scholarly journals Low mutational load and high mutation rate variation in gut commensal bacteria

PLoS Biology ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. e3000617 ◽  
Author(s):  
Ricardo S. Ramiro ◽  
Paulo Durão ◽  
Claudia Bank ◽  
Isabel Gordo
Keyword(s):  
Mutation Rate ◽  
Commensal Bacteria ◽  
High Mutation Rate ◽  
Rate Variation ◽  
Mutational Load ◽  
Mutation Rate Variation

scholarly journals Low Mutational Load Allows for High Mutation Rate Variation in Gut Commensal Bacteria

2019 ◽  
Author(s):  
Ricardo S. Ramiro ◽  
Paulo Durão ◽  
Claudia Bank ◽  
Isabel Gordo
Keyword(s):  
Gut Microbiota ◽  
Mutation Rate ◽  
Microbial Evolution ◽  
Rate Variation ◽  
Mutational Load ◽  
Deleterious Mutations ◽  
Natural Ecosystems ◽  
Fluctuating Selection ◽  
Beneficial Mutations ◽  
Mutation Rate Variation

AbstractBacteria generally live in species-rich communities, such as the gut microbiota. Yet, little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensalEscherichia coliin the mouse gut. We observe the emergence of polymorphism for mutation rate, ranging from wild-type levels to 1000-fold higher. By combining experiments, whole-genome sequencing andin silicosimulations, we identify the molecular causes and evolutionary conditions that allow these hypermutators to emerge and coexist within a complex microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III, which increase mutation rate by ~1000-fold (a mutation in the proofreading subunit) and stabilize hypermutator fitness (mutations in the catalytic subunit). The strong mutation rate variation persists for >1000 generations, with coexistence between lineages carrying 4 to >600 mutations. Thisin vivomolecular evolution pattern is consistent with deleterious mutations of ~0.01-0.001% fitness effects, 100 to 1000-fold lower than currentin vitroestimates. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but by processes leading to negative frequency-dependent or temporally fluctuating selection. Thus, microbial evolution in the gut is likely characterized by partial sweeps of beneficial mutations combined with hitchhiking of very slightly deleterious mutations, which take a long time to be purged but impose a very weak mutational load. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we identified key evolutionary processes shaping the genetic composition of this community.

Minisatellite mutation rate variation associated with a flanking DNA sequence polymorphism

1994 ◽  
Vol 8 (2) ◽  
pp. 162-170 ◽  
Author(s):  
Darren G. Monckton ◽  
Rita Neumann ◽  
Tara Guram ◽  
Neale Fretwell ◽  
Keiji Tamaki ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Mutation Rate ◽  
Sequence Polymorphism ◽  
Rate Variation ◽  
Dna Sequence Polymorphism ◽  
Mutation Rate Variation

scholarly journals Reply to: Mutation rate variation in eukaryotes: evolutionary implications of site-specific mechanisms

2007 ◽  
Vol 8 (11) ◽  
pp. 902-902
Author(s):  
Charles F. Baer ◽  
Michael M. Miyamoto ◽  
Dee R. Denver
Keyword(s):  
Mutation Rate ◽  
Rate Variation ◽  
Site Specific ◽  
Mutation Rate Variation

scholarly journals Robustness of Coalescent Estimators to Between-Lineage Mutation Rate Variation

2006 ◽  
Vol 23 (12) ◽  
pp. 2355-2360 ◽  
Author(s):  
M. K. Kuhner
Keyword(s):  
Mutation Rate ◽  
Rate Variation ◽  
Mutation Rate Variation

scholarly journals The architecture of intra-organism mutation rate variation in plants

PLoS Biology ◽  
2019 ◽  
Vol 17 (4) ◽  
pp. e3000191 ◽  
Author(s):  
Long Wang ◽  
Yilun Ji ◽  
Yingwen Hu ◽  
Huaying Hu ◽  
Xianqin Jia ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Rate Variation ◽  
Mutation Rate Variation

scholarly journals Mutation Rate Variability across Human Y-Chromosome Haplogroups

2020 ◽  
Author(s):  
Qiliang Ding ◽  
Ya Hu ◽  
Amnon Koren ◽  
Andrew G Clark
Keyword(s):  
Y Chromosome ◽  
Mutation Rate ◽  
Cultured Cells ◽  
Sex Chromosome ◽  
Branch Length ◽  
Rate Variation ◽  
Sequencing Data ◽  
Chromosome Mutations ◽  
Mutation Rate Variation

Abstract A common assumption in dating patrilineal events using Y-chromosome sequencing data is that the Y-chromosome mutation rate is invariant across haplogroups. Previous studies revealed interhaplogroup heterogeneity in phylogenetic branch length. Whether this heterogeneity is caused by interhaplogroup mutation rate variation or nongenetic confounders remains unknown. Here, we analyzed whole-genome sequences from cultured cells derived from >1,700 males. We confirmed the presence of branch length heterogeneity. We demonstrate that sex-chromosome mutations that appear within cell lines, which likely occurred somatically or in vitro (and are thus not influenced by nongenetic confounders) are informative for germline mutational processes. Using within-cell-line mutations, we computed a relative Y-chromosome somatic mutation rate, and uncovered substantial variation (up to 83.3%) in this proxy for germline mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity.

scholarly journals Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation

Science ◽  
2016 ◽  
Vol 351 (6277) ◽  
pp. 1094-1097 ◽  
Author(s):  
S. Uphoff ◽  
N. D. Lord ◽  
B. Okumus ◽  
L. Potvin-Trottier ◽  
D. J. Sherratt ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Mutation Rate ◽  
Rate Variation ◽  
Cell Mutation ◽  
Damage Response ◽  
Mutation Rate Variation
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