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Pros and Cons of the Genotyping Approach
| Content Provider | Semantic Scholar |
|---|---|
| Abstract | The hybrid approach we have used to reconstruct the phylogeographic history of Y. pestis has several limitations. Traces of strong selection that might be present in the genomes may have been eradicated by our exclusion of homoplasies, repetitive DNA and variable sequences. Indeed, the ratio of non-synonymous to synonymous mutations was near unity in the maximum parsimony genomes tree (Fig. 1; Supplementary Table 14), which indicates the absence of either purifying or diversifying selection in the core-genome that was studied here. The relative distances between populations along the main branches of the MSTree (Fig. 2) are accurate, because most of the tips in the tree terminate in genomic sequences. However, the tips of the tree are largely based on SNPs discovered from only 17 genomic sequences, resulting in phylogenetic discovery bias. As a result, the true diversity of populations in the MSTree is strongly underestimated, and the lengths of branches that are not on the path to a genomic sequence are much too short because they only reflect the diversity revealed by low resolution SNP discovery. Nevertheless, the genomes and minimal spanning trees share an identical branching order, which is fully parsimonious and reflects unidirectional, clonal evolution. These properties indicate that our genealogical reconstruction is very robust. The branches are defined by sequential fixed mutations, each of which only occurred once prior to multiplication and spread. Mutation rate in nature. Historical records show that an initial plague epidemic reached Madagascar in 1898 and that a second wave began in 1921 11. We calculated mutation rates per year in nature based on the frequencies of SNPs discovered by dHPLC with 81 isolates from Madagascar of known dates of isolation (Madagascar isolate 1494 was excluded because its date of isolation was unknown). Mutation rates Page 2 were inferred using a full maximum likelihood model which assumes that after introduction in Madagascar, demographic expansion was strong enough to result in |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://wrap.warwick.ac.uk/81946/5/SupplementaryNote.pdf |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
