Tuesday, January 27, 2015

50 years of applying theory to ecological problems: where are we now?

Fifty years ago, the seminal volume ‘The Genetics of Colonizing Species’ edited by Herbert G. Baker and G. Ledyard Stebbins was published, and it marked a new phase for the nascent sciences of ecology and evolutionary biology –namely applying theories and concepts to understanding applied issues. Despite the name, this book was not really about genetics, though there were several excellent genetics chapters, what it was really about was the collective flexing of the post-modern synthesis intellectual muscles. Let’s back up for a minute.

The modern synthesis, largely overlooked and forgotten by modern course syllabi, is the single most important event in ecology and evolution since the publication of Darwin’s Origin of the Species. Darwin’s concepts of evolution stand as dogma today, but after publishing his book, Darwin and others recognized that he lacked a crucial mechanism –how organismal characteristics were passed on from parent to offspring. He assumed that whatever the mechanisms, offspring varied in small ways from parents and that there was continuous variation across a population.

For more than 30 years, from about 1900-1930, evolution via natural selection was thought disproven. With the rediscovery of Mendel’s garden pea breeding experiments in 1900, many influential biologists of the day believed that genetic variation was discontinuous in ‘either-or’ states and that abrupt changes typified the appearance of new forms. Famously, this thinking lead to the belief that ‘hopeful monsters’ were produced with some becoming new species instantaneously. This model of speciation was referred to ‘saltationism’

Of course there were heretics, most notably the statisticians who worked with continuous variation (e.g., Karl Pearson, and Ronald Fisher) who refuted the claims made by saltationists in the 1920s. Some notable geneticists changed their position on saltationism because their experiments and observations provided evidence that natural selection was important (most notably T.H. Morgan). However, it wasn't until WWII that the war was won. A group of scientists working on disparate phenomena published a series of books from 1937-1950 that showed how genetics was completely compatible with Darwinian natural selection and could explain a wide variety of observations from populations to biogeography to paleontology. These ‘architects’ and their books were: Theodosius Dobzhansky (Genetics and the Origin of Species); Ernst Mayr (Systematics and the Origin of Species); E. B. Ford (Mendelism and Evolution); George Gaylord Simpson (Tempo and Mode in Evolution); and G. Ledyard Stebbins (Variation and Evolution in Plants). With this, they unified biology and thus the modern synthesis was born.
Now back to the edited volume. Which such a powerful theory, it made sense that there should be a theoretical underpinning to applied ecological problems. The book grew out of a symposium held in Asilomar, California Feb. 12-16, 1964[1], organized by C. H.Waddington, who originally saw an opportunity to bring together thinkers on population genetics. But the book became so much more. According to Baker and Stebbins:
“…the symposium … had as its object the bringing together of geneticists, ecologists, taxonomists and scientists working in some of the more applied phases of ecology –such as wildlife conservation, weed control, and biological control of insect pests.”

Thus the goal was really about modern science and the ability to inform ecological management. The invitees include a few of the ‘architects’ (Dobzhansky, Mayr, and Stebbins) and their academic or intellectual progeny, which includes many of the most important thinkers in ecology and evolution in the 1960s and 70s (Wilson, Lewontin, Sakai, Birch, Harper, etc.).

Given the importance of the Genetics of Colonizing Species in establishing the role that theory might play for applied ecology, it is important to reflect on two important questions: 1) How much have our basic theories advanced in the last 50 years; and perhaps more importantly, 2) has theory provided key insights to solving applied problems?

This book is the fodder for a graduate seminar course I am teaching, and these two questions are the focus of our comparing the chapters to modern papers. Over the next couple of months, students in this course will be contributing blog posts that examine the relationship between the classic chapters and modern work, and they will muse on these two questions. Hopefully by the end of this ongoing dialogue, we will have a better feeling of whether basic theory has advanced our ability to solve applied problems.

Friday, January 23, 2015

Equalizing and stabilizing traits?

Plant functional traits and the multidimensional nature of species coexistence. 2015. Nathan J. B. Kraft, Oscar Godoy, and Jonathan M. Levine. PNAS.

(This isn’t a brand new paper, but somehow I’m already behind on reading papers in the new year...) 
A recent paper from Kraft et al. in PNAS does a really nice job in filling a gap that has been in literature for a while, which is to extend the influential theoretical work on coexistence from Chesson (and extended more recently by Jonathan Levine et al.) to explicitly incorporate functional traits and trait-based approaches to ecology. Chesson’s work (particularly ARES 2000) lays out a framework for understanding coexistence and competitive interactions, which focuses on the importance of stabilizing effects (niche differences) and equalizing effects (fitness differences) between competing species (e.g.). This theory makes strong predictions of when and how coexistence is expected (for example, when species have strong enough niche differences). However, accurate application of the theory is somewhat difficult, perhaps because identifying and calculating niche and fitness differences requires heavy use of mathematical models and careful experimental design.

In contrast, the value of the focus on functional traits in ecology is that they are readily measured, easily conceptualized, and databases of values already exist. In common with equalizing/stabilizing effects, traits are meant to inform our understanding of species' niches, but in contrast, traits are empirically friendly. One of the more common critiques of the Chesson framework was that empirical measures, particularly traits, couldn't be shoehorned into it. After all, traits likely contribute to both equalizing and stabilizing forces in complicated ways that may well shift during a species' life.

What Nathan Kraft and coauthors have done is show that this is not a limitation - traits can contribute to both equalizing and stabilizing forces, and mathematical models can tease these effects apart. They relate detailed measurements of leaf, root, seed and whole plant traits for 18 California annual plants with the results of mathematical models of competition and coexistence between these species. The authors found strong and exciting relationships between the theoretically motivated measures of competitive processes and species' traits. Average fitness differences had significant correlations with functional traits, particularly maximum height, leaf [N], leaf area, rooting depth, and phenology.
From Kraft et al. 2015: Correlations between species traits and A) Stabilizing niche differences, and B) Average fitness differences.
The key to interpreting these plots is to understand that where the coloured line overlaps with the grey shading, the correlation is not different than the null model. When the line is between the null and the center of the figure, the correlation is significant and negative; where it is between the null and the external edge, the correlation is significant and positive.
No individual traits correlated with niche differences, but models including multiple traits considered together do correlate with niche differences. A rather nice bit of support for the multidimensional view of the niche.

This paper does a nice job of expanding Chesson's framework a little bit farther towards empirical applications. Further, it reinforces the value of trait approaches. There are still some important limitations - the first is that this particular system of annual plants has been studied in great detail. It seems unlikely that the traits identified in this paper can necessarily be generalized as "equalizing" traits. A trait with an equalizing effect in a California grassland may well contribute less to fitness in a desert system, for example. Perennial species are altogether less integrated into experimental applications of Chesson's framework (life time fitness, among other things, being much easier to capture in annual plants). But this paper is a suggestion of a useful way forward, albeit a way that requires much more data and careful experimentation. The authors acknowledge that more study is due, but also the potential: “These complex relationships argue against the simple use of single traits to infer community assembly processes but lay the foundation for a theoretically robust trait-based community ecology.”

Monday, January 12, 2015

#ibs2015 – Confronting uncertainty, biases and the unknown

The 2015 meeting of the International Biogeography Society just came to an end, and even for someone who wouldn’t traditionally consider themselves a ‘biogeographer’ there were many interesting topics and talks to see.

The focus of most talks was on biological patterns over space and/or time (or ‘deep time’, which is a fun phrase to throw around), and the talks emphasized how sophisticated statistical methodologies for such questions have become. The extent and complexity of approaches for making inferences from limited existing information, be it phylogenetic, distributional, or fossil and pollen records, is pretty amazing.

Such complicated inference needn't and shouldn't come at the cost of careful scientific work, and must include recognition of uncertainty and biases. The final sessions of the conference acted as an excellent (and at times provocative) reminder of this. For example, Joaquin Hortal advocated the development of ‘maps of ignorance’, which instead of showing the typical distributions of known information, highlight where information is missing and new sampling should be emphasized. Not only is information sometimes missing, but its value degrades over space and time. The value of a sample declines the further away you get from that site or the more different the spatial scale; samples over 50 years old may not represent current conditions any more. Predictions should consider or even incorporate this uncertainty.

Catherine Graham, David Nipperess, and Jon Chase all gave talks similarly emphasizing how fundamental consideration of scale and extent is. This is as true for phylogenetic community analysis (Graham, what extent or size of tree should be considered for analyses of community phylogenetics?); for rarefaction of phylogenetic diversity (Nipperess); or for measures of beta-diversity (Chase). Without this context, we are likely to be misunderstanding our results.

Finally, David Currie gave a damning critique of macroecology. Unfortunately, he said, macroecology seems to be a field where hypothesis testing is rare and conclusions are drawn based on spurious correlations with little explanatory and even less predictive ability. For example, why has the study of latitudinal gradients in richness progressed little beyond a list of possible correlates after more than 30 years of attention? Though Currie was focused on his own field, his comments were relevant to many ecological approaches. Currie expressed concerns about areas where scientific methods were being given short shift. In particular, he noted a lack of appropriate hypothesis testing and strong inference. Instead there is a tendency for studies to look for evidence in support of a hypothesis of interest, rather than attempting to falsify a hypothesis. Supporting evidence, sadly, does not actually increase the probability that a hypothesis is true, since the evidence could equally support some other, currently unconsidered, hypothesis. Further, correlations between variables of interest are at best a weak test of a hypothesis. The most important suggestions were that macroecologists and others should be testing the predictive ability of their hypotheses on new data sets: model fitting, in his opinion, is too often confused with model testing.