The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning

DNA Microarrays for Identifying Fishes

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products

Sperm Competition, Sperm Numbers and Sperm Quality in Muroid Rodents

Sperm competition favors increases in relative testes mass and production efficiency, and changes in sperm phenotype that result in faster swimming speeds. However, little is known about its effects on traits that contribute to determine the quality of a whole ejaculate (i.e., proportion of motile, viable, morphologically normal and acrosome intact sperm) and that are key determinants of fertilization success. Two competing hypotheses lead to alternative predictions: (a) sperm quantity and quality traits co-evolve under sperm competition because they play complementary roles in determining ejaculate's competitive ability, or (b) energetic constraints force trade-offs between traits depending on their relevance in providing a competitive advantage. We examined relationships between sperm competition levels, sperm quantity, and traits that determine ejaculate quality, in a comparative study of 18 rodent species using phylogenetically controlled analyses. Total sperm numbers were positively correlated to proportions of normal sperm, acrosome integrity and motile sperm; the latter three were also significantly related among themselves, suggesting no trade-offs between traits. In addition, testes mass corrected for body mass (i.e., relative testes mass), showed a strong association with sperm numbers, and positive significant associations with all sperm traits that determine ejaculate quality with the exception of live sperm. An “overall sperm quality” parameter obtained by principal component analysis (which explained 85% of the variance) was more strongly associated with relative testes mass than any individual quality trait. Overall sperm quality was as strongly associated with relative testes mass as sperm numbers. Thus, sperm quality traits improve under sperm competition in an integrated manner suggesting that a combination of all traits is what makes ejaculates more competitive. In evolutionary terms this implies that a complex network of genetic and developmental pathways underlying processes of sperm formation, maturation, transport in the female reproductive tract, and preparation for fertilization must all evolve in concert

Pollinator foraging modifies nectar sugar composition in Helleborus foetidus

We experimentally tested the hypothesis that the extensive within-plant variation of nectar sugar composition in Helleborus foetidus (Ranunculaceae) and other species results from differences between flowers and nectaries in pollinator visitation history. Experiments were conducted to mimic single-nectary visits by wild-caught individuals of the main bee pollinators of H. foetidus, which were assayed for their capacity to modify the sugar composition of natural and artificial nectar. Experimental nectar probing with bee mouthparts induced extensive changes in proportional sugar composition 48 h after treatment, and bee taxa differed widely in their effects. Nectar probing by Andrena, medium-sized Anthophoridae, Apis mellifera, and Lasioglossum had no subse- quent effects on nectar sugar composition, while probing by Bombus terrestris and B. pratorum induced an extensive reduction in percentage sucrose, a marked increase in percentage fructose, and a slight increase in percentage glucose. Results support the hypothesis that stochastic variations among flowers or nectaries in the taxonomic identity of recent visitors and their relative visita- tion frequencies may eventually generate very small-scale mosaics in nectar sugar composition. Changes in nectar sugar composi- tion following bumblebee probing may be the consequence of nectar contamination with pollinator-borne nectarivorous yeastsPeer reviewe

Molecular identification and pathogenicity assessment of a rust fungus infecting common ragweed (Ambrosia artemisiifolia) in its native North American range

A rust fungus collected from common ragweed (Ambrosia artemisiifolia) in Texas, USA, was identified as belonging to the Puccinia xanthii morphospecies based on its nrDNA ITS sequence. Pathogenicity studies carried out with this rust accession under quarantine conditions in the UK showed that the fungus was highly virulent on A. artemisiifolia plants from Australia. Recently, P. xanthii has been proposed as a potential classical biological control agent (CBCA) for common ragweed in its invasive range, focusing on Europe, despite previous doubts about its biocontrol potential. The results of the pathogenicity tests reported here support the suitability of this pathogen as a CBCA for common ragweed