GC/MS data reduction using retention time alignment and spectral subtraction

The identification of chemical compounds in a complex mixture is a challenge. In the context of drug surveillance for the sporting world, large-scale screening of urine and blood samples is undertaken using methods such as GC/MS with low-resolution mass spectrometers that measure integer values of m/z ratio. The analysis of the GC/MS data can be automated using standard mass spectrometry software to detect peaks in the chromatograms and to search a library of mass spectra of known drugs. Because of noise and the presence of co-eluting compounds, the mass spectra are usually not exactly the same as those in the library. The match quality for a genuine match can be quite low, and the library search settings must be sufficiently sensitive so as not to miss positive samples. Therefore many false matches are reported for checking and validation by human analysts, and, since almost all the samples are negative, this process of checking is tedious, time-consuming and cost-inefficient. The usual technique to remove unwanted background is to subtract the spectrum of an adjacent scan of the same sample. Our proposed method instead subtracts the spectrum of a second similar sample. The intention is that any contributions from a substance common to the two samples will be eliminated, and that any substance that is in the first sample but not in the second will still be recorded in the subtracted dataset. Assuming a suitable second sample is available that does not contain banned substances, those that are present in the first sample can be more easily detected. The subtraction is applied to each scan of the test sample. For this to work, it is essential that retention times are precisely aligned so that a corresponding scan of the second sample can be chosen. Although many methods of alignment are described in the literature, simple linear alignment based on a correlation measure is found to be sufficient. It is also necessary to scale the spectra being subtracted to allow for differences between the two samples in the concentration of the common compounds. Subtracting a similar dataset will reduce the number of peaks to be considered, and our hypothesis is that a library search of the resulting dataset will produce a smaller number of false matches than the same library search applied to the original data. An experiment was carried out to test this and the number of false matches was indeed found to be reduced. The more similar the second sample was to the first, the better was the result. It was also verified that true matches of compounds of interest are still reported by the library search of the subtracted data

Geographic and taxonomic patterns of extinction risk in Australian squamates

Australia is a global hotspot of reptile diversity, hosting similar to 10% of the world's squamate (snake and lizard) species. Yet the conservation status of the Australian squamate fauna has not been assessed for >25 years; a period during which the described fauna has risen by similar to 40%. Here we provide the first comprehensive conservation assessment of Australian terrestrial squamates using IUCN Red List Categories and Criteria. Most (86.4%; n = 819/948) Australian squamates were categorised as Least Concern, 4.5% were Data Deficient, and 7.1% (range 6.8%-11.3%, depending on the treatment of Data Deficient species) were threatened (3.0% Vulnerable, 2.7% Endangered, 1.1% Critically Endangered). This level of threat is low relative to the global average (similar to 18%). One species (Emoia nativitatis) was assessed as Extinct, and two species (Lepidodactylus listeri and Cryptoblepharus egeriae) are considered Extinct in the Wild: all three were endemic to Christmas Island. Most (75.1%) threat assessments were based on geographic range attributes, due to limited data on population trends or relevant proxies. Agriculture, fire, and invasive species were the threats that affected the most species, and there was substantial geographic variation in the number of species affected by each threat. Threatened species richness peaked on islands, in the Southern Alps, and across northern Australia. Data deficiency was greatest in northern Australia and in coastal Queensland. Approximately one-in-five threatened species were not represented in a single protected area. Our analyses shed light on the species, regions, and threats in most urgent need of conservation intervention

Conservation status of the world's skinks (Scincidae): taxonomic and geographic patterns in extinction risk

Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation status of skinks (Scincidae), a speciose reptile family with a worldwide distribution. Using International Union for Conservation of Nature (IUCN) criteria, we report that ~20% of species are threatened with extinction, and nine species are Extinct or Extinct in the Wild. The highest levels of threat are evident in Madagascar and the Neotropics, and in the subfamilies Mabuyinae, Eugongylinae and Scincinae. The vast majority of threatened skink species were listed based primarily on their small geographic ranges (Criterion B, 83%; Criterion D2, 13%). Although the population trend of 42% of species was stable, 14% have declining populations. The key threats to skinks are habitat loss due to agriculture, invasive species, and biological resource use (e.g., hunting, timber harvesting). The distributions of 61% of species do not overlap with protected areas. Despite our improved knowledge of the conservation status of the world's skinks, 8% of species remain to be assessed, and 14% are listed as Data Deficient. The conservation status of almost a quarter of the world's skink species thus remains unknown. We use our updated knowledge of the conservation status of the group to develop and outline the priorities for the conservation assessment and management of the world's skink species