Minimal Model for Genome Evolution and Growth

Abstract

Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random mutation but primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and intragenomic and intergenomic homologous genes are preponderant across all life forms.

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“…2, 3, 4 and 5 results that agree quite well with genomic data for all k= 2 to 9, it is far easier than not for our model to generate results that are good for one particular k and not for the other k's. For example, in our first application of the model in which a much longer average duplicated segment length than 25 b was used, only 6-distributions were well reproduced but not the others [14].…”

“…This model hasl = 25 and δ l = 11.2. There is nothing special about the Erlang function except that it was a simple generalize function of the exponential functionthat we used in the first instnace -and that it provided a simple setting for discrete parameter search: after we realizedl needed to be less than 50, we scannedl in intervals of 5 and n in intervals The following are some examples that gave very good k-distributions for specific k-mers but not generally; all were generated with L 0 = 1000 and n = 0: for 6-mer, σ = 13, 000 ± 2, 000 and on average 0.04σ mutations per duplication (these parameters also work for genomes with biased base compositions) [14]; for 2-mer, σ = 50, no mutation; for 5-mer, σ = 30, no mutation; for 9-mer, σ = 15, no mutation.…”

Evaluation of the current models for the evolution of bacterial DNA uptake signal sequences

“…There are at least two ways around this firstly, the genome might already contain highly repeated subsequences; one of those might then be used as a signal sequence, thus avoiding the difficulty of having to evolve one. Recent research has established that typical genomes do indeed contain highly over-represented oligomeres (Hsieh et al, 2003).…”

Crossover operators to control size growth in linear GP and variable length GAs

“…One example where this could be the case is the evolution of chemical systems, such as for example cell signaling networks [5]. Furthermore, there is strong evidence that growth phenomena are important in the evolution of real genomes [9].…”