DNA barcoding plants with citizen science

28 08 2013

hikingI was contacted recently by Oscar Jaslowski of Microryza (a web platform that allows scientists to post research  ideas and collect contributions from web visitors) about a project getting underway in Alaska by Ellen Jorgensen of Genspace. He suggested it might make a good post for ConservationBytes.com, and I agreed. Thanks for the contribution, Ellen & Oscar.

There’s nothing so final as watching the bush pilot take off in his tiny plane, leaving you stranded in the Alaskan backcountry. We had plenty of food for a three-day expedition, but no satellite phone or any other way to contact anyone. In Alaska, the phrase ‘primordial indifference’ pretty much sums up your relationship with the vast, glacier-carved landscape. Mother Nature does not care if an ant like you lives or dies.

Our destination, the Skolai Valley, is located about 480 km (300 miles) east of Anchorage, in the heart of Wrangell-St. Elias National Park. At a whopping 5.3 million hectares (13 million acres), it is the largest national park in the United States, and probably one of the least-visited. Much of its forbidding territory is snow-covered and similar to the Himalayas. In fact, the size of the massive ice fall that towers over the town of McCarthy, the origin of our flight, is exceeded only by one near Mt. Everest. But winding through the glaciers and snowfields are alpine valleys that are a backpacker’s dream. And Genspace, the nonprofit science-based organisation that I direct, was lucky enough to have received funding in 2012 to launch this expedition to Skolai.

Our  mission: to barcode wild Alaskan plant life. Two of us headed down into the river valley and the other two climbed up to the level of the mountain pass to survey more alpine vegetation. We were carrying portable plant presses – normally something too bulky for backpacking, but necessary for this trip. Read the rest of this entry »





De-extinction is about as sensible as de-death

15 03 2013

Published simultaneously in The Conversation.


On Friday, March 15 in Washington DC, National Geographic and TEDx are hosting a day-long conference on species-revival science and ethics. In other words, they will be debating whether we can, and should, attempt to bring extinct animals back to life – a concept some call “de-extinction”.

The debate has an interesting line-up of ecologists, geneticists, palaeontologists (including Australia’s own Mike Archer), developmental biologists, journalists, lawyers, ethicists and even artists. I have no doubt it will be very entertaining.

But let’s not mistake entertainment for reality. It disappoints me, a conservation scientist, that this tired fantasy still manages to generate serious interest. I have little doubt what the ecologists at the debate will conclude.

Once again, it’s important to discuss the principal flaws in such proposals.

Put aside for the moment the astounding inefficiency, the lack of success to date and the welfare issues of bringing something into existence only to suffer a short and likely painful life. The principal reason we should not even consider the technology from a conservation perspective is that it does not address the real problem – mainly, the reason for extinction in the first place.

Even if we could solve all the other problems, if there is no place to put these new individuals, the effort and money expended is a complete waste. Habitat loss is the principal driver of species extinction and endangerment. If we don’t stop and reverse this now, all other avenues are effectively closed. Cloning will not create new forests or coral reefs, for example. Read the rest of this entry »





Declining biodiversity in… your filthy mouth

18 02 2013

green teethIt still amazes me that the more we look, the more we realise just how important intact ecosystems are for our own well-being. I guess this is why I’m still a scientist.

Our latest paper that just came out today in Nature Genetics is a bit of a departure for me (again!); I really must not take much credit for this given that it was a huge effort among a big team of people and I played a comparatively minor role. Still, I can definitely say this is one of the more interesting papers I’ve co-authored in a while.

For me the involvement started after Alan Cooper (Director of the Australian Centre for Ancient DNA) asked me for a bit of help with a cool paper he and some of his colleagues were working on. When he told me what the subject was, my initial reaction was (yawn): Dentistry? Teeth? You’ve got to be joking. Why would an ecologist be even remotely interested in that stuff? Then he went into more detail, and I was hooked.

Before I get into that detail, I have to tell you a story about a colleague of mine (name withheld, but true story) who recently went to the dentist to have some routine cleaning and maintenance done. There was nothing particularly special about his visit – no local anaesthetic, no extractions, no caps, and certainly no surgery. Two weeks later he was in the hospital theatre getting his chest cracked open for open-heart surgery. Jesus H. Christ!, I said to myself. Read the rest of this entry »





Ghosts of bottlenecks past

25 05 2012

© D. Bathory

I’ve just spent the last week at beautiful Linnaeus Estate on the northern NSW coast for my third Australian Centre for Ecological Analysis and Synthesis (ACEAS) (see previous post about my last ACEAS workshop).

This workshop is a little different to my last one, and I’m merely a participant (not the organiser) this time. Alan Cooper and members of his Australian Centre for Ancient DNA (Jeremy Austin, Vicki Thomson & Julien Soubrier) combined forces this week with Craig Mortiz, Margaret Byrne, Steve Donnellan, Tania Laity, Leo Joseph, Xander Xue and Gabriele Cybis. Our task was to examine the mounting evidence that many Australian species appear to show a rather shallow genetic pool from a (or several) major past bottlenecks.

What’s a ‘bottleneck’? In reference to the form after which it was named, a genetic bottleneck is the genetic diversity aftermath after a population declines to a small size and then later expands. The history of this reduction and subsequent expansion is written in the DNA, because inevitably gene ‘types’ are lost as most individuals shuffle off this mortal coil. In a way, it’s like losing a large population of people who all speak different languages – inevitably, you’d lose entire languages and the recovering population would grow out of a reduced ‘pool’ of languages, resulting in fewer overall surviving languages.

Our workshop focus started, as many scientific endeavours do, rather serendipitously. Several years ago, Jeremy Austin noticed that devils who had died out on the mainland several thousand years ago had a very low genetic diversity, as do modern-day devils surviving in Tasmania. He thought it was odd because they should have had more on the mainland given that was their principal distribution prior to Europeans arriving. He mentioned this in passing to Steve Donnellan one day and Steve announced that he had seem the same pattern in echidnas. Now, echidnas cover most of Australia’s surface, so that was equally odd. Then they decided to look at another widespread species – tiger snakes, emus, etc. – and found in many of them, the same patterns were there. Read the rest of this entry »





Does conservation biology need DNA barcoding?

5 01 2012

In November last year I was invited to participate in a panel discussion onthe role of DNA barcoding in conservation science. The discussion took place during the 4th International Barcode of Life Conference (which I didn’t actually attend) in Adelaide, and was hosted by that media-tart-and-now-director-of-the-Royal-Institution, Dr. Paul Willis.

Paul has recently blogged about the ‘species’ concept as it relates to DNA barcoding, which I highly recommend. It also prompted me to write this post because now the video of the discussion is available online (see below).

Now, the panel was a bit of a funny set-up in a way – I was really one of the only ‘conservation biologists’ represented (Patrick O’Connor and Andy Lowe perhaps excepted), with the rest mainly made up of molecular people (Pete Hollingsworth, Bob Hanner, Karen James) – and I was told prior to the ‘debate’ that I was meant to be the contrarian (i.e., that there is no role for DNA barcoding in conservation).

Fundamentally, I don’t actually embrace the contrarian view on this one given that I see no reason why DNA barcoding can’t enhance or refine our conservation knowledge and skills. But the ‘debate’ did raise some important issues about technological advancements in the application of conservation science to real conservation.

I suppose that prior to getting stuck into the polemic I should define DNA barcoding for the uninitiated; it’s a basic technique that analyses short sequences of DNA with the sole purposes of identifying from which species they come. Imagine walking through the bush with a barcode scanner and pointing at random species you see and getting an instant identification read-out without actually knowing the species beforehand. You can see why it’s called ‘barcoding’ because it is like running products through the check-out to get instant price details. Read the rest of this entry »





Environmental Genomics PhD and Postdoc positions

8 08 2010

My colleague, Professor Alan Cooper of the Australian Centre for Ancient DNA at the University of Adelaide, asked me to advertise a couple of cool research positions that he’d like to fill by the end of this year.

Environmental Genomics: PhD and Postdoc opportunities

We are looking for interested postgraduate students who are highly motivated and enjoy independent and unusual research. An interest in environmental biodiversity is a key requirement, and a background in any of the following would be useful: molecular ecology, molecular biology, genetics, bioinformatics, chemistry/biochemistry. The project is for 3 years, and starts in early 2011.

New environmental genomics approaches for biodiversity studies of soils, water, forensics, grasses and Antarctic biota

A number of PhD positions are available in a large-scale project to apply high throughput sequencing approaches to the analysis of environmental samples and develop a new range of methods to perform biodiversity surveys, taxonomic discovery, and environmental impact reports. The project will employ multiplexed PCR, 2nd/3rd gen sequencing, bioinformatics and phylogenetics to develop novel systems for rapid and accurate biodiversity assessment. Key topics within the project are the analysis of Australian soils, natural and re-use water supplies, Australian native grasses, Antarctic biota, and forensic material. A strong molecular biology and/or bioinformatics background is required. The project is a $1M Australian Research Council-industry partnership.

1-2 postdoc positions will also be available for this project, and will carry supervisory responsibilities for the PhD projects. It is anticipated that one position will be oriented towards data generation, and another towards bioinformatics/database analysis.

International Students wishing to study at The University of Adelaide in 2011 should check the available scholarship opportunities as they provide payment of full academic fees plus an annual living allowance of approximately AUD$21,000 tax free.

Note the closing date for international scholarship enrolment 31 August 2010 or 30 October for Australian/NZ applicants.

Both the Australian Department of Immigration and University of Adelaide expect international applicants to meet English Language Proficiency (ELP) requirements. The ELP is based on high scores in IELTS (International English Language Testing System) or TOEFL (Test of English as a Foreign Language). For further information please refer to this website and this document.

Expressions of interest from applicants with strong graduate marks, a good TOEFL score, and a background in evolution/bioinformatics/molecular biology are encouraged to apply. Please contact the following supervisors and provide your curriculum vitae:

Prof. Alan Cooper (e-mail)

Australian Centre for Ancient DNA
School of Earth & Environmental Sciences
Darling Building, THE UNIVERSITY OF ADELAIDE
SA 5005, AUSTRALIA
Telephone: +61 8 8303 3952
Facsimile: +61 8 8303 4364

Add to FacebookAdd to DiggAdd to Del.icio.usAdd to StumbleuponAdd to RedditAdd to BlinklistAdd to TwitterAdd to TechnoratiAdd to Yahoo BuzzAdd to Newsvine








Follow

Get every new post delivered to your Inbox.

Join 5,316 other followers

%d bloggers like this: