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DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area.

ABSTRACT: BACKGROUND:The North American Trichoptera larvae are poorly known at the species level, despite their importance in the understanding of freshwater fauna and critical use in biomonitoring. This study focused on morphological diagnoses for larvae occurring in the Churchill, Manitoba area, representing the largest larval association effort for the caddisflies at any given locality thus far. The current DNA barcode reference library of Trichoptera (available on the Barcode of Life Data Systems) was utilized to provide larval-adult associations. RESULTS:The present study collected an additional 23 new species records for the Churchill area, increasing the total Trichoptera richness to 91 species. We were able to associate 62 larval taxa, comprising 68.1% of the Churchill area Trichoptera taxa. This endeavor to identify immature life stage for the caddisflies enabled the development of morphological diagnoses, production of photographs and an appropriate taxonomic key to facilitate larval species analyses in the area. CONCLUSIONS:The use of DNA for associations of unknown larvae with known adults proved rapid and successful. This method should accelerate the state-of-knowledge for North American Trichoptera larvae as well as other taxonomic lineages. The morphological analysis should be useful for determination of material from the Churchill area.

SUBMITTER: Ruiter DE

PROVIDER: S-EPMC3691766 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area.

Ruiter David E DE Boyle Elizabeth E EE Zhou Xin X

BMC ecology 20130220

<h4>Background</h4>The North American Trichoptera larvae are poorly known at the species level, despite their importance in the understanding of freshwater fauna and critical use in biomonitoring. This study focused on morphological diagnoses for larvae occurring in the Churchill, Manitoba area, representing the largest larval association effort for the caddisflies at any given locality thus far. The current DNA barcode reference library of Trichoptera (available on the Barcode of Life Data Syst ...[more]

PMID: 23425021

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Project description:BackgroundBecause arctic plant communities are highly vulnerable to climate change, shifts in their composition require rapid, accurate identifications, often for specimens that lack diagnostic floral characters. The present study examines the role that DNA barcoding can play in aiding floristic evaluations in the arctic by testing the effectiveness of the core plant barcode regions (rbcL, matK) and a supplemental ribosomal DNA (ITS2) marker for a well-studied flora near Churchill, Manitoba.ResultsThis investigation examined 900 specimens representing 312 of the 354 species of vascular plants known from Churchill. Sequencing success was high for rbcL: 95% for fresh specimens and 85% for herbarium samples (mean age 20 years). ITS2 worked equally well for the fresh and herbarium material (89% and 88%). However, sequencing success was lower for matK, despite two rounds of PCR amplification, which reflected less effective primer binding and sensitivity to the DNA degradation (76% of fresh, 45% of herbaria samples). A species was considered as taxonomically resolved if its members showed at least one diagnostic difference from any other taxon in the study and formed a monophyletic clade. The highest species resolution (69%) was obtained by combining information from all three genes. The joint sequence information for rbcL and matK distinguished 54% of 286 species, while rbcL and ITS2 distinguished 63% of 285 species. Discrimination of species within Salix, which constituted 8% of the flora, was particularly problematic. Despite incomplete resolution, the barcode results revealed 22 misidentified herbarium specimens, and enabled the identification of field specimens which were otherwise too immature to identify. Although seven cases of ITS2 paralogy were noted in the families Cyperaceae, Juncaceae and Juncaginaceae, this intergenic spacer played an important role in resolving congeneric plant species at Churchill.ConclusionsOur results provided fast and cost-effective solution to create a comprehensive, effective DNA barcode reference library for a local flora.

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Project description:BackgroundOrbivirus-induced hemorrhagic diseases cause high mortality in wild and captive white-tailed deer in North America. The role of different Culicoides species in Orbivirus transmission outside of areas of intensive animal production has not been established. At our study location, bluetongue virus (BTV) RNA-positive female Culicoides debilipalpis pools have been detected annually since 2012 when BTV transmission was noted in a captive deer herd. Identifying specific larval habitats of suspected vectors at active transmission sites is crucial both for identifying the source of the vectors and for subsequently planning intervention actions. Since C. debilipalpis larvae are known to develop in tree holes, this study was designed to use DNA barcoding to identify larvae collected from tree holes.MethodsAdult female Culicoides were collected using light or emergence traps and morphologically identified to 11 species. Culicoides sonorensis were also obtained from a laboratory colony. Substrate was collected from tree holes and flooded with water to harvest floating larvae. Total DNA from three to seven adult females per species and 19 larvae was extracted. Two loci of the nuclear 18S ribosomal RNA (rRNA) gene, one locus each of the mitochondrial cytochrome oxidase subunit I (COI) gene and the nuclear 28S rRNA gene were amplified using loci-specific primers.ResultsAll 61 adults were sequenced at each of the four loci under study. Since no single locus delineated all putative species and the COI locus yielded unreliable pseudogenes for two individuals of C. arboricola, sequences of all four loci were concatenated to maximize species separation and allow for larval association with identified adults. Sixteen larvae were clearly assigned to species based on DNA barcoding and phylogenetic results. Multiple larvae were assigned to each of the C. debilipalpis clade, the C. villosipennis clade, the C. arboricola clade and the C. nanus clade.ConclusionsOf the approximately 62 species described in the southeast USA, 21 have now been barcoded and sequences are publicly available. In this study, we constructed a database composed of species-specific sequences of adult Culicoides and then identified larvae to species by matching their corresponding sequences with adults. Since Culicoides larvae are difficult to identify, using DNA barcoding to facilitate larval habitat surveys can be a valuable tool.

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Dataset Information

DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area.

Publications

DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area.

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