Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine‐scale, ongoing genetic divergence in a wild microbial metapopulation

@article{Carbone2001MultilocusNH,
  title={Multilocus nested haplotype networks extended with DNA fingerprints show common origin and fine‐scale, ongoing genetic divergence in a wild microbial metapopulation},
  author={Ignazio Carbone and Linda Myra Kohn},
  journal={Molecular Ecology},
  year={2001},
  volume={10}
}
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… 
A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum
TLDR
The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens, which may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.
Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum.
TLDR
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.
Microsatellite Markers Reveal Genetic Variation within Sclerotinia sclerotiorum Populations in Irrigated Dry Bean Crops in Brazil
Microsatellites are powerful markers to infer population genetic parameters. We used 10 microsatellite loci to characterize the genetic diversity and structure of 79 samples of Sclerotinia
Phylogeography of Cavernularia hultenii: evidence of slow genetic drift in a widely disjunct lichen
TLDR
Mismatch distributions indicate exponential population growth, probably during postglacial invasion of C. hultenii into formerly glaciated areas of western North America and the presence of one southern and at least one northern glacial refugium in South Central Alaska is inferred.
2 - Inferring Process from Pattern in Fungal Population Genetics
CRYPTIC SPECIATION IN THE COSMOPOLITAN AND CLONAL HUMAN PATHOGENIC FUNGUS ASPERGILLUS FUMIGATUS
TLDR
The discovery of a globally distributed A. fumigatus species clade highlights the need for ecological studies of the fungus to either document global dispersal or propose alternative mechanisms by which it persists as single, global phylogenetic population.
Phylogeography of two closely related species of Allium endemic to East Asia: Population evolution in response to climate oscillations
TLDR
The results suggest the speciation event of the two species was triggered by violent climatic changes during the Quaternary glaciation, suggesting a significant phylogeographic structure.
Selective sweeps in populations of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum
TLDR
This study lays the foundation for further work into investigation of the differing selective pressures that S. sclerotiorum populations are subjected to on a global scale.
Molecular phylogenetics suggest a North American link between the anthropogenic dry rot fungus Serpula lacrymans and its wild relative S. himantioides
TLDR
Phylogenetic analyses indicate that the Domesticus group may have originated from an ancient lineage related closely to the Shastensis group, suggesting a recent worldwide dispersal, possibly linked to human activity.
Clonal lineages of Sclerotinia sclerotiorum previously known from other crops predominate in 1999-2000 samples from Ontario and Quebec soybean
TLDR
Results indicate that soybean is infected mainly by pathogen genotypes residual from other crop or weed hosts and that a few pathogen Genotypes are responsible for a large proportion of infections.
...
1
2
3
4
...

References

SHOWING 1-10 OF 41 REFERENCES
PATTERNS OF DESCENT IN CLONAL LINEAGES AND THEIR MULTILOCUS FINGERPRINTS ARE RESOLVED WITH COMBINED GENE GENEALOGIES
TLDR
Comparison of gene genealogies with a phylogeny inferred from DNA fingerprints and a combined phylogeny of the entire dataset identified convergent or parallel changes in fingerprints.
A microbial population–species interface: nested cladistic and coalescent inference with multilocus data
Using sequence data from seven nuclear loci in 385 isolates of the haploid, plant parasitic, ascomycete fungus, Sclerotinia, divergence times of populations and of species were distinguished. The
Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome.
TLDR
Genetic variability appears to be much more structured by lineage than by population, and the deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.
TLDR
An algorithm for defining a nested statistical design under cladogram uncertainty and recombination is presented and it is illustrated that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
TLDR
A strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination is presented.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila.
TLDR
A cladogram is produced that partially reconstructs the evolutionary history of the present-day haplotype variability in Drosophila melanogaster by producing a nested analysis of variance that simultaneously detects phenotypic effects, localizes the effects within the cladogram, and identifies haplotypes that are potentially heterogeneous in their Phenotypic associations.
Extraordinary ribosomal spacer length heterogeneity in a neotyphodium endophyte hybrid: implications for concerted evolution.
TLDR
Evidence for a combination of homogenization mechanisms that drive the concerted evolution of the Lp1 rDNA is discussed, and potential refinements of the molecular details of unequal crossing over are presented.
Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
TLDR
The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region that may be useful in identifying phenotypic associations with variable sites in this gene.
Clonal dispersal and spatial mixing in populations of the plant pathogenic fungus, Sclerotinia sclerotiorum
TLDR
Nine of the 30 most frequently sampled clones from this study were previously recovered in a macrogeographical sample from western Canada in 1990, suggesting spatial mixing of ascospore inoculum from resident or immigrant sources.
Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.
TLDR
It was suggested that some of the subrepeat array types are quite old, at least predating the recolonization of pond habitats in the midwestern United States after the last glaciation, and that the populations were quite divergent.
...
1
2
3
4
5
...