Essential papers you’ve probably never read

14 09 2015
library

Hmmm. What to read next?

“What would you consider to be the most important papers to read in your discipline?”.

That was the question a colleague with whom I’m working closely at the moment (you can probably figure out who that is) asked me last year. “Jesus H. Bloody Christ”, I thought, “What a question!”. How long is a piece of string?

In some ways, there is no way to answer that question well. Every research project requires reading a specific set of papers, and very few traverse the divide between projects. I seem to have to read a new set of papers every time I write one myself, although I admit I tend to stray from a single ‘discipline’ far too often than is probably considered healthy. Let’s also not forget those essential methods papers; you know, the ones that actually show you how to do the thing you’re trying to do? You can’t get much more essential than those.

But if I really sit down and think about it (and I have), it sort of comes down to what I’d expect my postgraduate students to know by the time they finish their degrees. In other words, they should read and retain the information in the papers that transcend research projects and all sub-disciplines of conservation ecology.

So I’ve picked a dozen of my ‘favourite’ papers that I think have something really important to tell us. They tend to be a little generic in terms of the broadness of their implications, but they are also, in my view, brilliant demonstrations of fundamental processes that all conservation ecologists should know.

While many of them are in the ‘big’ journals, not all of them are, nor are they necessarily the most cited papers in this field. I’ve also tended to avoid papers that document the things we know pretty well by now (e.g., effects of fragmentation, extinction patterns, etc.), and I haven’t really included any ‘methods’ papers for the simple reason I explained above that there are so many and they are very project-specific. I’ve even been a little cheeky and included one of my own, so take that for what it’s worth.

I present the list below in broad categories, and I include a little blurb about why I chose each one. There are, of course, 100s if not 1000s of others out there that others would choose, and I suppose that an inventory of such papers across many ecologists would be a good idea to put together. If you know this blog at all, you’ll know that I’ve also published my list of conservation ‘classics’, so I’m not going to repeat those here. Neither am I presenting those older papers that we should all have read, yet despite citing them for decades, few of us have (which has all sorts of implications for bullshit perpetuating over time, but that’s a topic for another blog post). For now, this is my tuppence.

ECOLOGICAL PRINCIPLES

  • Margalef, R, 1963. On certain unifying principles in ecology. American Naturalist 97: 357-374. doi:10.1086/282286 [PDF]

I chose this very old, but wonderfully written paper because it contains so many of the original gems of the discipline that everyone should be able to discuss without hesitation. Margalef talks about community structure, sampling issues, biomass-production ratios, succession, stochastic fluctuations, homeostasis, ecosystem resilience, hysteresis, biotic exchange, ecological entropy, and many other wonderful concepts. Some of the terms might be a little out-of-date, but this should be essentially reading for all ecologists. As in indication of how heavy-hitting this paper is, Ramón Margalef thanks some truly legendary ecological minds in the second paragraph for honing his thinking (Odum, MacArthur, Hutchinson, et alia).

  • Belovsky, GE, DB Botkin, TA Crowl, KW Cummins, JF Franklin, ML Hunter, A Joern, DB Lindenmayer, JA MacMahon, CR Margules, JM Scott. 2004. Ten suggestions to strengthen the science of ecology. BioScience, 54: 345–351. doi:10.1641/0006-3568(2004)054[0345:tststs]2.0.co;2 [PDF]

I love this paper. While it was written over 10 years ago, ever single one of the ten suggestions is still hugely relevant today. This is the kind of paper that should be re-read every few years just to remind ourselves of what we’re still missing, or at least, what we could be doing better. I get a particular kick out of this line: “… a recurring criticism of ecology is that concepts are often not clearly defined or, if they are, the definitions do not hold …”. Amen.

RESILIENCE

  • Kennedy, TA, S Naeem, KM Howe, JMH Knops, D Tilman, P Reich. 2002. Biodiversity as a barrier to ecological invasion. Nature 417: 636–638. doi:10.1038/nature00776 [PDF]

This is a wonderful piece of work that I think sets the bar for much of applied ecology. Not only is the experimental framework brilliant (yet simple), it demonstrates pretty much the raison d’être for all biodiversity science: more = better. In this case, ‘more’ is more diversity, and ‘better’ is fewer nasty invasive species.

  • Haas, SE, MB Hooten, DM Rizzo, RK Meentemeyer. 2011. Forest species diversity reduces disease risk in a generalist plant pathogen invasion. Ecology Letters 14: 1108-1116. doi:10.1111/j.1461-0248.2011.01679.x [PDF]

In a similar vein to the Kennedy and colleagues paper above, although this time using a mensurative experiment, Haas and colleagues set the standard for establishing the relationship between diversity and disease. Like the invasives story above, this time more diversity leads to lower disease risk from what has been called the ‘dilution effect’. If you need any more justification for keeping biodiversity high, then this and the previous paper should be on top of the list.

  • Cadotte, MW, R. Dinnage, D Tilman. 2012. Phylogenetic diversity promotes ecosystem stability. Ecology 93: S223-S233. doi:10.1890/11-0426.1 [PDF]

I’ve had the privilege of publishing with Marc Cadotte, and his wonderful body of work — including this paper — has inspired me greatly. A product of the great Tilman lab, Marc shows how (in his words): “… communities where species are evenly and distantly related to one another are more stable compared to communities where phylogenetic relationships are more clumped”. In this case, ‘stability’ is the temporal variation in aboveground biomass. This experimental evidence is really the third story in the ‘why more is better’ trilogy.

BIODIVERSITY & EXTINCTIONS

  • Stephens, DW, WJ Sutherland, RP Freckleton. 1999. What is the Allee effect? Oikos 87: 185-190. doi:10.2307/3547011 [PDF]

This was one of the first papers to nail down the concept of the Allee effect, and so is essential reading in my book. We know now that inbreeding depression (one type of Allee effect) is a massive contributor to extinction risk, and so we should be taking Warder Clyde Allee‘s concept seriously (although Warder never coined the term ‘Allee effect’ to describe the concept — that would have been just a little too arrogant).

  • Dudgeon, D, AH Arthington, MO Gessner, ZI Kawabata, DJ Knowler, C Lévêque,RJ Naiman, AH Prieur-Richard, D Soto, MLJ Stiassny, CA Sullivan. 2006. Freshwater biodiversity: importance, threats, status and conservation challenges. Biological Reviews 81: 163-182. doi:10.1017/S1464793105006950 [PDF]

This was one of the first papers that really scared me. We’re so focussed on the big things going out that we forget that some ecosystems are on the verge of complete biodiversity collapse. So is the case with the enormously diverse and almost completely fucked freshwater biota. This paper has stats to chill anyone to the bone, but it also has some brilliant suggestions of how to fix some of the worst of it. If we’d only listen …

  • Brook, BW, NS Sodhi, CJA Bradshaw. 2008. Synergies among extinction drivers under global change. Trends in Ecology and Evolution 25: 453-460. doi:10.1016/j.tree.2008.03.011 [PDF]

Time to be cheeky. Yes, I’m a co-author on this one, but I really do think it’s one of the few papers out there (and certainly one of the first) that really goes to the heart of the whole extinction synergies concept (reiterated by Belovsky and colleagues above). We can’t treat the individual symptoms separately – it’s the 1-2-3 (or more) combination of drivers that causes extinctions.

STATISTICS

  • Burnham, KP, DR Anderson. 2004. Understanding AIC and BIC in model selection. Sociological Methods and Research 33: 261-304. doi:10.1177/0049124104268644 [PDF]

I said I wasn’t going to present methods papers, but it reality, this is more of a ‘philosophical’ paper. Yes, it has a few equations, but it’s more about why we need to deal with model uncertainty as much as parameter uncertainty in our models. It’s also one of the main reasons why I completely abandoned using the term ‘significant’ in all my subsequent work. This paper was a statistical revolution, in my view.

Following the last paper, Bill Link and Richard Barker do a marvellous job of explaining how multi-model inference works, and what the real differences between different information criteria are, and what they mean for making strong statistical inferences in ecology. This paper should ideally be read after Burnham and Anderson (2004) to appreciate it fully. I’m obliged to reveal here, in the interest of exposing any potential conflict of interest, that Richard Barker was an unofficial supervisor on my PhD committee, and is someone with whom I’ve published a few times. However, that was well before he published this pearl of a paper.

HUMAN POPULATION

As some of you might know, I’ve dabbled in a bit of what is easily the main reason behind the Anthropocene biodiversity crisis: too many of us. This is the paper that sets out the problem so clearly and with such convincing evidence that it should be considered the ‘source’ for all sustainability issues relative to human over-population. It’s short, so read it.

In contrast to the 44 year-old paper above, this relative newbie nicely outlines why no matter which way you look at it, human over-population is the heart of all sustainability issues. This is because of the diminishing returns problem — every extra person requires resources of ever-increasing ecological cost. Understanding this concept is essential.

Post scriptum: You might have noticed that David Tilman‘s work features heavily in my list. I maintain however that this is entirely an emergent property of my choice rather than some affiliation to David’s (admittedly brilliant) career. I barely know the man (I’ve met him only once, and I doubt he’d even know who I am). Nonetheless, I can’t help but conclude that he’s probably one of the most brilliant ecologists alive.

CJA Bradshaw


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23 09 2015
What makes all that biodiversity possible? | ConservationBytes.com

[…] how?’ with elegance, style and a lifetime of experience. I just might have to update my essential-ecology-papers list. If I had to introduce someone to 60 years of ecological theory on biodiversity, there’s no […]

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