Duplicate genes from the whole-genome duplication (WGD) in yeast are often dispensable--removing one copy has little or no phenotypic consequence. It is unknown, however, whether such dispensability reflects insignificance of the ancestral function or compensation from paralogs. Here, using precise competition-based measurements of the fitness cost of single and double deletions, we estimate the exposed fitness contribution of WGD duplicate genes in metabolism and bound the importance of their ancestral pre-duplication function. We find that the functional overlap between paralogs sufficiently explains the apparent dispensability of individual WGD genes. Furthermore, the lower bound on the fitness value of the ancestral function, which is estimated by the degree of synergistic epistasis, is at least as large as the average fitness cost of deleting single non-WGD genes. These results suggest that most metabolic functions encoded by WGD genes are important today and were also important at the time of duplication.

Background: Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists.

With the capability of interfacing an extensive band of instruments, the General Purpose Interface Bus (GPIB) has become an integral part of computer systems. For the purpose of optimizing its universality, an interface between the user and the GPIB devices can be implemented to allow nonspecific commands to be used. In addition to writing a generic interface that can be applied in MATLAB, GPIB instruments can also be accessed through the Experimental Physics and Industrial Control System (EPICS). This option was initially explored when the EPICS support for GPIB was built, and then added to the Input Output Controller (IOC). Subsequently, hardware modules could be attached to the VME crate of the IOC, and configuration data could then be read to the database layer. This procedure, however, did not meet generality of the specifications, so the former option was investigated. When the interface was ready, the oscilloscope, arbitrary waveform generator, and various other GPIB devices were connected to the LAN-GPIB gateway for testing. This project would be useful as a diagnostic tool for several Next Linear Collider Research and Development (NLC R&D) applications such as the NLC Test Accelerator (NLCTA) and 8-pack, used to demonstrate beam acceleration; feedback on nanosecond timescales (FONT), used to demonstrate control of beam collisions; and the vibration project, used to demonstrate final focus vibration stabilization.