Shanan S. Tobe

• B.Sc. Honours, M.Sc., Ph.D.
• Associate Professor at Murdoch University

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci i...

Despite their wide use, the limits of presumptive tests can be poorly understood. The aim of this study was to investigate the specificity and sensitivity of conventional, as well as innovative, presumptive tests for blood, semen and saliva. We investigated Kastle-Meyer (KM) and leucomalachite green (LMG) tests for blood with regard to their sensit...

Sexual assault samples are some of the most common samples encountered in forensic analysis. These samples can require a significant time investment due to differential extraction processes. We report on the first record of successful direct amplification of semen for STR analysis. Neat seminal fluid, dilutions ranging from 1:5 to 1:160 and GEDNAP...

1. The current classification of the Felidae was reviewed by a panel of 22 experts divided into core, expert and review groups, which make up the Cat Classification Task Force CCTF of the IUCN Cat Specialist Group. 2. The principal aim of the CCTF was to produce a consensus on a revised classification of the Felidae for use by the IUCN. 3. Based on...

Real-time PCR (qPCR) is widely used in the life sciences. For quantifying DNA, a standard curve is required. Common methods for standard development are time consuming, costly, necessitate a specific skill set, and pose a contamination risk. Using a targeted synthetic oligonucleotide, such as a gBlocks® Gene Fragment, overcomes these drawbacks and...

Bone and teeth, specialised bio-mineralized connective tissues, are left after the typical decomposition process of any vertebrate organism. Their analysis can reveal insights into an organism's life and retrace the history of the remains after death (also known as taphonomy), which ultimately evolves to destruction or fossilization. Studies on the...

Unlike the chemical composition and diagenetic modification of buried bones, subaqueous archaeological bone diagenesis has not been studied in detail. This observational work presents a macroscopic and microscopic characterization of eleven variably preserved archaeological terrestrial mammalian bones submerged in seawater and/or surrounded by mari...

Foraminifera are marine single-celled organisms, ubiquitous in marine environments, present in brackish waters and absent in terrestrial locations. Their presence has been associated with archaeological and forensic studies only rarely, and just once and superficially with bones of terrestrial mammals. In this study, a new association is presented...

Diagenesis is the collective word for the physical, biological, and chemical processes that bones undergo in the post-mortem period, until their physical destruction or fossilization. In forensic anthropology, the analysis of macroscopic and microscopic bone alterations, alongside the taphonomy of the soft tissues of a body, has proven valuable for...

Wildlife crimes and the threats they present to elephant populations raise the need to develop and implement DNA-based methodology as an aid for wildlife forensic investigations and conservation efforts. This study describes the development of a tetra-nucleotide repeat STR multiplex, genotyping assay that will identify Asian elephant (Elephas maxim...

A framework for the development and validation of a qPCR assay for species identification and DNA quantification for conservation and forensic purposes is presented. Elephants are commonly poached for their ivory tusks, which is the primary driving force behind their endangered status. In addition to poaching and trade, habitat loss due to logging...

Groundwater is increasingly used globally for domestic, industrial and agricultural production. While many studies have focused on groundwater as a resource, the diverse ecosystems within are often ignored. Here, we assess 54 Southern South Australian groundwater microbial communities from the populated part of the state to assess their status and...

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Her...

Two-dimensional contour plots showing the presence of hotspots and coldspots in A LDNA, B HDNA, C V1, D V2 and E Total virus. Faint gridlines indicate sampling interval. Minimum contour value of ≥ 10000 chosen. Solid red regions indicate sample points higher than the maximum contour level selected. Solid white point indicates empty sample well. Col...

MLE-calculated optimal Pareto (power) law truncation point, estimated best-fit exponent, and goodness of fit test information for genus abundance distributions across all samples. (DOCX)

Total prokaryotic abundances determined via flow cytometry. (DOCX)

SIMPER similarity comparisons between subsamples with no removal and removal of genera with heightened relative abundance. (DOCX)

SIMPER similarity comparisons between samples with no removal and removal of genera with heightened relative abundance. (DOCX)

F-statistics and change points in the total prokaryote rank-abundance profile resulting from the supF criterion for optimal distribution breaks between (A) hotspots-background (B) background-coldspot and (C) within background data. (TIF)

Normal QQ plots of the residuals (top) and residuals vs fitted (bottom) scatterplots for the chosen rank-abundance models for (L-R): hotspots; background (1); background (2); and coldspots. (TIF)

Representative flow cytometric biparametric cytogram of SYBR Green fluorescence vs. side scatter (size) showing the presence of two prokaryotic (LDNA and HDNA) and two viral (V1 and V2) subpopulations. (TIF)

Phylogenetic heatmaps of A hotspot, B coldspots and C background subsamples showing the heightened abundance of Firmicutes, Proteobacteria and Bacteroidetes. For clarity, only phyla representing > 2% average abundance are shown. OTUs determined via RDP Classifier within the UPARSE pipeline. (TIF)

Maximum likelihood parameter estimates and AICc ranks and weights for genus abundance distributions across all samples. (DOCX)

Mitochondrial DNA (mtDNA) can provide a means for forensic identity testing when genotyping of nuclear DNA (nuDNA) targets is not possible due to degradation or lack of template. For degraded samples, an indication of the quantity and quality of mtDNA is essential to allow selection of appropriately sized targets for hypervariable region (HVR) anal...

Many archaeological science studies use the concept of “provenance”, where the origins of cultural material can be determined through physical or chemical properties that relate back to the origins of the material. Recent studies using DNA profiling of bacteria have been used for the forensic determination of soils, towards determination of geograp...

Order level relative proportion of matches to the Greengenes (13_08) database. (PDF)

Plot showing the relative abundance in each sample of 70 different orders. (PDF)

Number of sequences obtained for each ochre sample. (PDF)

A European Endangered Species Programme (EEP) was established in the early 1990s, in order to manage a captive population of Asian lions (Panthera leo leo) within European zoos. The founders of this population comprised of nine individuals that originated from a captive population in India. During 2007–2009, 57 lions were born in the European capti...

The composition and diversity of bacteria forming the microbiome of parasitic organisms have implications for differential host pathogenicity and host-parasite co-evolutionary interactions. The microbiome of pathogens can therefore have consequences that are relevant for managing disease prevalence and impact in affected hosts. Here we investigate...

The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B, were analyzed. These strains were isolated from surface-sterilized roots of lucerne plants from South Australia and were found to promote the growth of the rhizobial partner in vitro and significantly increased nodulation and nitrogen fixation in lucerne pla...

The complete genome sequences of three endophytic Streptomyces species were compared. Strains EN16, EN23, and EN27 were isolated from surface-sterilized roots of wheat plants from South Australia. In field trials, these strains are effective in suppressing fungal root diseases of wheat when added as spore coatings to wheat seed.

Here, we evaluate Diamond Nucleic Acid Dye (DD) for use in quantitative PCR (qPCR) applications. Although DD is a commercially available stain for detection of DNA separated by gel electrophoresis, its use as a detection dye in qPCR has yet to be described. To determine if DD can be used in qPCR, we investigated its inhibitory effects on qPCR at co...

More than 97% of the world’s freshwater reserves are found in aquifers, making groundwater one of the most important resources on the planet. Prokaryotic communities in groundwater underpin the turnover of energy and matter while also maintaining groundwater purity. Thus, knowledge of microbial transport in the subsurface is crucial for maintaining...

Microscale microbial distributions are patchy, with abundance hotspots and cold - spots that provide important microenvironments for microbial interactions. However, studies are often restricted to abundance estimates alone. At the riverbed of the Murray River, we used taxonomy to complement quantitative analysis to show that abundance hotspots, co...

It is known that DNA can be deposited onto a surface by touch yet few means have been developed for its in situ detection. Collecting touch-DNA samples can be difficult as likely locations rather than the DNA is targeted leading to many samples that are submitted to a forensic laboratory containing little or no DNA. A range of dyes are available th...

We report on the effects of six dyes used in the detection of DNA on the process of DNA extraction, amplification and detection of STR loci. While dyes can be used to detect the presence of DNA, their use is restricted if they adversely affect subsequent DNA typing processes. Diamond™ Nucleic Acid Dye, GelGreen™, GelRed™, RedSafe™, SYBR(®) Green I...

Current histological investigation of vaginal swabs after alleged sexual assault includes the scoring of spermatozoa (0, + to ++++) and the recording of visible tails. It is a method that is universally employed. Despite this method being used for 40 years, there has never been a study investigating its suitability for forensic science. Here, we in...

Non-invasive genetic sampling using scats has a well established role in conservation biology, but has rarely been applied to reptiles. Using scats from captive and wild Egernia stokesii (Squamata, Scincidae) we evaluated two storage and six DNA-extraction methods and the reliability of subsequent genotype and sequence data. Accurate genotype and s...

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically the most common dye used for gel staining is ethidium bromide however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now availabl...

An identification assay has been developed that allows accurate detection of 19 of the most common terrestrial mammals present in New Zealand (cow, red deer, goat, dog, horse, hedgehog, cat, tammar wallaby, mouse, weasel, ferret, stoat, sheep, rabbit, Pacific rat, Norway rat, ship rat, pig, and brushtail possum). This technique utilizes species-spe...

Wildlife forensic science is a relatively new field in both research and its use in criminal investigations. It should be acknowledged from the outset that wildlife forensic science encompasses many areas of the analytical sciences and each plays a potentially crucial role. This book is focused on the use of DNA in wildlife forensic science while n...

This chapter leads the reader through the process of designing, testing and validating a species testing. This is conducted using step by step worked examples that can be followed by the user. In this chapter, the phylogenetic definition of a species is used. All members of the same species share a large amount of their DNA. Closely related species...

Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was succe...

The complete mitochondrial genomes of five tiger samples from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed Panthera-specific primer sets. The genome organization and gene arrangement of the five tiger samples were similar to each other; however polymorphic tandem repe...

NOTE - An erratum is available at http://dx.doi.org/10.1007/s11033-012-1879-2. This adds an additional author and also corrects miss-classification of samples. The complete mitochondrial genomes of five tiger samples from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed P...

Poaching is a worldwide crime that can be difficult to investigate due to the nature of the evidence. Previous studies have focused on the identification of endangered species in cases of poaching. Difficulties arise if the poached animal is not endangered. In the UK deer have hunting seasons whereby they can legally be hunted. Therefore, identific...

Species identification is a tool used extensively in forensic science; particularly in the investigation of wildlife crime. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b), and identification is generally carried out through the use of DNA sequencing. Howeve...

Despite renewed public interest, education, research and legislation, Traditional East Asian Medication (TEAM) continues to incorporate animal parts from endangered species and can be obtained openly in many countries. Products sold as having medicinal properties include plasters, pills, ointments, tonic wine and others. Due to the low population l...

The Convention on the International Trade in Endangered Species of Wild Fauna and Flora (CITES) monitors the international trade in endangered animal and plant species; a high profile example is the tiger, Panthera tigris. We report on the application of a SNaPshot multiplex technique to simultaneously identify tiger species and subspecies; this te...

This work was based upon earlier studies which exploited indels located in the mitochondrial genome to discriminate between different varieties of grass. The nad7 and nad5 indels were amplified from the DNA of nine different varieties of amenity grass species typical of lawn and recreational use. Discrimination was achieved by differences in Tm val...

Poaching is a crime that occurs worldwide and can be extremely difficult to investigate and prosecute due to the nature of the evidence available. If a species is protected by international legislation such as the Convention on International Trade in Endangered Species of Wild Fauna and Flora then simply possessing any part of that species is illeg...

The tiger (Panthera tigris) is currently listed on Appendix I of the Convention on the International Trade in Endangered Species of Wild Fauna and Flora; this affords it the highest level of international protection. To aid in the investigation of alleged illegal trade in tiger body parts and derivatives, molecular approaches have been developed to...

The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage...

Supplementary references. (0.05 MB DOC)

The evolutionary history inferred using the Maximum Likelihood method as calculated using MrBayes [S111–112] for COI. Markov chain Monte Carlo (MCMC) [S121] was executed in two independent analyses starting from different random seeds, parameters were DNA data type, a 4×4 nucleotide model, Nst of 6 with a Dirichlet prior, no covarion, four states w...

The evolutionary history inferred using the Minimum Evolution method [S115] for COI. The optimal tree with the sum of branch length = 17.26235975 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) [S116] are show as symbols on the branches (for values >75%). The tree...

The evolutionary history inferred using the Maximum Parsimony method [S120] for cyt b. The consensus tree inferred from 15 most parsimonious trees is shown. The consistency index is 0.065208, the retention index is (0.508168), and the composite index is 0.034876 (0.033137) for all sites and parsimony-informative sites (in parentheses). The percenta...

The evolutionary history inferred using the Neighbor-Joining method [S119] for cyt b. The optimal tree with the sum of branch length = 19.31726074 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) [S116] are shown as symbols on the branches (for values >75%). The tre...

The evolutionary history inferred using the Maximum Likelihood method as calculated using RAxML [S113] for cyt b. Rapid bootstrapping was used followed by searching for the best ML Tree. Bootstrapping was performed using a random seed, 100 repetitions, a general time reversible model of nucleotide substitution [S124] with the I model of rate hetero...

Legend for Figures S1–S10. Phylogenetic trees based on the aligned sequences for cyt b and COI of 236 mammals (compromising 29 Orders, 89 Families, 174 genera and 217 species). Color ranges are the same for all trees and correspond to the Order of the species. Minimum Evolution, Maximum Parsimony and Neighbor-Joining phylogenetic trees were created...

Supplementary Figure 2 caption. (0.03 MB DOC)

The evolutionary history inferred using the Maximum Likelihood method as calculated using RAxML [S113] for COI. Rapid bootstrapping was used followed by searching for the best ML Tree. Bootstrapping was performed using a random seed, 100 repetitions, a general time reversible model of nucleotide substitution [S124] with the I model of rate heteroge...

The evolutionary history inferred using the Minimum Evolution method [S115] for cyt b. The optimal tree with the sum of branch length = 19.25186677 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) [S116] are shown as symbols on the branches (for values >75%). The tr...

Receiver Operator Characteristic (ROC) curves for COI and cyt b. A reference line is given. The two genes cannot be differentiated based on their ROC curves. Area under the curves and statistical results can be found in Table S5. Calculated in SPSS 17.0.0. (1.26 MB EPS)

The evolutionary history inferred using the Maximum Parsimony method [S120] for COI. The consensus tree inferred from 15 most parsimonious trees is shown. The consistency index is 0.051612, the retention index is (0.500358), and the composite index is 0.027801 (0.025824) for all sites and parsimony-informative sites (in parentheses). The percentage...

The evolutionary history inferred using the Neighbor-Joining method [S119] for COI. The optimal tree with the sum of branch length = 17.29940543 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) [S116] are show as symbols on the branches (for values >75%). The tree i...

The evolutionary history inferred using the Maximum Likelihood method as calculated using MrBayes [S111–112] for cyt b. Markov chain Monte Carlo (MCMC) [S121] was executed in two independent analyses starting from different random seeds, parameters were DNA data type, a 4×4 nucleotide model, Nst of 6 with a Dirichlet prior, no covarion, four states...

The statistical results from the Maximum Likelihood phylogenetic trees calculated using MrBayes [S111–112] from 15,002 trees sampled. Tree length, six reversible substitution rates, four stationary state frequencies (pi), the shape of the gamma distribution (α) and the proportion of invariable sites (pinvar) are displayed. (0.07 MB DOC)

The statistical results from the Maximum Likelihood phylogenetic trees calculated using RAxML [S113] from 100 trees sampled. Tree length, six reversible substitution rates, four stationary state frequencies (pi), the shape of the gamma distribution (α) and the proportion of invariable sites (pinvar) are displayed. (0.03 MB DOC)

The Rs values for COI (A) and cyt b (B) over the entire genes represented by the blue bars. A value of 2 represents 100% conservation over all species at that base. Moving averages of homology are shown for blocks of 101 bp (red) 401 bp (purple) and 601 bp (yellow). (8.24 MB EPS)

The list of complete mitochondrial sequences used for the cyt b and COI alignments. Accession number, common name, Order, Family, species and reference as given by the NCBI listing are shown. DS: Direct Submission. (0.40 MB DOC)

The statistical results from the ROC curve (Figure S3). Calculated in SPSS 17.0.0. (0.03 MB DOC)

The list of human (Homo sapiens), domestic cattle (Bos taurus) and domestic dog (Canis familiaris) complete mitochondrial sequences used for the cyt b and COI alignments. Accession number, ethnicity/breed (if known) and reference as given by the NCBI listing are shown. (0.27 MB DOC)

Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneou...

DNA profiles can be obtained from fabrics where a person has made direct contact with clothing. A standard approach is to cut out a section of the fabric and then use a commercially available method to extract and isolate the DNA. Alternative methods to isolate DNA include the use of adhesive tape to remove traces of cellular material from the fabr...

Species identification for forensic purposes is being increasingly used, as the value of non-human evidence is realized. This requires the identification of the species before individual analysis can take place. Traditionally the cytochrome b (cyt b) gene was used for species identification, but in 2003 the cytochrome c oxidase subunit 1 (CO1) gene...

The trade in samples of tiger (Panthera tigris), or parts derived from tiger, is controlled through the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), which lists all subspecies as protected at the highest level. Tiger has been used as a component in traditional medicines for centuries, often as powder thus...

Although endangered species are afforded protection under national and international laws, trade in products containing endangered species is still one of the most lucrative criminal enterprises in the world. Forensic science is employed to determine if endangered species are present in commercial products but runs into problems due to the extremel...

Species identification using mitochondrial DNA (mtDNA) loci is a standard method for mammalian species testing. Less is understood about the conservation and variability in the avian mitochondrial genome, yet many exotic bird species are threatened with extinction and are traded illegally. In this study 80 different avian species were chosen from 2...