Synthetic eco-evolutionary dynamics in simple molecular environment

The understanding of eco-evolutionary dynamics, and in particular the mechanism of emergence of species, is still fragmentary and in need of test bench model systems. To this aim, we developed a variant of SELEX in-vitro selection to study the evolution of a population of ∼ 10^15 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼ 10^12 DNA oligomers of fixed sequence (‘resources’) over which they compete. At each cycle (‘generation’), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences (‘species’) drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual-resource b..., Please see the paper. All the methods are clearly explained there. Our experimental design takes advantage of a selective capture mechanism where magnetic beads carrying single-stranded DNA filaments of fixed length and sequence target DNA individuals present in a DNA library based on their level of complementarity. Sequences are selected, amplified via PCR, sequenced, and analysed with the home-made codes present also in this repository., , # Synthetic Eco-Evolutionary Dynamics in Simple Molecular Environment

Dataset: experimental files for the \"oligo1\" dataset, in fastq format.

## Description of the data and file structure

The name of each file is as follows:

RX_06_RY.fastq

X: is the round (from 1 to 24)

Y: either 1 or 2, for reverse/forward sequences

oligo1_R1/R2 files are data relative to cycle 0.

## Sharing/Access information

Analysis code and other materials can be also found: here

## Code/Software

These codes have been written by Francesco Mambretti (2021-2023). They are meant to analyze experimental FASTQ files from the SEDES experiment.

\------------------------------------- REQUIREMENTS -------------------------------------

* `python3` with `numpy, matplotlib, itertools, more_itertools, biopython, pandas, difflib`
* `C++` installed and a `C++` compiler supporting (at least) `C++ - 2011`

\------------------------------------- input_params.py -------------------------------------

1. first, mod...