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The vast majority of conservation work concentrates on the fragments of natural vegetation that remain, and ignores the matrix in which they occur. However, most of the world's biodiversity is located in the tropical world, which is a patchwork of fragments in a matrix of agriculture. The bias that favors concentrating efforts on fragments while ignoring the matrix is far more damaging to conservation efforts than first meets the eye. This chapter argues that the matrix matters in a variety of social and political ways, but, more importantly, it matters in a strictly biological sense. There is now little doubt that isolating fragments of natural vegetation in a landscape of low quality matrix, such as a pesticide-drenched banana plantation, is a recipe for disaster from the point of view of preserving biodiversity. Whatever arguments exist in favor of constructing a high quality matrix, and there are many, strictly from the point of view of biodiversity conservation, the quality of the matrix is, perhaps, the most critical issue. The concept of “the quality of the matrix” must be related to the natural habitat that is being conserved, but most importantly, it involves, at its core, the management of agroecosystems.

Human activities superimpose complexity onto spatially and temporally variable successional processes. Biotic and anthropogenic legacies of land-use transitions and forest regrowth are intricately connected through effects of landscape suitability for crop cultivation or pasture establishment; these phenomena strongly affect rates and scale of land clearing for agriculture, duration of land use, rates of agricultural abandonment, and seedling establishment following abandonment. Studies in the Old and New World tropics have documented pervasive, long-term human impacts on species composition and forest structure in tropical secondary forests. The rate, structure, and composition of forest regrowth are strongly affected by soil disturbance, residual vegetation, and proximity to seed sources. Long-term effects emerge from cascading effects of initial abundance, composition, and spatial patchiness of species that colonize abandoned agricultural areas. Thus secondary forests are particularly sensitive to human impacts and land use intensity. This chapter analyzes five major ways in which human activities influence secondary forest regeneration in Costa Rica and presumably other regions of the wet tropics: (1) remnant trees in pastures; (2) hunting and density of mammalian seed predators; (3) duration and intensity of agricultural land use; (4) landscape structure and distribution of forest patches; and (5) invasion of exotics.

Since the 1970s, there has been a growing global awareness of the El Niño–Southern Oscillation (ENSO) phenomenon, especially in regard to its impacts on humans, natural ecosystems, and agriculture. The three strongest events of these decades (1972–73, 1982–83, and 1997–98) each marked a milestone in this progression. To be sure, not all climate extremes during any given ENSO year are necessarily due to that phenomenon; for example, the intense drought that occurred in 1982–83 in the West African Sahel does not appear to be causally linked to the strong ENSO event of that period (Glantz, 1987). However, even unrelated climate anomalies can exacerbate the effects of an El Niño or La Niña on world food supplies. Here we summarize the major effects of the three most recent very strong El Niño events (see box 4.1) with a focus on their agricultural manifestations. Table 4.1 summarizes the effects by region and continent and for the world food system as a whole. Evolving understanding of ENSO (and its related phenomena) appears to be contributing to the development of improved resilience to such major climate shocks in some regions (see chapter 6 for use of ENSO predictions in agriculture and chapter 8 on building adaptive capacity). However, continuing progress in affected regions is needed for agriculture to withstand (or benefit from) very strong El Niño events in the future, especially since global climate change may be affecting conditions as well. The El Niño of 1972–73 awakened international attention to the ENSO cycle. Besides the failure of the fishery industry in Peru, there were droughts, floods, and food shortages in various locations around the world that also appeared to be associated with El Niño. Consequently, scientists and the public began to realize that El Niño teleconnections and their impacts could extend beyond the West Coast of South America (Glantz, 2001). During the El Niño event of 1972–73, the reduced anchoveta harvest, combined with overfishing, caused the collapse of the Peruvian fishmeal industry and the dislocation of entire fishing communities.

Sustainable agriculture can be defined in many different ways. In industrial nations, sustainable agriculture means improving energy use efficiency, reducing environmental pollution, and increasing and sustaining profitability. For millions of small-holder farmers throughout the tropics, sustainable agriculture means providing basic food needs for the farming family, improving the farmer’s ability to replenish soil nutrients and control soil degradation, and optimizing crop yield per unit area of land. Soil utilization for agricultural production in the tropics during the past two centuries, to a large extent, has been influenced by the technological and economic changes in temperate regions. Research and development for agriculture during the colonial era were mainly focused on the needs of industrial nations, while the production of food crops for the indigenous inhabitants was largely left in the hands of the traditional slash-and-burn cultivators. Large and small cash crop plantations were developed on fertile, high-base-status allophanic and oxidic soils for coffee, cocoa, banana, and sugarcane production throughout the humid and subhumid tropics. Cotton was cultivated on smectitic soils and high-base-status kaolinitic soils in the subhumid and semiarid regions of Africa for the textile industries in temperate regions. In tropical America, cattle ranching, a production system introduced by European immigrants, still occupies most of the fertile flat land today, while food grains are usually cultivated on less fertile land or in shallow soils on steep slopes. In tropical Africa and Latin America, a wide range of food crops, such as maize and beans, potato, cowpea, sorghum, millet, cassava, and yam are mostly produced under the traditional slash-and-burn system of cultivation on less fertile kaolinitic soils. In tropical Asia, the indigenous intensive rice-based agriculture on wet smectitic soil has been practiced over many centuries and has been able to meet the basic food needs for the increasing population in the region. Generally, upland food crop production in the tropics has not kept pace with human population growth in the tropics during the past century. It was not until the 1950s and 1960s, following the independence of many nations in tropical Asia and Africa, that more attention was given to the research and development of food crop production.