Policy discussions of the future of small farms, for example, emphasize the role of small farms in agricultural development in part because of their superior efficiency . This argument leans heavily on the inverse farm size – productivity relationship, but requires that small farms be more efficient with their use of all resources and not just land. Whereas a farm size – land productivity relationship does not provide clarity on this issue, a farm size – total factor productivity relationship does. In this light, we argue that the inverse relationship literature needs to shift its focus from land productivity to total factor productivity. In fact, empirical studies assessing the productivity – farm size relationship in the developed world, such as Garcia et al. , Alvarez and Arias , and Rasmussen , almost exclusively use measures of technical efficiency or total factor productivity. Similarly, the literature estimating national level agricultural productivity is clear in its use of total factor productivity as a preferred measure . We illustrate the importance of productivity measures with new empirical evidence on the farm size – productivity relationship across regions of Brazil from 1985 to 2006 . Our evidence is only suggestive because we are unable to correct for potential issues of measurement error in farm size, output, and inputs that have been identified in recent literature. However, this period in Brazil provides an excellent case study because it includes regions with relatively advanced agricultural sectors, those characterized by more traditional agricultural production, and others experiencing rapid agricultural transformation, allowing us to assess the farm size – productivity relationship and its dynamics at different stages of agricultural development. Using a pseudo-panel of farms aggregated at the municipality by farm size level, square black flower bucket we show that estimating the farm size – productivity relationship using land productivity is potentially misleading.

While we always identify an inverse relationship using land productivity, we find disparate results when using total factor productivity. In the modern agricultural regions of Brazil, we find a direct relationship between farm size and total factor productivity, and in the rapidly transforming region of the Center-West we identify dynamics that suggest the inverse relationship is disappearing over time. The analysis highlights that the relationship between total factor productivity and farm size has evolved with modernization, shedding some light on the issues raised by Mill over 150 years ago. The remainder of this paper is organized as follows. In Section 2 we seek to clarify the common measures, their relationships, and their advantages and limitations in empirical work. Section 3 presents the empirical exercise, generating new evidence on the relationship between size and productivity in several macro regions of Brazil. In Section 4 we summarize and conclude with policy implications.Farm size may be related to a broad range of economic outcomes, such as employment, poverty, inequality, food security, efficiency and growth. While these are important issues connected to the role of farm size in development, here, as with most of the literature on the inverse relationship , we focus specifically on the concept of productivity. The following discussion seeks to clarify the relationships between the various productivity measures most commonly used in the literature, allowing us to draw conclusions on the impact that choice of measure may have on finding an IR and the potential implications for policy.The relationship captured by is unconditional in the sense that it is the simple bivariate relationship between land productivity and farm size. Using land productivity as a measure is inherently limited—as would be any partial measure of productivity—whenever there is more than one factor of production.

If use of other factors vary systematically with farm size, the IR between land productivity and farm size may simply reflect more input intensive practices of small farms. Higher land productivity may reflect overuse of fertilizer, for example, which would not necessarily reflect any underlying productivity advantage of small farms. In such situations, estimates of the farm size – land productivity relationship introduces omitted variable bias into estimates of the underlying farm size – productivity relationship. From this perspective, a focus on the relationship between land productivity and the size of farms may be misplaced. Similarly, analysis using different partial productivity measures may result in conflicting policy recommendations. Indeed, Sen’s seminal contribution revealed precisely this type of systematic relationship between the intensity of labor use and farm size, leading to his formal exposition of the dual labor market hypothesis . Figure 1.2 illustrates the problem in the case of Brazil. While there is an inverse relationship between land productivity and farm size, there is a direct relationship between labor productivity and size. Analysis of the farm size and productivity relationship using labor productivity suggests that larger farms are more productive than are their smaller counterparts. Policy recommendations from the two partial measures of productivity would differ, underscoring the need for a comprehensive measure of productivity when identifying any relationship with farm size.We now provide an example using data on Brazilian agriculture. The intention here is not to explain the relationship between farm size and productivity by controlling for its potential determinants. Rather, we seek to use a regional analysis within Brazil to highlight how the choice of measure influences the observed relationship and how these patterns can change across stages of agricultural development. Our evidence is only suggestive because we are unable to correct for the measurement issues in farm size, outputs, and inputs that recent literature has focused on. We discuss this further below. The results provide an important counterpoint to much of the literature that has focused on countries in Africa and Asia where the overwhelming majority of farms have less than 2 hectares . Mean and median farm size in Brazil, in contrast, were around 65 and 10 hectares in 2006. The data come from the 1985, 1995/1996, and 2006 rounds of the Brazilian agricultural census. For confidentiality reasons, we constructed a pseudo-panel in which all farms in the census are aggregated into five farm size classes within each municipality of Brazil.9 Aggregation requires that we assume homogeneity within each observation . We call these “representative-farms,” as they reflect the average behavior of a given farm size in a given municipality. The pseudo-panel approach has been used recently to study agricultural productivity growth by Key and Rada et al. . Antmann and McKenzie demonstrate that, in the context of mobility studies, pseudo-panels can be used to consistently estimate parameters of interest. The averaging within cells in each period reduces the influence of individual-level measurement error, and the fact that it is not a true panel of farms makes it less vulnerable to non-random attrition. They show the approach is also robust to some forms of non-classical measurement error. We begin with 47,365 representative farms for all of Brazil across the three survey years. Due to concern about the comparability of a small number of extremely large observations, square black flower bucket wholesale we remove all representative farms in the Northeast and South over 4,000 ha and all of those over 5,000 ha in the North, Southeast, and Center-West. We then identify land productivity outliers taking into account the IR shown in Figure 1.1 and potential non-linearities. Thus, rather than trim the tails of the unconditional land productivity distribution, we use a quadratic specification to regress land productivity on farm size with municipal fixed effects and survey year dummy variables.

From this regression we identify and remove outliers, defined as all representative farms with residuals greater than four standard deviations from their size specific predicted values. Together, the data cleaning exercises remove 1.8% of the initial sample. The Census data were gathered by the Brazilian Institute of Geography and Statistics through end of season in-person farmer interviews based on recall. Output is measured as the real value of total agricultural production, deflated to 2006 with a price index developed from the data in Gasques et al. . Farm size is measured in hectares , and unlike in many African and Asian countries the overwhelming majority of farms operate a single plot. Additional factors of production used in the production function are family labor, purchased inputs including hired labor, and an index of capital. The number of male, female, and child family members working on each farm are used to develop a family labor index measured in adult male equivalents. The index assigns weights of 1.0 to men, 0.75 to women and 0.5 to children under 14. In 2006 around two thirds of family labor was provided by men, and over 90% of working family members were 14 years or older. The real value of purchased inputs, including expenditure on fertilizer, seeds, hired labor, fuel, energy, soil amendments, and other items, are deflated with the same price index used for output. A proxy for the total capital stock is calculated as a quantity index comprised of machine, animal, and tree capital stock sub-indices following Moreira et al. and Butzer et al. . The machine capital stock index values tractors of five horsepower classes, trucks, harvesters and other agricultural equipment using a constant set of sale prices drawn from the Instituto de Economia Agrícola in São Paulo. The stock of animal capital is measured in cattle equivalents of the nine most important animal stocks and aggregated with a set of time invariant relative prices . The stock of tree capital is measured as the present discounted value of expected future profits for thirteen different tree crops, using region-specific estimates of expected profits. The subindices are aggregated using region-specific weights estimated by regressing output on the three capital stock sub-indices in the base year 1985.13 Additionally, we control for unexpected shocks in rainfall and temperature to each municipality in each survey year utilizing data described in Wilmott and Matsuura . These quarterly shocks are measured as standardized deviations from 25-year moving averages ending in the year prior to each Census. The data are transformed into categorical variables capturing extremely low, below average, average, above average, and extremely high values relative to the historical municipal average. Weather shocks between -1 and 1 standard deviations are treated as normal weather years and are the reference category, with extremely high and extremely low values occurring at more than ±1.645 standard deviations. The data used are drawn from a nation-wide decennial census and are potentially subject to multiple sources of measurement error. The literature on measurement error and its implications for the IR has grown rapidly in recent years. Of greatest concern are non-classical types of measurement error that are correlated with farm size. Carletto et al. , Carletto et al. , Abay et al. and Dillon et al. examine measurement error in self-reported farm size relative to more accurate approaches to measuring land . They demonstrate clearly that farmers report area with error, that this error varies systematically with farm size, and that whereas small farms tend to overestimate farm size, large farms tend to underestimate their size. The implications for the IR literature are mixed, as Carletto et al. and Abay et al. find that the IR becomes stronger when measurement error in farm size is the sole correction made, but Carletto et al. and Dillon et al. both find that correcting for such measurement error partially mitigates the IR in some of their data but has no statistically significant impact elsewhere. Similarly, several recent papers have explored the implications of non-classical measurement error in output. Desiere and Jolliffe , Gourlay et al. , and Lobell et al. show non-classical measurement error in self-reported output when compared to “crop cuts” as the gold standard measure. Importantly, small farms overreport output more so than larger farms in their data. Conditional on GPS land measurement, the IR disappears in these papers when they utilize the more objective measure of output. Abay et al. explore measurement error in both farm size and output, and concur that in their data the IR disappears when land is measured objectively and then crop cuts are used to correct for measurement error in production. However, they caution that the IR strengthens when land is self-reported and measurement error in output alone is corrected. Lastly, measurement error in the use of inputs such as labor is potentially an issue. Relative to weekly surveys conducted in-person or by phone, end of season surveys of labor usage can contain substantial errors .

The four new fungicides were moderately to highly effective in reducing PRR and P. cinnamomi populations in rhizosphere soil of the avocado seedlings and rootstocks used. Overall, oxathiapiprolin was the most effective among fungicides evaluated. In experiments with Zutano seedlings, the efficacy of oxathiapiprolin at the low rate of 70 g/Ha was 2- to 33-times higher than that of the other fungicides and 2- to 4-times higher than that of mandipropamid, a CAA fungicide. In a study on managing P. capsici on peppers , the difference in effectiveness of oxathiapiprolin at 30 g/Ha as compared to the CAA dimethomorph at 262.5 g/Ha was similar to our study using the same FRAC codes of fungicides. In response to reducing PRR, avocado plants treated with oxathiapiprolin generally developed more shoot and root growth as compared with untreated plants. On the avocado seedlings and rootstocks used, fluopicolide, mandipropamid, and ethaboxam treatments also effectively reduced the incidence of PRR compared with the control. P. cinnamomi propagules in the rhizosphere soil were only significantly reduced on the Zutano seedlings and the Dusaâ rootstock. These latter treatments were often significantly more effective than potassium phosphite or mefenoxam; whereas fluopicolide often performed statistically similar to oxathiapiprolin. Still, the efficacy of potassium phosphite was demonstrated with significant reductions in PRR on the seedlings and rootstocks although its overall performance may have been compromised by the use of three P. cinnamomi isolates with reduced sensitivities to the fungicide in our soil inoculations. These results also could explain why potassium phosphite is still effectively used in managing PRR in California since many growers cultivate avocado trees grafted on the Dusaâ rootstock. Thus, flower buckets wholesale highly effective alternatives to mefenoxam and the phosphonates were identified by us for the management of avocado PRR.

Oxathiapiprolin used at low rates provided similar or better efficacy than the other fungicides. Oxathiapiprolin, fluopicolide, mandipropamid, and ethaboxam previously demonstrated high efficacy against selected foliar and root diseases of vegetable and tree crops caused by Oomycota organisms in greenhouse and field studies. Thus, the four fungicides were highly efficacious in reducing Phytophthora root rot of citrus caused by P. nicotianae and P. citrophthora . Oxathiapiprolin, fluopicolide, and mandipropamid were more effective in managing P. capsici on watermelon than mefenoxam or potassium phosphite . In other studies, oxathiapiprolin was shown to be highly effective in managing diseases of vegetable crops caused by Phytophthora species including P. capsici and P. infestans and controlled black shank of tobacco caused by P. nicotianae . Ethaboxam was shown to be an effective treatment for tomato late blight , as well as Phytophthora blight of pepper . Based on our studies, registration of oxathiapiprolin for use on avocado has been initiated through the Inter-regional Research Project No. 4 , and ethaboxam, fluopicolide, and mandipropamid are proposed for further development on avocado. Additional evaluations will have to be done under field conditions using rootstocks with different growth characteristics and susceptibilities to PRR. The availability of fungicides with new modes of action and options for rotation and mixture programs using previously registered and new fungicides will help reduce the risk of development and spread of resistance in P. cinnamomi populations in California avocado production. Growers currently rely heavily on the use of phosphonate-based fungicides, and as we demonstrated, pathogen populations are shifting towards reduced sensitivity to this fungicide class. Thus, there is an urgent need to register fungicides with new modes of action. In our greenhouse studies, overall treatment efficacy in reducing PRR and soil inoculum levels of the pathogen on the susceptible PS.54 was reduced as compared with the more tolerant Dusa rootstock, indicating additive effects of fungicide use and rootstock selection. In an integrated approach for a durable and effective management of PRR that allows the continued economical production of avocados in P. cinnamomiinfested soils, the use of tolerant rootstocks is critical along with irrigation management and cultural practices such as using mulching and planting in areas with good soil drainage.

There are Phytophthora species that can infect only one, or a few different hosts like Phytophthora infestans de Bary, and then there are species that can infect hundreds or even thousands of different plant species such as P. cinnamomi Rands . P. cinnamomi is of particular interest in California because it causes Phytophthora root rot of avocado, in fact, PRR is the most destructive disease of avocado production worldwide . PRR limits production of avocado by killing feeder roots which reduces fruit yield and can cause tree death . P. cinnamomi impacts other fruit crops such as peach, pineapple, and high bush blueberry, as well as affecting natural stands of eucalyptus, pine, and oak . Areas that have become infested with P. cinnamomi will never completely remove this pathogen from the soil. Current chemical treatments are being challenged by the emergence of isolates that are more virulent and less sensitive to potassium phosphite . The current challenges of PRR treatment of avocado necessitates a better understanding of the molecular and genetic basis of plant-P. cinnamomi interactions. Taking advantage of the wide host range of P. cinnamomi, we developed a detached leaf assay in Nicotiana benthamiana to elucidate the molecular and genetic basis of plant immunity against P. cinnamomi . The hemibiotrophic lifestyle of P. cinnamomi was confirmed in this model system through differential staining and quantitative PCR pathogen DNA quantification. The model plant, N. benthamiana , has been widely used to study the pathogenicity and virulence of similar broad range and root Phytophthora pathogens such as P. capsici , P. palmivora , and P. parasitica . Furthermore, several studies using model plants, crops, and tree crops to study pathogenicity, virulence, and fungicide efficacy of root rot pathogens such as P. sojae, P. capsici, P. parasitica, P. palmivora, P. cinnamomi, and P. ramorum have been performed using detached-leaf assays . Using the tools developed in previous studies and combining them with RNAseq analysis as well as functional assays using this model plant it becomes possible to gain a better understanding of plant defense responses against P. cinnamomi infection.

Previous transcriptomic studies on avocado and model systems provides important information on plant gene expression in response to infection by P. cinnamomi. Avocado defense gene expression has been analyzed three separate times over the last eight years . Mahomed and Van den Berg used the tolerant avocado rootstock Dusa to study the gene expression changes after P. cinnamomi inoculation. By comparing expressed sequence tags and 454 pyrosequencing they were able to identify six defense related genes. The defense genes identified encoded: cytochrome P450-like TBP , thaumatin, PR10 , metallothionein-like protein, MLO transmembrane protein encoding gene, and a gene encoding a universal stress protein . In a follow up study, again on the resistant avocado rootstock Dusaâ , 16 additional defense genes encoding: WRKY transcription factors, phenylalanine ammonia-lyase , beta-glucanase, allene oxide synthase, allene oxide cyclase, oxophytodienoate reductase, 3-ketoacyl CoA thiolase, Fbox proteins, ethylene biosynthesis, isoflavone reductase, glutathione s-transferase, cinnamyl alcohol dehydrogenase, cinnamoyl-CoA reductase, cysteine synthase, quinone reductase, and NPR1 were differentially expressed after P. cinnamomi infection. Reeksting et al. found up-regulated transcripts corresponding to cytochrome P450, a germin-like protein , flower harvest buckets and chitinase genes after P. cinnamomi infection using microarray technology. It has been stated , that an important difference between gene expression in avocado and model systems is that the salicylic acid response is only seen in infected avocado, which is associated with a defense response to biotrophic and hemibiotrophic pathogens. It has been further asserted that P. cinnamomi infection of model plants initiates the jasmonic acid and ethylene pathways associated with necrotrophic pathogens. Although there are differences between expression patterns in avocado and the numerous model plants that have been studied to better understand plant defense to P. cinnamomi, there are also many similarities. Model plants used to better understand plant defense gene response to P. cinnamomi infection include; Zea mays, Arabidopsis thaliana, Lupinus angustifolius, Castanea sativa , Eucalyptus nitens, Lomandra longifolia, and most recently N. benthamiana . The gene expression in susceptible model hosts such as L. angustifolius and N. benthamiana can be compared to tolerant hosts like A. thaliana and L. longifolia to identify differences that may be associated with resistance to P. cinnamomi. Santos et al compared the gene expression between a susceptible and resistant variety of chestnut. They found that genes encoding for proteins involved in pathogen recognition proteins , were significantly upregulated in the resistant variety especially before inoculation. Six out of eight defense related genes including; WRKY31 and LRR-RLK’s were more highly expressed in the uninoculated C. crenata when compared to the uninoculated C. sativa. This increased basal defense to P. cinnamomi may contribute to this variety’s resistance. Gene expression in E. nitens in response to P. cinnamomi infection included up-regulated overrepresented gene ontology terms related to JA and ET signaling . Interestingly, pathogenesis-related gene 9 was down-regulated and represents a cross-species effector target during P. cinnamomi infection. Functional genomics and validation of these defense genes has only been performed in one study in A. thaliana. Eshraghi et al. reported that an auxin Arabidopsis mutant was more susceptible to P. cinnamomi infection than the wild type indicating the role of auxin pathways in P. cinnamomi defenses. The main challenges for the identification of P. cinnamomi resistance genes in avocado are the lack of tools available for functional genomic studies and limitations associated with tree crop biology. Next-generation sequencing has provided some information on the expression of defense-related genes in avocado infected with P. cinnamomi. However, the lack of the genome sequence and absence of functional genomic tools for avocado makes it difficult to determine and confirm their contributions to resistance against P. cinnamomi.

The N. benthamiana model plant provides the opportunity to conduct functional genomic studies to determine the role of defense response genes to P. cinnamomi resistance that is not yet available in the avocado system or other tree hosts. Model plants including A. thaliana , L. angustifolius , and Medicago truncatula have been previously reported as susceptible hosts for this oomycete pathogen and have been used to study P. cinnamomi pathogenesis and plant responses to this pathogen. Although whole genome sequencing was available for these pathosystems, functional assays were not conducted with the exception of one study in Arabidopsis implicating the auxin signaling pathway with defense response against P. cinnamomi . Conducting RNAseq studies in N. benthamiana system at different time points during the infection process will provide a foot-hold into the defense gene expression pattern during P. cinnamomi infection and will allow us to conduct functional studies of selected defense genes using this N. benthamiana–P. cinnamomi pathosystem. Differentially expressed pathways and genes can be then validated by RT-qPCR in N. benthamiana and in avocado inoculated with P. cinnamomi using a detached leaf assay. Functional validation of the most promising genes can be done in N. benthamiana by transient over expression or silencing to determine their contribution to P. cinnamomi resistance. If similar expression patterns are found in avocado it is reasonable to consider this gene a good candidate for marker assisted breeding or biotechnology in avocado. As genomic tools for avocado quickly become more available the methods developed in this system will become more applicable to this fruit tree crop. RNAseq analysis of infected N. benthamiana roots can complement this system by identifying what genes are universally expressed in the plant in response to P. cinnamomi infection and what gene expression is unique to the roots. Functional genomics are lacking in avocado; therefore, the objectives of this study were i) to establish a model system to look at defense gene expression in response to P. cinnamomi infection, ii) validate differentially expressed defense genes using overexpression in the same N. benthamiana model system, and iii) establishing connections to similarly expressed defense genes in avocado in response to P. cinnamomi infection. This information will help to select candidate defense genes in avocado for marker assisted breeding or biotechnology. The average total million reads for the sequenced mock-inoculated N. benthamiana samples were 66, 75, 75, 81, and 70 million for the 6, 12, 24, 36, and 48 hpi time points respectively. The average total reads for the inoculated N. benthamiana samples were 145, 123, 80, 62, and 70 million reads for the 6, 12, 24, 36, and 48 hpi time points respectively. The average percentage of reads mapped for the five-mock inoculated time points was between 86 and 88%.

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.

Extensive studies of community assembly of ants in the coffee agroecosystem reveal that both environmental filtering, which is frequently associated with nesting opportunities , and competitive interactions are likely involved . Here we divide that literature into two general groupings, ants that generally nest in the ground or leaf litter, broadly construed, versus ants that nest in hollow cavities, generally referred to as twig-nesting ants. The first, we suggest, are structured largely through competition for feeding resources, whereas the second are structured more through competition for nesting sites.The general spatial patterns seen with ground-foraging ants are frequently thought to result from interspecific competition . Part of the evident spatial structure is the existence of mosaics in which patches of dominant species are arranged in space something like a jigsaw puzzle. Ground-foraging ants on coffee farms seem also to form this mosaic spatial pattern; various species form patches that are relatively discrete, with each species occupying its own space and the patches fitting together almost as if they were pieces in a jigsaw puzzle . Studies in coffee farms suggest that much of the spatial pattern of ground-foraging ants is indeed a consequence of the underlying structure of competitive interactions among the various species , although that structure is not simple.For both arboreal ants that nest in hollow trees or shrub twigs and leaf litter ants that inhabit hollow twigs on the ground, the size, number, or diversity of available twigs may be an important determinant of community structure. For arboreal ants in coffee agroforests, hollow coffee twigs and shade-tree twigs and branches comprise the vast majority of available nest sites, and there can be considerable variation in the size of twigs available. However, in the coffee plants themselves, most ants prefer to nest in similar-sized twigs . Although one larger ant species, Procryptocerus hylaeus, occupied twigs with larger cavities in the field and selected larger twigs in choice experiments in the lab, 30 planter pot nine other species examined showed no difference in the mean nest size occupied .

Nest availability also strongly varies, and competition for nesting resources may be an extremely important determinant of community structure and contribute to community assembly processes in tropical communities. Work in coffee farms has enabled learning the importance of diversity, quality, and size of nesting resources for community assembly. Ants compete for nesting resources, and among indications of nest limitation in ants are the occupation of a large fraction of available resources, takeovers of nests by different colonies or species, and occupation of artificial nests . Coffee agroforests that differ in shade structure,and therefore in the overall availability of nest sites, have been used to demonstrate the importance of nest-site limitation for ants, and the fact that nest-site limitation can contribute to a loss of ant diversity . In a comparison of two different coffee farms varying in the amount of shade, nest-site limitation was stronger in farms with less shade. In addition, increasing the number of artificial nests in high-shade coffee farms resulted in a large increase in the number of species colonizing twig nests, but there were less dramatic increases in richness in low-shade sites . Thus nest limitation, but also other processes must be important drivers of community assembly in large, intensively managed farms. In coffee agroforests in Colombia, nest-site limitation is important for twignesting ants both on coffee plants and in the leaf litter. With a similar technique, Armbrecht et al. added artificial nests to coffee plants and added artificial nests and leaf litter in forests and in three coffee systems varying in shade management to examine the bottom-up influences of resources on ant assembly. Both litter addition and twig addition increased the number of ant colonies, indicating that ant colonies in these habitats are litter- and nest-limited. The numbers of ant species colonizing resources did not increase with litter or twig addition but did increase with increasing shade in coffee farms, a similar result to that found in Mexico . Nest diversity may also be important in determining the numbers of species that can colonize and survive in tropical environments. In Colombia, Armbrecht et al. tested whether the diversity of nesting resources affected colonization by litter-dwelling ants.

They collected branches of eight species of shade trees and drilled holes in the branches so that they would resemble natural hollow twigs found in the leaf litter. They then placed the nests in bags and added the bags to the leaf litter on the ground in either single-species bags, containing eight twigs of the same tree species, or mixed bags, containing one twig of each of eight tree species. They found that the mixed bags were colonized by a significantly greater diversity of ants but not for the reasons expected. Whereas it was expected that different species of ants would select different species of twigs, leading to an increase in ant diversity in mixed bags, they instead found that most ant species preferred the mixed bags, but not due to strong tree-species and ant-species associations. Thus, diversity in a nesting resource greatly influenced ant assembly and led to a more diverse ant community. Ecological interactions with other species, such as dominant ants or parasites, may also contribute to the structure and maintenance of ant communities. The presence of aggressive, dominant ants may influence the foraging by arboreal ants and may also limit their abilities to colonize new areas as well as limit their access to food resources and perhaps survival once they are established. But little experimental work has documented the importance of arrival and survival processes for ant communities . Two interesting studies in coffee farms have documented the importance of aggression from canopy-dominant ants on twig-nesting ants that belong to a different nesting guild. A. sericeasur ants are aggressive toward many types of arthropods, including even birds. In a manipulative field experiment, Philpott added artificial nests on coffee plants with A. sericeasur foragers and on coffee plants without A. sericeasur foragers to assess their impact on nest colonization. Fewer nests were colonized by twig-nesting ant species when A. sericeasur were present, and six out of ten common species occupied significantly more artificial nests placed on plants without A. sericeasur. Nest colonization increased with tree density , indicating that both abiotic and biotic factors are contributing to assembly processes for this community.

In a clever experiment to test the influences of the A. sericeasur–C. viridis or ant-scale mutualism on foraging by A. sericeasur and other arboreally foraging ant species, MacDonald et al. sprayed scale insect populations near clusters of A. sericeasur nests with an aqueous solution of L. lecanii, a fungal parasite of the scale insects. TheL. lecanii killed significant numbers of scales and resulted in increases in the foraging of other ant species proportional to the reduction in the numbers of A. sericeasur foraging on coffee plants. Thus A. sericeasur likely affects not only arrival but also survival of the twig-nesting ant colonies in coffee farms. As an aside, plastic growers pots the same sorts of reductions in foraging by A. sericeasur are also experienced frequently when they are under attack by Pseudacteon spp. phorid flies, resulting in similar increases in resource access for twig-nesting ant species . Such manipulative experiments have rarely been conducted in natural habitats, highlighting the role of coffee farms as model systems for ecological tests. Coffee farms have also provided a natural laboratory for simultaneously testing multiple hypotheses for community assembly. Livingston & Philpott used twig-nesting ants to investigate drivers of community assembly, including nest-site preferences; environmental filters, such as nest-site abundance and disturbance by A. sericeasur; influences of competition among ant species; and stochastic dispersal. They examined co-occurrence patterns of 25 twig-nesting ant species and used a “core/satellite” approach to address dispersal heterogeneity among species in the community . Species were divided into four groups: core species that are common at both local and regional scales, regional dominants that are found globally and dominant locally, local dominants that are dominant locally but not well distributed globally, and satellite species that are neither dominant locally nor well distributed. According to theory, competition among core species should result in overdispersed co-occurrence patterns , whereas dispersal effects should result in random or aggregated co-occurrence for satellite species. Several patterns emerged from the field analysis. First, >60% of twigs were occupied, demonstrating strong nest-site limitation. Second, most ant species inhabited similar-sized twigs, all species examined had proportionally similar responses to gradients in nest-site abundance, and A. sericeasur presence had little influence on richness or composition of ants occupying coffee twigs. Thus, Livingston & Philpott concluded that species sorting through environmental filters plays a minor role. Third, all ant species showed random patterns of co-occurrence with respect to each other in the absence of the “core” species, Pseudomyrmex simplex. But in the presence of P. simplex, regional dominants, local dominants, and satellite species showed aggregated patterns of co-occurrence with respect to one another. Thus, P. simplex likely plays an important role in “assembling” the community by providing a core meta population into which the other species fall.

Fourth, there was evidence for priority effects, as two ant species of equal competitive rank rarely co-occurred. Taken together, these data provide support for a competitive meta-community structure and suggest that competition for nest sites should be the dominant species interaction in this community. In a follow up paper, Livingston et al. used an expanded data set, coupled with data on dispersing alates , to examine evidence for species sorting and mass effects . They used data on twig-nesting ants from natural twig nests in five microhabitat types in a shaded coffee agroecosystem and coupled this with data on artificial nest occupation and numbers of alates caught in light traps. They then used community similarity and a variance decomposition to partition community variance into spatial and environmental components. Twig-nesting ant communities were distinct in each of the five microhabitats, and dissimilarity among communities was largely driven by changes in relative abundance of dominant and subdominant species but also by extensive turnover in the rare species. Space and environment together predicted 24.5% of the variation in the ant community, and space and environment explained unique fractions of the variance, indicating that both species sorting and mass effects are likely important drivers in this community. Alate abundancefor a species was correlated with colony abundance of species, indicating that microhabitats are dominated by internal dispersal. Finally, ant richness in artificial nests was higher than that in natural nests in coffee; however, natural nests had higher richness than artificial nests in shade trees and in the forest. Thus, abundances of the dominant and subdominant species are predominant in community dynamics, and dispersal of rare species from the canopy or adjacent forest patches may support mass effects into coffee microhabitats. To summarize, evidence to date for this twig-nesting ant community suggests that environmental filtering at the level of the nest may not occur but that some differences in habitat may impact ant assembly. Furthermore, dispersal and competition appear to be highly important in this community.Azteca sericeasur nests in trees and is common in the Mesoamerican tropics, where it is frequently encountered on casual walks in the forest. However, discerning any spatial pattern of its colonies in a tropical forest is inevitably obstructed by the heterogeneity of the habitat. In a 45-ha plot regular surveys revealed that Azteca colonies were distributed neither randomly nor uniformly within the plantation. Rather, they were strongly clustered . Examining a variety of environmental factors, such as slope, identity of nesting tree, and size of nesting tree, showed that nothing external to the ant population was correlated with the clusters, suggesting that the underlying biology of the ant was potentially the source of a self-organized pattern. The basic biology of the ant is not unusual for a species that has multiple queens and may be quite general for species that acquire most of their energy from hemipterans . After a queen establishes a colony in a tree, the colony may grow to the point that new nests are established in neighboring trees, evidently one part of the mechanism whereby patchiness is generated. However, unabated new nest formation would obviously result in a continuous expansion of colonies, which means that some force must limit this expansion. Turing’s concept of diffusive instability is a useful metaphor , with the tendency of the ants to disperse to neighboring trees equivalent to the “activator” of the system. However, there must also be some “suppressor,” otherwise the ants would simply disperse over the whole farm.

Although highly mobile, lechugueros represent a much more stable labor force than, for example, migrant strawberry pickers. Santa Barbara County’s fourth value crop is cauliflower. It engaged 8,920 acres of the Santa Maria Valley’s prime farmland and generated $29.5 million in 1992 . Like other crops described above, cauliflower boomed from under 1,500 acres in the late 1970s to nearly 9,000 today . Crop prolificacy also has risen from under 9,000 pounds per acre to 15,000 in the same period of time . As the close relative to broccoli that it is, cauliflower presents similar production and employment characteristics. It is, for example, farmed nearly year round and, as a result, offers a relatively steady source of employment to a number of local farm workers. Demanding 96.5 man-hours per acre to produce , Santa Maria’s current cauliflower acreage consumes 860,000 man-hours. Two-thirds of the labor requirement is used to harvest and field pack, and the remainder to plant and cultivate. We estimate that some 800 workers are employed regularly but intermittently by local cauliflower farms to complete these tasks. Harvest crews surveyed in 1993 revealed that all employees, like broccoli crews, are local permanent residents. Weeding and thinning crews, moreover, revealed that they are, in great measure, made up by the same local workers who execute similar tasks in the broccoli fields. Wine grapes are Santa Barbara County’s sixth value crop. Vineyards issued $28 million in 1992 and occupied 9,532 acres . Prior to 1970 there were no commercial vineyards in Santa Barbara but soon afterwards the industry took-off owing to growing national demand for wine, blueberry in container especially for the premium varieties Santa Barbara is capable of producing . In 1975 some 7,000 acres had been appropriated by the crop and by the early 1980s growth had leveled to the current acreage .

Although many of Santa Barbara’s vineyards are located in the neighboring Santa Ynes Valley, much of the new growth has occupied the hills and slopes that surround the Santa Maria Valley. Moreover, much of the labor employed by the county’s vineyards finds temporary or permanent lodging in the Santa Maria area. Wine grapes require approximately 110 man-hours per acre to cultivate and harvest . Much of the vineyard work is spread throughout the year and, consequently,requires only small crews to, among other things, prune the vines, till the soil, inspect and repair trellises and drip irrigation lines, fertilize and spray, and complete pre-harvest leaf removal. Harvest, in contrast, claims one-half of the annual labor requirement during a brief and intense moment in the early fall. Because Santa Barbara wine grapes are used to craft premium wines, the fruit must be picked in its prime, that is, during a short, fleeting window of opportunity when a large number of workers must labor in a frenzy to gather the grapes and transport them to the wineries for processing. Although mechanical means are currently available to harvest wine grapes and, in fact, most Santa Barbara vineyards have been designed and trellised with this in mind, growers continue to hand-harvest their crops in order to ensure the highest possible quality product. Santa Barbara vineyard acreage, according to available man-hour/acre computations, requires some one million man-hours to cultivate and harvest. We estimate that three hundred workers, employed intermittently during the course of the year, supply the labor needed to complete all the production tasks with the exception of harvest. All non-harvest employees are local resident workers, and many combine intermittent employment in the vineyards with employment in other local crops. Harvest crews, in contrast, are made up by both local and migrant workers.

Our 1993 survey of grape harvest crews, in effect, revealed a prevalence of transient migrants with a smattering of local residents, including many who had participated in other valley crops, especially strawberries, during the course of the summer. With just 2,724 acres, celery yielded an impressive $16.9 million in 1992, making it the county’s seventh value crop . Celery acreage and value are both down relative to 1989 production when 3,478 acres yielded $23.6 million. Nonetheless, it represents another vegetable crop with a healthy consumer demand, especially that which is designed to supply specialty markets. Most Santa Maria celery is, in effect, grown for premium markets and, as a result, is pampered during cultivation and then hand harvested. Celery is essentially a cool-temperature crop which thrives in the temperate winters of the California coast. In the Santa Maria Valley, plantings are established during the late summer and early autumn to be harvested from November to July when the long summer days and increased temperatures impel the plant to bolt. The cultivation of celery actually begins in nurseries where seedlings are started and prepared for transplantation to the fields. Growers stagger transplanting activities in a way that will assure an extended but steady harvest. Although mechanical planters are normally used, work crews are also needed to feed and assist the machine, and to correct frequent planter errors. When the ground is too wet, owing to rain or irrigation, the use of the mechanical planter must be forgone altogether. Weeding is intense and harvest constitutes a major enterprise. Depending on whether mechanical planters are used or not, celery requires from 240 to 320 man-hours per acre to produce, much of it, about 150, during the harvest alone . The celery harvest is arduous, back-breaking and, considering the presence of a large number of workers swinging razor sharp instruments in a fairly restricted space, it is deemed to be quite dangerous indeed. Harvest crews, as a result, are made up almost exclusively of young men. Based on available man-hour/acre computations, Santa Maria celery acreage requires some 800,000 man-hours to produce. Field observations, moreover, allow us to estimate that harvest crews employ about 400 workers who enjoy a seven-to-eight-month season of reliable but intermittent employment.

Transplanting and farming crews employ about 175 workers on a fairly regular schedule during at least six months of the year, while nursery work employs some 50 workers year-round. The celery industry, like lettuce, has established specialized harvest crews that move about California coastal celery-growing sites . In contrast with the lechugueros who tend to live in the United States-Mexico border area and enjoy a relatively stable relationship with their employers, celery cutters are typically migrants from the interior of Mexico and suffer high attrition rates. The celery harvest offers young men an excellent opportunity to make good money, but few workers remain in its employment for more than a few years. Nursery employees and celery cultivators , on the other hand, are mostly derived from the local, settled farm-working population and enjoy stable employment. The six fruit and vegetable crops described above create a 15 million man-hour labor demand in the Santa Maria Valley. However, in order to correctly estimate the valley’s entire fruit and vegetable labor demand it is necessary to make two additional adjustments. First, a myriad of other labor-intensive vegetable crops which occupied 11,230 valley acres and generated $41 million in 1992, augment the valley’s labor demand by at least 1.5 million man-hours. Second, because one-fifth of the Santa Maria Valley belongs to neighboring San Luis Obispo County and we have thus far based our estimates on crop data from Santa Barbara County alone, it is necessary to augment our first estimate by twenty percent. With these two adjustments, the valley’s fruit and vegetable labor demand ascends to nearly 20 million man-hours. If the aforementioned labor demand were to be evenly distributed throughout the year, plastic planters bulk it would create approximately 9,500 full-time jobs. In actuality, because farm employment is not uniformly distributed, Santa Maria’s fruit and vegetable farms employ as many as 23,000 different workers during the course of the year. Controlled field observations and work crew interviews conducted in 1993 suggest that in the Santa Maria Valley: Only ten percent of all farm employees enjoy full-time, year-round employment; twenty percent experience regular but intermittent employment during eight to ten months of the year; forty-five percent attain continuous employment during an extended season of four to six months and, hence, encounter long periods of unemployment; and twenty-five percent are employed only during a short, intense work season of two months or less. Finally, also based on controlled field observations and work crew interviews, we conclude that forty-three percent of Santa Maria’s 23,000 strong fruit and vegetable work force are immigrants who have established themselves permanently in the valley with their families.

The remaining fifty-seven percent are migrants who maintain a home base away from Santa Maria in either the border area or in the interior of Mexico. It is important to note that the number and mix of immigrant and migrant farm workers in the Santa Maria Valley has been in constant flux ever since we initiated our observations there several years ago. This is, in part, the logical outcome of an agricultural economy undergoing rapid, profound change. Two other conflicting forces, however, have also exerted considerable influence over this affair in recent times: On one hand, IRCA’s special provisions for farm workers which, to be sure, invited many former migrants and their dependents to settle down permanently in the valley, have contributed to increase the count of both authorized and unauthorized immigrants, and, on the other, the increasing prominence and rapid proliferation of farm labor contractors who, by preferring to hire new sojourners over established immigrants, stimulate migratory practices while displacing immigrants from their jobs. Nevertheless, in light of 1993 observations, the pulse of the valley is for both immigration and migration to continue growing unabated, probably at a rate which exceeds the creation of new farm jobs. Regarding the April 1 date when the Census Bureau undertakes its decennial count of population, it is important to note that although most immigrants are in the valley at that time, only one-half or less of the migrants are actually there. By early April the strawberry and lettuce harvest is just beginning to build-up steam but is not yet in full swing. Moreover, having just arrived, most migrants are still in the process of making their living arrangements for the season, creating with their great numbers havoc in the local housing situation and probably producing the worst possible conditions for the completion of a sound and accurate population count. Finally, in April the wine grape harvest is still six months away and, as a result, most of the migrant workers who participate in it will be missed as well. According to estimates made in the previous section, some 23,000 farm workers become involved in the valley’s agricultural endeavors during the course of the year. A little over one half of them are migrants who remain in the valley only as long as employment is available, some for just a few weeks, others for as long as eight to ten consecutive months. The other half, more than 10,000, have established themselves permanently in the valley with their families, accounting for as many as one-third of the valley’s inhabitants. The immigrant and migrant farm-working population of Santa Maria, moreover, continues to grow owing to: the farm employment opportunities the valley continues to offer; the dynamics of migration itself as settled migrants draw family and friends from their home communities in Mexico; and ongoing IRCA reverberations. In view of prevailing conditions and observable behaviors, there is no reason to assume that the flow will cease or diminish any time soon despite the fact that the valley already suffers a considerable labor oversupply. Farm workers in the Santa Maria Valley are not an homogeneous lot. The stereotypical view that once served to describe the California farm worker as a nomadic, young, single male campesino from Mexico is of little value today. Among the valley’s numerous farm workers are young and old, male and female , single and married. Some, as we have seen, are settled while others move about. They are, in effect, a broad array of different people displaying diverse and distinct behaviors. Farm workers continue to come from traditional sending communities located primarily in the Mexican central states of, for example, Guanajuato, Jalisco, Michoacan and Zacatecas, but also from new sending communities located in the southern states of, for example, Oaxaca and Guerrero; and some are from as far south as Central America, especially from Guatemala.

The low-ranking, newly important species found in seasonally dry forests were subject to human interest and manipulation, either intentional or inadvertent, routed into cultivation and eventually domesticated . Because they were sparsely distributed over the landscape, hence relatively unattractive to human foragers, there arose an immediate advantage for those who manipulated through burning or harvested species from these habitats so as to increase their density and yield of useful energy or materials. Piperno and Pearsall cite three rationales for using the diet breadth model in this analysis : the archaeological evidence shows that early hunter-gatherer/horticultural residents of the neotropics had an expandingdiet breadth followed by increasing subsistence commitment to low-ranked species; the prehistoric changes of concern are evident enough that short-term precision in the use of the model isn’t necessary ; and finally evidence from ethnographic tests shows that this model and an energy currency are commonly successful in predicting the economic response of foragers to changing environmental circumstances. They conclude, “[b]ehavioral ecology seems to us to be the most appropriate way to explain the transition from human foraging to food production” . Many of the dozen or so early HBE papers on domestication and agricultural origins are fairly general and conjectural. They ask, without too much attention to specific cases or the empirical record of prehistoric findings on this topic, how might the ideas of HBE be used to address the question of agricultural origins? By and large, their authors are ethnographers whose experience is with extant hunter-gatherer societies. And, growing berries in containers they generally have been written by people who already placed themselves within the research tradition of HBE. By contrast, most of the papers in this volume are based on empirical case studies, and they are written largely by archaeologists.

Most are authored by individuals for whom behavioral ecology is a new analytic tool. We do not claim that the HBE research tradition is a complete replacement for the other approaches that we have identified and briefly described. We view it rather as a sometimes complementary and sometimes competing form of explanation. It is complementary in two respects: HBE takes up issues rarely or never addressed in these approaches; search and pursuit trade-offs in the harvest of low-ranking resource species; risk-sensitive adaptive tactics; and, it frames these issues in quite a different manner than other, sometimes older, anthropological and archaeological research traditions by focusing on the costs and benefits associated with individual-level subsistence decisions in localized ecological settings. This framing difference is determined largely by the analytical effort of modeling and hypothesis testing within an explicitly selectionist, neo-Darwinian theoretical framework . In both respects, HBE provides tools that complement or make other traditions more complete. At the very least, HBE provides a theoretically well grounded set of tools to begin exploring the transition to agriculture in a variety of environmental and social contexts. For instance, although Hayden presents his competitive feasting model as a sufficient social explanation for the origins of agriculture, in effect as an alternative to models drawing on materialist or ecological explanations, we would prefer a more cooperative form of analytic engagement. We might assume that social stratification and competitive feasting increase the demand for resources and then ask how this source of ecological change would be represented in terms of foraging models—those extant, adapted, or developed specifically for this purpose—and with what consequences for predictions about subsistence choices and the co-evolution of humans and their resources. Taking this a step further, HBE might help us to identify the socio-ecological circumstances and evolutionary processes that combine to generate a competitive social hierarchy like that expressed in feasting .

A signal strength of HBE is its ability to carry into hypothesis generation a wide variety of postulated sources of causation—global climate change to the aggrandizement of dominant individuals. Nonetheless, to the extent that HBE is successful in addressing the question of agricultural origins, it will raise doubts about or contradict elements of other research traditions. In the process it will help us sort out, appraise and discard faulty elements of these approaches. Thus, for reasons of parsimony as well as theory, those working in the HBE tradition are skeptical of the adequacy of explanations couched at the level of global prime movers such as climate change. Likewise we doubt the efficacy of explanations made in terms of universal, directional pressures,such as Childe’s postulated trend of increasing energy capture or ecosystem approaches premised on cybernetic properties such as homeostasis .Behavioral ecology begins with an optimization premise. As a result of natural and cultural evolutionary processes, behavior will tend toward constrained optimization . This assumption makes operational the long-standing view of anthropologists that hunter-gatherers tend to be skilled and effective in the food quest . Efficiency, say in capturing food energy, is important even if food is not in short supply because it affords hunter gatherers the time and resources to engage fully in other essential or fitness-enhancing activities . We state this premise as constrained optimization because we do not expect behavior to be fully optimal. Temporal lags in adaptation and compromises among conflicting adaptive goals impede this outcome. Optimization likewise must be determined within the cognitive capacities, beliefs and goals of the organism under study. We adopt the assumption of constrained optimization rather than “satisficing” because the latter—while it may lead to superficially similar predictions—is an empirical concept and is therefore not able to generate theoretically robust predictions . Constrained optimization is an analytically powerful starting point that does not entail the belief that behavior is routinely optimal, only that there be a tendency towards optimal forms of behavior.

Behavioral ecology likewise is grounded in the observation, now well confirmed by non-human as well as anthropological studies, that some fundamental economic concepts transcend their scholarly origins in microeconomic attempts to explain the functioning of market-oriented economies. They are useful for studying adaptive decision making whether the questions concern the behavior of capitalists and workers, or the subsistence choices of hunter-gatherers, horticulturalists, and agriculturalists, not to say juncos and bats . At a minimum this list would include marginal valuation, opportunity costs, discounting, and risk sensitivity. marginal value. For most tasks we pursue and things we consume, immediate value changes with quantity, be it duration of the activity or the amount of a good obtained or ingested. The first breakfast sausage is more satisfying than the sixth or seventh; an hour-long bath is a delight, but four hours in the tub makes even insipid alternatives attractive. This would be trivial except for the additional observation that the decision to suspend consuming something like sausage or doing something like taking a bath is based on its marginal rather than initial, average or total value. Because of marginal valuation we move from doing one thing to another even though the intrinsic qualities of the options themselves may be unchanging. The formulation of marginal analysis was fundamental to microeconomics , and the careful reader will find marginal trade-offs in each of the foraging models we discuss below. opportunity costs. The idea of opportunity costs is closely related: the decision to switch from one behavior—a kind of consumption; a work activity—to another depends not only on its marginal value, but on the return to be gained from the available alternatives. Thus, one ceases to consume sausage when it becomes more attractive to sip orange juice; one stops bathing when preparing a ceremony is more compelling. More to the point of our subject, blueberry containers one ceases to forage for mussels when the opportunity and benefits of doing something else take precedence. In each case we assess the current activity, be it consumption or purchase against what we might be doing instead. In technical terms, the opportunity cost of an activity refers to the value of the opportunity that is foregone or displaced by continuing it. For instance, the diet breadth model sets the decision to pursue a particular resource against the opportunity cost of ignoring it in favor of searching for a more profitable resource to pursue. Much of microeconomics is a logical and mathematical elaboration on the workings of marginal valuation and opportunity costs, as they are manifested in the environment of a market economy. Using these ideas, economists ask how a wage earner’s consumption patterns change in response to an increase in her income.

By contrast, the behavioral ecologist analyzes how these two concepts play out as an organism interacts with a natural environment of physical processes and other organisms in the roles of predators, competitors, food resources, potential mates, and offspring. She asks, how might the resource choices of a forager shift as a consequence of a decline in the density of a highly valued resource, or an improvement in the technology used to harvest a particular species? The most basic claim of the papers in this volume is that these same ideas can be adapted to an understanding of decisions faced by humans during the evolutionary transition between foraging and agriculture. discounting. Discounting refers to the situation in which we assign a future reward less value than if it were available immediately and with certainty. For instance, we would pay less at planting time for a corn crop which might after all fail, than for that same crop at harvest time when the yield is certain. We discount in this manner when the cost of an activity such as planting occurs immediately but the reward, the harvest, is delayed and, perhaps because of that delay, uncertain. Delay alone can be important because the opportunity to benefit, even from a completely assured harvest in the most extreme case might diminish or pass, were the cultivator to die in the meantime. Delay also offers opportunities for hailstorms, locust plagues and other unforeseen events to reduce the value of the reward itself. For both reasons, effective behavior will hedge, finding it economical to discount delayed rewards. Use of this concept is fairly recent in behavioral ecology theory . Because the shift from hunting and gathering to agriculture represents a shift from immediate- to delayed reward activities this basic concept likely will be quite important in economic analyses of the transition from foraging to farming. risk-sensitive behavior. Basic behavioral ecology models assume that all environmental variables are constants and that a forager pursuing an optimal set of resources gets the expected reward at all times. By contrast, risk-sensitive models aim to be more realistic by introducing a stochastic element to the relevant environmental variables. All hunters recognize the large role of chance in the discovery and successful capture of game. In a risk-sensitive model the acquisition rate experienced by the forager is expressed by a statistical distribution; outcomes can be assigned probabilities but the actual rate at any time is unpredictable. Therefore, the optimization problem must take into account both the long-term average and the inevitable periods of shortfall. Risk-sensitive models do this. They are generally more realistic and more complicated than deterministic models, sometimes generate like predictions and, given the heuristic nature of the modeling effort, may not always be the preferred option for analysis . There is a well-developed literature regarding the risk-sensitive behavior of foragers and food producers, taken separately , but little has been written about risk sensitive adaptation during the transition from one of these subsistence systems to the other .The concepts just reviewed—marginal valuation, opportunity cost, discounting, and risk sensitive analysis—signal that behavioral ecology is an attempt to assess the costs and benefits of alternative courses of action under a range of environmental conditions. In operational terms, we accomplish this task with models that have in common four features: an alternative set, constraints, some form of currency, and a goal. Within a particular model, the range of possible behavioral actions is known as the alternative set. For instance, the diet breadth model specifies an alternative set of ranked combinations of potential resources . In the marginal value theorem, the alternative set refers to patch residence times. The alternative set is the dependent variable in the analysis; a particular socioenvironmental factor constitutes the independent variable. The model itself does not specify what might cause the independent variable to take on a certain value, or to change. It thus leaves open the opportunity for exploring how diverse influences such as habitat or climate change, seasonal variations in population density, over exploitation, competition from another predator or pressure to extract a surplus might affect a behavior like resource selection.

In the global market, shade-grown coffee is often advertised using particular imagery, which is meant to remind us of “conserved natural forests” or places with vast natural resources, rather than agricultural systems where both humans and non-humans play an important role in processes of commodity production. The result has been the construction of a coffee imaginary that paints shade-grown coffee plantations as lush gardens with tropical birds, jaguars, and foraging tapirs. Although an attractive and marketable vision of the coffee landscape, this imaginary is an inaccurate representation of the social reality of these spaces. At the core of this coffee imaginary is a conservation narrative2 that places responsibility of environmental degradation and species extinctions on exploitation by humans, and growing human populations . As a result, humans are excluded from places and the use of natural resources commonly used for social reproduction and the sustenance of human livelihoods. This conservation narrative incorporates some aspects of the “protected-area” discourse of conservation, emphasizing the maintenance of critical ecosystem functions and structures . Although this conservation narrative is based on strong scientific evidence, it is often presented under a framework of “crisis” , which potentially dehumanizes places and intensifies the human-nature dichotomy through the exclusion of the human experience . The impact of this conservation narrative on human communities has been explored in the context of exclusionary practices around protected areas, such as national parks, coral reefs, and fisheries . However, despite the prevalence of this conservation narrative in organic shade-grown coffee plantations, container growing raspberries no studies have explored its impact on plantation workers, and whether the embodiment of such narrative through potentially exclusionary practices further marginalizes vulnerable peoples.

This is particularly relevant for three reasons: first, seasonal workers in labor-intensive systems are one of the most vulnerable and marginalized actors within the coffee production chain . Research suggests that about 30% of the coffee currently consumed worldwide comes from large plantation systems , where seasonal workers face food and labor inequalities . Second, although literature on organic agriculture suggests that organic markets and price premiums from certifications can potentially support livelihoods in rural areas, farm workers continue to suffer inequalities and forced labor . In fact, the priorities of such ecolabeling initiatives focus primarily on certification criteria and privilege ecological goals while paying scarce attention to social processes and labor issues , and fail to question inequalities experienced by farm workers . And third, although shade grown coffee has been a critical system for conservation efforts and in some cases, supports peasant households , it is possible that the conservation narrative in organic shade-grown coffee plantations helps construct a coffee imaginary that misrepresents the human experience. This chapter examines the tensions that arise when conservation narratives meet the everyday-lived-experience of migrant farm workers in organic shade-grown coffee plantations in Soconusco, Mexico. I draw attention to the ways in which conservation narratives embodied in organic shade-grown coffee plantations have material and symbolic effects on farm workers’ everyday lived-experience, and argue that they contribute to farm workers’ vulnerability and marginalization. The relevance of this work lies in exposing the social intricacies of coffee production and biodiversity conservation within this labor intensive system as I demystify coffee production as a fair and just imaginary. First, I address the labor aspect of coffee plantations in the Soconusco region. Second, I discuss conservation narratives in the context of organic shade-grown coffee plantations, and the ways in which conservation narratives are embodied in organic shade-grown coffee plantations.

Finally, I discuss the implications of these conservation narratives on the everyday-lived-experience of migrant farm workers.In order to understand conservation narratives in coffee plantations and how they are perceived and contested by farm workers, I carried out ethnographic research in an organic shade-grown coffee plantation in the Soconusco region. The extension of this plantation is approximately 300ha and can be categorized as a mix between traditional and commercial polyculture, with hired wage labor, both permanent and temporary. The epistemological basis of my research is rooted in the interpretivist tradition of anthropology using a phenomenological approach, which emphasizes the importance of symbols and experiences as well as individual opinions, values and categories to understand societies . This methodological approach allowed me to capture meaningful experiences of farm workers, as well as to understand how farm workers perceive themselves in the plantation. During the harvest season between October 2015-January 2016, I picked coffee with 15 families of migrant farm workers. I also lived in their shacks and joined them in daily activities such as collecting edible wild plants, hunting, and preparing meals. My research consisted of participant observation and informal interviews that took place while picking coffee during the day, in the evenings over meals, and while performing other activities. Along with my interlocutors I experienced the physical struggles of picking coffee and, in return for their time, I contributed my portion of harvested coffee at the end of each day to their totals. The population of migrant farm workers with which I carried out my research were mestizo from Guatemala, although indigenous laborers also work in the plantation during the earliest part of the harvest season. I complemented my ethnographic research with interviews of three coffee plantation owners which allowed me to understand their engagement with conservation narratives, as well as their own struggles as coffee growers in a highly competitive market.

Farm owners are often blamed for the social conditions experienced in their farms, yet we should not assume that owners can automatically change this reality . Therefore, research about farm workers should also consider the experiences of the growers themselves. As suggested by Holmes “The fact that the perspectives of farm management are generally overlooked, inadvertently encourages the assumption that growers may be wealthy, selfish, or unconcerned” . This may reinforce a superficial understanding of the reality of farm workers, and therefore the fact that the complexity of their struggles and structural challenges are not often recognized. Due to my interest in analyzing how conservation narratives weave with the popular public perception of shade-grown coffee, I also visited coffee plantation lodges along the touristic Ruta del Café , where I collected written comments representing the public discourse surrounding shade grown coffee plantations. Plantations are highly specialized, large-scale agricultural operations, which are characterized by their intensive use of capital investments, as well as the exploitation of wage labor . Although plantations are primarily concerned with the production of agricultural products grown on land, in scale and method of operation plantations are more akin to a modern factory or industrialized agriculture than they are to a small-scale family farm . The plantation model of agriculture has affected the ecologies of place, including the interaction between humans, non-humans, and their environment, as it embodies both the control of nature and of people. The essence of plantations–with defined social stratification and a controlling character, full labor control, and the transmission of agricultural management instructions from top to bottom – continues to have a presence in agricultural production in Latin America. In its origins, plantation economies were entirely controlled by foreign capital, and labor would be primarily imported, but profits would be invested overseas. Knowledge and technology were also imported from abroad, often by sending the owner’s offspring to their country of origin to study, as part of the colonial emulation of the plantation economy . The primal organizational aspects of plantations slowly disappeared in most places in Latin America, blueberries in pots giving way to communal land and small holdings that followed land reforms and land grabs lead by displaced peasants. However, in some places plantations continue to shape the landscape and the lives of people that live in, of and around plantations. This is the case in the Soconusco region of Chiapas, Mexico. Coffee production in the Soconusco region– one of the most important coffee producing regions in Mexico– is particularly interesting, as it played a key historical role in incorporating the state into the global capitalist market . By the end of the XIX Century, factors such as the economic policies of the Mexican government , strong foreign capital and adequate ecological conditions, allowed the expansion of coffee plantations in the Soconusco region . In its expansion, the coffee plantation economy became not only a powerful mode of production, but also a way of life for both plantation owners and laborers , which remains an integral part of the cultural identity of Soconusco. The expansion of German plantations in this region was characterized by the adoption of a production system that did not fall too far from the hacienda system of the pre-revolutionary period . Coffee production in large volumes was done primarily by these large plantations, which had access to commercialization routes and the required capital investments . Today, the subsistence peasant economy coexists alongside the export-oriented economy of coffee plantations, generating a rich cultural, social and economic rural patchwork . Plantations in Soconusco maintain a social organization based on a centralized political structure and the employment of wage labor . At the center of this organization is the Patron, or owner of the plantation who often lives outside of the plantation; followed by an administrator; a sideman or mayordomo; a set of foremen or caporales in charge of crews of laborers; and the laborers themselves .

Although labor has been historically sourced from the highlands of Chiapas, most laborers today are currently seasonal migrants that come from Guatemala, primarily during the harvest season . The increasing migration of labor from Central and South America directly to the United States has generated a labor shortage in the region of Soconusco , which in turn has promoted alternative strategies of labor recruitment, including the provisioning of temporary visas and permits granted by the patrons of large operations, extended for up to five years of work . Such permits are only legally granted to individuals and not to entire families, meaning that only one or two family members are legally represented in the migratory destination . This situation only exacerbates the already vulnerable position of migrant laborers in coffee plantations, where living and working conditions are overwhelmingly unfair . Once migrating, the vulnerabilities that come with illegal status and high dependency from the contractors increase the stress experienced by farm workers . Additionally, the barriers to transnational mobility limits the ability of farm workers to claim better labor conditions and wages . Issues of migration, illegal status, and poor working conditions are accompanied by differences among farm workers in terms of their ethnicity, farming abilities, and their permanency in the farms, as has been shown for other agricultural systems that rely heavily on migrant labor . In coffee plantations, multiple ecological knowledges and imaginaries meet farm workers’ experience, which makes farm workers important actors for providing meaning to these spaces despite the fact they are often overlooked in the coffee production cycle. The harsh reality of laborers in coffee plantations contrasts with the coffee imaginary of shade-grown organic coffee and fails to show its reality, therefore obscuring the lives of people . Additionally, the social sustainability of organic agriculture can be widely questioned for the contradictions posed to laborers. On the one hand, organic agriculture provides a safer space to laborers in terms of limiting the exposure to pesticides , while on the other hand, it does not address structural inequalities, occupational injuries, and other health related concerns common in the community of farm laborers . In an ideal world, the benefits of organic shade-grown coffee should be perceived not only through the conservation of biodiversity, but also through improving social justice and human livelihoods. Yet, as Guthman argues, “the organic movement has fallen woefully short of addressing the social justice issues that are often assumed to be part and parcel of organic farming” .The Soconusco region is famous for its Ruta del Café, repeatedly advertised as a “magical destination on the coast of Chiapas”. Plantation-style lodges embedded in the tropical perennial forest overlook what is hard to not categorize as a dreamlike landscape for the avid nature lover: a mosaic of greens, the coffee within the dense natural forest, the sound of the river, and the singing of the birds.

Overall, the gene pool of cultivated fig analyzed possesses substantial genetic polymorphism and exhibits narrow differentiation. It is evident that fig accessions from Turkmenistan are somewhat genetically different from the rest of the Mediterranean and the Caucasus figs. A long history of domestication and cultivation with extensive dispersal of cultivars has often resulted in a great deal of confusion in the identification and classification of cultivars.Coffee, a highly demanded commodity supporting the livelihoods of more than 20 million families , has been traditionally cultivated under the shade of trees within tropical and subtropical biodiversity hotspots, making it relevant for conservation, food provisioning for rural families and the delivery of ecosystem services, meaning the processes and conditions provided by natural ecosystems with the potential to sustain and fulfill human welfare . Important ecosystem services in coffee plantations are pest control and pollination . However, coffee agroecosystems continue to experience a dramatic change in their management, characterized by the reduction of shade trees and increased use of chemical inputs . This intensification has had severe ecological implications, including the decline of ecosystem services ; and social consequences like food insecurity and seasonal hunger for farming families . Much research on the benefits of biodiversity in coffee agroecosystems – has pointed out that highly bio-diverse habitats have the potential to sustain a number of species and interactions that support ecosystem services . However, less is known about the specific ecological mechanisms supporting more biodiversity and higher abundance of natural enemies of coffee pests in complex agroecosystems . Previous studies have suggested that resource heterogeneity, large pots plastic meaning the variability of available resources through space and time and accessible refuges provided by surrounding vegetation could be important factors for arthropod communities . Yet, this is still an ongoing scientific exploration in coffee systems .

A second area of attention in coffee studies comprises the benefits that humans perceive from the planned and associated biodiversity in coffee agroecosystems. Most of these studies have highlighted the importance of bio-diverse coffee smallholdings in delivering food security and contribute to livelihoods of peasant households . However, research has suggested that established and temporary farm workers are a highly marginalized sector of the coffee production chain , which indicates that further attention needs to be put in terms of the overall lived experience– and specifically food-related experiences– of this sector. Ecological theory provides foundations for explaining higher abundance and diversity of natural enemies in complex habitats. Two complementary hypothesis have been developed and are useful in this sense: the first one suggests that different habitat types– meaning a variety of plants, strata, microhabitats, the spatial arrangement and temporal overlap of the plants –can support greater biodiversity of predators and reduce crop damage . This hypothesis considers that an increase in resources such as floral and extrafloral nectar and provisioning of shelter through improving non-crop vegetation, favors generalist and specialist predators and parasitoids through the delivery of alternative food . A second hypothesis suggests that niche complementarity, which occurs when higher diversity in the system allows for a grater range of functional traits to be represented, favors a more efficient use of resources and promotes diversity at higher trophic levels . Following these hypotheses communities of natural enemies could potentially thrive in coffee agroecosystems to the extent that these systems provide the necessary resources to survive when the main prey are not available. My dissertation departs from two socio-ecological understandings: 1) Resource heterogeneity– expressed in temporal variation of a particular resource, differences in quality and nutritional variation of resources, or differences in microhabitats – is considered an important factor influencing communities.

More complex habitats provide diversity of niches and ways to exploit resources in a particular environment , which in turn supports more biodiversity , influences the distribution and interactions of species and may favor niche partitioning and species coexistence in a given environment . 2) Ecological diversity exists along a gradient of social complexity, allowing the co-creation of spaces. The subsistence value of bio-diverse coffee systems draws upon the potential of growing and using a variety of resources other than coffee within the agroecosystem and adjacent plots . There is an increase interest and awareness that biodiversity conservation can have positive effects on food production and livelihoods . Such is the case of traditional coffee polycultures and indigenous agroforestry systems . Despite benefits of highly bio-diverse coffee plantations, coffee farmers frequently experience seasonal hunger and food shortages . Food related challenges are mostly reported from smallholdings; however a smaller but important sector of coffee production happens in large plantations, which represent a historically and currently important sector of the coffee production in Central America and issues of food security have not been explored enough. Under this framework, this dissertation evaluates three intertwined areas. First – I examine the influence of the availability of three resources on ant community dynamics such as colonization, reproduction, and two species interactions: predator-prey and parasitoid-host interactions. Ants and parasitoids are important natural enemies of coffee pests and are model systems to understand the mechanisms that favor diversity in complex habitats. Second, I examine the influence of local habitat factors on community dynamics. Third, I explore the every-day lived experiences of farm workers in coffee plantations, a scantily explored area that requires attention in coffee growing regions in Mexico. Community assembly is the process that leads to particular patterns of colonization of interacting species, that may share a particular resource , and a process that reflects survival of species in a particular habitat . The study of communities and their assemblage processes is important for explaining community dynamics, but also because it can provide important insights into spatiotemporal factors that maintain ecosystem services in face of global change, destruction of natural biomes, and intensification of managed systems .

Ants are a diverse and an interesting group of insects to use for studies of community assembly and drivers of coexistence because they are found almost everywhere and in the tropics they can represent up to 80% of the animal biomass . Understanding drivers of ant diversity and co-occurrence is of relevance, as ants participate in competitive, mutualistic and predatory interactions, as well as trait mediated interactions that often result in ecosystem services . Ants are important pollinators , predators of pests in agricultural systems , square planter pots seed dispersers and protectors of plants that provide resources useful for ants . Local and regional factors influence ant assemblages, however there is no single cause or dynamic that explains nest colonization patterns of entire communities of ants. Thus, recognizing that community assemblages can be structured through multiple ecological and evolutionary processes interacting synergistically is essential in community studies . By examining the community of arboreal ants that nest in hollow twigs in a coffee plantation, we investigated how availability of resources, such as diversity of nests with different sized entrances, and the vegetation strata in which nests are located influence colonization and nesting patterns for a community of twig-nesting ants. The role of cavity entrance diversity on Neotropical arboreal ants has been previously shown to strongly influence cavity colonization in a natural ecosystem . Although the present study shares a number of similarities with the previous study in terms of the experimental design, the novelty of our study lies in the examination of the assembly process of the arboreal ant community in an agroecosystem considering the vegetative strata as a potentially significant local factor influencing ant assembly. Other studies have also made important contributions to the understanding of the influence of resource availability, interspecific competition from dominant ants, and changes in environmental conditions on ant colonization, survival and community assembly ; similarly, studies have reported that niche differentiation and interspecific competition for similar resources structure ant communities . In the litter environment, factors such as patchiness in nest site availability can influence ground ants . For other communities, however, nesting sites might not be a limiting factor, although nest-site limitation may increase with agricultural habitat intensification or disturbance . Moreover, increases in diversity of nesting sites can influence species richness and composition . Only few studies examine factors that influence ant communities at the colonization stage, despite the importance of priority effects for community assembly . Recruitment limitation can affect colony density and incidence of less competitive species, thus examining initial phases of colonization may be important for understanding species coexistence . Moreover, the dispersal stage of colony formation maybe strongly influenced by community assembly mechanisms such as habitat filtering because ants must find suitable habitats .

The present study asked the following questions: 1) Does nest strata or diversity of nest entrance sizes influence the percent of nests colonized by arboreal twig-nesting ants, 2) Does nest strata or diversity of nest entrance sizes influence the species richness of arboreal twig-nesting ants colonizing nests? 3) Does nest strata or diversity of nest entrance sizes influence the community composition of twig-nesting ants colonizing nests? 4) Are nests with certain nest entrance sizes more frequently occupied, or have a higher species richness of ants? 5) Do individual ant species more frequently occupy nests in a certain strata or nests of a certain entrance size?We conducted field research in a 300-ha shaded coffee farm in the Soconusco region of Chiapas, Mexico between March and June 2012. The farm is located between 900-1100 m a.s.l. Between 2006-2011, annual rainfall at the farm was between 4000-5000 mm. During the time of the research, the production style of the farm could be classified as a mix of commercial polyculture and shaded monoculture according to the system of Moguel & Toledo . The farm has ~50 species of shade trees that provide 30-75% canopy cover to the coffee buses in the understory. We studied ant occupation of nests in 44 locations on the farm. Each study site was separated by a minimum of 100 m, and consisted of two neighboring Inga micheliana trees of approximately the same size and two coffee plants directly underneath the trees. In order to characterize the vegetation of each study site, we measured trees, canopy cover, and coffee density. For all measurements, we used the midway point between the two Inga micheliana trees as the center point. In a 25 m radius circle around the center, we identified and counted each tree and measured the circumference and height of all tress. We sampled canopy cover at the circle center, and 10 m to the N, S, E, and W of the circle center with a convex spherical densitometer. We counted the number of coffee plants within 5 m of each focal Inga tree in each site. With the vegetation data, we calculated a vegetation complexity index . To calculate the index, we divided values for each vegetation variable by the highest observed value for each variable. For the number of coffee plants and the percent of trees in the genus Inga, we subtracted the product from 1 as these two factors generally negatively correlate with vegetation complexity. Then, we took the average of all values for each site to obtain a single value between 0 and 1 .Treatments were randomly assigned to plants in each site. We attached nests to plants with twist ties and plastic string between 0.5 to 1.5 m above ground on coffee plants, and between 4 to 6 m above ground for Inga trees. We placed nests flush with coffee or tree branches. We placed nests between 5-7 March and harvested all nests 14 weeks later . The period of the study encompassed part of the rainy season. Rain and moisture have a significant effect on colony phenology because they regulate alate’s flights in the absence of temperature variation . Although nests were placed long enough to be colonized by ants, longer time periods may have allowed us to capture colonization dynamics across time. To determine effects of nest entrance size, entrance size diversity, and nest vegetation strata on colonization, we collected artificial nests, placed them in bags, froze them, and then cut open all nests to remove the contents. We noted whether each nest was occupied or not. We stored ants in 70% ethanol and later identified them according to the Ants of Costa Rica , and AntWeb . For all species found, we obtained an approximate head width measurement from AntWeb .

Despite higher recorded GDD in the present study, titratable acidity at harvest was maintained around 7 g•L-1 . Ultimately the reduction in cluster temperature imparted by the shading impeded organic acid degradation therefore maintaining berry acidity. It was identified that anthocyanin accumulation was maximized at 875 GDD and a daily mean light intensity of 220klm⸱m-2 after which anthocyanin content decreased in Cabernet Sauvignon. Previous works that used partial shading that transmitted 60% of solar radiation had also resulted in increased anthocyanin content compared to unshaded fruit in under similar growing season and climatic conditions . In 2021, shade films did not affect the anthocyanin content in berry skins at harvest, due to the cooler growing season limiting anthocyanin degradation post-veraison. The reduction in anthocyanin content observed in 2020 may result from repressed anthocyanin biosynthesis at hot temperatures via the MYB4 repressor . However, it is also highly likely that elevated temperatures in 2020 resulted in increased anthocyanin degradation in exposed fruit compared to shaded fruit, leading to shaded fruit having greater anthocyanin content. Flavonols are photoprotectants and free radical scavengers in the plant kingdom . As such, these compounds are directly responsive to light exposure of the cluster. In the phenylpropanoid pathway, MYBF1 is a transcriptional regulator ofFLS, the key gene in flavonoid synthesis . It has been shown that MYBF1 is upregulated by UV-B light, resulting in increased flavonols in grape berry skins . Thresholds for optimal sunlight exposure have been elucidated in previous solar radiation exclusion experiments, where Martínez-Lüsher et al. tracked flavonol development over the growing season under 20% and 40% shading conditions. It was determined that net flavonol biosynthesis occurs until approximately 570 MJ m-2 of accumulated global radiation which corresponds with 7.6% molar abundance of kaempferol in grape skins .

Beyond these thresholds, plastic gutter flavonols started to be degraded in the grape berries. Our study showed a similar trend for flavonol content in hot years like 2020. The control treatments in 2020 exceeded 8.6% kaempferol abundance, while shade films were effective in maintaining kaempferol abundance below this overexposure threshold. In cooler years like 2021, flavonol degradation was not observed at the global radiation threshold as a result of the cooler growing season. Rather, biosynthesis continued to increase flavonol content until harvest in 2021. Shade films effectively lengthened the period of flavonol biosynthesis and reduced the amount of time during ripening where clusters are under flavonol degrading conditions. Anthocyanins are comprised of two aromatic rings linked by three carbons in an oxygenated heterocycle . Hydroxylation and methylation of the B- ring is responsible for color and hue of each anthocyanin molecule. Increasing free hydroxyl groups on the B-ring enhances blueness while methylation of the hydroxyl groups increases redder hues in grape skins . From a winemaking perspective, 3’4’5-OH anthocyanins are more resistant to degradation during fermentation, leading to stable wine color . In this study, overhead shade films did not affect anthocyanin hydroxylation by harvest in either year of this study. However, shifts in anthocyanin hydroxylation have been previously documented: colored shade nets reducing solar radiation by 40%, showed higher anthocyanin and flavonol hydroxylation compared to unshaded treatments . Previous studies reported increases in the ratio of di-tri hydroxylated anthocyanins in grapevines under water deficits . The absence of this shift in anthocyanin hydroxylation under shade films was most likely due to similar grapevine water status among the shaded and control treatments, as the vines were not under water deficit conditions. However, shade films altered flavonol hydroxylation under hot growing conditions in 2020, with hydroxylation being the highest in the least exposed shade films . Shade films D4 and D5 transmitted 60% and 40% of UV-B radiation respectively, resulting in less flavonol hydroxylation than D1 and D3, but more hydroxylation than the control. In cooler growing conditions in 2021, all shade films had comparable levels of flavonol hydroxylation, yet hydroxylation was still greater under shade films than the control.

These results may be due to the upregulation of flavonoid 3’ hydroxylase . This enzyme is responsive under sun exposure and is responsible for the generation of 3’4’ hydroxylated flavonoid precursors .It has been long recognized that the quality of wines is closely associated with the accumulation of secondary metabolites, specifically flavonoids and volatile organic compounds that have a direct effect on wine color, taste and aroma . Flavonoids in wine include anthocyanins, flavonols and flavan-3-ols. Wine color, particularly its hue and intensity, are strongly determined by anthocyanin methylation, acetylation, hydroxylation of the anthocyanin B-ring, and co-pigmentation with cofactors such as flavonols . Partial solar radiation exclusion was shown to effect anthocyanin hydroxylation. Tarara et al. demonstrated increased dihydroxylation of anthocyanins in grape berries exposed to direct solar radiation compared to shaded fruit. Likewise, Martínez-Lüscher et al. monitored anthocyanin hydroxylation under colored photo selective shade nets and found that by reducing solar radiation by 40% with black polyethylene shade nets, the ratio of tri- to dihydroxylated anthocyanins was increased compared to uncovered control fruit. Such shifts in anthocyanin hydroxylation can impact anthocyanin hue and wine antioxidant capacity. Wine aroma in both red and white wines is a matrix formed by a variety of volatile compounds. However, the composition of the matrix can be impacted by grape cultivar, vineyard conditions and fermentation conditions. Contribution of volatiles to wine flavor composition is related to its chemical structure . The most abundant class of volatile compounds found in the wine matrix are higher alcohols . These by-products of yeast nitrogen metabolism are usually described by unpleasant “solvent” or “fusel” aromas when present in concentrations greater than 400 mg/L . The more pleasant “fruity” aromas described in wine are associated with esters. Esters are often in highest concentrations in young red wines and decrease in concentration with aging . C-13 norisoprenoids and terpenes are key aromas compounds found in both red and white wines, contributing fruity and floral aromas at low olfactory concentrations . C-13 norisopenoids are understood to be derivatives of enzymatic or photochemical degradation of carotenoid pigments in the grape berry . In plants, carotenoids have photo protectant and antioxidant properties, making these pigments responsive to solar radiation in grape berries. Carotenoids in grape berries have been shown to increase in berries with increased in solar radiation pre-veraison . However, under extreme exposure to heat and solar radiation, there is a documented decrease in carotenoid concentrations during ripening . To preserve the carotenoid concentrations in the grape berry and to promote C-13 norisoprenoids in resulting wines under more frequent heat wave events and increases in air temperature, artificial shading with black polyethylene cloth has been trialed and found that shaded fruit contained more carotenoids than unshaded fruit . However, the effect of partial solar radiation exclusion on wine C-13 norisoprenoid content seems to be more nuanced. Wines produced from the shaded fruit contained more β- damascenone as well as esters compared to wines produced from unshaded fruit . Yet, there are conflicting reports showing no effect of UV exposure on β- damascenone concentrations in Shiraz wines made from clusters that underwent solar radiation exposure via varying rates of leaf removal and polycarbonate UV screens . Like C-13 norisoprenoids, final terpene concentrations in wines depends on the net accumulation in grape clusters exposed to excessive temperatures and UV radiation . The effect of photo selective overhead shade films on whole plant physiology and temporal development of berry flavonoids of Cabernet Sauvignon development over two growing seasons was previously studied in a hot region . Grape berries growing under reduced near-infrared radiation exposure in hotter than average years, resulted in a 27% increase in anthocyanin content at harvest than the exposed control due to decreases inanthocyanin degradation due to high berry temperatures . Moreover, flavonol degradation was similarly decreased, thus optimizing flavonol content in the grape berry under reduced near-infrared radiation exposure .

The objectives of this study aimed to determine the extent to which the impact of photo selective overhead shade films on flavonoid development transfer to wine and the cascading effects of partial solar radiation exclusion had on aroma composition of resultant wines. The experiment was conducted in Oakville, CA, USA during two consecutive growing seasons at the University of California Davis, Oakville Experimental Vineyard. The vineyard was planted with “Cabernet Sauvignon” clone FPS08 grafted onto 110 Richter rootstock. The grapevines were planted at 2.0 m × 2.4m and oriented NW to SE. The grapevines were trained to bilateral cordons, blueberry container vertically shoot positioned, and pruned to 30-single bud spurs. Irrigation was applied uniformly from fruit set to harvest at 25% evapotranspiration as described elsewhere . The photo selective shade film treatments were previously described in Marigliano et al. and their properties presented in Figure 1. Shade films were designed to target portions of the electromagnetic spectrum previously observed and measured at the experimental site . Briefly, four photo selective shade films and an untreated control were installed in 3 adjacent rows on 12 September 2019. The shade films remained suspended over the vineyard until 20 October 2021. The shade films were 2 m wide and 11m long and were secured on trellising approximately 2.5 m above the vineyard floor. Each experimental unit consisted of 15 grapevines in 3 adjacent rows. Grape clusters were harvested by hand from each experimental unit when berry total soluble solids reached 25o Brix on 9 September 2020, and 7 September 2021, respectively. Vinification was conducted in 2020 and 2021 at the UC Davis Teaching and Research Winery. Upon arrival at the winery, grapes were destemmed and crushed mechanically. Must from each field experimental unit was divided into three technical fermentation replicates . K2S2O2 was added to each treatment- replicate and must was allowed to cold-soak overnight at 5o C in jacketed stainless-steel tanks controlled by an integrated fermentation control system . The following day each treatment-replicate was inoculated with EC- 1118 yeast to initiate fermentation. Musts were fermented at 25°C and two volumes of must were pumped over twice per day by the integrated fermentation control system. During the winemaking process, TSS was monitored daily using a densitometer and fermentations were considered complete once residual sugar contents were less than 3 g⸱L-1 . Wines were then mechanically pressed using a screw-type basket press. Following pressing, wine samples were collected for flavonoid analysis. Malolactic fermentation was initiated with the addition of Viniflora® Oenococcus oeni . Malolactic fermentation was carried out at 20o C. Upon completion of MLF, free SO2 levels were then adjusted to 35 mg⸱L-1 and wines were bottled. Using a spectrophotometer , color intensity , hue, total polyphenolic index and % of polymeric anthocyanins was determined following procedures described by Ribéreau-Gayon, Glories, Maujean, and Dubourdieu . Wine samples were diluted in water and absorbance readings were taken at 280, 420, 520, and 620nm. The absorbance at 740 nm was subtracted from all absorbance readings to eliminate turbidity. CI was calculated as the sum of absorbance at 420, 520 and 620nm. Hue was calculated as the ratio between the absorbance at 420 and 520nm. The percentage of polymeric anthocyanins was determined via absorbance measurements at 520nm after anthocyanin bleaching with a sodium bisulfite solution . TPI was determined by diluting wines with water and recording absorbance at 280nm. Volatile compounds in wine samples were analyzed following procedures described previously . Briefly, 10-mL of each wine sample was transferred to a 20-mL amber glass vial . Each vial also contained 3 g of NaCl and 50μg of an internal standard solution of 2-undecanone . After agitating at 500 rpm for 5 mins at 30o C, samples were exposed to 1 cm polydimethylsiloxane/divinylbenzene/Carboxen , 23-gauge SPME fiber for 45 mins. Helium was used as a carrier gas at a flow rate of 0.8636 mL/min in a DB-Wax 231 ETR capillary column  with constant pressure and temperature at 5.5311 psi and 40o C, respectively. The oven temperature was kept at 40o C for 5 mins and then incrementally increased by 3o C/min until reaching 180o C. Oven temperature was then increased by 30o C/min until reaching 260o C, at which temperature was maintained for 7.67min. The SPME fiber was desorbed split mode with a 10:1 split for wine samples and held in the inlet for 10min to prevent carryover effects. The method was retention time-locked to the 2-undecanone internal standard.

DCA-treated colon cancer cells exhibited higher ROS generation, membrane blebbing, activation of mitochondrial apoptotic pathway, and formation of apoptotic bodies compared to untreated cells. DCA exposure also resulted in micronuclei formation accompanied by a dose-dependent response in NFκb activation that was attenuated by cotreatment. The above studies clearly demonstrate that hydrophobic BAs induce cellular oxidative stress through elevated reactive oxygen and nitrogen species production with similar results observed between human liver and colon cell lines. Interestingly, human HCC cells treated with hydrophobic primary CDCA also displayed cell cycle arrest, caspase-9-like activity, poly ADP-ribose polymerase cleavage, dose-dependent sites of DNA lesions, and extensive nuclear fragmentation. These cells also showed activation of ERK1/2 leading to the phosphorylation and stabilization of myeloid cell leukemia sequence 1 in a mitogenactivated protein kinase-dependent manner which conferred greater resistance to chemotherapeutic drugs. These findings strongly support that excessive levels of hydrophobic BA can exert a carcinogenic effect on enterohepatic tissues by promoting genomic instability through oxidative injury. Figure 3 provides an overview of the implicated carcinogenic consequences of BA dysregulation, gut dysbiosis, and insulin resistance. Several synthetic drugs such as colesevelam and colestimide, designed to sequester BAs, have demonstrated efficacy in improving insulin resistance and glucose tolerance. BA receptor agonists also appeared to be promising in the management of obesity and diabetes related symptoms. Specifically, synthetic retinoid such as acyclic retinoid was investigated for its beneficial effect on obesity-related liver tumorigenesis, since RXRα, a heterodimer partner of FXR, square plastic plant pot was found to be repressed in early stages of HCC due to phosphorylation by the Ras/MAPK signaling pathway. Results indicate that ACR inhibited the Ras/MAPK pathway, ameliorated liver steatosis, improved insulin sensitivity, and decreased inflammation.

Ultimately, ACR appears promising in restoring RXRα function in the liver, making it an effective chemoprevention drug against HCC progression. With the intestinal microbiota implicated as one of the key players in the progression of liver and colon carcinogenesis in obese and diabetic patients, selective modification of the gut microbial composition has been extensively researched as a viable alternative or additive to current treatment plans. Prebiotics promote the growth of beneficial bacteria while probiotics are live microorganisms, administered exogenously, which provide a benefit beyond nutrition. Most prebiotics exist in the form of non-digestible carbohydrates and exert protective effects against liver and colon cancer. Dietary fibers shortened GI transit time to reduce the length of exposure to toxic metabolites such as hydrophobic BAs and bacterial toxins while aiding in their incorporation in feces for excretion. In addition, these fibers enhanced the growth of beneficial bacteria such as Bifidobacteria, lowered intestinal pH, and inhibited the growth of harmful bacteria. An increase in bifidobacteria is the signature of prebiotic treatment using insulintype fructans or galactooligosaccharides. Other resistant dietary fibers such as pomegranate peel extract and natural phytoalexin resveratrol can alter the gut microbiome in favor of bifidobacteria while lowering inflammatory markers in the colon and visceral adipose tissue. Short chain fatty acids , the fermented end products of dietary fibers, are recognized for their ability to inhibit growth and promote apoptosis in colon and liver cancer cells. SCFAs can also activate various drug metabolizing enzymes to decrease DNA mutation and reduce cancer risk. Complementing SCFAs with fish oil selectively reduced unsaturated fatty acid accumulation in the liver, improving hepatic fat oxidation and inflammation. Furthermore, probiotics have been suggested as a tool to manage inflammatory bowel disease. Although no general consensus exists for the beneficial effects of probiotics in obese, diabetic, and NAFLD patients, reduced hepatic total fatty acid content and serum alanine aminotransferase levels were noted in rodent models treated with probiotics.

A synergistic effect of probiotics and blueberry husks in preventing colon carcinomas and subsequent liver tumors has been observed in rats. Blueberry husks alone significantly decrease the number of colonic ulcers and dysplastic lesions while probiotics alone improved liver function by decreasing parenchymal infiltration and bacterial translocation. Thus, the combination treatment of probiotics and blueberry husks delayed colonic carcinogenesis and prevented hepatic injuries. The combined treatment also reduced endotoxin-producing enterobacteriaceae and increased beneficial, anti-inflammatory lactobacilli. Synbiotics, mixtures of probiotics and prebiotics, were noted to lower colon cancer risk through improved insulin resistance, reduced inflammation, and preservation of gut barrier integrity in rats fed a high-fat diet. In terms of gut microbial ecology, synbiotic treatment significantly increased fecal Lactobacillus species at the expense of potentially pathogenic E. coli and Staphylococcus, thus lowering the endotoxin level in cirrhotic patients. Simple dietary changes can also aid in reversing BA dysregulation and intestinal microbiome derangement. Vitamin B6 can improve colon health by significantly reducing hydrophobic LCA levels in the colon, creating a reduced LCA to DCA ratio. LCA was 20- fold more toxic than DCA toward liver and colon cancer cells, and vitamin B6 helped with detoxifying enzymes and decreased DNA damage.170 Moreover, various naturally derived products are also under investigation including the antioxidant tempol which reduced obesity and improved insulin resistance in mice fed a high-fat diet by activating bile salt hydrolase to increase intestinal tauro-beta-muricholic acid, an FXR antagonist. Tempol appears to exert its antiobesity effects through FXR since inhibition of intestinal FXR promoted diet-induced obesity and insulin resistance. Tempol was also able to shift the gut microbial profile from firmicutes toward bacteroidetes dominance. Plant-based products such as burdock powder and genistein also showed moderate efficacy in normalizing BA homeostasis and the gut microbiome in animal models. The proposed beneficial effects on BA dysregulation and gut dysbiosis by pharmacological and dietary intervention are described in Figure 4. In this genome release, we report on the first assembled genome of a member of the genus Arctostaphylos. 

Our genome assembly is part of the California Conservation Genomics Project , the goal of which is to establish patterns of genomic diversity across the state of California and its many habitats. The CCGP will sequence the complete genomes of approximately 150 carefully selected species projects. Many of these taxa are threatened or endangered, and therefore in need of conservation management in the face of rapidly accelerating biodiversity decline. The combined reference genome plus landscape genomics approach of the CCGP, based on the resequencing of many individuals of each target species across the state, will allow the identification of hotspots of diversity across California and provide a framework for informed conservation decisions and management plans. Manzanitas are among the most conspicuous and dominant native chaparral species in the California Floristic Province , a biodiversity hotspot characterized by a Mediterranean-type climate with hot, dry summers and cool, wet winters. These plants comprise the most diverse woody genus in the CFP , and their diversity has long fascinated taxonomists. Manzanitas serve essential roles in their native ecosystems, including rapidly regenerating in fired-disturbed areas, and providing food resources for pollinators and fruit-eating animals . In addition, these plants are of great importance for conservation management: over half of the more than 100 morphologically defined manzanita species and subspecies are narrow endemics with highly restricted distributions and are considered rare and/or endangered . In contrast to their importance in ecology, evolution, and conservation studies, genomic resources for manzanitas are nearly nonexistent beyond investigations into karyotypes of diploid and tetraploid species . In this study, we present the first genome sequence of a manzanita. Big berry manzanita, Arctostaphylos glauca , is a widespread diploid species common in northern Baja California and across southern and coastal central California that is hypothesized to be the progenitor of several potential hybrid manzanita species . With funding and support from the CCGP, 25 liter square pot we created this scaffold-level assembly using a hybrid de novo assembly approach that combines Hi-C chromatin-proximity and PacBio HiFi long-read sequencing data. This genome assembly will provide a robust basis for studying the diversification and evolutionary history of Arctostaphylos in the CFP.A Dovetail Hi-C library was prepared in a similar manner as previously described . For each library, chromatin was fixed in place with formaldehyde in the nucleus. Extracted, fixed chromatin was digested with DpnII, the 5′ overhangs were filled in with biotinylated nucleotides, and free blunt ends were ligated. After ligation, crosslinks were reversed, and the DNA purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. The DNA was then sheared to ~350 bp mean fragment size and sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of each library. The libraries were prepared and sequenced on an Illumina HiSeq X by Dovetail Genomics .The CCGP assembly protocol version 1.0 uses PacBio HiFi reads and Hi-C chromatin capture data for the generation of high-quality and highly contiguous nuclear genome assemblies. The output corresponding to a diploid assembly consists of two pseudo haplotypes .

The alternate consists of haplotigs in heterozygous regions and is not as complete and more fragmented. Given the characteristics of the latter, it cannot be considered on its own but as a complement of the primary assembly . Arctostaphylos is the third genus with a genome assembly in the heath family, Ericaceae, following release of assembled genome sequences of Rhododendron and Vaccinium . These two genera are of significant economic importance: many species, hybrids, and cultivars of Rhododendron, including rhododendron and azalea, are important landscape and ornamental plants, and the fruits of many Vaccinium species, which include cranberry, blueberry, and huckleberry, are consumed by humans and other animals. Species in the Ericaceae are also notable for their ability to tolerate acidic and nutrient-poor soils that often characterize boreal forests and bogs, allowing them to thrive in habitats that are inaccessible to most species. Their tolerance for these conditions is due in part to the formation of mutualistic associations between the roots of the plants and soil fungi of a type unique to the heath family known as ericoid mycorrhizae. Ericoid mycorrhizae are distinct from common mycorrhizal associations found in most angiosperms, and are far less well understood . Complete genome sequences from three genera in this family will provide a strong foundation for investigating the basis of this unique mutualism and its ability to promote survival in inhospitable soils. The size of the A. glauca assembly is 547Mb, which is similar to the two Rhododendron genomes and half that of V corymbosum, which is tetraploid . The tetraploid nature of V. corymbosum also explains the vastly greater number of duplicated genes in its assembly compared to the two diploid assemblies. The scaffold N50 of the A. glauca assembly is longer than R. williamsianum, and close to R. simsii and V. corymbosum, suggesting that the contiguity of Arctostaphylos is comparable to the other taxa . Analysis using Repeat Modeler indicated that 57.71% of the A. glauca genome is composed of different categories of repetitive elements . In contrast, analysis using RepeatModeler identified only 26%, 47.5%, and 44.3% of the genome comprising repeat elements in R. williamsianum, R. simsii, and V. corymbosum respectively. The BUSCO completeness assessment of the A. glauca assembly is higher than R. williamsianum and close to the V. corymbosum , indicating that our final assembly is high quality . Overall, the A. glauca, R. simsii and V. corymbosum genomes are of comparably high contiguity and completeness. The lower contiguity and completeness of the R. williamsianum genome may be due to the lack of HiFi or other longread data in the assembly. This explanation is consistent with other studies demonstrating improved assembly with the inclusion of longer reads . Although the big berry manzanita is a common and widespread species, nearly half of the 60+ manzanita species are rare or threatened. Many are now represented by only one or two populations, and are thus vulnerable to complete eradication by the increasingly common and intense wildfires experienced across California each year. Our manzanita genome sequence will help fulfill the overall goal of the CCGP, serving as a key resource to assess genetic diversity in these threatened endemics and move forward with coordinated conservation programs.Sangiovese is the most important Italian red grape variety, with origins in Tuscany and Calabria in the south of Italy. Through time, Sangiovese has always been considered as a good-quality cultivar for wine production. Today, it is the basis of internationally known DOC and DOCG wines from Tuscany in Italy, the region where it is most cultivated. Sangiovese is also grown in Argentina, California, France, and in other countries such Australia and Chile, but to a lesser extent.