Tuesday, December 04, 2007

Using OpenID for comments

I added the option of using OpenIDs to comment on this blog, per phydeaux3's blog post. So it should now be possible to leave comments using AOL/AIM, LiveJournal, TypeKey, WordPress or other OpenID logins.

Phydeaux3 also has instructions on how to alter the settings on to allow this on Blogger.

Friday, November 16, 2007

This week

This week in Science
  • Hurricane Katrina's Carbon Footprint on U.S. Gulf Coast Forests - Jeffrey Q. Chambers et al. found that "[s]patially explicit forest disturbance maps coupled with extrapolation models predicted mortality and severe structural damage to ~320 million large trees totaling 105 teragrams of carbon, representing 50 to 140% of the net annual U.S. forest tree carbon sink"
This week in Proceedings of the National Academy of Sciences USA

Thursday, November 08, 2007

What's new

Since I called this blog Plant News, I am going to try something new - posting links to new papers related to plant biology in major journals (Science, Nature, etc.) This first posting will focus in part on last weeks articles.

This week in Nature:

Last week in Science:
Current issue of PLOS Biology
Recent papers at PLOS ONE

Monday, October 29, 2007

Water repulsion off montane forest leaves

A study published in the November issue of the journal Biotropica looks at the ability of trees in tropical montane forests to repel water from their leaves. Holder hypothesised that trees in montane forests should be better at repelling water than trees from drier environments - dry forests in Guatemala and a semiarid grassland-foothills ecotone in Colorado. However, he found montane forest trees were less able to repel water than dry forest or temperate grassland-foothill species. Holder suggested that the increased wettability of the montane forest species may be driven by their coating of epiphylls (plant and other organisms growing on the leaf surface), while increased ability to shed water may be selected for in dry environments because it may help channel water to the roots of the plants in arid environments.
  1. Holder, Curtis D. 2007. Leaf Water Repellency as an Adaptation to Tropical Montane Cloud Forest Environments. Biotropica 39 (6), 767-770. doi:10.1111/j.1744-7429.2007.00303.x
[Read the rest of my post Like water off the back of a duck]

Monday, October 22, 2007

Poor showing for fall colours

Warmer weather has been blamed for less than impressive Fall foliage in New England. According to Dave Gram, writing in the Buffalo News:

Forested hillsides usually riotous with reds, oranges and yellows have shown their colors only grudgingly in recent years, with many trees going straight from the dull green of late summer to the rust-brown of late fall with barely a stop at a brighter hue.

"It's nothing like it used to be," said University of Vermont plant biologist Tom Vogelmann, a Vermont native.

He says autumn has become too warm to elicit New England's richest colors.

While I'm no expert on this, the idea seems intuitively appealing. Brilliant Fall colours are a feature of the Great Lakes region - down here, leave tend to go from green to brown, often with only the slightest nod to yellows and reds. Unfortunately, "intuitively appealing" arguments can be misleading - after all, many people are attracted to creationism for just that reason.

It shouldn't be too difficult to answer the question of whether there is a correlation between Fall colours and climate change. The more interesting question is why there is such a correlation, why might drive such a change. The Gram article attempts to address this:

Warming climate affects trees in several ways.

Colors emerge on leaves in the fall, when the green chlorophyll that has dominated all spring and summer breaks down.

The process begins when shorter days signal leaves to form a layer at the base of their stems that cuts off the flow of water and nutrients. But in order to hasten the decline of chlorophyll, cold nights are needed.

In addition, warmer autumns and winters have been friendly to fungi that attack some trees, particularly the red and sugar maples that provide the most dazzling colors.

"The leaves fall off without ever becoming orange or yellow or red. They just go from green to brown," said Barry Rock, a forestry professor at the University of New Hampshire.

So where do the pigments come from? Why do the plants produce these pigments? While I didn't know the answer to that question, it didn't cross my mind that this was in any way a mystery. Turns out that it is a mystery. There are several hypotheses, including
  1. to attract fruit-dispersing birds (this only works for species with bird-disperse fruit and is, at best, an incomplete explanation; Hoch et al. 2001)
  2. anti-herbivore or anti-microbial defenses
  3. protection against drought or freezing tolerance
  4. protection against photoinhibition that might otherwise interfere with the recovery of nutrients from leaves (Holopainen and Peltonen 2002)
  5. as a means of signaling to aphids that a tree has invested heavily in chemical defenses (Hamilton and Brown 2001)
If Fall pigments play a protective role, it's reasonable to suggest that a shortened period of leaf senescence (triggered by a warmer Fall) might lead to reduced production of these compounds. It is, as I said before, an interesting story. Sadly, it seems like it's still just that - a story.
  1. Hoch, W. A., Zeldin, E. L. and Mccown, B. H.. 2001. Physiological significance of anthocyanins during autumnal leaf senescence. –Tree Physiol. 21: 1–8.
  2. Holopainen, J. K. and Peltonen, P. 2002. Bright autumn colours of deciduous trees attract aphids: nutrient retranslocation hypothesis.Oikos 99 (1), 184–188.
  3. Hamilton, W. D. and Brown, S. P. 2001. Autumns tree colours as a handicap signal. –Proc. R. Soc. Lond. B Biol. Sci. 268: 1489–1493.

Friday, October 19, 2007

Human impacts on pre-Columbian tropical forests

Blogging on Peer-Reviewed Research

When European naturalists first visited the New World Tropics they saw vast forests that seemed untouched by humans. While indigenous people often lived in these forests, their populations were small. This led to a perception of tropical forests as primeval, “virgin” forests. In the last few decades, this perception has changed - large areas now covered by mature forests have a history of cultivation. In many cases, “primeval” forests are less than 500 years old.

La Selva biological station in Costa Rica is one of the premier research stations for Neotropical biology. Prior to archaeological study of the site, much of it was assumed to be free of human influence. However, the discovery of pre-Columbian artefacts led to the discovery that the site had been occupied at least 3000 years ago. Charcoal was more abundant in alluvial terraces (flatter areas with deeper, more fertile soil) and less abundant in the less fertile upland soils. A chronology, established by Sol (2000)*, divided the La Selva into four archaeological phases: La Cabaña 1000 – 1550 CE; La Selva 500 – 1000 CE; El Bosque 300 BCE– 500 CE; La Montaña 1500 –300 BCE.

To better understand the history of the site, Lisa Kennedy of Virginia Tech and Sally Horn of the University of Tennessee, Knoxville, undertook a study of sediment cores extracted from the Cantarra swamp*, a 0.5 ha wetland dominated by perennial herbs. They used pollen, charcoal and macrofossils to reconstruct the environmental history of the site. Wetlands are frequently used to reconstruct vegetation histories. As sediments accumulate in bodies of water, plant pollen, fern spores and charcoal fragments are trapped. Pollen coats are extremely tough, and decay takes place very slowly in waterlogged soils. If the vegetation surrounding the site changes, different types of pollen will be deposited into the site. Someone with the patience to sort through these cores can observe thousands of years of history in a few metres of sediment.

[Read the rest of the post]

  1. Sol, C., R. F. 2000. Asentamientos prehispánicos en la Reserva Biológica La Selva, Sarapiquí, Costa Rica: Sistemas de explotación de recursos naturales en un bosque tropical lluvioso. Licenciatura thesis, School of Anthropology and Sociology, University of Costa Rica.
  2. Lisa M. Kennedy, Sally P. Horn. A Late Holocene Pollen and Charcoal Record from La Selva Biological Station, Costa Rica. Biotropica (OnlineEarly Articles). doi:10.1111/j.1744-7429.2007.00334.x

Tuesday, October 09, 2007

Indian fruit genebank threatened

Jeremy at Agricultural Biodiversity Weblog reports that the government of Jharkand State in India plans to bulldoze the field genebanks of the Horticulture and Agro Forestry Research Programme in order to build housing for Members of Parliament and Members of the Legislative Assembly.

According to a story in the The Indian Express, the plan will take 288 acres of HARP's land, including 88 acres of Farm 2, and will destroy
5253 plants of different varieties of mango and litchi, 6,500 trees more than 30 years old, eight greenhouse nurseries, each with 4000-5000 plants of guava and jackfruit and a gene bank developed over 20 years to have a germplasm base of 239 varieties of mango and litchi.
As the story goes on to say, this goes beyond destroying decades of work - destruction of a gene bank will also hurt regional farmers
Not just that. “The gene bank of these valuable fruit-bearing tress will be destroyed for ever. It will seriously affect horticulture prospects of the farmers in this belt,” says HARP’s Principal Scientist Shivendra Kumar.
Not only is this a political decision, it's a decision being made by the state legislature to benefit state legislators. So it isn't too surprising that they are unmoved by external forces.
This also flies in the face of a letter from Union Agriculture Minister Sharad Pawar earlier this year asking Chief Minister Madhu Koda to shelve the plan and instead issue mutation certificate of this land whose title was transferred to the ICAR by the Ranchi Deputy Commissioner in 1976. In 1979, HARP was set up with 100 percent funding by the Union government.

Wednesday, October 03, 2007

Fighting to save Greene Prairie

The University of Wisconsin-Madison's Arboretum is famous for its restored prairies. The most famous is the Curtis Prairie, established in the 1930s and 40s. Less well known is the 50-acre Greene Prairie, which was restored almost single-handed by Henry Greene in the 1940s and 50s.

Greene Prairie is currently under threat from Reed Canary Grass (Phalaris arundinacea) a perennial grass native to Eurasia. In North America it is invasive in wet sites; the Wisconsin DNR estimates that it dominates 10% of the state's wetlands. The Greene Prairie initially lacked permanently flooded areas, but runoff from suburban have altered the site. Reed Canary Grass currently dominates 10 acres of the 50-acre site. (Reed Canary Grass at Greene Prairie from: Zedler, J.B. and J. Wilcox. 2005. Interconnected Restoration Challenges: Controlling invasives and reestablishing natives, Arboretum Leaflet 1).

So far, restoration efforts have had limited success. University of Wisconsin-Madison News reports on new efforts to incorporate students in the restoration project.

In the new plan, Arboretum staff will burn the experimental site and apply sethoxydim in the spring. Then, each fall, the ecology students will sow native seeds, survey plant diversity and abundance, and otherwise monitor the project's progress. In keeping with its experimental nature, researchers will review the data carefully each year and make adjustments to the approach as needed.

The team hopes not only to keep reed canary grass from spreading further, but also to push it back eventually toward the south. No matter what the final outcome, however, Herrick has no doubts about the benefits.

"At a time when resources are stretched, we could never, as Arboretum staff, pull off this experiment on our own. So, incorporating the students is a perfect way to do this," he says. "It's an education for them - first and foremost. But we also get to advance restoration ecology research and answer land care questions. It's a win, win, win, all the way around."

Friday, September 28, 2007

Serendipity and the origin of crops

In Puerto Rican dry forest, one of the most striking dichotomies is between forests dominated by native species and forests dominated by exotic Leucaena leucocephala. Most forests that have regrown on abandoned agricultural land are dominated by Leucaena. The colonisation of these areas by native tree species is slow - either the native species are poor colonisers, or Leucaena resists invasion. Its importance on the landscape and apparent stability made me fascinated with the species.

One of the things which struck me early on was the fact that many published sources listed Leucaena as a native species in Puerto Rico. To me, its behaviour shouted “exotic”, but when I spoke to Liogier at the University of Puerto Rico herbarium (author of the Flora of Puerto Rico) he said that it was probably introduced, but there were no records to say anything conclusive, one way or the other. So I was very happy when I came across Colin Hughes’ Monograph of Leucaena. Based on the diversity of hyperparasitoids Hughes concluded that Leucaena leucocephala was native to Central Mexico. He concluded that the abundant populations in the Yucatan (which often formed pure stands in disturbed areas) were, in fact, introduced. And that was the last I had heard on the subject for almost a decade.

When a post entitled “How domestication happens” popped up on my RSS reader, I was curious. The post was minimal, and I almost didn’t click through to the link. When I did so I was rewarded with a post entitled “Biodiversity, trash heaps and the evolutionary origin of crops” and a picture I recognised instantly as Leucaena leucocephala. The post described a paper published in the Proceedings of the National Academy of Sciences entitled: “Serendipitous backyard hybridization and the origin of crops“.

According to Hughes and coauthors, Leucaena leucocephala is one of several domestic species in central Mexico which are believed to have originated through the hybridisation of related species that were brought together in backyard dumps.

Seeds of 13 species of Leucaena are used for food across S-C Mexico…. Food
use is widespread and intensive in Chiapas, Oaxaca, Puebla, Guerrero, and Morelos and more sporadic further north, but unknown further south despite the availability of native species of Leucaena. Present-day food use varies from gathering of pods from local free-living populations for home consumption to intensive harvesting of commercial quantities from cultivated trees and transportation of seeds to regional markets…. This spectrum of increasing human intervention involves transitions from wild to managed to cultivated, from home consumption to local to wider regional marketing, and from very
local to regional to much wider translocation of species.

[This whole thing forced me to reevaluate Leucaena. While I have always thought of it as “useful” for revegetation and perhaps for animal fodder or green manure, the idea of growing it as a food crop for its pods is alien to me. Even the green pods don’t strike me as “food”.]

In Mexico, there is a continuum of use, from Leucaena cuspidata, which is collected from wild populations and used locally, through L. confertiflora and L. collinsii, which are more widely cultivated and tranlocated, to L. eculenta, L. pallida and L. leucocephala which are intensively cultivated. The pods of these latter species are commercial crops which are distributed to markets several hundred kilometres away.

Five of the 13 species are polyploids, and the authors concluded that they are likely to be allopolyploids (polyploids which originated through the bybridisation of two species) whose origins can be traced to backyard gardens and dumps. The underlying idea is that human activity can bring together species which would not normally encounter one-another in the wild. In the case of Leucaena leucocephala and L. pallida the hybrid origin theory is strengthened by the lack of wild populations of the species.

They go on to point out that this hypothesis is not only plausible for Leucaena, but also for the other two major perennial crops in south-central Mexico, Agave and Opuntia, which show similar trends, but are less thoroughly studied than Leucaena species.

  1. Hughes, Colin E. (1998). Monograph of Leucaena (Leguminosae-Mimosoideae), Systematic Botany Monographs 55:1-244
  2. Hughes, C.E., R. Govindarajulu, A. Robertson, D.L. Filer, S.A. Harris, and C.D. Bailey. 2007. Serendipitous backyard hybridization and the origin of crops. Proceedings of the National Academy of Sciences USA 104:14389-14394.

Thursday, July 26, 2007

Wolves bring aspen back to Yellowstone

Blogging on Peer-Reviewed Research
Aspen (Populus tremuloides) was a major species in Yellowstone, but over the twentieth century populations declined and there was little regeneration. While elk were initially blamed for this lack of regeneration, changing policies by the Park Service led to a change in this policy:
Until 1968, Park Service officials contended that an unnaturally large elk population, which had built up in Yellowstone during the late 1800s and early 1900s, had severely damaged the park’s northern winter range, including aspen (Populus tremuloides) communities. However, agency biologists now hypothesize that elk and other ungulates in Yellowstone are “naturally regulated,” being resource (food) limited, and that the condition of the ecosystem today is much like it was at park formation (Houston 1982; Despain et al. 1986). Elk influences on Yellowstone’s vegetation are now thought to be “natural” and to represent the “pristine” condition of the park.
According to the Park Service, Yellowstone is not now nor has it ever been
overgrazed, and all previous studies to that effect are wrong (Houston 1982).
[Kay, Charles E. 2001. Long-Term Aspen Exclosures in the Yellowstone Ecosystem. USDA Forest Service Proceedings RMRS-P-18.]

This conclusion was challenged by available evidence. For example, Kay showed the change in herbivore exclosures between 1946, 1963 and 1987 (images from Kay, 2001). The aspen clone is bisected by the exclosure's fence. While the two portions of the clone seem fairly similar in 1963, by 1987 the portion of the clone that was protected from herbivores has spread considerably.

William Ripple
and Eric Larsen found* that the aspens had stopped regenerating in 1920, about the same time that wolves were eliminated from Yellowstone. However, there were questions on the role that wolves might play in regulating the elk population.

To this end, Ripple and Robert Beschta** looked at the level of browsing and the height of aspen saplings in areas with and without logs (which can provide cover for wolves). In both upland and riparian sites, aspen saplings were taller when downed logs were present.

The reintroduction of wolves has allowed allowed aspen to return to riparian areas (although not, so far, in upland areas). Willows and cottonwoods also returned - more quickly than the aspen, which are a preferred browse for elk. While populations reductions have played a role, so has the 'ecology of fear'.

*Ripple,W.J., Larsen, E.J., 2000. Historic aspen recruitment, elk, and wolves in northern Yellowstone National Park, USA. Biological Conservation 95, 361–370.
**Ripple, W.J., Beschta, R.L., Restoring Yellowstone’s aspen with wolves, Biological Conservation (2007), doi:10.1016/j.biocon.2007.05.006

Story at Science Daily.

Thursday, July 19, 2007

Can organic agriculture sustain current levels of food production?

A recent report by Ivette Perfecto, Catherine Badgley and others at the University of Michigan suggests the organic agriculture is capable of sustaining or increasing current levels of food production globally.
Organic farming can yield up to three times as much food as conventional farming on the same amount of land—according to new findings which refute the long-standing assumption that organic farming methods cannot produce enough food to feed the global population.
According to the press release, the authors found that organic agriculture, which they define as "practices referred to as sustainable or ecological; that utilize non-synthetic nutrient cycling processes; that exclude or rarely use synthetic pesticides; and sustain or regenerate the soil quality", can maintain current levels of production in developed countries, and as much as triple production in developing countries.

The original article was published in Renewable Agriculture and Food Systems. There's a more detailed review at New Scientist and a two-part story(part 1, part 2) at OrganicAuthority.com.

H/T Meteor Blades at dKos.

Thursday, June 21, 2007

Open access in botany journal

The Journal of Experimental Botany has provided open access to papers if the authors' institutions subscribe to the journal. Other authors who want their papers to be freely accessible will have to pay the full cost of publication which is estimated at £1500/$2800/€2250.

Over the last three years the journal has conducted an experiment in which they made about 30% of their papers freely available. They have found that these papers are more widely cited:
Early indications show that OA publication increases impact as full text downloads are, on average, 17% higher and citations 14% higher than for those publications kept under subscription control.
H/T Chronicle of Higher Education News Blog.

Monday, June 18, 2007

Ceiba pentandra: dispersal, vicariance and press releases

Ceiba pentandra (the silkcotton, kapok or ceiba tree) has a broad distribution including across the Neotropics and Africa. A cultivated form is grown across a wider range for kapok fibres. The trans-Atlantic distribution of C. pentandra has attracted attention for a long time - based on the fact that there are nine species in the Neotropics and only one in Africa, it has generally been assumed that it is a Neotropical species that dispersed to Africa. How it got there has long been a question.

EurekaAlert! published a press release attributed to the National Science Foundation about a paper published in Molecular Ecology concerning the trans-Altantic distribution of Ceiba pentandra, the silk cotton or kapok tree. The paper* considers three mechanisms by which the species could have come to be present on both sides of the Atlantic: Gondwana vicariance, Boreotropical dispersal (and subsequent vicariance) and long-distance dispersal.

In the case on Gondwana vicariance, the distribution would reflect the fact that South America and Africa were connected (as parts of Gondwana) until 96 million years ago. In the case of Boreotropical dispersal, the species would have colonised Africa about 35 million years ago through a then warmer North America and Europe, only to be lost from those areas as the climate warmed. Both of these would be expected to produce deep divergence between African and South American C. pentandra populations. On the other hand, if long-distance dispersal across the Atlantic took place more recently, the divergence would be smaller.

The paper found evidence for recent dispersal. The authors noted that:

Ceiba pentandra has the weakest phylogeographical structure yet reported for a widespread rainforest tree species. Apart from the cluster of sites in Western Ecuador having a variant psbB-psbF haplotype, there was no cpDNA variation across Mesoamerica, the Amazon basin, and West Africa. In fact, this study found less cpDNA variation across three continents than some rainforest tree species exhibit within putative breeding populations in French Guiana and Brazil (Hamilton 1999b; Dutech et al. 2000; Latouche-Halle et al. 2003) or among sample sites at regional scales in French Guiana and across Mesoamerica (Caron et al. 2000; Cavers et al. 2003).

In this regard, C. pentandra is by no means unique - several other species have been found that have recently crossed the Atlantic, including Symphonia globulifera, which apparently colonised the Americas from Africa.

One thing that bothers me is the press release. It opens with

Celebrated in Buddhist temples and cultivated for its wood and cottony fibers, the kapok tree now is upsetting an idea that biologists have clung to for decades: the notion that African and South American rainforests are similar because the continents were connected 96 million years ago.

It’s obvious that whoever wrote the press release didn’t spend much time looking at the paper. While the issue of Gondwanan roots is considered, it’s by no means a new idea. At the same time, it’s a fairly limited suite of trees that are shared between the two areas, and evidence of recent trans-Atlantic dispersal by a few species does not “[upset] an idea that biologists have clung to for decades”. That’s nonsense.

* Christopher W. Dick, Eldredge Bermingham, Maristerra R. Lemes and Rogerio Gribel. Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics. Molecular Ecology (OnlineEarly Articles). doi:10.1111/j.1365-294X.2007.03341.x

H/T Agricultural Biodiversity Weblog.

[Crossposted from my Wordpress blog]

Saturday, May 19, 2007


ScienceDaily has an article today about a new biofuel based on wood chips which can be blended with biodiesel and petroleum diesel. It's based on pyrolysis of wood chips in an oxygen-free environment, and yields charcoal as a waste product. It's supposed to be nearly carbon-neutral (as long as the forests are being replanted), and actually carbon-neutral if the charcoal can be added back to the soil as a fertiliser (presumably since the carbon in charcoal is pretty much out of circulation forever).

Link to the paper is here.

Of course, the thing that pops into my head is the question of how much land is available for growing trees. Will a wood-based biofuel lead to further deforestation - like the Brazilian forests that were cleared to plant Eucalyptus to produce charcoal for an iron smelter? Will it shorten the rotation time on current forest plantations? Will it lead to pressure to convert natural and semi-natural areas to tree monocultures? Will it compete with land for food production? Obviously we can't continue to depend on fossil fuels indefinitely, but alternative fuels seem to raise as many questions as answers.

Saturday, January 20, 2007

The impact of farming on biodiversity

Globally, the demand for food is expected to double by 2050, which could require the conversion of an additional 10 billion hectares of natural ecosystems to cropland. With 37% of the available land already under agriculture, agroecosystems represent an important component of global biodiversity. Since agricultural intensification is usually associated with biodiversity declines, being able to estimate the effects of land use change on biodiversity is an important tool for land management. In the latest issue of Science, Butler et al. were able to use six historical measures of agricultural land use change to successfully explain population changes in 57 bird species over the a forty-year period.