Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi, Segrate, Italy.
Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, Padova, Italy.
Elife. 2024 Mar 26;12:RP90156. doi: 10.7554/eLife.90156.
The understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence 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 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼10 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 binding dominates the selection in the first generations, while inter- and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.
对生态进化动力学的理解，特别是物种共存的机制，仍然是零碎的，需要有测试台模型系统。为此，我们开发了一种体外选择 SELEX 的变体，以研究大约 10 个单链 DNA 寡核苷酸“个体”的种群进化。我们从大约 10 个固定序列的 DNA 寡聚物（“资源”）中通过亲和力捕获开始，这些寡聚物与它们竞争。在每个循环（“代”）中，通过对幸存者进行 PCR 扩增来补充生态系统。大规模平行测序表明，随着世代的推移，序列的多样性（“物种”）急剧减少，而其中一些变得丰富并主导着生态系统。我们的方法很简单，通过杂交赋予了生存能力，通过对结合能进行统计分析，可以对适应性进行定量研究。我们发现，在最初的几代中，个体资源结合的强度主导着选择，而个体间和个体内的相互作用在后期变得重要，同时也出现了互惠和寄生的原型形式。
