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1. Historical Contingency Causes Divergence in Adaptive Expression of the lac Operon

   https://doi.org/10.1093/molbev/msab077  

   Karkare, Kedar; Lai, Huei-Yi; Azevedo, Ricardo B.R.; Cooper, Tim F. (March 2021, Molecular Biology and Evolution)

   Wittkopp, Patricia (Ed.)

   Abstract Populations of Escherichia coli selected in constant and fluctuating environments containing lactose often adapt by substituting mutations in the lacI repressor that cause constitutive expression of the lac operon. These mutations occur at a high rate and provide a significant benefit. Despite this, eight of 24 populations evolved for 8,000 generations in environments containing lactose contained no detectable repressor mutations. We report here on the basis of this observation. We find that, given relevant mutation rates, repressor mutations are expected to have fixed in all evolved populations if they had maintained the same fitness effect they confer when introduced to the ancestor. In fact, reconstruction experiments demonstrate that repressor mutations have become neutral or deleterious in those populations in which they were not detectable. Populations not fixing repressor mutations nevertheless reached the same fitness as those that did fix them, indicating that they followed an alternative evolutionary path that made redundant the potential benefit of the repressor mutation, but involved unique mutations of equivalent benefit. We identify a mutation occurring in the promoter region of the uspB gene as a candidate for influencing the selective choice between these paths. Our results detail an example of historical contingency leading to divergent evolutionary outcomes. 

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2. Divalent Cations and the Divergence of βγ -Crystallin Function

   https://doi.org/10.1021/acs.biochem.9b00507  

   Roskamp, Kyle W.; Kozlyuk, Natalia; Sengupta, Suvrajit; Bierma, Jan C.; Martin, Rachel W. (October 2019, Biochemistry)
3. The mode of expression divergence in Drosophila fat body is infection-specific

   https://doi.org/10.1101/gr.269597.120  

   Ramirez-Corona, Bryan A.; Fruth, Stephanie; Ofoegbu, Oluchi; Wunderlich, Zeba (June 2021, Genome Research)

   Transcription is controlled by interactions of cis -acting DNA elements with diffusible trans -acting factors. Changes in cis or trans factors can drive expression divergence within and between species, and their relative prevalence can reveal the evolutionary history and pressures that drive expression variation. Previous work delineating the mode of expression divergence in animals has largely used whole-body expression measurements in one condition. Because cis -acting elements often drive expression in a subset of cell types or conditions, these measurements may not capture the complete contribution of cis -acting changes. Here, we quantify the mode of expression divergence in the Drosophila fat body, the primary immune organ, in several conditions, using two geographically distinct lines of D. melanogaster and their F1 hybrids. We measured expression in the absence of infection and in infections with Gram-negative S. marcescens or Gram-positive E. faecalis bacteria, which trigger the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans -acting effects dominating in response to Gram-negative infection and cis -acting effects dominating in Gram-positive and preinfection conditions. Expression divergence in several receptor proteins may underlie the infection-specific trans effects. Before infection, when the fat body has a metabolic role, there are many compensatory effects, changes in cis and trans that counteract each other to maintain expression levels. This work shows that within a single tissue, the mode of expression divergence varies between conditions and suggests that these differences reflect the diverse evolutionary histories of host–pathogen interactions. 

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4. Balanced polymorphisms and their divergence in a Heliconius butterfly

   https://doi.org/10.1002/ece3.8423  

   Ogilvie, James_G; Van_Belleghem, Steven; Range, Ryan; Papa, Riccardo; McMillan, Owen_W; Chouteau, Mathieu; Counterman, Brian_A (December 2021, Ecology and Evolution)

   Abstract The evolution of mimicry in similarly defended prey is well described by the Müllerian mimicry theory, which predicts the convergence of warning patterns in order to gain the most protection from predators. However, despite this prediction, we can find great diversity of color patterns among Müllerian mimics such asHeliconiusbutterflies in the neotropics. Furthermore, some species have evolved the ability to maintain multiple distinct warning patterns in single populations, a phenomenon known as polymorphic mimicry. The adaptive benefit of these polymorphisms is questionable since variation from the most common warning patterns is expected to be disadvantageous as novel signals are punished by predators naive to them. In this study, we use artificial butterfly models throughout Central and South America to characterize the selective pressures maintaining polymorphic mimicry inHeliconius doris. Our results highlight the complexity of positive frequency‐dependent selection, the principal selective pressure driving convergence among Müllerian mimics, and its impacts on interspecific variation of mimetic warning coloration. We further show how this selection regime can both limit and facilitate the diversification of mimetic traits. 

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5. Ad fontes : divergence‐time estimation and the age of angiosperms

   https://doi.org/10.1111/nph.20076  

   Smith, Stephen_A; Beaulieu, Jeremy_M (August 2024, New Phytologist)

   Summary Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the older ages inferred from molecular data and relaxed‐clock models are misled by lineage‐specific rate heterogeneity resulting from life history changes that occurred several times throughout the evolution of vascular plants. To overcome persistent discrepancies in age estimates, more biologically informed and realistic models should be developed, and our results should be considered in the context of their biological implications before we accept inferences that are a major departure from our strongest evidence. 

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