A Model for Biased Fractionation after Whole Genome Duplication

Background: Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversial, as is the question of fractionation bias, namely whether one homeologous chromosome is more vulnerable to gene deletion than the other. Results: As a null hypothesis, we first assume deletion events, on either homeolog, excise a geometrically distributed number of genes with unknown mean μ, and a number r of these events overlap to produce deleted runs of length l. There is a fractionation bias 0 ≤ j ≤ 1 for deletions to fall on one homeolog rather than the other. The parameter r is a random variable with distribution π(·). We simulate the distribution of run lengths l, as well as the underlying π(·), as a function of μ, j and θ, the proportion of remaining genes in duplicate form. We show how sampling l allows us to estimate μ and j. The main part of ...

• Type: Journal
• Year: 2012
• Where: RECOMB
• Authors: David Sankoff, Chunfang Zheng, Baoyong Wang
• Keywords: Chromosomal Segments, Computational Biology, Dna Segments, Null Hypothesis, RECOMB 2012