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During that time period, the effective population size has undergone expansion, reduction, and recent expansion.
Mutations, some of which inactivate genes, have occurred continuously over the history of Paratyphi A, as has the gain or loss of accessory genes.
We conclude that Darwinian selection is not responsible for increased frequency of enteric fever and suggest that environmental changes may be more important for the frequency of disease.
We used vertically acquired mutations identified by a novel algorithm to reconstruct the genealogy of Paratyphi A over the period of 450 y since its MRCA.
In turn, this genealogy led to a reconstruction of the history of global transmissions since the mid-1800s.
Mapping of all polymorphic sites within the core genome to ATCC 9150 identified only 4,584 SNPs (Table 1), which is comparable to the diversity found in (3), serovar Typhi (25), and other genetically monomorphic bacterial pathogens (26).
These SNPs yielded a single (unambiguous) maximum parsimony tree, except for several polytomies and a few homoplasies (repeated, independent, convergent mutations) (Phylogeny and demography of Paratyphi A.
We also identified 273 mutations that were under Darwinian selection.
However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries.
To strengthen dating estimates, we included 42 old strains (1917–1980) from the historical, global collection at the Institut Pasteur (Paris) (Dataset S1, tab 1).
The remaining strains were isolated between 19 and represent the current global distribution of Paratyphi A, including isolates from India (42 genomes) and Pakistan (12), where Paratyphi A is now most common.
For each of these strains, as well as for publicly available short reads from five additional Chinese isolates (16), we performed de novo assemblies and mapped the reads to those assemblies to avoid assembler errors that result in false SNP calls (24).
The final set of 149 genomes, including the completed genomes of ATCC 9150 (20) and AKU 12601 (21), yielded a 4,073,403-bp core genome after removing repetitive DNA (henceforth core genome).
Indeed, the dynamics of changes in the contents of the pan-genome are unclear for almost all bacterial taxa, as are the selective forces that shape genomic content with time.Tags: Adult Dating, affair dating, sex dating