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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.

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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: www.eol.org)

Waterhemp, Amaranthus tuberculatus (photo credit: www.eol.org)

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.