Figure 5. Model for the Relation between Ungapped and Functional Segments.

Indel events (modeled as point events, and represented by arrows) affecting functional DNA (red) are purified from the population and are not observed in extant species. The remaining indels (green arrows) delineate ungapped segments. Those subtending a segment of functional DNA (dark blue) are longer than the functional element itself, and the amount of neutral sites included in these long ungapped segments is on average twice the expected distance between indels on neutrally evolving DNA (see Materials and Methods).