1
|
Dopson M, Emary C. The persistence of bipartite ecological communities with Lotka-Volterra dynamics. J Math Biol 2024; 89:24. [PMID: 38955850 PMCID: PMC11219392 DOI: 10.1007/s00285-024-02120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
The assembly and persistence of ecological communities can be understood as the result of the interaction and migration of species. Here we study a single community subject to migration from a species pool in which inter-specific interactions are organised according to a bipartite network. Considering the dynamics of species abundances to be governed by generalised Lotka-Volterra equations, we extend work on unipartite networks to we derive exact results for the phase diagram of this model. Focusing on antagonistic interactions, we describe factors that influence the persistence of the two guilds, locate transitions to multiple-attractor and unbounded phases, as well as identifying a region of parameter space in which consumers are essentially absent in the local community.
Collapse
Affiliation(s)
- Matt Dopson
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
| | - Clive Emary
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| |
Collapse
|
2
|
Casiraghi L, Mambretti F, Tovo A, Paraboschi EM, Suweis S, Bellini T. Synthetic eco-evolutionary dynamics in simple molecular environment. eLife 2024; 12:RP90156. [PMID: 38530348 PMCID: PMC10965223 DOI: 10.7554/elife.90156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
| | - Francesco Mambretti
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Anna Tovo
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi MontalciniPieve EmanueleItaly
- IRCCS, Humanitas Clinical and Research CenterRozzanoItaly
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
| |
Collapse
|
3
|
Shao J, Rong N, Wu Z, Gu S, Liu B, Shen N, Li Z. Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters. iScience 2023; 26:107396. [PMID: 37701813 PMCID: PMC10494312 DOI: 10.1016/j.isci.2023.107396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 07/11/2023] [Indexed: 09/14/2023] Open
Abstract
Microbes shape their habitats by consuming resources and producing a diverse array of chemicals that can serve as public goods. Despite the risk of exploitation by cheaters, genes encoding sharable molecules like siderophores are widely found in nature, prompting investigations into the mechanisms that allow producers to resist invasion by cheaters. In this work, we presented the chemostat-typed "resource partition model" to demonstrate that dividing the iron resource between private and public siderophores can promote stable or dynamic coexistence between producers and cheaters in a well-mixed environment. Moreover, our analysis shows that when microbes not only consume but also produce resources, chemical innovation leads to stability criteria that differ from those of classical consumer resource models, resulting in more complex dynamics. Our work sheds light on the role of chemical innovations in microbial communities and the potential for resource partition to facilitate dynamical coexistence between cooperative and cheating organisms.
Collapse
Affiliation(s)
- Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhenchao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Beibei Liu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| |
Collapse
|
4
|
Saeedian M, Pigani E, Maritan A, Suweis S, Azaele S. Effect of delay on the emergent stability patterns in generalized Lotka-Volterra ecological dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210245. [PMID: 35599557 DOI: 10.1098/rsta.2021.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Understanding the conditions of feasibility and stability in ecological systems is a major challenge in theoretical ecology. The seminal work of May in 1972 and recent developments based on the theory of random matrices have shown the existence of emergent universal patterns of both stability and feasibility in ecological dynamics. However, only a few studies have investigated the role of delay coupled with population dynamics in the emergence of feasible and stable states. In this work, we study the effects of delay on generalized Loka-Volterra population dynamics of several interacting species in closed ecological environments. First, we investigate the relation between feasibility and stability of the modelled ecological community in the absence of delay and find a simple analytical relation when intra-species interactions are dominant. We then show how, by increasing the time delay, there is a transition in the stability phases of the population dynamics: from an equilibrium state to a stable non-point attractor phase. We calculate analytically the critical delay of that transition and show that it is in excellent agreement with numerical simulations. Finally, following a similar approach to characterizing stability in empirical studies, we investigate the coefficient of variation, which quantifies the magnitude of population fluctuations. We show that in the oscillatory regime induced by the delay, the variability at community level decreases for increasing diversity. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
Collapse
Affiliation(s)
- Meghdad Saeedian
- Dipartimento di Fisica 'G. Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Emanuele Pigani
- Dipartimento di Fisica 'G. Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Amos Maritan
- Dipartimento di Fisica 'G. Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Samir Suweis
- Dipartimento di Fisica 'G. Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Sandro Azaele
- Dipartimento di Fisica 'G. Galilei', Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| |
Collapse
|
5
|
Gotta D, Amaro F, Anagnostopoulos D, Bühler P, Covita D, Fuhrmann H, Gorke H, Gruber A, Hennebach M, Hirtl A, Ishiwatari T, Indelicato P, Jensen T, Le Bigot EO, Liu YW, Manil B, Markushin V, Marton J, Nekipelov M, Pomerantsev V, Popov V, el Hassani AJR, dos Santos JMF, Schlesser S, Schmid P, Simons L, Strauch T, Theisen M, Trassinelli M, Veloso JFCA, Zmeskal J. Pionic hydrogen and deuterium. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202226201005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The strong-interaction effects both in pionic hydrogen and deuterium atoms have been re-determined with improved precision. The hadronic shift and width in pionic hydrogen together with the hadronic shift in pionic deuterium constitute a one-fold constraint for the two independent pion-nucleon scattering lengths. Furthermore, the hadronic width in pionic deuterium measures the transition strength of s-wave pions on an isoscalar nucleon-nucleon pair which is an independent quantity not related to the pion-nucleon scattering lengths. The experiment was performed at the Paul Scherrer Institute by stopping a high-intensity low-energy pion beam in gaseous targets using the cyclotron trap. The X-rays emitted by the πH and πD atoms were analysed with a high resolution Bragg spectrometer equipped with spherically bent crystals. The pion-nucleon scattering lengths and other physical quantities extracted from the atom data are in good agreement with the results obtained from pionnucleon and nucleon-nucleon scattering experiments and confirm that a consistent picture is achieved for the low-energy pion-nucleon sector with respect to the expectations of chiral perturbation theory.
Collapse
|
6
|
OxDNA to Study Species Interactions. ENTROPY 2022; 24:e24040458. [PMID: 35455121 PMCID: PMC9029285 DOI: 10.3390/e24040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
Abstract
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity, among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on the fact that species compete for resources. More in generally, it is now recognized that species interactions play a crucial role in determining the coexistence and abundance of species. However, experimentally controllable platforms, which allow us to study and measure competitions among species, are rare and difficult to implement. In this work, we suggest exploiting a Molecular Dynamics coarse-grained model to study interactions among single strands of DNA, representing individuals of different species, which compete for binding to other oligomers considered as resources. In particular, the well-established knowledge of DNA–DNA interactions at the nanoscale allows us to test the hypothesis that the maximum consecutive overlap between pairs of oligomers measure the species’ competitive advantages. However, we suggest that a more complex structure also plays a role in the ability of the species to successfully bind to the target resource oligomer. We complement the simulations with experiments on populations of DNA strands which qualitatively confirm our hypotheses. These tools constitute a promising starting point for further developments concerning the study of controlled, DNA-based, artificial ecosystems.
Collapse
|
7
|
Garcia Lorenzana G, Altieri A. Well-mixed Lotka-Volterra model with random strongly competitive interactions. Phys Rev E 2022; 105:024307. [PMID: 35291125 DOI: 10.1103/physreve.105.024307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The random Lotka-Volterra model is widely used to describe the dynamical and thermodynamic features of ecological communities. In this work, we consider random symmetric interactions between species and analyze the strongly competitive interaction case. We investigate different scalings for the distribution of the interactions with the number of species and try to bridge the gap with previous works. Our results show two different behaviors for the mean abundance at zero and finite temperature, respectively, with a continuous crossover between the two. We confirm and extend previous results obtained for weak interactions: at zero temperature, even in the strong competitive interaction limit, the system is in a multiple-equilibria phase, whereas at finite temperature only a unique stable equilibrium can exist. Finally, we establish the qualitative phase diagrams and compare the species abundance distributions in the two cases.
Collapse
Affiliation(s)
- Giulia Garcia Lorenzana
- Laboratoire de Physique de l'École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, 75005 Paris, France
- Laboratoire Matière et Systèmes Complexes (MSC), Université de Paris, CNRS, 75013 Paris, France
| | - Ada Altieri
- Laboratoire Matière et Systèmes Complexes (MSC), Université de Paris, CNRS, 75013 Paris, France
| |
Collapse
|