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This pattern of loci with and without Cas proteins has been reported previously in E. faecalis (Palmer and Gilmore, 2010).
The segregation pattern of loci detected by 17 EST-SSR and 6 genomic SSR primer pairs that were polymorphic between ICMB 841-P3 and 863B-P2 were assessed using 149 F2 individuals.
The patterns of locus length variation for CDS-AE and CDS-ANE were similar to those for FL-AE and FL-NAE, respectively (Figure 1c,d, Table 3).
Focusing on Ty coding-elements, we observed that contrary to what occurs with the LTRs, the patterns of locus occupancy are mostly either specific to a given strain or shared by just a few strains (only 18 out of the 130 occupied loci are common to more than five strains).
Second, for the same loci used in step one, we estimate patterns of locus-specific introgression in admixed populations.
For example, loci under selection may deviate from the expected patterns of loci solely under demographic pressure and might mimic alternate demographic patterns [ 20].
The read processing patterns of loci with low expression levels may be biased by random fluctuations, thus we have only included patterns with a minimum expression of 50 reads.
The expression pattern of the locus is reflected by its organization in space.
To estimate phylogenetic informativeness, prior data on the molecular evolutionary pattern of a locus is required.
In addition, several studies have reported that the imprinting pattern of a locus can be variable over ontogenetic time [ 31] or under different environmental effects [ 32].
Our results also show that early-firing origins can override the original replication timing pattern of the locus by converting genuinely late-replicating chromatin into early-replicating regions.
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