TY - JOUR T1 - Estimate of Within Population Incremental Selection Through Branch Imbalance in Lineage Trees JF - bioRxiv DO - 10.1101/002014 SP - 002014 AU - Gilad Liberman AU - Jennifer Benichou AU - Lea Tsaban AU - Yaakov Maman AU - Jacob Glanville AU - Yoram Louzoun Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/01/23/002014.abstract N2 - Incremental selection within a population, defined as a limited fitness change following a mutation, is an important aspect of many evolutionary processes and can significantly affect a large number of mutations through the genome. Strongly advantageous or deleterious mutations are detected through the fixation of mutations in the population, using the synonymous to non-synonymous mutations ratio in sequences. There are currently to precise methods to estimate incremental selection occurring over limited periods. We here provide for the first time such a detailed method and show its precision and its applicability to the genomic analysis of selection.A special case of evolution is rapid, short term micro-evolution, where organism are under constant adaptation, occurring for example in viruses infecting a new host, B cells mutating during a germinal center reactions or mitochondria evolving within a given host.The proposed method is a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations.This method does not suffer from the need of a baseline model and is practically not affected by sampling biases. In order to show the wide applicability of this method, we apply it to multiple cases of micro-evolution, and show that it can detect genes and intergenic regions using the selection rate and detect selection pressures in viral proteins and in the immune response to pathogens. ER -