Multispecies population dynamics of prebiotic compositional assemblies
Open accessAbstract
Present life portrays a two-tier phenomenology: molecules compose supramolecular structures, such as cells or organisms, which in turn portray population behaviors, including selection, evolution and ecological dynamics. Prebiotic models have often focused on evolution in populations of self-replicating molecules, without explicitly invoking the intermediate molecular-to-supramolecular transition. Here, we explore a prebiotic model that allows one to relate parameters of chemical interaction networks within molecular assemblies to emergent population dynamics. We use the graded autocatalysis replication domain (GARD) model, which simulates the network dynamics within amphiphile-containing molecular assemblies, and exhibits quasi-stationary compositional states termed compotype species. These grow by catalyzed accretion, divide and propagate their compositional information to progeny in a replication-like manner. The model allows us to ask how molecular network parameters influence assembly evolution and population dynamics parameters. In 1000 computer simulations, each embodying different parameter set of the global chemical interaction network parameters, we observed a wide range of behaviors. These were analyzed by a multi species logistic model often used for analyzing population ecology (r-K or Lotka-Volterra competition model). We found that compotypes with a larger intrinsic molecular repertoire show a higher intrinsic growth (r) and lower carrying capacity (K), as well as lower replication fidelity. This supports a prebiotic scenario initiated by fast-replicating assemblies with a high molecular diversity, evolving into more faithful replicators with narrower molecular repertoires.
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Only when too many mutations sequentially occur, the GARD assembly exits one basin of composomal attraction, transiting to drift or entering another composome.
“Only when too many mutations sequentially occur, the GARD assembly exits one basin of composomal attraction, transiting to drift or entering another composome.”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [64]
There is a correlation between a composome's restricted repertoire size NMOL and the ecology-like population-growth rate in simulations of composomal populations.
“In a broader realm, this is exemplified by a correlation seen between a composome's restricted repertoire size NMOL (the subset of environmental molecular types taking part in this composome) and the ecology-like population-growth rate in simulations of composomal populations [64].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [64]
Typical GARD simulations show that the internal kinetics leads from a completely random composition to a composome in a relatively small number of growth-split cycles.
“Despite such sparse fitness landscape, typical GARD simulations show that the internal kinetics leads from a completely random composition to a composome in a relatively small number of growth–split cycles.”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [64]
In constant population reactor simulations, one observes several compotypes of a given β matrix at the same time, as well as drift.
“In such simulations, one observes several compotypes (clusters of similar composomes) of a given β matrix at the same time, as well as drift (weakly reproducing or non-reproducing assemblies).”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [64]
When the assembly is in or near reproducing composomes, the average internal repertoire drops to NMOL = 15.9 ± 5.5, with the rest of the compounds absent.
“By contrast, when the assembly is in or near reproducing composomes, the average internal repertoire drops to NMOL = 15.9 ± 5.5 [64], with the rest of the compounds absent (figure 9a).”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [64]
Cites
Segré, D., Ben-Eli, D., Deamer, D. W., & Lancet, D. (2001) · Origins of life and evolution of the biosphere · doi:10.1023/a:1006746807104 · Cited by 620 · see citing works
Self-citationCompositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies
Segré, D., Ben-Eli, D., & Lancet, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4112 · Cited by 398 · see citing works
Self-citationMaurer, S. E., Deamer, D. W., Boncella, J. M., & Monnard, P.-A. (2009) · Astrobiology · doi:10.1089/ast.2009.0384 · Cited by 121 · see citing works
The Molecular Roots of Compositional Inheritance
SEGRÉ, D., SHENHAV, B., KAFRI, R., & LANCET, D. (2001) · Journal of Theoretical Biology · doi:10.1006/jtbi.2001.2440 · Cited by 82 · see citing works
Self-citationExcess mutual catalysis is required for effective evolvability
Markovitch, O., & Lancet, D. (2012) · Artificial Life · doi:10.1162/artl_a_00064 · Cited by 68 · see citing works
Self-citationCoevolution of compositional protocells and their environment
Shenhav, B., Oz, A., & Lancet, D. (2007) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2073 · Cited by 40 · see citing works
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Systems protobiology: origin of life in lipid catalytic networks
Lancet, D., Zidovetzki, R., & Markovitch, O. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0159 · Cited by 182 · see citing works
Self-citationChemical Evolution and the Evolutionary Definition of Life
Higgs, P. G. (2017) · Journal of Molecular Evolution · doi:10.1007/s00239-017-9799-3 · Cited by 58 · see citing works
Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate
Kahana, A., Schmitt-Kopplin, P., & Lancet, D. (2019) · Astrobiology · doi:10.1089/ast.2019.2029 · Cited by 40 · see citing works
Self-citationQuasispecies in population of compositional assemblies
Gross, R., Fouxon, I., Lancet, D., & Markovitch, O. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0265-1 · Cited by 20 · see citing works
Self-citationPredicting species emergence in simulated complex pre-biotic networks
Markovitch, O., & Krasnogor, N. (2018) · PLOS ONE · doi:10.1371/journal.pone.0192871 · Cited by 19 · see citing works
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- Authors
- Markovitch, O., & Lancet, D.
- Affiliations
- Weizmann Institute of Science (IL)
- Corresponding author
- Lancet, Doron
- Venue
- Journal of Theoretical Biology
- Publisher
- Elsevier BV
- Published
- 2014-09
- Volume
- 357
- Pages
- 26-34
- ISSN
- 0022-5193 (ISSN-L)
- OpenAlex
- W2165108069
- Cited by
- 43
- References
- 6
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 7 · 2023: 5 · 2022: 1 · 2021: 2 · 2020: 4 · 2019: 2 · 2018: 6 · 2017: 1 · 2016: 2 · 2015: 6 · 2014: 3
- FWCI
- 2.16
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Journal of Theoretical Biology (publishedVersion)
- PubMed (publishedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Weizmann Institute of Science
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- prebiotic evolution, molecular assembly, amphiphile self-assembly, population dynamics, Lotka-Volterra competition, replication fidelity, carrying capacity
- MeSH terms
- Computer Simulation, Models, Chemical, Prebiotics
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