1
|
Meng Y, Cornelius SP, Liu YY, Li A. Dynamics of collective cooperation under personalised strategy updates. Nat Commun 2024; 15:3125. [PMID: 38600076 PMCID: PMC11006938 DOI: 10.1038/s41467-024-47380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
Collective cooperation is essential for many social and biological systems, yet understanding how it evolves remains a challenge. Previous investigations report that the ubiquitous heterogeneous individual connections hinder cooperation by assuming individuals update strategies at identical rates. Here we develop a general framework by allowing individuals to update strategies at personalised rates, and provide the precise mathematical condition under which universal cooperation is favoured. Combining analytical and numerical calculations on synthetic and empirical networks, we find that when individuals' update rates vary inversely with their number of connections, heterogeneous connections actually outperform homogeneous ones in promoting cooperation. This surprising property undercuts the conventional wisdom that heterogeneous structure is generally antagonistic to cooperation and, further helps develop an efficient algorithm OptUpRat to optimise collective cooperation by designing individuals' update rates in any population structure. Our findings provide a unifying framework to understand the interplay between structural heterogeneity, behavioural rhythms, and cooperation.
Collapse
Affiliation(s)
- Yao Meng
- Center for Systems and Control, College of Engineering, Peking University, Beijing, 100871, China
| | - Sean P Cornelius
- Department of Physics, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Aming Li
- Center for Systems and Control, College of Engineering, Peking University, Beijing, 100871, China.
- Center for Multi-Agent Research, Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
| |
Collapse
|
2
|
Dagg JL, Derry JF. The book of Matthew 'On naval timber and arboriculture'. Its structure and development. Ann Sci 2024:1-20. [PMID: 38572665 DOI: 10.1080/00033790.2024.2306141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/30/2023] [Indexed: 04/05/2024]
Abstract
The book of Patrick Matthew (1790-1874) 'On Naval Timber and Arboriculture' has regularly thwarted readers' attempts of interpretation. The problems seem to extend beyond analysing and interpreting its evolutionary passages. Building upon previous studies, this analysis presents evidence that the book's structure itself may have contributed significantly to its reception by sundry readers as somehow either clear or obscure, consequently leading to a diversity of interpretations. First, the book does not have a consistent literary form. Second, it presents a miscellany of juxtaposed contents. Third, its readers approach it from different contexts. Internal evidence shows that Patrick Matthew added a lot of material, while the manuscript was already in the proof-reading or press stage. This explains why it provides no consistent literary form or integrated content that would have helped interpretation. Hence readers have been left to their own devices, and their interpretation depended more strongly than usual on their own contexts.
Collapse
Affiliation(s)
| | - J F Derry
- Ronin Institute, Montclaire, NJ, USA
- Edinburgh, UK
| |
Collapse
|
3
|
Hanley KA, Cecilia H, Azar SR, Moehn BA, Gass JT, Oliveira da Silva NI, Yu W, Yun R, Althouse BM, Vasilakis N, Rossi SL. Trade-offs shaping transmission of sylvatic dengue and Zika viruses in monkey hosts. Nat Commun 2024; 15:2682. [PMID: 38538621 PMCID: PMC10973334 DOI: 10.1038/s41467-024-46810-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Mosquito-borne dengue (DENV) and Zika (ZIKV) viruses originated in Old World sylvatic (forest) cycles involving monkeys and canopy-living Aedes mosquitoes. Both viruses spilled over into human transmission and were translocated to the Americas, opening a path for spillback into Neotropical sylvatic cycles. Studies of the trade-offs that shape within-host dynamics and transmission of these viruses are lacking, hampering efforts to predict spillover and spillback. We infected a native, Asian host species (cynomolgus macaque) and a novel, American host species (squirrel monkey) with sylvatic strains of DENV-2 or ZIKV via mosquito bite. We then monitored aspects of viral replication (viremia), innate and adaptive immune response (natural killer (NK) cells and neutralizing antibodies, respectively), and transmission to mosquitoes. In both hosts, ZIKV reached high titers that translated into high transmission to mosquitoes; in contrast DENV-2 replicated to low levels and, unexpectedly, transmission occurred only when serum viremia was below or near the limit of detection. Our data reveal evidence of an immunologically-mediated trade-off between duration and magnitude of virus replication, as higher peak ZIKV titers are associated with shorter durations of viremia, and higher NK cell levels are associated with lower peak ZIKV titers and lower anti-DENV-2 antibody levels. Furthermore, patterns of transmission of each virus from a Neotropical monkey suggest that ZIKV has greater potential than DENV-2 to establish a sylvatic transmission cycle in the Americas.
Collapse
Affiliation(s)
- Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Hélène Cecilia
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Sasha R Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Center for Tissue Engineering, Department of Surgery, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Brett A Moehn
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Jordan T Gass
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Wanqin Yu
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Ruimei Yun
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Benjamin M Althouse
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
- Information School, University of Washington, Seattle, WA, 98105, USA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Shannan L Rossi
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| |
Collapse
|
4
|
Tang S, Liu Y, Zhu J, Cheng X, Liu L, Hammerschmidt K, Zhou J, Cai Z. Bet hedging in a unicellular microalga. Nat Commun 2024; 15:2063. [PMID: 38453919 PMCID: PMC10920660 DOI: 10.1038/s41467-024-46297-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Understanding how organisms have adapted to persist in unpredictable environments is a fundamental goal in biology. Bet hedging, an evolutionary adaptation observed from microbes to humans, facilitates reproduction and population persistence in randomly fluctuating environments. Despite its prevalence, empirical evidence in microalgae, crucial primary producers and carbon sinks, is lacking. Here, we report a bet-hedging strategy in the unicellular microalga Haematococcus pluvialis. We show that isogenic populations reversibly diversify into heterophenotypic mobile and non-mobile cells independently of environmental conditions, likely driven by stochastic gene expression. Mobile cells grow faster but are stress-sensitive, while non-mobile cells prioritise stress resistance over growth. This is due to shifts from growth-promoting activities (cell division, photosynthesis) to resilience-promoting processes (thickened cell wall, cell enlargement, aggregation, accumulation of antioxidant and energy-storing compounds). Our results provide empirical evidence for bet hedging in a microalga, indicating the potential for adaptation to current and future environmental conditions and consequently conservation of ecosystem functions.
Collapse
Affiliation(s)
- Si Tang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China
| | - Yaqing Liu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China
| | - Xueyu Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China
| | - Lu Liu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China
| | | | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China.
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China.
- Technology Innovation Center for Marine Ecology and Human Factor Assessment of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, Guangdong Province, PR China.
| |
Collapse
|
5
|
Jay P, Aubier TG, Joron M. The interplay of local adaptation and gene flow may lead to the formation of supergenes. Mol Ecol 2024:e17297. [PMID: 38415327 DOI: 10.1111/mec.17297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.
Collapse
Affiliation(s)
- Paul Jay
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas G Aubier
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| |
Collapse
|
6
|
Draghi JA, McGlothlin JW, Kindsvater HK. Demographic feedbacks during evolutionary rescue can slow or speed adaptive evolution. Proc Biol Sci 2024; 291:20231553. [PMID: 38351805 PMCID: PMC10865011 DOI: 10.1098/rspb.2023.1553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
Populations declining toward extinction can persist via genetic adaptation in a process called evolutionary rescue. Predicting evolutionary rescue has applications ranging from conservation biology to medicine, but requires understanding and integrating the multiple effects of a stressful environmental change on population processes. Here we derive a simple expression for how generation time, a key determinant of the rate of evolution, varies with population size during evolutionary rescue. Change in generation time is quantitatively predicted by comparing how intraspecific competition and the source of maladaptation each affect the rates of births and deaths in the population. Depending on the difference between two parameters quantifying these effects, the model predicts that populations may experience substantial changes in their rate of adaptation in both positive and negative directions, or adapt consistently despite severe stress. These predictions were then tested by comparison to the results of individual-based simulations of evolutionary rescue, which validated that the tolerable rate of environmental change varied considerably as described by analytical results. We discuss how these results inform efforts to understand wildlife disease and adaptation to climate change, evolution in managed populations and treatment resistance in pathogens.
Collapse
Affiliation(s)
- Jeremy A. Draghi
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Joel W. McGlothlin
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Holly K. Kindsvater
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| |
Collapse
|
7
|
Abstract
Repeated interactions provide an evolutionary explanation for one-shot human cooperation that is counterintuitive but orthodox1-3. Intergroup competition4-7 provides an explanation that is intuitive but heterodox. Here, using models and a behavioural experiment, we show that neither mechanism reliably supports cooperation. Ambiguous reciprocity, a class of strategies that is generally ignored in models of reciprocal altruism, undermines cooperation under repeated interactions. This finding challenges repeated interactions as an evolutionary explanation for cooperation in general, which further challenges the claim that repeated interactions in the past can explain one-shot cooperation in the present. Intergroup competitions also do not reliably support cooperation because groups quickly become extremely similar, which limits scope for group selection. Moreover, even if groups vary, group competitions may generate little group selection for multiple reasons. Cooperative groups, for example, may tend to compete against each other8. Whereas repeated interactions and group competitions do not support cooperation by themselves, combining them triggers powerful synergies because group competitions constrain the corrosive effect of ambiguous reciprocity. Evolved strategies often consist of cooperative reciprocity with ingroup partners and uncooperative reciprocity with outgroup partners. Results from a behavioural experiment in Papua New Guinea fit exactly this pattern. They thus suggest neither an evolutionary history of repeated interactions without group competition nor a history of group competition without repeated interactions. Instead, our results suggest social motives that evolved under the joint influence of both mechanisms.
Collapse
Affiliation(s)
- Charles Efferson
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland.
| | - Helen Bernhard
- Department of Economics, University of Zurich, Zurich, Switzerland
| | - Urs Fischbacher
- Department of Economics, University of Konstanz, Konstanz, Germany
- Thurgau Institute of Economics, Kreuzlingen, Switzerland
| | - Ernst Fehr
- Department of Economics, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
8
|
Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nat Commun 2024; 15:810. [PMID: 38280868 PMCID: PMC10821953 DOI: 10.1038/s41467-024-45028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
Recent studies reveal that de novo gene origination from previously non-genic sequences is a common mechanism for gene innovation. These young genes provide an opportunity to study the structural and functional origins of proteins. Here, we combine high-quality base-level whole-genome alignments and computational structural modeling to study the origination, evolution, and protein structures of lineage-specific de novo genes. We identify 555 de novo gene candidates in D. melanogaster that originated within the Drosophilinae lineage. Sequence composition, evolutionary rates, and expression patterns indicate possible gradual functional or adaptive shifts with their gene ages. Surprisingly, we find little overall protein structural changes in candidates from the Drosophilinae lineage. We identify several candidates with potentially well-folded protein structures. Ancestral sequence reconstruction analysis reveals that most potentially well-folded candidates are often born well-folded. Single-cell RNA-seq analysis in testis shows that although most de novo gene candidates are enriched in spermatocytes, several young candidates are biased towards the early spermatogenesis stage, indicating potentially important but less emphasized roles of early germline cells in the de novo gene origination in testis. This study provides a systematic overview of the origin, evolution, and protein structural changes of Drosophilinae-specific de novo genes.
Collapse
Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
9
|
Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
Collapse
Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
| |
Collapse
|
10
|
Sheen JK, Rasambainarivo F, Saad-Roy CM, Grenfell BT, Metcalf CJE. Markets as drivers of selection for highly virulent poultry pathogens. Nat Commun 2024; 15:605. [PMID: 38242897 PMCID: PMC10799013 DOI: 10.1038/s41467-024-44777-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
Theoretical models have successfully predicted the evolution of poultry pathogen virulence in industrialized farm contexts of broiler chicken populations. Whether there are ecological factors specific to more traditional rural farming that affect virulence is an open question. Within non-industrialized farming networks, live bird markets are known to be hotspots of transmission, but whether they could shift selection pressures on the evolution of poultry pathogen virulence has not been addressed. Here, we revisit predictions for the evolution of virulence for viral poultry pathogens, such as Newcastle's disease virus, Marek's disease virus, and influenza virus, H5N1, using a compartmental model that represents transmission in rural markets. We show that both the higher turnover rate and higher environmental persistence in markets relative to farms could select for higher optimal virulence strategies. In contrast to theoretical results modeling industrialized poultry farms, we find that cleaning could also select for decreased virulence in the live poultry market setting. Additionally, we predict that more virulent strategies selected in markets could circulate solely within poultry located in markets. Thus, we recommend the close monitoring of markets not only as hotspots of transmission, but as potential sources of more virulent strains of poultry pathogens.
Collapse
Affiliation(s)
- Justin K Sheen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Fidisoa Rasambainarivo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Mahaliana Labs SARL, Antananarivo, Madagascar
| | - Chadi M Saad-Roy
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| |
Collapse
|
11
|
Roy S, Brännström Å, Dieckmann U. Ecological determinants of Cope's rule and its inverse. Commun Biol 2024; 7:38. [PMID: 38238502 PMCID: PMC10796397 DOI: 10.1038/s42003-023-05375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/19/2023] [Indexed: 01/22/2024] Open
Abstract
Cope's rule posits that evolution gradually increases the body size in lineages. Over the last decades, two schools of thought have fueled a debate on the applicability of Cope's rule by reporting empirical evidence, respectively, for and against Cope's rule. The apparent contradictions thus documented highlight the need for a comprehensive process-based synthesis through which both positions of this debate can be understood and reconciled. Here, we use a process-based community-evolution model to investigate the eco-evolutionary emergence of Cope's rule. We report three characteristic macroevolutionary patterns, of which only two are consistent with Cope's rule. First, we find that Cope's rule applies when species interactions solely depend on relative differences in body size and the risk of lineage extinction is low. Second, in environments with higher risk of lineage extinction, the recurrent evolutionary elimination of top predators induces cyclic evolution toward larger body sizes, according to a macroevolutionary pattern we call the recurrent Cope's rule. Third, when interactions between species are determined not only by their body sizes but also by their ecological niches, the recurrent Cope's rule may get inverted, leading to cyclic evolution toward smaller body sizes. This recurrent inverse Cope's rule is characterized by highly dynamic community evolution, involving the diversification of species with large body sizes and the extinction of species with small body sizes. To our knowledge, these results provide the first theoretical foundation for reconciling the contrasting empirical evidence reported on body-size evolution.
Collapse
Affiliation(s)
- Shovonlal Roy
- Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading, RG6 6DW, UK.
| | - Åke Brännström
- Advancing Systems Analysis Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, A-2361, Laxenburg, Austria
- Department of Mathematics and Mathematical Statistics, Umeå University, 90187, Umeå, Sweden
- Complexity Science and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan
| | - Ulf Dieckmann
- Advancing Systems Analysis Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, A-2361, Laxenburg, Austria
- Complexity Science and Evolution Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna, Kunigami, Okinawa, 904-0495, Japan
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, 240-0193, Japan
| |
Collapse
|
12
|
Sudakow I, Reinitz J, Vakulenko SA, Grigoriev D. Evolution of biological cooperation: an algorithmic approach. Sci Rep 2024; 14:1468. [PMID: 38233462 PMCID: PMC10794236 DOI: 10.1038/s41598-024-52028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024] Open
Abstract
This manuscript presents an algorithmic approach to cooperation in biological systems, drawing on fundamental ideas from statistical mechanics and probability theory. Fisher's geometric model of adaptation suggests that the evolution of organisms well adapted to multiple constraints comes at a significant complexity cost. By utilizing combinatorial models of fitness, we demonstrate that the probability of adapting to all constraints decreases exponentially with the number of constraints, thereby generalizing Fisher's result. Our main focus is understanding how cooperation can overcome this adaptivity barrier. Through these combinatorial models, we demonstrate that when an organism needs to adapt to a multitude of environmental variables, division of labor emerges as the only viable evolutionary strategy.
Collapse
Affiliation(s)
- Ivan Sudakow
- School of Mathematics and Statistics, The Open University, Milton Keynes, MK7 6AA, UK.
| | - John Reinitz
- Departments of Statistics, Ecology and Evolution, Molecular Genetics and Cell Biology, University of Chicago, Chicago, 10587, IL, USA
| | - Sergey A Vakulenko
- Institute for Problems in Mechanical Engineering, Russian Academy of Sciences, Saint Petersburg, 199178, Russia
- Saint Petersburg Electrotechnical University, Saint Petersburg, 197022, Russia
| | - Dima Grigoriev
- CNRS, Mathématiques, Université de Lille, Villeneuve d'Ascq, Lille, 59655, France
| |
Collapse
|
13
|
Sandhu S, Mikheev V, Pasternak A, Taskinen J, Morozov A. Revisiting the role of behavior-mediated structuring in the survival of populations in hostile environments. Commun Biol 2024; 7:93. [PMID: 38216662 PMCID: PMC10786947 DOI: 10.1038/s42003-023-05731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
Increasing the population density of target species is a major goal of ecosystem and agricultural management. This task is especially challenging in hazardous environments with a high abundance of natural enemies such as parasites and predators. Safe locations with lower mortality have been long considered a beneficial factor in enhancing population survival, being a promising tool in commercial fish farming and restoration of threatened species. Here we challenge this opinion and revisit the role of behavior structuring in a hostile environment in shaping the population density. We build a mathematical model, where individuals are structured according to their defensive tactics against natural enemies. The model predicts that although each safe zone enhances the survival of an individual, for an insufficient number of such zones, the entire population experiences a greater overall mortality. This is a result of the interplay of emergent dynamical behavioral structuring and strong intraspecific competition for safe zones. Non-plastic structuring in individuals' boldness reduces the mentioned negative effects. We demonstrate emergence of non-plastic behavioral structuring: the evolutionary branching of a monomorphic population into a dimorphic one with bold/shy strains. We apply our modelling approach to explore fish farming of salmonids in an environment infected by trematode parasites.
Collapse
Affiliation(s)
- Simran Sandhu
- School of Computing and Mathematical Sciences, University of Leicester, LE1 7RH, Leicester, UK
| | - Victor Mikheev
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Anna Pasternak
- Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Jouni Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Andrew Morozov
- School of Computing and Mathematical Sciences, University of Leicester, LE1 7RH, Leicester, UK.
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
14
|
Guo R, He Y, Tian X, Li Y. New energy vehicle battery recycling strategy considering carbon emotion from a closed-loop supply chain perspective. Sci Rep 2024; 14:688. [PMID: 38184743 PMCID: PMC10771451 DOI: 10.1038/s41598-024-51294-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024] Open
Abstract
The negative impact of used batteries of new energy vehicles on the environment has attracted global attention, and how to effectively deal with used batteries of new energy vehicles has become a hot issue. This paper combines the rank-dependent expected utility with the evolutionary game theory, constructs an evolutionary game model based on the interaction mechanism between decision makers' emotions and decision making, and studies the recycling strategy of new energy automobile trams under the heterogeneous combination of emotions. The study shows that: (1) In addition to the establishment of effective external norms, the subjective preference of decision makers can also positively affect the recycling strategy of new energy vehicle batteries. (2) Fairness preferences can have a significant nonlinear effect on new energy vehicle battery recycling strategies by changing the utility function of decision makers. (3) When new energy vehicle manufacturers remain optimistic and new energy vehicle demanders remain rational or pessimistic, the new energy vehicle battery recycling strategy can reach the optimal steady state.
Collapse
Affiliation(s)
- Rong Guo
- School of China Alcoholic Drinks, Luzhou Vocational and Technical College, Luzhou, 646000, China
| | - Yongjun He
- Intelligent Policing and National Security Risk Management Laboratory, Sichuan Police College, Luzhou, 646000, China.
| | - Xianjun Tian
- Intelligent Policing and National Security Risk Management Laboratory, Sichuan Police College, Luzhou, 646000, China
| | - Yixin Li
- School of Management, Xi'an University of Science and Technology, Xi'an, 710054, China
| |
Collapse
|
15
|
Abstract
We explore the interpersonal origins of human culture, arguing that culture emerges as a necessary consequence of our helplessness in infancy, which in turn requires a greater degree of collaboration and social organization than is necessary for other mammals. We propose a model of cultural transmission that depends on a dyadic interpersonal process whose vicissitudes can have a lifelong impact. We explore the role played by imagining subjectively experienced psychological states and processes in others, which we have defined as mentalizing, in the process of cultural transmission, and propose that mentalizing is key to the establishment of epistemic trust-that is to say, an experience of trust that enables the individual to absorb and use the knowledge they are being offered. We suggest that psychoanalysis can be viewed as a paradigmatic example of a process of transferring knowledge from one human being (the teacher, the caregiver, the analyst) to another (the learner, the young person, the patient) and argue that the mechanisms of psychic change in analysis cannot be fully understood without appreciating this aspect of the biological/evolutionary origins of our essential humanity. Finally, we discuss the clinical implications of the model we are proposing for the psychoanalytic process.
Collapse
Affiliation(s)
- Peter Fonagy
- Division of Psychology and Language Sciences, University College London, Gower Street, London WC1E 6BT
| | - Elizabeth Allison
- Division of Psychology and Language Sciences, University College London, Gower Street, London WC1E 6BT
| |
Collapse
|
16
|
Carrillo-Bustamante P, Costa G, Lampe L, Levashina EA. Evolutionary modelling indicates that mosquito metabolism shapes the life-history strategies of Plasmodium parasites. Nat Commun 2023; 14:8139. [PMID: 38097582 PMCID: PMC10721866 DOI: 10.1038/s41467-023-43810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Within-host survival and between-host transmission are key life-history traits of single-celled malaria parasites. Understanding the evolutionary forces that shape these traits is crucial to predict malaria epidemiology, drug resistance, and virulence. However, very little is known about how Plasmodium parasites adapt to their mosquito vectors. Here, we examine the evolution of the time Plasmodium parasites require to develop within the vector (extrinsic incubation period) with an individual-based model of malaria transmission that includes mosquito metabolism. Specifically, we model the metabolic cascade of resource allocation induced by blood-feeding, as well as the influence of multiple blood meals on parasite development. Our model predicts that successful vector-to-human transmission events are rare, and are caused by long-lived mosquitoes. Importantly, our results show that the life-history strategies of malaria parasites depend on the mosquito's metabolic status. In our model, additional resources provided by multiple blood meals lead to selection for parasites with slow or intermediate developmental time. These results challenge the current assumption that evolution favors fast developing parasites to maximize their chances to complete their within-mosquito life cycle. We propose that the long sporogonic cycle observed for Plasmodium is not a constraint but rather an adaptation to increase transmission potential.
Collapse
Affiliation(s)
| | - Giulia Costa
- Vector Biology Unit, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Lena Lampe
- Vector Biology Unit, Max Planck Institute for Infection Biology, 10117, Berlin, Germany
- Physiology and Metabolism Laboratory, The Francis Crick Institute, NW11AT, London, UK
| | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, 10117, Berlin, Germany.
| |
Collapse
|
17
|
Daybog I, Kolodny O. A computational framework for resolving the microbiome diversity conundrum. Nat Commun 2023; 14:7977. [PMID: 38042865 PMCID: PMC10693575 DOI: 10.1038/s41467-023-42768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/20/2023] [Indexed: 12/04/2023] Open
Abstract
Recent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term 'the microbial β- diversity conundrum'. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals' microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host's fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
Collapse
Affiliation(s)
- Itay Daybog
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Oren Kolodny
- Department of Ecology, Evolution and Behavior, The A. Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| |
Collapse
|
18
|
Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
Collapse
Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| |
Collapse
|
19
|
Moore NA, Morales-Castilla I, Hargreaves AL, Olalla-Tárraga MÁ, Villalobos F, Calosi P, Clusella-Trullas S, Rubalcaba JG, Algar AC, Martínez B, Rodríguez L, Gravel S, Bennett JM, Vega GC, Rahbek C, Araújo MB, Bernhardt JR, Sunday JM. Temperate species underfill their tropical thermal potentials on land. Nat Ecol Evol 2023; 7:1993-2003. [PMID: 37932384 PMCID: PMC10697837 DOI: 10.1038/s41559-023-02239-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023]
Abstract
Understanding how temperature determines the distribution of life is necessary to assess species' sensitivities to contemporary climate change. Here, we test the importance of temperature in limiting the geographic ranges of ectotherms by comparing the temperatures and areas that species occupy to the temperatures and areas species could potentially occupy on the basis of their physiological thermal tolerances. We find that marine species across all latitudes and terrestrial species from the tropics occupy temperatures that closely match their thermal tolerances. However, terrestrial species from temperate and polar latitudes are absent from warm, thermally tolerable areas that they could potentially occupy beyond their equatorward range limits, indicating that extreme temperature is often not the factor limiting their distributions at lower latitudes. This matches predictions from the hypothesis that adaptation to cold environments that facilitates survival in temperate and polar regions is associated with a performance trade-off that reduces species' abilities to contend in the tropics, possibly due to biotic exclusion. Our findings predict more direct responses to climate warming of marine ranges and cool range edges of terrestrial species.
Collapse
Affiliation(s)
- Nikki A Moore
- Department of Biology, McGill University, Montreal, Quebec, Canada.
| | - Ignacio Morales-Castilla
- Department of Life Sciences, Global Change Ecology and Evolution Group, Universidad de Alcalá; Alcalá de Henares, Madrid, Spain
| | | | - Miguel Ángel Olalla-Tárraga
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | | | - Piero Calosi
- Marine Ecological and Evolutionary Physiology Laboratory, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Quebec, Canada
| | - Susana Clusella-Trullas
- Department of Botany and Zoology and School for Climate Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Juan G Rubalcaba
- Department of Biology, McGill University, Montreal, Quebec, Canada
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Adam C Algar
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Brezo Martínez
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Laura Rodríguez
- Department of Biology (Grupo en Biodiversidad y Conservación, IU-ECOAQUA), Marine Sciences Faculty, University of Las Palmas de Gran Canaria; Las Palmas de G.C., Canary Islands, Spain
| | - Sarah Gravel
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Joanne M Bennett
- Fenner School of Environment & Society, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Greta C Vega
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Carsten Rahbek
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Ecology, Peking University, Beijing, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M, Denmark
| | - Miguel B Araújo
- Department of Biogeography and Global Change, National Museum of Natural Sciences, CSIC, Madrid, Spain
- 'Rui Nabeiro' Biodiversity Chair, MED Institute, University of Évora, Évora, Portugal
| | - Joey R Bernhardt
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | | |
Collapse
|
20
|
Wang X, Zhou L, McAvoy A, Li A. Imitation dynamics on networks with incomplete information. Nat Commun 2023; 14:7453. [PMID: 37978181 PMCID: PMC10656501 DOI: 10.1038/s41467-023-43048-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Imitation is an important learning heuristic in animal and human societies. Previous explorations report that the fate of individuals with cooperative strategies is sensitive to the protocol of imitation, leading to a conundrum about how different styles of imitation quantitatively impact the evolution of cooperation. Here, we take a different perspective on the personal and external social information required by imitation. We develop a general model of imitation dynamics with incomplete information in networked systems, which unifies classical update rules including the death-birth and pairwise-comparison rule on complex networks. Under pairwise interactions, we find that collective cooperation is most promoted if individuals neglect personal information. If personal information is considered, cooperators evolve more readily with more external information. Intriguingly, when interactions take place in groups on networks with low degrees of clustering, using more personal and less external information better facilitates cooperation. Our unifying perspective uncovers intuition by examining the rate and range of competition induced by different information situations.
Collapse
Affiliation(s)
- Xiaochen Wang
- Center for Systems and Control, College of Engineering, Peking University, Beijing, 100871, China
| | - Lei Zhou
- School of Automation, Beijing Institute of Technology, Beijing, 100081, China
| | - Alex McAvoy
- School of Data Science and Society, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aming Li
- Center for Systems and Control, College of Engineering, Peking University, Beijing, 100871, China.
- Center for Multi-Agent Research, Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
| |
Collapse
|
21
|
Ng ETH, Kinjo AR. Plasticity-led evolution as an intrinsic property of developmental gene regulatory networks. Sci Rep 2023; 13:19830. [PMID: 37963964 PMCID: PMC10645858 DOI: 10.1038/s41598-023-47165-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
The modern evolutionary synthesis seemingly fails to explain how a population can survive a large environmental change: the pre-existence of heritable variants adapted to the novel environment is too opportunistic, whereas the search for new adaptive mutations after the environmental change is so slow that the population may go extinct. Plasticity-led evolution, the initial environmental induction of a novel adaptive phenotype followed by genetic accommodation, has been proposed to solve this problem. However, the mechanism enabling plasticity-led evolution remains unclear. Here, we present computational models that exhibit behaviors compatible with plasticity-led evolution by extending the Wagner model of gene regulatory networks. The models show adaptive plastic response and the uncovering of cryptic mutations under large environmental changes, followed by genetic accommodation. Moreover, these behaviors are consistently observed over distinct novel environments. We further show that environmental cues, developmental processes, and hierarchical regulation cooperatively amplify the above behaviors and accelerate evolution. These observations suggest plasticity-led evolution is a universal property of complex developmental systems independent of particular mutations.
Collapse
Affiliation(s)
- Eden Tian Hwa Ng
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam
| | - Akira R Kinjo
- Department of Mathematics, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam.
| |
Collapse
|
22
|
Brauns F, Iñigo de la Cruz L, Daalman WKG, de Bruin I, Halatek J, Laan L, Frey E. Author Correction: Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast. Nat Commun 2023; 14:7163. [PMID: 37935655 PMCID: PMC10630505 DOI: 10.1038/s41467-023-42928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Affiliation(s)
- Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Leila Iñigo de la Cruz
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Werner K-G Daalman
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Ilse de Bruin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jacob Halatek
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539, Munich, Germany.
| |
Collapse
|
23
|
Leeks A, Bono LM, Ampolini EA, Souza LS, Höfler T, Mattson CL, Dye AE, Díaz-Muñoz SL. Open questions in the social lives of viruses. J Evol Biol 2023; 36:1551-1567. [PMID: 37975507 DOI: 10.1111/jeb.14203] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 11/19/2023]
Abstract
Social interactions among viruses occur whenever multiple viral genomes infect the same cells, hosts, or populations of hosts. Viral social interactions range from cooperation to conflict, occur throughout the viral world, and affect every stage of the viral lifecycle. The ubiquity of these social interactions means that they can determine the population dynamics, evolutionary trajectory, and clinical progression of viral infections. At the same time, social interactions in viruses raise new questions for evolutionary theory, providing opportunities to test and extend existing frameworks within social evolution. Many opportunities exist at this interface: Insights into the evolution of viral social interactions have immediate implications for our understanding of the fundamental biology and clinical manifestation of viral diseases. However, these opportunities are currently limited because evolutionary biologists only rarely study social evolution in viruses. Here, we bridge this gap by (1) summarizing the ways in which viruses can interact socially, including consequences for social evolution and evolvability; (2) outlining some open questions raised by viruses that could challenge concepts within social evolution theory; and (3) providing some illustrative examples, data sources, and conceptual questions, for studying the natural history of social viruses.
Collapse
Affiliation(s)
- Asher Leeks
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA
| | - Lisa M Bono
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Elizabeth A Ampolini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lucas S Souza
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Thomas Höfler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Courtney L Mattson
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
| | - Anna E Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Samuel L Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| |
Collapse
|
24
|
Long X, Weissing FJ. Transient polymorphisms in parental care strategies drive divergence of sex roles. Nat Commun 2023; 14:6805. [PMID: 37884497 PMCID: PMC10603145 DOI: 10.1038/s41467-023-42607-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
The parental roles of males and females differ considerably between and within species. By means of individual-based evolutionary simulations, we strive to explain this diversity. We show that the conflict between the sexes creates a sex bias (towards maternal or paternal care), even if the two sexes are initially identical. When including sexual selection, there are two outcomes: either female mate choice and maternal care or no mate choice and paternal care. Interestingly, the care pattern drives sexual selection and not vice versa. Longer-term simulations exhibit rapid switches between alternative parental care patterns, even in constant environments. Hence, the evolutionary lability of sex roles observed in phylogenetic studies is not necessarily caused by external changes. Overall, our findings are in striking contrast to the predictions of mathematical models. We show that the discrepancies are caused by transient within-sex polymorphisms in parental strategies, a factor largely neglected in current sex-role theory.
Collapse
Affiliation(s)
- Xiaoyan Long
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, The Netherlands
- Institute of Biology I, University of Freiburg, Freiburg im Breisgau, 79104, Germany
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, The Netherlands.
| |
Collapse
|
25
|
Wang TY, Zhang H. Research on the game of manufacturing capacity sharing based on prospect theory. Sci Rep 2023; 13:18093. [PMID: 37872181 PMCID: PMC10593761 DOI: 10.1038/s41598-023-45189-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
In order to investigate the strategy choice of each player in capacity sharing, the article constructs a tripartite game model based on capacity provider-capacity demander-government, introduces the prospect theory and conducts numerical simulation analysis using MATLAB. The results show that capacity sharing in the manufacturing industry is related to three parties: capacity providers, capacity demanders and the government, and their strategies in the game process influence each other; the sensitivity of capacity providers and capacity demanders is higher than that of the government; the increase of risk-return coefficient and loss-avoidance coefficient is conducive to the evolution of subjects to the ideal state.
Collapse
Affiliation(s)
- Tian-Yu Wang
- School of Economics and Management, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Hao Zhang
- School of Economics and Management, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
| |
Collapse
|
26
|
Wodarz D, Komarova NL. Mutant fixation in the presence of a natural enemy. Nat Commun 2023; 14:6642. [PMID: 37863909 PMCID: PMC10589345 DOI: 10.1038/s41467-023-41787-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/19/2023] [Indexed: 10/22/2023] Open
Abstract
The literature about mutant invasion and fixation typically assumes populations to exist in isolation from their ecosystem. Yet, populations are part of ecological communities, and enemy-victim (e.g. predator-prey or pathogen-host) interactions are particularly common. We use spatially explicit, computational pathogen-host models (with wild-type and mutant hosts) to re-visit the established theory about mutant fixation, where the pathogen equally attacks both wild-type and mutant individuals. Mutant fitness is assumed to be unrelated to infection. We find that pathogen presence substantially weakens selection, increasing the fixation probability of disadvantageous mutants and decreasing it for advantageous mutants. The magnitude of the effect rises with the infection rate. This occurs because infection induces spatial structures, where mutant and wild-type individuals are mostly spatially separated. Thus, instead of mutant and wild-type individuals competing with each other, it is mutant and wild-type "patches" that compete, resulting in smaller fitness differences and weakened selection. This implies that the deleterious mutant burden in natural populations might be higher than expected from traditional theory.
Collapse
Affiliation(s)
- Dominik Wodarz
- Department of Population Health and Disease Prevention, University of California, Irvine, CA, 92697, US.
- Department of Mathematics, University of California, Irvine, CA, 92697, US.
- School of Biological Sciences, Ecology, Behavior & Evolution Department, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Natalia L Komarova
- Department of Mathematics, University of California, Irvine, CA, 92697, US
- Department of Mathematics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
27
|
Brauns F, Iñigo de la Cruz L, Daalman WKG, de Bruin I, Halatek J, Laan L, Frey E. Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast. Nat Commun 2023; 14:6504. [PMID: 37845215 PMCID: PMC10579396 DOI: 10.1038/s41467-023-42100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
How can a self-organized cellular function evolve, adapt to perturbations, and acquire new sub-functions? To make progress in answering these basic questions of evolutionary cell biology, we analyze, as a concrete example, the cell polarity machinery of Saccharomyces cerevisiae. This cellular module exhibits an intriguing resilience: it remains operational under genetic perturbations and recovers quickly and reproducibly from the deletion of one of its key components. Using a combination of modeling, conceptual theory, and experiments, we propose that multiple, redundant self-organization mechanisms coexist within the protein network underlying cell polarization and are responsible for the module's resilience and adaptability. Based on our mechanistic understanding of polarity establishment, we hypothesize that scaffold proteins, by introducing new connections in the existing network, can increase the redundancy of mechanisms and thus increase the evolvability of other network components. Moreover, our work gives a perspective on how a complex, redundant cellular module might have evolved from a more rudimental ancestral form.
Collapse
Affiliation(s)
- Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Leila Iñigo de la Cruz
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Werner K-G Daalman
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Ilse de Bruin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jacob Halatek
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539, Munich, Germany.
| |
Collapse
|
28
|
Ogbunugafor CB. Mutations that enhance evolvability may open doors to faster adaptation. Nat Commun 2023; 14:6310. [PMID: 37813831 PMCID: PMC10562388 DOI: 10.1038/s41467-023-41914-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023] Open
Affiliation(s)
- C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
- Santa Fe Institute, Santa Fe, NM, USA.
| |
Collapse
|
29
|
Sharma A, Czégel D, Lachmann M, Kempes CP, Walker SI, Cronin L. Assembly theory explains and quantifies selection and evolution. Nature 2023; 622:321-328. [PMID: 37794189 PMCID: PMC10567559 DOI: 10.1038/s41586-023-06600-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life's origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena. Evolutionary theory explains why some things exist and others do not through the lens of selection. To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary3-5. We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an 'object' on which these laws act. AT conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units. We introduce a measure called assembly (A), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly. By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists.
Collapse
Affiliation(s)
| | - Dániel Czégel
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | | | | | - Sara I Walker
- BEYOND Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA.
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA.
| | - Leroy Cronin
- School of Chemistry, University of Glasgow, Glasgow, UK.
| |
Collapse
|
30
|
Alfieri F, Botton-Divet L, Wölfer J, Nyakatura JA, Amson E. A macroevolutionary common-garden experiment reveals differentially evolvable bone organization levels in slow arboreal mammals. Commun Biol 2023; 6:995. [PMID: 37770611 PMCID: PMC10539518 DOI: 10.1038/s42003-023-05371-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023] Open
Abstract
Eco-morphological convergence, i.e., similar phenotypes evolved in ecologically convergent taxa, naturally reproduces a common-garden experiment since it allows researchers to keep ecological factors constant, studying intrinsic evolutionary drivers. The latter may result in differential evolvability that, among individual anatomical parts, causes mosaic evolution. Reconstructing the evolutionary morphology of the humerus and femur of slow arboreal mammals, we addressed mosaicism at different bone anatomical spatial scales. We compared convergence strength, using it as indicator of evolvability, between bone external shape and inner structure, with the former expected to be less evolvable and less involved in convergent evolution, due to anatomical constraints. We identify several convergent inner structural traits, while external shape only loosely follows this trend, and we find confirmation for our assumption in measures of convergence magnitude. We suggest that future macroevolutionary reconstructions based on bone morphology should include structural traits to better detect ecological effects on vertebrate diversification.
Collapse
Affiliation(s)
- Fabio Alfieri
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany.
- Museum Für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany.
| | - Léo Botton-Divet
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Jan Wölfer
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - John A Nyakatura
- Comparative Zoology, Institute for Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117, Berlin, Germany
| | - Eli Amson
- Paleontology Department, Staatliches Museum für Naturkunde, Rosenstein 1-3, 70191, Stuttgart, Germany
| |
Collapse
|
31
|
Zhao K, Yang X, Zeng Q, Zhang Y, Li H, Yan C, Li JS, Liu H, Du L, Wu Y, Huang G, Huang T, Zhang Y, Zhou H, Wang X, Chu Y, Zhou X. Evolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung. Nat Commun 2023; 14:5976. [PMID: 37749088 PMCID: PMC10519970 DOI: 10.1038/s41467-023-41704-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
Chronic infection with the bacterial pathogen Pseudomonas aeruginosa often leads to coexistence of heterogeneous populations carrying diverse mutations. In particular, loss-of-function mutations affecting the quorum-sensing regulator LasR are often found in bacteria isolated from patients with lung chronic infection and cystic fibrosis. Here, we study the evolutionary dynamics of polymorphic P. aeruginosa populations using isolates longitudinally collected from patients with chronic obstructive pulmonary disease (COPD). We find that isolates deficient in production of different sharable extracellular products are sequentially selected in COPD airways, and lasR mutants appear to be selected first due to their quorum-sensing defects. Polymorphic populations including lasR mutants display survival advantages in animal models of infection and modulate immune responses. Our study sheds light on the multistage evolution of P. aeruginosa populations during their adaptation to host lungs.
Collapse
Affiliation(s)
- Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China.
| | - Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Qianglin Zeng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yige Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Heyue Li
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, 610064, Chengdu, China
| | - Chaochao Yan
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Jing Shirley Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Huan Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Liangming Du
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yi Wu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Gui Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Ting Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yamei Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Hui Zhou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Affiliated Hospital of Chengdu University, Chengdu University, 610106, Chengdu, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
| |
Collapse
|
32
|
Wu F, Wang W, Chen J, Wang Z. A dynamic multi-objective optimization method based on classification strategies. Sci Rep 2023; 13:15221. [PMID: 37709788 PMCID: PMC10502025 DOI: 10.1038/s41598-023-41855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
The dynamic multi-objective optimization problem is a common problem in real life, which is characterized by conflicting objectives, the Pareto frontier (PF) and Pareto solution set (PS) will follow the changing environment. There are various dynamic multi-objective algorithms have been suggested to solve such problems, but most of the methods suffer from the inability to balance the diversity of populations with convergence. Prediction based method is a common approach to solve dynamic multi-objective optimization problems, but such methods only search for probabilistic models of optimal values of decision variables and do not consider whether the decision variables are related to diversity and convergence. Consequently, we present a prediction method based on the classification of decision variables for dynamic multi-objective optimization (DVC), where the decision variables are first pre-classified in the static phase, and then new variables are adjusted and predicted to adapt to the environmental changes. Compared with other advanced prediction strategies, dynamic multi-objective prediction methods based on classification of decision variables are more capable of balancing population diversity and convergence. The experimental results show that the proposed algorithm DVC can effectively handle DMOPs.
Collapse
Affiliation(s)
- Fei Wu
- College of Computer Science and Technology, Zhejiang University of Technology, HangZhou, ZheJiang, 310023, China
| | - Wanliang Wang
- College of Computer Science and Technology, Zhejiang University of Technology, HangZhou, ZheJiang, 310023, China
| | - Jiacheng Chen
- College of Computer Science and Technology, Zhejiang University of Technology, HangZhou, ZheJiang, 310023, China
| | - Zheng Wang
- School of Computer and computational Sciences, Zhejiang University City College, Hangzhou, Zhejiang, 310015, China.
| |
Collapse
|
33
|
Bukkuri A, Pienta KJ, Austin RH, Hammarlund EU, Amend SR, Brown JS. A mathematical investigation of polyaneuploid cancer cell memory and cross-resistance in state-structured cancer populations. Sci Rep 2023; 13:15027. [PMID: 37700000 PMCID: PMC10497555 DOI: 10.1038/s41598-023-42368-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023] Open
Abstract
The polyaneuploid cancer cell (PACC) state promotes cancer lethality by contributing to survival in extreme conditions and metastasis. Recent experimental evidence suggests that post-therapy PACC-derived recurrent populations display cross-resistance to classes of therapies with independent mechanisms of action. We hypothesize that this can occur through PACC memory, whereby cancer cells that have undergone a polyaneuploid transition (PAT) reenter the PACC state more quickly or have higher levels of innate resistance. In this paper, we build on our prior mathematical models of the eco-evolutionary dynamics of cells in the 2N+ and PACC states to investigate these two hypotheses. We show that although an increase in innate resistance is more effective at promoting cross-resistance, this trend can also be produced via PACC memory. We also find that resensitization of cells that acquire increased innate resistance through the PAT have a considerable impact on eco-evolutionary dynamics and extinction probabilities. This study, though theoretical in nature, can help inspire future experimentation to tease apart hypotheses surrounding how cross-resistance in structured cancer populations arises.
Collapse
Affiliation(s)
- Anuraag Bukkuri
- Cancer Biology and Evolution Program and Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, USA.
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | | | - Emma U Hammarlund
- Tissue Development and Evolution Research Group, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sarah R Amend
- The Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, USA
| | - Joel S Brown
- Cancer Biology and Evolution Program and Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, USA
| |
Collapse
|
34
|
Abstract
Spatial heterogeneity in antibiotic concentrations is thought to accelerate the evolution of antibiotic resistance, but current theory and experiments have overlooked the effect of cell motility on bacterial adaptation. Here, we study bacterial evolution in antibiotic landscapes with a quantitative model where bacteria evolve under the stochastic processes of proliferation, death, mutation and migration. Numerical and analytical results show that cell motility can both accelerate and decelerate bacterial adaptation by affecting the degree of genotypic mixing and ecological competition. Moreover, we find that for sufficiently high rates, cell motility can limit bacterial survival, and we derive conditions for all these regimes. Similar patterns are observed in more complex scenarios, namely where bacteria can bias their motion in chemical gradients (chemotaxis) or switch between motility phenotypes either stochastically or in a density-dependent manner. Overall, our work reveals limits to bacterial adaptation in antibiotic landscapes that are set by cell motility.
Collapse
Affiliation(s)
- Vit Piskovsky
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK
| | - Nuno M Oliveira
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK.
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| |
Collapse
|
35
|
Roper M, Green JP, Salguero-Gómez R, Bonsall MB. Inclusive fitness forces of selection in an age-structured population. Commun Biol 2023; 6:909. [PMID: 37670147 PMCID: PMC10480192 DOI: 10.1038/s42003-023-05260-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 08/20/2023] [Indexed: 09/07/2023] Open
Abstract
Hamilton's force of selection acting against age-specific mortality is constant and maximal prior to the age of first reproduction, before declining to zero at the age of last reproduction. The force of selection acting on age-specific reproduction declines monotonically from birth in a growing or stationary population. Central to these results is the assumption that individuals do not interact with one another. This assumption is violated in social organisms, where an individual's survival and/or reproduction may shape the inclusive fitness of other group members. Yet, it remains unclear how the forces of selection might be modified when inclusive fitness, rather than population growth rate, is considered the appropriate metric for fitness. Here, we derive such inclusive fitness forces of selection, and show that selection on age-specific survival is not always constant before maturity, and can remain above zero in post-reproductive age classes. We also show how the force of selection on age-specific reproduction does not always decline monotonically from birth, but instead depends on the balance of costs and benefits of increasing reproduction to both direct and indirect fitness. Our theoretical framework provides an opportunity to expand our understanding of senescence across social species.
Collapse
Affiliation(s)
- Mark Roper
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jonathan P Green
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Roberto Salguero-Gómez
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Max Planck Institute for Demographic Research, Konrad-Zuse-Straße 1, 18057, Rostock, Germany
| | - Michael B Bonsall
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| |
Collapse
|
36
|
Glunčić M, Vlahović I, Rosandić M, Paar V. Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly. Sci Rep 2023; 13:14420. [PMID: 37660151 PMCID: PMC10475015 DOI: 10.1038/s41598-023-41517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
Collapse
Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia.
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (Ret.), 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
- Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
| |
Collapse
|
37
|
Lion S, Sasaki A, Boots M. Extending eco- evolutionary theory with oligomorphic dynamics. Ecol Lett 2023; 26 Suppl 1:S22-S46. [PMID: 36814412 DOI: 10.1111/ele.14183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023]
Abstract
Understanding the interplay between ecological processes and the evolutionary dynamics of quantitative traits in natural systems remains a major challenge. Two main theoretical frameworks are used to address this question, adaptive dynamics and quantitative genetics, both of which have strengths and limitations and are often used by distinct research communities to address different questions. In order to make progress, new theoretical developments are needed that integrate these approaches and strengthen the link to empirical data. Here, we discuss a novel theoretical framework that bridges the gap between quantitative genetics and adaptive dynamics approaches. 'Oligomorphic dynamics' can be used to analyse eco-evolutionary dynamics across different time scales and extends quantitative genetics theory to account for multimodal trait distributions, the dynamical nature of genetic variance, the potential for disruptive selection due to ecological feedbacks, and the non-normal or skewed trait distributions encountered in nature. Oligomorphic dynamics explicitly takes into account the effect of environmental feedback, such as frequency- and density-dependent selection, on the dynamics of multi-modal trait distributions and we argue it has the potential to facilitate a much tighter integration between eco-evolutionary theory and empirical data.
Collapse
Affiliation(s)
| | - Akira Sasaki
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Mike Boots
- Integrative Biology, University of California, Berkeley, California, USA
- Department of Ecology and Conservation, University of Exeter, Penryn, UK
| |
Collapse
|
38
|
Lecointre G, Aish A, Améziane N, Chekchak T, Goupil C, Grandcolas P, Vincent JFV, Sun JS. Revisiting Nature's "Unifying Patterns": A Biological Appraisal. Biomimetics (Basel) 2023; 8:362. [PMID: 37622967 PMCID: PMC10452652 DOI: 10.3390/biomimetics8040362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Effective bioinspiration requires dialogue between designers and biologists, and this dialogue must be rooted in a shared scientific understanding of living systems. To support learning from "nature's overarching design lessons" the Biomimicry Institute has produced ten "Unifying Patterns of Nature". These patterns have been developed to engage with those interested in finding biologically inspired solutions to human challenges. Yet, although well-intentioned and appealing, they are likely to dishearten biologists. The aim of this paper is to identify why and propose alternative principles based on evolutionary theory.
Collapse
Affiliation(s)
- Guillaume Lecointre
- Institut de Systématique, Évolution et Biodiversité, UMR ISYEB 7205 CNRS MNHN SU EPHE UA, Muséum National d’Histoire Naturelle, CP 50, 45 Rue Buffon, 75005 Paris, France
| | - Annabelle Aish
- Bioinspire-Museum, Direction Générale Déléguée à la Recherche, l’Expertise, la Valorisation et l’Enseignement (DGD REVE), Muséum National d’Histoire Naturelle, 57 Rue Cuvier, CP 17, 75005 Paris, France
| | - Nadia Améziane
- Institut de Systématique, Évolution et Biodiversité, UMR ISYEB 7205 CNRS MNHN SU EPHE UA, Muséum National d’Histoire Naturelle, CP 50, 45 Rue Buffon, 75005 Paris, France
| | - Tarik Chekchak
- Institut des Futurs Souhaitables, 127 Avenue Ledru Rollin, 75011 Paris, France
| | - Christophe Goupil
- Laboratoire Interdisciplinaire des Énergies de Demain (LIED), UMR 8236 CNRS, Université Paris-Cité, 75013 Paris, France
| | - Philippe Grandcolas
- Institut de Systématique, Évolution et Biodiversité, UMR ISYEB 7205 CNRS MNHN SU EPHE UA, Muséum National d’Histoire Naturelle, CP 50, 45 Rue Buffon, 75005 Paris, France
| | - Julian F. V. Vincent
- Nature Inspired Manufacturing Centre, School of Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Jian-Sheng Sun
- Structure et Instabilité des Génomes, UMR 7196—U1154, MNHN CNRS INSERM, Muséum National d’Histoire Naturelle, 43 Rue Cuvier, 75005 Paris, France
| |
Collapse
|
39
|
Jiang D, Cope AL, Zhang J, Pennell M. On the Decoupling of Evolutionary Changes in mRNA and Protein Levels. Mol Biol Evol 2023; 40:msad169. [PMID: 37498582 PMCID: PMC10411491 DOI: 10.1093/molbev/msad169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here, we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level; this observation held true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and the translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic data.
Collapse
Affiliation(s)
- Daohan Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alexander L Cope
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
40
|
Majic P, Payne JL. Developmental Selection and the Perception of Mutation Bias. Mol Biol Evol 2023; 40:msad179. [PMID: 37556606 PMCID: PMC10443735 DOI: 10.1093/molbev/msad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a nonrandom association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, that is selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population-genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.
Collapse
Affiliation(s)
- Paco Majic
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
41
|
Rouzine IM. Long-range linkage effects in adapting sexual populations. Sci Rep 2023; 13:12492. [PMID: 37528175 PMCID: PMC10393966 DOI: 10.1038/s41598-023-39392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
In sexual populations, closely-situated genes have linked evolutionary fates, while genes spaced far in genome are commonly thought to evolve independently due to recombination. In the case where evolution depends essentially on supply of new mutations, this assumption has been confirmed by mathematical modeling. Here I examine it in the case of pre-existing genetic variation, where mutation is not important. A haploid population with [Formula: see text] genomes, [Formula: see text] loci, a fixed selection coefficient, and a small initial frequency of beneficial alleles [Formula: see text] is simulated by a Monte-Carlo algorithm. When the number of loci, L, is larger than a critical value of [Formula: see text] simulation demonstrates a host of linkage effects that decrease neither with the distance between loci nor the number of recombination crossovers. Due to clonal interference, the beneficial alleles become extinct at a fraction of loci [Formula: see text]. Due to a genetic background effect, the substitution rate varies broadly between loci, with the fastest value exceeding the one-locus limit by the factor of [Formula: see text] Thus, the far-situated parts of a long genome in a sexual population do not evolve as independent blocks. A potential link between these findings and the emergence of new Variants of Concern of SARS-CoV-2 is discussed.
Collapse
Affiliation(s)
- Igor M Rouzine
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint-Petersburg, Russia, 194223.
| |
Collapse
|
42
|
Lewin-Epstein O, Jaques Y, Feldman MW, Kaufer D, Hadany L. Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis. Commun Biol 2023; 6:782. [PMID: 37495841 PMCID: PMC10372008 DOI: 10.1038/s42003-023-05099-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Recent studies revealed mechanisms by which the microbiome affects its host's brain, behavior and wellbeing, and that dysbiosis - persistent microbiome-imbalance - is associated with the onset and progress of various chronic diseases, including addictive behaviors. Yet, understanding of the ecological and evolutionary processes that shape the host-microbiome ecosystem and affect the host state, is still limited. Here we propose that competition dynamics within the microbiome, associated with host-microbiome mutual regulation, may promote dysbiosis and aggravate addictive behaviors. We construct a mathematical framework, modeling the dynamics of the host-microbiome ecosystem in response to alterations. We find that when this ecosystem is exposed to substantial perturbations, the microbiome may shift towards a composition that reinforces the new host state. Such a positive feedback loop augments post-perturbation imbalances, hindering attempts to return to the initial equilibrium, promoting relapse episodes and prolonging addictions. We show that the initial microbiome composition is a key factor: a diverse microbiome enhances the ecosystem's resilience, whereas lower microbiome diversity is more prone to lead to dysbiosis, exacerbating addictions. This framework provides evolutionary and ecological perspectives on host-microbiome interactions and their implications for host behavior and health, while offering verifiable predictions with potential relevance to clinical treatments.
Collapse
Affiliation(s)
- Ohad Lewin-Epstein
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Yanabah Jaques
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720, USA
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Daniela Kaufer
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lilach Hadany
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel.
- Sagol school of neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
| |
Collapse
|
43
|
Alfieri F, Caravagna G, Schaefer MH. Author Correction: Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions. Nat Commun 2023; 14:4423. [PMID: 37479721 PMCID: PMC10362046 DOI: 10.1038/s41467-023-40060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
Affiliation(s)
- Fabio Alfieri
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139, Milan, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, 34127, Trieste, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139, Milan, Italy.
| |
Collapse
|
44
|
Jiang B, He Y, Elsler A, Wang S, Keating JN, Song J, Kearns SL, Benton MJ. Extended embryo retention and viviparity in the first amniotes. Nat Ecol Evol 2023; 7:1131-1140. [PMID: 37308704 PMCID: PMC10333127 DOI: 10.1038/s41559-023-02074-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/17/2023] [Indexed: 06/14/2023]
Abstract
The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles, birds and mammals. It is debated whether these fetal membranes evolved in eggs on land as an adaptation to the terrestrial environment or to control antagonistic fetal-maternal interaction in association with extended embryo retention (EER). Here we report an oviparous choristodere from the Lower Cretaceous period of northeast China. The ossification sequence of the embryo confirms that choristoderes are basal archosauromorphs. The discovery of oviparity in this assumed viviparous extinct clade, together with existing evidence, suggests that EER was the primitive reproductive mode in basal archosauromorphs. Phylogenetic comparative analyses on extant and extinct amniotes suggest that the first amniote displayed EER (including viviparity).
Collapse
Affiliation(s)
- Baoyu Jiang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China.
| | - Yiming He
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Armin Elsler
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Shengyu Wang
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Joseph N Keating
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Junyi Song
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Stuart L Kearns
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| | - Michael J Benton
- School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, UK
| |
Collapse
|
45
|
Mukherjee A, Ealy J, Huang Y, Benites NC, Polk M, Basan M. Coexisting ecotypes in long-term evolution emerged from interacting trade-offs. Nat Commun 2023; 14:3805. [PMID: 37365188 PMCID: PMC10293278 DOI: 10.1038/s41467-023-39471-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
Evolution of complex communities of coexisting microbes remains poorly understood. The long-term evolution experiment on Escherichia coli (LTEE) revealed the spontaneous emergence of stable coexistence of multiple ecotypes, which persisted for more than 14,000 generations of continuous evolution. Here, using a combination of experiments and computer simulations, we show that the emergence and persistence of this phenomenon can be explained by the combination of two interacting trade-offs, rooted in biochemical constraints: First, faster growth is enabled by higher fermentation and obligate acetate excretion. Second, faster growth results in longer lag times when utilizing acetate after glucose is depleted. This combination creates an ecological niche for a slower-growing ecotype, specialized in switching to acetate. These findings demonstrate that trade-offs can give rise to surprisingly complex communities with evolutionarily stable coexistence of multiple variants in even the simplest environments.
Collapse
Affiliation(s)
- Avik Mukherjee
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Jade Ealy
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Yanqing Huang
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Nina Catherine Benites
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Mark Polk
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Markus Basan
- Harvard Medical School, Department of Systems biology, 200 Longwood Avenue, Boston, MA, 02115, USA.
| |
Collapse
|
46
|
Wagner A. Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein. Nat Commun 2023; 14:3624. [PMID: 37336901 PMCID: PMC10279741 DOI: 10.1038/s41467-023-39321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Can evolvability-the ability to produce adaptive heritable variation-itself evolve through adaptive Darwinian evolution? If so, then Darwinian evolution may help create the conditions that enable Darwinian evolution. Here I propose a framework that is suitable to address this question with available experimental data on adaptive landscapes. I introduce the notion of an evolvability-enhancing mutation, which increases the likelihood that subsequent mutations in an evolving organism, protein, or RNA molecule are adaptive. I search for such mutations in the experimentally characterized and combinatorially complete fitness landscapes of a protein and an RNA molecule. I find that such evolvability-enhancing mutations indeed exist. They constitute a small fraction of all mutations, which shift the distribution of fitness effects of subsequent mutations towards less deleterious mutations, and increase the incidence of beneficial mutations. Evolving populations which experience such mutations can evolve significantly higher fitness. The study of evolvability-enhancing mutations opens many avenues of investigation into the evolution of evolvability.
Collapse
Affiliation(s)
- Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.
- The Santa Fe Institute, Santa Fe, NM, USA.
| |
Collapse
|
47
|
Alfieri F, Caravagna G, Schaefer MH. Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions. Nat Commun 2023; 14:3594. [PMID: 37328455 PMCID: PMC10276008 DOI: 10.1038/s41467-023-39313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/01/2023] [Indexed: 06/18/2023] Open
Abstract
Cancers evolve under the accumulation of thousands of somatic mutations and chromosomal aberrations. While most coding mutations are deleterious, almost all protein-coding genes lack detectable signals of negative selection. This raises the question of how tumors tolerate such large amounts of deleterious mutations. Using 8,690 tumor samples from The Cancer Genome Atlas, we demonstrate that copy number amplifications frequently cover haploinsufficient genes in mutation-prone regions. This could increase tolerance towards the deleterious impact of mutations by creating safe copies of wild-type regions and, hence, protecting the genes therein. Our findings demonstrate that these potential buffering events are highly influenced by gene functions, essentiality, and mutation impact and that they occur early during tumor evolution. We show how cancer type-specific mutation landscapes drive copy number alteration patterns across cancer types. Ultimately, our work paves the way for the detection of novel cancer vulnerabilities by revealing genes that fall within amplifications likely selected during evolution to mitigate the effect of mutations.
Collapse
Affiliation(s)
- Fabio Alfieri
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, 34127, Italy
| | - Martin H Schaefer
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, 20139, Italy.
| |
Collapse
|
48
|
Tzung KW, Lalonde RL, Prummel KD, Mahabaleshwar H, Moran HR, Stundl J, Cass AN, Le Y, Lea R, Dorey K, Tomecka MJ, Zhang C, Brombacher EC, White WT, Roehl HH, Tulenko FJ, Winkler C, Currie PD, Amaya E, Davis MC, Bronner ME, Mosimann C, Carney TJ. A median fin derived from the lateral plate mesoderm and the origin of paired fins. Nature 2023; 618:543-549. [PMID: 37225983 PMCID: PMC10266977 DOI: 10.1038/s41586-023-06100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/19/2023] [Indexed: 05/26/2023]
Abstract
The development of paired appendages was a key innovation during evolution and facilitated the aquatic to terrestrial transition of vertebrates. Largely derived from the lateral plate mesoderm (LPM), one hypothesis for the evolution of paired fins invokes derivation from unpaired median fins via a pair of lateral fin folds located between pectoral and pelvic fin territories1. Whilst unpaired and paired fins exhibit similar structural and molecular characteristics, no definitive evidence exists for paired lateral fin folds in larvae or adults of any extant or extinct species. As unpaired fin core components are regarded as exclusively derived from paraxial mesoderm, any transition presumes both co-option of a fin developmental programme to the LPM and bilateral duplication2. Here, we identify that the larval zebrafish unpaired pre-anal fin fold (PAFF) is derived from the LPM and thus may represent a developmental intermediate between median and paired fins. We trace the contribution of LPM to the PAFF in both cyclostomes and gnathostomes, supporting the notion that this is an ancient trait of vertebrates. Finally, we observe that the PAFF can be bifurcated by increasing bone morphogenetic protein signalling, generating LPM-derived paired fin folds. Our work provides evidence that lateral fin folds may have existed as embryonic anlage for elaboration to paired fins.
Collapse
Affiliation(s)
- Keh-Weei Tzung
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Robert L Lalonde
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Karin D Prummel
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Harsha Mahabaleshwar
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Hannah R Moran
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Amanda N Cass
- Biology Department, Wesleyan University, Middletown, CT, USA
| | - Yao Le
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Robert Lea
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Karel Dorey
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika J Tomecka
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Changqing Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Eline C Brombacher
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - William T White
- CSIRO National Research Collections Australia, Australia National Fish Collection, Hobart, Tasmania, Australia
| | - Henry H Roehl
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Frank J Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Christoph Winkler
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Enrique Amaya
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Marcus C Davis
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Tom J Carney
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
49
|
Scott TW, West SA, Dewar AE, Wild G. Is cooperation favored by horizontal gene transfer? Evol Lett 2023; 7:113-120. [PMID: 37251586 PMCID: PMC10210433 DOI: 10.1093/evlett/qrad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 05/31/2023] Open
Abstract
It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
Collapse
Affiliation(s)
- Thomas W Scott
- Corresponding author: Department of Biology, University of Oxford; Oxford, OX1 3SZ, United Kingdom.
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Geoff Wild
- Department of Mathematics, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
50
|
Awasthi K, M Henshaw J. Can low-quality parents exploit their high-quality partners to gain higher fitness? J Evol Biol 2023; 36:795-804. [PMID: 37036579 DOI: 10.1111/jeb.14174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/10/2023] [Accepted: 03/15/2023] [Indexed: 04/11/2023]
Abstract
An individual's optimal investment in parental care potentially depends on many variables, including its future fitness prospects, the expected costs of providing care and its partner's expected or observed parental behaviour. Previous models suggested that low-quality parents could evolve to exploit their high-quality partners by reducing care, leading to the paradoxical prediction that low-quality parents could have higher fitness than their high-quality partners. However, these studies lacked a complete and consistent life-history model. Here, we challenge this result, developing a consistent analytical model of parental care strategies given individual variation in quality, and checking our results using agent-based simulations. In contrast to previous models, we predict that high-quality individuals always outcompete low-quality individuals in fitness terms. However, care effort may differ between high- and low-quality parents in either direction: low-quality individuals care more than high-quality individuals if their baseline mortality is higher, but less if their mortality increases more steeply with increasing care. We also highlight the ambiguity of the term 'quality' and stress the need for 'genealogical consistency' in evolutionary models.
Collapse
Affiliation(s)
| | - Jonathan M Henshaw
- Institute of Biology I, University of Freiburg, Hauptstraße 1, D-79104, Freiburg, Germany
| |
Collapse
|