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1. Precise measurement of the fitness effects of spontaneous mutations by droplet digital PCR in Burkholderia cenocepacia

   https://doi.org/10.1093/genetics/iyab117  

   Rana, Anita; Patton, David; Turner, Nathan T; Dillon, Marcus M; Cooper, Vaughn S; Sung, Way (July 2021, Genetics)

   Wittkopp, P J (Ed.)

   Abstract Understanding how mutations affect survivability is a key component to knowing how organisms and complex traits evolve. However, most mutations have a minor effect on fitness and these effects are difficult to resolve using traditional molecular techniques. Therefore, there is a dire need for more accurate and precise fitness measurements methods. Here, we measured the fitness effects in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines using droplet-digital polymerase chain reaction (ddPCR). Overall, the fitness measurements from ddPCR-MA are correlated positively with fitness measurements derived from traditional phenotypic marker assays (r = 0.297, P = 0.05), but showed some differences. First, ddPCR had significantly lower measurement variance in fitness (F = 3.78, P < 2.6 × 10−13) in control experiments. Second, the mean fitness from ddPCR-MA measurements were significantly lower than phenotypic marker assays (−0.0041 vs −0.0071, P = 0.006). Consistent with phenotypic marker assays, ddPCR-MA measurements observed multiple (27/43) lineages that significantly deviated from mean fitness, suggesting that a majority of the mutations are neutral or slightly deleterious and intermixed with a few mutations that have extremely large effects. Of these mutations, we found a significant excess of mutations within DNA excinuclease and Lys R transcriptional regulators that have extreme deleterious and beneficial effects, indicating that modifications to transcription and replication may have a strong effect on organismal fitness. This study demonstrates the power of ddPCR as a ubiquitous method for high-throughput fitness measurements in both DNA- and RNA-based organisms regardless of cell type or physiology. 

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2. Selection on heritable social network positions is context-dependent in Drosophila melanogaster

   https://doi.org/10.1038/s41467-021-23672-1  

   Wice, Eric Wesley; Saltz, Julia Barbara (June 2021, Nature Communications)

   Abstract Social group structure is highly variable and can be important for nearly every aspect of behavior and its fitness consequences. Group structure can be modeled using social network analysis, but we know little about the evolutionary factors shaping and maintaining variation in how individuals are embedded within their networks (i.e., network position). While network position is a pervasive target of selection, it remains unclear whether network position is heritable and can respond to selection. Furthermore, it is unclear how environmental factors interact with genotypic effects on network positions, or how environmental factors shape selection on heritable network structure. Here we show multiple measures of social network position are heritable, using replicate genotypes and replicate social groups ofDrosophila melanogasterflies. Our results indicate genotypic differences in network position are largely robust to changes in the environment flies experience, though some measures of network position do vary across environments. We also show selection on multiple network position metrics depends on the environmental context they are expressed in, laying the groundwork for better understanding how spatio-temporal variation in selection contributes to the evolution of variable social group structure. 

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3. Changes in Cell Size and Shape during 50,000 Generations of Experimental Evolution with Escherichia coli

   https://doi.org/10.1128/JB.00469-20  

   Grant, Nkrumah A.; Abdel Magid, Ali; Franklin, Joshua; Dufour, Yann; Lenski, Richard E. (April 2021, Journal of Bacteriology)

   Brun, Yves V. (Ed.)

   ABSTRACT Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. In this study, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last time point. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest that larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells. IMPORTANCE Bacteria exhibit great morphological diversity, yet we have only a limited understanding of how their cell sizes and shapes evolve and of how these features affect organismal fitness. This knowledge gap reflects, in part, the paucity of the fossil record for bacteria. In this study, we revived and analyzed samples extending over 50,000 generations from 12 populations of experimentally evolving Escherichia coli to investigate the relation between cell size, shape, and fitness. Using this “frozen fossil record,” we show that all 12 populations evolved larger cells concomitant with increased fitness, with substantial heterogeneity in cell size and shape across the replicate lines. Our work demonstrates that cell morphology can readily evolve and diversify, even among populations living in identical environments. 

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4. The importance of comparative physiology: mechanisms, diversity and adaptation in skeletal muscle physiology and mechanics

   https://doi.org/10.1242/jeb.245158  

   Mendoza, E.; Moen, D. S.; Holt, N. C. (April 2023, Journal of Experimental Biology)

   ABSTRACT Skeletal muscle powers animal movement, making it an important determinant of fitness. The classic excitation–contraction coupling, sliding-filament and crossbridge theories are thought to describe the processes of muscle activation and the generation of force, work and power. Here, we review how the comparative, realistic muscle physiology typified by Journal of Experimental Biology over the last 100 years has supported and refuted these theories. We examine variation in the contraction rates and force–length and force–velocity relationships predicted by these theories across diverse muscles, and explore what has been learnt from the use of workloop and force-controlled techniques that attempt to replicate aspects of in vivo muscle function. We suggest inclusion of features of muscle contraction not explained by classic theories in our routine characterization of muscles, and the use of phylogenetic comparative methods to allow exploration of the effects of factors such as evolutionary history, ecology, behavior and size on muscle physiology and mechanics. We hope that these future directions will improve our understanding of the mechanisms of muscle contraction, allow us to better characterize the variation in muscle performance possible, and enable us to infer adaptation. 

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5. The landscape of transcriptional and 1translational changes over 22 years of bacterial adaptation

   https://doi.org/10.7554/eLife.81979  

   Favate, John S; Liang, Shun; Cope, Alexander L; Yadavalli, Srujana Samhita; Shah, Premal (October 2022, eLife)

   Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here we use the E. coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution. 

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