Latest papers from ACG Lep inventory

Joining Inventory by Parataxonomists with DNA Barcoding of a Large Complex Tropical Conserved Wildland in Northwestern Costa Rica
By Daniel H. Janzen, Winnie Hallwachs  

Reading the Complex Skipper Butterfly Fauna of One Tropical Place
By Daniel H. Janzen, Winnie Hallwachs, John M. Burns, Mehrdad Hajibabaei, Claudia Bertrand, Paul D. N. Hebert

A Tri-Oceanic Perspective: DNA Barcoding Reveals Geographic Structure and Cryptic Diversity in Canadian Polychaetes

By Christina M. Carr, Sarah M. Hardy, Tanya M. Brown, Tara A. Macdonald, Paul D. N. Hebert

Polychaete Barcoding Studies

My labmate Christy Carr recently pulished a paper from her MSc thesis about Polychaete diversity in Canadian waters. The paper on barcoding is to follow soon in PLoS One. Christy is very good at creating eye-catching figures.

Polychaete diversity and distribution patterns in Canadian marine waters
 By Christina May Carr

Fish Barcoding Studies

[Photo: Me and brazilian visiting scientists at Niagara Falls]
A special on fish barcoding in the journal Mitochondrial DNA has recently been released online. Two papers were written by researchers visiting the Hanner Lab at the University of Guelph from the developing world. I was lucky enough to interact with these researchers and help with the development of the studies.

DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species By Christopher D. Nwani, Sven Becker, Heather E. Braid, Emmanuel F. Ude, Okechukwu I. Okogwu, Robert Hanner

DNA barcodes discriminate freshwater fishes from the Paraíba do Sul River Basin, São Paulo, Brazil By Luiz H. G. Pereira, Gláucia M. G. Maia, Robert Hanner, Fausto Foresti, Claudio Oliveira

A cryptic, intergeneric cytochrome c oxidase I pseudogene in tyrant flycatchers (family: Tyrannidae)

My former labmate Kevin Kerr found a numt in a group of birds.

A cryptic, intergeneric cytochrome c oxidase I pseudogene in tyrant flycatchers (family: Tyrannidae)

Kerr, Kevin C.R.

Nuclear mitochondrial pseudogenes, or “numts”, are nonfunctional copies of mitochondrial genes that have been translocated to the nuclear genome. Numts have been used to study differences in mutation rates between the nuclear and mitochondrial genomes, but have also been implicated as troublesome for phylogenetic studies and DNA-based species identification (i.e., DNA barcoding). In this study, a suspected numt discovered during a study of mitochondrial cytochrome c oxidase I (COI) diversity in North American birds was targeted and sequenced from tyrant flycatchers (family: Tyrannidae). In total, the numt was found in five taxa representing two genera. Substitution rates were compared between COI and numt sequences. None of the numt sequences harboured stop codons nor frameshift mutations, but phylogenetic analysis revealed they had accumulated more amino acid substitutions than the mitochondrial COI sequences. Mitochondrial COI appeared to be preferentially amplified in most cases, but methods for numt detection are discussed for cases like this where sequences lack obvious features for identification. Because of its persistence across a broad taxonomic lineage, this numt could form a valuable model system for studying evolution in numts. The full size of the numt and its location within the nuclear genome are yet to be determined.

Accelerated construction of a regional DNA-barcode reference library: caddisflies (Trichoptera) in the Great Smoky Mountains National Park

A paper has recently been published in Journal of the The North American Benthological Society, 2011, 30(1):131-162 (available as part of a barcodeoflife.net discussion from here). The paper details how 645 COI sequences, representing 80 species, were obtained from specimens collected in a 3-day bioblitz (short-term, intense sampling program) in the Great Smoky Mountains National Park. I was lucky to be part of the BioBlitz team back in 2007, and am very happy to see the results published!