A ‘synthetic’ review of a year of PEGE


Conifer phylogeny from Willamette Biology
Conifer phylogeny from Willamette Biology’s photostream

Lynsey McInnes

Lynsey McInnes

We’ve come to the end of a year of PEGE! Well done us! We only skipped one week in the whole year (and it was the week in which I got married) and we managed 16 guest posters. It’s been an entertaining year. Will and I set up PEGE mostly as an excuse to keep in regular contact with each other, to ensure we regularly checked the literature and to learn how to write something more or less thoughtful in a short timeframe (for me, within the length of the train journey from Stirling to Edinburgh). I think we succeeded in all three.

A secondary aim was to get an online discussion going along the lines of a journal club. In this, we did less well. Although we know that the site got substantial traffic (from our fanatical checking of site stats), few people commented. From perusing other blogs, I think this is a hard thing to get going and we’re not going to beat ourselves up about it. I know I read other blogs, more or less regularly, and have never commented on a single one. It’s enough for us if a paper we have highlighted or a comment we have made has impacted someone’s research in any which way. I know that writing these posts has had a positive impact on the way I think about my own research and the links between what I do and am interested in and what else is going on in the PEGE world.

It was almost amusing how quickly it became apparent where Will’s and my interest lie. Regular readers can by now easily guess who wrote which post in an instance. I’ve found PEGE helpful in identifying my emerging interests and I hope to follow up some of these new found leads in my future research.

Apparently, I am super keen on intraspecific diversity and how it affects species’ responses to climate change, niche evolution and range movements. I am not a fan of community phylogenetics and can’t quite believe there is a good way to identify source pools for such analyses. I really like the idea of mesocosm experiments (although I
have no experience of them myself) and am prone to want to roll out any neat analysis on a particular study system to some sort of broad-scale comparative study. If only I had the cash and the expertise (and the time). Both Will and I are concerned with scale, the appropriate scale for various analyses (temporal and spatial), how scale affects the inferences possible and how, ultimately, a sound understanding of diversity patterns requires analyses across scales. Scale, scale, scale.

What’s up next for PEGE? We’ve decided to shake things up a little and to par down to fortnightly posts. In each, we will focus on a classic (we decide what constitutes a classic) paper from the PEGE world and hopefully spend a little more time (TWO train journeys) thinking about the paper and developing our thoughts. It’s been fun scanning the literature for new papers to discuss this year, but we often found ourselves choosing a paper based on an intriguing title and being disappointed by its content (bet you can guess which posts I’m referring to). Now we’ve had the chance to flex our commenting muscles, we’re going to try to put them to better use on ‘bigger’ papers.

Finally, thanks for reading. You know who you are. We’re hopeful that readers have enjoyed our posts and ever hopeful that our readership might grow alongside our comments column. Any tips to make PEGE better, suggestions for classics to discuss next year or requests to be a guest poster, just let us know.

Merry Christmas!

Will Pearse

Will Pearse

Wow, a whole year. I can hardly believe we’ve made it! Everything Lynsey has said is true; I’d just like to add I’m really grateful to everyone who’s read the blog. I’ve been lucky enough to talk with some of you at conferences, in comments beneath articles, and through email, and it’s always fun doing that. Thank you!

If, like I used to be, you’re skeptical of why something like PEGE is worthwhile, please believe me when I say this has been one of the most useful things I have ever done. It’s not just that this lets me constructively engage with scientists I could never otherwise hope to meet, it’s that my reading and writing skills have qualitatively improved. Every week for a year I have had to be constructively critical and engage positively with an article, then scribble out something that people will (hopefully!) find interesting. It makes you leaner, it makes you faster, and it makes you better.

If no one were reading PEGE it would be worth it for the impact its had on me alone. Many bloggers obsessively monitor site statistics – Lynsey and I are no different, but we haven’t actively sought-out more readers in the way I know others do. That’s not to say we haven’t engaged with people – we’ve replied to every comment, and I would like to think the diversity of our guest posters speaks for itself (thank you all!). I’m very happy with the audience we’ve built up (thank you again!) and if you’re thinking about setting up your own blog (do!) be reassured that you don’t have to dedicate hours every week to selling yourself on the Internet. Build it and they will come – but do make sure you email your friends!

As Lynsey said, we’re both obsessed about scale-dependency. Unlikely Lynsey, I like community phylogenetics – while I agree with her that defining source pools is tricky, I prefer to see it as a way of asking questions and don’t expect a single ‘answer’. Moreover, there’s more to community/eco-phylogenetics than source pools. Looking back through what we’ve chosen, I’m struck that there are a number of what I would call ‘case study’ papers, where there is a central story that verifies established theory and fleshes-out specific details for a particular system. Many say scientists are no longer interested in filling in the gaps with studies that have little conceptual novelty; I think it’s re-assuring that Lynsey and I have found so many excellent papers that do buck that trend. Maybe there’s hope yet!

Thanks again for reading, thanks again to all our guest posters, and thanks again Lynsey for writing, listening, and continuing to be my emotional supervisor. On to 2014!


Will plant movements keep up with climate change?

Richard T. Corlett and David A. Westcott. Trends in Ecology and Evolution 28(8): 482-488. DOI:10.1016/j.tree.2013.04.003. Will plant movements keep up with climate change?

It's a plant moving. Look, do you have any idea how hard it is to find a picture every week?

This plant can move fast enough… From Wikipedia

Will Pearse

Will Pearse

I picked this paper (out of Lynsey’s selection) because I had a long chat with someone about this at ESA. We concluded then that we didn’t really know whether plants could move fast enough, and to be honest that’s pretty much the conclusion I came to at the end of this review.

Box 4 of the review lists outstanding problems that include “ignorance of the factors that currently limit species ranges”, “largely unknown to what extent plants can acclimate to climate change”, and a number of other factors. The section “can plants track climate change?” lasts only two paragraphs – we apparently have no idea whether plants can track climate change or not. The authors give a number of (for what it’s worth, quite reasonable) reasons they probably can’t, but I think they’d agree that we don’t actually know. Frankly, I’m slightly shocked that we don’t know more about this.

I’m not convinced that animal-dispersed species are necessarily going to fare much better in the face of climate change. This assumes that animals with larger territories are going to move more easily (not necessarily true), particularly given we don’t fully understand the mechanisms by which species would shift their ranges. An animal that eats fruits that moves when it’s hungry is not going to disperse that fruit polewards, because it’s hungry and hasn’t eaten that fruit!

Long-distance dispersal as a mechanism by which individuals trapped in a sea of bad habitat can save the species is an interesting idea. I think this would benefit from a simulation study, but I sense it would require species to be able to colonise in the face of a quite severe numerical disadvantage (small number of immigrants, lots of incumbents). Still, this is a nice idea I’d like to think about for longer…

Lynsey McInnes

Lynsey McInnes

This is a funny paper. On the one hand, a very useful, succinct review of the different factors involved in thinking about how plants might respond to climate change and why this is of interest to ecologists/conservation scientists/mankind and on the other hand, a frustratingly on-the-fence expose of plant movement research to date and its likely next steps.

The authors undoubtedly do a great job in summarizing many recent studies (check out the reference list, its stacked with refs from post 2010). This subject is most definitely timely and popular. And yet it seems we don’t know much. For example, conclusive answers are absent for questions such as what determines a plant species’ current range? How much more range could a species occupy with unlimited dispersal/removing other species/new climates? Is this period of climate change different to past ones (cities in the way, etc.)? The author’s box 4 neatly summarizes the extent of our lack of knowledge!

I got to the end of the paper and found myself wondering (a bit like last week), should we worry? Or should we worry in a more focused way? Does the identity of individual plant species matter as long as the ecosystem is still functioning healthily? If you are a ‘rubbish’ species, has your time come? Perversely, I do just find the outstanding questions listed in box 4 of interest in and of themselves, but firmly, firmly believe that for conservation purposes, they are not the correct ones to be focusing on. I’m not a conservation scientist so I’m allowed (have allowed myself) to ponder these questions, but if wanted to be practical, I reckon we need to think more about functional types (mentioned in box 1), more about corridors to facilitate movement, more about redundancy, more about … ?

Can we ever know – ‘Will plant movements keep up with climate change?’ Seems like this is not a yes or no question. It will depend on the specific set of traits the plant species has/the environment it is found in/the interactions with other species (plants, dispersers, pollinators) it has now and could have in the future? Different camps want an answer for different reasons. Generalities seem to be in place already (and are well-summarised in the paper). However, if we want to conserve species or functions, we need more than these generalities, it seems. If want to use this broad question to learn some fundamentals on the biology of plants, my suggestion would be we need more of everything: more field studies, more theory and perhaps most importantly more of a recognition and exploration of interacting forces: a bit of evolution, a few influential abiotic factors, one or two key biotic interactions, a whole host of more minor ones, across and within trophic levels, some anthropogenic effects, short- and long-distance dispersal and this whole shebang playing out against a shifting climate.

I think the paper left me unsatisfied as it was pitched too broad and thus felt too shallow. What are these authors interested in? What piece of the puzzle will they tackle? Ja, perhaps that’s unfair to ask of from a review, but I’m curious anyway.

Finally – I did very much appreciate this line from the paper: ‘The involvement of government agencies, nongovernmental organizations, and citizen-science networks will be essential, given the focus of academic science on novelty.’

Heat freezes niche evolution

Araújo, Ferri-Yañez et al. Heat freezes niche evolution. Ecology Letters, early view.


Some pretty exciting datasets used in this study (above)

Will Pearse

Will Pearse

I’m sorry everyone, because a number of work commitments (including preparing for ESA) mean I haven’t been able to spend the time I would normally devote to PEGE this week. I’m particularly annoyed, because this paper has a story, and stories require sitting in a quiet room with a beer and thinking, which I really don’t have right now.

Let’s assume that the tropical origin theories are right, and that the tropics are a huge source of diversity. If so, I completely buy more variability in cold tolerance – that’s what allowing species to spread towards the poles, and that’s what’s allowing species to radiate out into new niches. We should expect variation, because it’s that variation that’s driving speciation / it’s speciation that’s driving that variation.

When I look at the evolution of species traits, I assume I can measure them fairly accurately, and describe them with a single value. Well, this paper (and in particular figure 7a) really makes me think I should stop doing that, because tolerances seem to be things that are described by distributions with long (or at least variable) tails, and quite strong asymmetries. Perhaps even some kind of linkage with the traits that underly cold tolerance, and how those work physiologically, might help. So, maybe it’s time to crack out that dusty old physiology textbook!

Lynsey McInnes

Lynsey McInnes

Oops, I’ve managed to pick a paper that merits more consideration than either Will and I have had time to give it this week. But in the spirit of publishing PEGE more or less on time each week (less this week given Latvian wifi collapse), here are some initial thoughts on this paper.

Well, it looks like we are finally beginning the next generation of niche conservatism type analyses and that physiology is about to take centre stage. For a while now, we have been bandying about the notion that we can’t really look at niches by summarising the different climates found within species’ range polygons, that really niches relate to physiology and that we need to address physiological mechanisms head on. However, physiological traits are way harder to measure! The authors here do a great job of collating all available date on physiological tolerances and asking some interesting questions with this dataset (as an aside, I am extremely fond of papers that dare to use data from variety of sources and measuring slightly different things, rather than restricting themselves to more ‘perfect’ homogeneous datasets).

They conclude that upper thermal limits are much less variable than lower ones and that this indicates that upper limits are much more conserved. This in turn suggests that species living in regions close to these limits are most likely to be most screwed in the face of increasing temperatures. I really need more time to think about this, but on first glance, this sounds pretty reasonable and sits well with similar assessments of latitudinal gradients of climate change risk that have not used real physiological data.

I really appreciated that authors tackled head on what their results mean for all those studies (mine included) that make loose handwavey gestures that realised niches should be correlated in some nicely linear way with fundamental niches. I also liked the way they highlight how their findings deal (another) blow to using bioclimatic modelling to make robust assessments of species likely responses/range movements in the face of climate change.

Some thoughts that popped into my head…

How are these results affected by there just not being higher temperatures around at the moment? And by there being more species in the tropics, with smaller ranges? Is there any conflation going on?

Are there any experimental evolution studies around that have selected for increased temperature tolerance/looked at the genetic mechanisms behind this? (I expect yes!)

What is the relationship between upper and lower thermal limits and the absolute range of thermal tolerance for each species? (Not sure what I mean here, but I think I mean what about the physiology analogue of the effect of range size/intraspecific variation?).

How would these results change if studied in an explicitly phylogenetic context (harping back to my musings on what is niche conservatism without the ‘phylogenetic’ bit?).

Given the apparent complexity in species’ (thermal) niches is there any real hope that we are able to make accurate predictions of species’ likely responses to climate change (and then go on to use these predictions to take useful conservation decisions)? The typical trio – move, evolve, perish – still stand but how much progress have we made in working out what is more likely (my feeling is most species will have a bit of all three in different/overlapping parts of the range). Pragmatically, maybe we need to give up on these species by species assessments and instead look at emergent community/ecosystem assessments to insure healthy ecosystems (whatever that might mean) rather than persistence of individual species. I.e. go more macro instead of less?

Alternatively, if our aim is not necessarily to conserve, but just to understand what on earth is going on and how niches ‘work’, it looks like we are going to have heat up a lot more organisms on hot plates and digitise a few less maps…

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