Ancient Darwinian replicators nested within eubacterial genomes

Bertels, Frederic; Rainey, Paul B.

doi:10.1101/2021.07.10.451892

Cited by 3 publications

(28 citation statements)

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“…Similarly, genomes without RAYTs have smaller REPIN populations in the purple population than genomes with the corresponding RAYT ( Figure 3D ). A similar observation has been made previously in E. coli, P. chlororaphis and Neisseria where the loss of the RAYT gene is followed by a decay of the REPIN population (Bertels, Rainey 2022).…”

Section: Resultssupporting

confidence: 86%

“…RAREFAN can identify REPINs and their corresponding RAYTs in a set of – ideally fully sequenced – bacterial genomes. The RAREFAN algorithm has been used in previous analyses to identify and characterize REPINs and RAYTs in Pseudomonas (Bertels, Rainey 2011, 2022), Neisseria (Bertels, Rainey 2022), and Enterobacteria (Bertels, Gallie, et al . 2017; Park et al .…”

Section: Resultsmentioning

confidence: 99%

“…The algorithm to determine REP sequence groups has been described in previous papers and is slightly improved in our implementation (Bertels, Rainey 2011, 2022; Bertels, Gokhale, et al . 2017).…”

Section: Methodsmentioning

confidence: 99%

“…2017; Park et al . 2021; Bertels, Rainey 2022), in the absence of horizontal transfer of RAYT transposases or REPIN populations (Bertels, Gallie, et al . 2017; Park et al .…”

Section: Introductionmentioning

confidence: 99%

“…2017; Park et al . 2021; Bertels, Rainey 2022). These evolutionary characteristics are consistent with REPIN-RAYT systems providing a benefit to the host (Bertels, Rainey 2022).…”

Section: Introductionmentioning

confidence: 99%

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RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Fortmann-Grote

Balk

Bertels

2022

Preprint

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Compared to eukaryotes, mobile genetic elements are rare in bacterial genomes and usually do not persist for long in the genome. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN's capabilities by analyzing a set of 49 Stenotrophomonas maltophilia genomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems across S. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find the correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…2017; Park et al . 2021; Bertels, Rainey 2022), in the absence of horizontal transfer of RAYT transposases or REPIN populations (Bertels, Gallie, et al . 2017; Park et al .…”

Section: Introductionmentioning

confidence: 99%

“…2017; Park et al . 2021; Bertels, Rainey 2022). These evolutionary characteristics are consistent with REPIN-RAYT systems providing a benefit to the host (Bertels, Rainey 2022).…”

Section: Introductionmentioning

confidence: 99%

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RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Fortmann-Grote

Balk

Bertels

2022

Preprint

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Major evolutionary transitions in individuality between humans and AI

Rainey

2023

Phil. Trans. R. Soc. B

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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’.

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Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

Dijk

Farr

Buffard

et al. 2023

Preprint

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Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome - the zoo of Darwinian replicators that depend on microbial hosts - remains poorly characterised. New experimental approaches and analyses are necessary to advance our understanding beyond simple pairwise MGE-host interactions. To detect horizontal transfer, a bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples, which was then applied to metagenomic data from evolving compost communities. These communities were routinely exposed to an "MGE cocktail" derived from allopatric communities. We show that this results in horizontal transfer of a multitude of previously undetected MGEs, including bacteriophages, phage-plasmids, megaplasmids, and even nanobacteria. Sequences that spread from one community to another are shown to disproportionally carry characteristics of phages and insertion-sequences, i.e., traits of canonically parasitic MGEs. We also show that one particularly prolific mobile element - a 313 kb plasmid - correlates substantially with rates of ammonia production, which under nitrogen limitation is likely beneficial. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the drivers of microbial community evolution.

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Ancient Darwinian replicators nested within eubacterial genomes

Cited by 3 publications

References 98 publications

RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes

Major evolutionary transitions in individuality between humans and AI

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

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