Conversion of AFLP markers to high-throughput markers in a complex polyploid,sugarcane

The application of DNA markers linked to traits of commercial value in sugarcane may increase the efficiency of sugarcane breeding. The majority of markers generated for quantitative trait locus mapping in sugarcane have been single sequence repeats or AFLPs (amplified fragment length polymorphisms). Since AFLP markers are not adapted for large-scale implementation in plant breeding, our objective was to assess the feasibility of converting AFLP markers to fast, cheap and reliable PCR-based assays in a complex polyploid, sugarcane. Three AFLP markers were selected on the basis of an association to resistance to the fungal pathogen Ustilago scitaminea, the causal agent of smut in sugarcane. We developed an approach which enabled the identification of polymorphisms in these AFLP markers. Towards this goal, we employed GenomeWalking and 454 sequencing to isolate sequences adjacent to the linked AFLP markers and identify SNP (single nucleotide polymorphisms) haplotypes present in the homo(eo)logous chromosomes of sugarcane. One AFLP marker was converted to a cleavage amplified polymorphic sequence marker, another to a SCAR (sequence characteristered amplified region) marker and the final AFLP marker to a SNP PCR-based assay. However, validation of each of the markers in 240 genotypes resulted in 99, 90 and 60% correspondence with the original AFLP marker. These experiments indicate that even in a complex polyploid such as sugarcane, polymorphisms identified by AFLP can be converted to high-throughput marker systems, but due to the complexity this would only be carried out for high-value markers. In some cases, the polymorphisms identified are not transferable to more sequence-specific PCR applications.     

Analysis of the causes of declines in Western Siberian outbreaks of the nun moth <Emphasis Type=Italic>Lymantria monacha</Emphasis>

This study presents the results of an investigation into the causal factors of precipitous population declines after five mass outbreaks of nun moths (Lymantria monacha) in territories of Western Siberian (Novosibirsk and Tyumen oblasts, Russia). Nucleopolyhedrovirus (NPV) and parasitoids represented by the families Tachinidae and Sarcophagidae (Diptera) were found to be major contributors to the degradation of these outbreaks. Viable occlusion bodies persisted on pine needles during a two-year observation period and contaminated nun moth eggs, resulting in the death of the insects from NPV infection. A high probability of insect/virus contacts was largely attributable to the poor flying ability of female moths. Moreover, a latent virus was apparently activated in part of the insect population due to asynchrony between the growth rate of larvae and pine phenology.     

Taxon-specific multiplex-PCR for quick,easy, and accurate identification of encyrtid and aphelinid parasitoid species attacking soft scale insects in California citrus groves

Citricola scale, Coccus pseudomagnoliarum Kuwana (Hemiptera: Coccidae), is a serious pest of citrus in California’s San Joaquin Valley, but not in southern California where a complex of Metaphycus spp. Mercet (Hymenoptera: Encyrtidae) suppress it. This has created interest in using these (and other Metaphycus) species for biological control in the San Joaquin Valley. A critical step in assessing an organism’s potential for biological control is the ability to accurately identify it. For Metaphycus spp., this currently requires slide mounted adult specimens and expert taxonomic knowledge. We present a simple, quick and accurate method to identify any life stage of the ten major parasitoids of soft scales in California citrus, based on amplification of ribosomal DNA, using the polymerase chain reaction (PCR). Three multiplex-PCR protocols amplify products of taxon-specific sizes, allowing direct diagnosis of taxa accommodated by the PCR, and reducing identification time to a fraction of that of existing methods.     

The Harlequin ladybird continues to invade southeastern Europe

The ladybird Harmonia axyridis (Pallas) is considered one of the most serious invasive species around the globe. It has spread all over North America and Western Europe, while data from southeastern Europe, especially in the Mediterranean region, are scarce. In this study we present the first confirmed data of the spread of H. axyridis throughout Croatia. Specimens were sampled and identified during the period 2008–2010. The species was recorded at 18 localities in all three colour forms in various habitat types. Light trapping was found to be a satisfactory method for collecting H. axyridis. Since there is no evidence to suggest the deliberate introduction of H. axyridis in Croatia, it can be assumed that it has spread southwards from Central and Eastern Europe, and that it will probably continue to spread. Further investigations should focus on monitoring and detailed mapping of H. axyridis in Croatia and neighbouring countries, especially in the Mediterranean region, to determine whether stable populations are present.     

Ring-based versus disc-based separation of spatial scales: a case study on the impact of arable land proportions on invertebrates in freshwater streams

The impact of different land-use types on species is traditionally estimated by correlating landscape proportions recorded in buffer areas around focal points with species data observed at these sites. If a high proportion of a specific land-use type exists within a small radius, it will be accumulated in larger buffers and may confound the interpretation at larger scales. We sampled freshwater invertebrates in ten streams using cages with artificial substrate and compared the effects of arable land proportions calculated in disc-shaped buffers of increasing radius versus areas calculated from non-overlapping rings of increasing radius. We hypothesize that (1) the accumulative disc-based approach leads to confounding effects across increasing buffer size and that (2) the use of ring-based methods facilitates the identification of relevant scales for conservation measures. The abundance of crustaceans showed a positive relationship with arable land proportions, but Plecoptera abundance and the taxonomic richness of Ephemeroptera and Plecoptera decreased with increasing arable land proportions in the surrounding landscape. Our results further support the presence of confounding effects in disc-based analyses, as correlations between arable land proportions and Crustacea, or Plecoptera, respectively, were affected by the accumulation of small-scale area proportions. The distance at which arable land proportions significantly affected benthic fauna in freshwater streams was consistently shorter if calculated from rings rather than from discs. Although an a priori definition of ring width introduces new challenges, a combined use of disc- and ring-based techniques for the estimation of land-use effects may substantially improve the realization of conservation and protection measures in terrestrial and aquatic systems.     

Increased abundance of the non-indigenous zooplanktivore, <Emphasis Type=Italic>Bythotrephes longimanus</Emphasis>, is strongly correlated with greater spring prey availability in Canadian Shield lakes

The non-indigenous zooplanktivore, Bythotrephes longimanus, is a large Palaearctic cladoceran that is spreading rapidly in the Great Lakes watershed in North America. As a voracious predator, Bythotrephes can reduce herbivorous cladoceran abundance and diversity; however, the variables that affect its abundance are not well understood. To determine what bottom-up factors are associated with the abundance and seasonal dynamics of established Bythotrephes populations, two Bythotrephes datasets from lakes in south-central Ontario, Canada, were analysed using multiple regression and multivariate analyses: a multi-lake dataset of nine lakes sampled in 2003 and a multi-year dataset of one of these lakes, Harp Lake, sampled from 1994–1998 and 2001–2004. Bottom-up variables tested were Secchi disk depth, epilimnetic temperature, cladoceran (prey) density, total phosphorus, dissolved organic carbon and Chlorophyll a, as well as maximum depth for the multi-lake dataset. In both analyses and datasets, springtime abundance of herbivorous cladocerans was consistently found to be a significant factor associated with Bythotrephes (June–September) abundance; Bythotrephes annual abundance was significantly and positively associated with mean May and June prey abundance, along with mean Secchi disk depth for the multi-lake dataset, and groups of lakes or years with similar Bythotrephes seasonal abundance patterns were predicted by June prey abundance. Additionally, prey availability was the dominant contributor towards changes in weekly Bythotrephes birth rates calculated for two of the study lakes. Our study suggests that prey availability influences Bythotrephes abundance, which provides evidence that Bythotrephes establishment success is affected by the abundance of its prey.     

Correlation between the leaf turnover rate and anti-herbivore defence strategy (balance between ant and non-ant defences) amongst ten species of <Emphasis Type=Italic>Macaranga</Emphasis> (Euphorbiaceae)

We measured variation in the intensities of ant and non-ant anti-herbivore defences amongst ten Macaranga species in Sarawak, Malaysia. Intensities of non-ant defences were estimated by measuring effects of fresh leaves (provided as food) of these Macaranga species on survival of common cutworm larvae [Spodoptera litura (Fabricius), Lepidoptera: Noctuidae]. Intensities of ant defences were estimated by measuring ant aggressiveness in the presence of artificial damage inflicted on plants. As part of our examination of non-ant defences, we measured leaf toughness (punch strength, by penetrometry), and the contents of total phenols and condensed tannin. We demonstrated interspecific variation in intensities of both ant and non-ant defences amongst ten Macaranga species and showed that the rank order of ant defence intensity was negatively correlated with the intensity of non-ant defence. We also found that the balance between ant and non-ant defence intensity was correlated with the rates of leaf turnover and shoot growth. Species investing more in ant defence tended to have higher leaf turnover rates. Macaranga species that occur preferentially in shadier microhabitats had lower leaf turnover rates, suggesting that non-ant defences are more cost-effective in more shade-tolerant species. Our results also suggest that the total intensity of non-ant defences is positively correlated with both leaf toughness and total phenol content.     

Invasion of the African sharp-tooth catfish <Emphasis Type=Italic>Clarias gariepinus</Emphasis> (Burchell, 1822) in South China

We record here the invasion of the African sharp-tooth catfish Clarias gariepinus in the South China biodiversity hotspot, an area rich in endemic and endangered fish fauna. C. gariepinus was introduced into the natural systems as escapees from aquaculture ponds. These catfishes are very large, top predators, and thus have the potential to cause serious threats to the native fish fauna. The impact of C. gariepinus needs more investigation with emphasis on developing techniques for controlling its dispersal.