For a photo montage of what we do check out the following PHOTO GALLERY
The TrEnD laboratory uses it expertise in isolating and characterising trace and environmental DNA to addess a variety of biological questions - collectively our reseach can be divided into eight core areas 1) Ancient DNA, 2) Environmental DNA (or eDNA), 3) Eggshell genetics, 4) Complementary and alternative medicines, 5) MicroWine, 6) Wildlife forensics 7) Fish population Genetics/genomics and 8) Coral Biology. Each of these areas is discussed in more detail below.
Ancient DNA. One of the core area’s of expertise in the TrEnD laboratory is the study of ancient DNA (aDNA). Over the past 10 years the lab has applied aDNA techniques to address a variety of biological questions including; 1) Extinction processes (Allentoft et al. PNAS 2014) 2) Conservation biology (Pacioni et al 2015, in press) 3) DNA decay rates (Allentoft et al. 2012) 4) human migration into Australia (Rasmussen et al. 2011) 5) Zooarchaeology ( Murray et al. 2013) and 6) Avian Phylogeny and evolutionary history (Bunce et al. 2009, White et al. 2011, Jervis et al. 2014).
Most recently the lab has focused on using bulk-bone metabarcoding to rapidly assess biodiversity from ‘scrap’ bone (pictured left) recovered from archaeological and paleontological excavations. The method involves grinding a collection of bone fragments into a homogenous powder then using new sequencing technologies to assay all the species present. The method is a cost-effective way of obtaining ecosystem data from thousands of bones. First described from work in south-west WA (Murray et al. 2013) we have now applied this method to sites across Australia, New Zealand, USA, Hawaii, Armenia and Madagascar.
Environmental DNA (eDNA). DNA isolated and characterised from a variety of substrates including sediments and water is collectively referred to as environmental DNA. DNA is shed from a variety of biological secretory processes and provides a means to audit species composition. When combined with next generation sequencing (NGS) and metabarcoding, eDNA can provide a wealth of information for studies of biodiversity, food web dynamics, diet analysis and invasive species monitoring. Metabarcoding eDNA has become feasible only because it is now possible to simultaneously sequence millions of copies of DNA from complex multi-species environmental samples.
The use of eDNA isolated from marine water is a new technology. First described in 2012 (Thomsen et al. 2012) at the University of Copenhagen - the work demonstrated the potential to characterise vertebrates that live in the water that is sampled. Since this finding a number of other studies have investigated the potential of the eDNA approach in a marine context including biodiversity assessments (e.g. Miya et al. 2015) and Biosecurity (e.g. Pochon et al. 2013). The Trace and environmental DNA (TrEnD) laboratory, together with its partners in Copenhagen have extensive experience in DNA metabarcoding from a variety of DNA substrates including water. Since 2014 TrEnD has actively pursued how its expertise in DNA metabarcoding and NGS can be applied to the growing eDNA field particularily in the marine sectors of biosecurity, food webs, diet and aquaculture. We have an active program of research with Prof. Euan Harvey at Curtin University that is integrating baited baited remote underwater video (BRUV - see picture) technologies and eDNA as a cutting-edge survellience tool for best-practice ecosystem management.
Complementary and alternative medicines. Over recent years, the popularity of complementary medicine has risen substantially, particularly in Western societies. Along with increased uptake in the use of complementary medicine, there have also been concerns and questions raised over honesty in package labelling and overall safety of such products. Leading on from a PLoS Genetics paper published in 2012 by members of the TrEnD laboratory, which revealed endangered species and toxic plants in certain traditional Chinese medicines (TCMs), the National Health and Medical Research Council funded the Complementary and Alternative Medicine (CAM) study, commencing in 2014.
The CAM study is a joint collaborative project run out of the TrEnD laboratory, the Trace Research Advanced Ultra-Clean Environment (TrACE) facility at Curtin University (A/Prof Ross Edwards) , the Separation Science and Metabolomics laboratory at Murdoch University (Dr Garth Maker, Prof Rob Trengove, Elly Crighton), and the University of Adelaide (Dr Ian Musgrave, Prof Roger Byard, Claire Hoban). Through a combination of next generation DNA sequencing, and toxicological and heavy metal analyses, the CAM study aims to audit the composition of a wide range of CAMs down to trace levels. The safety and legality of approximately 300-400 CAMs will be assessed in total, which at the conclusion of this study, will help to inform health practitioners and the wider community on the content of products that have been largely unscrutinised previously.
MicroWine and Wine Research Curtin University (Mike Bunce and Tom Gilbert) is a member of the EU training network called Microwine.
the Microwine proposal was conceived, under the hypothesis that thanks to the recent, principally sequencing, based developments in microbiology, it is a timely and unique opportunity for academia and the wine industry to pair up, in order to use state-of-the-art laboratory and computational metagenomics in order to gain a more comprehensive understanding of the complex processes through which microbes affect, thus may benefit, the vines and wines upon which the industry is based. The aim of microwine is to train a new generation of interdisciplinary experts who will strengthen the industry through application of the state- of-the-art techniques spanning the disciplines of geochemistry, genomics, systems and computational biology.
The TrEnD laboratory (Dr Nicole White and Elizabeth Compton), along with the microwine network, has an active research program in the Margaret River region. Using metabarcoding methods we have investigated the fermentative yeasts on grapes and together with Tom Gibert and PhD student Christian Carøe we are investiagting the DNA profiles in old wine from the region - Cullen Wines kindly provided a vertical series of wine for this project (pictured).
Fish population genetics/genomics. We are in the process of developing genomic approaches to address questions of connectivity and adaptability in a number of non-model reef fish on the coast of Western Australia and into the broader Indo-Pacific. In most cases, this involves a combination of traditional mitochondrial sequencing (i.e. DNA barcoding and mitogenomes), identifying Single Nucleotide Polymorphisms (SNPs) within and across our study species, and integrating with available ecological and oceanographic information. We are particularly interested in characterising barriers to larval dispersal, source-sink dynamics, and the origins of the unique biodiversity in this geologically complex region. This project has direct applications to the fields of biogeography, phylogeography, population genetics, meta-population dynamics, and regulating the international exchange of marine resources.
Complimentary streams of research in the TrEnD Lab, such a metabarcoding of gut contents for dietary analysis or gut flora to assess microbial community dynamics, will add to this study. This work forms part of an Early Career Research Fellowship to Joseph DiBattista at Curtin University and is in partnership with the Department of Fisheries Western Australia
For detailed description of RAD-seq experiments on Illumina Sequencers and our bench protocol see: Etter, P. D. Sequenced RAD Markers for Rapid SNP Discovery and Genetic Mapping. This protocol is easily adapted to non-fish species simply by using a different restriction enzyme for digestion and adjusting the concentration of P1 adapters. For a detailed description of the bioinformatics pipeline package for processing RAD data see here.
Coral Biology; (Richards and Stat)