eDNA provides researchers with 'more than meets the eye'
March 24, 2020
Researchers from Curtin University have used next generation DNA sequencing to learn more about the different species of plants, insects and animals present in the Pilbara and Perth regions of Western Australia.
Lead researcher Curtin PhD candidate Mieke van der Heyde, from the ARC Centre for Mine Site Restoration said that DNA metabarcoding is a growing field in the biological monitoring space, with the potential to provide fast, accurate, and cost effective assessments of biodiversity.
"Traditionally, biomonitoring has relied on scientists setting traps and visually monitoring a certain area, counting the number of species, and then extrapolating that data to come up with regional analysis," Ms van der Heyde said.
"Understandably, that method of data collecting is expensive, time consuming and challenging, especially when looking into remote areas of Australia, which often present a harsh climate.
"As animals and organisms interact with their environment, they leave behind traces of their DNA through things like droppings, skin cells, saliva, and pollen. When this DNA is found in the environment, it's known as environmental DNA, or eDNA.
"Our research looked in to the feasibility of using this eDNA as an additional tool for biomonitoring. Not only to see if this type of analysis could potentially make things a bit easier for biologists out in the field, but as well as providing researchers with more accurate field information then what they can visually identify."
The study analysed samples of soil, animal droppings, plant and insect material, collectively known as 'substrates,' taken from two different areas of Western Australia: The Pilbara, a hot desert climate, and the Swan Coastal Plain, a hot Mediterranean-type climate.
"We tested common environmental substrates including soil, bulk scat, bulk plant material, and bulk arthropods from pitfall traps and vane traps, using four eDNA barcoding assessments to detect a wide range of plants, vertebrates and arthropods," Ms van der Heyde said
"This study was the first of its kind to systematically test terrestrial substrates for eDNA, and it also was the first time that some of these particular substrates were analysed.
"Results show that bulk arthropods and animal droppings detected the most biodiversity, with at least a third of the biodiversity detected in only one substrate. Soil samples detected the least, and fewer samples had usable DNA, especially in the Pilbara. We believe this is most likely due to the hot climate, which potentially degraded the eDNA.
"Biomonitoring is necessary for effective ecosystem management. Our study shows that eDNA can detect biodiversity in an area, and collecting more substrates will increase the breadth of biodiversity detected.
"However, surveys must be carefully considered, as DNA may come from organisms outside the study area," Ms van der Heyde said.
This research was completed at the Trace and Environmental DNA (TrEnD) Laboratory at Curtin University's Perth campus.
Curtin PhD Candidate Ms Mieke van der Heyde collecting samples for eDNA analysis.
Mieke Heyde, Michael Bunce, Grant Wardell‐Johnson, Kristen Fernandes, Nicole E. White, Paul Nevill. Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding. Molecular Ecology Resources, 2020; DOI: 10.1111/1755-0998.13148
Art in times of crisis
March 24, 2020
Scientia Professor Jill Bennett says the arts offer useful ways of dealing with complex mental health and emotional challenges.
Body mapping session in Virtual Reality using EmbodiMap developed by UNSW fEEL Lab Scientia Professor Jill Bennett and lead immersive media designer Volker Kuchelmeister. Image: Dr Jill Bennett
People often think that prioritising art in a time of crisis is counterintuitive but ARC Laureate Fellow and UNSW Professor of Experimental Arts, Professor Jill Bennett says it’s very important.
“I think it's exactly now that we need these kinds of tools,” she says. “One of the things that art does well – and has done for hundreds of years – is to investigate challenging human experiences. This opens up the potential for reflecting on and understanding our own and others mental states and feelings of distress and anxiety.”
Professor Bennett notes that evidence suggests that 65% or more of Australians with a mental health issue don’t seek help. That’s why she is advocating for work around mental health to also be done outside the health sector.
“We need to support people in more ways than just medically,” she says.
For Professor Bennett, who is also the founding Director of The Big Anxiety festival, art exists beyond the gallery or the museum - and creative mental health interventions take place in environments that people want to be in, and enjoy being in, rather than a medical space.
“The creative process is very different from, say, a course of cognitive behaviour therapy or something medicalised,” she says. Art doesn’t substitute for medical interventions, but it offers something else that is beneficial.
“Art can be a means of reflecting on and processing difficult emotions or complex mental states. It can help us gain perspective, insight and agency, as well as the capacity to communicate”.
On one level, that increased understanding can come through casual engagement with art or it can come through the form of larger art-based projects, Professor Bennett says. But in both cases, it’s like a form therapy insofar as it helps us develop agency and emotional awareness.
Professor Bennett has an ARC funded Lab called fEEL (felt Experience & Empathy Lab) where psychologists and art specialists work together developing techniques and practises that are beneficial in a whole range of mental health, trauma and anxiety contexts.
Body mapping session in Virtual Reality using EmbodiMap developed by UNSW fEEL Lab Scientia Professor Jill Bennett and lead immersive media designer Volker Kuchelmeister. Image: Dr Jill Bennett
Through fEEL she has recently developed EmbodiMap - a therapeutic body mapping tool that uses Virtual Reality to allow users to engage with and map their feelings, thoughts and emotions.
“We often feel anxiety in the body. You may feel a response in your throat or your gut, for example. Body mapping, which is used extensively by my colleague, Professor Katherine Boydell at Black Dog Institute, is a process of mapping those embodied feelings, by drawing. EmbodiMap allows us to do this in VR, interacting in a physical way with 3D body images.
“When you feel anxious it can be useful to think about what's happening in your body. You need to notice the patterns of what's happening, and develop a way of intervening when stress or anxiety occurs.”
She says that the EmbodiMap is a good illustration of this because it works with those processes. It gives people a potent way of visualising what’s happening to them by encouraging them to paint internal sensations as they are experienced onto a 3D facsimile of the body, which can also be posed and manipulated, thus creating an interactive tool to exert some control over anxious thoughts and feelings.
“That’s not to say you can instantly and mechanically make anxiety go away,” she says. “But having that sort of perspective and insight and being able to see much more clearly what's going on, does give you a much greater degree of agency and insight. Those things we know are really critical when it comes to managing anxiety and emotional health.”
Professor Bennett’s team is looking for participants to be involved in the testing phase of EmbodiMap, which can be used in conjunction with body-focused therapies or as stand-alone activity.
Ancestor of all animals identified in Australian fossils
March 23, 2020
A wormlike creature that lived more than 555 million years ago is the earliest bilaterian
A team led by UC Riverside geologists has discovered the first ancestor on the family tree that contains most familiar animals today, including humans.
The tiny, wormlike creature, named Ikaria wariootia, is the earliest bilaterian, or organism with a front and back, two symmetrical sides, and openings at either end connected by a gut. The paper is published today in Proceedings of the National Academy of Sciences.
An artist's rendering of Ikaria wariootia. (Sohail Wasif/UCR)
The earliest multicellular organisms, such as sponges and algal mats, had variable shapes. Collectively known as the Ediacaran Biota, this group contains the oldest fossils of complex, multicellular organisms. However, most of these are not directly related to animals around today, including lily pad-shaped creatures known as Dickinsonia that lack basic features of most animals, such as a mouth or gut.
The development of bilateral symmetry was a critical step in the evolution of animal life, giving organisms the ability to move purposefully and a common, yet successful way to organise their bodies. A multitude of animals, from worms to insects to dinosaurs to humans, are organized around this same basic bilaterian body plan.
Evolutionary biologists studying the genetics of modern animals predicted the oldest ancestor of all bilaterians would have been simple and small, with rudimentary sensory organs. Preserving and identifying the fossilised remains of such an animal was thought to be difficult, if not impossible.
For 15 years, scientists agreed that fossilised burrows found in 555 million-year-old Ediacaran Period deposits in Nilpena, South Australia, were made by bilaterians. But there was no sign of the creature that made the burrows, leaving scientists with nothing but speculation.
Scott Evans, a recent doctoral graduate from UC Riverside; and Mary Droser, a professor of geology, noticed minuscule, oval impressions near some of these burrows. With funding from a NASA exobiology grant, they used a three-dimensional laser scanner that revealed the regular, consistent shape of a cylindrical body with a distinct head and tail and faintly grooved musculature. The animal ranged between 2-7 millimetres long and about 1-2.5 millimetres wide, with the largest the size and shape of a grain of rice -- just the right size to have made the burrows.
Ikaria wariootia impressions in stone. (Droser Lab/UCR)
"We thought these animals should have existed during this interval, but always understood they would be difficult to recognise," Evans said. "Once we had the 3D scans, we knew that we had made an important discovery."
A 3D laser scan of an Ikaria wariootia impression. (Droser Lab/UCR)
The researchers, who include Ian Hughes of UC San Diego and James Gehling of the South Australia Museum, describe Ikaria wariootia, named to acknowledge the original custodians of the land. The genus name comes from Ikara, which means "meeting place" in the Adnyamathanha language. It's the Adnyamathanha name for a grouping of mountains known in English as Wilpena Pound. The species name comes from Warioota Creek, which runs from the Flinders Ranges to Nilpena Station.
"Burrows of Ikaria occur lower than anything else. It's the oldest fossil we get with this type of complexity," Droser said. "Dickinsonia and other big things were probably evolutionary dead ends. We knew that we also had lots of little things and thought these might have been the early bilaterians that we were looking for."
In spite of its relatively simple shape, Ikaria was complex compared to other fossils from this period. It burrowed in thin layers of well-oxygenated sand on the ocean floor in search of organic matter, indicating rudimentary sensory abilities. The depth and curvature of Ikaria represent clearly distinct front and rear ends, supporting the directed movement found in the burrows.
The burrows also preserve crosswise, "V"-shaped ridges, suggesting Ikaria moved by contracting muscles across its body like a worm, known as peristaltic locomotion. Evidence of sediment displacement in the burrows and signs the organism fed on buried organic matter reveal Ikaria probably had a mouth, anus, and gut.
"This is what evolutionary biologists predicted," Droser said. "It's really exciting that what we have found lines up so neatly with their prediction."
Scott D. Evans, Ian V. Hughes, James G. Gehling, and Mary L. Droser. Discovery of the oldest bilaterian from the Ediacaran of South Australia. PNAS, March 23, 2020 DOI: 10.1073/pnas.2001045117
Aboriginal scars from frontier wars
March 18, 2020
Hundreds of Aboriginal men who became native mounted police in colonial Australia carried a significant burden of responsibility for law and order for white settlers in Queensland and other settlements.
An historical photo of Native Mounted Police troopers.
A long-running ARC-funded archaeology project has turned the lens on the recruitment to the Queensland Native Mounted Police and their part in the violent 'frontier wars' -- which created long-term traumatic impacts on the lives of the Indigenous people involved.
"We argue that the massacres, frontier violence, displacement, and the ultimate dispossession of land and destruction of traditional cultural practices resulted in both individual and collective inter-generational trauma for Aboriginal peoples," says Flinders University Professor Heather Burke in a new article published in the Journal of Genocide Research.
"Despite the Australian frontier wars taking place over a century ago, their impacts continue to reverberate today in a range of different ways, many of which are as yet only partially understood."
Professor Burke, and Queensland researchers, say official records show of the history of the Queensland Mounted Police in terms of its development, its white officers, some day-to-day operations of the force, and how many people were killed during the frontier wars.
The article looks at the ongoing psychological impacts of the historical dispossession and frontier violence.
Based on more than four years of research, the Archaeology of the Queensland Native Mounted Police project combined historical records, oral and historical evidence from a range of sites across central and northern Queensland to understand more fully the activities, lives and legacies of the native police.
It strives to present an alternative perspective on the nature of frontier conflict during Australian settlement, in order to initiative new understandings of the Aboriginal and settler experience, and contribute to global studies of Indigenous responses to colonialism.
Background:
The Queensland Native Mounted Police was organised along paramilitary lines, consisting of detachments of Aboriginal troopers led by white officers. It covered the whole of Queensland, including 170 camps, and was explicitly constituted to protect the lives, livelihoods and property of settlers and to prevent (and punish) any Aboriginal aggression or resistance.
This was often accomplished through violence in many forms, leading Australian historian Henry Reynolds to characterise the NMP as "the most violent organisation in Australian history."
The project's new publicly available national database covers the 50-year history of the Queensland Native Mounted Police (1849-1904) and stories of many of the 800 troopers and 400 officers. It is the only publicly available historical and archaeological dataset of their lives and activities. The excavations conducted over the past four years were the first archaeological investigations of any native police force operating anywhere in Australia.
Heather Burke, Bryce Barker, Lynley Wallis, Sarah Craig, Michelle Combo. Betwixt and Between: Trauma, Survival and the Aboriginal Troopers of the Queensland Native Mounted Police. Journal of Genocide Research, 2020; 1 DOI: 10.1080/14623528.2020.1735147