Shelley L Ball’s research while affiliated with Bates College and other places

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

We measured infection rates of a putative parasitic castrating ciliate, in a population of the obligately parthenogenetic mayfly, Centroptilum triangulifer. Eleven percent of females sampled contained ciliates. All infected females oviposited ciliates when their abdomen contacted the water surface during oviposition trials. Furthermore, none of these females possessed eggs, yet all females contained gonadal tissue remnants within their abdomens, suggesting that ciliates were directly consuming gonadal tissue.

Early detection of economically important insects is critical to preventing their establishment as serious pests. To accomplish this, tools for rapid and accurate species identification are needed. DNA barcoding, using short DNA sequences as species "genetic identification tags," has already shown large potential as a tool for rapid and accurate detection of economically important insects. DNA extraction is the critical first step in generating DNA barcodes and can be a rate-limiting step in very large barcoding studies. Consequently, a DNA extraction method that is rapid, easy to use, cost-effective, robust enough to cope with range of qualities and quantities of tissue, and can be adapted to robotic systems will provide the best method for high-throughput production of DNA barcodes. We tested the performance of a new commercial kit (prepGEM), which uses a novel, streamlined approach to DNA extraction, and we compared it with two other commercial kits (ChargeSwitch and Aquapure), which differ in their method of DNA extraction. We compared performance of these kits by measuring percentage of polymerase chain reaction (PCR) success and mean PCR product yield across a variety of arthropod taxa, whichincluded freshly collected, ethanol-preserved, and dried specimens of different ages. ChargeSwitch and prepGEM performed equally well, but they outperformed Aquapure. prepGEM was much faster, easier to use, and cheaper than ChargeSwitch, but ChargeSwitch performed slightly better for older (> 5-yr-old) dried insect specimens. Overall, prepGEM may provide a highly streamlined method of DNA extraction for fresh, ethanol-preserved, and young, dried specimens, especially when adapted for high-throughput, robotic systems.

It is currently proposed that there are two species of honeydew-producing sooty beech scale insects (Ultracoelostoma spp.) in New Zealand. It is thought that U. brittini lives exclusively on trunks of southern beech (Nothofagus spp.) trees, while U. assimile occurs mainly on branches. This study aimed to confirm this habitat specialisation by using a molecular genetic approach. We sequenced the c. 650 base pair DNA 'barcode' region of the mitochondrial gene cytochrome c oxidase I (COI) from specimens collected from Mount Grey/Maukatere (North Canterbury), Greymouth, and the Nelson Lakes region. Although the COI sequences supported the existence of two species, there was no evidence of the two species specialising on trunk or branch microhabitats. The excess sugar that these insects excrete as honeydew is an important energy source upon which many native birds and insects depend. Further geographic sampling is needed to determine the distribution and extent of sympatry of the two species detected in this study, which might have implications for forest management decisions.

We tested the efficacy of DNA barcodes in identifying mayfly species primarily from the northeastern United States and central Canada. We sequenced a 630-base-pair segment of the mitochondrial gene, cytochrome c oxidase 1 (COI), from 1 individual of each of 80 species to create a reference sequence profile. We used these reference sequences to identify 70 additional specimens representing 32 of the species that were in the profile. DNA barcodes correctly identified 69 of the 70 test specimens. The sole exception was an individual identified morphologically as Maccaffertium modestum that showed deep genetic divergence from other M. modestum specimens. Mean sequence divergence within species was 1%, whereas mean divergence among congeneric species was an order of magnitude greater (18%). We conclude that DNA barcoding can provide a powerful tool for mayfly species identification.

We tested the efficacy of DNA barcodes in identifying mayfly species primarily from the northeastern United States and central Canada. We sequenced a 630-base-pair segment of the mitochondrial gene, cytochrome c oxidase 1 (COI), from 1 individual of each of 80 species to create a reference sequence profile. We used these reference sequences to identify 70 additional specimens representing 32 of the species that were in the profile. DNA barcodes, correctly identified 69 of the 70 test specimens. The sole exception was an individual identified morphologically as Maccaffertium modestum that showed deep genetic divergence from other M. modestum specimens. Mean sequence divergence within species was 1%, whereas mean divergence among congeneric species was an order of magnitude greater (18%). We conclude that DNA barcoding can provide a powerful tool for mayfly species identification.

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.