We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative polymerase chain reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self-prime under defined conditions. Selection acts on the phenotype of self-priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools for the Oli system here and demonstrate that it can be used as a conventional experimental evolution model system by test-driving it in an experiment investigating adaptive evolution under different rates of environmental change.
Roche SFF sequence files for all 16 Oli populations
These are the SFF files from Roche 454 titanium sequencing of the Oli populations. Populations were barcode indexed using the Roche MIDs, sequenced on the 454 titanium, base-called using the Roche pipeline version 2.53, then split into the 16 separate populations using the MID index. These sff files have been bzip2'ed into one tar archive for easier upload and download.
sff_files_from_all_16_oli_populations.tar.bz2
Perl script to filter reads by start and end primer sequences
A Perl script to filter 454 reads by the start and end primer sequence. Input reads are in fasta format. Outputs several files for reads that match the primers, and reads that are too short or too long, or don't match.
filter_by_primers_for_Sinead_Collins.pl
Perl script to count unique sequences
Script to count unique sequences from fast input file, reverse complementing if necessary so forward primer is at start of the sequence.
count_unique_sequences_for_Sinead_Collins.pl
README
This Readme file gives details about the initial submission of manuscript to arXiv.org, before it subsequently accepted by the Journal of Evolutionary Biology.
