Population history and process, nested clade and coalescent analysis of multiple gene genealogies in a parasite of agricultural and wild plants

grantor: University of TorontoThe goal of the studies initiated in this thesis is to understand the history of population divergence and speciation in a cosmopolitan group of plant parasitic fungi, the Sclerotiniaceae. DNA sequence data from seven loci, developed through a novel discovery procedure exploiting the GenBank database, and collapsed into haplotypes from sequence alignments using a new program, CONVERT, that I co-developed, were used to infer and analyze multiple gene genealogies. To achieve maximum resolution of patterns of descent among clones in agricultural populations, gene genealogies were combined with DNA fingerprints. Some recombination against a background of predominant clonality was detected. Several tests were used to assess congruence among data partitions and the effects of combining data sets. Four clades (populations) were identified from a sample of agricultural and wild isolates of 'S. sclerotiorum' from North America, Northern Europe and New Zealand. Nested clade analysis with geographical distance indicated a pattern of divergence among these populations that started with a fragmentation event, followed by extensive geographic and host dispersal and a recurrent pattern of restricted gene flow resulting from isolation by distance. Coalescent estimates of the time to the most recent common ancestor (TMRCA) suggested an independent and simultaneous origin of a geography-specific clade in the Southeastern USA and a host-specific clade in Norway during the Pleistocene Ice Age. Host shifts may have accompanied the fragmentation event in some clades. The clades have contiguous geographical boundaries; a population sample was not equivalent to a population (clade). Estimates of mutation, recombination and migration rates based on coalescent models showed no distinction between agricultural crop samples and samples from wild 'Ranunculus ficaria'. Divergent populations were phylogenetically distinct from taxonomic species in a combined genealogy of four genomic regions from a sample spanning the population-species interface. 'Sclerotinia' is monophyletic and includes 'S. sclerotiorum', 'S. minor', ' S. trifoliorum' and a new species with a host range spanning cultivated and wild plants. Species boundaries and the diversifying forces driving speciation in 'Sclerotinia' will be investigated using nested clade analysis as the studies reported in this thesis are continued.Ph.D