The taxonomy and phylogeny of the Cherax destructor complex (Decapoda : Parastacidae) examined using mitochondrial 16S sequences

This study uses nucleotide sequences from the 16S rRNA mitochondrial gene to investigate the taxonomy and phylogeny of freshwater crayfish belonging to the 'Cherax destructor' complex. The sequencing of an approximately 440-bp fragment of this gene region from freshwater crayfish sampled from 14 locations identified significant haplotype diversity. Phylogenetic analysis found three distinct clades that correspond to the species C. rotundus, C. setosus and C. destructor. C. rotundus is largely confined to Victoria, and C. setosus is restricted to coastal areas north of Newcastle in New South Wales. C. destructor is widely distributed in eastern Australia and shows significant phylogeographic structure, with three well supported clades. None of these clades, however, correspond to species previously recognised as C. esculus, C. davisi or C. albidus. The failure to genetically distinguish these morphologically defined species is consistent with reproductive information and morphological plasticity relating to habitat similar to that documented for other Cherax species.

Molecular phylogeny of the Cheilodactylidae and Latridae (Perciformes: Cirrhitoidea) with notes on taxonomy and biogeography

Phylogenetic relationships among cheilodactylid and latrid fishes were estimated from cytochrome oxidase I and cytochrome b mitochondrial DNA sequences. Two South African cheilodactylids, Cheilodactylus fasciatus and Cheilodactylus pixi, were divergent from the remaining members of their genus and family, and the monophyly of these groups was rejected based on parametric bootstrap analysis. As C. fasciatus is the nominal species for the genus and family, widespread taxonomic reassignment is implicated for the remaining 12 and 17 members of these groups, respectively. As these 17 cheilodactylids are not genetically or morphologically distinct from the latrids, it is proposed that the Latridae should be expanded to encompass them. The inferred relationships among those Cheilodactylus requiring generic reassignment were largely unresolved, and hence few recommendations can be made regarding their placement. Divergence time estimates indicate that chance oceanic dispersal subsequent to Gondwanan fragmentation best explains the Southern Hemisphere radiation of cheilodactylids.

Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy, and the convergent evolution of abbreviated larval development

There has hitherto been little research into evolutionary and taxonomic relationships amongst species of the freshwater prawn genus Macrobrachium Bate across its global distribution. Previous work by the authors demonstrated that the endemic Australian species did not evolve from a single ancestral lineage. To examine whether other regional Macrobrachium faunas also reflect this pattern of multiple origins, the phylogeny of 30 Macrobrachium species from Asia, Central/South America and Australia was inferred from mitochondrial 16S rRNA sequences. Phylogenetic relationships demonstrate that, despite some evidence for regional diversification, Australia, Asia and South America clearly contain Macrobrachium species that do not share a common ancestry, suggesting that large-scale dispersal has been a major feature of the evolutionary history of the genus. The evolution of abbreviated larval development (ALD), associated with the transition from an estuarine into a purely freshwater lifecycle, was also mapped onto the phylogeny and was shown to be a relatively homoplasious trait and not taxonomically informative. Other taxonomic issues, as well as the evolutionary origins of Macrobrachium, are also discussed.

Molecular taxonomy and phylogenetics of some species of Australian palaemonid shrimps

The evolutionary history and classification of the palaemonid shrimps has been the subject of constant speculation and debate. At present, all major systematic treatments have been based on morphological characteristics. To help resolve the phylogenetic relationships, and thus enable the creation of a classification system that reflects evolutionary history, a region of the 16S mitochondrial rRNA gene was sequenced for a number of Australian Palaemonidae. The resulting phylogenetic analyses indicated the presence of major anomalies in the current classification of Australian Palaemonidae. Significantly, three species belonging to three separate genera, Macrobrachium intermedium, Palaemon serenus, and Palaemonetes australis, are closely related, with genetic differences more characteristic with that of congeneric species. The results also demonstrate non-monophyly in Australian palaemonids with respect to both Palaemonetes and Macrobrachium.

Taxonomy and biology of two new species of gall midge (Diptera: Cecidomyiidae) infesting Sarcocornia quinqueflora (Chenopodiaceae) in Australian salt marshes

Two new species of gall midge associated with two distinct galls on the succulent creeping shrub Sarcocornia quinqueflora are described from salt marshes in south-eastern Australia. The infestations caused by the new species hinder the growth of S. quinqueflora, the seeds of which are the major food of the critically endangered orange-bellied parrot Neophema chrysogaster. Asphondylia floriformis sp. n. Veenstra-Quah & Kolesik transforms leaf segments into flower-like galls, whereas Asphondylia sarcocorniae sp. n. Veenstra-Quah & Kolesik produces simple swellings on branches. Both galls have fungal mycelium growing in the apoplast of the gall tissue and lining the inner surface of the larval chamber where it is presumably grazed by the larva. Descriptions of the larvae, pupae, males, females and the geographical distribution of the two gall midges in south-eastern Australia are given.

Taxonomy and survey of location management systems

In wireless mobile computing, location management is introduced whenever users move from one place to another. In order to track a mobile user, the system must store information about their current location and report new locations to a home base station. Numerous techniques have been proposed to optimally manage the location of mobile hosts in mobile networks. This paper attempts to present a more structured and comprehensive analysis of the current location management techniques architectures and their technology enablers. We discuss some of the principal issues involved in location management and present a taxonomy and survey of location management strategies that have been proposed in the literature over the years for mobile computing systems.

POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons

Background: The existence of exons and introns has been known for thirty years. Despite this knowledge, there is a lack of formal research into the categorization of exons. Exon taxonomies used by researchers tend to be selected ad hoc or based on an information poor de-facto standard. Exons have been shown to have specific properties and functions based on among other things their location and order. These factors should play a role in the naming to increase specificity about which exon type(s) are in question.

Results: POEM (Protein Oriented Exon Monikers) is a new taxonomy focused on protein proximal exons. It integrates three dimensions of information (Global Position, Regional Position and Region), thus its exon categories are based on known statistical exon features. POEM is applied to two congruent untranslated exon datasets resulting in the following statistical properties. Using the POEM taxonomy previous wide ranging estimates of initial 5' untranslated region exons are resolved. According to our datasets, 29–36% of genes have wholly untranslated first exons. Untranslated exon containing sequences are shown to have consistently up to 6 times more 5' untranslated exons than 3' untranslated exons. Finally, three exon patterns are determined which account for 70% of untranslated exon genes.

Conclusion: We describe a thorough three-dimensional exon taxonomy called POEM, which is biologically and statistically relevant. No previous taxonomy provides such fine grained information and yet still includes all valid information dimensions. The use of POEM will improve the accuracy of genefinder comparisons and analysis by means of a common taxonomy. It will also facilitate unambiguous communication due to its fine granularity

Cholesterol-lowering effects of plant sterol esters and non-esterified stanols in margarine, butter and low-fat foods

Objectives: To determine the efficacy on plasma cholesterol-lowering of plant sterol esters or non-esterified stanols eaten within low-fat foods as well as margarine.
Design: Randomised, controlled, single-blind study with sterol esters and non-esterified plant stanols provided in breakfast cereal, bread and spreads. Study 1 comprised 12 weeks during which sterol esters (2.4 g) and stanol (2.4 g) -containing foods were eaten during 4 week test periods of cross-over design following a 4 week control food period. In Study 2, in a random order cross-over design, a 50% dairy fat spread with or without 2.4 g sterol esters daily was tested.
Subjects: Hypercholesterolaemic subjects; 22 in study 1 and 15 in study 2.
Main outcome measures: Plasma lipids, plasma sterols, plasma carotenoids and tocopherols.
Results: Study 1¾median LDL cholesterol was reduced by the sterol esters (-13.6%; P<0.001 by ANOVA on ranks; P<0.05 by pairwise comparison) and by stanols (-8.3%; P=0.003, ANOVA and <0.05 pairwise comparison). With sterol esters plasma plant sterol levels rose (35% for sitosterol, 51% for campesterol; P<0.001); plasma lathosterol rose 20% (P=0.03), indicating compensatory increased cholesterol synthesis. With stanols, plasma sitosterol fell 22% (P=0.004), indicating less cholesterol absorption. None of the four carotenoids measured in plasma changed significantly. In study 2, median LDL cholesterol rose 6.5% with dairy spread and fell 12.2% with the sitosterol ester fortified spread (P=0.03 ANOVA and <5% pairwise comparison).
Conclusion: 1. Plant sterol esters and non-esterified stanols, two-thirds of which were incorporated into low-fat foods, contributed effectively to LDL cholesterol lowering, extending the range of potential foods. 2. The LDL cholesterol-raising effect of butter fat could be countered by including sterol esters. 3. Plasma carotenoids and tocopherols were not reduced in this study.

Plant variety protection and traditional agricultural knowledge in Southeast Asia

This article provides an overview of the emerging plant variety protection (PVP) systems in Southeast Asia. The case studies are from countries that form part of the regional Association of Southeast Asian Nations (ASEAN), mainly Indonesia, Malaysia, Philippines and Thailand. The focus will be on the intersection between intellectual property rights (IPRs) and popular demands for the protection of the traditional knowledge (TK) of local communities. Factors that fuelled the emergence and shaped the content of the PVP laws were the obligation to comply with art 27(3)(b) of the Agreement on Trade Related Aspects of Intellectual Property Rights (TRIPS Agreement), aspirations for the development of the biotechnology industry, avoidance of possible sanction under the US ‘Special 301’ procedure, Free Trade Agreements (FTAs), the role played by the International Union for the Protection of New Plant Varieties (UPOV), technical assistance from UPOV member countries, membership of international biodiversity treaties and demands from civil society organisations for protection of TK. The PVP laws that resulted present an uneasy amalgam of conventional property rights with some aspects of protection of TK. It is very likely that the local communities claiming TK rights will face legal hurdles, in as much as government agencies implementing the law will face administrative and technical complications.

Invertebrate diversity of the unexplored marine western margin of Australia: taxonomy and implications for global biodiversity

However derived, predictions of global marine species diversity rely on existing real data. All methods, whether based on past rates of species descriptions, on expert opinion, on the fraction of undescribed species in samples collected, or on ratios between taxa in the taxonomic hierarchy, suffer the same limitation. Here we show that infaunal macrofauna (crustaceans and polychaetes) of the lower bathyal depth range are underrepresented among available data and documented results from Australia. The crustacean and polychaete fauna (only partially identified) of the bathyal continental margin of Western Australia comprised 805 species, representing a largely novel and endemic fauna. Overall, 94.6% of crustacean species were undescribed, while 72% of polychaete species were new to the Australian fauna, including all tanaidaceans, amphipods, and cumaceans, as well as most isopods. Most species were rare, and the species accumulation rate showed no sign of reaching an asymptote with increasing area sampled. Similar data are likely for the largely unexplored bathyal regions. This leads us to conclude that the numbers upon which extrapolations to larger areas are based are too low to provide confidence. The Southern Australian and Indo-West Pacific deep-sea regions contribute significantly to global species diversity. These regions and bathyal and abyssal habitats generally are extensive, but are so-far poorly sampled. They appear to be dominated by taxonomically poorly worked and species-rich taxa with limited distributions. The combination of high species richness among infaunal taxa-compared to better known taxa with larger individuals, higher endemism than presently acknowledged because of the presence of cryptic species, the low proportion of described species in these taxa, and the vast extent of unexplored bathyal and abyssal environments-will lead to further accumulation of new species as more and more deep sea regions are explored. It remains to be tested whether ratios of 10 or more undescribed to described species, found in this study for the dominant taxa and for the deep Southern Ocean and the Indo-West Pacific, are replicable in other areas. Our data and similar figures from other remote regions, and the lack of faunal overlap, suggest that Appeltans et al.'s (Current Biology 22:1-14, 2012) estimate that between one-third and two-thirds of the world's marine fauna is undescribed is low, and that Mora et al.'s (PLoS Biol 9(8):e1001127. doi:10.1371/journal.pbio.1001127, 2011) of 91% is more probable. We conclude that estimates of global species, however made, are based on limited data. © 2014 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg.

A taxonomy and mapping of computer-based critiquing tools

Critics have emerged in recent times as a specific tool feature to support users in computer-mediated tasks. These computer-supported critics provide proactive guidelines or suggestions for improvement to designs, code, and other digital artifacts. The concept of a critic has been adopted in various domains, including medical, programming, software engineering, design sketching, and others. Critics have been shown to be an effective mechanism for providing feedback to users. We propose a new critic taxonomy based on extensive review of the critic literature. The groups and elements of our critic taxonomy are presented and explained collectively with examples, including the mapping of 13 existing critic tools, predominantly for software engineering and programming education tasks to the taxonomy. We believe this critic taxonomy will assist others in identifying, categorizing, developing, and deploying computer-supported critics in a range of domains.