Traditionally there were two ways to map vegetation – ground surveys and aerial surveys. In the 19th century people like Charles Flauhert at Montpellier began mapping and classifying vegetation. People like Robert Smith brought this work back to Britain; after his death, his brother William Gardner Smith continued his work. W.G. Smith was one of the organising members of the British Vegetation Committee (together with Arthur Tansley and others), which later gave rise to the British Ecological Society. They used field surveys to map different vegetation types, and standardised sampling procedures to characterise the different forms of vegetation. In America, E. Lucy Braun, Edgar Transeau and William S. Cooper played a similar pioneering role in vegetation mapping.

The availability of aerial surveys, starting in the 1920s and 30s, added another dimension to vegetation surveys. Now, it was possible to collect data over a large area, but the quality of the data was low – you could probably distinguish forest from grassland, farmland from urban. As aerial photography developed it was possible to extract more information about vegetation – coniferous forest from deciduous forest, open forest from closed forest, even distinguish younger successional forest by the roughness of the canopy (younger forests tend to be dominated by even-aged stands of the same species, so the canopy is made up of relatively similar trees. Older forests are more uneven in age and species composition, leading to a canopy that varied more in height and colour.) Things began to take off as additional sensors, many of them space-based, became available. By measuring additional wavelengths, outside the visible spectrum, and by actually collecting quantitative data about the absolute reflectivity in each band, it was possible to develop much more structured data from remotely sensed data. Some of these sensors can estimate the amount of chlorophyll in vegetation, while others can measure vegetation structure.

In the March 2013 issue of Biotropica, Sebastián Martinuzzi, William Gould and others used LIDAR data to classify dry forest¹ in Guánica, Puerto Rico, into “forest type” (semi-deciduous forest, semi-evergreen forest, scrub forest, dwarf forest and mesquite forest, a “relatively homogeneous stand of Prosopis pallida with a dense herbaceous understory”) and beyond that, into successional stage: mid-secondary forest with a logging² past, late secondary forest with a logging past, late-secondary forest with an agricultural past, and ‘primary’ forest (undisturbed for more than 90 years). This part of their analysis they restricted to semi-deciduous forest areas. Since LIDAR penetrates the forest canopy, it can identity the underlying land surface (and thus, elevation and topography), and the height not only of the forest canopy, but also of various layers in the canopy.

It’s hard to explain how appealing the idea of being able to map and age these forests using remote sensing can be. I’ve mapped forest cover using aerial photographs – first you map current forest cover, then you map historical forest cover, and use that to estimate areas of “older growth” forest. Not only is it tedious, there’s also a risk of ending up with subjective results. If an area was cut-over and regrew in the interval between two images, you may never noticed it. And if an area lost all its understorey without losing its canopy, you’d probably be unaware.

While avoiding subjectivity in that regard, this approach added a different sort of subjectivity.

We used GPS surveys and visual interpretation of 1-m spatial resolution color aerial photos supported by expert knowledge, for a total of 83 sample locations. All samples represented an area of at least 30 m by 30 m of the same forest type (to coincide with the geospatial grain size used by this study), and were separated by >60 m (consistent with Agosto Diaz 2008).

As far as I know, the definitions of the different forest types in Guánica Forest are subjective. They are somewhat self-evident, as long as you stay in the park (and avoid certain grey areas), but I’m not aware of any formal delineations of these vegetation types. Granted, there’s nothing unique about that, but having poked around in Guánica Forest, uncertain (at times) whether I was in one forest type or another…I’m a tad bothered.

Perhaps the thing that interested me most was this

The most important predictors in the LiDAR canopy model included the median absolute deviation of vegetation heights (HMAD), the 90th percentile of vegetation heights (H90th), and the percent of returns >1.0 m (CDENSITY2; Table 3).

Canopy closure is a useful, but incomplete predictor of forest type. The most closed canopies tend to be in ravines and arroyos (semi-evergreen forest), but certain young secondary forests could also have a closed canopy (like the Prosopis forest they mentioned). But when you combine that with with the variation in vegetation height, you can probably separate out the species-poor secondary forests dominated by Prosopis or Leucaena leucocephala, since these forests lack structural diversity – most of the trees are the same age and belong to just a single species. This has me wondering…

1. Martinuzzi, Sebastián, William A. Gould, Lee A. Vierling, Andrew T. Hudak, Ross F. Nelson, and Jeffrey S. Evans. 2013. Quantifying Tropical Dry Forest Type and Succession: Substantial Improvement with LiDAR. Biotropica 45(2): 135-146
2.  Logging in this case means harvest for fence posts and charcoal production; this process left the rootstocks intact and allowed rapid coppice regeneration.
3. Lugo, Ariel E., Jose A. Gonzalez-Liboy, Barbara Cintron, and Ken Dugger . 1978. Structure, productivity, and transpiration of a subtropical dry forest in Puerto Rico. Biotropica, 10: 278–291.

What ecology blogs am I missing?

In a general sense, time sensitive science writing tends to focus on the latest discoveries, or failing that, the latest issue of one journal or another. This sort of stuff can be fun to write about – exciting new finds, or just stuff that’s cool because of its newness. But you can also do the same sort of writing on something dredged out of the older literature. The value of immediacy can be tempered by the fact that it’s impossible to assess impact within a few days of publication. If you’re writing for the general public, it can also be difficult to balance the need to explain the background with the need to tell the current story. Too much background and the ‘story’ gets lost. Too little, and the reader gets lost.

The other type of writing is more about narrative. You can write about basic concepts. Lots of background for the general reader, plenty of opportunity to actually convey some real information…but apart from questions of tone (who’s really my audience?) there’s the problem of trying to stay on track. At some point you either have to assume a certain amount of background knowledge…or you’ll end up writing Wikipedia, all over again.

Back in the dark ages (2007) Dave Munger and Sister Edith Bogue launched BPR3 (Bloggers for Peer-Reviewed Research Reporting; sadly the original website is lost to link-rot) which later grew into researchblogging.org (which is still chugging along, by the look of things). More recently, Dave launched ScienceSeeker, which seems to have similar, but more all-encompassing goals. I loved the idea of clearly marking (and aggregating) posts about peer-reviewed research, but it doesn’t deal with the problem of recentism. Writing at BioDiverse Perspectives, Fletcher Halliday took a look at what gets blogged about when it comes to papers about biodiversity. Unsurprisingly, it’s not the classic papers, it’s not the papers that have attracted hundreds of citations. Rather, it’s the new stuff. Scientists like writing about what’s new and novel. And why plumb the depths of decades-old literature when there’s more new stuff coming out than anyone can keep track of?

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My first serious attempt at science blogging came about a year later, when Bill Dembski came to campus peddling intelligent design. This time everything was different – I had already started to blog (although mostly about politics and religion) and I was in the process of getting to know the science blogging community. Over the next several months my blogging output grew, peaking in February of 2008. By July 2008 it was mostly over. Blogging had gone from fun to work. Since then, from time to time I have tried to re-launch my blog(s), but with limited success. At some point, blogging stopped being easy.

The idea behind blogging was ‘easy’ writing. The medium is immediacy, the ability to post whatever you’re thinking. But the more I wrote, the more I thought about what I wrote.

Short posts have their value, but they quickly get old. Short posts don’t really stand alone. You can build a narrative of short posts (some people have done really well with that on Twitter) but it leaves very little room for nuance, for background, for explanation. But the longer your posts get, the more you realise the value of editing…not copy-editing, that’s something you can fix later (or, if you’re careful, while you write). No, what’s difficult about long posts is that they require a plan. You need some vision of how you’re going to write them without getting lost, without repeating yourself, without losing sight of your point entirely. And writing turns into work. A post that you might otherwise have thrown up in 10 or 15 minutes now takes hours or, worse yet, after days of editing simply sinks into the growing pile of drafts. And other priorities, like work, take over…

[More later]

This isn’t the first time I’ve given thought to this issue. In the opening chapter of my dissertation I wrote:

The viability of small populations can also be affected by the loss of genetic diversity. Most tropical trees are outbreeders with complex incompatibility systems (Bawa 1974, Zapata and Arroyo 1978, Bawa et al. 1985, Bawa 1990). Since they are less prone to inbreeding in natural conditions, outbreeders are likely to carry a moderately high genetic load of slightly deleterious alleles (Lande 1995). Minimum viable population sizes for tropical forest trees needed to ensure long-term survival have been estimated at effective populations sizes (N_e) of about 5000 (Alvarez-Buylla et al. 1996).

Although the literature was far from cutting edge even when I wrote it (and more than a little long-of-tooth today), I think the basic point is applicable to the fragmentation question – inbreeders should be expected to purge genetic load, outbreeders more likely to tolerate moderate genetic load. So inbreeders and outbreeders are likely to experience fragmentation differently. (There’s are important caveats here, of course: plants may not respond to fragmentation the same way that animals do; tropical plants may differ from extra-tropical plants; trees will probably not react in the same way that shorter-lived species would.)

Thinking about this point reminded me of something other than Preston Aldrich’s work – Gemma White worked on gene flow in fragmented populations of Swietenia humilis, a species of mahogany restricted to the Pacific coast of Mexico. White and colleagues found that increased gene flow between populations in a fragmented landscape counteracted the effects of fragmentation (in this one species in this one context). The problem with this is that Aldrich and Hamrick’s paper was published in 1998, while White et al. is a 2001 vintage. So what has happened since?

This is where Google Scholar becomes both a boon and a trap. Not only does it make it much easier to find literature, it also makes it easy to find who has cited the papers that interest you. Granted, Web of Knowledge does the same thing, but Google Scholar is quicker and has a more intelligent search engine (as you’d expect from Google). White’s PNAS paper, it turns out, has been cited about 226 times, far too often for casual curiosity. And searching those 226 papers can itself be difficult – the top hits may not be the ones that cite White et al. for precisely the reasons you’re interested. At the same time, it does make an exercise in casual curiosity, like this one, feasible.

So what does the literature say? Not surprisingly (given the question posed), it says “we’re not sure”. Caesalpinia echinata in fragmented Brazilian Atlantic Rainforest fragments showed substantial genetic structure in forest fragments – populations in different fragments have become different, presumably due to reduced gene flow. On the other hand, the Australian rainforest tree Elaeocarpus grandis, showed reduced diversity and increased inbreeding in fragmented landscapes, but no increase in genetic structure. But Andrea Kramer and colleagues found that although “theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce”, and suggested that ecological degradation, rather than genetic degradation, might be a far more important cause for concern.

These are just a few random excerpt from the literature, but it makes me think that I might been on the right track when I wrote:

However, the studies that led to these conclusions were not done on insular populations. Species native to the Greater and Lesser Antilles should be adapted to much smaller populations than are mainland populations; historically small populations are likely to be more inbred and, as a consequence of this, to carry lower genetic loads (Alvarez-Buylla et al. 1996). This makes them less susceptible to inbreeding depression (reduced viability, seed production and growth rates caused by the segregation of partially recessive lethal alleles).

There’s still a long way to go, but I suspect that a lot of insight from naturally fragmented systems, especially areas like the Caribbean (and obviously, some people have done just that).

The authors grouped the questions into six group which were, more or less, what you’d expect them to be: evolution and ecology, populations, diseases and microorganisms, communities and diversity, ecosystems and functioning, and humans impacts and global change. One thing I found notable was how things I would consider to be within my area of interest, were scattered up and down the list. It probably says something both about ecology itself (its subfields are notoriously poorly demarcated), but it probably also explains why I sometimes find the term “plant community ecologist” to be an ill-fitting label. Communities are, after all, made up of populations nested within species which are nested within landscapes and ecosystems, shaped by evolution and biogeography, and structured by human disturbance (both at the local and global level). So…Puerto Rican dry forests, you say…

1. What are the evolutionary consequences of species becoming less connected through fragmentation or more connected through globalization?

Listed under “evolution and ecology”, this encapsulated the nature of ecological questions nicely. If a formerly continuous population is fragmented, you’d generally expect a reduction in gene flow between populations. The consequences of reduced gene flow cover a wide spectrum from extinction due to inbreeding depression to speciation. If you had just read a conservation biology textbook you’d probably come away with the former answer. If you had read an evolution text, you’d be more likely to come up with the latter. Still, given the simplified way in which we teach ecology and evolutionary biology, you’d probably think that this wouldn’t be the kind of problem that would called a “fundamental question”.

Reality is always more complicated than we like to imagine. To begin with, the population genetic impact of fragmentation differs between species. Is the species unisexual or bisexual, and if it is the latter, is it an obligate (or even predominant) outcrosser? I always remember Preston Aldrich’s work on Symphonia globulifera in Costa Rica. Dan Janzen characterised individual trees in pasture as “the living dead” – although adults could survive in pasture, there was almost no recruitment. Although the tree might still have many decades of life ahead of it, the odds of it passing its genes on to future generations was almost nil. Aldrich and Hamrick showed that, in fact, a single individual growing in the middle of a pasture was, in fact, supplying most of the pollen to trees in surrounding forest fragments. Despite growing in a habitat that was inhospitable for seedlings, it had a disproportionate impact on the next generation. This was probably tied to the fact that the tree in the pasture experienced less competition and had greater access to light. This gave it more resources to dedicate to flower production and allowed it to dominate pollen flow locally. This doesn’t mean that living in a pasture amidst forest fragments is good for a species – rather, it means that these things can be difficult to predict. The harder it is to predict something, the longer it’s likely to linger on a list of fundamental (and unanswered) questions in ecology.

Difficult, of course, does not mean intractable. Nor must a rule be perfect. If “in general” is known, and we understand something of the nature of the deviations from it, we’d still have made great substantial progress.

The same cannot be said about the history of ecology. It seems like everywhere I turn I come across a new and important figure that I’ve never heard of before. Today on Wikipedia, for example, I encountered Frank Edwin Egler. A student of William S. Cooper, he went on to play a role in Rachel Carson’s Silent Spring. And his property in Connecticut now forms a protected area, Aton Forest.

There’s also this bit in the article that intrigues me. Like too much in Wikipedia, it’s written by someone who failed to include much back-story or context:

A consequence was that a passage in Silent Spring having some of Egler’s sarcasm received the most criticism from Ian Baldwin in his famously negative review in Science ([13]). Egler rose to defend Carson’s (and his) views in a series of publications that led to his censure by the Entomological Society of America—and censure of a journal that published his views. That incident helped both to focus and to polarize the issues of professionalism and environmentalism in the science of ecology ([14]; [15]).

Like much of the article, this passage refers back to the Aton Forest website, which contains a long biography of Egler. But without reading it, much of the article is obscure. (Ian Baldwin’s famously negative review? I’m familiar with neither Baldwin – the source calls him “an agricultural scientist at the University of Wisconsin” – nor his review. And Wikipedia contains neither a biography of Baldwin nor mention of his review in its Silent Spring article.)

The average biology class starts with cells and molecules, go on to tissues and organs, moving finally onto organisms and ecology. Small to large, the way it’s always been…except, of course, that molecular biology is a product of the second half of the twentieth century. Still, it makes sense to start with the basic building blocks and work upward into more complex structures, right? Or is it just climbing the tree of life, from simple to complex? So maybe it’s an older idea? It probably wouldn’t be a difficult question to answer, but not tonight.

And what about educational theory? What about learning theory? How does that fit in? Is this constructivist? Are students going to construct their ideas of complexity from simple structures? My experience teaching undergrads doesn’t exactly make me hopeful in this regard. Students don’t learn to scale from cells to landscapes – very few people ever learn to see the world that way. Instead, they tend to compartmentalise knowledge.

When I was an undergrad in botany we went the other way – we started with diversity, worked our way up the plant kingdom, before moving on to anatomy and physiology, and then finally to ecology. If I had to guess, that was probably the way introductory botany had been taught for much of the twentieth century. Still, it had the benefit of working from something more or less familiar – the organism – and moving to less familiar things. Unfortunately, since we worked our way up the plant kingdom, starting, I suspect, in the weird and wonderful world of algal life cycles, it probably wasn’t really a matter of working from “knowns”.

This gets me to my current thought: how do I design my course for next semester? In Creating Significant Learning Experiences, Dee Fink lays out a system for course design (that I need to revisit), working backward from your learning goals to your classroom activities. While very useful, this doesn’t tell me the best way to present things so that students build connections between the material – and it doesn’t tell me how to do that in the specific context of introductory biology or environmental science.

So where to you start? Students know a little bit about the world, about biomes. So should that be the starting place? In the principle of moving from knowns to unknowns, do you start big and move small? Or do you start small and move big? And does any of this even matter in an environmental science class wherein you have to teach your students about the natural world, teach them ecology, population growth, minerals and mining, pollution and waste management, energy, climate change, ethics, environmental justice, sustainability science…The volume of material you need to master in a class like that, the amount of basic knowledge you need in order to have an educated conversation – is vast. So how do you present it?

I’m really interested to see how he develops this model, but my initial reaction is very positive. While it may not possess the simplicity and tractability of Hubbell’s neutral model, it identifies from the very start what’s missing from so much in community ecology: a role for species as something more than interchangeable placeholders.