In biology all things must be proved several times — Cyril Dean Darlington, The Facts of Life, 1953.
How Prokaryotes Evolve
Updates | Earlier notices
This webpage began as a What'sNEW notice, 10 Mar 2021
New genes can be acquired only via HGT, whereas other mechanisms, such as duplication followed by divergence and de novo gene birth, are disregarded.
 "Assessment of assumptions underlying models of prokaryotic pangenome evolution" [open-access link], by Itamar Sela, Yuri I. Wolf and Eugene V. Koonin, doi:10.1186/s12915-021-00960-2, BMC Biology, 10 Feb 2021.
There is a basic set of genes shared by almost all prokaryotes, the "core" genome. But far more prokaryotic genes are "singletons," found in only one genome. Not too many land in between. What accounts for this U-shaped distribution?
Koonin et al., experts in biotechnology information, have studied this phenomenon. They compared the gene distribution in bacterial genomes to computer models that might generate the same distribution. Following various assumptions about the rates of gene gain and loss, and about the size of the available gene pool, the modelling succeeded. Among the E. coli genomes graphed here (blue circles) almost 4,000 genes are singletons, and 20 genes are shared among almost 2,000 of the genomes. The model (red boxes and x's) fits almost perfectly. The first assumption in the successful model is quoted above in bold italics.
Evidence leading to this conclusion as been accumulating for decades, but established opinions are stubborn. Even now,
mainstream biology does not recognize the reach and profundity of this new paradigm of prokaryotic evolution.
Updates since 2021
"Genetic exchange networks bridge mobile DNA vehicles in the bacterial pathogen Listeria monocytogenes," by Muller, H., Ikhimiukor, O.O., Montoya-Giraldo, M. et al, Nat Commun, 04 Nov 2025. Our findings reveal a structured but interconnected network of genetic exchanges between different mobile DNA vehicles.
"Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization," by Lingchen He1, Jonasz B. Patkowski et al, Cell, online 09 Sep 2025. ...tailless capsids... can hijack different phage tails to form chimeric infectious particles... contributing to bacterial evolution.
"Giant extrachromosomal element 'Inocle'...," by Kiguchi, Y, Hamamoto, N, Kashima, Y et al, doi:10.1038/s41467-025-62406-5, Nat Commun, 11 Aug 2025. ...plasmid-like circular elements of 395kb....
"Cross-kingdom RNA communication in plant–bacterial interaction," by Ronald Palermo and Arne Weiberg, doi:10.1016/j.tig.2025.07.004, TiG, 30 Jul 2025; re:
"Vesicular and non-vesicular extracellular small RNAs direct gene silencing in a plant-interacting bacterium," by Antinéa Ravet, Jérôme Zervudacki et al, doi:10.1038/s41467-025-57908-1, pdf, Nature Communications, 14 Apr 2025.
Maybe not incorporated into the bacterial genome, but they're phenotypically active, transferred sRNAs.
"...microbiomes in ruminants," by Tang, Y., Zhan, P., Wu, Y. et al, doi:10.1186/s40168-025-02139-1, Microbiome, 1 Jul 2025.
Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution....
"Mobile integrons encode phage defense systems," by Nicolas Kieffer, Alberto Hipólito et al, Science, 08 May 2025.
"Diverse bacteria use extracellular structures called competence type IV pili (T4P)
to take up DNA from their environment.," [from abstract] by Nicholas D. Christman and Ankur B. Dalia, PLoS Pathog, 21 Apr 2025.
"Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats," by Biller, S.J., Ryan, M.G., Li, J. et al, Nat Commun, 03 Mar 2025.
 18 Nov 2024: Transferred genes likely brought along their own regulatory elements.
"Intragenc DNA inversions expand bacterial coding capacity," by Rachael B. Chanin, Patrick T. West et al, Nature, 25 Sep 2024.
"Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements," by Manuel Ares-Arroyo et al, PLoS, 29 Aug 2024.
"Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer," by Taru Verma et al, overview, Front. Microbiol., accepted 08 Oct 2024.
"The extent and characteristics of DNA transfer between plasmids and chromosomes," by A. Samer Kadibalban et al, doi:10.1016/j.cub.2024.06.030, Current Biology, 22 Jul 2024.
07 Jun 2024: De novo bacterial genes by reverse transcription of a "rolling circle" of RNA?
30 May 2024: GTAs ...package host DNA into virus-like capsids and transfer this DNA....
12 Jan 2024: Heterologous cell fusion is said to be another way for bacteria to exchange genes, wholesale.
06 Nov 2023: Extracellular vesicles play a much greater role in horizontal gene transfer....
30 Aug 2023: Microbial evolution is driven by ...horizontal gene transfer (HGT).
29 Apr 2023: ...clouds can transport these genes....
14 Nov 2022: Viral GTAs can supply repair templates.
05 Apr 2022: Bacteriophage and MGEs beneficial to bacteria.
25 Jan 2022: Defense cassettes are supplied by mobile genetic elements.
11 Nov 2021: ...This pattern is the same as that for prokaryotes.
Earlier evidence in What'sNEW notices
 15 Oct 2020: HGT can potentiate future adaptation.
18 Dec 2018: Horizontal Gene Transfer (HGT) is the only source....
28 Oct 2018: The lateral transfer of bacterial genes by viruses....
14 Jun 2018: "...Bacteria Harpoon and Swallow DNA to Evolve" (w/ video)
28 Dec 2017: ...the predator cell can acquire antibiotic resistance.
31 Mar 2017: Cyanobacteria acquired the genes for photosynthesis relatively late....
09 Jul 2015: ...the entire basic genome is continually exchanged....
10 Sep 2014: HGT ...is the principal contributor....
more about HGT among prokaryotes, 2014-2006.
03 May 2006: Genes undergo rapid mutation and selection immediately after transfer.
15 Mar 2006: The paradigm for evolution ...has completely shifted.
26 Sep 2005: Common bacteria share an infinite gene pool?
01 Jul 2005: A new microbial tree of life.
01 Jan 2005: Gene exchange among archaebacteria from salt pools....
17 Jan 2003: HGT is no longer an explanation of last resort....
15 Oct 2000: Entire genetic regions appear to have been transferred....
12 Jun 2000: Among bacteria, HGT is "all there is," says Ernst Mayr.
18 May 2000: HGT produces extremely dynamic bacterial genomes.
14 Apr 2000: The microbial biosphere resembles a "World Wide Web," says Joshua Lederberg.
09 Apr 2000: "In bacteria and their DNA viruses, the major process of genetic adaptation and evolution involves the horizontal transfer of genetic elements...," writes Luis P. Villarreal in 1999.
12 Aug 1998: The paradigm continues to move toward lateral gene transfer as the primary driver of evolution.
24 Apr 1998: A distinctive class of integron in the Vibrio cholerae Genome
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