Show us your spots! Quoll trapping in northern Queensland.

Recently, I went on a little data-collecting trip. The scenery was pretty cool and I was collecting parasites from some rather cute marsupials, so I thought it might be nice to share it with you.


One of our rockier sites – a creek running through a gorge.

The field sites were on the Atherton Tableland, northern Queensland. Sites were in hilly, rocky areas, because we were trapping northern quolls (Dasyurus hallucatus), and they live in hilly, rocky habitats. Northern quolls are classified as ‘endangered’ by the federal government, which was one reason why this fieldwork was done – a colleague was collecting samples for population genetics analysis. Live mammal trapping involves getting up before sunrise to check traps nice and early (so the animals don’t get caught in the sun!), even though all our traps were covered with a thick layer of vegetation for protection. Walking around in the dawn light for the purposes of handling little marsupials is definitely one of those “I love my job” moments.

being at work at sunrise is not all bad.

Being at work at sunrise is not all bad.

It turns out that northern quolls are pretty easy to catch. Using collapsible cage traps baited with chicken frames from the butcher, we caught ourselves many quolls. The traps were treadle-operated, meaning that there was a little flap on the floor attached to the door of the trap by a metal rod. As an animal steps on the flap on its way in to eat the bait, it dislodges the rod and the door swings down, trapping the animal.

Northern quoll, Dasyurus hallucatus, in a bag.

Northern quoll, Dasyurus hallucatus, in a bag.

Once caught, the quolls get transferred to a handling bag where they had their measurements taken, and were examined for ectoparasites. Generally, they do not get checked for parasites, but because I was there, I collected any ectoparasites I found on each animal.

Me, collecting parasites from a quoll.

Me, collecting parasites from a quoll.

Paydirt! Ticks on the back of a quoll's ear.

Paydirt! Ticks on the back of a quoll’s ear.

After I’d finished picking at their ears and combing their fur (for fleas!), they got their photo taken – in a kitchen garbage bin, no less. It was the best thing to show up their spots, and they couldn’t jump out of it. Usually. We did have a couple of escape attempts. The purpose of the photography was as an identification method for upcoming remote camera trapping, as quolls have individual spot patterns. Then, they were done, and released at the site of capture. We caught several quolls again and again. Seems they didn’t mind the indignity of a night in a trap as long as they could have a chicken dinner!

Quoll showing us its good side.

Quoll showing us its good side.

Getting released - going...

Getting released – going…



Back at the lab, I have a collection of ticks, mites, fleas and lice from the quolls that were captured. I sorted them into separate vials and am now going through the process of identifying them. Some are easier than others! Very little is known about the parasites of northern quolls, so my work will shed a bit more light on the ecology of parasites on an increasingly rare marsupial.

It's like Christmas came early in the parasite lab!

Christmas came early in the parasite lab!


A new species of Acanthocephala (shameless self-promotion!)

My first paper for 2013 is out. If you’re interested in learning about a new species of Acanthocephala from fish, then this is the paper for you.

Weaver HJ and Smales LR (2013) Filisoma filiformis n. sp. (Echinorhynchida: Cavisomidae), a New Species of Acanthocephala from Kyphosus spp. (Perciformes: Kyphosidae) from the South Pacific, and a Key to the Genus Filisoma. Comparative Parasitology 80, 33 – 38.

Find it here: If you can’t access it, let me know by leaving a comment and I can email it to you.

Here’s the abstract: 

“We describe a new species of acanthocephalan from the reef fish Kyphosus bigibbus Lacepede, Kyphosus sydneyanus (Gunther) and Kyphosus vaigiensis (Quoy and Gaimardi)  from Heron Island, Queensland; Ningaloo Reef, Western Australia; and Moorea, French Polynesia, respectively. Filisoma filiformis n. sp. is differentiated primarily from other species by its long, slender proboscis, with 16–18 longitudinal rows of 42–48 hooks. The wide distribution and multiple host species of F. filiformis suggest that it could be found in other localities around the Indo-Pacific region where kyphosid fish occur. The differing patterns of host range and geographic distribution within the genus Filisoma are discussed.”


It’s been so long since I posted last. But my current project is nearly finished, so hopefully the blogging can recommence soon.

Heligmosomoides polygyrus: a twirly taxonomic customer.

Heligmosomoides polygyrus (or is it H. bakeri?) Image via Wikipedia.

(post edited 6 October)

Last week, I taught in an undergraduate parasitology prac class. My job was to remove nematodes from lab mice so the students could examine them. The nematodes were were using were Heligmosomoides polygyrus, and they’re quite cool, because they  are coiled, and look a bit like twirly telephone cords. As I dissected the worms out the mice, I explained to the students how special these worms are. Why, you ask? Well, I’ll tell you.

Heligmosoloides polygyrus is a really nice model for exploring host-parasite relationships, for example in understanding  Th1/Th2 immune responses, and other aspects of immune system function. It’s also good as a model for drug targets for parasites of livestock. It is easy to work with, but it’s name is a problem.

As synthesised by Behnke and Harris (2010), the nematode was first described in 1842 from wood mice, Apodemus spp. as Strongylus polygyrus. It was synonomised with another species as Heligmosomoides polygyrus in 1922. Not long after, another species from Apodemus wood mice was described as Nematospiroides dubius. Between the late 1920s and the late 1960s, there was much confusion over the name of this nematode(s), and its range of hosts. During the 1930s, the parasite had been collected from Peromyscus maniculatus (an American mouse species) and was begun to be used in laboratory experiments.  This served to cause more confusion over what name should be used for the lab strains and the wild strains, because its host was not the usual one. To complicate the story even further, H. polygyrus had also been isolated from wild house mice, Mus musculus in America (as opposed to Europe where the wood mice lived). Were they the same species? They looked the same, but people still wrote about the worms using both names.

The name N. dubius was officially abandoned in 1991, and later in 2001 the species was split into two subspecies – H. p. polygyrus (wild strain) and H. p. bakeri (lab strain). Essentially, people were getting hung up on the host species (Apodemus vs. Mus) and the distribution (Europe vs. North America). To complicate it just a little more (as if it wasn’t confusing enough already), the lab strains were also being compared to the wild strains. Molecular evidence presented in 2006 (Cable et al. 2006) showed that there was indeed a difference between the two taxa, enabling them to be named as separate species – this creating two new species from one: H. polygyrus in Apodemus and H. bakeri in Mus (including lab mice).

But it doesn’t end there. Maizels et al (2011) contended that the methods used by Behnke and Harris were not that great, and that differences in infectivity of lab strains vs. wild strains of Heligmosomoides polygyrus/bakeri could not reasonably be used to split species. The issue of infectivity (or lack thereof) was most likely because the number of generations of nematodes that had passed through mice had probably resulted in selection of infectivity to lab mice over the years. They recommended the use of two subspecies of H. polygyrus as per the previous idea. But as they had no taxonomic evidence for this assertion, the current taxonomy of the two species is retained. Therefore, according to the current evidence, I was showing students H. bakeri, not H. polygyrus. Unfortunately, most undergraduate students don’t care for taxonomy, and when I explained the history of the names of these worms to them, several pairs of eyes glazed over…. But when they saw the worms down the microscopes, they seemed genuinely excited, so I’ll take that as a win.

And that’s where we’re at today. A complicated and convoluted early history has led to an ongoing complicated and convoluted taxonomy for this parasite(s). Chances are, we’re actually seeing evolution in action, as the lab strains become more distant genetically from the wild strain due to manipulation through many, many generations of host mice.


Behnke and Harris (2010) Heligmosomoides bakeri: new name for an old worm? Trends Parasitol 26, 524-529.

Cable, Harris, Lewis, Behnke (2006) Molecular evidence that Heligmosomoides polygyrus from laboratory mice and wood mice are separate species. Parasitology 133, 111-122.

Maizels, Hewitson and Gause (2011) Heligmosomoides polygyrus: one species still. Trends Parasitol 27, 100-101.

This just in: There are no big cats in Victoria.

Puma concolor (image via Wikipedia)

A report ordered by the Victorian State Government on the status of ‘big cats’ in the state has just been released. You can read about it here at the ABC News or here at The Age. The authors of the report, from the Department of Sustainability and Environment, did not find any evidence to support the (crackpot) idea that large cats are roaming around the country areas of the state. The Minister for Agriculture, Peter Walsh has said, “Some preliminary DNA evidence also cannot be entirely dismissed but it is not sufficiently conclusive to prove beyond a reasonable doubt the identity of an animal.” Uh-huh. In amongst the Bureaucratese, I got ‘we had DNA but were told it was just from a domestic cat and we were disappointed’ from that statement. This may be because there are so many feral cats lurking around the place, who annoyingly would share much of their DNA with other species of cats, and also because labs that can tell you the name, address and birthday of someone/thing from a piece of DNA only exist on TV shows like CSI.

From The Age:

While the report author says it is impossible to prove something doesn’t exist, his survey of about a century’s worth of anecdotal evidence alleging big cats exist in Victoria has concluded it is highly unlikely.

“We can’t say 100 per cent there are no big cats in Victoria but we can say it is highly unlikely,” Department of Sustainability of Environment zoologist Peter Menkhorst said on Tuesday.

Mr Menkhorst examined more than 1000 pieces of data, including anecdotal reports collected by community groups and the government.

He said instances where people had blamed the mauling of livestock or other wildlife on a big cat pointed to a lack of understanding of how known predators behaved.

Some people seem to assume that big cats like pumas exist in parts of Australia, but the evidence points to regular domestic cats adapting to life as ferals and becoming really large (see here for a nice discussion on this). Obviously this takes time to occur, and over many generations. But cats were introduced into Australia in the late 1700s as part of European colonisation, and, when conditions are good, they can breed like rabbits (another environmental invader).
Let’s throw some taxonomy in while we’re here (after all, it’s what I’m all about). The article from The Age lists “pumas, leopards, jaguars or cougars” as potentially roaming around the place. This is an excellent example of why common names are stupid and confusing. The cat Puma concolor (it has been moved from the genus Felis into its own) has a wide distribution across most of the Americas, and this has led to various common names being used across different regions – a puma and a cougar are the same thing and they are also a mountain lion too. Cougars can also be called panthers, although generally ‘panther’ refers to a jaguar (Panthera onca) that is all-black in appearance instead of spotted. Finally, leopards (P. pardus) which occur in Asia and Africa but not the Americas, also come in a black morph that is referred to as a ‘panther’. So I’m not entirely sure whether the government report wanted three different species of cats serached for, or just one.

While this finding does not astound me in the slightest, what I do find jaw-droppingly incredible is that the government sought to have this report completed in the first place. They aren’t telling us how much it cost to produce, but I’d guess it was a substantial amount (as in, a decent small-research-grants’-worth). Feral cats (and dogs and foxes) have done so much harm to the overall biodiversity of the state (and the country), and their numbers go more or less unchecked. Surely the money spent on this report would have better used for developing control measures for feral cats, dogs and/or foxes?

Final note: Perhaps the Minister for Agriculture might like to turn his attention to yowies next? There are highly unsubstantiated claims that they roam around the countryside too…

Science round-up: What morsels have I found this week?

Oh, I have been neglectful. I’ve started a new project and it is leaving little time to wander the interwebs, get distracted reading things and write blog posts.

I have some very mammal-related offerings this week. A new species of African monkey has been described, panic about hantavirus in Yosemite NP is escalating, and population crashes of arctic lemmings is a bad thing.

New monkey species.

Cercopithecus lomamiensis juveniles, image from Hart et al. 2012.

Published in PLoS One, Hart et al. describe the second new species of African primate in 28 years. They don’t say how long it had been beyond that other species 28 years ago. These monkeys are commonly known as guenons, and are semi-arboreal, with records of them using spaces all the way between the canopy and the forest floor. This paper is really neat because it presents a very thorough description, including morphology, molecular data, ecological information and vocalisation data. And, because PLoS journals are online, they included the necessary information pertaining to hard-copy availability of the description (as the manuscript would have pre-dated the changes to the Code of Zoological Nomenclature that I posted about last week). The highlight of the article for me was learning that males of this new monkey have a blue perineum.

Hantavirus in Yosemite.

Peromyscus maniculatus, from Nebraska (photo from IncreasingDisorder’s camera)

Hantavirus is not really a new thing, and but this is the first time that an outbreak on this scale has occured. The virus is rodent-borne, with deermice, Peromyscus spp., being the main culprits. The current outbreak at Yosemite National Park in California has killed 3 people out of the nine confirmed cases so far. But because of the popularity of the site as a tourist destination, officials have sent health advisory notices out to almost a quarter of a million people who have visited the park (info from BBC News). Hantavirus is potentially deadly, so it’s not such a bad thing that these precautions are being taken.

Lemming population crashes are bad….

Stoat with lemming (image via ScienceNOW)

…if you rely on them to eat. Research published in Proc R Soc B and reported by ScienceNOW indicate that recent population crashes of collared lemming populations has had implications for the survival of various carnivores who mainly eat lemmings. As keystone species, the lemmings essentially hold the arctic ecosystems they inhabit together. The natural cycles of population fluctuation observed in arctic lemmings was interrupted by a severe decrease in numbers over the years since 2000. This is thought to be a result of decreased snow cover, and by extension, climate change. Population sizes of lemming predators have also decreased as a result of the population decline.

A revolution in taxonomy: electronic-only publication OK’d by ICZN.

I’m excited.

The International Commission on Zoological Nomenclature (ICZN) has published an amendment to the International Codeof Zoological Nomenclature (which confusingly can also be abbreviated to ICZN, but is usually called the Code instead) allowing for publication of taxonomic works in online-only journals.

This is great news. Previously, all taxonomic works (i.e., species descriptions, revisions etc) had to be published in such a way that they had a permanent hard-copy. In the old days, ALL journals were published in hard-copy, so this wasn’t a problem. But in our new  digital age, there have been several journals spring up that do not have a hard-copy version – they’re only available online, for example the journals in the PLoS and BMC stables. Any taxonomic works published in those journals have been invalid until now.

The major change to the Code is that if you wish to publish a description in an online-only journal, you must register your new species with ZooBank, and include information on where the permanent (electronic) record of your work will be held, along with the ISSN or ISBN for the publication.

Go forth and describe!

Taxonomy goings-on.

Perhaps as a taxonomist, I don’t get terribly excited about new species in the same way that the general public does. I do love the satisfaction of discovering and describing something new, but I have not yet named a species after a famous person (only my Honours supervisor, who thought having a parasite named after him was a rather dubious honour), or found anything exceptional-looking. But, this week, I’ve found newly described species who are both those things. And I also found some other extra-interesting bits.

David Attenborough’s spider

P. attenboroughi (image via Museum WA)

Via the BBC News, I learned that taxonomists from the Queensland Museum and the Museum of Western Australia have described a new species of goblin spider and named it after Sir David Attenborough. It’s called Prethopalpus attenboroughi, lives in a very small island off northern Queensland, and is less than 2mm long. I’d be far too timid to name something so tiny after someone so great, but maybe there’s an irony there that I’m missing.

The genus Homo gets larger

Taxonomy papers rarely get published in Nature. So I won’t begrudge Maeve Leakey et al. for having the audacity to submit a species description to said journal, because it’s on a new species of Homo. Fossils examined suggest that there was more than just H. erectus and H. habilis roaming around Africa about 2 million years ago. NewScientist has a nice summary for those who can’t get through the Nature paywall. Homo rudolfensis was found in the 1970s and initially considered to be a morphological anomaly and was disregarded. More recent discoveries of similarly-shaped skulls enabled the comparison with the original and the hypothesis that they were anomalus H. habilis was rejected, reinstating H. rudolfensis as a species. Nice.

New caecilian looks like a penis…

…well, it does. I quote a tweet I got from Science Mag: “The penis-snake is an amphibian![link to]”. A new species of caecilian, Atretochoana eiselti, was discovered in Brazil last year, during the earthworks for a new dam. It’s quite large, around 75cm long (twice the size of your usual, garden-variety caecilian), and, it looks fairly phallic. Most unfortunate.

Atretochoana eiselti (photo by Matt Roper, via MongaBay)

This photo of A. eieslti is necessary for context. Same credit as above.

Want to name a new species?

All this could be yours, via

Conservation scientists in South Africa have found a new species of iris. Not knowing what to name it, they have set up an online auction, to let the highest bidder have a crack at it instead. Check it out at the NewScientist website. Proceeds from the auction will go to the Overberg Lowlands Conservation Trust, which includes looking after the critically endangered habitats where the iris lives. I think it’s a nice way of generating some interest in taxonomy and species discovery, and also generating some funding for research and conservation at the same time. Get your thinking caps on, and your wallets out. When I looked, the auction was at 1100 pounds sterling (I don’t have the little wiggly pounds sign on my Australian computer).

So there you have it – some highlights of taxonomy from the past week. The beauty of taxonomy is that you never know what you might find!