Parallel genetic adaptation across environments differing in mode of growth or resource availability

Abstract

Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under all combinations of high or low carbon availability and selection for either planktonic or biofilm modes of growth. Populations that evolved in environments with shared selection pressures (either level of carbon availability or mode of growth) were more genetically similar to each other than populations from environments that shared neither characteristic. However, not all shared selection pressures led to parallel evolution. Genetic parallelism between low‐carbon biofilm and low‐carbon planktonic populations was very low despite shared selection for growth under low‐carbon conditions, suggesting that evolution in low‐carbon environments may generate stronger trade‐offs between biofilm and planktonic modes of growth. For all environments, a population's fitness in a particular environment was positively correlated with the genetic similarity between that population and the populations that evolved in that particular environment. Although genetic similarity was low between low‐carbon environments, overall, evolution in similar environments led to higher levels of genetic parallelism and that genetic parallelism, in turn, was correlated with fitness in a particular environment.

Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

“…The presence of a pre-existing mutation would 234 also help explain the rapid rise of wspA mutations to nearly 100% frequency in the populations. Several 235 rpfR mutations were detected in multiple populations, raising the possibility of their presence at low 236 frequency in the shared ancestral culture, though repeated independent mutations of the same rpfR 237 nucleotide have been observed in prior experiments (Turner et al 2018). Other rpfR alleles, however, were 238 unique to individual populations and thus de novo mutations.…”

SARS-CoV-2 genome evolution exposes early human adaptations

“…Beneficial mutations can be readily identified in laboratory evolution experiments 75 through parallel mutations that arise in multiple independent replicates (16,17), also known as 76 homoplasies. We applied this intuition to search for beneficial mutations in the SARS-CoV-2 77 genome as it diversifies across many hosts.…”

Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network

“…Examples of such convergence exist in natura such as the well-known case of pelvic reduction in freshwater stickleback (Chan, et al 2012). In experimental evolution systems such as yeast or bacteria, parallel de novo mutations have been often observed at the gene and even nucleotide level during adaptation to antibiotic dosage (Laehnemann, et al 2014), to nutrient availability and growth conditions (Spor, et al 2014;Turner, et al 2018) , and during acclimation to high temperature . In this last example, first-step mutations in the evolved lines have been observed in multiple replicates at a single gene: a trans-acting factor 22 modulating the expression of hundreds of downstream genes (Rodriguez-Verdugo, et al 2016).…”