Breakthrough allows scientists to determine the age of endangered native fish using DNA

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Benjamin Mayne, CSIROIdentifying the age of animals is fundamental to wildlife management. It helps scientists know if a species is at risk of extinction and the rate at which it reproduces, as well as determining what level of fishing is sustainable.

Determining the age of fish has been difficult in the past — primarily involving extracting the inner ear bone, also known as the “otolith”. Layers of growth in the otolith are counted like rings on a tree to reveal an individual’s age. Unless a dead specimen is available, this method requires killing a fish, making it unsuitable for use on endangered populations.

However a non-lethal DNA test developed by the CSIRO enables researchers to determine fish age for three iconic and threatened Australian freshwater species: the Australian lungfish, the Murray cod and the Mary River cod. We outline the technological breakthrough in our research just published.

Our fast, accurate and cost-effective test can be adapted for other fish species. We now hope to share this method to improve the protection of wild fish populations and help promote sustainable fisheries around the world.

Traditionally, age could only be determined on a dead fish. The new method is non-lethal.
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Iconic species at risk

Human activity has led to the population declines of the three Australian fish species at the centre of our research.

The threatened Australian lungfish is found in rivers and lakes in southeast Queensland. It’s often referred to as a “living fossil” because its extraordinary evolutionary history stretches back more than 100 million years, before all land animals including dinosaurs.

Man-made barriers in rivers reduce the movement of water, which lowers lungfish breeding rates.

Older lungfish do not have hard otolith structures, which makes determining their age difficult. Bomb radiocarbon, which analyses carbon levels in organic matter, has been used to age Australian lungfish, but this method is too expensive to be widely used.

In the past, determining the age of Australian lungfish has been challenging.

The threatened Murray cod is Australia’s largest freshwater fish. The Mary River cod is one of Australia’s most endangered fish, found in less than 30% of its former range in Queensland’s Mary River.

Habitat destruction and overfishing are major threats to Murray cod and Mary River cod populations.

Otoliths can be used to determine age for both these cod species, however this has only been done on a population-wide scale for the more prevalent Murray cod.

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CSIRO estimated the age of Mary River cod.

Our DNA breakthrough

When cells divide to make new cells, DNA is replicated. This can lead to DNA methylation, which involves the addition or the loss of a “methyl group” molecule at places along the DNA strand.

Research has found the level of DNA methylation is a reliable predictor of age, particularly in mammals, including humans.

To develop our test, we first worked with zebrafish. This species is useful when studying fish biology because it has a short lifespan and high reproductive rates. We took zebrafish whose ages were known, then removed a tiny clip of their fin. We then examined DNA methylation levels in the fin sample to identify the fish’s age.

Following this successful step, we transferred the method to Australian lungfish, Murray cod and Mary River cod. Again, we used fish of known ages, as well as bomb radiocarbon dating of scales and ages determined from otoliths.

We found despite the zebrafish and the study fish species being separated by millions of years of evolution, our method worked in all four species. This suggests the test can be used to predict age in many other fish species.

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The test uses co-called DNA methylation to estimate age.
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A conservation management boom?

In the same way human population demographers use census data to understand and model human populations, we now have the tools to do this with animals.

We are looking to expand this DNA-based method to determine the age of the endangered eastern freshwater cod and trout cod. We will also continue to test the method across other species including reptiles and crustaceans.

This work is part of CSIRO’s ongoing efforts to use DNA to measure and monitor the environment. This includes estimating the lifespan of vertebrate species such as long-lived fish and surveying biodiversity in seawater using DNA extracted from the environment.

We envisage that in the not too distant future, these methods may be used by other researchers to better understand and manage wild animal populations.

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A new study shows an animal’s lifespan is written in the DNA. For humans, it’s 38 years

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Benjamin Mayne, Molecular biologist and bioinformatician, CSIRO

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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A virus is attacking koalas’ genes. But their DNA is fighting back

Keith Chappell, The University of Queensland

A virus that infects koalas is steadily integrating itself into their DNA, ensuring that it is passed down from generation to generation. But the koala genome is defending itself, revealing that DNA has its own immune system to shut down invaders.

The virus, called koala retrovirus (KoRV), is linked to weakened immunity, cancer, and chlamydia infection in koalas. All retroviruses hijack the DNA in some cells of their host’s body, but not all of them manage to be transmitted to the host’s offspring.

Your DNA is 8% virus

Over the millions of years of evolutionary history, retroviruses have at one time or another made their way into the genomes of all species of vertebrates that we have studied.

We know about these ancient infections because retroviruses sometimes infect the animal’s sperm or egg cells, which means the virus incorporates its own DNA sequences into the genome that is passed from generation to generation.

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These viral sequences can contribute to disease, but have also been “co-opted” by the host animals for processes that are essential to normal development. As much as 8% of the human genome is made up of the remnants of infectious viruses.

While we know that retroviruses have frequently appeared during evolutionary history, we don’t know much about how retroviral sequences infiltrate sperm and egg cells, or how these cells react.

Catching a retrovirus in the act

Almost all known retrovirus genome invasions happened millions of years ago. However, KoRV is a recently identified exception. The virus spreads between individuals, but is also infecting sperm and egg cells, so many koalas are born with this pathogen as part of their genome.

My colleagues and I at the University of Queensland are collaborating with scientists from the University of Massachusetts Medical School to analyse how koala sperm and egg cells respond to KoRV-A infection.

Our findings, published today in Cell, suggest these cells mount a novel “innate genome immune response” to viral infection, which may help control the spread of infectious KoRV.

Within this project, the team analysed DNA and RNA from different tissue samples from deceased wild koalas from South East Queensland. (Like DNA, RNA also contains genetic information about the koalas – but it is also what KoRV’s own genome is made of.)

The team specifically looked for short sequences of RNA, between 23 and 35 nucleotides long, known as PIWI Interacting RNAs (piRNAs). Clusters of piRNA sequences are retained within the genome and serve as a kind of memory bank of undesirable sequences – signatures of invading viruses – to be targeted.

An immune system for the genome

Based on our new findings, we suggest that there is a specialised immune system to defend against retroviral genome invasion. Like the ordinary immune system, this one includes an innate response – a sort of general-purpose defence against attackers – and an adaptive response, which learns to recognise specific pathogens and take them down.

At the early stages of egg or sperm infection, the altered DNA sequence results in a “molecular pattern” that is recognised by an innate genome immune system, which stops the activity of the virus and starts producing signature piRNA sequences to recognise the invader.

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The innate immune response works until a memory of the genome invader is created and a sequence-specific adaptive response kicks in.

We propose a framework through which a sequence from an invading retrovirus can first have its genes “silenced”, and then through targeted processes it eventually becomes an integral part of the host genome.

This “genome immune system” changes our understanding of what shapes the genomes of all animals. No more can we view the genome as a defenceless entity governed purely by natural selection – it fights back.

Keith Chappell, Senior Research Fellow, School of Chemistry and Molecular Biosciences, The University of Queensland

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Monster hunt: using environmental DNA to survey life in Loch Ness

With the help of environmental DNA, scientists are compiling a census of life in Loch Ness, which should establish if there is any scientific basis to the centuries-old legend of the Loch Ness monster.
Supplied, CC BY-SA

Neil Gemmell

Reported sightings of the Loch Ness monster go back to the Dark Ages, but now our Super Natural History team is using the 21st-century technology of environmental DNA to survey all life in the famous Scottish lake.

The premise of environmental DNA (eDNA) is simple. Life is messy, and living things leave behind skin, hair, feathers, poo, bark, pollen and spores as part of their day-to-day activities.

These traces result in a potpourri of organic material in our soil and water from which DNA can be extracted and sequenced. Our aim is to produce a census of life in Loch Ness and to establish if there is any scientific basis for the centuries-old monster legend.

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Sampling a legend

There have been more than 1,000 registered sightings of the Loch Ness “monster”, including two in the last month. They have sparked various theories. Some say the loch is home to a prehistoric relic, while others believe it’s a giant sturgeon, catfish, or just a log or a boat wake.

Obviously, the hook here is that if Nessie is present in the deep, dark and mysterious waters of Loch Ness (for the record I am not a believer, but open to being wrong) then we might find DNA sequences that will help us figure out its biological basis.

We have now finished two weeks of field work for this project, having collected 259 water samples from various parts of the loch, including its chilly depths, more than 200 metres down.

The team took water samples from several sites on the lake, as well as from deep waters.
Kieran Hennigan, CC BY-SA

Miraculously, for the Highlands, the wind stayed light and the rain stayed away which meant we were able to send teams out to sample right around Loch Ness by car and small boat, as well as several nearby lochs as controls. We have also used the Loch Ness Centre boat to sample up and down Loch Ness, particularly targeting the loch’s depths.

Decoding life

Our days were long, frequently starting as early as 6am and finishing as late as midnight. Our project was also hard on equipment – we broke two of our three sampling devices deploying to depth. Now, with sample collection behind us, we are onto the next phase of work.

The DNA is currently being extracted from our filtered water samples at the University of Hull. From there it will go to French and Swiss laboratories to be metabarcoded and sequenced.

What will we find? Well undoubtedly there will be DNA sequences derived from bacteria, protists, algae, invertebrates, and the traces of fish, birds and other vertebrate life known from the loch.

What we’ll get is a comprehensive survey of the biodiversity of Loch Ness, but whether we’ll find anything unusual, such as a giant catfish, sturgeon or eel, or a species unknown to science, who knows. Nessie believers will have to wait a few more months for the final results.

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Bigfoot, the Kraken and night parrots: searching for the mythical or mysterious

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It all started with a tweet

About two years ago Darren Naish had just published a book, Hunting Monsters, which included a section on Loch Ness. Over a few tweets I asked him if, in his research for the book, he had stumbled on anyone who was using eDNA to search for evidence of Nessie. The answer was no, but we both thought it a splendid idea.

I was becoming increasingly enamoured with the power of eDNA as a means to monitor the natural environment. Our team at the University of Otago was undertaking eDNA work that demonstrated amazing accuracy at identifying the species that resided in the marine ecosystems we studied.

Based on this, I was already thinking about how we might use eDNA to search for and identify the creatures that live in areas of our planet that are hard to investigate using traditional approaches – deep oceans, subterranean water systems and the like. Loch Ness seemed a perfect fit for that sort of project.

Career killer or opportunity?

As with many science ideas, that tweet ended up going into the “this is quite interesting” basket and there it sat until I got an email from Scottish journalist John Paul Breslin. When his article appeared in early April, many took it for an April Fool’s joke, but the story rapidly spread from Scotland to the rest of the world.

The media interest was overwhelming but I wasn’t sure if this was something I really wanted to do. At the time I was the head of a large department at a respected university, with an international reputation for doing quality work in the areas of molecular ecology and evolution. Some colleagues suggested the idea might be a career killer.

The turning point arrived one morning when I was dropping my son off at school. A large posse of eight- and nine-year-olds told me they thought the idea of hunting for the Loch Ness monster was the coolest thing ever. It resonated with me and led to this opportunity to engage the public, particularly kids, in the scientific process.

Loch Ness expert, Adrian Shine (right), had dredged the deep lake many times and is now helping to sample DNA traces of life.
Kieran Hennigan, CC BY-SA

One of the first stops was Loch Ness expert, Adrian Shine, who had dredged Loch Ness many times with nets and other devices and agreed to provide a boat and skipper. Several other colleagues all agreed to join the project and the team grew as we realised the Loch Ness monster hunt would describe the biodiversity of the lake in unprecedented fashion, add information about the movements of migratory fish species such as salmon, eels and lamprey, and be a hell of a science communication platform.

So, our project is not a simple monster hunt (although wouldn’t it be amazing if we did find something extraordinary during our investigation). Rather it is an amalgam of basic science, linked to major current initiatives, with a strong science communication aspect. Ultimately, we may find no DNA evidence that explains the monster myth, but I doubt that will ever dent belief. As Adrian Shine quips, absence of evidence is not evidence of absence, and those that wish to will continue to believe in monsters.

Neil Gemmell, Professor of Reproduction and Genomics

This article was originally published on The Conversation. Read the original article.

New DNA test traces illegal ivory back to African herds from which they came

How DNA Could Help Catch Elephant Poachers

CROCODILE ATTACK: HUMAN REMAINS FOUND IN CROCODILE

A 4.3m long crocodile has been caught and tested following the disappearance of Arthur Booker in the Endeavour River near Cooktown (Queensland, Australia) two weeks ago. Male human remains have been found within the crocodile and police have been notified of the find. DNA tests are now to be carried out to confirm the identity of the human remains, though it is more than likely to be those of Arthur Booker.

MYSTERY SOLVED: PLANE IS THAT OF STEVE FOSSETT

There is now more information on the story I posted yesterday regarding the disappearance of Steve Fossett at:

https://kevinswildside.wordpress.com/2008/10/02/steve-fossett-mystery-solved/

The wreckage discovered during the renewed search for Steve Fossett (following the discovery of several items belonging to Steve Fossett by a bushwalker) has turned out to be that of the missing Steve Fossett. Human remains have also been found in the wreckage with DNA testing to be used to confirm whether the remains are indeed those of Steve Fossett.