At the end of the harvest season, when the seasonal farm workers prepare to return home, established workers sell their good hunting dogs for up to $1000 pesos to migrant workers who purchase them using the earnings from the harvest season. In the process of describing the everyday-lived-experience of farm workers, is important to also recognize that the experience of the finqueros themselves is often overlooked, which in turn encourages a shallow understanding of the complexity of the problems faced by migrant workers in coffee plantations. Similar to what Holmes describes in the case of migrant farm workers in US agriculture, the increasingly corporatized market “squeezes growers such that they cannot easily imagine increasing the pay of the pickers or improving the labor camps without bankrupting the farm” . As he continues, “perhaps instead of blaming the growers, it is more appropriate to understand them as human beings doing the best they can in the midst of an unequal and harsh system” . The struggle in coffee plantations is experienced on its own way by the finqueros, who find themselves “squeezed” between the pressure of the market, increasing indebtedness and the social stigma that accompanies large plantations in this region. The finqueros I interviewed for this work were generally concerned about the living conditions of their workers and expressed future plans to improve mostly infrastructure, but find themselves with their hands tied in the face of low prices and few economic benefits from the premiums offered by the specialty market. On the one hand finqueros most catch up with current trends that include roasting their own coffee, which requires special infrastructure, special training, as well as high investments. On the other hand, growers have also had to incorporate the touristic aspect of their plantations, create and recreate the colonial stories that forged these places, build attractive bungalows and spas, black plastic plant pots wholesale and sell coffee as a whole new “experience of the senses”, that includes biodiversity conservation at its center and the recasting of colonial narratives .

As one of them puts it: “el turismo hace maravillas” . In addition, in order to increase economic gain, finqueros have also started to diversify their income, not only through tourism, but also through the production of ornamentals, cardamom, timber, and medicinal plants, which marketable value increases when being planted along with coffee. Low and unstable coffee prices, in combination to a changing climate and disease outbreaks, add to the struggle of coffee growers, which blends with the problem of low productivity of their shade-grown coffee plantations, and labor shortages for this region7 , a problem that is not new to the region . To add to this problematic, Renard points out: “ The liberalization of the international coffee market combined with a sharply reduced state intervention engendered the control over coffee production by a few transnational companies and the collapse of the economy of small producers. Combined with natural disasters whose effects were not addressed by the neoliberal state, this situation caused the region to be bypassed by Guatemalan labor that now prefers direct migration to the United States” . Moreover, in the past decade, finqueros in Soconusco and Central America were also challenged by two important coffee leaf rust disease outbreaks caused by the fungus Hemileia vastatrix, that practically swept entire coffee plantations in the region in 2008 and 2013 . This disease is highly associated with climate change , another important environmental challenge that is projected to increase climatic variability and the intensity of rain for this region . At the center of the imaginary is the shade-grown coffee farm, which is offered to the world as a steward of the land, a guardian of endangered species, a place for retreat within lush gardens overlooking a seemingly natural, remote land. However, within the wrinkles and creases of this portrait lies the experience of farm workers laboring in the fields, the struggles, the joys, and the stories that give meaning to this place.

Considering that various visions, knowledge, and experiences converge within the coffee plantation, we can begin to understand it as a co-produced space, one that is constructed through the ecological views and social relations of diverse actors that produce this space : the market and the consumers, the workers and their everyday labor experiences, the owners with their own struggles and desires, and dominant conservation narratives. In some ways, the convergence of ecological knowledges in the coffee plantation, the alternative market boom, and the conservation narrative sold in “First World” cafeterias, has created a particular coffee tropical imaginary. In this sense, coffee produced on shaded and biodiverse plantations is often targeted toward a specific environmentally conscious, upper class consumer that engages with these narratives by both directly buying the coffee as commodity, and through ecotourist vacations to coffee plantations. Shaded plantation coffee is also presented as a luxurious commodity associated with a type of tropical imaginary that, in actuality, is produced at the expense of farm workers’ living and working conditions. This work questions the practices and narratives surrounding biodiversity conservation in the context of farm workers’ lives. Farmworkers in coffee plantations are a highly vulnerable sector in the coffee production chain. In these labor-intensive systems, they not only suffer unfair living and working conditions, but also face fears and anxieties posed by conservation practices and discourses: the need to harvest coffee in the dense vegetation or abundant leaf litter, and the strict regulation around the use of resources to supplement their daily diets. Multiple imaginaries have shape this landscape dominated by coffee. On the one hand, neoliberal market trends in coffee production– which have brought the multiple certification schemes we can find in the supermarket– have imposed dogmatic regimes around the production of coffee , which– as I have shown– are at odds with people’s needs and desires. On the other hand, scientists have often promoted an imaginary around shade-grown coffee production, which reminds us of a natural or seemingly natural portrait, in which humans are nonexistent . These imaginaries, supported by an exclusionary narrative of biodiversity conservation, obscure the lived experience of farm workers. I also bring attention to an important problem in organic production, which is the fact that it does not question social conditions, particularly of farm workers, despite presenting itself as a label with social responsibility. Issues such as poor wages, structural violence, social segregation, and racism are aspects of the daily lives of farm workers in systems that depend heavily on migrant labor . However, there is a strong emphasis on ecological sustainability goals, that ignore such issues. The social implications of these labels and discourses about conservation in a labor-intensive system are striking. Therefore, in the practice of questioning our current food regime, we must reflect and recognize how narratives of conservation might reinforce farm workers’ marginalization. A change of paradigm in the conservation narrative in shaded coffee plantations should acknowledge workers’ experiences, but not only the ways in which farm workers experience injustices in the plantation, such as prohibitions, unequal pay, forced labor, bodily pain, and unfair living conditions; also, the potential subtle and creative ways of contesting them, which challenges a potential passive and subjugated vision that their experiences might provoke on the reader. For example, disregarding hunting prohibitions, using the work in coffee plantations to reproduce the peasant living back at home, appropriating land in abandoned areas of the plantation, and gossiping and character assassination of powerful figures within the hierarchy of the plantation , all as an act of autonomy or “everyday resistance”. Similarly, I acknowledge the fact that plantation owners also find themselves squeezed in various narratives: the push to be more ecologically sustainable, the unforgiving reputation that many of them receive by the media and the adjacent ejidos, black plastic plant pots bulk the push to be more productive in a competitive market while being socially just, all within a reality of low coffee prices, and increasing indebtedness to international buyers and powerful corporations, such as Nestle and Starbucks.

In some way, finqueros benefit from the conservation narratives and the imaginary of shade grown coffee plantations, as they are able to accommodate their coffee with much more identity and value in the market. Finally, this research invites all of us as scientists, tourists, and coffee consumers to rethink our political actions as we construct the spaces that we visit, study, and imagine. In a time of increasing violence towards immigrants, and a food regime increasingly dominated by corporations, it is pertinent to ask how our actions change and perpetuate current neoliberal models, that are ultimately detrimental to the lives of people that live with and from coffee. Coffee is an important agricultural system for Latin America, supporting millions of farmers and national economies. A large portion of coffee in Latin America is produced under the shade of forests, making this habitat important for the conservation of biodiversity and ecosystem functions, as well as the sustenance of human livelihoods. Through the analysis of species interactions and human lived-experiences I provide a glimpse to the social and ecological complexities of organic shade-grown coffee plantations. Shaded coffee plantations are complex socioecological systems constructed through our scientific understandings of ecological interactions, insects and other organisms, as well as by the experience of people making a living in these spaces. My work contributes to our understanding of complexity through the lens of humans and non-humans, and paints a portrait of shade grown coffee that shows Los claroscuros del café, or the disambiguation of this space. On the one hand, my research contributes to our understanding of the mechanisms that maintain species diversity and complex interactions in complex agroecosystems. From an agroecological perspective, resource heterogeneity, and the availability of a diverse suit of resources, including food, nesting and connectivity resources can promote species richness and biological pest control in coffee systems. My research highlights the importance of conserving specific resources for insects in the face of increasing agricultural simplification. From a political ecology perspective, my research brings attention to an overlooked aspect of shadedcoffee systems, which is the lived experience of farm workers, and indirectlyinvites all of us to rethink our political actions as we construct the spaces that we study. Highly parallel genotyping has become an important component of genomics. Hybridization of genomic DNA and RNA to microarrays has been used in the past for detection of polymorphisms between genotypes. However, the previously available arrays for complex genomes only provided limited transcriptome coverage. We developed an array designed to maximize transcriptome coverage while maintaining the possibility of performing other analyses. Our custom designed Lettuce GeneChipW combined the benefits of overlapping probes across unigenes, similar to that demonstrated by Gresham et al. for yeast, with the use of anti-genomic probes to maximize the possible coverage of unigenes while maintaining the sensitivity to detect polymorphisms and retaining appropriate controls to normalize and correct for background noise. The tiling path design allows for multiple assessments of hybridization differences between lines for single positions rather than single assessments of a few positions as obtained with most expression arrays. We developed custom scripts for analysis of our hybridization data taking into account the multiple probes covering a single position as well as filtering out poorly performing probes. We used recent advances in high throughput sequencing technology to validate our SPP calls as well as filter out potentially unreliable data. Genomic DNA and cDNA are two options for hybridization to an array for SFP detection. The decision of which to use becomes more difficult as genome size and complexity increases. DNA as well as cDNA are both viable targets for species with smaller genomes such as Arabidopsis and rice. However, with larger and more complex genomes such as barley, cDNA was indicated as a more reliable option for hybridization even with the added difficulty of subtracting out expression effects. The genome of lettuce is nearly 17x larger than Arabidopsis although it is half the size of barley. Given the difficulty of accounting for spatiotemporal expression effects as seen in cDNA, we focused on developing methods to use genomic DNA. Rostokset al.suggested that genomic DNA may be a feasible target in larger genomes with added replication. With the redundancy of the overlapping probes in the lettuce array, the need for additional replication was reduced because they provide technical replicates within a chip.