World Heritage Species

17 08 2014

horseshoe crabHaving just attended the Baker & Stebbins Legacy Symposium on Invasion Genetics in Pacific Grove, California, I have had a rare bit of leisure time between my book-writing commitments and operating in conference mode. It’s summer here in California, so I’ve taken the opportunity to read a bit of The New Yorker in my accommodation. It is indeed a pleasure to have these micro-moments of ‘leisure’ reading. As it turns out though, work subjects are never far from my mind as I do this.

So it interested me greatly when I read another fantastic article in the ‘Yorker about horseshoe crabs, and their precarious state despite having survived half a billion years on this planet. While I was generally interested in the science, biomedical applications, conservation and systematics of the species, what really caught my eye was the proposal to list them as a ‘World Heritage Species’.

A what? Never heard of that classification, you say? Neither had I. Not to worry though – it doesn’t exist yet. Read the rest of this entry »





50/500 or 100/1000 debate not about time frame

26 06 2014

Not enough individualsAs you might recall, Dick Frankham, Barry Brook and I recently wrote a review in Biological Conservation challenging the status quo regarding the famous 50/500 ‘rule’ in conservation management (effective population size [Ne] = 50 to avoid inbreeding depression in the short-term, and Ne = 500 to retain the ability to evolve in perpetuity). Well, it inevitably led to some comments arising in the same journal, but we were only permitted by Biological Conservation to respond to one of them. In our opinion, the other comment was just as problematic, and only further muddied the waters, so it too required a response. In a first for me, we have therefore decided to publish our response on the arXiv pre-print server as well as here on ConservationBytes.com.

50/500 or 100/1000 debate is not about the time frame – Reply to Rosenfeld

cite as: Frankham, R, Bradshaw CJA, Brook BW. 2014. 50/500 or 100/1000 debate is not about the time frame – Reply to Rosenfeld. arXiv: 1406.6424 [q-bio.PE] 25 June 2014.

The Letter from Rosenfeld (2014) in response to Jamieson and Allendorf (2012) and Frankham et al. (2014) and related papers is misleading in places and requires clarification and correction, as follows: Read the rest of this entry »





We’re sorry, but 50/500 is still too few

28 01 2014

too fewSome of you who are familiar with my colleagues’ and my work will know that we have been investigating the minimum viable population size concept for years (see references at the end of this post). Little did I know when I started this line of scientific inquiry that it would end up creating more than a few adversaries.

It might be a philosophical perspective that people adopt when refusing to believe that there is any such thing as a ‘minimum’ number of individuals in a population required to guarantee a high (i.e., almost assured) probability of persistence. I’m not sure. For whatever reason though, there have been some fierce opponents to the concept, or any application of it.

Yet a sizeable chunk of quantitative conservation ecology develops – in various forms – population viability analyses to estimate the probability that a population (or entire species) will go extinct. When the probability is unacceptably high, then various management approaches can be employed (and modelled) to improve the population’s fate. The flip side of such an analysis is, of course, seeing at what population size the probability of extinction becomes negligible.

‘Negligible’ is a subjective term in itself, just like the word ‘very‘ can mean different things to different people. This is why we looked into standardising the criteria for ‘negligible’ for minimum viable population sizes, almost exactly what the near universally accepted IUCN Red List attempts to do with its various (categorical) extinction risk categories.

But most reasonable people are likely to agree that < 1 % chance of going extinct over many generations (40, in the case of our suggestion) is an acceptable target. I’d feel pretty safe personally if my own family’s probability of surviving was > 99 % over the next 40 generations.

Some people, however, baulk at the notion of making generalisations in ecology (funny – I was always under the impression that was exactly what we were supposed to be doing as scientists – finding how things worked in most situations, such that the mechanisms become clearer and clearer – call me a dreamer).

So when we were attacked in several high-profile journals, it came as something of a surprise. The latest lashing came in the form of a Trends in Ecology and Evolution article. We wrote a (necessarily short) response to that article, identifying its inaccuracies and contradictions, but we were unable to expand completely on the inadequacies of that article. However, I’m happy to say that now we have, and we have expanded our commentary on that paper into a broader review. Read the rest of this entry »





Cleaning up the rubbish: Australian megafauna extinctions

15 11 2013

diprotodonA few weeks ago I wrote a post about how to run the perfect scientific workshop, which most of you thought was a good set of tips (bizarrely, one person was quite upset with the message; I saved him the embarrassment of looking stupid online and refrained from publishing his comment).

As I mentioned at the end of post, the stimulus for the topic was a particularly wonderful workshop 12 of us attended at beautiful Linnaeus Estate on the northern coast of New South Wales (see Point 5 in the ‘workshop tips’ post).

But why did a group of ecological modellers (me, Barry Brook, Salvador Herrando-Pérez, Fréd Saltré, Chris Johnson, Nick Beeton), ancient DNA specialists (Alan Cooper), palaeontologists (Gav Prideaux), fossil dating specialists (Dizzy Gillespie, Bert Roberts, Zenobia Jacobs) and palaeo-climatologists (Michael Bird, Chris Turney [in absentia]) get together in the first place? Hint: it wasn’t just the for the beautiful beach and good wine.

I hate to say it – mainly because it deserves as little attention as possible – but the main reason is that we needed to clean up a bit of rubbish. The rubbish in question being the latest bit of excrescence growing on that accumulating heap produced by a certain team of palaeontologists promulgating their ‘it’s all about the climate or nothing’ broken record.

Read the rest of this entry »





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 »





Software tools for conservation biologists

8 04 2013

computer-programmingGiven the popularity of certain prescriptive posts on ConservationBytes.com, I thought it prudent to compile a list of software that my lab and I have found particularly useful over the years. This list is not meant to be comprehensive, but it will give you a taste for what’s out there. I don’t list the plethora of conservation genetics software that is available (generally given my lack of experience with it), but if this is your chosen area, I’d suggest starting with Dick Frankham‘s excellent book, An Introduction to Conservation Genetics.

1. R: If you haven’t yet loaded the open-source R programming language on your machine, do it now. It is the single-most-useful bit of statistical and programming software available to anyone anywhere in the sciences. Don’t worry if you’re not a fully fledged programmer – there are now enough people using and developing sophisticated ‘libraries’ (packages of functions) that there’s pretty much an application for everything these days. We tend to use R to the exclusion of almost any other statistical software because it makes you learn the technique rather than just blindly pressing the ‘go’ button. You could also stop right here – with R, you can do pretty much everything else that the software listed below does; however, you have to be an exceedingly clever programmer and have a lot of spare time. R can also sometimes get bogged down with too much filled RAM, in which case other, compiled languages such as PYTHON and C# are useful.

2. VORTEX/OUTBREAK/META-MODEL MANAGER, etc.: This suite of individual-based projection software was designed by Bob Lacy & Phil Miller initially to determine the viability of small (usually captive) populations. The original VORTEX has grown into a multi-purpose, powerful and sophisticated population viability analysis package that now links to its cousin applications like OUTBREAK (the only off-the-shelf epidemiological software in existence) via the ‘command centre’ META-MODEL MANAGER (see an examples here and here from our lab). There are other add-ons that make almost any population projection and hindcasting application possible. And it’s all free! (warning: currently unavailable for Mac, although I’ve been pestering Bob to do a Mac version).

3. RAMAS: RAMAS is the go-to application for spatial population modelling. Developed by the extremely clever Resit Akçakaya, this is one of the only tools that incorporates spatial meta-population aspects with formal, cohort-based demographic models. It’s also very useful in a climate-change context when you have projections of changing habitat suitability as the base layer onto which meta-population dynamics can be modelled. It’s not free, but it’s worth purchasing. 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 »








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