references.bib

---
---


@Article{McCook_2015,
author={McCook, Stuart and Vandermeer, John},
title={The Big Rust and the Red Queen: Long-Term Perspectives on Coffee Rust Research},
journal={Phytopathology review},
year={2015},
month={May},
day={24},
volume={105},
number={9}
}


@Article{Belachew_2020,
author={Belachew, Kifle and Senbeta, Girma Adugna and Garedew, Weyessa and Barreto, Robert W. and Del Ponte, Emerson Medeiros},
title={Altitude is the main driver of coffee leaf rust epidemics: a large-scale survey in Ethiopia},
journal={Tropical Plant Pathology},
year={2020},
month={Oct},
day={01},
volume={45},
number={5},
pages={511-521},
issn={1983-2052},
doi={10.1007/s40858-020-00383-4},
url={https://doi.org/10.1007/s40858-020-00383-4}
}

@article{Jha_2014,
    author = {Jha, Shalene and Bacon, Christopher M. and Philpott, Stacy M. and Ernesto Méndez, V. and Läderach, Peter and Rice, Robert A.},
    title = {Shade Coffee: Update on a Disappearing Refuge for Biodiversity},
    journal = {BioScience},
    volume = {64},
    number = {5},
    pages = {416-428},
    year = {2014},
    month = {04},
    abstract = {In the past three decades, coffee cultivation has gained widespread attention for its crucial role in supporting local and global biodiversity. In this synthetic Overview, we present newly gathered data that summarize how global patterns in coffee distribution and shade vegetation have changed and discuss implications for biodiversity, ecosystem services, and livelihoods. Although overall cultivated coffee area has decreased by 8 percent since 1990, coffee production and agricultural intensification have increased in many places and shifted globally, with production expanding in Asia while contracting in Africa. Ecosystem services such as pollination, pest control, climate regulation, and nutrient sequestration are generally greater in shaded coffee farms, but many coffee-growing regions are removing shade trees from their management. Although it is clear that there are ecological and socioeconomic benefits associated with shaded coffee, we expose the many challenges and future research priorities needed to link sustainable coffee management with sustainable livelihoods.},
    issn = {0006-3568},
    doi = {10.1093/biosci/biu038},
    url = {https://doi.org/10.1093/biosci/biu038},
    eprint = {https://academic.oup.com/bioscience/article-pdf/64/5/416/14094027/biu038.pdf},
}

@article{Bebber_2016,
author = {Bebber, Daniel P.  and Castillo, Ángela Delgado  and Gurr, Sarah J. },
title = {Modelling coffee leaf rust risk in Colombia with climate reanalysis data},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
volume = {371},
number = {1709},
pages = {20150458},
year = {2016},
doi = {10.1098/rstb.2015.0458},
URL = {https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2015.0458},
eprint = {https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2015.0458}
}


@article{Brown_2018,
    author = {Brown, Nick},
    title = {Coffee is Rapidly Losing Its Resistance to Rust, Says WCR Science Director},
    journal = {Daily Coffee News},
    year = {2018},
    month = {09},
    url = {https://dailycoffeenews.com/2018/09/24/coffee-is-rapidly-losing-its-resistance-to-rust-says-wcr-science-director/}
}

@article{Brown_2021,
    author = {Brown, Nick},
    title = {Colombian Researchers Discover Aggressive New Variants of Coffee Leaf Rust},
    journal = {Daily Coffee News},
    year = {2021},
    month = {04},
    url = {https://dailycoffeenews.com/2021/04/30/colombian-researchers-discover-aggressive-new-variants-of-coffee-leaf-rust/}
}

@article{WCR_2017,
    author = {World Coffee Research},
    title = {Colombian Researchers Discover Aggressive New Variants of Coffee Leaf Rust},
    journal = {World Coffee Research},
    year = {2017},
    month = {05},
    url = {https://worldcoffeeresearch.org/news/2017/coffee-leaf-rust-resistant-coffee-variety-overcome-in-honduras}
}



@article{Perfecto_1996,
    author = {Perfecto, Ivette and Rice, Robert A. and Greenberg, Russell and Van der Voort, Martha E.},
    title = {Shade Coffee: A Disappearing Refuge for Biodiversity: Shade coffee plantations can contain as much biodiversity as forest habitats},
    journal = {BioScience},
    volume = {46},
    number = {8},
    pages = {598-608},
    year = {1996},
    month = {09},
    issn = {0006-3568},
    doi = {10.2307/1312989},
    url = {https://doi.org/10.2307/1312989},
    eprint = {https://academic.oup.com/bioscience/article-pdf/46/8/598/650215/46-8-598.pdf},
}


@article{Tadesse_2014,
title = {Coffee landscapes as refugia for native woody biodiversity as forest loss continues in southwest Ethiopia},
journal = {Biological Conservation},
volume = {169},
pages = {384-391},
year = {2014},
issn = {0006-3207},
doi = {https://doi.org/10.1016/j.biocon.2013.11.034},
url = {https://www.sciencedirect.com/science/article/pii/S0006320713004205},
author = {Getachew Tadesse and Erika Zavaleta and Carol Shennan},
keywords = {Woody species diversity, Shade coffee, Deforestation, Conservation, Regeneration},
abstract = {Land-use changes threaten biodiversity and ecosystem services. Some of the last remaining forest fragments in Ethiopia, and the world’s only habitats that retain genetically diverse wild Arabica coffee populations, have experienced rapid recent conversion to coffee farms, plantations and agricultural fields. We examined patterns of remnant woody plant diversity in the remaining forests, and assessed the potential and limitations of coffee agroforests to maintain this diversity. We explored patterns of woody biodiversity, structure, and regeneration in forest fragments and on adjacent smallholder and large-scale state-owned shade-coffee farms. A total of 155 native woody species including rare/threatened species of Baphia, Cordia, Manilkara, and Prunus were recorded. Of these species, 56 (36.2%) and 18 (12%) were restricted to forest fragments and coffee farms respectively. Smallholder and large-scale coffee farms maintained 59% and 26% of the 155 recorded native woody species compared to the 137 species (88%) found in forest fragments. Native woody species regeneration in state-owned plantations was lower than in smallholder farms, which in turn was lower than forest fragments. Coffee farms could support a considerable portion, though not all, of the woody biodiversity of disappearing forests. Persistence of forest woody diversity and associated ecosystem services depends strongly on the scale and type of shade coffee cultivation pursued.}
}

@ARTICLE{Le_2022,
  
AUTHOR={Le, Cham Thi Mai and Okane, Izumi and Ono, Yoshitaka and Tsuda, Yoshiaki and Yamaoka, Yuichi},   
	 
TITLE={Incidence of Coffee Leaf Rust in Vietnam, Possible Original Sources and Subsequent Pathways of Migration},      
	
JOURNAL={Frontiers in Plant Science},      
	
VOLUME={13},           
	
YEAR={2022},      
	  
URL={https://www.frontiersin.org/articles/10.3389/fpls.2022.872877},       
	
DOI={10.3389/fpls.2022.872877},      
	
ISSN={1664-462X},   
   
ABSTRACT={This research focused on the incidence and population genetics of coffee leaf rust (CLR) fungus, Hemileia vastatrix, to estimate the possible original source(s) and subsequent migration pathways of wind-borne and human-aided spores in three main coffee production regions (Northwest, Central Highlands, and Southeast) in Vietnam. In southern Vietnam (Central Highlands and Southeast), Coffea canephora covers the majority area, while Catimor lines of C. arabica accounts for 95% of the coffee plantations in northwestern Vietnam. Field surveys conducted at eighty-five plantations, show coffee leaf samples infected by the rust fungus across forty-one plantations. Catimor varieties exhibited high levels of susceptibility with severe rust symptoms, while robusta varieties had varying degrees of susceptibility. We analyzed 863−869 base pairs of internal transcribed spacer (ITS) region from 83 samples (41 sequences from Vietnam, 2 from Thailand, and the remaining 40 from American countries); and fifty-two haplotypes consisting of 123 polymorphic sites were detected. Although the analysis of molecular variance (AMOVA) indicates significant genetic differentiation in the H. vastatrix populations in Vietnam, there was no clear genetic structure with respect to the three geographic areas surveyed. Based on the haplotype network, NeighborNet analysis, and geographical distribution patterns of the haplotypes, five haplotypes were identified as early established, from which most other haplotypes in Vietnam were derived. The early established haplotypes were found in the highest frequency in Northwest Vietnam. This finding corresponds to the earliest record of CLR in Vietnam. The phylogenetic network analysis also illustrated that H. vastatrix had expanded from the northwest to southern Vietnam. Pairwise genetic distance analysis and the geophylogenetic tree also suggests that CLR was first established in the Northwest. In addition, some scattered individuals on the principal coordinate analysis (PCoA) diagram and several separated haplotypes in the phylogenetic networks indicated that other branches of CLR in Vietnam were initiated in the Central Highlands. Hemileia vastatrix from these branches have been spreading in southern Vietnam.}
}


@ARTICLE{Talhinhas_2017,
  title    = {The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics},
  author   = {Talhinhas, Pedro and Batista, Dora and Diniz, Ines andnVieira, Ana and Silva, Diogo N and Loureiro, Andreia and Tavares, Silvia and Pereira, Ana Paula and Azinheira, Helena G and Guerra-Guimaraes, Leonor and Varzea, Vitor and Silva, Maria do Ceu},
  journal  = {Mol Plant Pathol},
  volume   =  {18},
  number   =  {8},
  pages    = {1039--1051},
  year     =  {2017}
}

@Article{Avelino_2015,
author={Avelino, Jacques and Cristancho, Marco and Georgiou, Selena and Imbach, Pablo and Aguilar, Lorena and Bornemann, Gustavo and Laderach, Peter and Anzueto, Francisco and Hruska, Allan J. and Morales, Carmen},
title={The coffee rust crises in Colombia and Central America (2008--2013): impacts, plausible causes and proposed solutions},
journal={Food Security},
year={2015},
month={Apr},
}

@article{Gullino_2021,
author={Gullino, Maria Lodovica},
title={Coffee Rust in Ceylon: Why English People Drink Tea},
bookTitle={Spores: Tulips with Fever, Rusty Coffee, Rotten Apples, Sad Oranges, Crazy Basil. Plant Diseases that Changed the World as Well as My Life},
year={2021},
publisher={Springer International Publishing},
address={Cham"},
pages={29--32"},
abstract={Today Ceylon (now Sri Lanka) is worldwide known for its tea production, but few of us know that in 1870 this island was the main international coffee producer.},
doi={10.1007/978-3-030-69995-6_5},
}


@article{Liebig_2019,
author = {Theresa Liebig and Fabienne Ribeyre and Peter Läderach and Hans-Michael Poehling and Piet van Asten and Jacques Avelino},
title = {Interactive effects of altitude, microclimate and shading system on coffee leaf rust},
journal = {Journal of Plant Interactions},
volume = {14},
number = {1},
pages = {407-415},
year  = {2019},
publisher = {Taylor & Francis},
doi = {10.1080/17429145.2019.1643934},
URL = {https://doi.org/10.1080/17429145.2019.1643934},
}



@article{Avelino_2020,
title = {Shade tree Chloroleucon eurycyclum promotes coffee leaf rust by reducing uredospore wash-off by rain},
journal = {Crop Protection},
volume = {129},
pages = {105038},
year = {2020},
issn = {0261-2194},
doi = {https://doi.org/10.1016/j.cropro.2019.105038},
url = {https://www.sciencedirect.com/science/article/pii/S0261219419303849},
author = {J. Avelino and S. Vílchez and M.B. Segura-Escobar and M.A. Brenes-Loaiza and E. de M. Virginio Filho and F. Casanoves},
keywords = {Coffea arabica, Deposition, Dispersal, , Raindrop kinetic energy, Sporulation, Throughfall},
abstract = {Shade trees stimulate many pathways that influence disease development in opposite directions, and that, in addition, may interact with environment. To better understand shade trees effects on coffee leaf rust (CLR), we studied three disease stages separately: sporulation, uredospore wash-off by rain, and uredospore deposition on leaves. The study was conducted during almost one year in the long-term trial on coffee-based agroforestry systems established by CATIE in 2000, in Turrialba, a low altitude area of Costa Rica. We only used the Full Sun and Shade provided by Chloroleucon eurycyclum treatments. For studying sporulation, we harvested diseased leaves every three weeks and collected the uredospores present on the lesions. For assessments of uredospore wash-off, we located containers at ground level below the coffee bushes and in the interval between rows of coffee bushes, and removed them after rainfall events (43 rainfall events studied) to count the number of uredospores collected. For uredospore deposition, we used varnish to capture deposited uredospores on apparently healthy coffee bush leaves (55 dates). We also studied the raindrop kinetic energy by using splashcups, on 19 rainy days. The number of uredospores produced and preserved was 2.22 times higher below shade trees than in full sun, whereas the number of uredospores lost by wash-off, below the coffee bush, was 1.62 times lower. Reduced wash-off was probably due to raindrop interception by shade trees and stemflow and to the increased kinetic energy of the raindrops in the understory of the Shade treatment (twice as high as that measured in full sun), which reduced the capacity of coffee leaves to intercept raindrops. In addition, we found 1.43 times more uredospores deposited on apparently healthy leaves below shade trees than in full sun, partly due to the higher number of uredospores produced and preserved below shade trees. Increasing throughfall and reducing raindrop kinetic energy below shade trees seem crucial to improved CLR regulation. This can be achieved by selecting specific shade tree functional traits and by implementing shade pruning during the rainy season.}
}

@ARTICLE{Toniutti_2017,
AUTHOR={Toniutti, Lucile and Breitler, Jean-Christophe and Etienne, Hervé and Campa, Claudine and Doulbeau, Sylvie and Urban, Laurent and Lambot, Charles and Pinilla, Juan-Carlos H. and Bertrand, Benoît},    
TITLE={Influence of Environmental Conditions and Genetic Background of Arabica Coffee (C. arabica L) on Leaf Rust (Hemileia vastatrix) Pathogenesis},      
JOURNAL={Frontiers in Plant Science},      
VOLUME={8},           
YEAR={2017},      
URL={https://www.frontiersin.org/articles/10.3389/fpls.2017.02025},       
DOI={10.3389/fpls.2017.02025},      
ISSN={1664-462X},   
   
ABSTRACT={Global warming is a major threat to agriculture worldwide. Between 2008 and 2013, some coffee producing countries in South and Central America suffered from severe epidemics of coffee leaf rust (CLR), resulting in high economic losses with social implications for coffee growers. The climatic events not only favored the development of the pathogen but also affected the physiological status of the coffee plant. The main objectives of the study were to evaluate how the physiological status of the coffee plant modified by different environmental conditions impact on the pathogenesis of CLR and to identify indicators of the physiological status able to predict rust incidence. Three rust susceptible genotypes (one inbred line and two hybrids) were grown in controlled conditions with a combination of thermal regime (TR), nitrogen and light intensity close to the field situation before being inoculated with the rust fungus Hemileia vastatrix. It has been demonstrated that a TR of 27-22°C resulted in 2000 times higher sporulation than with a TR of 23–18°C. It has been also shown that high light intensity combined with low nitrogen fertilization modified the CLR pathogenesis resulting in huge sporulation. CLR sporulation was significantly lower in the F1 hybrids than in the inbred line. The hybrid vigor may have reduced disease incidence. Among the many parameters studied, parameters related to photosystem II and photosynthetic electron transport chain components appeared as indicators of the physiological status of the coffee plant able to predict rust sporulation intensity. Taken together, these results show that CLR sporulation not only depends on the TR but also on the physiological status of the coffee plant, which itself depends on agronomic conditions. Our work suggests that vigorous varieties combined with a shaded system and appropriate nitrogen fertilization should be part of an agro-ecological approach to disease control.}
}

@Article{Belan_2015,
author={Belan, Leonidas Leoni and Pozza, Edson Ampelio and Freitas, Marcelo Loran de Oliveira and Pozza, Adelia Aziz Alexandre and de Abreu, Mario Sobral and Alves, Eduardo},
title={Nutrients distribution in diseased coffee leaf tissue},
journal={Australasian Plant Pathology},
year={2015},
month={Jan},
day={01},
volume={44},
number={1},
pages={105-111},
abstract={Knowing the structure and distribution of nutrients in plant tissues can clarify some mechanisms of pathogen attack in plants and plant defense against infection, thus helping management strategies. The aim of this study was verify differences in distribution of mineral nutrients in coffee leaf tissues around foliar lesions of bacterial blight of coffee, blister spot, cercospora leaf, phoma leaf spot and coffee leaf rust. Fragments of leaf tissue surrounding the lesions were dehydrated in silica gel, carbon covered and subjected to X-ray microanalysis (MAX). Thirty-three chemical elements were detected in leaf tissue; however, there was variation in potassium and calcium contents surrounding the lesions. The highest potassium content was found in asymptomatic tissues surrounding the lesions, decreasing toward the transition zone and reaching minimum content in symptomatic tissues. The highest calcium content was found in symptomatic tissues, decreasing toward the transition zone and reaching minimum content in asymptomatic tissues. Therefore, MAX can be used to analyze the composition and distribution of nutrients in plant tissues and, if associated with mineral nutrition, it may help understand host-pathogen relationships and plant disease management.},
issn={1448-6032},
doi={10.1007/s13313-014-0329-0},
url={https://doi.org/10.1007/s13313-014-0329-0}
}


@Article{vanderVossen_2015,
author={van der Vossen, Herbert and Bertrand, Benoit and Charrier, Andre},
title={Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review},
journal={Euphytica},
year={2015},
month={Jul},
day={01},
volume={204},
number={2},
pages={243-256},
abstract={Arabica coffees, 60 percent of current world coffee production) are generally sold at considerably better prices than robustas on account of superior beverage quality. However, costs of production are much higher, mainly due to more stringent demands for soil and climatic conditions, crop management, primary processing and control of several pests and diseases including the potentially very destructive coffee leaf rust (CLR) and berry disease (CBD). Breeding for disease resistance in combination with vigour, productivity and quality started in the early 1920s in India, but especially in the second half of the 20th century comprehensive breeding programmes have been implemented in several other coffee producing countries. Many of the resulting CLR- and CBD + CLR-resistant cultivars (true-breeding lines and F1 hybrids) meet the required standards of profitable and sustainable crop production. Challenges of more recent date include limited access to additional genetic resources of Coffea arabica, breakdown of host resistance to CLR, aggravating insect pest problems and the increasingly negative impact of climate change on arabica coffee production worldwide. This review discusses prospects of breeding and disseminating next generation (hybrid) cultivars of arabica coffee for sustainable coffee production under changing conditions of diseases, pests and climate. International networking on coffee breeding will facilitate sharing of resources (financial, genetic) and scientific information, application of genomics-assisted selection technologies, and pre-breeding for specific characters. Breeding and multiplication of new cultivars well adapted to the local environment will continue to be carried out at national or regional levels. A tree crop like arabica coffee does not lend itself to centralized variety development and dissemination on a global scale.},
issn={1573-5060},
doi={10.1007/s10681-015-1398-z},
url={https://doi.org/10.1007/s10681-015-1398-z}
}



@Article{Diola_2011,
author={Diola, Valdir and de Brito, Giovani Greigh and Caixeta, Eveline Teixeira and Maciel-Zambolim, Eunize and Sakiyama, Ney Sussumu and Loureiro, Marcelo Ehlers},
title={High-density genetic mapping for coffee leaf rust resistance},
journal={Tree Genetics and Genomes},
year={2011},
month={Dec},
day={01},
volume={7},
number={6},
pages={1199-1208},
abstract={Coffee leaf rust caused by the fungus Hemileia vastatrix causes considerable economic losses for coffee producers. Although agrochemical products can provide sufficient disease control, the use of resistant cultivars is a safer alternative. This resistance may be constrained by one or a few genetic factors, mainly those found in material originating from interspecific hybrids. In this study, the genetic analysis of an F2population consisting of 224 plants derived from a crossing of Hibrido de Timor UFV 427-15 (resistant) with Catuai Amarelo IAC 30 (susceptible) showed that a dominant gene confers the resistance of coffee to race II of H. vastatrix. From a genetic map saturated with 25 amplified fragment length polymorphism (AFLP) markers linked to the resistance gene, we developed a high-density genetic map with six sequence-characterized amplified region (SCAR) markers delimiting a chromosomal region of 9.45 cM and flanking the dominant gene at 0.7 and 0.9 cM. This is the first saturated and high-density genetic map obtained from this region containing the resistance gene. The results of this study are of great importance for the introduction of molecular markers for marker-assisted selection; they will also facilitate studies related to the cloning, structure, and function of race-specific genes involved in the resistance of coffee trees to H. vastatrix.},
issn={1614-2950},
doi={10.1007/s11295-011-0406-2},
url={https://doi.org/10.1007/s11295-011-0406-2}
}

@Article{Valencia_2018,
author={Valencia, Vivian and Garcia-Barrios, Luis and Sterling, Eleanor J. and West, Paige and Meza-Jimenez, Amayrani and Naeem, Shahid},
title={Smallholder response to environmental change: Impacts of coffee leaf rust in a forest frontier in Mexico},
journal={Land Use Policy},
year={2018},
month={Dec},
day={01},
volume={79},
pages={463-474},
keywords={Adaptation; Agroforestry; Autonomy; Environmental shock; Forest conservation},
issn={0264-8377},
url={https://www.sciencedirect.com/science/article/pii/S0264837718302436}
}

@article{De_resende_2021,
author = {De Resende, MLV and Pozza, EA and Reichel, T and Botelho, DMS},
title = {Strategies for Coffee Leaf Rust Management in Organic Crop Systems},
journal = {Agronomy},
year = {2021},
doi = {https://doi.org/10.3390/agronomy11091865}
}


@article{Sera_2022,
author = {Sera, GH and de Carvalho, CHS and de Rezende Abrahão, JC and Pozza, EA and Matiello, JB and de Almeida, SR and Bartelega, L and dos Santos Botelho, DM. },
title = {Coffee Leaf Rust in Brazil: Historical Events, Current Situation, and Control Measures},
journal = {Agronomy},
year = {2022},
doi = {https://doi.org/10.3390/agronomy12020496}
}

@article{Koutouleas_2019,
author = {Koutouleas, Athina and Jørgen Lyngs Jørgensen, Hans and Jensen, Birgit and Lillesø, Jens-Peter Barnekow and Junge, Alexander and Ræbild, Anders},
title = {On the hunt for the alternate host of Hemileia vastatrix},
journal = {Ecology and Evolution},
volume = {9},
number = {23},
pages = {13619-13631},
keywords = {coffee leaf rust, disease cycle, Hemileia vastatrix, hypothetical alternate host ranking},
doi = {https://doi.org/10.1002/ece3.5755},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.5755},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.5755},
abstract = {Abstract Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix, has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coffee by basidiospores of H. vastatrix has never been reported and thus far, no alternate host, capable of supporting an aecial stage in the disease cycle, has been found. Due to this, some argue that an alternate host of H. vastatrix does not exist. Yet, to date, the plant pathology community has been puzzled by the ability of H. vastatrix to overcome resistance in coffee cultivars despite the apparent lack of sexual reproduction and an aecidial stage. The purpose of this study was to introduce a new method to search for the alternate host(s) of H. vastatrix. To do this, we present the novel hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure, utilizing comprehensive biogeographical botanical data from the designated sites of interests (Ethiopia, Kenya and Sri Lanka) and plant pathology insights. With the HAHR/ATM methods, we produced prioritized lists of potential alternate hosts plant of coffee leaf rust. This is a first attempt to seek out an alternate plant host of a pathogenic fungus in this manner. The HAHR method showed the highest-ranking probable alternate host as Psychotria mahonii, Rubus apetalus, and Rhamnus prinoides. The cross-referenced results by the two methods suggest that plant genera of interest are Croton, Euphorbia, and Rubus. The HAHR and ATM methods may also be applied to other plant–rust interactions that include an unknown alternate host or any other biological system, which rely on data mining of published data.},
year = {2019}
}

@article{Kimberly_1997,
 ISSN = {00301299, 16000706},
 URL = {http://www.jstor.org/stable/3546007},
 abstract = {Neutral landscape models (NLMs) were developed from percolation theory nearly a decade ago. Since then, the original random percolation maps have undergone adaptive radiation and NLMs now include a diverse array of spatially explicit models based on theoretical distributions derived from fractal geometry and spectral synthesis. The purpose of NLMs is to provide null models of landscape structure as a baseline for comparison with real landscape patterns, or for evaluating the effects of landscape structure on ecological processes. As the use of NLMs has expanded beyond the domain of theoretical landscape ecology to applications in other areas of ecology, there is an increased risk that NLMs will be used inappropriately, or that their function will be misunderstood or misinterpreted. NLMs are being subjected to the same general criticisms levied against null models in other areas of ecology. For this reason, we clarify the purpose of NLMs, review the contributions of NLMs to ecology, and evaluate the appropriate use of NLMs in ecological research. NLMs have already made several contributions to ecology: (1) development of spatial indices to describe landscape patterns; (2) prediction of critical thresholds in ecological phenomena; (3) definition of landscape connectivity; (4) development of "species' perceptions" of landscape structure; (5) provision of a general model of spatial complexity; and (6) determination of the ecological consequences of spatial heterogeneity. In the future, emphasis on NLMs should shift from theoretical development to application and model testing.},
 author = {Kimberly A. With and Anthony W. King},
 journal = {Oikos},
 number = {2},
 pages = {219--229},
 publisher = {[Nordic Society Oikos, Wiley]},
 title = {The Use and Misuse of Neutral Landscape Models in Ecology},
 urldate = {2023-01-01},
 volume = {79},
 year = {1997}
}


@article{Etherington_2015,
author = {Etherington, Thomas R. and Holland, E. Penelope and O'Sullivan, David},
title = {NLMpy: a python software package for the creation of neutral landscape models within a general numerical framework},
journal = {Methods in Ecology and Evolution},
volume = {6},
number = {2},
pages = {164-168},
keywords = {artificial landscape, geographic information system, GIS, landscape generator, NLM, NumPy, SciPy, virtual landscape},
doi = {https://doi.org/10.1111/2041-210X.12308},
url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.12308},
eprint = {https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12308},
abstract = {Summary Neutral landscape models (NLMs) are widely used to model ecological patterns and processes across landscapes. However, the ability to generate NLMs is often made available through standalone bespoke software packages that have platform limitations. We have developed a python package that brings together some of the more popular NLM algorithms using a general numerical framework. The resulting NLMpy package: (i) allows for the creation of NLMs directly within a python modelling workflow or by other modelling software capable executing a python script, (ii) enables the first opportunity to create a NLM that combines different algorithms, (iii) provides easy integration with geographic information system data and (iv) creates a framework for developing other NLMs.},
year = {2015}
}



@Article{Beasley_2022,
author={Beasley, Emily M. and Aristizabal, Natalia and Bueno, Erika M. and White, Easton R.},
title={Spatially explicit models predict coffee rust spread in fragmented landscapes},
journal={Landscape Ecology},
year={2022},
month={Aug},
day={01},
volume={37},
number={8},
pages={2165-2178},
abstract={Landscape structure influences the spread of plant pathogens, including coffee leaf rust, a fungal disease affecting the coffee industry. Rust transmission is likely affected by landscape structure through the dispersal of wind-borne spores. Previous studies found positive associations between rust incidence and the proportion of pasture cover, suggesting deforestation may facilitate spore dispersal.},
issn={1572-9761},
doi={10.1007/s10980-022-01473-1},
url={https://doi.org/10.1007/s10980-022-01473-1}
}

@article{Rayner_1969,
author = {RAYNER, R. W.},
title = {Germination and penetration studies on coffee rust (Hemileia vastatrix B. \& Br.)},
journal = {Annals of Applied Biology},
volume = {49},
number = {3},
pages = {497-505},
doi = {https://doi.org/10.1111/j.1744-7348.1961.tb03641.x},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1744-7348.1961.tb03641.x},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1744-7348.1961.tb03641.x},
abstract = {SUMMARY Spore dispersal, germination, penetration and incubation-period studies on coffee rust (Hemileia vastatrix B. \& Br.) in Kenya, East Africa, are described. Evidence is produced that air-borne spores may be trapped effectively on the upper surfaces of leaves, thence to be liberated and transported to the undersurfaces of other leaves by rain splash. Germination requires liquid water and was observed to occur in 2.6–4.7 hr-(medians) at 23° C., the minimum being 1 hr. Appressoria were formed in 6.5–8.5 hr. (medians) with a 5.3 hr. minimum. Germination is inhibited by light and in the field by the rapid evaporation of water droplets on the lower leaf surface which occurs during daylight. Light inhibits the growth of germ tubes that are less than 30 μ long and reduces rate of growth if they are longer; appressoria may continue to form. In the field, appressorium formation and infection can occur between 10 p.m. and 8 a.m. If coffee trees are wet at dusk or rain falls before midnight, infection is probable and it is proposed that the number of occasions this occurs be used to forecast the severity of the annual rust maximum. The median incubation period throughout the year varied from 4 to 7 weeks, increasing with low temperatures and dry conditions. A multiple regression of mean maximum and minimum temperatures on incubation period gave fair agreement between observed and computed values for Ceylon and Mysore. Susceptibility and incubation period were strongly affected by coffee variety and rust biotype, but not by age of leaf or crop size.},
year = {1961}
}


@Article{Vandermeer_2018,
author={Vandermeer, John and Hajian-Forooshani, Zachary and Perfecto, Ivette},
title={The dynamics of the coffee rust disease: an epidemiological approach using network theory},
journal={European Journal of Plant Pathology},
year={2018},
month={Apr},
day={01},
volume={150},
number={4},
pages={1001-1010},
abstract={Dynamic modeling of plant pathogens has usually been accomplished with either a mean field or spatially explicit approach, searching generally for either broad generalization or precise prediction. In search of a qualitative intermediate that is able to query spatial particulars of transmission, we take an approximate approach using network theory. Some elements of network theory are applied to a specific case of the early spread of the coffee rust disease (agent = Hemileia vastatrix) on a single large shaded coffee farm in Chiapas, Mexico. We find that infection rates within connected components are more homogeneous than infection rates among components, suggesting that the initial stages of this disease show pattern that can be detected using simple ideas from network theory.},
issn={1573-8469},
doi={10.1007/s10658-017-1339-x},
url={https://doi.org/10.1007/s10658-017-1339-x}
}

@article{Djuikem_2021,
author = {Djuikem, Clotilde and Grognard, Frédéric and Tagne Wafo, Roger and Touzeau, Suzanne and Bowong, Samuel},
year = {2021},
month = {03},
pages = {},
title = {Modelling coffee leaf rust dynamics to control its spread},
volume = {16},
journal = {Mathematical Modelling of Natural Phenomena},
doi = {10.1051/mmnp/2021018}
}

@incollection{Townsend_2017,
title = {Chapter Seven - Phylogenetics and Phylogenomics of Rust Fungi},
editor = {Jeffrey P. Townsend and Zheng Wang},
series = {Advances in Genetics},
publisher = {Academic Press},
volume = {100},
pages = {267-307},
year = {2017},
booktitle = {Fungal Phylogenetics and Phylogenomics},
issn = {0065-2660},
doi = {https://doi.org/10.1016/bs.adgen.2017.09.011},
url = {https://www.sciencedirect.com/science/article/pii/S0065266017300391},
author = {M. Catherine Aime and Alistair R. McTaggart and Stephen J. Mondo and Sébastien Duplessis},
keywords = {Comparative genomics, Complex life cycles, Heteroecism, Obligate biotroph, Phytopathogen, Pucciniomycotina, Repetitive elements, Transposable elements, Uredinales},
abstract = {Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi. In this chapter, we provide an overview of the current status and special challenges of rust genomics, and we highlight how phylogenomics may provide new perspectives and answer long-standing questions regarding the biology of rust fungi.}
}

@ARTICLE{OEC_2022,
AUTHOR = {The Observatory of Economic Complexity},
TITLE = {Coffee},
Year = {2022},
URL = {https://oec.world/en/profile/hs/coffee}
}

@ARTICLE{Siles_2022,
  
AUTHOR={Siles, Pablo and Cerdán, Carlos R. and Staver, Charles},   
	 
TITLE={Smallholder Coffee in the Global Economy—A Framework to Explore Transformation Alternatives of Traditional Agroforestry for Greater Economic, Ecological, and Livelihood Viability},      
	
JOURNAL={Frontiers in Sustainable Food Systems},      
	
VOLUME={6},           
	
YEAR={2022},      
	  
URL={https://www.frontiersin.org/articles/10.3389/fsufs.2022.808207},       
	
DOI={10.3389/fsufs.2022.808207},      
	
ISSN={2571-581X},   
   
ABSTRACT={Sixty percent of global coffee is produced from farms of <5 ha. Studies show that returns from such farms do not generate a living income for producers or workers threatening supplies. Smallholders use agroforestry to reduce coffee production costs, diversify income and address livelihood needs. We undertook a three-phase analysis to test the following hypothesis. Current coffee agroforestry must shift from a low labor, low risk-stable return, slowly-changing matrix to more active management of species and stem turnover in system renovation cycles targeted to sustaining, reorienting and intensifying ecosystem-based benefits to coffee production, diversified income and household food. First, we conducted a document survey of current traditional tree diversity, research trends, and market drivers for more benefits-oriented agroforestry. Second, we proposed a framework for multiple benefits quantification converting tree use characteristics and density into five categories of benefits, each with sub-categories which we tested using previously collected data of stem density by species from coffee agroforestry in northern Nicaragua. Third, we modeled radiation in mixed canopy scenarios using the program SExI- FS based on modifications of species and density to target food and income diversification and tested our framework by quantifying benefits. We found that smallholder coffee faces farms decreasing coffee margins, labor scarcity, new pests and climate variability best addressed with targeted and adaptive shifts in coffee varieties and associated trees. Increasing data demands from certification and regulations provide a basis more data-driven coffee farm management. Our data bases of stem density by species of established agroforestry systems were sufficient to identify gaps in food and income benefits which were addressed in the scenarios thereby verifying the hypothesis. The benefits ranking both of current systems and three scenarios also provided insights into data collection specifications for a more rigorous academic test of the hypothesis and data-driven grower strategies for agroforestry transformation.}
}

@article{Helfer_2014,
author = {Helfer, Stephan},
title = {Rust fungi and global change},
journal = {New Phytologist},
volume = {201},
number = {3},
pages = {770-780},
keywords = {biogeography, fungal conservation, global change, pathogens, Pucciniales (rust fungi)},
doi = {https://doi.org/10.1111/nph.12570},
url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.12570},
eprint = {https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12570},
abstract = {Summary Rust fungi are important components of ecological communities and in ecosystem function. Their unique life strategies as biotrophic pathogens with complicated life cycles could make them vulnerable to global environmental change. While there are gaps in our knowledge, especially in natural plant–rust systems, this review of the exposure of rust fungi to global change parameters revealed that some host–rust relationships would decline under predicted environmental change scenarios, whereas others would either remain unchanged or become more prevalent. Notably, some graminicolous rusts are negatively affected by higher temperatures and increased concentrations of atmospheric CO2. An increase of atmospheric O3 appears to favour rust diseases on trees but not those on grasses. Combined effects of CO2 and O3 are intermediary. The most important global drivers for the geographical and host plant range expansion and prevalence of rusts, however, are global plant trade, host plant genetic homogenization and the regular occurrence of conducive environmental conditions, especially the availability of moisture. However, while rusts thrive in high-humidity environments, they can also survive in desert habitats, and as a group their environmental tolerance is large, with no conclusive change in their overall prevalence predictable to date.},
year = {2014}
}