Making sense of canopies

Béatrice Wedeux and David Coomes published a paper in Biogeosciences analysing how environmental factors and selective logging interact to shape the canopies of tropical forests. Using airborne laser scanning technology across a 750 km2peat swamp forest landscape in Borneo, the study reveals strong shifts in canopy height and gap patterns along environmental gradients linked to changing peat depth. In areas where logging roads were detected on historical satellite imagery, the canopy is lowered and has larger gaps, especially so on deep peat where tree growth is thought to be limited by low nutrient availability and waterlogging. The study identifies a close link between the height and the gap structure of tropical peat swamp forests at the landscape scale and reinforces the vulnerability of this ecosystem to human disturbance. The degradation of tropical peat swamps has been at the heart of climate negotiations in Paris, as emissions from fires in Indonesian peatlands over the last couple of months – exacerbated by a dry El Niño spell – approach the total annual emissions of Brazil (1.62 billion metric tons;


Airborne laser scanning allows the detection of openings at different height cross-sections of the canopies of old-growth and selectively logged forests.

Read online: Wedeux, BMM and Coomes DA (2015) Landscape-scale changes in forest canopy structure across a partially logged tropical peat swamp, BIOGEOSCIENCES 12(22):6707–6719, DOI: 10.5194/bg-12-6707-2015.

Summer of field work

Joanna Wolstenholme, a third year NatSci undergraduate, has just wrapped up seven weeks helping our field campaign in Canada.  She authored this entry, describing her experience.

Sudbury, on first inspection, is a rather spread-out mining town, inhabited by many trucks (most of them blue).  However the more you explore, the more remarkable the town becomes.  It is one of the few areas of the world where remediation has really worked, and the next generation will inherit a greener and cleaner city than the one that their parents inherited.  This remarkable change, from a barren ‘moonscape’ caused by years of acid rain (Sudbury was once the world’s largest point source of sulphur dioxide emissions, thanks to large-scale nickel and copper mining), to an area with burgeoning forest cover and recovering lakes, is a great success story that the area can be immensely proud of.

With this backstory, Sudbury, with its 330+ lakes, makes an ideal experimental location for a group dealing in ecosystems and global change. Our study lake, Daisy Lake, is perfectly set up for studying the effects of terrestrial influences on aquatic ecosystems.  Along its length, the shores and wetlands have recovered to various degrees. One catchment has even been limed – covered with calcium carbonate to neutralise the acidic soils, and so plant growth is relatively lush. Other areas, closer to the smelter at the north end of the lake, are far more barren; bare, stained rock predominates, with a few stunted trees.

One of the streams we study

One of the streams we study

In Daisy, we were studying eight stream deltas, each with very different personalities.  At each site Erik and I measured algae, sediment, and water. This all sounds very easy in theory, but in practice (as with any fieldwork, as I came to learn) things were far harder and more complicated… and often involved some rather novel solutions. If nothing else, this placement has certainly given me plenty of opportunities to stretch my problem solving skills!

My first job was to build algae-collectors, which were plastic tubes with cut up swim floats attached from which 6 microscope-slides dangled from fluorescent string. These floated on the surface, but we also sank clay pot holders as another surface for algae to grow on. We left these in the lake (on a beautiful sunny day) at each of the deltas and then returned to collect them 3 weeks later.  On a more high-tech note, we also made use of two chlorophyll fluorometers to characterise the algal species found in the water column and benthic layer. After several dry runs measuring the amount of algae on Erik’s office floor, we took them out to the lake, and used them at each of the deltas. The unseasonal amount of rain that Sudbury was experiencing, however, complicated things, and meant that in some sites Erik had to swim with the fluorometers, as we couldn’t reach the sediment from the boat.

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As well as working on Daisy with Erik, I also helped Andrew collect additional data for his survey of terrestrial resource use by aquatic organisms. This meant going out to six other lakes around Sudbury, and six down in the Muskokas, to collect water samples, use fluorometers, and deploy and collect the microscope slide contraptions. Key to the project was collecting clean leaf and algal samples, to go off for stable isotope analysis, to allow Andrew to calculate the influence of the terrestrial systems on the lake ecosystems.

In order to grow clean algal samples without the influence of terrestrial DOM, we collected water from each of the lakes, then filtered it into jars and re-inoculated each jar with a small amount of unfiltered lake water, from which we hoped the algae would regrow. This seemed simple in theory, but involved hours of standing by a vacuum pump watching water drip through a filter. One night, we actually filtered water outside a hotel, so as not to set the fire alarms off! Safe to say we got many odd looks. However, the field trip down to the Muskokas was one of the best perks of the summer. We went down in September, almost at the peak of the colours changing, and had two lovely dry but crisp days. Driving down dirt tracks through beautiful forest, to find beautiful lakes to paddle out into was great fun, and a real adventure! It definitely offset the tedium of filtering.

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The 'Hollywood sign' of Sudbury

The ‘Hollywood sign’ of Sudbury

At the end of my seven weeks here I am very sad to be leaving. It was a great experience, with plenty of messing about on boats, exploring new places, and making new friends. I have learnt a lot about the complications of fieldwork, how to solve problems on the fly with limited supplies, and just what really goes on behind those simple sounding ‘Materials and Methods’.


This article is also published on PLANeT.  Joanna’s trip was supported by funding from the Department of Plant Sciences and NERC.

More ways of living on a bush than on a bluebell

Some years ago, a fascinating article in the National Geographic described the exceptional diversity of bat species to be found in Barro Colorado Island, Panama – incidentally where Ed Tanner is currently with some of his PhD students. Research by the Smithsonian Tropical Research Institute and others had described 74 species, which managed to coexist by carving out distinct, often ingenious, niches. Some bats are physically adapted to hunt in open spaces, others in gaps and along edges, still others in the fine interstitial spaces of lower understorey layers. It is a dramatic example of how habitat structural complexity is related to, and helps promote, species richness.

We explore this relationship between habitat structure and species richness, and its relevance, in an article recently published in Methods in Ecology and Evolution. Building on an earlier review (Tews et al 2004, J. Biogeog 31:79-92) through an analysis of 199 papers published 2004-2013, we find that a positive relationship between habitat complexity or heterogeneity and animal species richness or diversity is found in over 75% of investigated cases, across different taxonomic groups and ecosystem types. It seems that Lawton (1978) was right when he observed: “There are more ways of living on a bush than on a bluebell”. Given this common pattern, and building on Coomes Group’s developing experience of using airborne lidar to study forests, we argue that this powerful vertical-profiling tool could be used to deliver habitat structural indicators of species richness over large spatial extents. More spatially and temporally precise information on species richness and habitat quality is increasingly important in responding to the unceasing loss of biodiversity across the planet, so we hope the article might contribute to developing new tools to meet this challenge.


Fish are a forest product

Our latest paper has just been made freely available in Nature Communications, showing that freshwater fish, an important source of nutrition for humans, are in part produced by forests.  The study focuses on small boreal lakes, which contain upwards of 60% of the world’s freshwater. It suggests that any reductions in forest cover in the boreal ecoregion, such as from industrial activities, will threaten the production of healthy fish populations.

Forest stream at Daisy Lake

Forest stream at Daisy Lake

Small streams that drain forest floors bring microscopic particles of vegetation and soil into water. These get broken down by bacteria, which are then eaten by small invertebrate animals that are main food source for small fish. The research uses a gradient of forest cover in Canada to show that more of this forest organic matter is brought into lakes as the surrounding landscape is vegetated. This produces more bacteria in the near-shore water, which can support more zooplankton, and thus provide more food to small fish. Young fish survive winters and escape predators better if they are larger, so these effects are predicted to carry forward into larger and older animals.

Trapping zooplankton

Trapping zooplankton

The research also uses natural variation in the molecular mass of primary production from land versus water to estimate the proportional of terrestrial resources used by fish. At least 34% of fish biomass was supported by terrestrial vegetation, increasing to 66% with greater forest cover. This suggests that fish increasingly use forest food subsidies as they become available in the small nutrient poor lakes that are characteristic of the boreal ecoregion.

You can read more about the work at the BBC, Planet Earth,, Al Jazeera America,  or even watch a video at the Weather Network.  It is great to see the work receive this type of reception!  It took over 2 years of my life to produce in collaboration with a number of colleagues mainly at Laurentian University’s Living with Lakes Centre.

Spring ephemerals in ancient woods

We had the opportunity over the Easter weekend to visit Hayley Wood, an ancient woodland located outside of Cambridge that pre-dates medieval times.  Presently, the Wood is managed under traditional coppice by standards, with large oaks that are estimated to be ca. 300 years old.  Professor Oliver Rackham’s work on the British countryside has been heavily influenced by Hayley, and in turn, he has been instrumental in its conservation.

Hayley Wood is particularly important, however, for its sizeable population of oxslips (Primula elatior).  During spring, the oxslips burst to life along with much of the other ground flora to produce a spectacular display of colour.  Carpets of bluebells (Hyacinthoides non-scripta) line the various woodland rides and we even managed to count 20+ orchids interspersed throughout one section of the Wood.  These seemed to fit the description of the early purple orchid (Orchis mascula), especially the spotted foliage, but do comment if you know what it is!

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Having spent many years in the Carolinian forest, even doing research there on spring ephemerals such as the showy white trillium (Trillium grandiflorum), I don’t ever feel homesick in British woodlands.  There’s always something to see in the Spring, with among the most beautiful floral displays anywhere in the world.

Measuring forest recovery at Orokonui Ecosanctuary

This is part 2 of a 3-part series highlighting our work testing the effectiveness of fenced sanctuaries for biodiversity conservation.  You can read part 1 here.

It has taken longer than I wanted, but I’ve now found some time to revisit our work at Orokonui from earlier this year.  We were re-measuring permanent vegetation monitoring plots as part of a one-year project, primarily supported by a British Ecological Society Research Grant.  As mentioned previously, our aim has been to test whether eco-sanctuaries restore habitat for threatened fauna.

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Harnessing the Tree of Life for conservation

I spent Monday in London at The Royal Society for a discussion meeting on Phylogeny, extinction risks and conservation.  As someone who is increasingly using comparative phylogenetic tools to ask how evolutionary history might influence conservation decisions, I took away at least three points (several more rattling in my mind at present):

(1) Measures of phylogenetic diversity are increasingly being used to inform conservation decisions (or at least that was the perception I got).

Perhaps the most notable way this is being done is through the EDGE (evolutionarily distinct globally endangered) programme.  EDGE classifies species based on the product of their IUCN Red List category and their evolutionary distinctiveness (ED).  ED is itself calculated by dividing the lengths of each branch in a phylogenetic tree by the number of species that subtend that branch.  These values are then summed for all the branches from which a species is descended.

(2) Risk of extinction is fairly clustered within evolutionary lineages – and this can lead to rather large losses in phylogenetic diversity (PD).  Losing PD may reduce ecosystem function and limit the range of biodiversity features that can respond to future change – if in fact there is an association between PD and function – though this is debatable.

This of course also assumes that closely-related species are more likely to go extinct because they share similar traits that make them more vulnerable to threats.  Large mammals are an excellent example of such a group.  But this might not be true for plants, particularly in areas with rapid diversification where species most classified as threatened are the recently-evolved ones that cluster within short branches at the tips of phylogenies.

(3)  Systematists are developing great new tools for assembling dated phylogenetic trees.

We heard about two specific resources.  The first was TimeTree, which is essentially a curated database collating all published estimates of divergence times among organisms.  By visiting the website, you can instantly search for a divergence time between any two species and find all published estimates, allowing you to not only get a date but also a statistical distribution for that estimate.  Unfortunately this means that its only as good as the primary literature and the curators’ ability to keep up with it.  I tried it quickly for two of our NZ alpine species (Ourisia macrocarpa and Veronica odora) but was told that “No molecular data available for this query”, which was surprising considering they do exist.

The second resource we heard about was the Open Tree of Life.  As the name says, it’s essentially trying to assemble a giant “tree of life” that will be continuously updated by the scientific community.  This is a really nice complement to TimeTree because rather than focusing on branch lengths, it’s just concerned with synthesizing tree topologies.  You can begin to explore the tree here.

Red listing plants

Today’s group meeting focused on the IUCN Red List.  The red list has generated many high-profile publications in recent years, but plants have typically been under-represented in the assessment process.  Partly, this has been due to debate around the validity of transferring the assessment approach used for animals to plants.  That sounds like it’s now changing.

We heard about a new initiative focused on assessing the threat status, and informing the conservation, of plants important to people.  These include wild relatives of crops, timber trees, medicinal plants, and palms.  As many of these assessments will also include detailed range maps, it now seems like there a number of interesting analyses that could be done mapping how plants are moving with people and which “traits” pre-dispose species towards better protection.  For example, one could classify different groups of medicinal plants, maybe like in this recent PNAS paper, and test whether threat status differs among groups.  One could imagine that some groups of plants would be better conserved because they’re deemed more “valuable”.  Or, more threatened because of the very fact that they’re valuable.  My old friend Panax quinquefolius is a good example of this!