references.bib

@ARTICLE{Lehner2017-mm,
  title    = "Independently founded populations of {\textit{Sclerotinia sclerotiorum}} from a tropical and a temperate region have similar genetic structure",
  author   = "Lehner, Miller S and de Paula J{\'u}nior, Trazilbo J and Del
              Ponte, Emerson M and Mizubuti, Eduardo S G and Pethybridge, Sarah
              J",
  abstract = "Sclerotinia sclerotiorum populations from tropical agricultural
              zones have been suggested to be more variable compared to those
              from temperate zones. However, no data were available comparing
              populations from both zones using the same set of markers. In
              this study, we compared S. sclerotiorum populations from the
              United States of America (USA, temperate) and southeast Brazil
              (tropical) using the frequency of mycelial compatibility groups
              (MCGs) and 13 microsatellite (SSR) markers. Populations were
              sourced from diseased plants within leguminous crops in New York,
              USA (NY; n = 78 isolates), and Minas Gerais State, Brazil (MG; n
              = 109). Twenty MCGs were identified in NY and 14 were previously
              reported in MG. The effective number of genotypes based on Hill's
              number of order 0, which corresponded to the number of multilocus
              genotypes (MLGs) were 22 (95\% CI = 15.6-28.4) and 24 (95\% CI =
              18.9-29.1) in NY and MG, respectively. Clonal fractions of MLGs
              were 71.8\% (NY) and 78.0\% (MG). The effective number of
              genotypes based on Hill's number of orders 1 and 2 in NY were 8.9
              (95\% CI = 5.2-12.6) and 4.4 (95\% CI = 2.6-6.1), respectively.
              For MG these indices were 11.4 (95\% CI = 8.7-14.1) and 7.1 (95\%
              CI = 5.1-9.0), respectively. There were no significant
              differences of allelic richness, private allelic richness, gene
              diversity, effective number of alleles and genotype evenness
              between the NY and MG populations. The populations were
              differentiated, with 29\% of total variance attributed to
              differences between them and G''ST and Jost's D indices higher
              than 0.50. Cluster analysis revealed dissimilarity higher than
              80\% among most MLGs from both populations. Different alleles
              segregated in the populations but both had similar levels of
              genotypic variability.",
  journal  = "PLoS One",
  volume   =  12,
  number   =  3,
  pages    = "e0173915",
  month    =  mar,
  year     =  2017,
  language = "en"
}

@ARTICLE{Kohli1998-hh,
  title    = "Random association among alleles in clonal populations of {\textit{Sclerotinia sclerotiorum}}",
  author   = "Kohli, Y and Kohn, L M",
  abstract = "Multiple loci identified in DNA fingerprints were used to test
              for random association in two agricultural populations of S.
              sclerotiorum. In linkage disequilibrium tests among pairs of loci
              with frequencies between 0.1 and 0.9, 44.5 and 80.5\% of pairs of
              loci were consistent with random association in the
              clone-corrected samples of the Canadian canola and the North
              Carolina cabbage populations, respectively. In estimates of
              corrected (Bonferroni) P value, 70.66 and 98.89\% of pairs of
              loci were in random association. All four possible genotypes for
              each pair of loci were observed in the Canadian canola sample,
              consistent with random association among loci. In multilocus
              association tests across all loci, however, significant
              association was observed in both populations. In the Canadian
              canola population, 40 possible heterokaryons were identified. Our
              data suggest that populations of S. sclerotiorum are
              predominantly clonal and that occasional genetic exchange and
              recombination, and not mutation alone, may be a source of new
              genotypes.",
  journal  = "Fungal Genetics and Biology",
  volume   =  23,
  number   =  2,
  pages    = "139--149",
  month    =  mar,
  year     =  1998,
  language = "en"
}

@ARTICLE{Derbyshire2017-mx,
  title    = "The complete genome sequence of the phytopathogenic fungus {\textit{Sclerotinia sclerotiorum}} reveals insights into the genome architecture of broad host range pathogens",
  author   = "Derbyshire, Mark and Denton-Giles, Matthew and Hegedus, Dwayne
              and Seifbarghy, Shirin and Rollins, Jeffrey and van Kan, Jan and
              Seidl, Michael F and Faino, Luigi and Mbengue, Malick and Navaud,
              Olivier and Raffaele, Sylvain and Hammond-Kosack, Kim and Heard,
              Stephanie and Oliver, Richard",
  journal  = "Genome Biology and Evolution",
  doi = {10.1093/gbe/evx030},
  url = {https://doi.org/10.1093/gbe/evx030},
  month    =  feb,
  year     =  2017,
  volume = {9},
  number = {3},
  pages = {593--618},
  language = "en"
}

@ARTICLE{Hambleton2002-an,
  title   = "Clonal lineages of {\textit{Sclerotinia sclerotiorum}} previously known from
             other crops predominate in 1999-2000 samples from {Ontario} and
	     {Quebec} soybean",
  author  = "Hambleton, S and Walker, C and Kohn, L M",
  journal = "Canadian Journal of Plant Pathology",
  volume  =  24,
  number  =  3,
  pages   = "309--315",
  year    =  2002
}

@ARTICLE{Barari2012-dn,
  title    = "Genetic and morphological differences among populations of
              {\textit{Sclerotinina sclerotiorum}} by microsatellite markers,
              mycelial compatibility groups ({MCGs}) and aggressiveness in
              North Iran",
  author   = "Barari, H and Alavi, V and Badalyan, S M",
  abstract = "Sclerotinia sclerotiorum is a cosmopolitan, homothallic fungus
              and is the most important causal agent of stem rot diseases in
              field crops of Iran. During 2006 - 2007, 65 isolates of the
              fungus were obtained from infected rapeseed, lettuce, bean,
              tomato, cucumber and wild Sinapis plants in various fields of
              North provinces of Iran. Genetic diversity between the isolates
              was investigated by PCR, using five microsatellite primer pairs.
              These divided the isolates into 9 groups with 25 clear
              polymorphic alleles. A high level of genetic diversity was
              observed at about 67.6\% between some isolates. By mycelial
              compatibility grouping (MCG) tests, the isolates were classified
              into 39 groups of which 26 MCGs were individual. Molecular and
              phenotypic analyses results o f all of the isolates (except MCG1,
              MCG4 and MCG23) were similar; however the isolates in MCG1, MCG4
              and MCG23 groups, with variable microsatellite haplotypes, were
              morphologically dissimilar. The results shown here were possibly
              due to high rates of out crossing, as well as to the evolutionary
              potential within population of the pathogen in different
              locations in Iran",
  journal  = "Romanian Agricultural Research 29",
  number   =  29,
  pages    = "323--331",
  month    =  jan,
  year     =  2012
}

@ARTICLE{Grubisha2010-ld,
  title    = "Genetic isolation among sympatric vegetative compatibility groups
              of the aflatoxin-producing fungus {\textit{Aspergillus flavus}}",
  author   = "Grubisha, L C and Cotty, P J",
  abstract = "Aspergillus flavus, a fungal pathogen of animals and both wild
              and economically important plants, is most recognized for
              producing aflatoxin, a cancer-causing secondary metabolite that
              contaminates food and animal feed globally. Aspergillus flavus
              has two self/nonself recognition systems, a sexual compatibility
              system and a vegetative incompatibility system, and both play a
              role in directing gene flow in populations. Aspergillus flavus
              reproduces clonally in wild and agricultural settings, but
              whether a cryptic sexual stage exists in nature is currently
              unknown. We investigated the distribution of genetic variation in
              243 samples collected over 4 years from three common vegetative
              compatibility groups (VCGs) in Arizona and Texas from cotton
              using 24 microsatellite loci and the mating type locus (MAT) to
              assess population structure and potential gene flow among A.
              flavus VCGs in sympatric populations. All isolates within a VCG
              had the same mating type with OD02 having MAT1-2 and both CG136
              and MR17 having MAT1-1. Our results support the hypothesis that
              these three A. flavus VCGs are genetically isolated. We found
              high levels of genetic differentiation and no evidence of gene
              flow between VCGs, including VCGs of opposite mating-type. Our
              results suggest that these VCGs diverged before domestication of
              agricultural hosts (>10,000 yr bp).",
  journal  = "Molecular Ecology",
  volume   =  19,
  number   =  2,
  pages    = "269--280",
  month    =  jan,
  year     =  2010,
  language = "en"
}

@BOOK{Kuhn2012-hy,
  title     = "The Structure of Scientific Revolutions: 50th Anniversary
               Edition",
  author    = "Kuhn, Thomas S",
  abstract  = "A good book may have the power to change the way we see the
               world, but a great book actually becomes part of our daily
               consciousness, pervading our thinking to the point that we take
               it for granted, and we forget how provocative and challenging
               its ideas once were---and still are. The Structure of Scientific
               Revolutions is that kind of book. When it was first published in
               1962, it was a landmark event in the history and philosophy of
               science. Fifty years later, it still has many lessons to teach.
               With The Structure of Scientific Revolutions, Kuhn challenged
               long-standing linear notions of scientific progress, arguing
               that transformative ideas don't arise from the day-to-day,
               gradual process of experimentation and data accumulation but
               that the revolutions in science, those breakthrough moments that
               disrupt accepted thinking and offer unanticipated ideas, occur
               outside of ``normal science,'' as he called it. Though Kuhn was
               writing when physics ruled the sciences, his ideas on how
               scientific revolutions bring order to the anomalies that amass
               over time in research experiments are still instructive in our
               biotech age. This new edition of Kuhn's essential work in the
               history of science includes an insightful introduction by Ian
               Hacking, which clarifies terms popularized by Kuhn, including
               paradigm and incommensurability, and applies Kuhn's ideas to the
               science of today. Usefully keyed to the separate sections of the
               book, Hacking's introduction provides important background
               information as well as a contemporary context. Newly designed,
               with an expanded index, this edition will be eagerly welcomed by
               the next generation of readers seeking to understand the history
               of our perspectives on science.",
  publisher = "University of Chicago Press",
  month     =  apr,
  year      =  2012,
  language  = "en"
}

@ARTICLE{Atallah2004-es,
  title    = "High genetic diversity, phenotypic uniformity, and evidence of
              outcrossing in {\textit{Sclerotinia sclerotiorum}} in the columbia basin of
              {Washington} state",
  author   = "Atallah, Z K and Larget, B and Chen, X and Johnson, D A",
  abstract = "Sclerotinia sclerotiorum, the causal agent of potato
              stem rot, is prevalent and poorly managed on potatoes in the
              Columbia Basin of Washington. Because of the ubiquitous nature of
              the fungus and high crop diversity within the Columbia Basin,
              understanding the population structure and the potential for
              outcrossing of the pathogen would be helpful in developing
              disease management strategies. The population structure of S.
              sclerotiorum in the Columbia Basin from potato was examined using
              microsatellite markers and mycelial compatibility. Analysis of
              molecular variance revealed that 92\% of the variability among
              167 isolates was found within subpopulations, with limited, yet
              statistically significant impact of the collection date, but not
              the year or location of collection. Linkage disequilibrium and
              index of association analyses noted a potential for outcrossing
              in two locations, which was substantiated by the discovery of
              recombinant ascospores in three field-generated apothecia from
              the 12 apothecia examined. Microsatellite haplotypes were not
              correlated with mycelial compatibility groups. This high
              haplotypic diversity did not seem to impact pathologically
              important phenotypes. Greenhouse inoculations of potato plants
              exhibited no significant differences in aggressiveness on potato
              stems. Moreover, in vitro studies of response to fungicides and
              temperature stimuli yielded no significant differences among
              studied isolates. These findings illustrate the potential for
              outcrossing in warm temperate regions of North America, where a
              diversity of crops are planted simultaneously and in neighboring
              fields. This study also indicates that the unsatisfactory
              management of potato stem rot is likely not directly attributable
              to genetic factors, but to gaps in agricultural practices.",
  journal  = "Phytopathology",
  volume   =  94,
  number   =  7,
  pages    = "737--742",
  month    =  jul,
  year     =  2004,
  language = "en"
}

@ARTICLE{Micali2003-li,
  title    = "On the independence of barrage formation and heterokaryon
              incompatibility in {\textit{Neurospora crassa}}",
  author   = "Micali, Cristina O and Smith, Myron L",
  abstract = "A barrage is a line or zone of demarcation that may develop at
              the interface where genetically different fungi meet. Barrage
              formation represents a type of nonself recognition that has often
              been attributed to the heterokaryon incompatibility system, which
              limits the co-occurrence of genetically different nuclei in the
              same cytoplasm during the asexual phase of the life cycle. While
              the genetic basis of the heterokaryon incompatibility system is
              well characterized in Neurospora crassa, barrage formation has
              not been thoroughly investigated. In addition to the previously
              described Standard Mating Reaction barrage, we identified at
              least three types of barrage in N. crassa; dark line, clear zone,
              and raised aggregate of hyphae. Barrage formation in N. crassa
              was evident only when paired mycelia were genetically different
              and only when confrontations were carried out on low nutrient
              growth media. Barrages were observed to occur in some cases
              between strains that were identical at all major heterokaryon
              incompatibility (het) loci and the mating-type locus, mat, which
              acts as a heterokaryon incompatibility locus during the
              vegetative phase of N. crassa. We also found examples where
              barrages did not form between strains that had genetic
              differences at het-6, het-c, and/or mat. Taken together, these
              results suggest that the genetic control of barrage formation in
              N. crassa can operate independently from that of heterokaryon
              incompatibility and mating type. Surprisingly, barrages were not
              observed to form when wild-collected strains of N. crassa were
              paired. However, an increase in the frequency of pairings that
              produced barrages was observed among strains obtained by
              back-crossing wild strains to laboratory strains, or through
              successive rounds of inbreeding of wild-derived strains,
              suggesting the presence in wild strains of genes that suppress
              barrage.",
  journal  = "Fungal Genetics Biology",
  volume   =  38,
  number   =  2,
  pages    = "209--219",
  month    =  mar,
  year     =  2003,
  language = "en"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Yang2016-hy,
  title    = "A next-generation marker genotyping platform ({AmpSeq}) in
              heterozygous crops: a case study for marker-assisted selection in
              grapevine",
  author   = "Yang, Shanshan and Fresnedo-Ram{\'\i}rez, Jonathan and Wang,
              Minghui and Cote, Linda and Schweitzer, Peter and Barba, Paola
              and Takacs, Elizabeth M and Clark, Matthew and Luby, James and
              Manns, David C and Sacks, Gavin and Mansfield, Anna Katharine and
              Londo, Jason and Fennell, Anne and Gadoury, David and Reisch,
              Bruce and Cadle-Davidson, Lance and Sun, Qi",
  abstract = "Marker-assisted selection (MAS) is often employed in crop
              breeding programs to accelerate and enhance cultivar development,
              via selection during the juvenile phase and parental selection
              prior to crossing. Next-generation sequencing and its derivative
              technologies have been used for genome-wide molecular marker
              discovery. To bridge the gap between marker development and MAS
              implementation, this study developed a novel practical strategy
              with a semi-automated pipeline that incorporates trait-associated
              single nucleotide polymorphism marker discovery, low-cost
              genotyping through amplicon sequencing (AmpSeq) and decision
              making. The results document the development of a MAS package
              derived from genotyping-by-sequencing using three traits (flower
              sex, disease resistance and acylated anthocyanins) in grapevine
              breeding. The vast majority of sequence reads (⩾99\%) were from
              the targeted regions. Across 380 individuals and up to 31
              amplicons sequenced in each lane of MiSeq data, most amplicons
              (83 to 87\%) had <10\% missing data, and read depth had a median
              of 220-244$\times$. Several strengths of the AmpSeq platform that
              make this approach of broad interest in diverse crop species
              include accuracy, flexibility, speed, high-throughput, low-cost
              and easily automated analysis.",
  journal  = "Hortic Res",
  volume   =  3,
  pages    = "16002",
  month    =  feb,
  year     =  2016,
  language = "en"
}

@ARTICLE{Lachance2013-kq,
  title    = "Population Genomics of Human Adaptation",
  author   = "Lachance, Joseph and Tishkoff, Sarah A",
  abstract = "Recent advances in genotyping technologies have facilitated
              genome-wide scans for natural selection. Identification of
              targets of natural selection will shed light on processes of
              human adaptation and evolution and could be important for
              identifying variation that influences both normal human
              phenotypic variation as well as disease susceptibility. Here we
              focus on studies of natural selection in modern humans who
              originated ~200,000 years go in Africa and migrated across the
              globe ~50,000 - 100,000 years ago. Movement into new
              environments, as well as changes in culture and technology
              including plant and animal domestication, resulted in local
              adaptation to diverse environments. We summarize statistical
              approaches for detecting targets of natural selection and for
              distinguishing the effects of demographic history from natural
              selection. On a genome-wide scale, immune-related genes appear to
              be major targets of positive selection. Genes associated with
              reproduction and fertility also appear to be fast evolving.
              Additional examples of recent human adaptation include genes
              associated with lactase persistence, eccrine glands, and response
              to hypoxia. Lastly, we emphasize the need to supplement scans of
              selection with functional studies to demonstrate the physiologic
              impact of candidate loci.",
  journal  = "Annual Reviews of Ecology, Evolution, and Systematics",
  volume   =  44,
  pages    = "123--143",
  month    =  nov,
  year     =  2013,
  keywords = "adaptation; human genetics; population genetics; whole genome
              sequencing",
  language = "en"
}

@ARTICLE{Nodvig2015-ev,
  title    = "A {CRISPR-Cas9} System for Genetic Engineering of Filamentous
              Fungi",
  author   = "N{\o}dvig, Christina S and Nielsen, Jakob B and Kogle, Martin E
              and Mortensen, Uffe H",
  abstract = "The number of fully sequenced fungal genomes is rapidly
              increasing. Since genetic tools are poorly developed for most
              filamentous fungi, it is currently difficult to employ genetic
              engineering for understanding the biology of these fungi and to
              fully exploit them industrially. For that reason there is a
              demand for developing versatile methods that can be used to
              genetically manipulate non-model filamentous fungi. To facilitate
              this, we have developed a CRISPR-Cas9 based system adapted for
              use in filamentous fungi. The system is simple and versatile, as
              RNA guided mutagenesis can be achieved by transforming a target
              fungus with a single plasmid. The system currently contains four
              CRISPR-Cas9 vectors, which are equipped with commonly used fungal
              markers allowing for selection in a broad range of fungi.
              Moreover, we have developed a script that allows identification
              of protospacers that target gene homologs in multiple species to
              facilitate introduction of common mutations in different
              filamentous fungi. With these tools we have performed RNA-guided
              mutagenesis in six species of which one has not previously been
              genetically engineered. Moreover, for a wild-type Aspergillus
              aculeatus strain, we have used our CRISPR Cas9 system to generate
              a strain that contains an AACU\_pyrG marker and demonstrated that
              the resulting strain can be used for iterative gene targeting.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  7,
  pages    = "e0133085",
  month    =  jul,
  year     =  2015,
  language = "en"
}

@ARTICLE{Goss2015-ue,
  title    = "Genome-enabled analysis of plant-pathogen migration",
  author   = "Goss, Erica M",
  abstract = "Trade in plant and plant products has profoundly affected the
              global distribution and diversity of plant pathogens.
              Identification of migration pathways can be used to monitor or
              manage pathogen movement for proactive disease management or
              quarantine measures. Genomics-based genetic marker discovery is
              allowing unprecedented collection of population genetic data for
              plant pathogens. These data can be used for detailed analysis of
              the ancestry of population samples and therefore for analysis of
              migration. Reconstruction of migration histories has confirmed
              previous hypotheses based on observational data and led to
              unexpected new findings on the origins of pathogens and source
              populations for past and recent migration. The choice of software
              for analysis depends on the type of migration being studied and
              the reproductive mode of the pathogen. Biased sampling and
              complex population structures are potential challenges to
              accurate inference of migration pathways.",
  journal  = "Annual Reviews of Phytopathology",
  volume   =  53,
  pages    = "121--135",
  month    =  may,
  year     =  2015,
  keywords = "coalescent; colonization; gene flow; globalization",
  language = "en"
}

@ARTICLE{Neigel1983-gt,
  title    = "Clonal diversity and population structure in a
              reef-building coral, {\textit{Acropora cervicornis}}:
              Self-recognition analysis and demographic
              interpretation",
  author   = "Neigel, Joseph E and Avise, John C",
  journal  = "Evolution",
  volume   =  37,
  number   =  3,
  pages    = "437--453",
  month    =  may,
  year     =  1983,
  language = "en"
}

@ARTICLE{Carling1988-xk,
  title   = "Relatedness within and among intraspecific groups of {\textit{Rhizoctonia
             solani}}: A comparison of grouping by anastomosis and by {DNA}
             hybridization",
  author  = "Carling, D E and Kuninaga, S and Leiner, R H",
  journal = "Phytoparasitica",
  volume  =  16,
  number  =  2,
  pages   = "209--210",
  year    =  1988
}

@ARTICLE{Perkins1988-mt,
  title   = "Main features of vegetative incompatibility in {\textit{Neurospora}}",
  author  = "Perkins, D D",
  journal = "Fungal Genetic Reports",
  volume  =  35,
  number  =  1,
  pages   = "44",
  year    =  1988
}

@ARTICLE{Parks1993-nv,
  title   = "A Study of Spatial Features of Clones in a Population of Bracken
             Fern, {\textit{Pteridium aquilinum}} (Dennstaedtiaceae)",
  author  = "Parks, James C and Werth, Charles R",
  journal = "American Journal of Botany",
  volume  =  80,
  number  =  5,
  pages   = "537--544",
  year    =  1993
}

@ARTICLE{Jo2008-xj,
  title   = "Rapid Development of Fungicide Resistance by {\textit{Sclerotinia
             homoeocarpa}} on Turfgrass",
  author  = "Jo, Young-Ki and Chang, Seog Won and Boehm, Michael and Jung,
             Geunhwa",
  journal = "Phytopathology",
  volume  =  98,
  number  =  12,
  pages   = "1297--1304",
  year    =  2008
}

@ARTICLE{Leslie1993-ln,
  title   = "Fungal Vegetative Incompatibility",
  author  = "Leslie, J",
  journal = "Annual Reviews of Phytopathology",
  volume  =  31,
  number  =  1,
  pages   = "127--151",
  year    =  1993
}

@ARTICLE{Ford1995-wk,
  title   = "Heterokaryon formation and vegetative compatibility in {\textit{Sclerotinia
             sclerotiorum}}",
  author  = "Ford, E J and Miller, R V and Gray, H and Sherwood, J E",
  journal = "Mycological Research",
  volume  =  99,
  number  =  2,
  pages   = "241--247",
  year    =  1995
}

@ARTICLE{Lehner2015-oj,
  title   = "Low genetic variability in {\textit{Sclerotinia sclerotiorum}} populations from
             common bean fields in {Minas Gerais} State, {Brazil}, at regional,
             local and micro-scales",
  author  = "Lehner, M S and Paula J{\'u}nior, T J and Hora J{\'u}nior, B T and
             Teixeira, H and Vieira, R F and Carneiro, J E S and Mizubuti, E S
             G",
  journal = "Plant Pathology",
  volume  =  64,
  number  =  4,
  pages   = "921--931",
  year    =  2015
}

@ARTICLE{Arnaud-Haond2007-zo,
  title    = "Standardizing methods to address clonality in population studies",
  author   = "Arnaud-Haond, S and Duarte, C M and Alberto, F and Serr{\~a}o, E
              A",
  abstract = "Although clonal species are dominant in many habitats, from
              unicellular organisms to plants and animals, ecological and
              particularly evolutionary studies on clonal species have been
              strongly limited by the difficulty in assessing the number, size
              and longevity of genetic individuals within a population. The
              development of molecular markers has allowed progress in this
              area, and although allozymes remain of limited use due to their
              typically low level of polymorphism, more polymorphic markers
              have been discovered during the last decades, supplying powerful
              tools to overcome the problem of clonality assessment. However,
              population genetics studies on clonal organisms lack a
              standardized framework to assess clonality, and to adapt
              conventional data analyses to account for the potential bias due
              to the possible replication of the same individuals in the
              sampling. Moreover, existing studies used a variety of indices to
              describe clonal diversity and structure such that comparison
              among studies is difficult at best. We emphasize the need for
              standardizing studies on clonal organisms, and particularly on
              clonal plants, in order to clarify the way clonality is taken
              into account in sampling designs and data analysis, and to allow
              further comparison of results reported in distinct studies. In
              order to provide a first step towards a standardized framework to
              address clonality in population studies, we review, on the basis
              of a thorough revision of the literature on population structure
              of clonal plants and of a complementary revision on other clonal
              organisms, the indices and statistics used so far to estimate
              genotypic or clonal diversity and to describe clonal structure in
              plants. We examine their advantages and weaknesses as well as
              various conceptual issues associated with statistical analyses of
              population genetics data on clonal organisms. We do so by testing
              them on results from simulations, as well as on two empirical
              data sets of microsatellites of the seagrasses Posidonia oceanica
              and Cymodocea nodosa. Finally, we also propose a selection of new
              indices and methods to estimate clonal diversity and describe
              clonal structure in a way that should facilitate comparison
              between future studies on clonal plants, most of which may be of
              interest for clonal organisms in general.",
  journal  = "Molecular Ecology",
  volume   =  16,
  number   =  24,
  pages    = "5115--5139",
  month    =  dec,
  year     =  2007,
  language = "en"
}

@ARTICLE{Prugnolle2010-yb,
  title    = "Apparent high recombination rates in clonal parasitic organisms
              due to inappropriate sampling design",
  author   = "Prugnolle, F and De Meeus, T",
  abstract = "Sampling design is of primary importance for empirical studies,
              in particular, population genetics. For parasitic organisms, a
              rather frequent way of sampling individuals from local
              populations is to collect and genotype only one randomly chosen
              parasite (or isolate) per host individual (or subpopulation),
              although each host (subpopulation) harbors a set of parasites
              belonging to the same species (that is, an infrapopulation).
              Here, we investigate, using simulations, the consequences of such
              sampling design regarding the estimates of linkage disequilibrium
              and departure from the Hardy-Weinberg expectations (H-WE) in
              clonal parasites with an acyclic life cycle. We show that
              collecting and genotyping only one individual pathogen per host
              individual (or per subpopulation) and pooling them to form one
              'artificial' subpopulation may generate strongly misleading
              patterns of genetic variations that may lead to false conclusions
              regarding their reproduction mode. In particular, we show that
              when subpopulations (or infrapopulations) are genetically
              differentiated, (i) the level of linkage disequilibrium is
              significantly reduced and (ii) the departure from the H-WE is
              strongly modified, sometimes giving a forged picture of a
              strongly recombining organism despite high levels of clonal
              reproduction.",
  journal  = "Heredity",
  volume   =  104,
  number   =  2,
  pages    = "135--140",
  month    =  feb,
  year     =  2010,
  language = "en"
}

@ARTICLE{McDonald1997-ob,
  title   = "The Population Genetics of Fungi: Tools and Techniques",
  author  = "McDonald, Bruce A",
  journal = "Phytopathology",
  volume  =  87,
  number  =  4,
  pages   = "448--453",
  year    =  1997
}

@ARTICLE{Kamvar2017-cl,
  title   = "Population structure and phenotypic variation of {\textit{Sclerotinia
             sclerotiorum}} from dry bean ({\textit{Phaseolus vulgaris}}) in the {United
             States}",
  author  = "Kamvar, Zhian N and Sajeewa Amaradasa, B and Jhala, Rachana and
             McCoy, Serena and Steadman, James R and Everhart, Sydney E",
  journal = "PeerJ",
  volume  =  5,
  pages   = "e4152",
  year    =  2017
}

@article{Kamvar2015-ff,
  title={Novel {R} tools for analysis of genome-wide population genetic data with emphasis on clonality},
  author={Kamvar, Zhian N and Brooks, Jonah C and Gr{\"u}nwald, Niklaus J},
  journal={Frontiers in Genetics},
  volume={6},
  pages={208},
  year={2015},
  publisher={Frontiers Media SA},
  doi={10.3389/fgene.2015.00208},
  url={https://doi.org/10.3389/fgene.2015.00208},
}

@article{Bailleul2016-lw,
	doi = {10.1111/2041-210x.12550},
	url = {https://doi.org/10.1111%2F2041-210x.12550},
	year = 2016,
	month = {mar},
	publisher = {Wiley-Blackwell},
	volume = {7},
	number = {8},
	pages = {966--970},
	author = {Diane Bailleul and Solenn Stoeckel and Sophie Arnaud-Haond},
	editor = {Timoth{\'{e}}e Poisot},
	title = {{RClone}: a package to identify {MultiLocus} Clonal Lineages and handle clonal data sets in {R}.},
	journal = {Methods in Ecology and Evolution}
}

@ARTICLE{Aldrich-Wolfe2015-yd,
  title    = "Genetic Variation of {\textit{Sclerotinia sclerotiorum}} from Multiple Crops
              in the North Central {United States}",
  author   = "Aldrich-Wolfe, Laura and Travers, Steven and Nelson, Jr, Berlin D",
  abstract = "Sclerotinia sclerotiorum is an important pathogen of numerous
              crops in the North Central region of the United States. The
              objective of this study was to examine the genetic diversity of
              145 isolates of the pathogen from multiple hosts in the region.
              Mycelial compatibility groups (MCG) and microsatellite haplotypes
              were determined and analyzed for standard estimates of population
              genetic diversity and the importance of host and distance for
              genetic variation was examined. MCG tests indicated there were 49
              different MCGs in the population and 52 unique microsatellite
              haplotypes were identified. There was an association between MCG
              and haplotype such that isolates belonging to the same MCG either
              shared identical haplotypes or differed at no more than 2 of the
              12 polymorphic loci. For the majority of isolates, there was a
              one-to-one correspondence between MCG and haplotype. Eleven MCGs
              shared haplotypes. A single haplotype was found to be prevalent
              throughout the region. The majority of genetic variation in the
              isolate collection was found within rather than among host crops,
              suggesting little genetic divergence of S. sclerotiorum among
              hosts. There was only weak evidence of isolation by distance.
              Pairwise population comparisons among isolates from canola, dry
              bean, soybean and sunflower suggested that gene flow between
              host-populations is more common for some crops than others.
              Analysis of linkage disequilibrium in the isolates from the four
              major crops indicated primarily clonal reproduction, but also
              evidence of genetic recombination for isolates from canola and
              sunflower. Accordingly, genetic diversity was highest for
              populations from canola and sunflower. Distribution of
              microsatellite haplotypes across the study region strongly
              suggest that specific haplotypes of S. sclerotiorum are often
              found on multiple crops, movement of individual haplotypes among
              crops is common and host identity is not a barrier to gene flow
              for S. sclerotiorum in the north central United States.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  9,
  pages    = "e0139188",
  month    =  sep,
  year     =  2015,
  language = "en"
}

@ARTICLE{Grunwald2017-wd,
  title    = "Best Practices for Population Genetic Analyses",
  author   = "Gr{\"u}nwald, N J and Everhart, S E and Knaus, B J and Kamvar, Z
              N",
  abstract = "Population genetic analysis is a powerful tool to understand how
              pathogens emerge and adapt. However, determining the genetic
              structure of populations requires complex knowledge on a range of
              subtle skills that are often not explicitly stated in book
              chapters or review articles on population genetics. What is a
              good sampling strategy? How many isolates should I sample? How do
              I include positive and negative controls in my molecular assays?
              What marker system should I use? This review will attempt to
              address many of these practical questions that are often not
              readily answered from reading books or reviews on the topic, but
              emerge from discussions with colleagues and from practical
              experience. A further complication for microbial or pathogen
              populations is the frequent observation of clonality or partial
              clonality. Clonality invariably makes analyses of population data
              difficult because many assumptions underlying the theory from
              which analysis methods were derived are often violated. This
              review provides practical guidance on how to navigate through the
              complex web of data analyses of pathogens that may violate
              typical population genetics assumptions. We also provide
              resources and examples for analysis in the R programming
              environment.",
  journal  = "Phytopathology",
  volume   =  107,
  number   =  9,
  pages    = "1000--1010",
  month    =  sep,
  year     =  2017,
  language = "en"
}

@ARTICLE{Leslie1993-hj,
  title   = "Fungal Vegetative Compatibility",
  author  = "Leslie, John F",
  journal = "Annual Reviews of Phytopathology",
  volume  =  31,
  number  =  1,
  pages   = "127--150",
  year    =  1993
}

@ARTICLE{Wu2017-dx,
  title    = "Virus-mediated suppression of host non-self recognition
              facilitates horizontal transmission of heterologous viruses",
  author   = "Wu, Songsong and Cheng, Jiasen and Fu, Yanping and Chen, Tao and
              Jiang, Daohong and Ghabrial, Said A and Xie, Jiatao",
  abstract = "Non-self recognition is a common phenomenon among organisms; it
              often leads to innate immunity to prevent the invasion of
              parasites and maintain the genetic polymorphism of organisms.
              Fungal vegetative incompatibility is a type of non-self
              recognition which often induces programmed cell death (PCD) and
              restricts the spread of molecular parasites. It is not clearly
              known whether virus infection could attenuate non-self
              recognition among host individuals to facilitate its spread.
              Here, we report that a hypovirulence-associated mycoreovirus,
              named {\textit{Sclerotinia sclerotiorum}} mycoreovirus 4 (SsMYRV4), could
              suppress host non-self recognition and facilitate horizontal
              transmission of heterologous viruses. We found that cell death in
              intermingled colony regions between SsMYRV4-infected Sclerotinia
              sclerotiorum strain and other tested vegetatively incompatible
              strains was markedly reduced and inhibition barrage lines were
              not clearly observed. Vegetative incompatibility, which involves
              Heterotrimeric guanine nucleotide-binding proteins (G proteins)
              signaling pathway, is controlled by specific loci termed het
              (heterokaryon incompatibility) loci. Reactive oxygen species
              (ROS) plays a key role in vegetative incompatibility-mediated
              PCD. The expression of G protein subunit genes, het genes, and
              ROS-related genes were significantly down-regulated, and cellular
              production of ROS was suppressed in the presence of SsMYRV4.
              Furthermore, SsMYRV4-infected strain could easily accept other
              viruses through hyphal contact and these viruses could be
              efficiently transmitted from SsMYRV4-infected strain to other
              vegetatively incompatible individuals. Thus, we concluded that
              SsMYRV4 is capable of suppressing host non-self recognition and
              facilitating heterologous viruses transmission among host
              individuals. These findings may enhance our understanding of
              virus ecology, and provide a potential strategy to utilize
              hypovirulence-associated mycoviruses to control fungal diseases.",
  journal  = "PLoS Pathogens",
  volume   =  13,
  number   =  3,
  pages    = "e1006234",
  month    =  mar,
  year     =  2017,
  doi      = "10.1371/journal.ppat.1006234",
  url      = "https://doi.org/10.1371/journal.ppat.1006234",
  language = "en"
}

@ARTICLE{Atehnkeng2016-qb,
  title    = "Environmental distribution and genetic diversity of vegetative
              compatibility groups determine biocontrol strategies to mitigate
              aflatoxin contamination of maize by {\textit{Aspergillus flavus}}",
  author   = "Atehnkeng, Joseph and Donner, Matthias and Ojiambo, Peter S and
              Ikotun, Babatunde and Augusto, Joao and Cotty, Peter J and
              Bandyopadhyay, Ranajit",
  abstract = "Maize infected by aflatoxin-producing Aspergillus flavus may
              become contaminated with aflatoxins, and as a result, threaten
              human health, food security and farmers' income in developing
              countries where maize is a staple. Environmental distribution and
              genetic diversity of A. flavus can influence the effectiveness of
              atoxigenic isolates in mitigating aflatoxin contamination.
              However, such information has not been used to facilitate
              selection and deployment of atoxigenic isolates. A total of 35
              isolates of A. flavus isolated from maize samples collected from
              three agro-ecological zones of Nigeria were used in this study.
              Ecophysiological characteristics, distribution and genetic
              diversity of the isolates were determined to identify vegetative
              compatibility groups (VCGs). The generated data were used to
              inform selection and deployment of native atoxigenic isolates to
              mitigate aflatoxin contamination in maize. In co-inoculation with
              toxigenic isolates, atoxigenic isolates reduced aflatoxin
              contamination in grain by > 96\%. A total of 25 VCGs were
              inferred from the collected isolates based on complementation
              tests involving nitrate non-utilizing (nit(-)) mutants. To
              determine genetic diversity and distribution of VCGs across
              agro-ecological zones, 832 nit(-) mutants from 52 locations in 11
              administrative districts were paired with one self-complementary
              nitrate auxotroph tester-pair for each VCG. Atoxigenic VCGs
              accounted for 81.1\% of the 153 positive complementations
              recorded. Genetic diversity of VCGs was highest in the derived
              savannah agro-ecological zone (H = 2.61) compared with the
              southern Guinea savannah (H = 1.90) and northern Guinea savannah
              (H = 0.94) zones. Genetic richness (H = 2.60) and evenness (E5 =
              0.96) of VCGs were high across all agro-ecological zones. Ten
              VCGs (40\%) had members restricted to the original location of
              isolation, whereas 15 VCGs (60\%) had members located between the
              original source of isolation and a distance > 400 km away. The
              present study identified widely distributed VCGs in Nigeria such
              as AV0222, AV3279, AV3304 and AV16127, whose atoxigenic members
              can be deployed for a region-wide biocontrol of toxigenic
              isolates to reduce aflatoxin contamination in maize.",
  journal  = "Microbial Biotechnology",
  volume   =  9,
  number   =  1,
  pages    = "75--88",
  month    =  jan,
  year     =  2016,
  language = "en"
}

@ARTICLE{Phillips2002-pq,
  title    = "Phylogeography and Genotype-Symptom Associations in Early and
              Late Season Infections of Canola by {\textit{Sclerotinia sclerotiorum}}",
  author   = "Phillips, D V and Carbone, I and Gold, S E and Kohn, L M",
  abstract = "ABSTRACT Both typical late season stem infections and atypical
              early season rosette infections of canola, a relatively new crop
              in the southeastern United States, were caused by Sclerotinia
              sclerotiorum. The 51 DNA fingerprints (from 71 isolates) did not
              match any fingerprints from previous studies of canola or other
              crops. Single locus haplotypes from nuclear DNA sequences
              included 18 in the intergenic spacer (IGS) of the rRNA repeat,
              four in 44.11, six in translation elongation factor 1alpha, three
              in calmodulin (CAL), and two in chitin synthase 1. Contingency
              permutation testing for associations of infection type with DNA
              fingerprint, single- or multilocus haplotype, or hierarchically
              nested clades based on single locus haplotypes found significant
              association of haplotype with mycelial compatibility group and
              DNA fingerprint for all loci except CAL. Significant association
              of IGS haplotypes with symptom type was detected in one pathogen
              population. Southeastern U.S. canola was infected by both
              recently evolved, geographically dispersed pathogen genotypes and
              older, indigenous genotypes (Carbone and Kohn, 2001. Molecular Ecology
              10:947-964). Indigenous haplotypes are infection-type
              generalists, and the most frequently isolated from rosette
              infections. In contrast, haplotypes from the most recently
              evolved, dispersed population were associated one-to-one with
              infection type, with only the most recently evolved haplotypes
              infecting rosettes.",
  journal  = "Phytopathology",
  volume   =  92,
  number   =  7,
  pages    = "785--793",
  month    =  jul,
  year     =  2002,
  language = "en"
}

@ARTICLE{Lehner2017-ny,
  title   = "Are {\textit{Sclerotinia sclerotiorum}} populations from the tropics more
             variable than those from subtropical and temperate zones?",
  author  = "Lehner, Miller S and Mizubuti, Eduardo S G",
  journal = "Tropical Plant Pathology",
  volume  =  42,
  number  =  2,
  pages   = "61--69",
  year    =  2017
}

@ARTICLE{Schafer2006-ph,
  title    = "An optimized method for mycelial compatibility testing in
              {\textit{Sclerotinia sclerotiorum}}",
  author   = "Schafer, Michelle R and Kohn, Linda M",
  abstract = "Classification of isolates into mycelial compatibility groups
              (MCGs) is used routinely in many laboratories as a quick marker
              for genotyping {\textit{Sclerotinia sclerotiorum}} within populations.
              Scoring each new sample requires optimization of standardized
              conditions to support adequate growth of all paired isolates.
              Appropriate conditions for growth are especially important
              because diverse compatibility reactions are difficult to
              categorize and score (e.g., in samples from populations with high
              genetic diversity, such as those that receive immigration from
              genetically diverse sources or those that deviate from strict
              clonality). The current standard medium for MCG testing can be
              inhibitory to isolates from some samples, confounding scoring of
              compatibility. We identified two foci for optimization: (i)
              choice of medium, in this experiment, Patterson's medium amended
              with red food coloring (termed modified Patterson's medium, MPM,
              the current standard medium) versus potato dextrose agar (PDA)
              and (ii) amount of McCormick's red food coloring amended to the
              growth medium. The red food coloring often yields a red reaction
              line in incompatible interactions; alternative incompatible
              reactions are a line of thick or thin hyphae. Based on results to
              date, self-self pairings of S. sclerotiorum are compatible and
              are a reliable standard for scoring compatible self-nonself
              mycelial interactions. PDA amended with 75 microl/L of
              McCormick's red food coloring was identified as optimal for
              isolates inhibited by MPM from a highly diverse, recombining
              population sample. This precisely amended PDA was also suitable
              for isolates from highly clonal populations that were not
              inhibited by MPM or by higher concentrations of red food
              coloring. Under the optimized, standardized conditions all paired
              isolates grew together and produced interactions that could be
              scored in repeatedly identifiable categories, compatible or
              incompatible. Workers are advised to optimize conditions before
              screening a new population sample.",
  journal  = "Mycologia",
  volume   =  98,
  number   =  4,
  pages    = "593--597",
  month    =  jul,
  year     =  2006,
  language = "en"
}

@article{Gordon1992-fs,
	doi = {10.1016/0147-5975(92)90033-n},
	url = {https://doi.org/10.1016%2F0147-5975%2892%2990033-n},
	year = 1992,
	month = {sep},
	publisher = {Elsevier {BV}},
	volume = {16},
	number = {3},
	pages = {245--250},
	author = {Thomas R. Gordon and Dorothy Okamoto},
	title = {Variation in mitochondrial {DNA} among vegetatively compatible isolates of {\textit{Fusarium oxysporum}}},
	journal = {Experimental Mycology}
}

@ARTICLE{Jo2008-ft,
  title    = "Reassessment of vegetative compatibility of {\textit{Sclerotinia
              homoeocarpa}} using nitrate-nonutilizing mutants",
  author   = "Jo, Y-K and Chang, S W and Rees, J and Jung, G",
  abstract = "Nitrate-nonutilizing (nit) mutants were recovered for the first
              time from 21 isolates of Sclerotinia homoeocarpa collected in the
              United States. Mutants were selected from shredded mycelium of
              each isolate when cultured on water agar medium amended with 4\%
              (wt/vol) potassium chlorate. The mutants could be classified into
              three phenotypes: nit1, nit3, and NitM, based on their growth on
              minimal medium (Czapek solution agar) supplemented with NaNO(2)
              or hypoxanthine. Complementary heterokaryons were observed in
              pairings between different phenotypes of nit mutants derived from
              compatible isolates, but not in self-fusions or pairings between
              incompatible isolates. The vigor of prototrophic growth varied
              with isolates and mutant phenotypes. Strong and continuous
              heterokaryons, as well as weak and spontaneous ones, formed
              depending on pairings of nit mutants. Stable heterokaryons
              between compatible isolates, but apoptotic reactions between
              incompatible isolates, were observed immediately after hyphal
              fusion under the epifluorescence microscope. The 21 isolates used
              in this study, which were previously assigned into 11 different
              vegetative compatibility groups (VCGs) based on the formation of
              a barrage zone at the contact site of paired isolates on complete
              medium (potato dextrose agar), were regrouped into five VCGs
              based on heterokaryon formation between nit mutants on minimal
              medium.",
  journal  = "Phytopathology",
  volume   =  98,
  number   =  1,
  pages    = "108--114",
  month    =  jan,
  year     =  2008,
  language = "en"
}

@ARTICLE{Liu1996-dr,
  title   = "Diversity and Multilocus Genetic Structure in Populations of {\textit{Cryphonectria parasitica}}",
  author  = "Liu, Yir-Chung and Cortesi, Paolo and Double, Mark L and
             MacDonald, William L and {Milgroom} and Michael, G",
  journal = "Phytopathology",
  volume  =  86,
  number  =  12,
  pages   = "1344--1351",
  year    =  1996
}

@ARTICLE{Milgroom1996-we,
  title    = "Recombination and the multilocus structure of fungal populations",
  author   = "Milgroom, M G",
  abstract = "This review examines the relationship between recombination and
              the multilocus structure of populations. This discussion of
              population structure is based on the pattern of genetic variation
              within populations, especially the frequencies of multilocus
              genotypes, which can be used for making inferences about
              recombination. Three questions are addressed: Is population
              structure consistent with a random mating hypothesis? Is there
              evidence for recombination? How frequently does recombination
              occur?",
  journal  = "Annual Reviews of Phytopathology",
  volume   =  34,
  pages    = "457--477",
  year     =  1996,
  language = "en"
}

@ARTICLE{Kohn1991-wq,
  title   = {Mycelial Incompatibility and Molecular Markers Identify Genetic Variability in Field Populations of {\textit{Sclerotinia sclerotiorum}}},
  author  = {Kohn, L M and Stasovski, E and Carbone, I and Royer, J and Anderson, J B},
  journal = {Phytopathology},
  volume  =  81,
  number  =  4,
  pages   = {480},
  year    =  1991
}

@ARTICLE{Attanayake2014-uy,
  title    = "Inferring outcrossing in the homothallic fungus {\textit{Sclerotinia sclerotiorum}} using linkage disequilibrium decay",
  author   = "Attanayake, R N and Tennekoon, V and Johnson, D A and Porter, L D and del R{\'\i}o-Mendoza, L and Jiang, D and Chen, W",
  abstract = "The occurrence and frequency of outcrossing in homothallic fungal
              species in nature is an unresolved question. Here we report
              detection of frequent outcrossing in the homothallic fungus
              Sclerotinia sclerotiorum. In using multilocus linkage
              disequilibrium (LD) to infer recombination among microsatellite
              alleles, high mutation rates confound the estimates of
              recombination. To distinguish high mutation rates from
              recombination to infer outcrossing, 8 population samples
              comprising 268 S. sclerotiorum isolates from widely distributed
              agricultural fields were genotyped for 12 microsatellite markers,
              resulting in multiple polymorphic markers on three chromosomes.
              Each isolate was homokaryotic for the 12 loci. Pairwise LD was
              estimated using three methods: Fisher's exact test, index of
              association (IA) and Hedrick's D'. For most of the populations,
              pairwise LD decayed with increasing physical distance between
              loci in two of the three chromosomes. Therefore, the observed
              recombination of alleles cannot be simply attributed to mutation
              alone. Different recombination rates in various DNA regions
              (recombination hot/cold spots) and different evolutionary
              histories of the populations could explain the observed
              differences in rates of LD decay among the chromosomes and among
              populations. The majority of the isolates exhibited mycelial
              incompatibility, minimizing the possibility of heterokaryon
              formation and mitotic recombination. Thus, the observed high
              intrachromosomal recombination is due to meiotic recombination,
              suggesting frequent outcrossing in these populations, supporting
              the view that homothallism favors universal compatibility of
              gametes instead of traditionally believed haploid selfing in S.
              sclerotiorum. Frequent outcrossing facilitates emergence and
              spread of new traits such as fungicide resistance, increasing
              difficulties in managing Sclerotinia diseases.",
  journal  = "Heredity",
  volume   =  113,
  number   =  4,
  pages    = "353--363",
  month    =  oct,
  year     =  2014,
  language = "en"
}

@ARTICLE{Correll1987-hh,
  title   = "Nitrate Nonutilizing Mutants of {\textit{Fusarium oxysporum}} and Their Use in
             Vegetative Compatibility Tests",
  author  = "Correll, J C",
  journal = "Phytopathology",
  volume  =  77,
  number  =  12,
  pages   = "1640",
  year    =  1987
}

@ARTICLE{Strom2016-di,
  title    = "Two genomes are better than one: history, genetics, and
              biotechnological applications of fungal heterokaryons",
  author   = "Strom, Noah B and Bushley, Kathryn E",
  abstract = "Heterokaryosis is an integral part of the parasexual cycle used
              by predominantly asexual fungi to introduce and maintain genetic
              variation in populations. Research into fungal heterokaryons
              began in 1912 and continues to the present day. Heterokaryosis
              may play a role in the ability of fungi to respond to their
              environment, including the adaptation of arbuscular mycorrhizal
              fungi to different plant hosts. The parasexual cycle has enabled
              advances in fungal genetics, including gene mapping and tests of
              complementation, dominance, and vegetative compatibility in
              predominantly asexual fungi. Knowledge of vegetative
              compatibility groups has facilitated population genetic studies
              and enabled the design of innovative methods of biocontrol. The
              vegetative incompatibility response has the potential to be used
              as a model system to study biological aspects of some human
              diseases, including neurodegenerative diseases and cancer. By
              combining distinct traits through the formation of artificial
              heterokaryons, fungal strains with superior properties for
              antibiotic and enzyme production, fermentation, biocontrol, and
              bioremediation have been produced. Future biotechnological
              applications may include site-specific biocontrol or
              bioremediation and the production of novel pharmaceuticals.",
  journal  = "Fungal Biology and Biotechnology",
  volume   =  3,
  pages    = "4",
  month    =  may,
  year     =  2016,
  keywords = "Biotechnology; Complementation; Heterokaryon; Heterosis;
              Parasexual cycle; Protoplast fusion; Vegetative compatibility
              groups",
  language = "en"
}

@ARTICLE{Malvarez2007-jo,
  title    = "New Populations of {\textit{Sclerotinia sclerotiorum}} from Lettuce in
              {California} and Peas and Lentils in {Washington}",
  author   = "Malv{\'a}rez, Gabriela and Carbone, Ignazio and Gr{\"u}nwald,
              Niklaus J and Subbarao, Krishnamurthy V and Schafer, Michelle and
              Kohn, Linda M",
  abstract = "ABSTRACT Four populations of {\textit{Sclerotinia sclerotiorum}} in North
              America were inferred previously, based on analyses of both
              rapidly evolving markers (DNA fingerprint and mycelial
              compatiblity), and multilocus DNA sequence spanning the range
              between fast and slow evolution. Each population was defined as
              an interbreeding unit of conspecific individuals sharing a common
              recent ancestor and arising in a unique evolutionary event. The
              present study applies this standard to extend characterization of
              S. sclerotiorum populations to the Western United States.
              Isolates of S. sclerotiorum (N = 294) were determined to
              represent three genetically differentiated populations:
              California (CA, lettuce), Washington (WA, pea/lentil), and
              Ontario (ON, lettuce). CA was the most diverse population yet
              sampled in North America. Clonality was detected in ON and WA. No
              DNA fingerprints were common among the populations. The index of
              association (I(A)), based on fingerprint, was closer to zero (0)
              for CA than it was for the other populations. High diversity and
              lack of association of markers in California are consistent
              either with genetic exchange and recombination, or with large
              population size and high standing genetic variation. Intra- and
              interlocus conflict among three DNA sequence loci was consistent
              with recombination. The coalescent IGS genealogy confirmed
              subdivision and showed CA to be older than WA or ON. The Nearest
              Neighbor statistic on combined data confirmed subdivision among
              all present and previously defined populations. All isolates had
              both MAT1-1 and MAT1-2, consistent with uniform homothallism.",
  journal  = "Phytopathology",
  volume   =  97,
  number   =  4,
  pages    = "470--483",
  month    =  apr,
  year     =  2007,
  language = "en"
}

@ARTICLE{Puhalla1985-bq,
  title   = "Classification of strains of {\textit{Fusarium oxysporum}} on the basis of
             vegetative compatibility",
  author  = "Puhalla, John E",
  journal = "Canadian Journal of Botany",
  volume  =  63,
  number  =  2,
  pages   = "179--183",
  year    =  1985
}

@ARTICLE{Leslie1996-di,
  title   = "Heterokaryon incompatibility in fungi---more than just another way
             to die",
  author  = "Leslie, John F and Zeller, Kurt A",
  journal = "Journal of Genetics",
  volume  =  75,
  number  =  3,
  pages   = "415--424",
  year    =  1996
}

@ARTICLE{Chang2014-rn,
  title   = "Evidence for Genetic Similarity of Vegetative Compatibility
             Groupings in {\textit{Sclerotinia homoeocarpa}}",
  author  = "Chang, Seog Won and Jo, Young-Ki and Chang, Taehyun and Jung,
             Geunhwa",
  journal = "Plant Pathology",
  volume  =  30,
  number  =  4,
  pages   = "384--396",
  year    =  2014
}

@ARTICLE{Glass2000-cg,
  title    = "The genetics of hyphal fusion and vegetative incompatibility in
              filamentous ascomycete fungi",
  author   = "Glass, N L and Jacobson, D J and Shiu, P K",
  abstract = "Filamentous fungi grow as a multicellular, multinuclear network
              of filament-shaped cells called hyphae. A fungal individual can
              be viewed as a fluid, dynamic system that is characterized by
              hyphal tip growth, branching, and hyphal fusion (anastomosis).
              Hyphal anastomosis is especially important in such nonlinear
              systems for the purposes of communication and homeostasis.
              Filamentous fungi can also undergo hyphal fusion with different
              individuals to form heterokaryons. However, the viability of such
              heterokaryons is dependent upon genetic constitution at
              heterokaryon incompatibility (het) loci. If hyphal fusion occurs
              between strains that differ in allelic specificity at het loci,
              vegetative incompatibility, which is characterized by hyphal
              compartmentation and cell lysis, is induced. This review covers
              microscopic and genetic analysis of hyphal fusion and the
              molecular and genetic analysis of the consequence of hyphal
              fusion between individuals that differ in specificity at het loci
              in filamentous ascomycetes.",
  journal  = "Annual Reviews of Genetics",
  volume   =  34,
  pages    = "165--186",
  year     =  2000,
  language = "en"
}

@ARTICLE{Berbegal2010-ev,
  title   = "Genetic Diversity and Host Range of {\textit{Verticillium dahliae}} Isolates from Artichoke and Other Vegetable Crops in {Spain}",
  author  = "Berbegal, M and Ortega, A and Jim{\'e}nez-Gasco, M M and Olivares-Garc{\'\i}a, C and Jim{\'e}nez-D{\'\i}az, R M and Armengol, J",
  journal = "Plant Disease",
  volume  =  94,
  number  =  4,
  pages   = "396--404",
  year    =  2010
}

@ARTICLE{Kohn1990-po,
  title   = "Mycelial interactions in {\textit{Sclerotinia sclerotiorum}}",
  author  = "Kohn, Linda M and Carbone, Ignazio and Anderson, James B",
  journal = "Experimental Mycology",
  volume  =  14,
  number  =  3,
  pages   = "255--267",
  year    =  1990
}

@ARTICLE{Attanayake2012-mq,
  title   = "Genetic and phenotypic diversity and random association of {DNA} markers of isolates of the fungal plant pathogen {\textit{Sclerotinia sclerotiorum}} from soil on a fine geographic scale",
  author  = "Attanayake, R N and Porter, L and Johnson, D A and Chen, W",
  journal = "Soil Biology and Biochemistry",
  volume  =  55,
  pages   = "28--36",
  year    =  2012
}

@ARTICLE{Carbone2001-hi,
  title    = "Multilocus nested haplotype networks extended with {DNA} fingerprints show common origin and fine-scale, ongoing genetic divergence in a wild microbial metapopulation",
  author   = "Carbone, I and Kohn, L M",
  abstract = "Nested haplotype networks for three loci in a haploid, fungal
              plant pathogen, Sclerotinia sclerotiorum, in two natural,
              Norwegian populations of the woodland buttercup, Ranunculus
              ficaria, were extended with DNA fingerprints to determine
              fine-scale population divergence. To preserve the cladistic
              structure in the network for both nonrecombinant and
              postrecombinant haplotypes in highly recombinant clades,
              recombinant events were not removed ('peeled off'), but instead
              were examined in alternative (marginal) networks. Fungi from both
              sampling locations share a common origin with subsequent genetic
              divergence, consistent with expectations for metapopulation
              structure. Evidence for divergence includes (i) lack of shared
              fingerprints between the two locations, (ii) evolution of new
              fingerprints, via transposition and recombination, within 2 years
              on a fine spatial scale within one sampling location, and (iii)
              increase in the size of the intergenic spacer (IGS) in both
              sampling locations. Sites of microsatellite repeat expansion and
              of an insertion were consistent with the boundaries of two
              recombination blocks in the IGS. Both alternative networks based
              on the recombination blocks were essential to finding all
              associations of DNA fingerprints with IGS size, sampling site,
              sampling year and mycelial compatibility group. Variation in the
              elongation factor 1alpha and calmodulin loci supported the
              topologies and the recurrent, ongoing polarity of change in
              fingerprints and IGS size inferred from the IGS.",
  journal  = "Molecular Ecology",
  volume   =  10,
  number   =  10,
  pages    = "2409--2422",
  month    =  oct,
  year     =  2001,
  language = "en"
}

@ARTICLE{Cubeta1997-rr,
  title    = "Clonality in {\textit{Sclerotinia sclerotiorum}} on Infected Cabbage in Eastern {North Carolina}",
  author   = "Cubeta, M A and Cody, B R and Kohli, Y and Kohn, L M",
  abstract = "ABSTRACT Eighty-four isolates of {\textit{Sclerotinia sclerotiorum}} from
              four cabbage production fields in North Carolina and 16 isolates
              from an experimental cabbage field plot in Louisiana were
              DNA-fingerprinted and tested for mycelial compatibility. In a
              comparison with 594 unique DNA fingerprints of S. sclerotiorum
              from Canadian canola, no fingerprints were shared among Canadian,
              North Carolina, and Louisiana populations. DNA fingerprints from
              the North Carolina sample were distinctive from those of the
              Canadian and Louisiana samples, with significantly more
              hybridizing fragments in the 7.7- to 18-kilobase range. Forty-one
              mycelial compatibility groups (MCGs) and 50 unique DNA
              fingerprints were identified from the North Carolina sample.
              Three MCGs and three fingerprints were identified from the
              Louisiana sample. From the North Carolina sample, 32 MCGs were
              each associated with a unique fingerprint; of these, there were
              11 clones (i.e., cases in which two or more isolates belonged to
              the same MCG and shared the same DNA fingerprint). Six clones
              sampled from two or more fields represented approximately 29\% of
              the total sample (24 of 84 isolates), with six clones recovered
              from fields 75 km apart. There were 10 cases in which one MCG was
              associated with more than one DNA fingerprint and two cases in
              which one DNA fingerprint was associated with more than one MCG.
              The small sample from Louisiana was strictly clonal. The North
              Carolina sample had a clonal component, but deviated from
              one-to-one association of MCG with DNA fingerprint to an extent
              consistent with more recombination or transposition than the
              other two populations sampled.",
  journal  = "Phytopathology",
  volume   =  87,
  number   =  10,
  pages    = "1000--1004",
  month    =  oct,
  year     =  1997,
  language = "en"
}

@ARTICLE{Papaioannou2014-pe,
  title   = "Barrage formation is independent from heterokaryon incompatibility
             in {\textit{Verticillium dahliae}}",
  author  = "Papaioannou, Ioannis A and Typas, Milton A",
  journal = "European Journal of Plant Pathology",
  volume  =  141,
  number  =  1,
  pages   = "71--82",
  year    =  2014
}

@ARTICLE{Kohli1992-pe,
  title   = "Local and {Trans-Canadian} Clonal Distribution of {\textit{Sclerotinia sclerotiorum}} on Canola",
  author  = "Kohli, Y and Morrall, R A A and Anderson, J B and Kohn, L M",
  journal = "Phytopathology",
  volume  =  82,
  number  =  8,
  pages   = "480--485",
  year    =  1992
}

@ARTICLE{Attanayake2013-zn,
  title    = "{\textit{Sclerotinia sclerotiorum}} populations infecting canola from {China}
              and the {United States} are genetically and phenotypically distinct",
  author   = "Attanayake, Renuka N and Carter, Patrick A and Jiang, Daohong and
              Del R{\'\i}o-Mendoza, Luis and Chen, Weidong",
  abstract = "Genetic and phenotypic diversity and population differentiation
              of {\textit{Sclerotinia sclerotiorum}} isolates infecting canola from China
              and the United States were investigated. Genetic diversity was
              assessed with eight microsatellite markers and mycelial
              compatibility groups (MCGs). Phenotypic diversity was assessed
              with sensitivity to three fungicides, production of oxalate and
              sclerotia, growth rate, and virulence on two canola cultivars. No
              shared MCGs or multilocus haplotypes were detected between the
              two populations, and populations differed significantly (P <
              0.001). Recombination was detected in both populations but was
              greater in the Chinese population. A polymerase chain reaction
              detection assay showed that ~60\% of the isolates were
              inversion-plus at the mating type locus. The two populations
              differed significantly (P < 0.05) for all of the phenotypic
              traits except for sensitivity to fungicide fluazinam and
              virulence. Isolates in the Chinese population were unique in
              several aspects. Despite the phenotypic differentiation,
              heritabilities of the phenotypic traits were similar for both
              populations. Significant correlations were found among five
              phenotypic traits. Cross resistance to benomyl and iprodione was
              detected. Virulence was not significantly correlated with any
              other phenotypic trait and had the least heritability. However,
              both populations were equally virulent on either a susceptible or
              a moderately resistant canola cultivars.",
  journal  = "Phytopathology",
  volume   =  103,
  number   =  7,
  pages    = "750--761",
  month    =  jul,
  year     =  2013,
  language = "en"
}

@ARTICLE{Sirjusingh2001-sq,
  title   = "Characterization of microsatellites in the fungal plant pathogen, {\textit{Sclerotinia sclerotiorum}}",
  author  = "Sirjusingh, Caroline and Kohn, Linda M",
  journal = "Molecular Ecology Notes",
  volume  =  1,
  number  =  4,
  pages   = "267--269",
  month   =  dec,
  year    =  2001
}

@ARTICLE{Milgroom2003-mu,
  title   = "Population Biology of Plant Pathogens: The Synthesis of Plant Disease Epidemiology and Population Genetics",
  author  = "Milgroom, Michael G and Peever, Tobin L",
  journal = "Plant Disease",
  volume  =  87,
  number  =  6,
  pages   = "608--617",
  year    =  2003
}

@ARTICLE{Glass1992-af,
  title    = "Mating type and vegetative incompatibility in filamentous
              ascomycetes",
  author   = "Glass, N L and Kuldau, G A",
  journal  = "Annual Reviews of Phytopathology",
  volume   =  30,
  pages    = "201--224",
  year     =  1992,
  language = "en"
}