Summary auto-generated
This study examines the relationship between 16S rRNA sequence similarity (S) and DNA hybridization extent (D) across 387 prokaryotic organism pairs from 20 taxa. The researchers compiled published 16S rRNA sequences and corresponding DNA hybridization data, calculating sequence similarities and testing various mathematical relationships. Using complementary log-log transformation, they derived the equation ln(-lnD) = 0.53[ln(-lnS)] - 2.201, which explained 78% of D variability when accounting for taxa differences. The relationship is nonlinear: when S ranges from 1.0 to 0.95, D drops from 1.0 to 0.15, while from 0.95 to 0.90, D declines only to 0.06. Notably, about one-third of taxa examined exhibited non-ultrametric 16S rRNA properties, where S values were unexpectedly low relative to D, making S a poor indicator of relatedness for closely related strains in these groups. The relationship between D and S varied significantly among taxa but not between bacterial and archaeal domains. DNA hybridization method (S1 nuclease, membrane filter, hydroxyapatite, or thermal renaturation) had minimal impact on the overall relationship.
Key findings
- The relationship between 16S rRNA sequence similarity and DNA hybridization is nonlinear and best described by complementary log-log transformation, explaining 78% of D variance when taxa differences are controlled.
- Sequence similarity S values must exceed 0.992 to achieve 95% probability that DNA hybridization D > 0.70, indicating similar sequences don't guarantee high DNA reassociation.
- Approximately one-third of the prokaryotic taxa examined have non-ultrametric 16S rRNA sequences where similarity values are unexpectedly low relative to DNA hybridization, making S unreliable for these groups.
- The relationship between D and S varies significantly among different prokaryotic taxa and genera, even within the same higher-order groups, requiring taxon-specific predictions for accuracy.
- The relationship between D and S is consistent between bacterial and archaeal domains, suggesting similar evolutionary rates of sequence change across prokaryotic groups.
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Abstract
The relationship between 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) was well described by the equation ln(-lnD)=0.53 [ln(-lnS)]+2.201 when D was determined by either the S1 nuclease or membrane filter methods. When the presence of nonultrametric rRNA sequences and differences between genera or families were controlled, this relationship accounted for 78% of the variability of D given S, and it was possible to estimate the distribution of D from S with a known precision. Thus, D < 0.70 was expected to occur 50, 95 and 99% of the time when S was 0.998, 0.992 and 0.986, respectively. The relationship between D and S varied between prokaryotic taxa even within the same subphylum, and more precise estimates of D could be made when the relationship for a particular taxon was known. The relationship between D and S was not significantly different between the prokaryotic domains, and S appeared to be a quasi-molecular clock of approximately constant rate when averaging effects and stochastic factors were taken into account. The relationship between logD and logS was nonlinear, and D provided a very poor measure of relatedness for distantly related organisms. For instance, within the range 1.0 > S > 0.95, D decreased from 1.0 to 0.15; and within the range 0.95 > S > 0.90, D decreased from 0.15 to 0.06. Lastly, at least some of the rRNA sequences from about one-third of the taxa examined had nonultrametric properties where S was much lower than expected from the value of D. For these taxa, S was a poor indicator of relatedness for closely related strains. Thus, the ultrametric properties of rRNA sequences should be tested before making taxonomic or phylogenetic conclusions based upon S.