Calibration of sampling techniques and determination of sample size for the estimation of egg and larval populations of Helicoverpa spp. (Lepidoptera: Noctuidae) on irrigated soybean

Abstract  Informed spray decisions require accurate assessments of the target pest's density. Currently, no advice is provided to farmers on the best method for sampling soybean for insect pests, although spray thresholds for Helicoverpa larvae are provided. This article describes the results of a trial designed to calibrate relative sampling techniques for Helicoverpa larvae; visual inspection of plants in situ in the field, beat cloth, sweep net and D-vac sampling were compared with an absolute measure of population density. The absolute measure was derived from the bagging and removal of whole plants in the field, followed by subsequent examination in the laboratory. Analysis of the distribution of Helicoverpa larvae collected by the different samples was then used to calculate the number of samples required to determine whether the economic threshold had been reached to different levels of certainty and accuracy. Significant relationships were detected between all the relative sampling techniques and the absolute, suggesting that all could be used to estimate field populations. However, due to the high variance and therefore increased sample sizes required, or the length of time taken to collect samples, only beat-cloth sampling appeared to offer a realistic method for farmers in the field. The results also suggest that the current best practice of sampling six locations per crop provides an adequate assessment of the field populations at the currently accepted threshold level of 6 larvae m⁻². However, if the economic spray was reduced, the number of samples required to determine an accurate population estimate would increase dramatically.     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

Human-Assisted Invasions of Pacific Islands by Litoria Frogs: A Case Study of the Bleating Tree Frog on Lord Howe Island

There are substantial differences among taxonomic groups in their capacity to reach remote oceanic islands via long-distance overwater dispersal from mainland regions. Due to their permeable skin and intolerance of saltwater, amphibians generally require human-assisted dispersal to reach oceanic islands. Several Litoria frog species have been introduced to remote islands throughout the Pacific Ocean region. Lord Howe Island (LHI) is an oceanic island that lies approximately 600 km east of the Australian mainland and has a diverse, endemic biota. The bleating tree frog (Litoria dentata) is native to mainland eastern Australia, but was accidentally introduced to LHI in the 1990s, yet its ecology and potential impact on LHI has remained unstudied. We used a mitochondrial phylogeographical approach to determine that L. dentata was introduced from the Ballina region in northeastern New South Wales. The founding population was likely accidentally introduced with cargo shipped from the mainland. We also completed the first detailed investigation of the distribution, ecology and habitat use of L. dentata on LHI. The species is widespread on LHI and is prevalent in human habitat, cattle pasture and undisturbed forest. We discuss the potential impact of introduced Litoria species on Pacific islands and outline what biosecurity protocols could be implemented to prevent the introduction of further amphibian species to the ecologically sensitive oceanic area.     

Evolutionary origins and diversification of dragon lizards in Australia's tropical savannas

Australia's monsoonal tropics are dominated by the largest and least modified savanna woodlands in the world, and they are globally significant for their high biodiversity and regional endemism. Despite this, there have been very few molecular studies of the evolutionary origins and diversification of vertebrates in this region. The semi-arboreal dragon lizards of Lophognathus and Amphibolurus are widely distributed in the savanna and dry sclerophyll woodlands of Australasia, including the monsoon tropics. We sequenced a ~1400 bp region of mitochondrial DNA and a ~1400 bp nuclear gene (RAG1) to investigate the phylogenetic relationships and phylogeographic structuring of all seven species of Lophognathus and Amphibolurus. Our analyses show that there is a higher level of species and generic diversity in the monsoon tropics than previously thought, and a full morphological review and taxonomic revision of these genera is required. Relaxed molecular clock analyses indicate that species across both genera originated in the late Miocene and early Pliocene, with significant phylogeographic structure within species. We did not find any evidence that the monsoon tropics species were a monophyletic group that had diversified within the region; instead Amphibolurus and Lophognathus represent at least three independent evolutionary colonizations of the monsoon tropics. It is probable that the origins and phylogeographic patterns of the northern Lophognathus species have evolved under the climatic influence of the Australian monsoon, rather than being either an ancient Gondwanan lineage that pre-dates the monsoon or the result of a more recent dispersal event across Wallace's Line.     

A first estimate of white shark, Carcharodon carcharias, abundance off Central California

The decline of sharks in the global oceans underscores the need for careful assessment and monitoring of remaining populations. The northeastern Pacific is the home range for a genetically distinct clade of white sharks (Carcharodon carcharias). Little is known about the conservation status of this demographically isolated population, concentrated seasonally at two discrete aggregation sites: Central California (CCA) and Guadalupe Island, Mexico. We used photo-identification of dorsal fins in a sequential Bayesian mark-recapture algorithm to estimate white shark abundance off CCA. We collected 321 photographs identifying 130 unique individuals, and estimated the abundance off CCA to be 219 mature and sub-adult individuals ((130, 275) 95% credible intervals), substantially smaller than populations of other large marine predators. Our methods can be readily expanded to estimate shark population abundance at other locations, and over time, to monitor the status, population trends and protection needs of these globally distributed predators.     

The Effects on Lignin Structure of Overexpression of Ferulate 5-Hydroxylase in Hybrid Poplar1

Poplar (Populus tremula × alba) lignins with exceedingly high syringyl monomer levels are produced by overexpression of the ferulate 5-hydroxylase (F5H) gene driven by a cinnamate 4-hydroxylase (C4H) promoter. Compositional data derived from both standard degradative methods and NMR analyses of the entire lignin component (as well as isolated lignin fraction) indicated that the C4H∷F5H transgenic''s lignin was comprised of as much as 97.5% syringyl units (derived from sinapyl alcohol), the remainder being guaiacyl units (derived from coniferyl alcohol); the syringyl level in the wild-type control was 68%. The resultant transgenic lignins are more linear and display a lower degree of polymerization. Although the crucial β-ether content is similar, the distribution of other interunit linkages in the lignin polymer is markedly different, with higher resinol (β-β) and spirodienone (β-1) contents, but with virtually no phenylcoumarans (β-5, which can only be formed from guaiacyl units). p-Hydroxybenzoates, acylating the γ-positions of lignin side chains, were reduced by >50%, suggesting consequent impacts on related pathways. A model depicting the putative structure of the transgenic lignin resulting from the overexpression of F5H is presented. The altered structural features in the transgenic lignin polymer, as revealed here, support the contention that there are significant opportunities to improve biomass utilization by exploiting the malleability of plant lignification processes.In the continuing search for improved biomass utilization in processes including chemical pulping, natural ruminant digestibility, and biomass conversion to ethanol, considerable attention has focused on improving lignocellulosic feedstocks through genetic engineering. Perturbing plant biomass deposition by misregulating key genes/enzymes integral to major cell wall pathways can provide rich insights into cell wall development and architecture and also create significant opportunities for improved lignocellulosic utilization (Baucher et al., 2003; Boerjan et al., 2003; Ralph et al., 2004). Lignins comprise the second most abundant polymer class in the biosphere; however, their combinatorial biosynthesis renders them among the more complex biomacromolecules synthesized by plants. Alterations in plant cell wall chemistry or ultrastructure, including lignin content or structure, can have a profound effect on chemical or enzymatic degradability. For example, in chemical pulping, lignin structure and content have been shown to significantly impact delignification efficiency (both pulp yield and residual lignin [RL] content) and pulp bleachability (Chang and Sarkanen, 1973; Huntley et al., 2003; Stewart et al., 2006). Similarly, improvements in fermentable sugar yields have been reported in lignin-engineered Medicago sativa (Chen and Dixon, 2007).In recent years, the genes encoding enzymes specific to the lignin branch of the phenylpropanoid pathway have been cloned and their roles evaluated using a combination of forward and reverse genetics (Franke et al., 2002; Baucher et al., 2003; Boerjan et al., 2003). The down-regulation of genes early in the pathway may limit the overall flux of metabolites to lignin synthesis. In contrast, the genes common to the latter part of the pathway generally affect the distribution of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) lignin units resulting from the primary monomers (the three monolignols p-coumaryl, coniferyl, and sinapyl alcohols). And, in several cases when the biosynthesis of a normal monolignol is severely curtailed, lignins appear to incorporate unique phenolics (e.g. 5-hydroxyconiferyl alcohol, hydroxycinnamaldehydes, and ferulic acid) that have not traditionally been considered lignin monomers (Sederoff et al., 1999; Boerjan et al., 2003; Ralph et al., 2004, 2008a, 2008b).Ferulate 5-hydroxylase (F5H), also referred to coniferaldehyde 5-hydroxylase to reflect one of its preferred substrate (Humphreys et al., 1999; Osakabe et al., 1999), is a key enzyme involved in synthesizing the monolignol sinapyl alcohol and, ultimately, S lignin moieties. F5H therefore affects the partitioning between the two major traditional monolignols, coniferyl and sinapyl alcohols, and is fundamental to the evolutionary differences between gymnosperms (with no S components) and angiosperms (with compositions favoring the S monomers). For example, the fah1 Arabidopsis (Arabidopsis thaliana) mutant, deficient in F5H, has little to no S lignin (Meyer et al., 1998; Marita et al., 1999). Like gymnosperms, it produces G-rich lignins, derived almost exclusively from coniferyl alcohol. In contrast, the overexpression of F5H in the mutant background produces plants displaying substantially higher than normal sinapyl alcohol-derived S units and is consequentially severely depleted in coniferyl alcohol-derived G units. Wet chemical analyses of cell wall lignins estimated S contents of up to about 92% in F5H-up-regulated Arabidopsis (Meyer et al., 1998), up to 84% in tobacco (Nicotiana tabacum; Franke et al. 2000), and as high as 93.5% in hybrid poplar (Populus tremula × Populus alba; Huntley et al., 2003; Li et al., 2003). These engineered cell walls, rich in S units, exceed the highest reported in nature to date (Baucher et al., 1998), with kenaf (Hibiscus cannabinus) bast fiber lignin, at 85% S, being among the highest (Ralph, 1996; Morrison et al., 1999). In poplars, the final methylation step, catalyzed by caffeic acid 3-O-methyl transferase (COMT), appears to adequately accommodate the increased flux from coniferaldehyde to 5-hydroxyconiferaldehyde to produce sinapaldehyde and ultimately sinapyl alcohol (Li et al., 2000, 2003). In Arabidopsis, however, evidence suggests that the COMT is not able to keep pace with the increased 5-hydroxyconiferaldehyde generated by F5H overexpression, since the ensuing lignins comprise a significant component derived from 5-hydroxyconiferyl alcohol (Ralph et al., 2001a). Novel 5-hydroxyguaiacyl benzodioxane structures, which result from incorporation of 5-hydroxyconiferyl alcohol into the lignification scheme, were the same as those noted in COMT-deficient plants (Ralph et al., 2001a, 2001b; Marita et al., 2001, 2003).The availability of woody plant material possessing an extreme S lignin concentration affords unique opportunities to explore the mechanisms and consequences of pushing plants toward compositional limits and has both major fundamental and industrial consequences. Engineering lignin composition to extreme levels provides rare and novel insights into the ramifications on the structure of the lignin component and on other cell wall characteristics. Here, we investigate the nature of the chemical modifications to the lignin polymer in up-regulated cinnamate 4-hydroxylase (C4H)∷F5H poplar and propose a model for how such gene perturbation impacts lignin biosynthesis.     

Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations

Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.