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Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns


Cooper, Timothy; Moore, Francisco; Smith, Chelsea; Smith, Adam (2022), Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns, Dryad, Dataset,


Long term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments, and chance events all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2,000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor were evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing-returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.


One-day competitive fitness were used to quantify the relative fitness of evolved populations. Populations were started with three-fold replicaiton from one of 16 founder strains and were seperately evovled for 2000 generations in acetate, trypsin, casamino acids, or glucoxse. Evovled populaitons were able to utilize arabinose (Ara+) and were competed against otherwise isogenic Ara- derivatives of corresponding ancestral strains. After pre-conditioning competitors were mixed at equal ratios and diluted 1000-fold into competition cultures. A sample was immediately plated on TA agar to determine the initial frequency of each competitor. A second sample was plated following 24 hours of competition. The ratioj of Malthusian parameters of each competitor was used to estimate relative fitness of evolved strains. We also estimated absolute fitness of progenitor strains from analysis of growth curves in relevant environemtns. In some cases competitions were plated on multiple plates to increase the number of colonies of each competitor observed and reduce sampling error. In these cases the count of that competitor is reported as a mean over the plates that were counted.

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Royal Society Te Apārangi, Award: 19-MAU-082

National Science Foundation, Award: DEB-0844355

National Science Foundation, Award: DEB- 844198