PhD project announcement – Biology and ecology of freshwater whiprays, Urogymnus dalyensis

Macquarie University and Sharks And Rays Australia are looking for a suited PhD candidate to work with us on freshwater whiprays, Urogymnus dalyensis, in various locations in Far North Queensland. The student will be enrolled at Macquarie University in Sydney but will be largely based in Cairns, and work closely with Dr Barbara Wueringer at Sharks And Rays Australia (SARA, Associate Supervisor) and Prof Jane Williamson (Macquarie University, Primary Supervisor) The project will be implemented in collaboration with various established Aboriginal Land and Sea ranger groups through existing partnerships with SARA.  

Freshwater whiprays are a large bodied ray that is found across Northern Australia. It’s biology and ecology are not well understood. For example, the species is thought to not occur on the east coast of Queensland, but our recent work uncovered that the species is present here. These animals can grow to around 150 cm disk width.  

 

Potential research questions, depending on interest and skilbase:  

  • Movement and behaviours of the east coast population in Rinyirru (Lakefield) National Park (CYPAL) (acoustic tracking, habitat assessment 
  • Assessment of biological parameters (morphometric) 
  • Identification of life history traits through non-invasive methods (ultrasound, hormone analysis, blood)  
  • Population dynamics (genetics) 
  • Species Distribution Modelling 

 

Non-negotiable qualifications (confirmed via appropriate documentation): 

  • Australian Citizen or Permanent resident  
  • Successful securement of a Macquarie University (or equivalent) PhD scholarship. 
  • Publication record with one first author publication (in order to be competitive for scholarships) 
  • 4WD experience (river crossings, corrugations, towing trailers, etc). You do not necessarily require a 4WD course certificate, but proven experience is a must.  
  • Experience driving a boat in shallow waters, recreational boating licence 
  • Willingness and experience in working in remote locations, incl. camping 
  • Experience using Microsoft Office 
  • Good writing and communication skills, including report writing 
  • Experience in data analysis and scientific paper writing 

 

Preferred qualifications:  

  • Experience in handling animals and willingness to complete basic animal ethics training 
  • Current first aid course 

 

Additional desirable qualifications: 

  • Experience in handling large, potentially dangerous animals (this could be snakes, sharks, teleosts, crocodiles, rays) 
  • Experience working in Cape York 
  • Previous experience in working with Aboriginal Communities, TOs and/or Land and Sea Rangers 
  • Current Coxswains ticket 
  • Experience in working with various levels of government 
  • A sound understanding of the principles of conservation biology, ecological management, endangered species management and a willingness to expand this knowledge in pursuit of SARA’s mission 

 

Please send a cover letter outlining how your qualifications and previous experience address the essential and desirable qualifications outlined above, along with your CV, to Dr Barbara Wueringer (barbara@saw.fish). Include contact details for two academic referees. 

Recap of the ASFB Conference

Recap of the ASFB Conference

By Amica Benoit-Limosani

In November 2024, three of our researchers had the exciting opportunity to participate in the annual conference of the Australian Society for Fish Biology (ASFB) in Newcastle. For me, it was my first-ever scientific conference, and I felt incredibly fortunate to attend alongside Nikki and Barbara.  

Prior to the conference, we all attended the workshop that ASFB held this year, which focused on fish tagging techniques with a special emphasis on animal ethics. The workshop was both informative and inspiring. We learned about the latest advancements in acoustic tagging technologies and explored the wide range of research opportunities that tagging can open up. The session sparked new ideas that we’re excited to incorporate into our ongoing tagging projects at SARA.

Patricia J. Kailola and Barbara Wueringer, image by Nikki Biskis.

Nikki Biskis, Barbara Wueringer and Amica Benoit-Limosani with The misunderstood giants of Rinyirru (Lakefield) National Park (CYPAL) poster, image by Julia Constance.

In November 2024, three of our researchers had the exciting opportunity to participate in the annual conference of the Australian Society for Fish Biology (ASFB) in Newcastle. For me, it was my first-ever scientific conference, and I felt incredibly fortunate to attend alongside Nikki and Barbara.  

Prior to the conference, we all attended the workshop that ASFB held this year, which focused on fish tagging techniques with a special emphasis on animal ethics. The workshop was both informative and inspiring. We learned about the latest advancements in acoustic tagging technologies and explored the wide range of research opportunities that tagging can open up. The session sparked new ideas that we’re excited to incorporate into our ongoing tagging projects at SARA.

Next, Nikki took the stage to present a section of her PhD work. She discussed how she analyzes the teeth of sawfish that we receive through donations. By examining these teeth, which grow continuously, she is able to trace the sawfish’s origin across Queensland. This fascinating method has the potential to reveal valuable information about the behaviors and movements of sawfish over time.

Nikki Biskis presenting at the ASFB conference, image by Leo Guida.

Barbara Wueringer presenting at the ASFB conference, image by Paddy Burke.

Last but certainly not least, Barbara had her first talk not about sawfish at ASFB! Her presentation centered on freshwater whiprays, which we affectionately refer to as “pancakes”. Barbara discussed the significant gaps in current literature about these species and shared some of our recent breakthroughs in whipray research, including extending their known distribution to the East Coast of Australia. We’re just beginning to dive into this research, and we’re excited to announce that we’re officially looking for a PhD candidate who shares our passion for these unique creatures (www.saw.fish/whipray-PhD).

All in all, the ASFB conference was an incredible success! After the initial nerves of presenting, we were able to relax and reconnect with old friends, meet new colleagues, and share our enthusiasm for fish. My first conference experience was truly memorable, and I am very thankful I got to experience it with two conference connoisseurs who guided me through the experience. If you were intrigued by our presentation, stay tuned for upcoming papers on these exciting topics! 

A behind-the-scenes look at eDNA processing at the TropWATER laboratory, JCU Townsville

A behind-the-scenes look at eDNA processing at the TropWATER laboratory, JCU Townsville

By Christina Nardini (SARA intern 2024, Masters by Placement, James Cook University) 

Recently, as part of my internship with SARA, I had the chance to visit the TropWATER eDNA lab in Townsville. This lab’s purpose is to process water and soil samples from the field to detect the presence of species. It was an exciting opportunity to witness firsthand how eDNA (environmental DNA) is extracted and analyzed, and how crucial this work is to conservation efforts. 

A Non-Contamination Lab for a Clean Start 

As I entered the non-contamination lab, the first step in the eDNA process, I noticed how everything was carefully controlled to prevent contamination. Lab staff were required to wear shoe coverings, gloves, and lab coats. With every surface and tool sterilized with bleach or UV light, it was clear how important it is to eliminate contamination and ensure no outside DNA interfered with the samples. This level of precaution is necessary to maintain the integrity of the results. 

Step-by-Step: The eDNA Analysis Process The lab follows a five-step process to analyze eDNA, each with meticulous attention to detail: 

1. Sampling: Water samples are collected in the field and transported to the TropWATER lab in sealed jars. These samples can be stored for up to three months, thanks to a preservative solution called Longmire’s Buffer. Multiple samples from different sites are sent in, with replicates used to ensure accuracy. When it comes to searching for sawfish DNA, SARA’s samples arrive as filter paper stored in Longmire Solution, as we sample large quantities of water by filtering it through the filter paper.  

 

A)

B)

C)

Samples arrive to the lab in sample jars with lids taped shut and in bags to prevent any loss of samples (Figure A). These samples can be stored for up to 3 months thanks to the Longmire’s Buffer (Figure B). When setting up test tubes for the DNA extraction process, 25 test tubes are needed per sample/yellow-lidded jar (Figure C). Of these, 5 are used per replicate, where one is used as a control group and 4 as treatment groups.

2. DNA Extraction: This is where the real work begins. In the non-contamination lab, researchers first prepare the samples by carefully cleaning the jars and labelling all equipment. Each sample is divided into test tubes, with some used for treatment and others as controls. The samples are mixed with glycogen, NaCl, and isopropanol before being left overnight in a fridge. The next day, the samples are spun in a centrifuge, separating the DNA for extraction. 

D)

E)

Lab tech Emma seen adding glycogen to each test tube (Figure D.) Figure E shows one of the many centrifuges in the non-contamination lab.

3. Inhibition Tests: After extracting DNA, inhibition tests are conducted to ensure there are no substances in the sample that might interfere with the PCR process. 

4. qPCR (Quantitative Polymerase Chain Reaction): In this step, scientists use qPCR to detect the DNA of specific species, like sawfish, in the sample. The lab was color-coded by task—blue for the DNA extraction lab, and yellow and green for different sides of the pre-PCR labs. It was essential to maintain strict lab separation to avoid cross-contamination. The team even scheduled shifts so that those working in one area of the lab couldn’t potentially contaminate another. 

F)

G)

H)

Different sides of the lab are used for different steps in the qPCR process. These are colour-coded by step, blue for the DNA extraction lab (Figure F), yellow and green for different sides of the pre-PCR labs (Figures G and H).

5. Data Analysis: Once the DNA is amplified and species-specific markers are detected, the data is analyzed to determine whether sawfish DNA is present in the samples. This critical information is then sent back to those who sent in the samples, like Sharks and Rays Australia. This eDNA data is then used to write reports, inform conservation efforts, and aid in research.  

I)

J)

Figure I shows a qPCR machine used to detect DNA in samples. The amplification of the DNA is shown in Figure J, where the data is output for analysis and distribution.  

Why It Matters 

The analysis of eDNA is a new method that provides insights into species distributions and environments. This lab gives organizations and researchers the ability to use non-invasive sampling techniques to study species and environments. With TropWATER’s help, Sharks And Rays Australia can gather data on sawfish distribution quicker and easier than with previous methods.  

My visit to the TropWATER eDNA lab gave me a new appreciation for the precision and dedication that goes into this work. From the painstaking steps to avoid contamination to the advanced technology used in DNA detection, every part of the process is geared toward one goal: understanding and conserving our natural world. 

SARA’s eDNA work is supported by various funding bodies and grants, including the Sea World Research and Rescue Foundation Inc., the Reef Trust Partnership and Great Barrier Reef Foundation, and a Community Sustainability Action Grant from the Queensland Government.  

Species we encounter – Carcharhinids

Species we encounter – Carcharhinids

by Amica Limosani, Jake New, Barbara Wueringer

The Carcharhinidae family, also known as whaler sharks, includes 12 genera and 50 species worldwide, making it one of the largest families of sharks. These sharks are typically found in warm tropical waters, although some species can also be found in brackish and freshwater environments, therefore we encounter these often in the field. Carcharhinids are highly recognizable, often having the classic shark-like shape that many people associate with these animals.

Speartooth Shark, Glyphis glyphis

Imagine a shark with spear-like teeth navigating freshwater rivers! Meet the Speartooth Shark, Glyphis glyphis, found in selected tropical rivers and estuaries in northern Australia and New Guinea. They are one of the few shark species adapted to freshwater habitats. These elusive sharks are hard to study due to their cryptic nature and remote homes. Sadly, they are critically endangered because of habitat degradation, pollution, and accidental capture in fishing gear. Conservation efforts are crucial to ensure their survival.  

Sicklefin Lemon Shark, Negaprion acudentis   

 Introducing the striking Sicklefin Lemon Shark (Negaprion acutidens)! While most shark enthusiasts are familiar with the Atlantic lemon shark (N. breviostris), widely researched by the Bimini Biological Field Station, the Sicklefin Lemon Shark is equally fascinating. They are easily recognizable by their slender, curved fins, particularly their two equal-sized distinctive sickle-shaped dorsal fins. They often inhabit shallow coastal waters, including mangroves and coral reefs, but are also known to explore farther offshore. With a nocturnal hunting habit, they prey on fish, crustaceans, and cephalopods. Renowned for their relatively docile nature compared to other shark species, encountering them is an unforgettable experience. 

Pigeye shark, Carcharhinus amboinensis

Pigeye sharks are sporadically spread throughout the tropical waters of the Indo-West Pacific. They inhabit brackish coastal water and tend to swim close to the ocean floor. Pigeye sharks often get confused with Bull sharks because it is so hard to distinguish the two. Due to this misidentification, there is little information on the Pigeye sharks.  According to the IUCN Red List, pigeye sharks in Australia are classified as least concern, though their population sizes have never been recorded. However, they often end up as bycatch in gillnets and longline fisheries. Currently, they are not targeted by fisheries and are considered sustainable. However, they are caught in gillnets and longline fisheries as bycatch.

Coates or Australian blackspot shark, Carcharhinus coatesi

Have you ever heard of a Coates or Australian Blackspot Shark, (Carcharhinus coatesi)? Despite recent reclassification and its elusive nature, this species remains largely unstudied. Females give birth to small litters of 1-3 pups, each measuring between 38-40 cm at birth, with adults reaching lengths of up to 88-92 cm.

This species is differentiated from the spot-tail shark as it does not have black markings on the lower caudal fin.

Creek Whaler, Carcharhinus fitzroyensis  

Say hello to the intriguing Carcharhinus fitzroyensis (Creek Whaler)!  Endemic to the tropical waters of Northern Australia, this small shark species holds many secrets waiting to be discovered.  With a maximum length of 135 cm, most individuals measure between 80-90 cm.  Sporting a spindle-shaped, stocky body, five gill slits, and a long snout, this shark is a remarkable inhabitant of our oceans.

It is easily identified as it lacks any black fin markings.

Nervous Shark, Carcharhinus cautus

Have you ever seen a nervous shark, Carcharhinus cautus? Aptly named for its skittish behavior, this shark often darts away when approached by divers or boats, keeping its distance from potential threats. Found in tropical and subtropical waters, primarily in the Indo-Pacific region, they navigate their habitat with caution. Sporting a streamlined body, pointed snout, and large eyes, these features likely contribute to their cautious nature.

Do not confuse the nervous shark with a lemon shark, even though it is slightly greenish in body colour, its dorsal fins are not equal in height.

Bull Shark, Carcharhinus leucas   

With the unique ability to thrive in both saltwater and freshwater, these sharks are true survivors. They navigate rivers and estuaries, sometimes venturing hundreds of miles upstream in search of prey and new territories. Known for their aggressive behavior, they’re often regarded as one of the most formidable shark species to encounter in the wild. Despite coastal environments being heavily impacted by human development, Bull Sharks have adapted and expanded their habitat in Australia to the Gold Coast canals (J. Werry, 2016)! 

Blacktip Shark, Carcharhinus limbatus

Introducing the Blacktip Shark, Carcharhinus limbatus! These sharks have black markings on their fins which are not as pronounced as those of blacktip reef Carcharhinus melanopterus. Beware to not confuse the two! Blacktip sharks are common in tropical and subtropical coastal waters worldwide, and they can grow up to 250 cm TL but average around 150cm. They are frequently found nearshore around river mouths, bays, mangrove swamps, and estuaries, though they do not venture far into freshwater. Fun fact their ‘black tips’ fade over time (Compagno et al. 2005). Blacktip sharks are listed as Vulnerable globally (IUCN, 2020) and are targeted by multiple commercial fisheries around the world.

Australian Blacktip Shark, Carcharhinus tilstoni

Meet the Australian blacktip shark, Carcharhinus tilstoni! Named for their black-tipped dorsal and pectoral fins, these sharks are only found in shallow coastal waters across northern Australia, often swimming in schools near coral reefs and estuaries. With streamlined bodies and large eyes, they have excellent vision for hunting. Primarily fish-eaters, they feed on small fish and cephalopods, playing a crucial role in marine ecosystems. Previously the Australian Blacktip and the global Blacktip shark Carcharhinus limbatus could only be distinguished by genetic analysis. However, scientists from NT Fisheries have found that the markings of the anal fins of both species are different, making it possible to differentiate the two in the field!

Graceful Shark, Carcharhinus amblyrhynchoides

Named for their smooth swimming style and sleek, streamlined bodies, these sharks are a marvel to watch. With their slender bodies, rounded snouts, and large eyes, graceful sharks have excellent vision in low-light conditions, making them effective nocturnal hunters. Interestingly, graceful sharks are often mistaken for bull sharks because they both have a stocky build. Can you spot the difference?

Learn more about the Mylobatiform rays we encounter here

Learn more about the Rhinopristiform rays we encounter here

Learn more about the Sphyrnid sharks we encounter here

Species we encounter – Mylobatiformes

Species we encounter – Mylobatiformes

by Amica Limosani, Jake New, and Barbara Wueringer

The Mylobatiformes order includes eight families of stingrays, such as Mylobatidae (eagle rays), Urolophidae (round rays), and Dasyatidae (whiptail rays). Mylobatiformes are incredibly diverse but share the common characteristics of flattened disc or diamond-shaped bodies with tapering tails, often armed with venomous spines. Stingrays from this order are found worldwide in warm coastal waters and can either be bottom dwellers or migratory. They exhibit diverse swimming patterns, either undulating their whole bodies in a wave-like motion or flapping their fins to “fly” through the water column.

Spotted Eagle Ray, Aetobatus ocellatus   

Behold the stunning Spotted Eagle Ray, Aetobatus ocellatus! Named for the white spots on their dorsal surface, resembling stars in the night sky, these rays are a marvel. With flattened bodies and wing-like pectoral fins spanning up to 3 meters wide, they gracefully navigate the ocean. If you are lucky enough to spot them underwater, you’ll see them swimming acrobatically and often leaping out of the water. Found in shallow coastal waters and coral reefs, they play a crucial role in the marine ecosystem by feeding on crustaceans and small fish. 

Ornate Eagle Ray, Aetomylaeus vespertilio   

Meet the intriguing Ornate Eagle Ray, Aetomylaeus vespertilio. These rays showcase captivating coloration and intricate patterns, featuring dark bands and spots on their dorsal surface. In tropical and subtropical coastal waters, they gracefully roam shallow bays, lagoons, and coral reefs. With a flattened body and broad, wing-like pectoral fins, they move through the ocean depths with elegance. Yet, encountering them in the wild is a rare thrill—there have been fewer than 60 confirmed sightings worldwide. We have been fortunate enough to have four individuals in our dataset over the years!

Bluebanded eagle ray, Aetomylaus caeruleofasciatus

Introducing the Bluebanded Eagle Ray (Aetomylaus caeruleofasciatus). This majestic ray showcases a yellowish-brown color, beautifully complemented by seven vibrant blue bands adorning its body. Despite its long tail, stretching up to 1.5-1.8 times the diameter width, fear not—it’s spineless! Found in the subtropical and tropical waters of northern Australia, from Hervey Bay to the Dampier Archipelago in Western Australia. We have only ever caught, tagged, and released them once, and they were schooling.

Cownose Ray, Rhinoptera neglecta

What’s cuter than a Cownose Ray, Rhinoptera neglecta? These rays are as unique as their name suggests, with a forehead resembling the nose of a cow. But don’t let their quirky appearance fool you—they’re highly migratory and can travel long distances in massive schools, sometimes numbering in the thousands. Picture the ocean filled with their graceful gliding as they navigate the waters with their flattened bodies and wing-like pectoral fins. And when it comes to dining, they’re true connoisseurs of the seafloor, using their specialized mouths to crush and feast on shellfish, crustaceans, and other invertebrates. Unfortunately, the Aussie species is much less understood than its Atlantic counterpart, Rhinoptera bonasus

Australian Whipray, Himantura australis

Meet the Australian Whipray, Himantura australis! This yellowish-brown whipray is covered in dense brown spots, reticulations, or speckles. Juvenile pups have dark spots forming a reticulated or honeycomb pattern. Commonly found in rivers and estuaries in northern Australia, they’re active hunters of shrimp and small fish. Although once threatened by commercial fishing net bycatch, bycatch reduction devices have decreased accidental captures by 95%!

Black-spotted Whipray, Maculabatis astra

Say hello to the gorgeous Black-spotted Whipray, Maculabatis astra! With distinctive black and white spots adorning their dorsal surface, these beautiful creatures roam the sandy and muddy bottoms of coastal waters across the Indo-Pacific, often near coral reefs and estuaries. Sporting a diamond-shaped body, a long whip-like tail armed with venomous spines, and a triangular snout, they are truly captivating. Growing up to 80cm in diameter, the Black-spotted Whipray is a true marvel of the marine world! 

Broad cowtail ray, Pastinachus ater

Meet the Broad Cowtail Ray, Pastinachus ater a fascinating inhabitant of the ocean. This species thrives in sandy intertidal flats, feeding on mollusks and crustaceans while moving with the tides. Juvenile rays seek refuge and food in mangroves to evade predators. Recent genetic analysis has revealed its distinctiveness from cowtail rays, despite similar physical traits.  

Freshwater Whipray, Urogymnus dalyensis

Discover the Urogymnus dalyensis (Freshwater Whipray), a magnificent ray with an apple-shaped body, a prominent snout and a long, whip-like tail armed with venomous spines. These rays call the freshwater rivers and estuaries of New Guinea, northern parts of Australia, including Queensland home. Well-adapted to their environment, freshwater whiprays often bury themselves in sand or mud to ambush prey or evade predators. Sadly, like many freshwater elasmobranchs, they face significant habitat degradation, pollution, and overfishing threats. Advocating for effective management plans is especially difficult because there is so little information on this species in the literature.

Brown Whipray, Maculabatis toshi 

Meet the Brown Whipray, Maculabatis toshi, a stealthy mesopredator of the ocean! These rays have a greenish-brown body decorated with freckle-like white spot patterns, a long whip-like tail and a uniformly white unders. Find them cruising in tropical and subtropical coastal waters, where they dominate sandy or muddy bottoms near coral reefs and estuaries. With mottled brown coloration, they seamlessly blend into their surroundings, becoming masters of disguise. With a taste for invertebrates and small fish, they’re skilled hunters of the ocean floor.

Learn more about the Carcharhinid sharks we encounter here

Learn more about the Sphyrnid sharks we encounter here

Learn more about the Rhinopristiform rays we encounter here