Phylogenetic Relationship of Osmia spp. in Korea Based on Mitochondrial COI Gene Sequences (Hymenoptera: Megachilidae)
3
Citation
4
Reference
10
Related Paper
Citation Trend
Keywords:
Megachilidae
Megachilidae
Cite
Citations (2)
Megachilidae
Cite
Citations (5)
Emergence patterns of a natural population of Osmia lignaria subsp. lignaria Say were monitored during a 5-yr period (2003-2007) in relation to air temperature, bloom of eastern redbud (Cercis canadensis L.), and emergence of the parasitoid Chysura kyrae Krombein. Bee cocoons were placed in gelatin capsules and overwintered within shelters in their natural habitat. Mean emergence of female O. l. lignaria was observed at approximately 2 d after redbud bloom began; mean male emergence was approximately 1 wk earlier than for females and was nearly identical to that of C. kyrae. Horticultural models used to predict budburst for several tree species were evaluated with respect to redbud bloom and O. l. lignaria emergence. Each model indicated that both sexes of the bee and redbud had similar chill unit requirements. Differences in emergence and bloom dates were attributed to the different requirements for growing degree hours (GDHs) after chilling requirements were met. The close phenological relationship observed between eastern redbud and bee emergence suggests an important role for this common understory tree in the early nesting success of O. l. lignaria.
Megachilidae
Cite
Citations (11)
Environmental DNA (eDNA) metabarcoding, the process of sequencing DNA collected from the environment for producing biodiversity inventories, is increasingly being applied to assess fish diversity and distribution in marine environments. Yet, the successful application of this technique deeply relies on accurate and complete reference databases used for taxonomic assignment. The most used markers for fish eDNA metabarcoding studies are the cytochrome C oxidase subunit 1 (COI), 16S ribosomal RNA (16S), the 12S ribosomal RNA (12S) and cytochrome b (cyt b) genes, whose sequences are usually retrieved from GenBank, the largest DNA sequence database that represents a worldwide public resource for genetic studies. Thus, the completeness and accuracy of GenBank is critical to derive reliable estimations from fish eDNA metabarcoding data. Here, we have i) compiled the checklist of European marine fishes, ii) performed a gap analysis of the four genes and, within COI and 12S, also of the most used barcodes for fish, and iii) developed a workflow to detect potentially incorrect records in GenBank. We found that from the 1965 species in the checklist (1761 Actinopterygii, 189 Elasmobranchii, 9 Holocephali, 4 Petromyzonti and 2 Myxini), about 70% have sequences for COI, whereas less have sequences for 12S, 16S and cyt b (45-55%). Among the species for which COI ad 12S sequences are available, about 60% and 40% have sequences covering the most used barcodes respectively. The analysis of pairwise distances between sequences revealed pairs belonging to the same species with significantly low similarity and pairs belonging to different high level taxonomic groups (class, order) with significantly large similarity. In light of this further confirmation of presence of a substantial number of incorrect records in GenBank, we propose a method for identifying and removing spurious sequences to create reliable and accurate reference databases for eDNA metabarcoding.
Environmental DNA
Taxonomic rank
Cite
Citations (1)
Megachilidae
Cite
Citations (2)
Megachilidae
Cite
Citations (1)
This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.
DNA Barcoding
Species complex
Lineage (genetic)
Barcode
Cite
Citations (52)
This is the publisher's version, also available electronically from http://biostor.org/reference/347.
Megachilidae
Cite
Citations (48)