Search arXivSearch

arXiv · 2210.03677

Global epistasis on fitness landscapes

Abstract

Epistatic interactions between mutations add substantial complexity to adaptive landscapes, and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a mutation is well-predicted by the fitness of its genetic background, may actually be of help in our efforts to reconstruct fitness landscapes and infer adaptive trajectories. Microscopic interactions between mutations, or inherent nonlinearities in the fitness landscape, may cause global epistasis patterns to emerge. In this brief review, we provide a succinct overview of recent work about global epistasis, with an emphasis on building intuition about why it is often observed. To this end, we reconcile simple geometric reasoning with recent mathematical analyses, using these to explain why different mutations in an empirical landscape may exhibit different global epistasis patterns - ranging from diminishing to increasing returns. Finally, we highlight open questions and research directions.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Juan Diaz-Colunga, Abigail Skwara, Karna Gowda, Ramon Diaz-Uriarte, Mikhail Tikhonov, Djordje Bajic, Alvaro Sanchez. 2022-10-07. Global epistasis on fitness landscapes. https://arxiv.org/abs/2210.03677

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

From daylight to darkness: a nonlocal model of circadian activity cycles

An animal's ability to perceive its surroundings, as well as the ecological interactions it experiences, can be strongly influenced by the sleep patterns of both itself and surrounding species. Animals with limited sensory capabilities may struggle to navigate their habitat at night, while in a predator-prey system, it may be detrimental for prey to be inactive while predators are awake and hunting. Here, we develop a general mathematical framework to study these interactions using partial differential equations, incorporating activity cycles and daylight-dependent perception into existing models of animal movement. We show that both the dominant sensory mode and the length of daylight are key factors determining the strength of aggregation in social species. Extending this framework to a two-species predator-prey system, we use game-theoretic approaches to show that the equilibrium sleep strategy of each species is shaped not only by its own sensory capabilities, but also by those of its ecological opponent. Depending on the sensory capabilities of the two species, equilibrium strategies may consist of a single sleep pattern or a combination of multiple sleep patterns.

q-bio.PE

Evolution as fitness landscape navigation: concepts, measures, and emerging questions

Fitness landscapes are mappings between genotypes, phenotypes, and fitness that shape evolution. In recent years, empirical work and theoretical models have greatly advanced our understanding of how populations navigate rugged fitness landscapes. Here, we provide a timely review of the theoretical aspects of this field. Its rapidly growing literature employs a wide range of terms, which are sometimes used ambiguously or inconsistently. We therefore begin by defining the major concepts and the field's vocabulary, highlighting our own terminology choices wherever needed. We then review key results on the relationships between epistasis, ruggedness, accessibility, and navigability for genotype-fitness maps, highlighting several complex and sometimes counterintuitive connections that have emerged. Further, we review how the conserved structural properties of the underlying genotype-phenotype map, which can lead to the formation of large connected neutral networks of genotypes, influence dynamics on fitness landscapes. We then compare the two levels to study landscape navigation: the level of genotype-phenotype maps and the level of genotype-fitness maps. Our review leads us to propose a new measure of navigability, based on evolutionary outcomes, that is broadly applicable and overcomes limitations of existing measures. Finally, we highlight examples from the smaller body of work that relaxes the common assumption of fitness-monotonic paths on static landscapes, and discuss how this can fundamentally change the nature of fitness landscape navigation. Throughout the review, we identify directions for future work to fill existing gaps and to synthesize the disparate strands of research within the field.

q-bio.PE

Best Matches in Phylogenetic Networks

Best match graphs (BMGs) were introduced in mathematical phylogenetics to describe the concept of closest relatives for related genes (leaves of rooted tree) in different organisms (defining leaf colors). We generalize this concept here to leaf-colored rooted networks, where least common ancestors are in general neither unique nor comparable. We characterize BMGs of rooted networks as those vertex-colored digraphs that are properly colored and satisfy an easy-to-check condition that we call the sicor-in-hub property. BMGs can be recognized in linear time and an explaining network can be constructed in quadratic time. Analogous results are obtained for reciprocal best match graphs (RBMGs), where an edge $\{x,y\}$ corresponds to pairs of vertices with different color that are mutually closest relatives.

q-bio.PE