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Daniel Rubinoff

Publications and source records attributed to Daniel Rubinoff.

9 recordsLinked to original sources
PubMed2006

A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification.

Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.

Animals↗
PubMed2006

Utility of mitochondrial DNA barcodes in species conservation.

Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.

Biodiversity↗
PubMed2005

Are plant DNA barcodes a search for the Holy Grail?

In a recent study, Kress et al. compared two plant genomes to seek out plant DNA barcodes. Two promising markers balanced the variability that is needed to distinguish species with conserved primer regions that enable universal amplification. Although this study is the most rigorous effort to date, problems from earlier barcoding efforts, such as the use of non-evolutionary species concepts and differential sorting of genes and species, could reemerge. Single-gene barcoding might not be universally effective owing to inherent inaccuracies. Kress et al. suggest the use of multiple genes, reflecting an integrated approach that is likely to be the best answer to identifying species quickly and accurately.

Biodiversity↗
PubMed2005

Web-spinning caterpillar stalks snails.

Moths and butterflies compose one of the most diverse insect orders, but they are overwhelmingly herbivorous. Less than 0.2% are specialized predators, indicating that lepidopteran feeding habits are highly constrained. We report a Hawaiian caterpillar that specializes on snails, a unique food source requiring an unusual feeding strategy. The caterpillar uses silk to restrain live prey. All caterpillars have silk glands, but none are known to use silk in this spiderlike fashion. Considering the canalization of caterpillar diets, evolution to attack and feed on snails is an anomaly. Hawaii s isolation and consequently disharmonic biota likely promote evolutionary experiments that occur nowhere else.

Animals↗
PubMed2002

Evolution of ecological traits and wing morphology in Hemileuca (Saturniidae) based on a two-gene phylogeny.

We present a molecular phylogeny for the genus Hemileuca (Saturniidae), based on 624 bp of mitochondrial cytochrome oxidase I (COI) and 932 bp of the nuclear gene elongation factor 1 alpha (EF1alpha). Combined analysis of both gene sequences increased resolution and supported most of the phylogenetic relationships suggested by separate analysis of each gene. However, a maximum parsimony (MP) model for just COI sequence from one sample of most taxa produced a phylogeny incongruent with EF1alpha and combined dataset analyses under either MP or ML models. Time of year and time of day during which adult moths fly corresponded strongly with the phylogeny. Although most Hemileuca are diurnal, ancestral Hemileuca probably were nocturnal, fall-flying insects. The two-gene molecular phylogeny suggests that wing morphology is frequently homoplastic. There was no correlation between the primary larval hostplants and phylogenetic placement of taxa. No phylogenetic pattern of specialization was evident for single hostplant families across the genus. Our results suggest that phenological behavioral characters may be more conserved than the wing morphology characters that are more commonly used to infer phylogenetic relationships in Lepidoptera. Inclusion of a molecular component in the re-evaluation of systematic data is likely to alter prior assumptions of phylogenetic relationships in groups where such potentially homoplastic characters have been used.

Animals↗