Monthly Archives: June 2012

Tree Physiology: Carbon allocation special issue

Tree Physiology cover for Carbon Allocation of Trees and Forests issueCarbon allocation, the process by which plants invest carbon into stored reserves and structures such as new leaves, stem tissue and roots, has implications for topics as varied as drought tolerance, carbon sequestration and crop yield. An upcoming special issue of Tree Physiology addresses the issue of carbon allocation in a series of articles ranging from very general reviews of modeling approaches to the very specific, such as a study of the transport of 13C through young loblolly pine trees over a 3-week period. While the specific studies each warrant discussion, three articles should be of interest to anyone involved in plant biology.

Carbon allocation represents a poorly understood process with a proliferation of modeling approaches. The article by Franklin et al. contends that this is because carbon allocation represents not a single process, but several interacting ones. This review focuses on guiding principles in carbon allocation models, placing them in the broader classes of empirical, allometric, functional balance, eco-evolutionary, and thermodynamic models. Guiding much of the article is a discussion of when more complicated models are required to answer questions of interest. For example, empirical allometry does not address the plastic responses to environmental changes that are critical to assessing the effects of climate change.

Likewise, within the category of eco-evolutionary models, some explicitly address competition, such as approaches of game-theoretic maximization (King 1993) and adaptive dynamics (Dybzinski et al. 2011), while others only focus on the optimal response of individuals according to a fitness proxy (Franklin et al. 2009). The authors discuss how an individual optimal response may incorporate one dimension of competition implicitly by choice of a fitness proxy, e.g. height as a proxy for light competition. Since competition has more than one dimension in many systems, as when plants compete for both light and nutrients, the case is made that this is often an insufficient representation of competition. In addition to providing an excellent guide for modelers interested in specific types of questions surrounding allocation, this article provides guidance for empiricists who wish to generate appropriate data to impact the development of these models.

Commenting on this review, Mäkelä (2012) classifies carbon allocation models as mechanistic (bottom-up), decision rule (top-down) and those that address system dynamics as a whole. Mäkelä makes an excellent point in noting that any top-down model must be regarded as eco-evolutionary, as trees can hardly be said to make decisions in any other manner. Reshuffling categories of models is not a mere exercise in pigeonholing, however; it highlights another set of challenges facing these models.

While the prospect of understanding long-term carbon allocation from mechanistic principles no doubt represents an attractive goal in this area of research, the complexity of these models due to the number of interacting processes makes them difficult to parameterize and best suited for short-term questions. On the other hand, whole system approaches such as adaptive dynamics may also suffer from excessive complexity arising from tracking the dynamics of a structured population with plastic responses. Decision rule based models represent a range of simplifying assumptions, but involve decisions on which traits to accept as adaptive and which are taken as constraints. In the end, both Mäkelä and Franklin et al. agree that the choice of model is dependent on the questions being asked and all models must be carefully tested against observations.

Guiding principles and modeling approaches aside, the review by Sala, Woodruff and Meinzer highlights recent research into the timing of carbon supply and demand in tree species. Of particular interest are studies that indicate stored carbohydrates are not simply ‘passive overflow reservoirs,’ but may be actively competing with growth for carbohydrates. These authors discuss why large trees may be dependent on the large safety margins provided by carbohydrate reserves to maintain hydraulic transport during droughts and how droughts may also impact the long distance transport of stored reserves. This means that the location and availability of reserves become an issue under water stress. Indeed, stored carbon may become sequestered in xylem by embolism events and become inaccessible altogether. This review highlights how commonly held assumptions, such as the passive nature of carbohydrate storage, are being revisited and why carbon allocation processes remain an area of active inquiry in tree physiology research.

Bryophytes and the evolution of early land plants (Review)

Bryophytes and the evolution of early land plants

Bryophytes and the evolution of early land plants

Land plants arose from a common ancestor at least 470 million years ago and presently encompass four major lineages: liverworts, mosses, hornworts and tracheophytes. By integrating paleontological, morphological, developmental, genetic and phylogenetic data, Ligrone et al. reconstruct the divergence of these lineages and the evolution of fundamental land plant characters. They conclude that the last common ancestor of land plants was probably a leafless axial gametophyte bearing simple unisporangiate sporophytes, and suggest that since fundamental land plant characters primarily evolved in the bryophyte grade, the key to a better understanding of the early evolution of land plants is in bryophytes.

Genetic control of germination in Orobanche

Genetic control of germination in Orobanche

Genetic control of germination in Orobanche

The tiny seeds of the obligate root parasitic plants of the Orobanchaceae do not germinate unless they detect chemical signals from a suitable host plant. After crossing the two closely related species Orobanche cernua and O. cumana, Plakhine et al. find hybrid families that do not need chemical stimulation for germination. This lethal trait appears only in F3 and further generations, indicating that the dependence on external chemical stimuli is genetically controlled in the seed perisperm, which is the only seed tissue of maternal origin. The results suggest that the stimulant receptors are located in the cells of the perisperm that are located beneath the micropyle.

All the best journals are doing it

PLoS Biologue Starting a blog, that is. It’s good to see PLoS Biology following Annals of Botany’s lead and starting their own blog, PLoS Biologue ;-)

A recent post by Lisa Gross, Reach out and teach someone, gives some nice case studies of how the content of PLoS Biology is being used in education to stimulate students to think about science. There’s a nice open access repository of plant science materials in AoB PLANTS, so maybe it’s about time someone tried out some of these ideas to big up plant science in school and university curricula?

Temperature, latitude and forest plant regeneration

Temperature, latitude and forest plant regeneration

Temperature, latitude and forest plant regeneration

Early life history stages are among the most critical phases in the life cycle of plants. De Frenne et al. assess the response of plant regeneration from seed of two forest understorey plants (Anemone nemorosa and Milium effusum) to variations in temperature along a latitudinal gradient. They find decreasing seedling emergence and fitness towards the northern edge of the distribution range of the species, as well as stronger growth responses to temperature increases in northern than in southern seedlings of the grass M. effusum. They conclude that wide intraspecific variation in plant regeneration in response to warming may differentially alter future plant dynamics across broad spatial scales.

Phenotypic plasticity in Suaeda maritima

Phenotypic plasticity in Suaeda maritima

Phenotypic plasticity in Suaeda maritima

Suaeda maritima shows morphologically different forms on high and low areas of the same salt marsh. Wetson et al. demonstrate that roots of this halophyte have a constitutively very high activity of lactate dehydrogenase (LDH) regardless of whether they are growing in aerated or severely hypoxic conditions, and not the inducible increase in activity that has been demonstrated in other plants during hypoxia. This high LDH activity is likely to be a factor in the high phenotypic plasticity observed in reciprocal transplants between high- and low-marsh field sites and in simulated tidal-flow tanks in a glasshouse.

Uses and Abuses of Plant-Derived Smoke: Its Ethnobotany as Hallucinogen, Perfume, Incense, and Medicine by Pennachio, Jefferson and Havens

Uses and Abuses of Plant-Derived Smoke coverUses and Abuses of Plant-Derived Smoke is a book I stumbled upon while looking for something else. It’s tempting to say it’s a very niche subject; the authors say this is the first book on the topic. After reading the introduction I’ve no reason to doubt what the authors say is true, but they make such a strong case that plant smoke has been neglected that it is surprising that more study hasn’t been done. One reason why plant smoke may prove a fertile ground for research in the future, the authors point out, is that many of the compounds in smoke are created by the act of burning and so aren’t found in the plant itself. There are potentially a vast number of compounds to analyse and these may have valuable properties that have been overlooked.

This isn’t the first collaboration between the authors. Previous has also looked at the uses of plant smoke, particularly as a trigger for germination. Marcello Pennacchio has also researched plants used by Australian aboriginals. Lara V Jefferson is clearly botanically informed. She has a weblog that talks about her environmental work with the mining industry. I’m not familiar with the intensity of mining in Western Australia. It’s not clear to what extent the authors are familiar with anthropology or history. Additionally there’s a short foreword by Peter Raven, which should be a sign that what follows is going to be worth a lot of attention.

The introduction gives examples of some the uses. The current bad reputation of smoking is tackled with anthropological examples of smoke being used for medicinal purposes. This seems particularly well attested among the aboriginal people of Australia, but this is also where one of the authors did much of his fieldwork. Hallucinogens are also shown as is incense, which is generally viewed as a more socially acceptable way of having a good time with smoke. Depending on where you draw the line this can segue in magical uses. There are other less obvious uses, but the examples are well-known, like the use of smoke for pest control and for communication via smoke signals. There were one or two places where I thought a few more references would have been useful. For example, my first degree was in Ancient History and Archaeology so I feel a bit foolish for having no idea of when Mark Anthony’s soldiers were driven mad – possibly by jimsonweed. The only ancient source I have found is Plutarch’s Life of Antony 45.5-6. Mark Antony isn’t a major interest for me so I hope there are better sources I’ve missed. Despite that, the introduction is good as far as it goes. Unfortunately as far as discussion matters that’s more or less it for the book. The rest is an alphabetical list of species and the possible uses they have been put to.

The descriptions vary, understandably due in part the how common their use is around the world and the work that has been done. One the first page of the list “Abies lasiocarpa (Hook.) Nutt. (Pinaceae). Rocky Mountain fir” gets an entry that details its use as incense for the Crow, a headache cure, a treatment for tuberculosis and a treatment for venereal diseases by the Blackfoot. A tranquilliser for those sacred of thunder by the Cheyenne and an incense for sweathouses by the Nex Perce. The following entry, “Abies spectabilis Spach (Pinaceae). Himalayan fir”, could have fitted on one line if Manandahar, the author cited as the source, had had a shorter name. This isn’t bad, but it reflects the patchy nature of knowledge at the current time, which means quite a few entries are extremely short.

In some cases the descriptions might be a bit too short. The entry for “Antennaria margaritacea (L) Sweet (Asteraceae)” reads; “Ross (2002) suggest that the dried leaves of this species can be smoked for pleasure. No other details about its use were given.” This is a bit of a problem in that it doesn’t mention who smoked the leaves. You could flip to the back of the book, but the entry above “Antennaria aprica Greene (Asteraceae)” also refers to Ross (2002) and mentions that the people in question are the Navajo. It’s not an insurmountable problem, but it seemed as though the authors were expecting the book to be read alphabetically. I could see anthropologists search for information by region, or possibly to compare treatments for tuberculosis or other diseases, but I wasn’t convinced that they’d look for species in alphabetical order as a first choice.

This turns out to be an unfair criticism as after the plants come a couple of indices, including one that is useful for exactly the sort of questions that anthropologists would ask. Given that and the range of questions that could be asked, alphabetical order is eminently sensible. Indeed if I hadn’t started reading in alphabetical order I may not have noticed that Antennaria margaritacea was an odd entry.

Looking at how the book will be used, I wonder if the authors are going to get all the credit they deserve for this work. They acknowledge that the value of the entries is only as good as the report they are based upon. This depends on many factors, including whether or not the fieldworker has correctly identified the plant. Therefore while this is a good first point of call, any research has to move into the original reports and work around those. When it comes to citation is there a need to cite this work? This book is adding nothing original in the entry itself, it’s value lies in putting this information into an accessible volume. There is also a matter of whether hard-copy is the right format for this work. Here the search function of a Kindle works for tracking information through the work and perhaps an updatable wiki could have been a better system. As long as an OUP volume has more academic cachet than a wiki it would be a poor career move for anyone to take the wiki option. However it may work for future editions if it sparks more work in this field.

If there’s any justice, this book should provoke more work into plant smoke. There is plenty of material for research in here. Some questions may seem obvious, like looking for chemical similarities in medicinal smoke remedies. The range of uses also allows for some odder questions to be asked. A number of plants are burned to ward off evil spirits. Is there something biological that smells like evil spirit? Another possibility is that it’s not merely the smoke that makes a plant useful against evil but maybe also the location it grows. Are such plants found in liminal zones like the edge of settlements, or on the borders of unused land? A few minutes thought could suggest a few possible lines of research when I wasn’t even aware of the question till reading through the entries.

To large extent this is what matters in an academic book, does it further conversation? Uses and Abuses of Plant-Derived Smoke definitely does. There are the tools there with the referenced entries and indices to create ideas and provide direction to take enquiries further. It helps that the book is readable too. It’s the way that this book opens new questions that makes it academically useful, but potentially disappointing to a general reader. There is still a good lengthy synthesis to be written on the use of plant smoke, and this isn’t it. The range of detailed research to write such a book probably doesn’t exist yet. My hopes are that it will inspire the large amount of work that makes such a synthesis possible in such volume that the book will rapidly appear dated to the extent a new edition is needed. I am a bit overworked at the moment so I shouldn’t be looking at new projects, but the next time I’m in a half-decent library I might have a few more articles on my to-photocopy list that I’ll want to follow-up.

Aside from the book, browsable on Google Books, Lara V Jefferson’s Environmental Applications in Mining weblog looks like it will be worth following if you have an interest in conservation and environmental impacts associated with mining.

Pitcher plant uses power of the rain to trap prey

Nepenthes gracilis The Nepenthes gracilis pitcher plant, found in southeast Asia, has a unique, semi-slippery wax crystal surface on the underside of the pitcher lid. Researchers have found that ants could cling to this surface under normal conditions, but a rain drop falling on the lid is enough to dislodge the insects, catapulting them into the pitcher where they are digested. This behavior can be seen in videos accompanying the published article:

With a Flick of the Lid: A Novel Trapping Mechanism in Nepenthes gracilis Pitcher Plants. (2012) PLoS ONE 7(6): e38951. doi:10.1371/journal.pone.0038951

Cretaceous flowers of Ericales

Cretaceous flowers of Ericales

Cretaceous flowers of Ericales

The rapid increase in knowledge of the fossil record of angiosperms in the past 30 years has provided important evidence on the antiquity of different lineages. Schönenberger et al. add to the fossil record of asterids with the description of an exceptionally well-preserved flower from Georgia, USA, from the Late Cretaceous named here as Glandulocalyx upatoiensis. The fossil is preserved as charcoal and investigations by standard scanning electron microscopy, as well as synchrotron-radiation X-ray tomographic microscopy, have made it possible to describe the flower in great detail. Morphological characterization of the fossil indicates a relationship to core Ericales and specifically to extant Actinidiaceae and Clethraceae.

Stochastic modelling in ecosystems – progress but we are not there yet

Modelling Of Ecosystems: the Cycle, Inputs and Ouputs

Modelling Of Ecosystems: the Cycle, Inputs and Ouputs

Modelling of processes lets one understand the functions of interacting components, helps to identify parts of processes, and can predict outcomes of changes in the system. Unfortunately, what was a major area of financial modelling is now largely discredited, much to the cost of the rest of us; other areas such as insurance are becoming so constrained by rules and regulation as to be useless. Biological modelling, in contrast is advancing rapidly, whether with respect to subcellular events, whole organism development, or disease epidemiology. This week, Professor Xueron Mao has organized a meeting (previous blog post) at the University of Strathclyde in Glasgow, Scotland, on “Stochastic Modelling in Ecosystems” (link to meeting programme).

In the week marking the 20th anniversary of the 1992 United Nations Conference on Environment and Development (“Rio Summit”), I wondered about the impact of ecosystem modelling on the major policies being discussed at the Rio+20 summit in June 2012. Had I missed a whole area of literature in the last 10 years? Weekly, the news media tell us about the results from the latest models of climate change, while I read  papers every month about crop and photosynthesis models, not to say stunning work on many individual plant species, including special issues and collected papers from Annals of Botany. Like many UN-related organizations and meetings, the Sustainable Development conference has a large amount of underpinning ‘grey literature’ – commissioned reports and research with strong scientific content (albeit, often not complete or definitive, and hence not suitable for publication in refereed journals). However, a search of the UN website does not show any attempts at ecosystem modelling (or, indeed, ‘modeling’): the 14 discussions of the topic of modelling are all about economics and finance. The Google Scholar search shows few major papers in the last decade with keywords of modelling/modeling and ecosystems.

Maybe the challenge of modelling a whole ecosystem is too difficult: a model needs to define inputs, outputs and flux through a system. The ecosystem involves cycles and networks involving hundreds of species and millions of interactions from sub-cellular level upwards. In my own talk opening the meeting, I concluded that the outputs can be classified in three areas. Firstly, chemical energy, largely in the form of the fixed carbon that is used as food, feed, fibres and fuel outside the direct ecosystem. Secondly, a small but important fraction of the flux is removed from the system, particularly to the long-term carbon stores in limestone and fossil fuels. The final group of outputs can be considered as ‘ecosystem services’ including purified (or indeed polluted) water that is changed from the input state in both purity and flow rate, or oxygen reduced from carbon dioxide. The slides from my talk are on under pathh, and maybe I will make a shortened commentary for YouTube at some point.

In the meeting, we were treated to a range of talks ranging from models of carbon cycles, through population and vegetation dynamics, through to disease epidemiology models. It is always exciting when different research communities come together, so it was very valuable to hear from and talk to the mathematicians at the meeting, even if there is some differences in our languages!
It is always invidious to pick out particular talks from a full programme, and the full listing is given here. Since this blog is plant-related, I will note the impressive talks from Mathew Williams (University of Edinburgh) discussing how gigatons of carbon move around the terrestrial (and indeed atmospheric) carbon cycles using global measurements in an experiment named FLUXNET, which, along with space-based measurements could examine large-scale forest biomass changes over timescales of only three years. My collaborator Jongrae Kim (University of Glasgow gave the next talk, discussing some formal approaches to modularization of complex networks in his talk on robustness analysis of community structures, of great relevance to making very large networks amenable to analysis. Francesco Accantino presented a model of abundance and changes of three Acacia species in humid savannas adding stochasticity to a matrix model, which linked nicely to Pierre Couteron (IRD, Montpellier) working at other sites in sub-Saharan Africa. Pierre modelled the distribution patterns of patchy vegetation, showing effects of rainfall and slope in both stable systems and the changes in the last 50 years. Remote sensing is giving much more data than ecologists have ever had, and interestingly Pierre is able to use freely available Google Earth for many of his analyses. After valuable talks related to aspects of epidemiology in several systems, the closing paper by Carlo de Michele (Politecnico di Milano, Italy) built on earlier talks about water as a main determinant of vegetation type – the topic of ecohydrology as the study of hydrology that underpins ecology. Like several other talks, modelling of water could give a bistable system with two solutions of bare soil (low rainfall) or of vegetative ground cover (high rainfall), taking into account the effects of rainfall stochasicity on soil water linked to vegetation systems. The surprise was that not only did the results describe behaviour of desert compared to topical forest ecosystems, but also annual changes in savannas with dry, bare periods followed by vegetation-covered wet seasons.

“Stochastic modelling in ecosystems” has some way to go before it becomes “Stochastic modelling of ecosystems”. Genetics, measurement methods and parameterization of properties are coming from the biologists are beginning to meet the modelling community with their increased understanding of robustness, oscillation and network reduction as well as computational approaches. I am looking forward to decisions at Rio+30 being underpinned by recommendations based on rigorous and robust models showing how we can exploit ecosystems without destroying the earth.

Stochastic Modelling in Ecosystems - University of Strathclyde - 2012 - Group Photograph