Category Archives: Rewilding

“Weighted” nestedness and “classical” nestedness analyses do not measure the same thing in species interaction networks

This post resulted from a question I posed on Twitter last week and hopefully summarises the issue as I see it and the results of the discussion with colleagues that followed.  Let me know if you disagree or if I have missed anything.


The use of network approaches to understanding how plants and their flower visitors interact has revolutionised the study of these and other mutualistic assemblages of species.  It’s a subject I’ve discussed on the blog before, highlighting some of the work we have published – for instance, see Plant-pollinator networks in the tropics: a new review just published and Local and regional specialization in plant–pollinator networks: a new study just published as two recent examples.

One of the recurring patterns that we see in mutualistic species networks (but not in antagonistic ones such as host-parasite and predator prey) is “nestedness”.  In a nested assemblage of species, generalists with lots of links to other species interact with other generalists and with specialists (those species which have few links to other species)Conversely, specialists tend only to link to generalists: specialist-specialist interactions are rare.  In nature, when we rank species in a network from most to least generalised, this sort of relationship looks like this:

South Africa nested

The rows are plants and the columns are pollinators, in this case from an assemblage of asclepiads and their pollinators we studied in South Africa.  A filled cell in the matrix indicates an interaction between that particular plant-pollinator combination.  It’s not perfectly nested by any means, but statistically this is not a random pattern and it comes out as nested when analysed.  There are a few ways of doing this but the most commonly used is the Nestedness metric based on Overlap and Decreasing Fill (NODF) developed by Almeida-Neto et al. (2008).

I first saw nestedness discussed in relation to plant-pollinator interactions in a presentation by Yoko Dupont of her PhD research at a SCAPE meeting in Sweden in 2001.  It was one of those “A-HA!” moments in science when the light bulb switches on and you realise that you are seeing an important new development which adds significant understanding to a field.  Yoko subsequently published her work as Structure of a plant–flower‐visitor network in the high‐altitude sub‐alpine desert of Tenerife, Canary Islands.

The nested pattern of interactions is conceptually derived from earlier work on island biogeography and species-area relationships and was initially developed to apply to interaction networks by Jordi Bascompte and colleagues in Spain and Denmark – see: The nested assembly of plant-animal mutualistic networks.

What was so exciting about this idea to me was that it provided a way to formally analyse what many of us had been observing and discussing for some time: that mutually specialised plant-pollinator interactions between species are rather rare, and that specialists tend to exploit generalists.  This makes perfect sense because specialist-specialist interactions may be more likely to go extinct, though why it does not also apply to host-parasite interactions is far from clear (and in fact the best known specialist-specialist interactions tend to derive from seed parasitism interactions such as fig-fig wasp and yucca-yucca moth relationships).

Fast forward 20 years and the plant-pollinator networks literature has exploded and our methods of analysis are much more sophisticated than they were in the late 1990s and early 2000s.  Every few months researchers are coming up with new ways in which to analyse these networks, mainly using the R environment for statistics and graphing.  Anyone entering the field would be forgiven for being bewildered as to which approaches to use: it’s bewildering enough for those of us who have been following it from the start!

One thing has been particularly bewildering me for a few years now, and that’s the introduction of “weighted” nestedness.  “Weighted” in this sense means that the abundance or interaction frequencies of the species in the network is taken into account in the analyses.  Visually it could look something like this if we code the cells in the network above to represent abundance or frequency (the darker the cell, the more abundant or frequent):

South Africa nested weighted

I’ve just mocked up the network above, it’s not the actual data.  But quite often networks look like this when we weight them: generalist interactions and/or species tend to be more frequent than specialist.  So far, so obvious.  But here’s the thing: networks that are statistically significantly nested when analysed by NODF tend to be not significantly nested when analysed by a new set of weighted metrics such as wNODF or WINE – see the documentation for the bipartite package for details.   And I don’t understand why.  Or rather I don’t understand why we should be using weights in an analysis of nestedness which is, at its heart, an analysis of presence-absence.  Species are either there or they are not, they are either interacting or they are not.  Their frequency or abundance is immaterial to whether a network is nested.  Indeed, assessing frequency of interactions in plant-pollinator networks is fraught with difficulties because (a) there are so many ways in which to do it; and (b) interactions between plants and pollinators in a community can vary HUGELY between years and across the geographical ranges of the species involved.

This should concern the interaction network community because recently I’ve had reviewers and co-authors saying things like: “don’t analyse for nestedness using NODF because wNODF/WINE is The Latest Thing, use that instead”.  But as far as I and the colleagues who commented on Twitter can tell, nestedness and weighted nestedness are different concepts and are not inter-changeable.  Indeed, many of us are struggling to really define exactly what weighted nestedness analyses are actually measuring.  I can define nestedness in simple terms as a verbal concept, without using the word “nested”, as you saw above.  I can’t do that with weighted nestedness, and I have yet to encounter anyone who can.

So the consensus from the Twitter discussion seems to be that:

  • for any study we should use only those analyses that are relevant to the questions we are asking rather than simply running every available analysis because there are lots to choose from.
  • weighted interaction networks that include abundance or frequency are not necessarily superior to binary presence-absence networks.  Again, it depends on the question being asked.
  • we should not treat weighted nestedness as an upgraded or superior version of classical nestedness.  If you are interested in nestedness, use a binary analysis like NODF.

My thanks to the colleagues who contributed to the Twitter discussion:  Nacho Bartomeus, Pedro Jordano, Pedro Luna, Marco Mello, Chris Moore, Timothée Poisot, and Kit Prendergast.  If you want to follow the Twitter discussion, start here:  https://twitter.com/JeffOllerton/status/1159377089319047168

 

Advertisements

13 Comments

Filed under Apocynaceae, Biodiversity, Rewilding

Why conservation is like paella: thoughts and photos from our Tenerife field trip

 

A couple of days ago I posted a photograph on Facebook with a comment that “after a hot day of collecting data there’s nothing better than a nice big Tenerife paella!”:

Karin and the paella.jpg

My wife Karin and I had ended up in the small town of Candelaria, tired and hungry after sweating our way through the Malpais de Guimar  counting and measuring plants.  Big plates of hot food were just what we needed!

After I posted the image a Spanish colleague commented that the dish was “closer to being an arroz con cosas than a paella”.  The term translates as “rice with things” and is used to convey the fact that the original Valencian dish of paella has been bastardised and changed across the Spanish-speaking world, and no longer reflects its culinary tradition.  Knowing nothing of that culinary tradition I took a look at the Wikipedia entry for paella.  It makes for interesting reading, not least the fact that in the original dish one of the main ingredients was the meat of water voles and that the dish was cooked on an open fire fuelled by wood from orange and pine trees to give a distinctive smoky flavour.  There was also a lot of geographic variation in the dish, so what constitutes an authentic paella is debatable.

Although there was no sign of rodent flesh or naked flames in the dish that we ate, it was certainly delicious!  But the comment about arroz con cosas got me thinking about shifting baselines in cooking and conservation.

The idea of a shifting baseline is that expectations of what is “correct” or “normal” or “natural” change over time depending upon what each generation has experienced.  It’s been mainly applied in conservation; for example, the Lake District of England is seen by many as a “natural” landscape of rolling hills and low mountains, but originally it would have been covered in deciduous forest.  Likewise large parts of Tenerife contain a high proportion of alien plants (such as agave and prickly pear) but local people and visitors see this as natural.  The baseline of “naturalness” has shifted for people.  Returning these landscapes to their original condition would mean a drastic shift in the composition of the vegetation.  And what point do we return that condition to?  One hundred years ago?  One thousand?  Ten thousand?  It’s an issue that is widely debated in the conservation literature, especially in relation to rewilding.

Likewise, over time paella has evolved and been adapted by different chefs, and what is currently cooked in restaurants only partially reflects how the dish was originally cooked.  Other than for epicurean purists, our culinary expectations have changed.  There’s been a shift in the paella baseline.

Anyway, enough metaphorising, here are some photographs from our trip.  To set the context, University of Northampton students and staff, including Pablo Gorostiague who is visiting from Argentina, and colleagues from the University of Sussex (Maria Clara Castellanos and Chris Mackin), were out with us last week.  Then we bade them farewell on Sunday before moving on to do some field work.

Field work on the lava fields at Santiago del Teide:

Santiago del Teide 2018-04-28 11.21.30.jpg

Santiago del Teide 2018-04-28 11.23.30.jpg

Santiago del Teide 2018-04-28 12.20.48.jpg

The landscape of Malpais de Guimar, which actually probably hasn’t changed much in the last 10,000 years:

P1040129

 

How many people can you fit around Pino Gordo, the largest Pinus canariensis on the island:

Pino Gordo 2018-04-24 12.10.41.jpg

Pino Gordo 2018-04-24 12.10.50.jpg

Pino Gordo 2018-04-24 12.11.09.jpg

The endemic Tenerife Blue Chaffinch:

P1040195.JPG

The cold, damp laurel forest:

P1040222.JPG

Team Nicotiana!  Helping Chris with locating Tree Tobacco populations for his PhD work:

Team Nicotiana - 2018-04-27 11.52.15.jpg

Team Nicotiana 2018-04-26 10.13.13.jpg

Pablito takes a break:

P1040235.JPG

 

 

 

5 Comments

Filed under Biodiversity, Biodiversity and culture, Rewilding, Tenerife, University of Northampton

Brexit and biodiversity: submissions invited to a Government inquiry

20160520_114743

Following on from my posts regarding how Brexit may affect the UK’s environmental policies and activities (see here and here) the Government has moved (surprisingly) quickly to begin an inquiry into how leaving the EU may affect issues that [quote] “include the future of funding for biodiversity and agri-environment schemes, the likely changes in the devolved administration, and the role that managed rewilding can play in conservation and restoration”.

I say “surprisingly” because the Government is no doubt focused on what they might see as more pressing concerns; but then much of this inquiry relates to how Brexit might affect biodiversity via subsidies to farmers, and the farming lobby is very powerful of course, and is no doubt pressing Defra to get a move on.

Here’s a link to the inquiry’s official website.  From that site I’ve pulled out the following text:

The Environmental Audit Committee invites submissions on some or all of the questions below:

  • What are the implications for UK biodiversity of leaving the EU, in particular the Common Agricultural Policy? To what extent do initiatives to support biodiversity in the UK depend on CAP-related payments? What risks and opportunities could developing our own agri-environment policy and funding present?
  • How should future support for UK agriculture be structured in order to ensure there are incentives for environmentally-friendly land management? What are the positives/negatives of current schemes (e.g. Countryside Stewardship) that should be retained/avoided?
  • How should future UK agri-environment support be administered, and what outcomes should it focus on?
  • What are the prospects and challenges for future environmental stewardship schemes in the devolved administrations? How much divergence in policy between the nations of the United Kingdom is likely? How can divergence be managed?
  • What are the future risks and opportunities to innovative land practices, such as managed rewilding? What role can rewilding play in conservation and restoration of habitats and wildlife? What evidence is there to support the incentivising of such schemes in any new land management policies?

There is a form for submissions (available on the website) and the deadline is Friday 9th September 2016.

I’ll be submitting a response via the Northamptonshire Local Nature Partnership, and welcome comments and ideas from any readers.

5 Comments

Filed under Biodiversity, Northants LNP, Rewilding

Emerging threats to the Białowieża Forest, one of Europe’s last remaining wilderness areas

From various news sources and personal contacts I’m hearing about some emerging threats to the Białowieża Forest, which at 216,200 ha (2,162 km2 or 835 square miles) is one of Europe’s largest and most ancient forested wilderness areas, and one of the few places where you’ll still see European bison (Bison bonasus)roaming free.

Despite its designation as a World Heritage Site, in recent months the Polish government has revealed plans to increase the amount of logging in the forest, ostensibly as a tree disease control measure.  However Polish scientists dispute this and claim that the real motivation is commercial – see the commentary and letters in this week’s Nature.  Here’s a quote from that article which provides some context to the concerns:

“[the] Białowieża management plan limits logging in the forest to 48,000 cubic metres of wood per year — enough to allow locals to gather firewood. But on 10 November, the local forest administration proposed an amendment that would allow large-scale logging in sections outside the central 17% of the forest that is a national park. They cited an outbreak of the bark beetle pest (Ips typographus) in Białowieża’s Norway spruce (Picea abies). In one forest district where logging is currently limited to 6,000 cubic metres per year, the allowable yearly volume would increase to 53,000 cubic metres”.

 

Interestingly, both Ips typographus and Picea abies are native to these forests and any large-scale outbreak would probably constitute a disturbance that is part of the natural dynamics of the forest. A recent piece on the National Geographic site by conservation biologist Stuart Pimm is worth quoting from in this regard:

“To…scientists studying biodiversity, the main value of the Białowieża Forest is accumulated in a massive occurrence of large and old trees, high amounts of dead-wood and natural dynamics of forest stands all being very unique to this area and supporting thousands of different specialised species ranging from birds and mammals using cavities or building nests in the canopy to lichens, fungi and microbes dependent on different stages of tree life and its decomposition.  It is not surprising that Białowieża Forest has been an invaluable reference area for scientists studying natural characteristics of European forests.” [my emphasis]

 

This is not the first time that concerns have been raised about the Białowieża Forest – here’s an article from the Guardian newspaper from 2011:  http://www.theguardian.com/world/2011/apr/06/poland-environmentalists-foresters-primeval-forest

Is it too much to hope that the Polish government takes notice and strengthens, not weakens, the protection of its natural heritage?  And allows natural processes to determine what happens in this woodland, rather than trying to manage every aspect of its ecology.

Leave a comment

Filed under Biodiversity, Biodiversity and culture, Mammals, Rewilding

Rewilding reconsidered: academic disagreements, big science, and beavers.

P1110320Rewilding has been the topic of a couple of blog posts over the last few years  (for example here, in relation to the George Monbiot-narrated video about the wolves of Yellowstone Park; and also here, about the notion that perhaps we should also think about rewilding the human digestive ecosystem).

Since then there’s been a lot of activity with respect to rewilding, some of it practical and adding to the evidence base, some of it conceptual and controversial.  So I thought I’d do a quick round up of rewilding-related items I’d seen recently: feel free to suggest others.

In an open-access paper in Current Biology, entitled “Rewilding is the new Pandora’s box in conservation” David Nogués-Bravo and colleagues ask “what exactly is rewilding, and is it based on sound ecological understanding?”  Their conclusion is that “there is a worrying lack of consensus about what rewilding is and what it isn’t” and that “scientific support for the main ecological assumptions behind rewilding, such as top-down control of ecosystems, is limited”.  They go on to discuss the potential dangers of (re)introducing species into existing ecosystems, including both ecological and economic concerns.

Meanwhile Jens-Christian Svenning and colleagues have an open access paper in Proceedings of the National Academy of the USA about “Science for a wilder Anthropocene: Synthesis and future directions for trophic rewilding research” which takes a much more positive view of the potential benefits of rewilding, though still urges caution and further research, pointing out that “empirical research on trophic rewilding is still rare, fragmented, and geographically biased, with the literature dominated by essays and opinion pieces.”  Science writer John Carey provides some useful wider context to this discussion in a companion piece.

Subsequently Dustin and Daniel Rubenstein critiqued the Svenning et al. paper with an opinion piece called “From Pleistocene to trophic rewilding: A wolf in sheep’s clothing“, to which Svenning and colleagues replied: “Time to move on from ideological debates on rewilding“.

Svenning et al.‘s request for more empirical data on the effects of rewilding has been heeded this month by a study in Freshwater Biology from Alan Law and colleagues on “Habitat engineering by beaver benefits aquatic biodiversity and ecosystem processes in agricultural streams“.  Focusing on the recent reintroduction of beaver to Scotland, these researchers documented positive effects of the beaver on removal of inorganic nutrients from streams, and overall freshwater invertebrate diversity.

I find it really exciting that so much interesting debate and data are now being generated on the topic of rewilding: it’s fascinating and important science with a clear practical component that could leave the planet richer and in better condition for future generations.  It certainly deserves to be better funded, perhaps taking a slice of the “big science” pie from physics and astronomy, an argument that has been raised several times by Charley Krebs on his Ecological Rants blog.

As a researcher I don’t have a horse in this race (or even a Konick pony, such as are being used in a small-scale rewilding project at Wicken Fen). However I do wonder what a “rewilded” landscape would look like for pollinators in Britain, given that most of their diversity and abundance is associated with open grassland and heathland habitats, which were rare in these islands prior to human deforestation.  Having said that, a greater density of large mammalian herbivores can certainly open up woodland – see Bakker et al.‘s paper on “Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation“.

As a teacher these discussions provide a lot of scope for interesting class exercises and seminars on the topic, which I’ll certainly be developing more next year.  Expect this to be an ongoing topic on the blog.

 

 

4 Comments

Filed under Biodiversity, Ecosystem services, Rewilding