Tasmanian tigers were going extinct before we pushed them over the edge



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Gone since 1936, and ailing since long before that.
Tasmanian Museum and Art Gallery, Author provided

Andrew Pask, University of Melbourne

There’s no doubt that humans killed off the Tasmanian tiger. But a new genetic analysis suggests this species had been on the decline for millennia before humans arrived to drive them to extinction.

The Tasmanian tiger, also known as the thylacine, was unique. It was the largest marsupial predator that survived into recent times. Sadly it was hunted to extinction in the wild, and the last known Tasmanian tiger died in captivity in 1936.

In a paper published in Nature Ecology and Evolution today, my colleagues and I piece together its entire genetic sequence for the first time. It tells us that thylacines’ genetic health had been declining for many millennia before they first encountered human hunters.


Read more: Will we hunt dingoes to the brink like the Tasmanian tiger?


Hounded by hunters.
Tasmanian Museum and Art Gallery, Author provided

Our research also offered the chance to study the origins of the similarity in body shape between the thylacine and dogs. The two are almost identical, despite having last shared a common ancestor more than 160 million years ago – a remarkable example of so-called “convergent evolution”.

Decoding the thylacine genome allowed us to ask the question: if two animals develop an identical body shape, do they also show identical changes in their DNA?

Thylacine secrets

These questions were previously difficult to answer. The age and storage conditions of existing specimens meant that most thylacine specimens have DNA that is highly fragmented into very short segments, which are not suitable for piecing together the entire genome.

We identified a 109-year-old specimen of a young pouch thylacine in the Museums Victoria collection, which had much more intact DNA than other specimens. This gave us enough pieces to put together the entire jigsaw of its genetic makeup.

The preserved young, thylacine with enough DNA to reveal its whole genome.
Museums Victoria, Author provided

Next, we made a detailed comparison of thylacines and dogs to see just how similar they really are. We used digital imaging to compare the thylacine’s skull shape to many other mammals, and found that the thylacine was indeed very similar to various types of dog (especially the wolf and red fox), and quite different from its closest living marsupial relatives such as the numbat, Tasmanian devil, and kangaroos.

Our results confirmed that thylacines and dogs really are the best example of convergent evolution between two distantly related mammal species ever described.

We next asked whether this similarity in body form is reflected by similarity in the genes. To do this, we compared the DNA sequences of thylacine genes with those of dogs and other animals too.

While we found many similarities between thylacines’ and dogs’ genes, they were not significantly more similar than the same genes from other animals with different body shapes, such as Tasmanian devils and cows.

We therefore concluded that whatever the reason why thylacines and dogs’ skulls are so similarly shaped, it is not because evolution is driving their gene sequences to be the same.

Family ties

The thylacine genome also allowed us to deduce its precise position in the marsupial family tree, which has been a controversial topic.

Our analyses showed that the thylacine was at the root of a group called the Dasyuromorphia, which also includes the numbat and Tasmanian devil.

By examining the amount of diversity present in the single thylacine genome, we were able to estimate its effective population size during past millennia. This demographic analysis revealed extremely low genetic diversity, suggesting that if we hadn’t hunted them into extinction the population would be in very poor genetic health, just like today’s Tasmanian devils.

The less diversity you have in your genome, the more susceptible you are to disease, which might be why devils have contracted the facial tumour virus, and certainly why it has been so easily spread. The thylacine would have been at a similar risk of contracting devastating diseases.

The last thylacine alive.
Tasmanian Museum and Art Gallery, Author provided

This loss in population diversity was previously thought to have occurred as a population of thylacines (and devils) became isolated on Tasmania some 15,000 years ago, when the land bridge closed between it and the mainland.

But our analysis suggests that the process actually began much earlier – between 70,000 and 120,000 years ago. This suggests that both the devil and thylacine populations already had very poor genetic health long before the land bridge closed.


Read more: How curiosity can save species from extinction


The ConversationNow that we know the whole genome of the Tasmanian tiger, we know much more about this extinct animal and the unique place it held in Australia’s marsupial family tree. We are expanding our analyses of the genome to determine how it came to look so similar to the dog, and to continue to learn more about the genetics of this unique marsupial apex predator.

Andrew Pask, Associate Professor, University of Melbourne

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

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Which square is bigger? Honeybees see visual illusions like humans do


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Flowers may take advantage of visual illusions to attract bees.
from www.shutterstock.com

Scarlett Howard, RMIT University and Adrian Dyer, RMIT University

When a human looks at a distant skyscraper, it appears small to the eye. It’s a visual illusion, and we use other contextual information to know the building is actually tall.

Our new study shows, for the first time, that honeybees see size-based visual illusions too. Whether a size illusion is seen, or not, depends on how a target object is viewed.

These new results help us understand how visual illusions evolved in different species over time.


Read more: Three visual illusions that reveal the hidden workings of the brain


How humans experience illusions

Humans see lots of different illusions such as mirages, illusions of shape, length, size, and even colour (remember that dress?).

The lines or shapes around an object can change the way your brain sees it.
Provided by Scarlett Howard

Visual illusions are errors in your own perception which can allow you to process the very complex visual information you see more easily.

One of the strongest geometric illusions we humans see is an illusion of size, called the Ebbinghaus Illusion.

Ebbinghaus Illusion: The central circles are of identical size, but are perceived as very different by humans because we use context to inform our vision.
Provided by Scarlett Howard

Interestingly, species such as bottlenose dolphins, bower birds, domestic chicks, and redtail splitfins see this illusion in the same way as humans. However, animals such pigeons, domestic dogs, and bantams see the opposite illusion to what we see, and baboons do not see an illusion at all.

To understand why different species see size illusions in such different ways, and how an insect with a miniature brain might view a size illusion, we developed an experimental design using honeybees.


Read more: Want a better camera? Copy bees and their extra light-sensing eyes


Bees can help us design better camera technology.

Why do animals perceive illusions differently?

It’s intriguing that some species view size illusions the same way as us, and some animals do not. Why is it that a baboon does not see any illusion when looking at the Ebbinghaus Illusion? Why do pigeons and dogs see the opposite illusion to us? Our team decided to look into the methodology of the past studies that had shown these differences.

When baboons, pigeons, dogs, and bantams were tested, they were looking at the illusion from either a set distance or from a forced close-range distance. For example, dogs had to touch the correct option with their noses, and birds had to peck the correct option meaning these species were viewing the illusion at a very close distance. Baboons, on the other hand, were viewing the illusion at a set distance, unable to move closer than a certain distance from a screen that presented the illusionary pictures.

With this knowledge, we decided to test honeybees using two study conditions:

  1. a free-flying set-up where bees could fly at any distance from the size illusion before making decisions, and
  2. a constrained viewing set-up where bees could only view and make decisions about the illusion from one set distance.

How does a bee view size illusions?

To determine if bees could perceive size illusions, we first had to find a way to ask them.

We trained one group of bees to always choose the larger black square on a square white background and another group of bees to always choose the smaller black square on a square white background.

When bees had learnt to either choose larger or smaller sized black square targets, we manipulated the size of the background, thus trying to induce the perception of a visual illusion (similar to the Delboeuf Illusion).

Stimuli used in experiments.
Provided by Scarlett Howard

We ran this experiment using our free-flying, unrestricted viewing condition and also using a restricted viewing condition where independent bees were unable to choose their own distance to make decisions.

Eureka! Training conditions explain why different animals see illusions differently. Bees in the unrestricted viewing condition perceived illusions, while bees in the restricted viewing condition did not see size illusions.

Now, we are interested in whether some past study results were due to experimental set-up: maybe more or even all animals could perceive illusions like humans, depending on the context in which they are viewing these illusions.

What does this mean for the evolution of vision?

Visual illusions are useful because they allow us to process complex scenes, with multiple pieces of information, as a whole by using context as a cue. Since different animals see size illusions, understanding how this works could help us learn more about how vision itself evolved.

One explanation of why such different animal species, from humans to bees, see size illusions is because an ancient ancestor had this ability, and it has been conserved throughout evolution. However, a more likely scenario is that the evolution of visual illusion perception is due to convergent evolution. This occurs when different species evolved the ability to perceive illusions separately.

The ability of bees to perceive a size illusion in a free-flying environment also has implications for flower evolution. Flowers could have evolved to exploit the ability of bees seeing illusions to make nectar areas look more appealing. One genus of flower, Wurmbea, appears to have illusionary properties such as differently sized flowers with patterns reminiscent of size illusions such as the Ebbinghaus and Delboeuf Illusions.

Wurmbea flower as seen through a special camera simulating bee vision.
http://ro.uow.edu.au/asj/vol5/iss1/7

The ConversationA very important lesson from this study is that viewing context can make scenes appear very different to reality. This is very important to remember when working on vision in humans or any other animal.

Scarlett Howard, PhD candidate, RMIT University and Adrian Dyer, Associate Professor , RMIT University

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

Bee aware, but not alarmed: here’s what you need to know about honey bee stings



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Bees don’t attack unless they feel threatened.
Shutterstock

Ronelle Welton, University of Melbourne and Kymble Spriggs, University of Melbourne

A Victorian man died yesterday after being stung by several bees. While bee sting deaths are rare (bees claim around two Australian lives each year), bees cause more hospitalisations than any venomous creature.

Bee stings cause nearly the same number of deaths each year as snake bites.
The University of Melbourne’s Pursuit/Internal Medicine Journal

Around 60% of Australians have been stung by a honey bee; and with a population of more than 20 million, that’s a lot of us who have just experienced pain and some swelling.

So what happens when we’re stung by a bee, and what determines whether we’ll have a severe reaction?


Further reading: Ants, bees and wasps: the venomous Australians with a sting in their tails


How do bees sting?

Honey bees work as collective group that live as a hive. The group protects the queen, who produces new bees, with worker bees flying out to collect nectar or pollen to bring back to the hive.

Bees have a venom sac and a barbed stinger at the end of their abdomen. This apparatus is a defensive mechanism that is used if they feel under attack; to defend the hive from destruction. The barb from a bee sting pierces the skin to inject the venom, with the bee releasing pheromones that can incite other nearby bees to join the defensive attack.

Honey bees work as a collective.
Shutterstock

The venom is a complex mixture of proteins and organic molecules, that when injected into our body can cause pain, local swelling, itching and irritation that may last for hours. The specific activity of some bee venom components have also been used to treat cancer.


Further reading: Curious Kids: Do bees ever accidentally sting other bees?


A single bee sting is almost always limited to these local effects. Some people, however, develop an allergy to some of these venom proteins. Anaphylaxis, a severe allergic reaction that is potentially life-threatening, is the most serious reaction our body’s immune system can launch to defend against the venom.

It is our body’s allergy to the bee venom, rather than the venom itself, that usually causes life-threatening issues and hospitalisation.

How do I know if I am allergic?

If you have not been stung by a bee before you are unlikely to be allergic to the venom. However, if you have been stung by a bee, there is the potential to develop an allergy. We do not know why some people become allergic and others don’t, but how often you are stung seems to play a role.

If you have experienced very large local reactions from a bee sting, or symptoms separate from the sting site (such as swelling, rashes and itchy skin elsewhere, dizziness or difficulty breathing) you may have an allergic sensitivity. Your doctor can assess you by taking a full history of reactions. Skin testing or blood allergy testing can help confirm or exclude potential allergy triggers.

An allergy specialist is key to assess people’s risk of severe allergic reactions (anaphylaxis).

There is an effective treatment for severe honey bee allergies, called immunotherapy. This involves the regular administration of venom extracts with doses gradually increased over a period of three to five years. This aims to desensitise the body’s immune system, essentially to “switch off” the allergic reaction to the venom.

Venom immunotherapy is very effective at preventing severe reactions and is available on the Pharmaceutical Benefit Scheme, whereas other immunotherapy treatments in Australia cost an average of A$1,200 per year.

First aid for a bee sting

Bees usually leave their barbed sting in the skin and then die. Remove the sting as soon as possible (within 30 seconds) to limit the amount of venom injected. Use a hard surface such as the edge of a credit card, car key or fingernail to flick/scratch out the barb.

For a minor reaction such as pain and local swelling, a cold pack may help relieve these symptoms.

If a bee stings you around your neck, or you find it difficult to breathe, or experience any wheezing, dizziness or light-headedness, seek medical advice urgently.

Prevention

Despite being a species introduced by European settlers, the honey bee (Apis mellifera) plays an essential role within Australian agriculture. We need to appreciate their essential functions, and try to prevent stings.


Read more: Losing bees will sting more than just our taste for honey


If you see a bee let it be (sorry); don’t swat it or step on them. Our bees don’t attack unless they feel they need to defend their hive.

Do not attempt to locate a hive, call an expert.

The ConversationFor more information on allergies go to the ASCIA website. Local bee keeping groups are a good source of knowledge about local bee populations.

Ronelle Welton, , University of Melbourne and Kymble Spriggs, Clinical Associate Professor, University of Melbourne

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

How we discovered a new species of orangutan in northern Sumatra



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The new species has a smaller head, and a distinctly ‘cinnamon’ colour compared with other orangutans.
Maxime Aliaga, Author provided

Colin Groves, Australian National University and Anton Nurcahyo, Australian National University

We have discovered a new species of orangutan – the third known species and the first new great ape to be described since the bonobo almost a century ago.

The new species, called the Tapanuli orangutan (Pongo tapanuliensis), has a smaller skull than the existing Bornean and Sumatran orangutans, but has larger canines.

As we and our colleagues report in the journal Current Biology, the new species is represented by an isolated population of fewer than 800 orangutans living at Batang Toru in northern Sumatra, Indonesia.

Orangutan populations in Sumatra and Borneo – the new species’ distribution is shown in yellow.
Curr. Biol.

Read more: The lengthy childhood of endangered orangutans is written in their teeth


The existence of a group of orangutans in this region was first reported back in 1939. But the Batang Toru orangutans were not rediscovered until 1997, and then confirmed in 2003. We set about carrying out further research to see whether this isolated group of orangutans was truly a unique species.

On the basis of genetic evidence, we have concluded that they are indeed distinct from both the other two known species of orangutan: Pongo abelii from further north in Sumatra, and Pongo pygmaeus from Borneo.

The Batang Toru orangutans have a curious mix of features. Mature males have cheek flanges similar to those of Bornean orangutans, but their slender build is more akin to Sumatran orangutans.

The hair colour is more cinnamon than the Bornean species, and the Batang Toru population also makes longer calls than other orangutans.

Making sure

To make completely sure, we needed more accurate comparisons of their body dimensions, or “morphology”. It was not until 2013 that the skeleton of an adult male became available, but since then one of us (Anton) has amassed some 500 skulls of the other two species, collected from 21 institutions, to allow for accurate comparisons.

Analyses have to be conducted at a similar developmental stage on male orangutan skulls, because they continue growing even when adult. Anton found 33 skulls of wild males that were suitable for comparison. Of 39 different measurement characteristics for the Batang Toru skull, 24 of them fall outside of the typical ranges of northern Sumatran and Bornean orangutans.

The new orangutans have smaller heads – but some impressive teeth.
Matthew G Nowak, Author provided

Overall the Batang Toru male has a smaller skull, but bigger canines. Combining the genetic, vocal, and morphological sources of evidence, we have confidently concluded that Batang Toru orangutan population is a newly discovered species – and one whose future is already under threat.

Under threat as soon as they’re discovered.
Maxime Aliaga, Author provided

Despite the heavy exploitation of the surrounding areas (hunting, habitat
alteration and other illegal activities), the communities surrounding the habitat of the Tapanuli orangutan still give us the opportunity to see and census the surviving population. Unfortunately, we believe that the population is fewer than 800 individuals.

Of the habitat itself, no more than 10 square km remains. Future development has been planned for that area, and about 15% of the orangutans’ habitat has non-protected forest status.


Read more: Orangutans need more than your well-meaning clicktivism


The discovery of the third orangutan in the 21st century gives us an understanding that the great apes have more diversity than we know, making it all the more important to conserve these various groups.

The ConversationWithout the strong support of, and participation from, the communities surrounding its habitat, the future of the Tapanuli orangutan will be uncertain. Government, researchers and conservation institutions must make a strong collaborative effort to make sure that this third orangutan will survive long after its discovery.

Colin Groves, Professor of Bioanthropology, Australian National University and Anton Nurcahyo, , Australian National University

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