Taxonomy and DNA sequence databases: A perfect match?

My latest review paper now available online.

Taxonomy and DNA sequence databases: A perfect match?
Terrestrial Arthropod Reviews

Preying on commercial fisheries and accumulating paralytic shellfish toxins: a dietary analysis of invasive Dosidicus gigas (Cephalopoda Ommastrephida

New paper now available online

By Heather Elizabeth Braid, Jonathan Deeds, Stacey Lea DeGrasse, John James Wilson, Josephine Osborne and Robert Harland Hanner

Read the story behind this paper at http://issuu.com/ibol/docs/ibol_bb_v1_n4_120610 page 10.

Assessing the Value of DNA Barcodes for Molecular Phylogenetics: Effect of Increased Taxon Sampling in Lepidoptera

My new publication out today.

Assessing the Value of DNA Barcodes for Molecular Phylogenetics: Effect of Increased Taxon Sampling in Lepidoptera.
PLoS ONE 6(9): e24769. doi:10.1371/journal.pone.0024769

When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths

My new paper out today.

When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths

John James Wilson, Rodolphe Rougerie, Justin Schonfeld, Daniel H Janzen, Winnie Hallwachs, Mehrdad Hajibabaei, Ian J Kitching, Jean Haxaire and Paul DN Hebert

BMC Ecology 2011, 11:18 doi:10.1186/1472-6785-11-18
Published: 1 August 2011

Identity of the ailanthus webworm moth (Lepidoptera, Yponomeutidae), a complex of two species: evidence from DNA barcoding, morphology and ecology

During extensive ongoing campaigns to inventory moths of North America and Area de Conservacion Guanacaste (ACG), northwestern Costa Rica, we discovered that morphologically similar yponomeutid moths were assigned two different names, Atteva ergatica Walsingham in Costa Rica and A. punctella (Stoll) in North America, but had identical DNA barcodes. Combining DNA barcoding, morphology and food plant records also revealed a complex of two sympatric species that are diagnosable by their DNA barcodes and their facies in Costa Rica. However, neither of the names could be correctly applied to either species, as A. ergatica is a junior synonym and A. punctella a junior homonym. By linking our specimens to type material through morphology and DNA barcoding, we determined that the ACG dry forest species, distributed from Costa Rica to southern Quebec and Ontario, should be called A. aurea, whereas the similar and marginally sympatric ACG rain forest species found in Central America should be called A. pustulella. Neotypes are designated for Phalaena Tinea punctella Stoll, 1781 and Deiopeia aurea Fitch, 1857. Atteva floridana has identical barcodes to A. aurea and provisionally maintained as a synonym.

Find my latest publication here

Assessing the Value of DNA Barcodes and Other Priority Gene Regions for Molecular Phylogenetics of Lepidoptera

Background: Despite apparently abundant amounts of observable variation and species diversity, the order Lepidoptera exhibits a morphological homogeneity that has provided only a limited number of taxonomic characters and led to widespread use of nucleotides for inferring relationships. This study aims to characterize and develop methods to quantify the value of priority gene regions designated for Lepidoptera molecular systematics. In particular, I assess how the DNA barcode segment of the mitochondrial COI gene performs across a broad temporal range given its number one position of priority, most sequenced status, and the conflicting opinions on its phylogenetic performance.

Methodology/Principal Findings: Gene regions commonly sequenced for Lepidoptera phylogenetics were scored using multiple measures across three categories: practicality, which includes universality of primers and sequence quality; phylogenetic utility; and phylogenetic signal. I found that alternative measures within a category often appeared correlated, but high scores in one category did not necessarily translate into high scores in another. The DNA barcode was easier to sequence than other genes, and had high scores for utility but low signal above the genus level.

Conclusions/Significance: Given limited financial resources and time constraints, careful selection of gene regions for molecular phylogenetics is crucial to avoid wasted effort producing partially informative data. This study introduces an approach to assessing the value of gene regions prior to the initiation of new studies and presents empirical results to help guide future selections.