Species identity: conserved inverted LINE repeat clusters (ILRC) in the vertebrate genome as indicators of population boundaries

The avian LINE CR1 generates multiply-superimposed insertions, resulting in apparently fortuitous inverted LINE repeat clusters (ILRCs). These loci display size micro-heterogeneity within populations, with few or no presence/absence polymorphisms, and yet only very closely related species share loci. Whilst the CR1 sequences that the ILRC loci are derived from are not species-specific, the loci themselves appear to be species-characteristic if not totally species specific. The mammalian LINE L1 is shown to act similarly to CR1 and also forms ILRCs. It is proposed that whilst the formation of these loci may be from a near-random process of super-insertion certain of them are in some way functional, explaining their conservation and rapid spread to population boundaries, whilst non-functional or inactive loci are quickly lost. ILRCs appear to decay from the element as formed by the accumulation of point mutations. ILRCs appear to an unusual example of non-polymorphic sequences being younger than polymorphic sequences with no obvious selective reason.