Ecology in the age of DNA barcoding: the resource,the promise and the challenges ahead

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.     

Efficient mucosal vaccination mediated by the neonatal Fc receptor

Almost all infectious diseases are initiated at mucosal surfaces, yet intramuscular or subcutaneous vaccination usually provides only minimal protection at sites of infection owing to suboptimal activation of the mucosal immune system. The neonatal Fc receptor (FcRn) mediates the transport of IgG across polarized epithelial cells lining mucosal surfaces. We mimicked this process by fusing a model antigen, herpes simplex virus type-2 (HSV-2) glycoprotein gD, to an IgG Fc fragment. Intranasal immunization, together with the adjuvant CpG, completely protected wild-type, but not FcRn knockout, mice after intravaginal challenge with virulent HSV-2 186. This immunization strategy induced efficient mucosal and systemic antibody, B- and T-cell immune responses, with stable protection for at least 6 months after vaccination in most of the immunized animals. The FcRn-IgG transcellular transport pathway may provide a general delivery route for subunit vaccines against many mucosal pathogens.     

Complexity at the mouse minor histocompatibility locusH-4

The fine immunogenetics of the chromosome 7 mouse minor histocompatibility (H) locusH-4 was investigated. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted helper T cells (TH) specifically reactive with H-4 antigens were isolated as clones and were used as genetic probes for classical backcross segregation analysis. Results of a four point cross indicated that theH-4 locus was actually comprised of two genes, that have been designatedH-46 andH-47. The former encodes antigens recognized by the TH and the latter encodes antigens recognized by the CTL. Moreover, these two genes could be separated from the gene pink-eyed dilution (p) which was found to be sandwiched between them. The functional significance of a minor H congenic strain differing by both TH-definedH-46 and CTL-definedH-47 was addressed using F₁ complementation tests. Such studies indicated that immune responses against H-46 antigens was required for generation of H-47-specific CTL. Altogether, these results suggest selective presentation of different minor H gene products by class I or class II MHC proteins and that the minor H locusH-4 may have necessarily included both TH and CTL-defined genes because of requisite TH-CTL collaboration. Address correspondence and offprint requests to: D. C. Roopenian.     

Chromosomal localization of GABAA receptor subunit genes: relationship to human genetic disease

Hybridization of GABAA receptor probes to human chromosomes in situ and to DNA from sorted human chromosomes has localized the genes encoding a beta subunit and three isoforms of the alpha subunit. The alpha 2 and beta genes are both located on chromosome 4 in bands p12-p13 and may be adjacent. The alpha 1 gene is on chromosome 5 (bands q34-q35) and the alpha 3 gene is on the X chromosome. The alpha 3 locus was mapped also on the mouse X chromosome using genetic break-point analysis in an interspecies pedigree. The combined results locate the human alpha 3 gene within band Xq28, in a location that makes it a candidate gene for the X-linked form of manic depression.     

Mapping of the phosphorylase kinase alpha subunit gene on the mouse X chromosome

Phosphorylase kinase is a glycogenolytic enzyme in several animal tissues. Within the last few years all four subunits of the enzyme have been cloned. The beta, gamma, and delta subunits are known to be autosomal. We have mapped the alpha subunit of phosphorylase kinase, recently cloned by Zander et al. (1988), in an interspecific mouse pedigree and localized it on the X chromosome, where it maps between the X-linked zinc finger protein and phosphoglycerate kinase genes, close to the latter. In man and mouse several X-linked disorders of this enzyme have been described. Although the X-linked phosphorylase kinase deficiency in mice may be caused by a mutation in the structural gene for the alpha subunit, mapped here, the existence of a separate regulatory locus, important in the normal expression or function of the enzyme in muscle, still remains a possibility.     

The extent of self-MHC restriction of cytotoxic T cells in nude mice varies from mouse to mouse

There are conflicting results as to whether the response of athymic nude mice to TNP-modified self determinants is or is not H-2 restricted. We cultured spleen cells from 29 individual RNC (H-2k) nude mice with TNP-modified self determinants and tested the cultures for their ability to lyse TNP-modified self (RNC-TNP) and TNP-modified allogeneic (BALB/c-TNP) target cells. Each mouse was stimulated by two different protocols: either by the addition of TNP-modified irradiated nu/+ spleen cells or by TNP modification of the nude responder cells without addition of other cells. All mice could lyse RNC-TNP targets and about one-half could also lyse BALB/c-TNP targets, i.e., there was a 50:50 division between restricted and unrestricted responses. The magnitude of the response against RNC-TNP and whether the response was restricted were both independent of the method of stimulation. We conclude that H-2 restriction in these mice is imposed by an as yet unidentified environmental influence that can vary from one nude mouse to the next. The influence appears to act through negative selection because the modified self response is, if anything, higher in mice showing an unrestricted response.     

Taxonomic implications for diaptomid copepods based on contrasting patterns of mitochondrial DNA sequence divergences in four morphospecies

Morphological identification methods do not provide reliable and meaningful species identifications for taxa where morphological differences among distinct species are either absent or overlooked (i.e., cryptic species). For example, due to the minute nature of the morphological characters used to delineate diaptomid copepod species and the apparent potential for copepod speciation to occur with little or no morphological change (i.e., morphological stasis), morphological identifications of diaptomid species may not adequately capture their true species diversity. Here, we present results from a geographic survey of mtDNA sequences from populations across the geographic ranges of four North American diaptomid species—Leptodiaptomus minutus, Skistodiaptomus pallidus, Skistodiaptomus reighardi, and Onychodiaptomus sanguineus. Shallow mitochondrial DNA sequence divergences (maximum of 1.1%) among haplotypes of L. minutus from across its geographic range suggest that current morphological identification techniques reliably identify this species. In contrast, we found large mitochondrial DNA sequence divergences (14–22%) among populations within the currently recognized morphospecies of S. pallidus, S. reighardi, and O. sanguineus. However, pairwise sequence divergences within four distinct S. pallidus clades and within populations of S. reighardi and O. sanguineus were similarly low (maximum of 1.5%) as found within L. minutus as a whole. Thus, the S. pallidus, S. reighardi, and O. sanguineus morphospecies may be considered best as cryptic species complexes. Our study therefore indicates that morphological identifications, while sufficient for some species, likely underestimate the true species diversity of diaptomid copepods. As such, we stress the need for extensive taxonomic revision that integrates genetic, morphological, reproductive, and ecological analyses of this diverse and important group of freshwater zooplankton. Furthermore, we believe an extensive taxonomic revision will shed important insight into major questions regarding the roles of geography, phylogeny, and habitat on the frequency of cryptic species on earth. Handling editor: S. I. Dodson     

Plasmolyseform- und Plasmolysezeit-Studien

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