Linda Kohn | University of Toronto (original) (raw)

Papers by Linda Kohn

Genetics, 2005

Rice, as a widely and intensively cultivated crop, should be a target for parasite host shifts an... more Rice, as a widely and intensively cultivated crop, should be a target for parasite host shifts and a source for shifts to co-occurring weeds. Magnaporthe oryzae, of the M. grisea species complex, is the most important fungal pathogen of rice, with a high degree of host specificity. On the basis of 10 loci from six of its seven linkage groups, 37 multilocus haplotypes among 497 isolates of M. oryzae from rice and other grasses were identified. Phylogenetic relationships among isolates from rice (Oryza sativa), millet (Setaria spp.), cutgrass (Leersia hexandra), and torpedo grass (Panicum repens) were predominantly tree like, consistent with a lack of recombination, but from other hosts were reticulate, consistent with recombination. The single origin of rice-infecting M. oryzae followed a host shift from a Setaria millet and was closely followed by additional shifts to weeds of rice, cutgrass, and torpedo grass. Two independent estimators of divergence time indicate that these host shifts predate the Green Revolution and could be associated with rice domestication. The rice-infecting lineage is characterized by high copy number of the transposable element MGR586 (Pot3) and, except in two haplotypes, by a loss of AVR-Co39. Both mating types have been retained in ancestral, well-distributed rice-infecting haplotypes 10 (mainly temperate) and 14 (mainly tropical), but only one mating type was recovered from several derived, geographically restricted haplotypes. There is evidence of a common origin of both ACE1 virulence genotypes in haplotype 14. Host-haplotype association is evidenced by low pathogenicity on hosts associated with other haplotypes. EMBL/GenBank Data Libraries under accession nos. AY944075-AY944131 and AY944359-AY944405. tent with cospeciation. The earliest report of a blast-like

Eukaryotic cell, 2014

The aims of this study were to determine (i) whether adaptation under strong selection occurred t... more The aims of this study were to determine (i) whether adaptation under strong selection occurred through mutations in a narrow target of one or a few nucleotide sites or a broad target of numerous sites and (ii) whether the programs of adaptation previously observed from three experimental populations were unique or shared among populations that underwent parallel evolution. We used archived population samples from a previous study, representing 500 generations of experimental evolution in 12 populations under strong selection, 6 populations in a high-salt environment and 6 populations in a low-glucose environment. Each set of six populations included four with sexual reproduction and two with exclusively asexual reproduction. Populations were sampled as resequenced genomes of 115 individuals and as bulk samples from which frequencies of mutant alleles were estimated. In a high-salt environment, a broad target of 11 mutations within the proton exporter, PMA1, was observed among the s...

Medical Care, 1994

There is increasing interest in the conduct of international studies that compare health care out... more There is increasing interest in the conduct of international studies that compare health care outcomes. This paper draws from the literature in sociology, anthropology, and psychology to examine the problems that can be encountered when collecting primary data for comparative purposes. Issues of study design, selection, development, and adaptation of instruments, problems encountered in collecting primary data, and techniques for analyzing comparative data are discussed. The paper is intended as a primer for health services researchers conducting comparative outcomes research in international settings.

by Kim Plummer, Darren Soanes, Muriel Viaud, Linda Kohn, Marc-henri Lebrun, Jeffrey Rollins, Nicholas Talbot, Oded Yarden, Luis Aguirrezabal Christine Granier, Sabine Fillinger, Emmanuel Quévillon, Baptiste Brault, Ulrich Güldener, and Pascale Cotton

PLoS Genetics, 2011

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic f... more Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to ,1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

Applied Mycology and Biotechnology, 2004

Our focus in this review is on powerful new methods for determining population patterning over ti... more Our focus in this review is on powerful new methods for determining population patterning over time and space and how from this, the dynamic processes leading to population divergence and speciation can be inferred. We focus on fungal populations, but draw from the wider literature on population genetics, evolutionary statistics, and, of course, phylogeography (see . We discuss the problems of gene duplication, paralogy, orthology, and deep coalescence as challenges to finding the interface between population divergence and speciation. Our main objective, however, is to guide the reader through the key phylogenetic, nested phylogenetic, coalescent and Bayesian operations with the aid of a set of figures based on a simple, hypothetical dataset of DNA haplotypes. Phylogenetic and compatibility approaches are presented with the goal of not only detecting recombination, but of detecting recombination when it is not widespread throughout a phylogeny. This is a major challenge in fungal systems with substantial asexual reproduction or with significant selfed sexual reproduction in a haploid genome. The key feature here is that recombination can be "localized" in some but not all clades in a phylogeny and that these clades can be identified. From this, contemporary versus historical patterns of recombination can be inferred from a phylogeny. Phylogenetic approaches based on conversion of the phylogeny to a nested hierarchical statistical design are presented for fuller exploration of associations between each nested level of the phylogeny and any variable, such as geographical location, host, or symptom type. The basic operations for both testing for population subdivision based on geographical associations, and for cladistic inference of population processes are presented. Our hypothetical dataset is also used to demonstrate how genealogical relationships and population parameters can be inferred using coalescent and Bayesian methods. The basic principles of these approaches are graphically presented, along with useful references and comments on key assumptions implicit in methods currently available.

Evolutionary Applications, 2010

All plants, including crop species, harbor a community of fungal endophyte species, yet we know l... more All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the 'assembly rules' concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant-fungal interactions, and (iii) investigation of microbe-microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host-fungus interactions and mechanisms of fungal-fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies.