Sexual segregation and flexible mating patterns in temperate bats

Angell et al. 2013 Sexual segregation and flexible mating patterns in temperate bats. PloS One. 8(1): e54194.  

Figure 3 from the paper. Posterior distributions for paternity probabilities at the group level. Posterior distributions for the probabilities that fathers (at the group level) came from roosts in the (blue) upper-elevation, (yellow) mid-elevation and (green) low-elevation, and from (red) swarming sites. For (A) low-elevation offspring (the inset graph shows the Wharfedale roost posterior distributions in greater detail), and (B) mid-elevation offspring. 

Following the last two discussions, this week’s paper was selected on the basis that it used non-lethal DNA collection techniques to determine how intra-specific niche separation influences mating patterns.

Matthew Guy

A large number of temperate bat species, including Myotis daubentonii, display sexual segregation along altitudinal gradients. In these species, mating usually occurs during autumn swarming events. However, at the upper limit of the female range, Senior et al. (2005), found evidence of summer mating within roosts where dominant males are tolerated by females. Using the same population of M. daubentonii, this paper extends this work to identify if this is the dominant mating strategy throughout the altitudinal range of the species and, if not, can the differences in mating strategy be explained by foraging habitat quality?

DNA was extracted from wing punches and a novel Bayesian approach was used to assign the probability of parentage of juveniles from low altitudinal roosts to males from different roosting sites and swarming sites. During our discussion, nobody had a lot of experience with the genetic methods used and we found the results section difficult to read. However, the figures clearly demonstrate that the probability that these juveniles are fathered by males from anywhere other than swarming sites is very low. We thought that this was a really nice example of how figures can be used to give a clear overall impression of complex data, especially for the lay person. This result was in contrast to that found by Senior et al. at mid-elevation roosts suggesting a flexible mating strategy over an altitudinal gradient.

Foraging habitat quality was assessed using bat activity, weight and temperature, all of which declined significantly with altitude. The paper surmises that by excluding males from roosts, pregnant and lactating females can reduce intra-specific competition for the high-quality foraging grounds. However, the carrying capacity at intermediate sites is lower and so supports fewer females. In these areas, the thermoregulatory benefits provided by males in the roost outweigh the costs incurred by additional competition. The paper pulls these results together qualitatively, stating that the mating strategy is adapted to the social structure, which, in turn has evolved in response to environmental conditions at a given altitude. However, we felt that an analysis of prevalent mating strategy (i.e. probability juveniles were fathered at swarming events) within individual roosts and local foraging habitat quality together would address the second part of the research question more directly.

Over all, we felt that the paper was well written and, in combination with the Senior et al. paper results, presented an interesting behavioural response. However, the scope of the paper is fairly limited, largely due to a combination of studying a single species and developing ideas of a previous single study. One potential way to widen the papers appeal could have been to incorporate a discussion on how the novel genetic technique developed in this study could be applied to other species populations.

The paper ends by posing the question: Is this flexible mating behaviour capable of dealing with changes in prey distribution and roost microclimate predicted by climate change? Our discussions came to the conclusion that climate change could cause a decrease in the success rate of mating during autumn swarming events, potentially reducing gene flow. An increase in temperature would drive prey species upstream, where the higher proportions of more turbulent water would reduce the quantity and quality of the forging grounds. This could lead to a reduction in females within local nursery roosts making them more reliant on males for roost thermoregulation, and hence, an increase in the prevalence of summer mating. We thought that actually addressing the question, at least to some extent, in the discussion would have made for interesting conclusion and again potentially widen the papers appeal.

A globally coherent fingerprint of climate change impacts across natural systems

Camille Parmesan and Gary Yohe. Nature 421: 37-42. A globally coherent fingerprint of climate change impacts across natural systems


What is climate change? (From Keep Queensland beautiful.)


Isabel Jones

A few weeks ago Lynsey bribed me with some really very delicious cake to write a guest blog here. Well I say bribe, it’s quite an honour really, so I chose one of my all-time favourite papers that I consider a ‘classic’: Parmesan & Yohe ‘A globally coherent fingerprint of climate change impacts across natural systems’ published in Nature, 2003. This research ties together the differing ways of viewing the world of biologists and economists, to clearly show that there are systematic biological trends being caused by climate change: poleward range shifts averaging 6.1 km per decade (or meters per decade in altitude) and spring events coming in on average 2.3 days earlier per decade.

This paper was in answer to disagreements within the IPCC as to whether changes in biological systems could be attributed to climate change, or not. And what a way to answer! Parmesan & Yohe combine methodologies of biologists and economists – engaging both schools of thought – and analyse a comprehensive dataset on species ranges and phenology, across diverse taxa and regions, to find out if there is a general response of species to climate change. They do this using meta-analysis, categorical analysis and probabilistic modelling of range-boundary shifts in birds, butterflies, and alpine herbs; and phenology changes in herbs, shrubs, trees, birds, butterflies and amphibians.

So often you can get lost in the murk of confounding factors which obscure small changes in a species’ range or phenology, when looking at a single species or region. Land-use change for example has huge impacts on species, and its immediate effects could overshadow the small and long-term changes caused by a steadily changing climate. These small, niggling, persistent changes in ranges and phenology have the ability to fundamentally alter communities over hundreds of years, their interactions, and even cause biomes to shift position or switch from one type to another. A whole biome switching. Quite a thought. I like that Parmesan and Yohe have stepped back from the immediate – and granted very pressing causes for biological responses – to see big picture changes coming from tiny alterations in range and phenology year on year.

Given the impacts that climate change could have from local- to biome-scale, it still baffles me that there isn’t more action being taken to curb emissions and mitigate negative impacts of climate change sooner rather than later. Perhaps one of the reasons is because there isn’t enough interaction between researchers and policy makers, but papers like this one, which help improve dialogue between different the parties and provide a nice summary of evidence, are surely what’s needed.

My one gripe with this paper is the use of the term ‘global’ as in ‘global fingerprint’, and that’s because the majority of studies used in the analyses come from the temperate Northern hemisphere. This is because long and high-quality datasets come from here, but I wonder what would happen to the global fingerprint of climate change impacts identified if we added more studies from the Southern hemisphere, the poles, and the tropics. If there was more time, perhaps long-term data collectors could switch their biomes too.

Lynsey McInnes

Lynsey McInnes

So far, I am really enjoying the ‘classics’ angle we are running on PEGE as it gives me a chance to actually re-read (sometimes just read) papers with 1000s of citations and remember why they are so. While writing up my PhD, the contrary part of me used to hate citing the ‘most cited’ paper on a topic because I liked a diversity of citations. Hm. Sometimes classics are classics for a reason.

This is an awesome paper. You can almost hear the authors’ sighs as they sit down at the their desks, hands on table and decide – let us sort this shit out. Enough of people swinging this way and that, let’s compile the evidence and just let it speak for itself. Beautiful.

Saying that, I’m sure many people remain that are unwilling to be convinced by the weight of evidence presented or just don’t care. Their world view is such that any evidence for responses in other directions or greater risk or impact from other factors is enough to convince them that climate change doesn’t matter.

Beyond being staggered by the strength of the argument being portrayed here and the admirable way in which it was portrayed, here follows a selection of thoughts that popped into my head (yep, it’s one of those posts).

– I wonder how much bigger the dataset could be made today, 11 years on.
– I wonder (like Izzy) what the ‘answer’ would be if the dataset was more evenly global in scope.
– I wonder what’s going on with annoyingly small and difficult to sample biodiversity.
– I wonder how to put together P&Y take two where community/ecosystem wide responses are recorded to see whether these distributional and phenological shifts actually matter for ecosystem functioning (however you might like to define that).
– I wonder, if you didn’t care about conservation of species from a – they are here and morally should be saved – outlook, what shifts and losses really matter for ‘functioning.’
– I wonder what is really going to happen to high latitude regions which are set (at least sometimes) to gain biodiversity.
– I wonder if you could do a P&Y take 2b and identify a combined fingerprint of climate change and other threats such as fragmentation (probably not land use change – when its gone its gone after all).
– I wonder if this hybrid biological – economic approach is well suited in the debate on what ecosystem functioning is. Can economic theory and practices be put to good to use when quantifying what a functioning ecosystem is and how to keep it that way.

I think that’s enough for now before I get overly-philosophical. In short, I really, really enjoyed reading this paper for its measured, no nonsense approach to evidence. I don’t think it is the final word on people believing climate change affects species. It’d be great to hear what the authors think about the ensuring 11 years of research and whether we are anywhere closer to a. understanding what is going on and b. doing something (what?) about it.

Yes, I’m aware the above was a very ‘academic’ post – I’m sure I could enter the non-academic literature and find out answers to a lot (though probably not all) of the musings above. Maybe I will.

Will Pearse

Will Pearse

This paper has been extremely influential, and I remember reading it in 2008 in my first undergrad conservation biology class. So I’d like to be self-indulgent and write about how my views on climate change have changed over the last few years. I’m no expert, so if you are you may well find what I have to say quite unsurprising.

The authors hope that if we measure enough things (range shifts), and then combine those things, we’ll understand more than if we just looked at each of those things separately. It isn’t helpful to ask whether each shift was ‘significant’ (), we’re interested in drawing inferences about the total ‘population’ of range shifts, and getting a good sample of that. If that sounds controversial to you, think of it like this: if you were measuring the average length of toads, you wouldn’t ask whether a particular toad was significant, you’d measure a sample of them to make an inference about the single population from which those toads were drawn. Each measurement has very little information, but the whole is equal to the sum of its parts, and samples help us understand the population they’re taken from.

In biology, small changes add up in the long-run, and the authors focus a lot on the different time-scales in economics and the rest of the world. Discount rates have a rather profound effect on what is rational behaviour! However, we now know that it’s wrong to characterise climate change as a strong, steady force – that would be scary enough, but it’s much worse than that. As the climate shifts every aspect of it becomes more erratic and unpredictable, and the its rapid fluctuations indicate an impending catastrophic shift (that’s actually the technical term). When you undergo such a shift, pretty much all information you had about the system before is now worthless. You’re now drawing from a different population. Using observed range shifts now to measure shifts in the future assumes that the basic properties of the system will stay the same – and once we pass the tipping point, they won’t. Under the conditions we’re approaching, all bets are off. Frankly, if that doesn’t scare you, I don’t know what will.

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…

Clade-specific consequences of climate change to amphibians in Atlantic Forest protected areas

Loyola et al. Ecography 36: 1-8. DOI:10.1111/j.1600-0587.2013.00396.x. Clade-specific consequences of climate change to amphibians in Atlantic Forest protected areas


Amphibian species recent now (left) and 2080 (right). A message… from the future! From Loyola et al.

Will Pearse

Will Pearse

Lynsey gave me a wide selection of papers this week, and I picked this one because I’m thinking a lot of about the phylogenetic structure of ecological communities and biogeography. The authors predict amphibians’ distirbutions in Brasil in 2080 on the basis of their present distributions, and then examine the implications for protected areas.

I found this paper quite hard to interpret, and I’d appreciate your input! I found figure 2c, which shows phylogenetic diversity in protected areas now and in 2080, hard to read, as did the authors: “phylogenetic diversity increased under future climatic conditions, albeit such increase was not clear (Fig. 2C)”. The magnitude of the change (0.04 is the biggest I could see) seems very small, but it looks to me like those areas with the greatest diversity now have lesser diversity in 2080, and vice-versa, so could there be some kind of interaction going on? I’d love to write about the within-clade results, but I simply don’t understand figure 3 where they’re presented. The authors seem to have made a matrix that represents clade composition in the protected areas, and then plot principal components of that matrix, but figure 3 shows present and future climatic conditions plotted on the same axes as monophyletic clades, and I don’t know how that’s possible. Help!

However, the general approach of examining variation in response among clades is interesting. I think making predictions about protected areas’ future phylogenetic diversity is particularly useful if we want to understand ecosystem function, and I think approaches like these have the potential to be of conservation importance.

Lynsey McInnes

Lynsey McInnes

Ouf, this was a strange paper. I do think the premise was well-intentioned, but the execution was really quite confusing. As I understand it, the authors were interested in seeing how climate change will affect amphibian richness, diversity and phylogenetic diversity in protected areas within the Atlantic Forest of Brazil. A fair enough intention, protected areas are, debatably, the best hope for the persistence of endangered species, and amphibians, more so than other vertebrate groups are undoubtedly endangered. Furthermore, it is of interest whether protected areas protect certain amphibian species better than others, so the phylogenetic perspective could be a valid and important one in order to predict what kinds of amphibians we will be left with in the future.

But this is kind of where I lost the plot. I really struggled with the authors’ approach to defining phylogenetic diversity and similar to Will struggled to interpret figure 3. I also thought they altered between considering the traits of vulnerable species vs. their basal vs. derived status in the phylogeny. Phylogenetic diversity and its maintenance is of interest, but ultimately, I’m more interested in maintaining a diverse amphibian fauna (and I think the authors are too) so they could have devoted more discussion to the traits that help amphibians persist in warmer, drier areas. They highlight that the increase in phylogenetic diversity that they predict should be interpreted with caution given that it comes hand in hand with a decrease in species richness and the paper could have used this interesting result as a springboard into a more philosophical discussion of whether or not this is an acceptable tradeoff.

The authors are also admirably open as to the deficiencies in the methods they employ, namely that their species’ distribution models do not incorporate realistic dispersal parameters or the effects of sustained or disrupted biotic interactions. These problems plague many similar studies and it seems like the field is changing so fast that soon these omissions might make publishingsuch studies harder and harder. On the one hand, this is good, we should as a research community be tough on ourselves, and on the other, is a shame, as this study, even with its flaws and difficulties, can provoke valid discussion on how to go about conservation with limited funds.

One last grumble, I am deeply sceptical on ensemble forecasting. My understanding is, all models are quite uncertain so we should take an average of all such uncertain models and this will give us an average model with much LESS uncertainty? Hm.

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