Although amenable to many genomic features, it notably leaves discontinuous genomic segments, such as transcripts, untreated.
However, the extracted rates of evolution exhibit a large spike at short evolutionary distances, possibly due to horizontal transfer of large genomic segments including many genes.
Our results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens.
This genome reduction arises from its parasitic lifestyle and is the result of many independent losses of genes and genomic segments.
In chickens, many independent studies reported that multiple genomic segments containing this gene were identified to be implicated in both egg weight and body weight [ 1, 3, 16, 19, 20, 53].
As shown in Additional file 1, many genes located in the same zebrafish genomic segments were also located in a single scaffold of the catfish draft genome sequence, and these scaffolds were mapped to similar locations on the linkage map.
Therefore, the use of the PP model implies little or no recombination in genomic segments and the 'infinitely many sites' assumption from population genetics.
In particular, our estimator should also be applicable to organisms that exchange genomic segments via horizontal transfer (many bacteria) and populations where levels of ancestral variation are very low, for instance in experimental evolution with clonal populations.
The 'raw' genome database included 301 935 distinct genomic segments (plasmids, chromosomes and other genomic segments) and contains 67 073 viral, 4366 bacterial and 236 archaea segments.
Many such rearrangements result in the loss or gain of specific genomic segments and thus are referred to as copy number variants (CNV).
