ESA 2013 Day 3: Bolkerisms

All the best quotes that I caught today were undeniably from Ben Bolker, who also gave an interesting talk.

"The hallmark of great theoretical ecology is that it is obvious in hindsight. When you explain it to someone, they say well, of course."

In relation to a philosophical issue: "That's a beer question, not a coffee question".

To explain the reason he and his coauthors chose to build a model to explore the question, Bolker showed a Dilbert cartoon illustrating the truism "When all you have is a hammer, everything looks like a nail".

Only one full day left to go, and it looks like it will be a good one!

ESA 2013, day 3: Like a kid in a candy store.

Sometimes there are moments in my career where feel truly fortunate. Today I was fortunate enough to be a speaker in a session on evolution, biodiversity and ecosystem function. The other talks in this session were outstanding, full of amazing insights into how historical evolutionary dynamics affect modern-day ecological patterns. The presentations were followed by a fantastic panel discussion stimulated by thoughtful questions from the audience. The talks covered a range of topics from including species interactions in models of evolutionary change to using traits to understand coexistence to trying to find patterns when close relatives do not coexist.

The first talk from Luke Harmon on finding phylogenetic signatures on species interactions was incredible. He is an entertaining speaker and included references to his kids finding leaf cutter ants.  He show us how one could fit phylogenetic models that include coevolution. The negative effects of coevolution should affect trait evolution and one should see this signature in variance-covariance matrices. Random evolutionary change generates covariance between species. Stabilizing selection will remove this covariance, while with competition there should be negative covariances apparent. From models we see an interesting signature where older species are able to diverge and fill niche space (thus diverging rapidly) while later species are constrained in their evolution (thus remaining similar). Older species can contribute more to ecosystem function because of historical competitive effects.

Next was Nathan Kraft talking about how traits can potential shed light on fitness and niche differences in coexisting species. In a plant experiment with focal species grown alone and at different densities with competitors, he showed that very few pairs met the conditions for coexistence. For those that do appear to be able to coexist, no traits were associated with fitness difference, but several traits appeared to be associated with fitness differences. Multivariate analyses  showed that an assortment of five traits collectively appeared to be associated with niche differences. Some of these traits appeared to also explain fitness differences, revealing the complexity in assigning traits to specific ecological effects.

In Jeannine Cavender-Bares’ talk, she examined how evolutionary transitions in seed dormancy helped explain modern day ecological patterns in the Fabaceae family (the pea and bean family). The Fabaceae includes species that have dormant and non-dormant  seeds. Dormancy should be favored in certain environments (e.g., less predictable and poor environments). Large seeds are much less likely to be dormant, as well as those occurring at lower latitudes. Historical transitions in dormancy seemed to be correlated with changes in temperature lineages experienced.

Finally, Sharon Strauss critically examine dhow to separate history form ecology. We need to be cognizant of scale effects, where larger scale observations will include more close relatives than we usually see at local scales. Communities contain ‘ghosts’ of past competition and assembly. If species originate allopatrically (in separate places), then we expect that close relatives should not coexist, which can skew our inference about how ecological differences have evolved. Within habitats we seldom see closely related species coexisting . She gave a number of great Californian examples of species appearing to co-occur at large scales but not locally. For example, Limnanthes plants occur in the same region but species never co-occur in the same vernal pool.

These talks represent the collective excitement about the fact that we are entering a new synthesis in ecology. Evolution is required to understand ecological patters and ecological interactions are need for understanding evolutionary change. These talks exhibited where the forefront of this synthesis is, and it was a great afternoon of talks.

ESA Day 2: The problem with statistics...

These are just my favourite quotes from talks on day two of ESA:

(All from great, but anonymous, speakers)

After showing the results of a spatial statistics test: "...But still I was worried because that would be using statistics to prove something and that feels wrong."

On being asked how the speaker quantified earthworm abundance: "I used a non-invasive electroshock technique".
(I'm sure this is normal procedure, it just sounds hilarious to the uninformed).

ESA day 2: The shampoo salesman and new questions.

Day two started off on a high note with Bernhard Schmid's talk on evolution in biodiversity-ecosystem function (BEF) experiments. He is one of the originators of the Jena biodiveristy experiment, for years they have been maintaining plant species in monocultures and in polycultures to assess how much more ecosystem function is produced by multi-species assemblages over single species monocultures. However, it occurred to Schmid that species in these two contexts face different pressures, which may have resulted in evolutionary changes. In monocultures, species face high intraspecific densities and thus competition is severe, as is negative indirect effects like pathogen sharing and herbivory rates. Within polycultures, intrraspecific interactions may involve niche differences, with opportunities for character divergence to further stabilize coexistence. He reported on an experiment that took seeds and cuttings from monoculture and polyculture populations and grew then in monoculture or polyculture. He showed that individuals originating from monoculture did better in monoculture and species originating from polyculture did better in polyculture. The implications are fascinating. If the rate of evolutionary change in performance are equivalent between monocultures and polycultures, the BEF relationships should remain constant. However, if the rates of change are greater for polyculture populations the BEF relationship should get stronger over time. Conversely, BEF relationships should became weaker if higher evolutionary change in monoculture. 

It was hard to top this talk, but there were several other impressive talks as well. Jacob Vander Laan used a country-wide dataset on aquatic insect diversity across the USA and showed that at larger scales, beta-diversity decreases with connectivity, but is seemingly unaffected by environmental heterogeneity.

Restoration is community assembly with management goals and Emily Grman gave an interesting talk on assessing the success of prairie restoration by accounting for management activities, landscape, historical and local abiotic factors. She showed that management activities were the most important, with species-rich sowings result in rich communities, even though many of the species are not those in the sown mixture. Sowing a high diversity of grasses did not increase diversity, but high diversity of forbes did. Other factors like landscape influences and local factors were not important.

Will Pearse examined plant diversity patterns and homogenization across six large urban centres. He showed that there has been little taxonomic homogenization, but substantial phylogenetic and moderate functional trait homogenization. Beyond the interesting questions about how urban centres may cause biotic homogenization is the new tools that Pearse created for these analyses, and that are available online. As a self described 'shampoo salesman', he created a general tool called Phylogenerator that creates a pipeline that makes estimating trees form sequence data more efficient -definitely a tool that ecologists should be using. He further created a way to quantify complex leaf shapes and has a tool available for that, called Stalkless.

All in all , this was a good day, one that has stimulated new questions and approaches. These talks got me thinking about some of my data and experiments and how I can extend them to new questions. 

ESA 2013 Day 1: Temporal variation, roller derby, and topics in between

With day 1 over, ESA 2013 was off to an excellent start. Minneapolis seems like a very friendly place, and I enjoyed perhaps the most chatty bus ride I've ever experienced. As always, I failed to determine the best point on the trade off plot between cherry-picking certain talks based on topic, speaker and friends, and staying put in a session with an interesting topic. Nonetheless I managed to see some really good talks.

Among them, I saw Lauren Shoemaker in the Theoretical Ecology section, who illustrated how to model the four metacommunity paradigms (I.e. species sorting, mass effects, neutral, and patch dynamics) with the Chessonian framework of equalizing and stabilizing forces. She illustrated how both deterministic and stochastic models could replicate dynamics from the four paradigms. This suggests that rather than the usual description of the neutral paradigm as stochastic and the mass effect and species sorting paradigms as niche-based and therefore deterministic, the terms niche and deterministic and neutral and stochastic should not be synonymous. Rather, in the Chessonian framework, fitness differences drive neutral-type dynamics and spatial niches structure the species sorting and mass effects paradigms. More importantly, the results show how the paradigms are just a few sets of points on the much broader set of parameter values that could describe metacommunity dynamics.

It must be funny for Peter Chesson to follow up a talk in which his name is used as an adjective. After the talk on the Chessonian framework, he spoke about the fact that environment is fluid and non-stationary, yet models of communities have almost always treated it as being at equilibrium. Since it is not, ideally models of community dynamics would begin to incorporate environmental variation, and ask questions more relevant to non-equilibrium systems. For example: when is long-term persistence expected, given this non-stationarity and can communities in a non-stationary system still be stable? He showed that including environmental fluidity into models doesn't mean that communities are necessarily unstable, for example, when spatial and temporal trends of environmental variation match, communities may be stationary.

In another of many good talks about temporal variation (seemingly a popular topic of late), Colin Kremer showed that altering the basic characteristics of abiotic temporal variation (amplitude, means, periodicity) changed the amount of diversity present as communities evolved over time. Temporal variation isn't a simple concept anymore than spatial variability is - it has different characteristics with different effects on ecological dynamics and needs to be considered in greater depth.

My biggest disappointment was that I had a time conflict and couldn't attend a talk titled "Significant changes in the skin microbiome mediated by the sport of roller derby".  No doubt I would have learned a lot.

EEB & Flow on summer vacation

We will be back in time to blog from the Ecological Society of America's annual meeting in Minneapolis (Aug 4-9)!

Carnival of Evolution is up!

The latest Carnival of Evolution (#61 if you are keeping track) is up and running at Teaching Biology. It is the Crustie Lovin' Edition.

MacArthur's words still resonate 40 years on

I recently received an old library copy of “Geographical Ecology: Patterns in the Distribution of Species” by Robert MacArthur (1972). It’s the last book that MacArthur wrote before his early death to cancer. It is an ambitious book that connects repeated ecological patterns to mechanisms as broad as the earth’s rotations (producing climate as we experience it) and as focused as organismal behaviour.

But honestly, the thing that has struck me most so far as I read is the timelessness and wisdom in MacArthur's introduction. Issues ranging from focusing on questions versus systems, the value of repeated patterns, complexity, and what generality really means, aren't at all new.

“To do science is to search for repeated patterns, not simply to accumulate facts, and to do the science of geographical ecology is to search for patterns of plant and animal life that can be put on a map. The person best equipped to do this is the naturalist who loves to note changes in bird life up a mountainside, or changes in plant life from mainland to island, or changes in butterflies from temperature to tropics. But not all naturalists want to do science; many take refuge in nature’s complexity as a justification to oppose any search for patterns. This book is addressed to those who do wish to do science. Doing science is not such a barrier to feeling or such a dehumanizing influence as is often made out. It does not take the beauty from nature. The only rules of scientific method are honest observations and accurate logic. To be great it must also be guided by a judgment, almost an instinct, for what is worth studying. No one should feel that honest and accuracy guided by imagination have any power to take away nature’s beauty.

Science should be general in its principles. A well-known ecologist remarked that any pattern visible in my birds but not in his Paramecium would not be interesting, because, I presume, he felt it would not be general. The theme running through this book is that the structure of the environment, the morphology of the species, the economics of species behaviour, and the dynamics of population changes are the four essential ingredients of all interesting biogeographic patterns. Any good generalization will be likely to build in all these ingredients, and a bird pattern would only be expected to look like that of a Paramecium if birds and Paramecium had the same morphology, economics, and dynamics, and found themselves in environments of the same structure.”
--Robert MacArthur

It's interesting that an introduction written in 1972 is so relevant that it could have been written today. The pessimistic view is that ecology is just iterating through the same problems and solutions, or progress is slow. Or maybe classic books remain as classics because their authors understood and explored the issues at the core of the science and had the benefit of being there in the formative years. It's fun to see that when MacArthur thanks particularly four friends who influenced his work most, he means G. Evelyn Hutchinson, E.O. Wilson, Richard Levins, and Jared Diamond. I suppose any book influenced by the combination of all these scientists and written by MacArthur will always have something interesting to say. 

Evidence for the evolution of limiting similarity in diving beetle communities

Remi Vergnon, Remko Leijs, Egbert H. van Nes, and Marten Scheffer. (2013) Repeated Parallel Evolution Reveals Limiting Similarity in Subterranean Diving Beetles. The American Naturalist, Vol. 182, pp. 67-75.

In 2006, Marten Scheffer and Egbert van Nes published a very nice paper showing the outcome of simulated evolution of competing species. Their results showed how patterns of evenly-spaced clusters of species along a niche axis could evolve to minimize competition via limiting similarity. 

From Scheffer and van Nes (2006): Evenly spaced clusters of species along a niche axis (x-axis) evolved in response to competition.

Within any cluster along the niche axis, species tended to be more similar than expected. The results suggested that complex self-organizing clustered patterns might result from simple competitive limitations. Interestingly, although the original paper suggested that clustered patterns in size distributions are common, only now are these theoretical expectations about the evolution of limiting similarity being tested with data. In fact, though theory has long suggested that patterns of limiting similarity should evolve to allow coexistence between competing species, empirical evidence is rather lacking. Despite this, limiting similarity and competition are staples of ecological thought: for example, patterns of overdispersion in traits or relatedness are often used as evidence for the importance of competition.

The follow-up paper -Vergnon et al. (2013)- tests for the pattern predicted in Scheffer and van Nes (2006) using communities of subterranean diving beetles (Coleoptera, Dytiscidae) in Australia. These species have evolved for over 5 million years in isolated aquifers. If limiting similarity structured beetle communities, the authors predicted that there should be regularity in the spacing of species along a niche axis. If competitive interactions determine species' positions on the niche axis, then their absolute positions on the niche axis could vary between communities so long as their relative positions are evenly spaced. If, in contrast, niches are driven by environmental conditions, species in different communities/aquifers should have similar absolute positions along the niche axis.

The authors used a nice combination of statistics, modelling and observational data (34 communities of beetles representing 75 total species) to test for these predicted patterns. They used beetle size as the measure of niche position, since size is often an indicator of niche position and food availability and identity. For almost all aquifers, co-occurring beetles were significantly different in size. Further, species in different aquifers classified as occurring in the same size classes (small, medium, large), had different absolute sizes (i.e. the largest beetle in one 2-species aquifer was not similar in size to the largest beetle in another 2-species aquifer).  

From Vergnon et al. (2013): Absolute sizes of diving beetles in aquifers with 3 species present. The absolute size in a size class (large - black; medium - white; small - grey) varies between aquifers.

Although the absolute size of species differed between aquifers, the ratio of sizes (regularity of spacing on the niche axis) was highly consistent. Further, simulations of evolution of body size due to competition were capable of reproducing the observed size structure of the diving beetles.

From Vergnon et al. (2013): regularity of spacing between competing diving beetles (measured as the body size ratio). 

This paper does a nice job of integrating theory and data, and combining pattern and process. The focus is on testing contrasting predictions, and the authors use complementary approaches to test statistically for the presence of patterns and to demonstrate with simulations the relationship between the evolution of limiting similarity and the observed pattern. The evidence is suggestive that limiting similarity and not pre-existing environmental niches explains the size structure of communities of competing diving beetles. There are still questions about how far these inferences can be extended. For example, do we expect that predefined environmental niches are really the same across aquifers? How important is competition in these communities - at the moment, the authors only have minimal evidence of gut content overlap from a single aquifer. Further the low diversity of aquifer communities (~1-5 diving beetle species) means that the prediction of clusters of multiple similar species made in the original Scheffer and van Nes paper can't be tested. But the fact that aquifer diving beetle communities have low diversity and are very simplistic is beneficial for the authors. Patterns in diverse communities where multiple processes (predation, migration, etc) are important may be too complex to show clear evidence in observational data. Simple systems (including microcosms) are a good place to find evidence that a process of interest actually occurs. Whether or not that process is important across many systems is of course a more difficult question to answer. 

Movement patterns in populations of early academics

Sometimes of the perks of academic life are also the most difficult parts – frequent travel opportunities mean you are also frequently away from friends and family (and spend too much time in airports). The nature of the university job market provides global opportunities for work, but also means that in reality opportunities and circumstances can constrain you to places you wouldn't have chosen otherwise. Your friends will cover the world, but you will rarely be in the same room together. The apprenticeship-like nature of early academic positions means that you will move, probably many times, before you find a permanent position (if you do). 

I have a friend who grew up with diplomat parents, which meant her family moved to a new place in the world every few years. The result was that she often felt like she didn’t have a strong connection to any one place or group of people. Academia isn’t quite so extreme, but you can understand why after moving to one place for undergrad, another for a Masters and/or PhD, one or two more for postdocs, your interactions and place in the world can feel rather impermanent. It also means that, for better or worse, your social circle includes other academics, and they are also shifting from place to place. When I tell non-academic friends and family (who mostly have settled in a single place) about upcoming moves, they are often more excited than I am about the opportunity to pick up and go. No doubt this is a grass-is-always-greener situation, but I often think that the most notable and difficult aspect of academic mobility is that you end up saying goodbye a lot.

I wonder whether some of the academic ambivalence expressed is aggravated by this early, necessary transience. Certainly there is lots of evidence that residential mobility (i.e. moving) relates to higher mortality and lowered health indicators, though some studies suggest that this effect may be more true for introverts than extroverts (presumably because extroverts form new friendships more easily). Academics share this phenomenon with groups like military families and third culture kids. The commonality is that, with every move it becomes harder to define home as a particular place – it is more like an intangible connection to multiple places and people. And maybe that's not so terrible - a good friend who was raised by an academic suggested that the key is to redefine your life and friendships as being global rather than local. And eventually professors settle down (I can think of a few people who have been at one university for 30+ years). But in the interim there is always the not-insignificant tension between the costs and benefits of uprooting yourself every few years, and the slow loss of individuals who are not capable of this mobility, from the academic pipeline.