Posts Tagged ‘species’

Notes from the international barcode of life conference #bol4

// December 5th, 2011 // 1 Comment » // Science Communication

Image by .jun, flickr

On Friday I went to day three of the international barcode of life conference, which happened to be in my hometown of Adelaide, actually at the home of my undergrad – The University of Adelaide – how convenient!

DNA barcoding matches a region of DNA to a species, at the moment there’s still plenty of work on building up that barcode database (called BOLD, though GenBank is also used). There are about a million and a half barcodes recorded so far and it’s streaming along.

The database is open access, and people can use it to match a barcode region from an unknown sample to a species.

So far, people have used this to check out the slice of fish in sushi, illegally collected shark fins, and plenty of other stuff.

It’s a powerful technique now in it’s ninth year and with some serious momentum behind it. There were 450-ish delegates at the conference from around the world, and Australia is a fair trek for most of them.

There’s talk that one day DNA sequencing will be so fast and cheap, you could take a sample while walking through the woods and be linked to species information on a handheld device – you would know if it was poisonous, endangered, new to science or what. Still a while away, but sci-fi in its possibilities.

This cool video gives a neat overview. It’s about a project proposal for student/citizen science in barcoding which is unfortunately currently unfunded and basically on ice at the moment. Nonetheless it’s a cute cartoons and great summary.

The region used for barcoding is called CO1 (found in mitochondira) in animals. It’s x base pairs long, and is generally very different between species, but pretty similar within one species. It’s short enough that sequencing is cheap and quick. A different region is used for fungi (called ITS, which was announced as the official fungi barcode at the conference), and plants use two regions, rbcL and matK, (found in chloroplasts).

The session I went to was on education and engagement – how to get people involved in DNA barcoding.

I love open access, power to the people, breaking down barriers stuff, and they’ve got some sweet plans. Already some projects have been successful, like the urban barcode project that gets high school students involved, and one group, who found the ingredients of tea didn’t always match what’s on the label, were even published in a journal (No less than Nature Scientific Reports! Amazing!) One group found a new species of cockroach, which is like my least favourite insect, but still a good effort.

What's in your tea? Image by massdistraction, flickr

BOLD are in the process of adding education and engagement to their online database so students can add to the database and store their results in a quarantined area. So they have a safe space to experiment with barcoding. Plus then they don’t screw it all up, right? Karen James, who moderated the session, actually pointed out that students may be less likely to make mistakes, as they are only working with a small number of samples and there’s less chance of losing track and accidental mislabeling.

Still in development, the BOLD 3.0 interface will look less intimidating than the current version, making it clearer for n00bs like me, and with links for educators at the bottom. They’re beta version is online here. Neat. I played around with BOLD before, taking a look at the barcode regions out of curiousity, and with my amateur skillz found it a bit tricky to navigate. Can’t wait to see the new one up and running so I can play with it.

If you want to read more about DNA barcoding, I recommend the iBOL website. I’ve got some more bits and pieces, but will post them separately once I’ve had a chance to flesh them out properly.

Hen mothers for ducklings, cross-fostering species

// August 25th, 2011 // 1 Comment » // Sex and Reproduction

hen and ducklings

Image by cod_gabriel

When I was young and living on a small farm in the Adelaide Hills, we used to raise ducklings under chickens. The hens were more inclined to sit and warm the eggs, and once hatched were better at protecting their young from rats. So we took duck eggs, placed them under brooding hens, and everything was cheery.

Those hens loved them little ducks, at least, they looked after them just as well as they did their own chicks. They’d go out foraging together, chattering away in their different tongues at a handful of scattered grain. But there was one place where their differences became obvious. The pond.

At the first sight of water, the ducklings would be in and swimming, having a great time duck-diving underwater and eating duckweed. Meanwhile, mother hen would be going absolutely spare! You could almost hear the concerned clucks saying “now get out of that water at once! Don’t you know you can’t swim? Oh heavens, what have I done to deserve such unruly children?”

What she’d done, somewhat unintentionally, was to be a cross-foster mother. A species which raises children of another species.

Peahen and guineafowl chicks

Image by Chicago Zoological Society

Chicago’s Brookfield Zoo recently raised two clutches of guineafowl chicks with peahen mothers. The parents protected their brood from hawks, and showed them the ropes of living free-range in the zoo – such as how to avoid pedestrians.

From the press release:

“‘Zoogoers may not notice anything unusual between the moms and chicks, but there are definitely differences and several barriers that they needed to overcome, including language and behaviors,’ said Tim Snyder, curator of birds for the Chicago Zoological Society, which manages Brookfield Zoo. ‘The first two weeks were a little precarious because the chicks needed to learn what the peahens’ vocalization meant and adapt to different behaviors that are not instinctual to them.’

“For instance, Guineafowl chicks naturally scatter and hide when frightened or threatened, while peachicks run toward their mother. Additionally, Guineafowl moms and chicks move as a group and help care for each others’ young, which is the opposite of independent peafowl.”

Black Robin on Rangatira Island

Image by Frances Schmechel

Cross-fostering for conservation helped bring Black Robins from the brink of extinction. In 1980, only five survived in the wild on Little Mangere island in New Zealand, including a just one fertile female called Old Blue.

Each Spring, the first clutch of eggs was raised under a Chatham Island tit, giving Old Blue time to breed twice in the season.

Bit by bit the population has crawled back and is now a relatively comfortable 250 individuals. The fostering program has been used as a model for other endangered bird species.

The Stupid Species – a science comedy

// March 11th, 2011 // Comments Off on The Stupid Species – a science comedy // Just for Fun, Science Communication

I just got home from seeing Daniel Keogh (from ABC’s the Hungry Beast, aka Professor Funk) performing in the 18+ science comedy show The Stupid Species – Why Everyone (except you) is an Idiot.

It. Was. Awesome.

From the complex and perplexing placebo effect to the Asch Conformity Test, it was a playful romp through the psychology of stupidity. Why is love risky (or whisky) business? How can different colours cure the sick? Why are expensive things deemed better than the cheap, but free things are the absolute best?

I could tell you, but not with as much pizazz as Professor Funk.

Go for the science. Stay for the hair (or the epic pants and jokes.)

I awarded major bonus points for starting the show with Venn Diagrams and Pie Graphs. Plus the video on the placebo effect was simply mind-blowing. Also there’s free wine testing *hell yeah!*

The show toured during last years National Science week, and is now in Adelaide on Saturday and Sunday night at the RiAus. Tickets are still available for Sunday at a tiny $10, or $8 for students (book here) and are worth double that. Take your friends, they’ll appreciate your confidence and good taste in comedy.

“We all like to think we’re special. In fact on average everyone thinks they’re above-average. Although we think we’re pretty smart our tendency towards irrational behaviour is what unites us all as humans – the stupid species,” says Daniel Keogh. Follow him @ProfessorFunk.

A Vampire Flying Frog by any other name…

// January 11th, 2011 // 2 Comments » // Recent Research

Rhacophorus vampyrus

Vampire Flying Frog. Image by Australian Museum

Actually, it’s not QUITE as cool as it sounds.

This new frog species, the Vampire Flying Frog, was discovered in Vietnam by scientists from the Australian Museum. Rhacophorus vampyrus was a latecomer to the International Year of Biodiversity, which yielded a wealth of newly discovered creatures.

But the name. The name. To be honest, it reminds me of the ten shelves in every bookstore devoted to vampire teen fiction. I’m all for making science sexy, but seriously. In the paper it doesn’t even say “Vampire flying frog” as in the media release and all the news articles. It actually says “Vampire tree frog” which sounds less vampiric and more like it drinks tree sap or something.

The name makes a promise that the frog doesn’t deliver on. Now if the frog looked like THIS then I would applaud the name.

Giant Vampire Frog

The Flying part is true enough. There are several species of tree frog that are called “flying frogs” because they can glide. It’s a good quality to have when you live up in trees. With larger hands and feet and extra webbing they can parachute through the air.

Vampire Flying Tadpole

Tadpole with fangs. Image by Australian Museum

The Vampire part is… well… it’s neat. The tadpoles have fangs.

Normally tadpoles have beak-like mouth pieces, but this one has two black, hard fang-shaped appendages made of keratin (the same stuff as your hair.)

According to the scientists, it looks too big to be involved in feeding but might help the tadpole hold onto tree bark. The frog creates foam nests, laying its eggs in water-filled tree-holes.

More details on the tadpoles will be published in another report. The original report can be downloaded in pdf by clicking through the citation: Rowley, J. et al. (2010). A new tree frog of the genus Rhacophorus (Anura: Rhacophoridae) from southern Vietnam Zootaxa

Another cool thing about the frog is it changes colour. In daylight it’s a pale tan, but at night it’s stunning brick red. I don’t know if that’s a normal thing for tree frogs. Any herpetologists in the house?

Genographics, Neanderthals and Cannibalism, an Interview with Carles Lalueza-Fox

// December 8th, 2010 // 1 Comment » // Recent Research, Science Communication, Sex and Reproduction

After the event last night about the worldwide Genographic Project, I caught up with Prof Dr Carles Lalueza‑Fox, the first speaker on the night, for a quick interview. He’s an expert on Neanderthals, or Neandertals I think we call them now. Named after the Neander Valley where the first specimen was discovered.

What first sparked your interest in studying Neandertals?

When the first Neandertal sequence was retrieved in 1997 I had been working on ancient DNA for a while, but then Neandertals seemed to be something in a different league.

In the first ten years it was only possible to get mitochondrial DNA from Neandertals.

For me, I really liked Neandertals and human evolution as a child. Ancient DNA was something particularly difficult at the time, and the thing that brought me to the subject.

How human do you think Neandertals were?

How human?

Yes, tricky question.

Haha, yes. It’s a very long question, a very difficult question. One must always take into mind our tendencies are always fluctuating. We saw them as a very primitive human lineage in the early 20th Century, but I’d say that now we’re turning to the point where we see them as very similar to us.

Maybe the best thing to think about Neandertals is they are more different from us than any modern human to any other modern human. That’s the way we should think about them.

If we want to think of them as a different species that’s fine for me, but there is a range of difference between us and the Neandertals.

The cuts found along Neandertal bones you suggest are evidence for cannibalism. Could they just be an example of de-fleshing prior to burial?

Well, yeah, it might be right in some circumstances. But this is not only cutting, you know de-fleshing the bones. It’s also fragmenting the bones with small stone tools, very small fragments, and even the skull, and the faces. For me it’s very difficult to think that this kind of post mortem activity is something more because this is a complete destruction of the bones.

It’s very similar to what we see in other sites with fauna, the bones are broken to extract the marrow in the same way.

And it’s a pretty common thing, well, not common these days, but certainly we humans have our own history of cannibalism.

Yes, well there are several sites with the signs in Neandertals. But you almost think that life was very tough and they were structured in very small groups, so the fact that you find another one… I mean you’d say “hey, we are Neandertals all of us,” but I’d say that’s a modern conception.

Whereas for them it might be “hey, you’re not one of my family I may as well eat you.”

Yeah, the idea of humankind, in fact, is very recent. After the second World War, and the UNESCO thing. So even the idea of humankind is more recent than we might think now.

And what do you think of the possibility of Neandertals and humans mating?

I think it’s plausible with the data we have. It was probably something that was a minority, restricted in time and space, it was nothing important in my view. The thing is we can detect it now in non-African modern humans is because this was an expanding population, so even a small event of just a few, say it was, this was amplified later on.






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