Synthetic eco-evolutionary dynamics in simple molecular environment
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 ∼1015 single-strand DNA ol...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2024-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/90156 |
| _version_ | 1797243559392313344 |
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| author | Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis Tommaso Bellini |
| author_facet | Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis Tommaso Bellini |
| author_sort | Luca Casiraghi |
| collection | DOAJ |
| description | 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 ∼1015 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼1012 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. |
| first_indexed | 2024-04-24T18:57:02Z |
| format | Article |
| id | doaj.art-21b9ad45226d463bb451093c0b48e8b1 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-24T18:57:02Z |
| publishDate | 2024-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-21b9ad45226d463bb451093c0b48e8b12024-03-26T14:49:54ZengeLife Sciences Publications LtdeLife2050-084X2024-03-011210.7554/eLife.90156Synthetic eco-evolutionary dynamics in simple molecular environmentLuca Casiraghi0Francesco Mambretti1https://orcid.org/0000-0002-3712-3595Anna Tovo2Elvezia Maria Paraboschi3Samir Suweis4Tommaso Bellini5https://orcid.org/0000-0003-4898-4400Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi, Segrate, ItalyDipartimento di Fisica e Astronomia, Università degli Studi di Padova, Padova, ItalyDipartimento di Fisica e Astronomia, Università degli Studi di Padova, Padova, ItalyDepartment of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, Pieve Emanuele, Italy; IRCCS, Humanitas Clinical and Research Center, Rozzano, ItalyDipartimento di Fisica e Astronomia, Università degli Studi di Padova, Padova, ItalyDipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli Cervi, Segrate, ItalyThe 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 ∼1015 single-strand DNA oligonucleotide ‘individuals’. We begin with a seed of random sequences which we select via affinity capture from ∼1012 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.https://elifesciences.org/articles/90156SELEXevolutionspeciationfitnessDNA interactionsrandom-sequence DNA |
| spellingShingle | Luca Casiraghi Francesco Mambretti Anna Tovo Elvezia Maria Paraboschi Samir Suweis Tommaso Bellini Synthetic eco-evolutionary dynamics in simple molecular environment eLife SELEX evolution speciation fitness DNA interactions random-sequence DNA |
| title | Synthetic eco-evolutionary dynamics in simple molecular environment |
| title_full | Synthetic eco-evolutionary dynamics in simple molecular environment |
| title_fullStr | Synthetic eco-evolutionary dynamics in simple molecular environment |
| title_full_unstemmed | Synthetic eco-evolutionary dynamics in simple molecular environment |
| title_short | Synthetic eco-evolutionary dynamics in simple molecular environment |
| title_sort | synthetic eco evolutionary dynamics in simple molecular environment |
| topic | SELEX evolution speciation fitness DNA interactions random-sequence DNA |
| url | https://elifesciences.org/articles/90156 |
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