  A morphogenic protein known as Dorsal patterns the embryonic dorsoventral
body axis of Drosophila by binding to transcriptional enhancers across the
genome. Each such enhancer activates a neighboring gene at a unique threshold
concentration of Dorsal. The presence of Dorsal binding site clusters in these
enhancers and of similar clusters in other enhancers has motivated models of
threshold-encoding in site density. However, we found that the precise length
of a spacer separating a pair of specialized Dorsal and Twist binding sites
determines the threshold-response. Despite this result, the functional range
determined by this spacer element as well as the role and origin of its
surrounding Dorsal site cluster remained completely unknown. Here, we
experiment with enhancers from diverse Drosophila genomes, including the large
uncompacted genomes from ananassae and willistoni, and report three major
interdependent results. First, we map the functional range of the
threshold-encoding spacer variable. Second, we show that the majority of sites
at the cluster are non-functional divergent elements that have been separated
beyond the encoding's functional range. Third, we verify an evolutionary model
involving the frequent replacement of a threshold encoding, whose precision is
easily outdated by shifting accuracy. The process by which encodings are
replaced by newer ones is facilitated by the palindromic nature of the Dorsal
and Twist binding motifs and by intrinsic repeat-instability in the specialized
Twist binding site, which critically impacts the length of the spacer linking
it to Dorsal. Over time, the dynamic process of selective deprecation and
replacement of encodings adds to a growing cluster of deadened elements, or
necro-elements, and strongly biases local sequence composition. ... [ABSTRACT
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