Evolutionary branching in distorted trait spaces

Ito, Hiroshi C.; Sasaki, Akira

doi:10.1101/794966

Cited by 4 publications

(4 citation statements)

References 27 publications

(79 reference statements)

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“…1d), much like a dominant effect in the NK model ( 14 ). This second way is consistent with a fitness landscape distortion, which occurs when certain mutations influence the interactions of many other genes ( 41 ). Geometrically, such a distortion constitutes a vertex split ( 42 ).…”

Section: Resultssupporting

confidence: 74%

High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

Eble

Joswig

Lamberti

et al. 2021

Preprint

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A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Yet biological interactions between genes, species, and different environmental contexts change the individual effects due to non-additive interactions, known as epistasis. In the fitness landscape concept, each gene/organism/environment is modeled as a separate biological dimension, yielding a high dimensional landscape, with epistasis adding local peaks and valleys to the landscape. Massive efforts have defined dense epistasis networks on a genome-wide scale, but these have mostly been limited to pairwise, or two-dimensional, interactions. Here we develop a new mathematical formalism that allows us to quantify interactions at high dimensionality in genetics and the microbiome. We then generate and also reanalyze combinatorically complete datasets (two genetic, two microbiome). In higher dimensions, we find that key genes (e.g. pykF) and species (e.g. Lactobacillus plantarum) distort the fitness landscape, changing the interactions for many other genes/species. These distortions can fracture a landscape with one optimal fitness peak into a landscape with many local optima, regulating evolutionary or ecological diversification, which may explain how a probiotic bacterium can stabilize the gut microbiome.

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Section: Resultssupporting

confidence: 74%

High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

Eble

Joswig

Lamberti

et al. 2021

Preprint

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“…We have based our analysis on the basic model by Ackermann & Doebeli [20] which extends directly from the classical work of MacArthur [21] and which formalizes the mechanism of the cost of individual generalization in a suitable and sufficient way. There are related models on the evolution of niche position and width, accounting for alternative aspects including behavioural optimal-and suboptimal-foraging processes [24], bimodal resource distributions [25] and the general assessment of branching lines of bivariate traits [26]. Such alternative models may be reviewed for additional insights or generality.…”

Section: Discussionmentioning

confidence: 99%

Principles of niche expansion

2018

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Niche expansion is attained by adaptations in two generalized phenotypical traits-niche position and niche width. This gives room for a wide range of conceptual ways of niche filling. The niche variation hypothesis reduces the range by predicting that expansion occurs by increasing variation in niche position, which has been debated on empirical and theoretical grounds as also other options seem possible. Here, we propose a general theory of niche expansion. We review empirical data and show with an eco-evolutionary model how resource diversity and a trade-off in resource acquisition steer niche evolution consistent with observations. We show that the range can be reduced to a discrete set of two orthogonal ways of niche filling, through (1) strict phenotypical differentiation in niche position or (2) strict individual generalization. When individual generalization is costly, niche expansion undergoes a shift from (2) to (1) at a point where the resource diversity becomes sufficiently large. Otherwise, niche expansion always follows (2), consistent with earlier results. We show that this either -or response can operate at both evolutionary and short-term time scales. This reduces the principles of niche expansion under environmental change to a notion of orthogonality, dictated by resource diversity and a resource-acquisition trade-off.

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“…The canonical equation of adaptive dynamics, as described above, can thus only describe the movement of populations in phenotype space, but not speciation or extinction events. Evolutionary branching is a well known phenomenon that occurs when there is an attracting equilibrium or nullcline [27–29] in trait space that is also a fitness minimum [19]. To model these we use a well described algorithm [18] where the adaptive dynamics are run for some period of time at which a random population is chosen and a small mutant is introduced nearby.…”

Section: Models and Methodsmentioning

confidence: 99%

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

Rubin

Ispolatov

Doebeli

2021

Preprint

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One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur’s classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lokta-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.Author summaryUnderstanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable stats, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.

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Evolutionary branching in distorted trait spaces

Cited by 4 publications

References 27 publications

High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

Principles of niche expansion

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

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