And the most cited ecology paper published in the last 10 years is…(UPDATEDx2)

Here are the contest results!

To identify the most cited ecology paper published in the last 10 years, on July 19 I searched Web of Science on the topic “ecology” for the years 2002-2012 and sorted the results by number of citations. I was just going to go with that, but then a guess by one of the contestants revealed that that search procedure unaccountably misses a few very highly cited ecology papers. So I redid the search, also including papers published in every leading ecology journal (and many not-so-leading ones). I can’t promise that I haven’t missed something, but I’ve done the best I can. As always, you get the background research you pay for on this blog. 😉 (UPDATE #2: my background research stinks; see below)

The most cited ecology paper published in the last 10 years is*…[drumroll]…wait for it!…

1. Milo, R. et al. 2002. Network motifs: simple building blocks of complex networks. Science 298:824-827. Cited 1544 times.

I remember this paper well. Milo et al. examine the relative frequencies of different “network motifs” in real-world networks of all sorts. A network motif is a small number of nodes and links arranged in a particular way. For instance, a “linear chain”, like website A links to site B, which links to site C; or species A eats B, which eats C. Milo et al. show that the relative frequencies of different motifs vary systematically across networks of different types, in ways that can be understood in terms of what the networks are designed (or in the case of food webs, not designed) to do. “Networks” have been a hot topic for about the last decade, both within and outside ecology, so Milo et al. is widely-cited in multiple fields. Also, it was published 10 years ago, so it’s had the maximum amount of time to accumulate citations.

Surprisingly, Milo et al. is an original research paper, not a review, a “perspectives” piece (which is really a sort of review), or a methods paper. But most of the remaining papers on the list do fall into one of those categories. The rest of the papers in the top 20 also tend to fall in certain topic areas: climate change, causes and consequences of biodiversity loss, and (to my surprise) modeling species’ geographic ranges. Only one on biodiversity and ecosystem function, to my mild surprise. Nothing on neutral theory, not to my surprise. Interest in that topic was kicked off before 2002, and kicked off by Hubbell’s book**, not by a highly-cited paper. The papers below also come mostly from certain journals: Science (want to publish a highly cited ecology paper? publish a review or perspectives piece in Science!), Ecology, Ecology Letters, AREES, and TREE (but not Nature or PNAS, surprisingly…). And a surprisingly large fraction of them (well, surprising to me) only have one or a small number of authors. By no means are they all from big working groups.

UPDATE: List numbering corrected

UPDATE #2. Dadgummit, my revised search procedure still missed at least two massively-cited ecology papers. Curse you, Web of Science topic fields! As a commenter points out, Walther et al. 2002 Nature (a review of ecological responses to recent climate change) has been cited 2238 times (not sure if that’s the WoS or Google Scholar number). So that’s actually the #1 paper. The real #2 is Thomas et al. 2004 Nature (a research paper estimating extinction risks from climate change), cited 1710 times. The commenter also suggests that Venter et al. 2004 Science (shotgun sequencing of the Sargasso Sea prokaryote fauna) should count, but I don’t consider that enough of an ecology paper to list. Well, at least these additions don’t change the contest winner. The addition of Walther et al. and Thomas et al. to the top of the list certainly reinforces the dominance of the list by papers on climate change and biodiversity loss. And Thomas et al. replaces Milo et al. as the number one original research paper on the list.

2. Hooper, D. U. et al. 2005. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs 75:3-35. Cited 1324 times. A major review of biodiversity and ecosystem function, written by a bunch of famous people, published in a leading journal. Probably the only surprise is that it’s not #1!

3. Eckburg, P.B. et al. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638. Cited 1256 times. An ecology paper, but also a microbiology and genomics paper, so like Milo et al. highly cited in part because it’s cited in multiple fields. Also the only other paper on the list besides Milo et al. that’s not a review, perspectives, or methods paper.

4. Elith et al. 2006. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29:129-151. 1213 citations.

5. Post, D.M. 2002. Using stable isotopes to estimate trophic position: Models, methods, and assumptions. Ecology 83:703-718. 1154 citations.

6. Parmesan, C. 2006. Ecological and evolutionary responses to recent climate change. Ann. Rev. Ecol. Evol. Syst. 37:637-669. 1134 citations.

7. Fahrig, L. 2003. Effects of habitat fragmentation on biodiversity. Ann. Rev. Ecol. Evol. Syst. 34:487-515.

8. Phillips. S.J. et al. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231-259. 1028 citations.

9. Brown, J.H. et al. 2004. Toward a metabolic theory of ecology. Ecology 85:1771-1789. 953 citations.

10. Guisan, A. and Thuiller, W. 2005. Predicting species distribution: offering more than simple habitat models. Ecology Letters 8:993-1009. 944 citations.

11. Johnson, J.B. and Omland, K.S. 2004. Model selection in ecology and evolution. Trends in Ecology and Evolution 19:101-108. 857 citations.

12. Pearson, R.G. and Dawson, T.P. 2003. Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful? Global Ecology and Biogeography 12:361-371. 758 citations.

13. Zane, L. et al. 2002. Strategies for microsatellite isolation: a review. Molecular Ecology 11:1-16. 722 citations. A methods paper, but one widely cited outside ecology as well as within ecology.

14. Worm, B. et al. 2006. Impacts of biodiversity loss on ocean ecosystem services. Science 314:787-790. 713 citations.

15. Leibold, M.A. et al. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters 7:601-613. Cited 649 times. This was my guess for #1. Given that I haven’t even heard of many of the papers on this list, I’m pretty pleased with myself for managing to guess a paper in the top 20.

16. Sitch, S. et al. 2003. Evaluation of ecosystem dynamics, plant geography and terrestrial carbon cycling in the LPJ dynamic global vegetation model. Global Change Biology 9:161-185. 645 citations.

17. Pimentel, D. et al. 2005. Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecological Economics 52:273-288. 629 citations.

18. Hoegh-Guldberg, O. et al. 2007. Coral reefs under rapid climate change and ocean acidification. Science 318:1737-1742. 617 citations. The most recent paper in the top 20.

19. MacKenzie, D.I. et al. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255. 614 citations.

20. Harvell, C.D. et al. 2002. Climate warming and disease risks for terrestrial and marine biota. Science 296:2158-2162. 609 citations.

So how did our contestants do?

butterflyskip: Tilman 2004 PNAS was cited 332 times through July 19, 2012. It’s a measure of how long the tail of the citation distribution is that a paper like this, by a famous guy, on a hot topic, published 8 years ago in one of the world’s most prominent venues, could be so highly cited and yet not even come close to making the top 20. Good guess though!

Jarrett Byrnes: Worm et al. 2006. Excellent guess, #14 on the list.

Gregor: Brown et al. 2004. Also an excellent guess, #9 on the list.

Dale Nimmo: Elith et al. 2006. Great guess, #4 on the list. A good enough to guess to win, if only it had come in sooner!

Similarly, Florian Schneider intended a guess that would’ve won if only our winner hadn’t guessed it first. So Florian guessed Finke and Denno 2004. A good guess, but as you’ve seen, original research papers needed to be more interdisciplinary than Finke and Denno (cited 177 times) to make this list.

Eric Pedersen wins for guessing Hooper et al. 2005! Great guess, #2 on the list. In retrospect, I’m actually kicking myself for not guessing this, I’m very familiar with this paper, not sure why I went with Leibold et al. instead. This is the guess that revealed to me that my original search procedure was flawed. I went to check how well our contestants did, discovered Hooper et al. had been cited over 1300 times but was not considered an “ecology” paper by WoS, and said a naughty word. 😉

For being the first to guess a paper in the top 5, Eric wins a beer from me at the ESA meeting. Thanks for playing everyone!

*Actually, according to Web of Science, the most cited “ecology” paper of the last 10 years is Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690, cited 1984 times. But I decided that this is really an evolution paper, not an “ecology” paper, so I omitted it from the list, along with a few other papers I judged not to be “ecology” papers. Obviously, if you’re really into phylogenetic approaches to ecology you could argue with me on the omission of this paper.

**By the way, younger readers may not be aware that Hubbell’s Princeton Monograph is not where he first proposed his neutral theory. He first proposed it in a paper in Coral Reefs in 1997.