There are also good reasons to believe that populations in Pleistocene Eurasia experienced frequent local extinctions or stochastic loss of small subpopulations.
In anopheles, it has been shown that there have been rapid stochastic loss of some retrotransposons [29], but whether this is directly related to the lack of recent retrogenes needs further investigation.
Furthermore, non-recombining populations may experience Muller's ratchet, which is the stochastic loss of the most fit genotype in the population due to the gradual accumulation of deleterious mutations [48] [50].
Wherever element numbers are low in a genome, such stochastic loss is likely.
This results in localised, stochastic loss of parental chromatin marks and changes in gene expression.
This might be explained by stochastic loss of BEL/Pao elements in early mammalian evolution.
Two alternative hypotheses for the cox1 intron were suggested: stochastic loss and horizontal transfer [ 50, 51].
The number of active copies also decreases due to random mutations, excision, purifying selection, and stochastic loss [ 2].
Transposons are believed to have evolved via three processes: horizontal transmission, vertical inactivation, and stochastic loss (Lohe et al. 1995).
The use of those four other species strengthened our results by preventing the detection of stochastic loss or ancestral polymorphisms.
This would explain the absence of roo elements in some species by stochastic loss (black branches in Figure 4).
