However, simulations from initial sequences that drive a pattern anticorrelated with the target has a negative effect on evolutionary time of several CRMs (supplementary fig. S5 B, Supplementary Material online).
This could drive a pattern of assortative mating between responsive, high-carotenoid-status females and colourful, high-carotenoid-status males, which together produce a relatively large number of offspring.
They drive a specific pattern of chiral flows which can be understood quantitatively based on the physics of active gels with chiral asymmetries (Kruse et al., 2005; Fürthauer et al., 2012, 2013).
However, as our method scores the statistical distribution of k-mers and not direct counts or identification of specific binding sites, it should also be able to predict CRMs which drive an altered pattern of gene expression due to gain or loss of a specific TF but which integrate an overall similar set of regulatory inputs.
However, the orchestrated emergence of pathologies and reduced activity in the elderly could potentially also drive a more uniform pattern of decline [1].
We used the PEBCRES simulation framework (He et al. 2012; Duque et al. 2014) (fig. 1 A and B) to evolve sequences that drive a predetermined expression pattern, simulating the process of evolutionary adaptation under a variety of scenarios.
This observation implies that MBONs are unlikely to function as command neurons to drive a specific motor pattern, as has been observed, for example, in recently identified descending neurons that induce only stereotyped backward walking (Bath et al., 2014; Bidaye et al., 2014).
In one set of experiments, we evolved an expression pattern from a sequence that already drove a similar pattern, by choosing the initial sequence for each simulation randomly from one of the 5 CRMs whose expression is most correlated with the target expression pattern.
Under normal 12 12 h LD conditions, a two oscillator network drives a bimodal pattern of activity that has pronounced morning and evening peaks of activity (Nitabach & Taghert, 2008).
The first experiment simulates evolution under the favorable scenario where a CRM evolves from a sequence that drives an expression pattern very similar to the target pattern (see Materials and Methods).
Each of the 12 true positives drove an expression pattern commensurate with the known or inferred (from homology to Drosophila) expression of its likely associated gene (see supplementary table S6, Supplementary Material online).
