Macroevolutionary dynamics in micro-organisms: Generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota.
dc.contributor.author | Padfield, D | |
dc.contributor.author | Kay, S | |
dc.contributor.author | Vos, R | |
dc.contributor.author | Quince, C | |
dc.contributor.author | Vos, M | |
dc.date.accessioned | 2024-06-20T10:58:19Z | |
dc.date.issued | 2024-05-08 | |
dc.date.updated | 2024-06-19T10:10:41Z | |
dc.description.abstract | Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity. However, relatively little is known about how prokaryotes successfully transition and persist across environments, and how these processes might vary between biomes and lineages. Here, we investigate biome transitions and specialization in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2,000 unique Myxococcota lineages, with the majority (77%) classified as biome specialists and with only <5% of lineages distributed across the salt barrier. Discrete character evolution models revealed that specialists in one biome rarely transitioned into specialists in another biome. Instead, evolved generalism mediated transitions between biome specialists. State-dependent diversification models found variation in speciation rates across the tree, but this variation was independent of biome association or specialization. Our findings were robust to phylogenetic uncertainty, different levels of species delineation, and different assumed amounts of unsampled diversity resulting in an incomplete phylogeny. Overall, our results are consistent with a "jack-of-all-trades" tradeoff where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists and shed light on how bacteria could transition between biomes. | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.description.sponsorship | Biotechnology and Biological Sciences Research Council (BBSRC) | en_GB |
dc.description.sponsorship | Biotechnology and Biological Sciences Research Council (BBSRC) | en_GB |
dc.description.sponsorship | Biotechnology and Biological Sciences Research Council (BBSRC) | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.format.extent | msae088- | |
dc.format.medium | ||
dc.identifier.citation | Vol. 41, No. 5, article msae088 | en_GB |
dc.identifier.doi | https://doi.org/10.1093/molbev/msae088 | |
dc.identifier.grantnumber | NE/T008083/1 | en_GB |
dc.identifier.grantnumber | BB/CSP1720/1 | en_GB |
dc.identifier.grantnumber | BBS/E/T/ 000PR9818 | en_GB |
dc.identifier.grantnumber | BBS/E/T/000PR9817 | en_GB |
dc.identifier.grantnumber | (NE/ W008890/1 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/136360 | |
dc.identifier | ORCID: 0000-0001-6799-9670 (Padfield, Daniel) | |
dc.identifier | ORCID: 0000-0002-3917-8151 (Vos, Michiel) | |
dc.language.iso | en | en_GB |
dc.publisher | Oxford University Press | en_GB |
dc.relation.url | https://www.ncbi.nlm.nih.gov/pubmed/38717941 | en_GB |
dc.relation.url | https://github.com/padpadpadpad/myxo_diversification | en_GB |
dc.relation.url | https://zenodo.org/doi/10.5281/zenodo.11210843 | en_GB |
dc.rights | © The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/ licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited | en_GB |
dc.subject | comparative phylogenetics | en_GB |
dc.subject | diversification | en_GB |
dc.subject | habitat transitions | en_GB |
dc.subject | macroevolution | en_GB |
dc.subject | microbes | en_GB |
dc.subject | myxobacteria | en_GB |
dc.subject | prokaryotes | en_GB |
dc.subject | specialization | en_GB |
dc.title | Macroevolutionary dynamics in micro-organisms: Generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota. | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2024-06-20T10:58:19Z | |
dc.contributor.editor | Pupko, T | |
dc.identifier.issn | 0737-4038 | |
exeter.article-number | ARTN msae088 | |
exeter.place-of-publication | United States | |
dc.description | This is the final version. Available from Oxford University Press via the DOI in this record. | en_GB |
dc.description | Data Availability: All raw sequencing data has been deposited on the European Nucleotide Archive (Study Accession number: PRJEB73761). Processed data and code to recreate all analyses are publicly available on GitHub (https://github.com/padpadpadpad/myxo_diversification) and is archived on Zenodo (https://zenodo.org/doi/10.5281/zenodo.11210843). The analysis code starts with the processed phyloseq objects created after the dada2 workflow. We thank two reviewers for their extensive and detailed comments that significantly improved the analyses. | en_GB |
dc.identifier.eissn | 1537-1719 | |
dc.identifier.journal | Molecular Biology and Evolution | en_GB |
dc.relation.ispartof | Mol Biol Evol, 41(5) | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2024-05-03 | |
dc.rights.license | CC BY | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2024-05-03 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2024-06-20T10:52:04Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2024-06-20T10:58:28Z | |
refterms.panel | A | en_GB |
refterms.dateFirstOnline | 2024-05-08 |
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