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  1. Article ; Online: Major evolutionary transitions in individuality between humans and AI.

    Rainey, Paul B

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2023  Volume 378, Issue 1872, Page(s) 20210408

    Abstract: That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central ... ...

    Abstract That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central to my argument is recognition that heritable variance in fitness at higher levels of organization can be externally imposed (scaffolded) by specific ecological structures and cultural practices. While ETIs to eusociality seem highly improbable, ETIs involving symbioses between humans and artificial intelligence (AI) can be readily envisaged. A necessary requirement is that fitness-affecting interactions between humans and AI devices are inherited by offspring. The Mendelian nature of human reproduction ensures that offspring resemble parents. Reproduction of AI devices requires nothing more than transference of algorithms from parental AI devices to devices that are assigned to offspring. This simple copying, combined with societal structures that require humans to carry AI devices, ensures heritable variance in fitness at the level of both interacting partners. Selection at the collective level will drive alignment of replicative fates and increase co-dependency, thus alleviating need for continual imposition of externally imposed scaffolds. I conclude by drawing attention to the immediacy of such transitions and express concern over possibilities for malevolent manipulation. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
    MeSH term(s) Humans ; Artificial Intelligence ; Biological Evolution ; Reproduction ; Algorithms ; Symbiosis
    Language English
    Publishing date 2023-01-23
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2021.0408
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Polar accumulation of pyoverdin and exit from stationary phase.

    Moreno-Fenoll, Clara / Ardré, Maxime / Rainey, Paul B

    microLife

    2024  Volume 5, Page(s) uqae001

    Abstract: Pyoverdin is a water-soluble metal-chelator synthesized by members of the ... ...

    Abstract Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus
    Language English
    Publishing date 2024-02-14
    Publishing country England
    Document type Journal Article
    ISSN 2633-6693
    ISSN (online) 2633-6693
    DOI 10.1093/femsml/uqae001
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  3. Article ; Online: Ancient Darwinian replicators nested within eubacterial genomes.

    Bertels, Frederic / Rainey, Paul B

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2022  Volume 45, Issue 2, Page(s) e2200085

    Abstract: Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by ... ...

    Abstract Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception - a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
    MeSH term(s) Bacteria/genetics ; DNA Transposable Elements/genetics ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences
    Chemical Substances repin (11024-67-2) ; DNA Transposable Elements
    Language English
    Publishing date 2022-12-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202200085
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  4. Article ; Online: Barcoding Populations of Pseudomonas fluorescens SBW25.

    Theodosiou, Loukas / Farr, Andrew D / Rainey, Paul B

    Journal of molecular evolution

    2023  Volume 91, Issue 3, Page(s) 254–262

    Abstract: In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver ... ...

    Abstract In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.
    MeSH term(s) Pseudomonas fluorescens/genetics ; Biological Evolution
    Language English
    Publishing date 2023-04-25
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s00239-023-10103-6
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  5. Article ; Online: Ancient Darwinian replicators nested within eubacterial genomes

    Bertels, Frederic / Rainey, Paul B.

    BioEssays. 2023 Feb., v. 45, no. 2 p.e2200085-

    2023  

    Abstract: Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by ... ...

    Abstract Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on non‐jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
    Keywords genome ; inheritance (genetics) ; population size ; transposases ; transposons
    Language English
    Dates of publication 2023-02
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202200085
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  6. Article ; Online: The effect of bottleneck size on evolution in nested Darwinian populations.

    Nitschke, Matthew C / Black, Andrew J / Bourrat, Pierrick / Rainey, Paul B

    Journal of theoretical biology

    2023  Volume 561, Page(s) 111414

    Abstract: Previous work has shown how a minimal ecological structure consisting of patchily distributed resources and recurrent dispersal between patches can scaffold Darwinian properties onto collections of cells. When the timescale of dispersal is long compared ... ...

    Abstract Previous work has shown how a minimal ecological structure consisting of patchily distributed resources and recurrent dispersal between patches can scaffold Darwinian properties onto collections of cells. When the timescale of dispersal is long compared with the time to consume resources, patch fitness increases but comes at a cost to cell growth rates. This creates conditions that initiate evolutionary transitions in individuality. A key feature of the scaffold is a bottleneck created during dispersal, causing patches to be founded by single cells. The bottleneck decreases competition within patches and, hence, creates a strong hereditary link at the level of patches. Here, we construct a fully stochastic model to investigate the effect of bottleneck size on the evolutionary dynamics of both cells and collectives. We show that larger bottlenecks simply slow the dynamics, but, at some point, which depends on the parameters of the within-patch model, the direction of evolution towards the equilibrium reverses. Introduction of random fluctuations in bottleneck sizes with some positive probability of smaller sizes counteracts this, even when the probability of smaller bottlenecks is minimal.
    MeSH term(s) Biological Evolution ; Population Dynamics ; Probability
    Language English
    Publishing date 2023-01-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2972-5
    ISSN 1095-8541 ; 0022-5193
    ISSN (online) 1095-8541
    ISSN 0022-5193
    DOI 10.1016/j.jtbi.2023.111414
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  7. Article ; Online: Toward a dynamical understanding of microbial communities.

    Rainey, Paul B / Quistad, Steven D

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2020  Volume 375, Issue 1798, Page(s) 20190248

    Abstract: The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a ... ...

    Abstract The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
    MeSH term(s) Bacteria/genetics ; Bacterial Physiological Phenomena/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; Metagenome ; Microbiota
    Language English
    Publishing date 2020-03-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2019.0248
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  8. Article ; Online: Genome Update for Pseudomonas fluorescens Isolate SBW25.

    Fortmann-Grote, Carsten / Hugoson, Eric / Summers, Joanna / Theodosiou, Loukas / Rainey, Paul B

    Microbiology resource announcements

    2023  Volume 12, Issue 2, Page(s) e0063722

    Abstract: We report a genome update for Pseudomonas fluorescens isolate SBW25. The updated genome assembly, which was derived from the original isolate, is based on PacBio long-read sequence data. It shows three minor differences, compared with the previously ... ...

    Abstract We report a genome update for Pseudomonas fluorescens isolate SBW25. The updated genome assembly, which was derived from the original isolate, is based on PacBio long-read sequence data. It shows three minor differences, compared with the previously published genome sequence. Original annotations were merged with recent automated annotations to preserve information.
    Language English
    Publishing date 2023-01-18
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00637-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A leader cell triggers end of lag phase in populations of

    Ardré, Maxime / Doulcier, Guilhem / Brenner, Naama / Rainey, Paul B

    microLife

    2022  Volume 3, Page(s) uqac022

    Abstract: The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the "inoculum effect." Its mechanistic basis is unclear with possible ... ...

    Abstract The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the "inoculum effect." Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of populations of cells. Here, we use a millifluidic droplet device in which the growth dynamics of hundreds of populations founded by controlled numbers of
    Language English
    Publishing date 2022-11-02
    Publishing country England
    Document type Journal Article
    ISSN 2633-6693
    ISSN (online) 2633-6693
    DOI 10.1093/femsml/uqac022
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  10. Article ; Online: Precarious development: the uncertain social life of cellular slime molds.

    Rainey, Paul B

    Proceedings of the National Academy of Sciences of the United States of America

    2015  Volume 112, Issue 9, Page(s) 2639–2640

    MeSH term(s) Dictyostelium/physiology ; Life Cycle Stages/physiology ; Spores, Protozoan/physiology
    Language English
    Publishing date 2015-02-23
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1500708112
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