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1. The effect of weak clonal interference on average fitness trajectories in the presence of macroscopic epistasis

   https://doi.org/10.1093/genetics/iyac028  

   Guo, Yipei; Amir, Ariel; Jain, ed., K. (February 2022, Genetics)

   Abstract Adaptation dynamics on fitness landscapes is often studied theoretically in the strong-selection, weak-mutation regime. However, in a large population, multiple beneficial mutants can emerge before any of them fixes in the population. Competition between mutants is known as clonal interference, and while it is known to slow down the rate of adaptation (when compared to the strong-selection, weak-mutation model with the same parameters), how it affects the shape of long-term fitness trajectories in the presence of epistasis is an open question. Here, by considering how changes in fixation probabilities arising from weak clonal interference affect the dynamics of adaptation on fitness-parameterized landscapes, we find that the change in the shape of fitness trajectory arises only through changes in the supply of beneficial mutations (or equivalently, the beneficial mutation rate). Furthermore, a depletion of beneficial mutations as a population climbs up the fitness landscape can speed up the rescaled fitness trajectory (where adaptation speed is measured relative to its value at the start of the experiment), while an enhancement of the beneficial mutation rate does the opposite of slowing it down. Our findings suggest that by carrying out evolution experiments in both regimes (with and without clonal interference), one could potentially distinguish the different sources of macroscopic epistasis (fitness effect of mutations vs change in fraction of beneficial mutations). 

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2. Migration feedback induces emergent ecotypes and abrupt transitions in evolving populations

   Barkan, Casey O; Wang, Shenshen (January 2024, arXiv)

   We explore the connection between migration patterns and emergent behaviors of evolving populations in spatially heterogeneous environments. Despite extensive studies in ecologically and medically important systems, a unifying framework that clarifies this connection and makes concrete predictions remains much needed. Using a simple evolutionary model on a network of interconnected habitats with distinct fitness landscapes, we demonstrate a fundamental connection between migration feedback, emergent ecotypes, and an unusual form of discontinuous critical transition. We show how migration feedback generates spatially non-local niches in which emergent ecotypes can specialize. Rugged fitness landscapes lead to a complex, yet understandable, phase diagram in which different ecotypes coexist under different migration patterns. The discontinuous transitions are distinct from the standard first-order phase transitions in statistical physics. They arise due to simultaneous transcritical bifurcations and exhibit a “fine structure” due to symmetry breaking between intra- and inter-ecotype interactions. We suggest feasible experiments to test our predictions. 

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3. Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants

   https://doi.org/10.3390/ijms22147533  

   Hinsch, Valerie; Adkins, Samuel; Manuela, Darren; Xu, Mingli (July 2021, International Journal of Molecular Sciences)

   Correct timing of developmental phase transitions is critical for the survival and fitness of plants. Developmental phase transitions in plants are partially promoted by controlling relevant genes into active or repressive status. Polycomb Repressive Complex1 (PRC1) and PRC2, originally identified in Drosophila, are essential in initiating and/or maintaining genes in repressive status to mediate developmental phase transitions. Our review summarizes mechanisms in which the embryo-to-seedling transition, the juvenile-to-adult transition, and vegetative-to-reproductive transition in plants are mediated by PRC1 and PRC2, and suggests that PRC1 could act either before or after PRC2, or that they could function independently of each other. Details of the exact components of PRC1 and PRC2 in each developmental phase transitions and how they are recruited or removed will need to be addressed in the future. 

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4. Estimating the net effect of functional traits on fitness across species and environments

   https://doi.org/10.1111/2041-210X.14079  

   Siefert, Andrew; Laughlin, Daniel C. (March 2023, Methods in Ecology and Evolution)

   Abstract Functional traits affect the demographic performance of individuals in their environment, leading to fitness differences that scale up to drive population dynamics and community assembly. Understanding the links between traits and fitness is, therefore, critical for predicting how populations and communities respond to environmental change. However, the net effects of traits on species fitness are largely unknown because we have lacked a framework for estimating fitness across multiple species and environments.We present a modelling framework that integrates trait effects on demographic performance over the life cycles of individuals to estimate the net effect of traits on species fitness. This approach involves (1) modelling trait effects on individual demographic rates (growth, survival and recruitment) as multidimensional performance surfaces that vary with individual size and environment and (2) integrating these effects into a population model to project population growth rates (i.e., fitness) as a function of traits and environment. We illustrate our approach by estimating performance surfaces and fitness landscapes for trees across a temperature gradient in the eastern United States.Functional traits (wood density, specific leaf area and maximum height) interacted with individual size and temperature to influence tree growth, survival and recruitment rates, generating demographic trade‐offs and shaping the contours of fitness landscapes. Tall tree species had high survival, growth and fitness across the temperature gradient. Wood density and specific leaf area had interactive effects on demographic performance, resulting in fitness landscapes with multiple peaks.With this approach it is now possible to empirically estimate the net effect of traits on fitness, leading to an improved understanding of the selective forces that drive community assembly and permitting generalizable predictions of population and community dynamics in changing environments. 

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5. Endorheic‐Exorheic Transitions of the Rio Grande and East African Rifts

   https://doi.org/10.1029/2018GC008176  

   Berry, M.; van Wijk, J.; Cadol, D.; Emry, E.; Garcia‐Castellanos, D. (July 2019, Geochemistry, Geophysics, Geosystems)

   Abstract Tectonic extension of continental lithosphere creates accommodation space in which sediments are deposited. Climate‐driven processes provide the mechanism by which mass is detached from hillslopes and sediments are transported into this accommodation space. These two forcings, climate and tectonics, act together to create either endorheic (internally drained) or exorheic (externally drained) rift basins. Here we use a large‐scale dynamic landscape evolution‐tectonics model to understand the contribution of tectonic processes in endorheic‐exorheic transitions. In the model, extension results in opening of an asymmetric half‐graben along a listric normal fault. Rift opening occurs in the models in wet, temperate, or semiarid climates where runoff and evapotranspiration are varied. Our numerical experiments show that slow rift‐opening rates, a slowing‐down of rift opening, or increase of headwater topography (e.g., upstream epeirogenic uplift), are tectonic situations that can cause a transition from an endorheic to an exorheic drainage state in a rift basin. Our results also show that wet climate conditions lead to a permanent exorheism that persists regardless of rift‐opening rates. In semiarid climates, endorheic conditions are favored and may last for the duration of rifting except for when rift opening is very slow. These results form an interpretive framework to study endorheic and exorheic drainage systems in natural continental rifts. In the slow‐opening Rio Grande rift, the endorheic‐exorheic transition may have occurred without dramatic climate changes. Lake‐level variations in East African rift basins are predicted by our models to result from variations in climate. 

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