Mycorrhizas in the Central European flora: relationships with plant life history traits and ecology

Stefan Hempel et al., 2013. Ecology 94(6): 1389-1399. DOI:10.1890/12-1700.1. Mycorrhizas in the Central European flora: relationships with plant life history traits and ecology

I'm reliably informed there are some mycorrhizae in this photo...

I’m reliably informed there are some mycorrhizae in this photo…


Will Pearse

Aaron David

One of the overarching goals in ecology is to understand the distributions of species and how interacting species shape these distributions. In the world of plant-symbiont interactions, one ongoing question is when is it advantageous to have a symbiont? Hempel et al. compile a dataset of Central European plants and their mycorrhizal associations in order to address several ecological hypotheses. Hempel et al. classify plants as obligate (OM), facultative (FM), or non-mycorrhizal (NM), and ask whether certain types of plants are more associated with various life-history traits (ie. life-form, life-span, pollination, etc.) or environments. The authors find support that different mycorrhizal statuses are over/underrepresented in with different traits and environments. The paper provides strong evidence that mycorrhizal associations may influence plant distributions, and that the benefit of such associations is very much environment dependent. Those such patterns have been shown for individual plant species, Hempel et al. show the generality of this pattern using a large set of plant species.

The authors tackle the exciting question of when it is advantageous to form mycorrhizal associations. For instance, they report that OM plants are found in higher than expected abundance with low soil acidity, while FM plants are found in higher abundance with high soil acidity (NM abundance wasn’t affected by acidity). This result was somewhat puzzling to me, as I would have expected the NM plants to be found with the high soil acidity and the FM to be unaffected. This could suggest that while some plants are able to adjust their associations in different environments, this may not be a general rule for FM plants. The authors define FM plants as those that can form a mycorrhizal association but are not always found with one. Therefore it’s possible that the FM plants as a whole might be composed of NM plants with the occasional mycorrhizal association. It would be interesting to see the FM group split into more definitive categories.

As a fungal ecologist, I found this paper provided interesting insights towards questions of fungal distributions. One of the burgeoning areas in fungal ecology is understanding the distributions of mycorrhizal associations (see the work of Peter Kennedy). Hempel et al.’s results suggest to me that these limitations to mycorrhizae distributions could arise from local environmental conditions or host plant distributions. Of course as the author’s note, it’s not necessarily clear which symbiont is limiting the other. One way to test this idea would be to overlay maps of mycorrhizae distributions with those of plant distributions. Environmental sampling of soil can be used to get a broader picture of mycorrhizae distributions, since many may live as saprobes in addition to being symbionts, though it’s likely the authors could generate a similar distribution map using their available data. Understanding both sides of symbiont distribution would more fully address how species are limited.


Will Pearse

Will Pearse

I’m no mycologist (for what it’s worth I love eating them), but I still thought this was an interesting paper. Literature reviews like this, where massive databases that are going to be of use to future scientists are just thrown out for all to enjoy, are exactly what science should be about. Hurrah.

I think the conclusions of this paper are sound, but I’m going to draw attention to two things just to be picky. Firstly, I have been brought up to think that the phylogenetic corrections employed here should be avoided (listen to Rob Freckleton please). This is a very touchy subject (I’ve heard of people bursting into tears over it!), but in brief the authors create eigenvectors that represent the phylogeny, and then by including them in their analyses hope to correct for phylogeny. A similar approach is used in spatial analyses, but for both it’s hard to know how many eigenvectors is ‘sufficient’, and it’s always unclear to me why you wouldn’t just other methods that directly incorporate the phylogenetic variance-covariance matrix you’re making eigenvectors to describe. Phew. Got that off my chest. Secondly, I wonder what effect the publication bias (that the authors find) will have on these results, particularly as the results are in agreement with what we might expect.

However, as I say, I think the results are pretty sound, and so I wonder whether we could model the co-evolution of plant and fungi. Indeed, there are some very neat new methods (we covered one recently) that examine these questions. More specifically, I wonder if the evolution of a tight association with mycorrhizae would allow a clade to break away from its close relatives and suddenly radiate out into as-yet unexplored habitats and niches. Equally, there could be links between mycorrhizal diversity and plant associations, although I’m almost certain this has already been looked at, and defining fungal species is hard (I think!). I’d quite like to hear from more fungus people!

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Is regional species diversity bounded or unbounded?

Howard V. Cornell, 2013. Biological Reviews 88(1): 140-165. DOI:10.1111/j.1469-185X.2012.00245.x. Is regional species diversity bounded or unbounded?

This post is PEGE’s contribution to the first PEGE/EvoBio journal clubs crossover. Add your comments to the bottom of this post and then come and join us with the guys over at EB-JC (evobiojournalclub.wordpress.com) next Monday (May 13th, 4:30p ET) to discuss things further over video chat.

EB-JC works a bit differently from us so we are keen to join forces and see what happens.

Is speciation rate bounded, unbounded, or... sort of both?

Is speciation rate bounded, unbounded, or… sort of both? (from Cornell 2013)


Will Pearse

Will Pearse

This paper is a brave attempt to reconcile the debate over what limits diversity through evolutionary time. Cornell’s ‘damped increase hypothesis’ is a compromise between a constant (unbounded) rate of speciation and one where clades have a (bounded) carrying capacity determined by ecological interactions. He acknowledges that diversity tends to increase through time, but this increase can be tempered by ecology; those looking for fireworks should look elsewhere (go read ‘that’ Wiens paper), because this is an attempt to reconcile and move forward.

It’s easy(ish) to derive models of evolutionary diversification, the problem is finding reliable data to validate them. You can’t sequence what isn’t here, so molecular phylogenies can’t incorporate extinct species, while the fossil record has biased sampling and makes it difficult to distinguish among species and higher taxonomic groups. Moreover, distinguishing between a clade becoming more diverse because of increased speciation or decreased extinction would be hard even with perfect data. Despite a number of really cool methods (I like these), I sometimes worry we may never be able to sort this mess out.

Much of this paper hinges on whether niche space ever gets filled. If species can fill up niche space, then it’s reasonable to expect that competitive effects would limit diversification, and Cornell’s first conclusion is that we need more experimental tests of whether these kinds of competitive effects exist. That’s not to say we need more research on competition – we have decades of that in ecology – but we need more explicit tests in extant clades that biogeographers are examining. We can’t turn back the clock, but we can validate the assumptions of our models in the present where we’re not data-limited. Now that is eco-evolutionary modelling!

Cornell spends a good deal of time discussing the importance of migration on clade dynamics, and species moving into an area and occupying niches is a rather thorny problem. However, I’m just not sure we’re ever going to be able to handle this; after decades of work, we’re only just beginning to understand how we can model species’ distributions in the present day, and attempting to do that using only biased fossil distributions for all of evolutionary time sounds like an incredibly tall order. Perhaps one thing we could do is look for correlated extinctions/speciations in the fossil record. Imagine a new species has just evolved that occupies a new kind of niche; if we assume it spreads essentially instantaneously in evolutionary time, any slow-down in other clades’ diversification rates should be immediately detectable.


Lynsey McInnes

Lynsey McInnes

This paper has been in my to read pile since I spotted it sometime last year. It probably remained there because it’s long, dense and comprehensive and takes more than a commuter train ride to get through. So when Rafael Maia over at Evo Bio journal club challenged Will and I to find a super cool paper on the geography of speciation, we decided to go with this one as it more or less covers ALL super cool papers on the geography of speciation ever published. So, thanks Howard Cornell for summarized this research field for us and providing us with plenty of food for thought for our first EB/PEGE journal club crossover.

For those of you who know me/have read my posts here at the site, you can guess that I chose this one and that it appeals to my interest in understanding the spatial nature of diversification. First, a note about the style of the paper. I really enjoyed reading it, and managed the whole thing in a single sitting and I think that is down to Cornell’s extremely clear writing style and his total command of the subject he is writing about. Wow. I was also impressed with his ability to navigate through a field that has become quite contentious in recent years; he managed to extract relevant points from a suite of Rabosky & Wiens papers without explicitly acknowledging the animosity apparent between these two camps. In fact, he elegantly concludes that regional diversity is, in effect, both bounded and unbounded and puts forward the damped increase hypothesis to cover this inclusive idea. Hoorah.

Enough rambling, what has Cornell left us to talk about?

First, I really liked his repeated emphasis on taxonomic scale. By this, he meant the conclusions we reach on the diversification of a clade will dependent on the breadth of diversity found within the clade (i.e., a subclade of mammals, a clade restricted to a single region, a clade found in a region with ecologically-similar species from different clades, a clade that has newly-colonised an area, and vice versa). I think this is an underappreciated point within macroevolution and one that deserves more explicit treatment in the future. If we are using a phylogeny to understand diversification of a group, we want to use a well-defined monophyletic clade, maybe we even want to compare two or more than two monophyletic clades. This is fine and admirable, but when doing so, we have to remember that the clade does not exist in isolation (ecologically-(dis)similar species probably occupy the same area, the clade probably included additional taxa that have now gone extinct, the size and nature of the area it currently occupies have probably changed substantially since the origin of the clade, and so and so on). If we really, really want to understand how clades diversify, we have to try really, really hard to account for at least some of the above. At the very least we have to circumscribe what we are trying to understand (How an area became populated? How a clade diversified? How extrinsic/intrinsic traits shape diversity/diversification?)

Years ago, I remember Joaquin Hortal – community ecologist extraordinaire – scoff in the face of the idea of ecological limits to diversity. His reasoning was that he knew of no system that was totally full, there was always scope to squeeze in new species if only the new species could be transported to the area in question. I kinda believed him, but somehow decided that he was talking at some kind of narrower scale than me, that at the continental scale or global scale of entire clade (what is an entire clade?!?!), limits could be reached. I think Cornell’s paper is the first I have read that both implicitly recognises and reconciles these multiple scales that I had in mind. I do wonder if we will ever work out a way to identify the optimal spatial and taxonomic scale to look at how diversity is generated or even if such an optimum exists?

To conclude a bit of a rambley post, I really appreciated this paper. It summarized the weight of evidence for two hypotheses that had somehow recently become quite polarized in the literature and emerged with a happier medium incorporating the best bits of both. Cornell also sets out his vision for making progress in this field and this involves taking a more thoughtful approach to improving our understanding of regional diversity patterns: collect more and better data, incorporate multiple types of data in any analysis, analyse it properly, and perhaps most importantly think about the SCALE of your analysis before you set out and as you interpret your results. Onwards and upwards!

Convergence, adaptation, and constraint

Jonathan B. Losos. Evolution 65(7): 1827-1840. DOI:10.1111/j.1558-5646.2011.01289.x. Convergence, adaptation, and constraint

Are these Anolis dewdaps constrained? Maybe more than you’d think… (PLoS One; click for source)


Will Pearse

Will Pearse

We’ve covered too many data papers recently (that’s not a joke, but it does read like one), and so I picked this paper to help us step back a little and think. I’m pleased with the result: this is an excellent essay, that really made me think about what convergent evolution actually is. I’m particularly keen to hear what you all think of my comments about history!

Losos argues convergence is scale-dependent: there are many ways to evolve a long beak, and while there may be divergent evolution of the actual genes involved, the resulting phenotype (a long beak) is convergent. We’ve covered convergent evolution in bacteria, where the same genes (but different regions of those genes) mutated in parallel in separate lineages. I like this scale-dependency – it allows us to define convergence so that it’s amenable to study at all levels from phenotype to genetic mechanism.

I think we can push this framework further, and compare very different systems in meaningful ways. For instance, maybe examining constraints to evolution in responses to predation in Daphnia is easier when you consider what constrains their tolerance of the abiotic environment. Maybe seeing particular stressors and evolved responses as analogous to one another allows us to better compare evolution among clades, and view constraints to evolution in a more holistic way..

Apparently, there are some who take the view that evolutionary changes are incomparable historical events, and so the whole idea of convergence is a nonsense. I think this is rather peculiar; while there is a debate in history as to whether the field is a science (I think it is, but I’m not a historian!), every historian I know compares periods and events in history, with the precise aim of drawing parallels among periods. Thus I think the argument that evolution is the study of history, and therefore will not allow us to compare events, is not one even a historian would agree with!


Lynsey McInnes

Lynsey McInnes

Commenting on a Losos paper is always going to be tricky, as this is a man who knows his evolutionary biology! You can tell this in two ways, first simply by the breadth of examples he draws on and second by his daring to question the be all and end all of phylogenetically-informed analyses, another recent examplesof his critique of such analyses can be found here.

Like Will, I appreciated having a week off from data bashing and am currently juggling all the different issues that Losos brings up on what is and is not convergence, parallelism, adaptation, exaptation, etc. The biggest take home message I got from the essay was that, as always, scale matters. Birds and bats both have wings that let them fly, are these convergent traits? Depends on your scale of comparison. It seems like identifying instances of convergent evolution would be simplified immeasurably if the researcher concerned just set out the scale across which he is looking and perhaps also mentions whether he is worried about the trait being the ‘same’ at the genetic, phenotypic, morphological and/or morphological level. Hey presto, confusion and agro could be gotten rid of.

I can’t help comparing the issues brought up here to the ones Losos, and plenty of others, have attempted to deal with concerning identifying instances of niche conservatism. Again, it all depends on scale. Cooper et al. provide an excellent roadmap for conducting analyses on nice conservatism, I’d like to see a companion piece to this essay detailing the practical approaches to sensible analyses of putative instances of convergent evolution.

I’ve recently shifted the scale of my own analyses to incorporate (currently to deal exclusively with) intraspecific variation. In practice, this has meant starting to think about different models of mutation (infinite site, infinite allele, shitty recombination raising its ugly head begging to be dealt with) so I find my scale of analysis shifting to the genetic level, wanting to see mutations in same genes, indeed at the same sites to qualify as parallel evolution. For this reason, I really appreciated this essay as it forced me to address my newfound genetics-only bias and realise that interesting, valid and evolutionarily important convergent changes at the functional (or even just phenotypic) level need not be produced from identical genetic changes.

The recent bacteria study that we discussed here at PEGE was a brilliant example of a standalone set-up for studying evolution across these different levels (genetic, phenotypic, etc.), the next step, as always, is to devise a set-up that facilitates similar inference in systems where access to all these levels might be patchy. Losos’ essay will undoubtedly be helpful in this regard.

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