Data from: The maintenance and emergence of diversity promotes open-ended evolution in a prebiotic context

This data was collected during the study entitled “The maintenance and emergence of diversity promotes open-ended evolution in a prebiotic context." We explored how selective contexts shape the evolution of innovation, using in vitro selection with single-stranded DNA (ssDNA) as an empirical model for pre-cellular evolution. During this selection regime, a diverse pool of 76-bp ssDNA (consisting of a random 40-nt region, flanked by 18-nt primer binding sites) was incubated with a target substrate, during which sequences were able to bind to the substrate. Following incubation, unbound sequences were discarded, while bound sequences were partitioned and amplified via PCR and used in subsequent rounds of selection.  Our experimental design consisted of 8 cycles of selection with either streptavidin-coated magnetic beads or yeast cells (Kluyveromyces lactis) as the binding substrate. We also included two variable selection regimes, where four rounds of selection were completed with one substrate before switching to the other target for the remaining four rounds (3 replicate populations per treatment). All replicates from rounds 1, 4, 7, and 8 were purified and submitted for next-generation sequencing (Illumina NovaSeq S4 2x150-bp lane), along with the random starting library. Sequencing generated a mean of 29,741,261 pair-end reads per sample, which were assembled and normalized to ~100,000 reads per sample used for analysis, which are included here. The file names are organized in the following format: Selection Treatment_Round of Selection_Replicate #. For example, “Beads_R1_1” indicates a population that was selected with beads as the binding substrate following Round 1 of selection, replicate population 1 (out of 3 replicates). Scripts used to list contigs (EditFastas.l) and measure the frequencies of each sequence (CountSeqs.l ) are also included.