Biodiversity Dips When Japanese Rice Paddies Go Fallow

Large-scale farms that generally grow a single crop at a time and are managed conventionally are, by design, lacking in biodiversity. Abandoning such farms and allowing nature to take its course should, not surprisingly, result in a dramatic uptick in biodiversity. Plant colonization of abandoned farmland (also referred to as old field succession) is well studied and is regularly used as an example of secondary succession in ecology textbooks. The scenario seems obvious: cease agriculture operations, relinquish the land back to nature, and given enough time it will be transformed into a thriving natural community replete with diverse forms of plants and animals. This is an oversimplification, of course, and results will vary with each abandoned piece of land depending on the circumstances, but it generally seems to be the story. So what about when it isn’t?

Rice farming in Japan began at least 2400 years ago. Rice had been domesticated in China long before that, and when it eventually arrived in Japan it shaped the culture dramatically. For hundreds of years rice was farmed in small, terraced paddies in the mountains of Japan. Dennis Normile writes about these traditional, rice paddies in a recent issue of Science. He describes how they were found in villages “nestled in a forested valley” accompanied by vegetable plots, orchards, and pasture. Today, farms like these are “endangered,” and as they have become increasingly abandoned, plants, insects, and other wildlife that have historically thrived there are suffering.

Since the 1960’s, a combination of factors has resulted in the decline of traditional rice farming in Japan. For one, large scale farming has led to the consolidation of paddies, which are farmed more intensively. Diets in Japan have also shifted, resulting in a preference for bread and pasta over rice. Additionally, Japan’s population is shrinking, and residents of rural areas are migrating to cities. Traditional rice farmers are aging, and younger generations are showing little interest in pursuing this career.

Red rice paddy in Japan - photo credit: wikimedia commons

Red rice paddy in Japan – photo credit: wikimedia commons

Demographic and dietary concerns aside, why in this case is the abandonment of agriculture imperiling species? The answer appears to be in both the way that the rice paddies have been historically managed and the length of time that they have been managed that way. Agriculture, by its very nature, creates novel ecosystems, and if the practice continues long enough, surrounding flora and fauna could theoretically coevolve along with the practice. When the practice is discontinued, species that have come to rely on it become threatened.

Traditional rice paddies are, as Normile describes, “rimmed by banks so that they can be flooded and drained.” Farmers “encouraged wild grassland plants to grow on the banks because the roots stabilize the soil.” The banks are mowed at least twice a year, which helps keep woody shrubs and trees from establishing on the banks. In some areas, rice farming began where primitive people of Japan were burning frequently to encourage grassland habitat. Maintaining grassland species around rice paddies perpetuated the grassland habitat engineered by primitive cultures.

As rice paddies are abandoned and the surrounding grasslands are no longer maintained, invasive species like kudzu and a North American species of goldenrod have been moving in and dominating the landscape resulting in the decline of native plants and insects. Normile reports that the abandoned grasslands are not expected to return to native forests either since “surrounding forests…are a shadow of their old selves.”

Additionally, like most other parts of the world, Japan has lost much of its natural wetland habitat to development. Rice paddies provide habitat for wetland bird species. On paddies that have been abandoned or consolidated, researchers are finding fewer wetland bird species compared to paddies that are managed traditionally.

The gray-faced buzzard (Butastur indicus) is listed as vulnerable in Japan. It nests in forests and preys on insects, frogs, and other animals found in grasslands and rice paddies. It's decline has been linked to the abandonment and development of traditionally farmed rice paddies. (photo credit: wikimedia commons)

The gray-faced buzzard (Butastur indicus) is listed as vulnerable in Japan. It nests in forests and preys on insects, frogs, and other animals found in grasslands and rice paddies. Its decline has been linked to the abandonment and development of traditionally farmed rice paddies. (photo credit: wikimedia commons)

All of this adds fodder to an ongoing debate: “whether allowing farmland to revert to nature is a boon to biodiversity or actually harms it.” Where agriculture is a relatively new practice or where conventional practices dominate, abandoning agriculture would be expected to preserve and promote biodiversity. However, where certain agricultural practices have persisted for millenia, abandoning agriculture or converting  to modern day practices could result in endangerment and even extinction of some species. In the latter case, “rewilding” would require thoughtful consideration.

The thing that fascinates me the most about this report is just how intertwined humans are in the ecology of this planet. In many ways humans have done great harm to our environment and to the myriad other species that share it. We are a force to be reckoned with. Yet, the popular view that we are separate, above, apart, or even dominant over nature is an absurd one. For someone who cares deeply about the environment, this view has too often been accompanied by a sort of self-flagellation, cursing myself and my species for what we have done and continue to do to our home planet. Stories like this, however, offer an alternative perspective.

Humans are components of the natural world. We evolved just like every other living thing here, and so our actions as well as the actions of other species have helped shape the way the world looks. If our species had met its demise early in its evolutionary trajectory, the world would look very different. But we persisted, and as it turns out, despite the destruction we have caused and the species we have eliminated, we have simultaneously played a role in the evolution and persistence of many other species as well. We must learn to tread lightly – for the sake of our own species as well as others – but we should also quit considering ourselves “other than” nature, and we should stop beating ourselves up for our collective “mistakes.” It seems that when we come to recognize how connected we are to nature we will have greater motivation to protect it.

Additional Resources:

Year of Pollination: Most Effective Pollinator Principle and Beyond, part two

“The most effective pollinator principle implies that floral characteristics often reflect adaptation to the pollinator that transfers the most pollen, through a combination of high rate of visitation to flowers and effective deposition of pollen during each visit.” – Mayfield, et al., Annals of Botany (2001) 88 (4): 591-596

In part one, I reviewed a chapter by Jose M. Gomez and Regino Zamora in the book Plant-Pollinator Interactions: From Specialization to Generalization that argues that the most effective pollinator principle (MEPP) “represents just one of multiple evolutionary solutions.” In part two, I summarize a chapter by Paul A. Aigner in the same book that further explains how floral characteristics can evolve without strictly adhering to the MEPP.

maximilian sunflower
Aigner is interested in how specialization develops in different environments and whether or not flowering plants, having adapted to interact with a limited number of pollinators, experience trade-offs. A trade-off occurs when a species or population adapts to a specific environmental state and, in the process, loses adaptation to another state. Or in other words, a beneficial change in one trait results in the deterioration of another. Trade-offs and specialization are often seen as going hand in hand, but Aigner argues that trade-offs are not always necessary for an organism to evolve towards specialization. Plant-pollinator interactions provide an excellent opportunity to test this.

“Flowers demand study of specialization and diversification,” Aigner writes, not only due to their ubiquity, “but because much of the remarkable diversity seen in these organisms is thought to have evolved in response to a single and conspicuous element of the environment – pollination by animals.” If pollinators have such a strong influence on shaping the appearance of flowers, pollination studies should be rife with evidence for trade-offs, but they are not. Apart from not being well-studied, Aigner has other ideas about why trade-offs are not often observed in this scenario.

Aigner is particularly interested in specialization occuring in fine-grained environments. A course-grained environment is “one in which an organism experiences a single environmental state for all of its life.” Specialization is well understood in this type of environment. A fine-grained environment is “one in which an organism experiences all environmental states within its lifetime,” such as “a flowering plant [being] visited by a succession of animal pollinators.” For specialization to develop in a fine-grained environment, a flowering plant must “evolve adaptations to a particular type of pollinator while other types of pollinators are also present.”

It’s important to note that the specialization that Aigner mainly refers to is phenotypic specialization. That is, a flower’s phenotype [observable features derived from genes + environment] appears to be adapted for pollination by a specific type of pollinator, but in fact may be pollinated by various types of pollinators. In other words, it is phenotypically specialized but ecologically generalized. Aigner uses a theoretical model to show that specialization can develop in a fine-grained environment with and without trade-offs. He also uses his model to demonstrates that a flower’s phenotype does not necessarily result from its most effective pollinator acting as the most important selection agent. Instead, specialization can evolve in response to a less-effective pollinator “when performance gains from adapting to the less-effective pollinator can be had with little loss in the performance contribution of the more effective pollinator.”

Essentially, Aigner’s argument is that the agents that are the most influential in shaping a particular organism are not necessarily the same agents that offer the greatest contribution to that organism’s overall fitness. This statement flies in the face of the MEPP, and Aigner backs up his argument with (among other examples) his studies involving the genus Dudleya.

Dudleya saxosa (panamint liveforever) - photo credit: wikimedia commons

Dudleya saxosa (panamint liveforever) – photo credit: wikimedia commons

Dudleya is ecologically generalized. Pollinators include hummingbirds, bumblebees, solitary bees, bee flies, hover flies, and butterflies. “Some Dudleya species and populations are visited by all of these taxa, whereas others seem to be visited by only a subset.” Aigner was curious to see if certain species or populations were experiencing trade-offs by adapting to a particular category of pollinators. Aigner found variations in flower characteristics among species and populations as well as differences in pollinator assemblages that visited the various groups of flowers over time but could not conclude that there were trade-offs “in pollination performance.”

In one study, he looked at pollination services provided by hummingbirds vs. bumblebees as corolla flare changed in size. In male flowers, bumblebees were efficient at removing pollen regardless of corolla flare size, while hummingbirds removed pollen more effectively as corolla flare decreased. Both groups deposited pollen more effectively as corolla flare decreased, but hummingbirds more strongly so. Ultimately, Aigner concluded that “the interactions did not take the form of trade-offs,” or, as stated in the abstract of the study, ” phenotypic specialization [for pollination by hummingbirds] might evolve without trading-off the effectiveness of bumblebees.”

Aigner goes on to explain why floral adaptations may occur without obvious trade-offs. One reason is that different groups of pollinators are acting as selective agents for different floral traits, “so that few functional trade-offs exist with respect to individual traits.” Pollinators have different reasons for visiting flowers and flowers use the pollination services of visitors differently. Another reason involves the “genetic architecture” of the traits being selected for. Results can differ depending on whether or not the genes being influenced are linked to other genes, and genetically based fitness trade-offs may not be observable phenotypically. Further studies involving the genetic architecure of specialized phenotypes are necessary.

And finally, as indicated in part one, pollinators are not the only floral visitors. In the words of Aigner, “if floral larcenists and herbivores select for floral traits in different directions than do pollinators, plants may face direct trade-offs in improving pollination service versus defending against enemies.” These “floral enemies” can have an effect on the visitation rates and per-visit effectiveness of pollinators, which can drastically alter their influence as selective agents.

Like pollination syndromes, the most effective pollinator principle seems to have encouraged and directed a huge amount of research in the field of pollination biology, despite not holding entirely true in the real world. As research continues, a more complete picture will develop. It doesn’t appear that it will conform to an easily digestible principle, but there is no question that, even in its complexity, it will be fascinating.

I will end as I began, with an excerpt from Thor Hanson’s book, The Triumph of Seeds: “The notion of coevolution implies that change in one organism can lead to change in another – if antelope run faster, then cheetahs must run faster still to catch them. Traditional definitions describe the process as a tango between familiar partners, where each step is met by an equal and elegant counter-step. In reality, the dance floor of evolution is usually a lot more crowded. Relationships like those between rodents and seeds [or pollinators and flowers] develop in the midst of something more like a square dance, with couples constantly switching partners in a whir of spins, promenades, and do-si-dos. The end result may appear like quid pro quo, but chances are a lot of other dancers influenced the outcome – leading, following, and stepping on toes along the way.”

Year of Pollination: Most Effective Pollinator Principle and Beyond, part one

Have you ever considered the diversity of flowers? Why do they come in so many different shapes, sizes, and colors? And why do they produce so many different odors – or none at all? Flowering plants evolved around 140 million years ago, a fairly recent emergence evolutionarily speaking. Along with them evolved numerous species of insects, birds, and mammals. In his book, The Triumph of Seeds, Thor Hanson describes the event this way: “In nature, the flowering plants put sex, seeds, and dispersal on full display, spurring not only their own evolution but also that of the animals and insects with which they became so entwined. In most cases, the diversity of dispersers, consumers, parasites – and, most especially, pollinators – rose right alongside that of the plants they depended upon.”

Speaking of dependence, most flowering plants depend upon pollinators for successful reproduction – it is, for the most part, a mutually beneficial relationship. Even the casual observer of flowers will note that a large portion of the creatures that visit them appear to be pollinators. Thus, it is no wonder that pollination biologists have given pollinators so much credit in shaping the flowers that we see today.

Consider G. Ledyard Stebbins and his Most Effective Pollinator Principle which he defined in a paper published in 1970: “the characteristics of the flower will be molded by those pollinators that visit it most frequently and effectively in the region where it is evolving.” He then goes on to reference pollination syndromes, a phenomenon that describes how the traits of flowers are best suited for their “predominant and most effective vector[s].” In my post about pollination syndromes a few months ago, I discussed how a strict adherence to this concept has waned. In the next two posts, I discuss how the Most Effective Pollinator Principle (MEPP) may not be the best way to explain why flowers look the way they do.


To make this argument I am drawing mainly from two chapters in the book Plant-Pollinator Interactions: From Specialization to Generalization. The first is “Ecological Factors That Promote the Evolution of Generalization in Pollination Systems” by Jose M. Gomez and Regino Zamora, and the second is “The Evolution of Specialized Floral Phenotypes in a Fine-grained Pollination Environment” by Paul A. Aigner.

According to Aigner the MEPP “states that a plant should evolve specializations to its most effective pollinators at the expense of less effective ones.” And according to Gomez and Zamora it “states that natural selection should modify plant phenotypes [observable characteristics derived from interactions between a plant’s genes and its surrounding environment] to increase the frequency of interaction [between] plants and the pollinators that confer the best services,” and so “we would expect the flowers of most plants to be visited predominantly by a reduced group of highly effective pollinators.” This is otherwise known as adaptive specialization.

Specialization is something that, in theory, plants are generally expected to evolve towards, particularly in regards to plant-pollinator relationships. Observations, on the other hand, demonstrate the opposite – that specialization is rare and most flowering plants are generalists. However, the authors of both chapters advise that specialization and generalization are extreme ends to a continuum, and that they are comparative terms. One species may be more specialized than another simply because it is visited by a smaller “assemblage” of pollinators. The diversity of pollinators in that assemblage and the pollinator availability in the environment should also be taken into consideration when deciding whether a relationship is specialized or generalized.

That pollinators can be agents in shaping floral forms and that flowering plant species can become specialized in their interactions with pollinators is not the question. There is evidence enough to say that it occurs. However, that the most abundant and/or effective pollinators are the main agents of selection and that specialization is a sort of climax state in the evolutionary process (as the MEPP seems to suggest) is up for debate. Generalization is more common than specialization, despite observations demonstrating that pollinators are drawn to certain floral phenotypes. So, could generalization be seen as an adaptive strategy?

In exploring this question, Gomez and Zamora first consider what it takes for pollinators to act as selective agents. They determine that “pollinators must first benefit plant fitness,” and that when calculating this benefit, the entire life cycle of the plant should be considered, including seed germination rate, seedling survival, fecundity, etc. The ability of a pollinator species to benefit plant fitness depends on its visitation rate and its per-visit effectiveness (how efficiently pollen is transferred) – put simply, a pollinator’s quantity and quality during pollination. There should also be “among-pollinator differences in the evolutionary effect on the plant,” meaning that one species or group of pollinators – through being more abundant, effective, or both – contributes more to plant fitness compared to others. “Natural selection will favor those plant traits that attract the most efficient or abundant pollinators and will also favor the evolution of the phenotypes that cause the most abundant pollinators to also be the most effective.” This process implies possible “trade-offs,” which will be discussed in part two.

When pollinators act as selective agents in this way, the MEPP is supported; however, Gomez and Zamora argue that this scenario “only takes place when some restrictive ecological conditions are met” and that while specialization can be seen as the “outcome of strong pollinator-mediated selection,” generalization can also be “mediated by selection exerted by pollinators…in some ecological scenarios.” This is termed adaptive generalization. In situations where ecological forces constrain the development of specialization and pollinators are not seen as active selection agents, nonadaptive generalization may be occurring.

Gomez and Zamora spend much of their chapter exploring “several causes that would fuel the evolution of generalization” both adaptive and nonadaptive, which are outlined briefly below.

  • Spatiotemporal Variability: Temporal variability describes differences in pollinator assemblages over time, both throughout a single year and over several years. Spatial variability describes differences in pollinator assemblages both among populations where gene flow occurs and within populations. Taken together, such variability can have a measurable effect on the ability of a particular pollinator or group of pollinators to act as a selective agent.
  • Similarity among Pollinators: Different pollinator species can have “equivalent abundance and above all comparable effectiveness” making them “functional equivalents from the plant perspective.” This may be the case with both closely and distantly related species. Additionally, a highly effective pollinator can select for floral traits that attract less effective pollinators.
  • The Real Effects on Plant Fitness: An abundant and efficient pollinator may select for one “fitness component” of a plant, but may “lead to a low overall effect on total fitness.” An example being that “a pollinator may benefit seed production by fertilizing many ovules but reduce seedling survival because it causes the ripening of many low-quality seeds.” This is why “as much of the life cycle as possible” should be considered “in assessing pollinator effectiveness.”
  • Other Flower Visitors: Pollinators are not the only visitors of flowers. Herbivores, nectar robbers, seed predators, etc. may be drawn in by the same floral traits as pollinators, and pollinators may be less attracted to flowers that have been visited by such creatures. “Several plant traits are currently thought to be the evolutionary result of conflicting selection exerted by these two kinds of organisms,” and “adaptations to avoid herbivory can constrain the evolution of plant-pollinator interactions.”

This, of course, only scratches the surface of the argument laid out by Gomez and Zamora. If this sort of thing interests you, I highly encourage you to read their chapter. Next week I will summarize Aigner’s chapter. If you have thoughts on this subject or arguments to make please don’t hesitate to comment or contact me directly. This is a dialogue, dudes.

How to Make Petrified Wood

petrified log 2

So, you want to petrify some wood, eh? Here is a list of the basic ingredients that you will need:

  • A log (or some other chunk of wood)
  • Sediment, mud, volcanic ash, lava, or some type of inorganic material in which to bury the log and create an oxygen-free environment
  • Groundwater rich in silica (or other mineral commonly found in rocks)
  • Additional minerals including iron, copper, and manganese for coloring
  • Time and patience (because this is going to take a while – millions of years perhaps)

petrified log 8

Petrification refers to organic material being converted entirely into stone through two main processes: permineralization and replacement. First, the log you intend to petrify must be buried completely, cutting off the oxygen supply and thereby slowing the decay process considerably. Over time, groundwater rich in silica and other minerals will deposit the minerals in the pore spaces between the cells of the log. Later, the mineral rich water will slowly dissolve the cells and replace them with the minerals as well. The slower the better, assuring that the textures of the bark and wood and details such as the tree rings will remain visible. After enough million years have passed, the log may find itself exposed, pushed out of the ground by an earthquake or landslide or some other act of nature. What entered the ground as a living or recently dead tree, is now 100% inorganic material. And it is much heavier.

The colors in your petrified log will vary depending on the presence and concentrations of minerals in the groundwater. Cobalt, copper, and chromium will create greens and blues. Iron oxides will give the log hues of red, orange and yellow. Manganese adds pink and orange. During the petrification process, various circumstances can cause the silica to form a variety of crystal structures and other formations within the log. These formations can include amethyst, agate, jasper, opal, citrine, and many others. When all is said and done, your petrified log will be a true work of art.

petrified log 1

Petrification is a fossilization process. Thus, a section of petrified wood is a fossil, and it can be used to help paint a picture of what a particular region was like back when the tree was alive. It can also help us gain a better understanding of how life has evolved on this planet. Areas with large concentrations of petrified wood are located throughout the world, each with its own unique story to tell about the tree species once found in the area and the circumstances that led to their petrification. One such location is Petrified Forest National Park in Arizona. The petrified wood found there came from trees living in the area over 200 million years ago.

petrified log 5

Is a few million years too long to wait? Scientists have developed ways to petrify wood in the laboratory in as little as four or five days. One such process was developed at Pacific Northwest National Laboratory about a decade ago. It involves soaking a section of wood in hydrochloric acid for two days and then in either a silica or titanium solution for another two days. After air-drying, the wood is placed in an argon gas filled furnace and slowly heated to 1400° Celsius over a period of two hours. It is then left to cool to room temperature in the argon gas. What results is a block of ceramic silicon carbide or titanium carbide. Probably not as beautiful and interesting to look at as the one that took millions of years to form, but cool nonetheless.

petrified log 6

Read more about petrified wood here and here.

The photos in this post were taken at Idaho Botanical Garden in Boise, Idaho. If you find yourself in the area, stop by and check out their petrified log which was found in the Owyhee Mountains.

A Rare Hawaiian Plant – Newly Discovered and Critically Endangered

Hawaii is home to scores of plant species that are found nowhere else in the world. But how did those plants get there? In geological time, Hawaii is a relatively young cluster of islands. Formed by volcanic activity occurring deep within the ocean, they only just began to emerge above water around 10 million years ago. At that point the islands would have been nearly devoid of life, and considering that they had never been connected to any other body of land and are about 2,500 miles away from the nearest continent, becoming populated with flora and fauna took patience and luck.

As far as plant life is concerned, seeds and spores had to either be brought in by the wind, carried across the ocean by its currents, or flown in attached to the feathers of birds. When humans colonized the islands, they brought seeds with them too; however, its estimated that humans didn’t begin arriving on the islands until about 1,700 years ago. The islands they encountered were no longer barren landscapes, but instead were filled with a great diversity of plant and animal life. A chance seed arriving on the islands once in a blue moon does not fully explain such diversity.

This is where an evolutionary process called adaptive radiation comes in. A single species has the potential to diverge rapidly into many new species. This typically happens in new habitats where little or no competition exists and there are few environmental stresses. Over time, as genetic diversity builds up in the population, individuals begin to adapt to specific physical factors in the environment, such as soil type, soil moisture, sun exposure, and climate. As individuals separate out into these ecological niches, they can become reproductively isolated from other individuals in their species and eventually become entirely new species.

This is the primary process that led to the great floral diversity we now see on the Hawaiian Islands. Adaptive radiations resulted in more than 1000 plant species diverging from around 300 seed introductions. Before western colonization, there were more than 1,700 documented native plant species. Much of this diversity is explained by the rich diversity of habitats present on the volcanic islands, which lead to many species becoming adapted to very specific sites and having very limited distributions.

A small population size and a narrow endemic range is precisely the reason why Cyanea konahuanuiensis escaped detection until recently. In September 2012, researchers on the island Oahu arrived at a drainage below the summit of Konahua-nui (the tallest of the Ko’olau Mountains). They were surveying for Cyanea humboldtiana, a federally listed endangered species that is endemic to the Ko’olau Mountains. In the drainage they encountered several plants with traits that differed from C. humboldtiana, including hairy leaves, smooth stems, and long, hairy calyx lobes. They took pictures and collected a fallen leaf  for further investigation.

Ko'olau Mountains of O'ahu (photo credit: wikimedia commons)

Ko’olau Mountains of O’ahu (photo credit: wikimedia commons)

Initial research suggested that this was a species unknown to science. More information was required, so additional trips were made, a few more individuals were found, and in June 2013, a game camera was installed in the area. The camera sent back three photos a day via cellular phone service and allowed the team of researchers to plan their next trip when they were sure that the flowers would be fully mature. Collections were kept to a minimum due to the small population size; however, using the material they could collect, further analyses and comparisons with other species in the Cyanea genus and related genera demonstrated that it was in fact a unique species, and so they gave it the specific epithet konahuanuiensis after the mountain on which it was found. It was also given a common Hawaiian name, Haha mili’ohu, which means “the Cyanea that is caressed by the mist.”

The hairy flowers and leaves of Cyanea konahuanuiensis. Purple flowers appear June-August. (photo credit:

The hairy flowers and leaves of Cyanea konahuanuiensis. Purple flowers appear June-August. (photo credit:

The total population of Cyanea konahuanuiensis consists of around 20 mature plants and a couple dozen younger plants. It is considered “critically imperiled” and must overcome some steep conservation challenges in order to persist. To start with, the native birds that pollinate its flowers and disperse its seeds may no longer be present. Also, it is likely being eaten by rats, slugs, and feral pigs. Add to that, several invasive plant species are found in the area and are becoming increasingly more common. While the researchers did find some seedlings in the area, all of the fruits that they observed aborted before they had reached maturity. Lastly, the population size is so small that the researchers say a landslide, hurricane, or flash flood “could obliterate the majority or all of the currently known plants with a single event.”

Seeds collected from immature fruits from two plants were sown on an agar medium at the University of Hawaii Harold L. Lyon Arboretum. The seeds germinated, and so the researchers plan to continue to collect seeds “in order to secure genetic representations from all reproductively mature individuals in ex situ collections.”

Single stem of Cyanea konahuanuiensis (photo credit:

Single stem of Cyanea konahuanuiensis (photo credit:

C. konahuanuiensis is not only part of the largest botanical radiation event in Hawaii, but also the largest on any group of islands. At some point in the distant past, a single plant species arrived on a Hawaiian island and has since diverged into at least 128 taxa represented in six genera, Brighamia, Clermontia, Cyanea, Delissea, Lobelia, and Trematolobelia, all of which are in the family Campanulaceae – the bellflower family. Collectively these plants are referred to as the Hawaiian Lobelioids. Cyanea is by far the most abundant genus in this group consisting of at least 79 species. Many of the lobelioids have narrow distributions and most are restricted to a single island.


Tales of Weedy Waterhemp and Weedy Rice

This is the eighth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Population Genetics and Origin of the Native North American Agricultural Weed Waterhemp (Amaranthus tuberculatus; Amarantheaceae) by Katherine E. Waselkov and Kenneth M. Olsen

Weeds are “the single greatest threat to agricultural productivity worldwide, costing an estimated $33 billion per year in the United States alone.” Understanding the origins, population structures, and genetic compositions of agricultural weeds will not only help us better mitigate current weed problems but may also help prevent the development of future weed species.

In the introduction, the authors present three modes of weed origination: 1. De-domestication (“domesticated species becoming feral”) 2. Hybridization of domesticated species with related wild species 3. Expansion of wild plants into agricultural ecosystems “through plasticity, adaptation, or exaptation [a shift in function of a particular trait].” In this study, the authors focused on the third mode – the wild-to-weed pathway – claiming that it receives “less attention by evolutionary biologists, even though all weeds without close crop relatives must have followed this pathway to agricultural invasion, and even though this type of weed species is the most common.”  Due to the dearth of research, there are several questions yet to be fully addressed: Does invasion require evolutionary changes in the plant and/or changes in agricultural practices? What is more common, single or multiple wild sources? What are the morphological, physiological, and ecological traits that might “predispose a wild species to expand into agricultural habitats?”

To help answer these questions, the authors turned to waterhemp (Amaranthus tuberculatus), a weed that, since first invading agricultural land in the 1950’s, has “become a major problem for corn and soybean farmers in Missouri, Iowa, and Illinois.” Waterhemp is native to the midwestern United States, where it can be found growing along riverbanks and in floodplains. It is a small seeded, dioecious (“obligately outcrossing”), wind-pollinated, annual plant with fruits that can be either dehiscent or indehiscent. Herbicide resistance has been detected in A. tuberculatus for at least six classes of herbicides, making it a difficult weed to control.

There is evidence that A. tuberculatus was previously in the process of diverging into two species, an eastern one and a western one, geographically separated by the Mississippi River. However, “human disturbance brought the taxa back into contact, and possibly gave rise to the agriculturally invasive strain through admixture.” Using population genetic data, the authors set out to determine if the present-day species would show evidence of a past divergence in progress prior to the 20th century. They also hypothesized that “the agricultural weed originated through hybridization between the two diverged lineages.”

Waterhemp, Amaranthus tuberculatus (photo credit:

Waterhemp, Amaranthus tuberculatus (photo credit:

After genotyping 38 populations from across the species range, the authors confirmed that A. tuberculatus was indeed diverging into two species. Today, the western variety (var. rudis) has expanded eastward into the territory of the eastern variety (var. tuberculatus), extending as far as Indiana. Its expansion appears to be facilitated by becoming an agricultural weed. Data did not confirm the hypothesis that the weedy strain was a hybridized version of the two varieties, but instead mainly consists of the western variety, suggesting that “admixture is not a pre-requisite for weediness in A. tuberculatus.”

Further investigation revealed that the western variety may have already been “genetically and phenotypically suited to agricultural environments,” and thus did not require “genetic changes to be successful” as an agricultural weed. “Finer-scale geographic sampling” and deeper genetic analyses may help determine whatever genetic basis there might be for this unfortunate situation.

The Evolution of Flowering Strategies in US Weedy Rice by Carrie S. Thurber, Michael Reagon, Kenneth M. Olsen, Yulin Jia, and Ana L. Caicedo

This paper looks at an agricultural weed that originated from the de-domestication of a crop plant (one of the three modes of weed origination stated above). A weed that belongs to the same species as the crop it invades is referred to as a conspecific weed, and weedy rice is “one of the most devastating conspecific weeds in the United States.”  Oryza sativa is the main species of rice cultivated in the US, and most varieties are from the group tropical japonica. The two main varieties of weedy rice are straw hull (SH) and black-hull awned (BHA), which originated from cultivated varieties in the groups indica and aus respectively. Because weedy rice is so closely related to cultivated rice, it is incredibly difficult to manage, and there is concern that cross-pollination will result in the movement of traits between groups. For this reason, the authors of this study investigated flowering times of each group in order to assess the “extent to which flowering time differed between these groups” and to determine “whether genes affecting flowering time variation in rice could play a role in the evolution of weedy rice in the US.”

Rice, Oryza sativa (illustration credit: wikimedia commons)

Rice, Oryza sativa (illustration credit: wikimedia commons)

Crop plants have typically been selected for “uniformity in flowering time to facilitate harvesting.” The flowering time of weed species helps determine their effectiveness in competing with crop plants. Flowering earlier than crop plants results in weed seeds dispersing before harvest, “thereby escaping into the seed bank.” Flowering simultaneously with crop plants can “decrease conspicuousness, and seed may be unwittingly collected and replanted” along with crop seeds. Simultaneous flowering of weeds and crops is of special concern when the two are closely related since there is potential for gene transfer, especially when the crop varieties are herbicide resistant as can be the case with rice (“60-65% of cultivated rice in [the southern US] is reported to be herbicide resistant”).

For this study, researchers observed phenotypes and gene regions of a broad collection of Oryza, including cultivated varieties, weed species, and ancestors of weed and cultivated species. They found that “SH weeds tend to flower significantly earlier than the local tropical japonica crop, while BHA weeds tend to flower concurrently or later than the crop.” When the weeds were compared with their cultivated progenitors, it was apparent that both weed varieties had “undergone rapid evolution,” with SH weeds flowering earlier and BHA weeds flowering later than their respective relatives. These findings were consistent with analyses of gene regions which found functional Hd1 alleles in SH weeds (resulting in day length sensitivity and early flowering under short-day conditions) and non-functional Hd1 alleles in BHA weeds (“consistent with loss of day-length sensitivity and later flowering under short-day conditions”). However, the authors determined that there is more to investigate concerning the genetic basis of the evolution of flowering time in weedy rice.

In light of these results, hybridization is of little concern between cultivated rice and SH weeds. BHA weeds, on the other hand, “have a greater probability of hybridization with the crop based on flowering time and Hd1 haplotype.” The authors “predict that hybrids between weedy and cultivated rice are likely to be increasingly seen in US rice fields,” which, considering the current level of herbicide resistant rice in cultivation, is quite disconcerting.