Author Archives: Morgan & Ethan
A new database for mammalian community ecology and macroecology
There are a number of great datasets available for doing macroecology and community ecology at broad spatial scales. These include data on birds (Breeding Bird Survey, Christmas Bird Count), plants (Forest Inventory & Analysis, Gentry’s transects), and insects (North American Butterfly Association Counts). However, if you wanted to do work that relied on knowing the presence or abundance of individuals at particular sites (i.e., you’re looking for something other than range maps) there has never been a decent dataset to work with for mammals.
Announcing the Mammal Community Database (MCDB)
Over the past couple of years we’ve been working to fill that gap as best we could. Since coordinated continental scale surveys of mammals don’t yet exist [1] we dug into the extensive mammalogy literature and compiled a database of 1000 globally distributed communities. Thanks to Kate Thibault‘s leadership and the hard work of Sarah Supp and Mikaelle Giffen, we are happy to announce that this data is now freely available as a data paper on Ecological Archives.
In addition to containing species lists for 1000 locales, there is abundance data for 940 of the locations, some site level body size data (~50 sites) and a handful of reasonably long (> 10 yr) time-series as well. Most of the data is restricted to the particular mode of sampling that an individual mammalogist uses and as a result much of the data is for small mammals captured in Sherman traps.
Working with data compilations like this is always difficult because the differences in sampling intensity and approaches between studies can make it very difficult to compare data across sites. We’ve put together a detailed table of information on how sampling was conducted to help folks break the data into comparable subsets and/or attempt to control for the influence of sampling differences in their statistical models.
The joys of Open Science
We’ve been gradually working on making the science that we do at Weecology more and more open, and the MCDB is an example of that. We submitted the database to Ecological Archives before we had actually done much of anything with it ourselves [2], because the main point of collecting the data was to provide a broadly useful resource to the ecological community, not to answer a specific question. We were really excited to see that as soon as we announced it on Twitter
We just published a new data set of 1000 mammal communities esajournals.org/doi/abs/10.189… Check it out and do something cool with it.
—
(@weecology) December 28, 2011folks started picking it up and doing cool things with it [3]. We hope that folks will find all sorts of uses for it going forward.
Going forward
We know that there is tons more data out there on mammal communities. Some of it is unpublished, or not published in enough detail for us to include. Some of it has licenses that mean that we can’t add it to the MCDB without special permission (e.g., there is a lot of great LTER mammal data out there). Lots of it we just didn’t find while searching through the literature.
If folks know of more data we’d love to hear about it. If you can give us permission to add data that has more restrictive licensing then we’d love to do so [4]. If you’re interested in collaborating on growing the database let us know. If there’s enough interest we can invest some time in developing a public portal.
The footnotes [5]
[1] We are anxiously awaiting NEON’s upcoming surveys, headed up by former Weecology postdoc Kate Thibault.
[2] We have a single paper that is currently in review that uses the data.
[3] Thanks to Scott Chamberlain and Markus Gesmann. You guys are awesome!
[4] To be clear, we haven’t been asking for permission yet, so no one has turned us down. We wanted to get the first round of data collection done first to show that this was a serious effort.
[5] Because anything that David Foster Wallace loved has to be a good thing.
Weecology at ESA
If folks are interested in seeing what Weecology has been up to lately we have a bunch of posters and talks at ESA this year. In order of appearance:
- Tuesday at 2:30 pm in Room 9AB our new postdoctoral researcher Dan McGlinn will be giving a talk on looking at community assembly using patterns of with- and between-species spatial variation.
- Tuesday afternoon at poster #28 Morgan will be presenting research on how the long-term community dynamics of the plant and rodent communities near Portal, AZ are related to decadal scale climate cycles. She’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look.
- Wednesday at 1:50 pm in Room 19A one of our new members, Elita Baldridge, will be giving a talk on her masters research on nested subsets.
- Wednesday at poster #139 Ethan will be presenting on our two attempts to make it easier to find and use ecological data. He’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look (or grab a computer and check out EcologicalData and the EcoData Retriever).
- Thursday at 1:50 pm in Room 10A another of our new members, Zack Brym, will be giving a talk on his masters research on controls on the invasion of an exotic shrub.
- Thursday at 4 pm in Room 8 Sarah Supp will give a talk on her work looking at the impacts of experimental manipulations on macroecological patterns (highlighted as a talk to see by Oiko’s blog)
- And last, but certainly not least, bright and early Friday morning at 8 am in Room 8 Kate Thibault (who has now moved on to fame and fortune at NEON) will be presenting on our work using maximum entropy models to predict the species abundance distributions of 16,000 communities.
Enjoy!
Michael Nielsen on the importance and value of Open Science
We are pretty excited about what modern technology can do for science and in particular the potential for increasingly rapid sharing of, and collaboration on, data and ideas. It’s the big picture that explains why we like to blog, tweet, publish data and code, and we’ve benefited greatly from others who do the same. So, when we saw this great talk by Michael Nielsen about Open Science, we just had to share.
(via, appropriately enough, @gvwilson and @TEDxWaterloo on Twitter)
Postdoc position in Jim Brown’s group studying the major patterns of biodiversity
There is a new postdoctoral research position available in Jim Brown’s lab at the University of New Mexico to study some of the major patterns of biodiversity. We know a bit about the research and it’s going to be an awesome project with a bunch of incredibly bright people involved. Jim’s lab is also one of the most intellectually stimulating and supportive environments that you could possibly work in. Seriously, if you are even remotely qualified then you should apply for this position. We’re both thinking about applying and we already have faculty positions 
. Here’s the full ad:
The Department of Biology at the University of New Mexico is seeking applications for a post-doc position in ecology/biodiversity. The post doc will be expected to play a major role in a multi-investigator, multi- institutional project supported by a four-year NSF Macrosystems Ecology grant. The research will focus on metabolic processes underlying the major patterns of biodiversity, especially in pervasive temperature dependence and requires a demonstrated working knowledge of theory, mathematical and computer
modeling skills.Applicants must have a Ph.D. in ecology or a related discipline.
Review begins with the first applications and continues until the position is filled. Applicants must submit a cover letter and a curriculum vitae along with at least three phone numbers of references, three letters of recommendation and PDF’s of relevant preprints and publications to be sent directly to ecohire@unm.edu attn: James Brown. Application materials must be received by July 25, 2011, for best consideration.
Questions related to this posting may be directed to Dr. James Brown at ecohire@unm.edu or to Katherine Thannisch at kthannis@unm.edu.
The University of New Mexico is an Equal Opportunity/Affirmative Action Employer and Educator. Women and underrepresented minorities are encouraged to apply.
Things you should read
We’ve been thinking a lot recently about the idea that the social web can/should play an increasing role in filtering the large quantity of published information to allow the best and most important work to float to the top (see e.g., posts by The Scholarly Kitchen and Academhack). In its simplest form the idea is that folks like us will mention publications that we think are good/important and then people who think we’re worth listening to will be more likely to read those papers and then pass on recommendations of their own. In concept this should allow for good papers to be found by the scientific community regardless of where they are published. Ecology is far from having reached the level of social media integration required to fully realize this possibility, but there are examples of other fields where this sort of thing has actually occurred.
We think this is a cool idea, but currently it is a relatively ineffective way to find interesting papers; primarily because there simply aren’t enough folks in ecology discussing what they’ve read. EEB and Flow does a great job of this and a few other blogs by practicing scientists make occasional contributions in this regard (e.g., I’m a chordata, urochordata), but there certainly isn’t a critical mass yet. Part of the reason for this is that putting together full posts on articles one has read can take quite a bit of time, and time isn’t something most of us have a lot of lying around. Here at JE we have half a dozen Research Blogging style posts that we keep planning on writing, but finding a couple of hours to reread the paper and a couple of related works and put together a full post just doesn’t seem to happen.
So, today Jabberwocky Ecology announces a new kind of post – Things you should read. The idea behind these posts is to reduce the activation energy for posting about papers that we like. As such, these might be as short as the title of the paper and a link. Most of the time we’ll try to contextualize things a bit with a few sentences or a paragraph to help you figure out if the linked material is relevant to you, but these won’t be full blown summaries because these are things you should read, not things you should read about.
Blogrolling graduate student ecology blogs
We’ve recently been following a couple of blogs by graduate students studying ecology and have been enjoying them enough that we thought we’d point folks in their direction.
Transient Theorist is a first year PhD student interested in quantitative and interdisciplinary approaches to ecology. How could we not love his blog. Particularly good recent posts include Ups and Downs and Intimidating questions.
Karina at Ruminations of an Aspiring Ecologist is a third year PhD student who travels to remote foreign lands for field work (we love her use of – Ukenzagapia – to pseudonymize the location). Good recent posts include Timescales in graduate school and Even more of my life in comics: writing to professors.
We are glad to see graduate students blogging for a variety of reasons. First, graduate school can sometimes be an incredibly isolating experience in that it can feel like some of the difficult situations are unique to you, when in fact hundreds of students are going through exactly the same thing. Having a cadre of students writing about these experiences helps their readers feel less alone in their struggles. As faculty we also appreciate the opportunity to be reminded of the graduate student perspective on academia. We’re not too far out of graduate school, but it is already difficult to recall what a committee meeting was like from a student perspective. Reading students thoughts, especially the sort of honest presentation of internal thoughts made possible by pseudonymous blogging, helps remind us that things often look very different to students than they do to us, which (we hope) helps make us better advisers, committee members, and teachers. Third, it provides opportunities for mentoring and interaction beyond the traditionally defined boundaries of one’s own department or university. Finally, and most importantly, it helps to build the nascent community of ecological bloggers. If you know of other good blogs by students studying ecology let us know in the comments.
Getting things done in academia
In a couple of days I’m participating in a panel to help young faculty be ready for their 3rd year review (the halfway step to tenure, which is kind of a big deal at my institution). This is the sort of thing that I normally say no to, but I’ve been to a couple of these things and I just couldn’t bear the thought of another group of young faculty being told that what they really needed to do to get tenure is to have a really spiffy tenure binder… so I’m going to talk about what they actually need to do to get tenure – get stuff done – and I thought it would be worth posting my thoughts on this here for broader consumption. This advice is targeted at assistant professors at research universities, but folks in other situations may be able to adapt it to their individual circumstances (e.g., if you’re at a small liberal arts college or other teaching centered school try swapping research and teaching below). Since the goal of the workshop is getting through the first phase of tenure, this is about what you need to do to accomplish that goal, not what you should be doing in any sort of broader philosophical sense. This advice is built on the lessons that Morgan (my wife and co-blogger for those of you new to JE; in fact she was so instrumental in developing these ideas that even though I’m using the first person singular this will be listed as a co-authored post) and I have learned during our time as assistant professors.
Laying the Groundwork for Change [Quote]
How then is it possible to modify and improve upon an academic culture populated by smart, creative individuals who are motivated by ideals more than by money, who have deep, intense interests, value substance over form, have little patience for conformity, think for themselves, do not defer to authority, and see their work not as a job but as a calling? Clearly the challenge is to find the incentives and rewards that will motivate this unique workforce to buy into desired changes and work willingly toward implementing them. But the first step is to explain clearly why change is nececessary and, even more important, why change does not mean abandoning core academic values. To win the hearts of academics, one first has to educate them.
- James C. Garland, Saving Alma Mater
This is just one of many brilliantly reasoned (and worded) arguments from Saving Alma Mater. If you are an academic, or an administrator at an academic institution, you really should read this book.
Amen brothers: why stimulus funding for science was a good idea
We just read this great piece from the Huffington Post by Todd Palmer and Rob Pringle on why including funds for NSF and NIH in the stimulus bill was a good idea (thanks to Ecotone for pointing us to the article). The great thing about the piece is that it doesn’t just make a cogent argument for the stimulus funds, but for why funding basic science is economically beneficial in general. Probably the high point of the article was this little gem:
Truthfully, the return on our relatively modest investment in basic research over the last half-century is so astronomical that it’s impossible to calculate. Science hasn’t just stimulated the economy; it has revolutionized the economy, and our lives along with it.
which seems like it must be hyperbole, but at least from our perspective it certainly is not. However, if we had to pick our favorite moment in the article it would definitely be the paraphrase of Paul Baskin’s concern about the utility of this funding:
Aren’t we just subsidizing a bunch of nerds who already have cushy academic jobs and buy fancy Japanese-made instruments? No.
This is definitely one of the clearest, best, and funniest explanations of why funding basic science is critical to the economy and to society in general. Go check it out.
