Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

Nearest Neighbor Distances on a Circle: Multidimensional Case

We study the distances, called spacings, between pairs of neighboring energy levels for the quantum harmonic oscillator. Specifically, we consider all energy levels falling between E and E+1, and study how the spacings between these levels change for various choices of E, particularly when E goes to infinity. Primarily, we study the case in which the spring constant is a badly approximable vector. We first give the proof by Boshernitzan-Dyson that the number of distinct spacings has a uniform bound independent of E. Then, if the spring constant has components forming a basis of an algebraic number field, we show that, when normalized up to a unit, the spacings are from a finite set. Moreover, in the specific case that the field has one fundamental unit, the probability distribution of these spacings behaves quasiperiodically in log E. We conclude by studying the spacings in the case that the spring constant is not badly approximable, providing examples for which the number of distinct spacings is unbounded.Comment: Version 2 is updated to include more discussion of previous works. 17 pages with five figures. To appear in the Journal of Statistical Physic