Repeatability and Predictability in Experimental Evolution

Lind, Peter A.

doi:10.1007/978-3-030-30363-1_4

Cited by 11 publications

(11 citation statements)

References 114 publications

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“…It is hard to explain this recurrence by rm/ns alone. This conclusion is consistent with other recent empirical findings connecting mutational phenomena to parallelism in evolution in general and adaptive evolution specifically (55)(56)(57)(58), such as the finding that the high rates of deletion of a specific enhancer are responsible for the parallel and likely adaptive loss of the pelvic hindfin in freshwater sticklebacks (55); and that the human hemoglobin S mutation, which protects against malaria in heterozygotes and causes sickle-cell anemia in homozygotes, originates significantly more rapidly than expected by chance for this mutation type, especially in Africans (51), strengthening the possibility that this mutation has after all arisen multiple independent times (59).…”

Section: Discussionsupporting

confidence: 93%

Genes used together are more likely to be fused together in evolution by mutational mechanisms: A bioinformatic test of the used-fused hypothesis

Bolotin

Melamed

Livnat

2021

Preprint

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Cases of parallel or recurrent gene fusions, whether in evolution or in cancer and genetic disease, are difficult to explain, as they require multiple of the same or similar breakpoints to repeat. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a certain context are more likely than otherwise to undergo a fusion mutation in the course of evolution–reminiscent of the Hebbian learning rule where neurons that fire together wire together. This mutational hypothesis offers to explain both evolutionary parallelism and recurrence in disease of gene fusions under one umbrella. Here, we test this hypothesis using bioinformatic data. Various measures of gene interaction, including co-expression, co-localization, same-TAD presence and semantic similarity of GO terms show that human genes whose homologs are fused in one or more other organisms are significantly more likely to interact together than random genes, controlling for genomic distance between genes. In addition, we find a statistically significant overlap between pairs of genes that fused in the course of evolution in non-human species and pairs that undergo fusion in human cancers. These results provide support for the used-together-fused-together hypothesis over several alternative hypotheses, including that all gene pairs can fuse by random mutation, but among pairs that have thus fused, those that have interacted previously are more likely to be favored by selection. Multiple consequences are discussed, including the relevance of mutational mechanisms to exon shuffling, to the distribution of fitness effects of mutation and to parallelism.

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Section: Discussionsupporting

confidence: 93%

Genes used together are more likely to be fused together in evolution by mutational mechanisms: A bioinformatic test of the used-fused hypothesis

Bolotin

Melamed

Livnat

2021

Preprint

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“…Thus, it is of interest that the overall point mutation rate in this region is significantly higher than expected, and that it is significantly higher in the African than in the European population. These results provide a clear case of a connection between mutation rates and adaptive evolution, thus moving beyond previous literature on the relevance of mutation rates to adaptive evolution and its repeatability (Crow et al, 2009;Dumas et al, 2012;Xie et al, 2019;Lind, 2019).…”

Section: Discussionsupporting

confidence: 70%

“…In contrast, technological limitations have precluded measuring mutation rates at particular base positions and of particular mutations at such positions. However, such high-resolution knowledge of the mutation rate variation would bear on multiple open questions in genetics and evolution—from the relative importance of mutation rate variation to the site frequency spectrum (SFS) ( Harpak et al 2016 ; Lek et al 2016 ; Mathieson and Reich 2017 ), to its importance for adaptive evolution and parallelism ( Inoue et al 2001 ; Crow et al 2009 ; Dumas et al 2012 ; Losos 2017 ; Kratochwil et al 2019 ; Kratochwil and Meyer 2019 ; Lind 2019 ; Xie et al 2019 ), to its contribution to recurrent genetic disease and cancer ( Lupski 1998 ; McClellan and King 2010 ; Veltman and Brunner 2012 ; Shendure and Akey 2015 ).…”

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confidence: 99%

De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease

et al. 2022

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While it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the 'HbS mutation' when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.

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“…However, we believe the latter would be unlikely, given the detectable differences in ARD vs. FSD coevolutionary dynamics and that the trade-off coincided only with ARD. The lack of repeatability and predictability during microbial evolution observed here may be due to the perpetuating effects of early-occurring mutations for phage resistance and whether these tend to send the bacterial population along a trajectory of ARD coupled with the expected phenotypic trade-off, versus FSD and low likelihood of the pleiotropic link between evolved phage and antibiotic resistance traits (Elena & Lenski, 2003;Lind, 2019). It is important to note that impact of phenotypic consequences of coevolutionary dynamics (ARD vs. FSD) for the applied use of phage is both unknown and understudied.…”

Section: Discussionmentioning

confidence: 99%

Arms race and fluctuating selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1

Kortright

Evans

Turner

2022

J of Evolutionary Biology

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Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms‐race dynamics (ARD) and fluctuating‐selection dynamics (FSD). Here, we tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory, whether ARD versus FSD coevolution occurred, and how coevolution affected a predicted phenotypic trade‐off between phage resistance and antibiotic sensitivity. We used a unique “deep” sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage infection and resistance to antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD, whereas the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade‐off. Whole genome sequencing revealed that treatment populations of bacteria accrued more de novo mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type‐IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade‐off in the ARD‐coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria‐phage system and that occurrence of predicted phage‐driven evolutionary trade‐offs may depend on the genetics underlying evolution of phage resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics.

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Repeatability and Predictability in Experimental Evolution

Cited by 11 publications

References 114 publications

Genes used together are more likely to be fused together in evolution by mutational mechanisms: A bioinformatic test of the used-fused hypothesis

Genes used together are more likely to be fused together in evolution by mutational mechanisms: A bioinformatic test of the used-fused hypothesis

De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease

Arms race and fluctuating selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1

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