, from grassland at agroecological interface in West Slovenia. Species identity of males and females has been determined using multiple criteria. In the first step, the characterization of the collected individuals included recordings of vibrational signals used in mating behaviour and morphometric analyses. In addition, a 442 nt sequence of the mitochondrial cytochrome oxydase I (COI) gene was obtained for some individuals and compared to COI sequences of the Psammotettix leafhoppers available in public databases. In the cereal fields in France, P sammotettix alienus was the most numerous species; however, it sometimes occurred together with Psammotettix confinis, while in the grasslands in Slovenia, the third syntopic species in Psammotettix community was Psammotettix helvolus. The temporal parameters of the P. alienus male calling song that were measured in this study were very similar to those measured in a previous study. The local biotic and/or abiotic parameters most likely influence the life history of Psammotettix leafhoppers, and the proportion of viruliferous individuals collected in cereal fields was 14.9%, while leafhoppers collected in Slovenia were virus-free. Taken together, results show that more detailed information on population structure of Psammotettix leafhoppers is crucial for providing an insight into the epidemiology of wheat dwarf disease.

Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels.

Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada. Many of these are potentially sympatric, and 14 species have been formally assessed as endangered, threatened, or special concern. We investigated whether there was sufficient variation within the cytochrome oxidase region (COI) to develop species-specific eDNA markers for at-risk unionids. We developed 32 COI markers for eight unionid species, and tested each of these on the target species plus 29 potentially sympatric unionid taxa. Six of these markers amplified DNA only from the intended target species. We then extracted and amplified mussel eDNA from rearing-tank water samples. We conclude that despite high species diversity, it should be possible to develop eDNA COI markers and screen water samples for habitat occupancy by unionid mussels.