Category Archives: Botany

‘Ferns have not bowed to the ages’

When I started my undergrad, botany was something of an afterthought – I just needed a third course to go along with chemistry and zoology, which had been my mainstays in A Levels. But once I sat down in Dr Duncan’s class, I was enthralled – while chemistry and zoology largely rehashed what I had learned in A Levels, botany took me into an entirely new world. As we partook in an old-fashioned march across the plant kingdom, I was amazed. Lectures were interesting, but it was the labs that truly drew me in.

By the time we got to ferns, we had covered a variety of algae and simpler plants. Much of what I was taught slipped past me, adrift without a proper foundation. The difference between isotomous and dichotomous branching in the thallus. Steles, and steles within steles. But one thing that stuck with me was a quote from Frederick Orphen Bower: ferns, he said, had not bowed to the ages. While other ancient groups like the liverworts and horsetails had retained only a shadow of their former diversity, ferns were not only diverse, much of their diversity reflected a (relatively) recent diversification that had occurred ‘in the shadow of angiosperms‘.

The simple fact that ferns diversified after the rise of the group that is generally seen as replacing and displacing them is in itself remarkable. It clashes, not with evolutionary theory, but rather, with our (mistaken) perception of an orderly progression of evolution. If we can put aside our evolutionary misconceptions, it becomes less disconcerting. Or it did, until recently.

A recent paper by Fay-Wei Li and colleagues uncovers the mechanism by which ferns were able to diversify in the shadows: a gene from a hornwort. In is usual way, Ed Yong does an great job of explaining the research, as does Carl Zimmer. While the discovery is a great story, what really intrigues me is the mechanism of gene transfer. Horizontal gene transfer (i.e., transfer from one species to another) is no big deal in bacteria. Migration of genes from the mitochondrial and chromosome genome to the nuclear genome is strange, but it’s still the kind of thing for which you can envision a reasonable mechanism. Gene flow between species via introgression (hybridisation followed by extensive backcrossing to one parental species) is intuitive (or can be, if you don’t think about it too much). But transfer of a gene from a hornwort to a fern. How is that supposed to happen?

As odd as it sounds, I’m sure there’s a reasonable way for genes to make that journey. I’ve heard about people coaxing plants to take up RNA molecules. Viruses could also have unwittingly played a part. I suppose the most important message in this story may be the realisation that transgenic higher plants may not be as unusual as we tend to think they are.

Course design

Why are courses designed the way they are?

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?

Disturbance and recovery in tropical dry forests

[Repost from my old blog]
When people think about the destruction and degradation of tropical forests, they tend to focus on rainforests. Tropical dry forests tend to get overlooked. They aren’t as striking – no cathedral-like understorey, no mind-boggling biodiversity. But more importantly, they often just aren’t there. Over much of their potential range they have simply been erased from the landscape. They may have covered as much as 42% of the land area in the tropics1, but have been reduced to less than 27% of their former range in Mexico2, and as little as 2% in Central America3 and New Caledonia4.

Despite the fact this, tropical dry forests are often seen as being quite well-adapted to human disturbance. Being less species-rich than wetter forests, they tend to support fewer rare species, and may be less extinction-prone. In addition, dry forests are dominated by trees that sprout after being cut. This means that if you cut down a patch of dry forest, most of the stumps will re-sprout. This type of recovery is much quicker than you would get if the trees had to germinate from seeds – not only does it take much longer for seedlings to grow large (stump sprouts can draw on resources stored in the roots of the tree), but there’s likely to be a time lag as seeds disperse into the area from surviving trees (tropical forests tend to lack long-lived seedbanks).

Much of our understanding of succession in tropical dry forests comes from Jack Ewel’s dissertation work. Ewel looked at the effect of cutting and herbicide application on succession in a series of plots across the Neotropics. One of his important findings was the dry forests were quicker to recover their stature that wetter forests. Since most of the recovery comes from stump sprouts, the recovering forest is also close to the original forest in terms of species composition.

While lightly used dry forest sites recover rapidly, recovery is slower in more intensively used sites. Seedling survival rates are very low in dry forests – while seedlings establish in the wet season, most (often all) of them die in the subsequence dry season. So while intensively used sites in Guánica Forest recovered well in terms of structure, biomass and leaf fall in 50 years after abandonment, the recovery of species composition was very slow6.

Resilience is the rate of recovery of disturbed sites to their pre-disturbed state. Ewel’s work helped to establish the idea that dry forests are more resilient than wetter forests. But there is no single rate – or pathway – of recovery. Measures of “recovery” depend on the parameter measured – canopy height, biomass, species richness, nutrient cycling… It also depends on the baseline against which recovery is measured: if the same site is measured before and after disturbance, you need to know if the site represented “mature” forest before disturbance. If another site is used, you need to wonder if it is really representative of initial conditions in your experimental plot.

In an article7 published in the journal Biotropica, Edwin Lebrija-Trejos and coauthors looked at what it really means to say that tropical dry forests are more resilient than wetter forests. They looked at a sequence of 15 sites in Oaxaca, Mexico, which had been cultivated and then abandoned for 0-40 years, and compared them with nearby mature forest. All of the sites had been cultivated for a short period (1-2 years) and then abandoned without being converted to pasture8. They considered a variety of different ways to measure resilience – they looked at forest height, plant density, basal area (the area occupied by tree stems), crown cover, species richness, species density (number of species per 100 m2), Shannon evenness and Shannon diversity. Not surprisingly, they found that certain features (canopy height, plant density, crown cover) recovered rapidly (in less than 20 years) while others (including basal area and species richness) had not recovered after 40 years.

When compared their sites with other comparable studies, they found that their sites were among the quickest to recover canopy cover and height. On the other hand, they found that their sites were among the slowest to recover species diversity and average in terms of the recovery of species richness. Overall, in terms of the structural measures that Ewel focussed on, it’s reasonable to conclude that dry forests are more resilient that wetter forests. On the other hand, with regards to things like basal area and species richness, the assertion of resilience for dry forests isn’t well supported.

  1. Brown, S., and A. E. Lugo. 1982. The storage and production of organic matter in tropical forests and their role in the global carbon cycle. Biotropica 14:161-187.
  2. Trejo, I., and R. Dirzo. 2002. Floristic diversity of Mexican seasonally dry tropical forests. Biodiversity and Conservation 11:2063–2084
  3. Janzen, D. H. 1988. Tropical dry forests: The most endangered major ecosystem. In E. O. Wilson (Ed.). Biodiversity, pp. 130–137. National Academy Press, Washington, DC
  4. Gillespie, T. W., and T. Jaffré. 2003. Tropical dry forests in New Caledonia. Biodiversity and Conservation 12:1687–1697.
  5. Ewel, J. J. 1971. Experiments in arresting succession with cutting and herbicide in five tropical environments. Ph.D. University of North Carolina, Chapel Hill.
  6. Molina Colón, S., and A. E. Lugo. 2006. Recovery of a subtropical dry forest after abandonment of different land uses. Biotropica 38:354–364.
  7. Lebrija-Trejos, E., Bongers, F., Pérez-García, E.A., Meave, J.A. (2008). Successional Change and Resilience of a Very Dry Tropical Deciduous Forest Following Shifting Agriculture. Biotropica 40(4):422-431 DOI: 10.1111/j.1744-7429.2008.00398.x
  8. Conversion to pasture tends to slow recovery significantly; not only does the prolonged period eliminate almost all root stocks, it also establishes a grassy layer that makes it more difficult for tree seedlings to establish.