Populations & Evolution
Population dynamics, evolutionary biology, and epidemiological modeling.
q-bio.PE · 93 papersThe Co-evolution of Costly Signaling and Cooperation in Social Dilemmas
This paper models how costly signaling and cooperation co-evolve in social dilemmas, showing signals are selected by cooperative responses they elicit.
Logarithmic scaling of selective sweep curves: from tents to houses
Logarithmic scaling transforms selective sweep curves from logistic to tent-like, then to a house shape, with proven convergence regularity.
Dual Fear Mechanisms Shaping Stochastic Population Dynamics under the Allee Effect
This paper models how dual fear mechanisms influence stochastic population dynamics under the Allee effect, revealing noise-induced and fear-controlled regime changes.
Higher-order interactions in ecology can be hidden in plain sight
This paper shows that higher-order ecological interactions are often indistinguishable from pairwise models using only time-series data, leading to misinterpretations.
A $μ$-distance for semidirected orchard phylogenetic networks
This paper introduces a new μ-distance for comparing semidirected orchard phylogenetic networks, enabling their distinction and reconstruction.
Towards a unified framework for multiple stable states in ecological systems
This paper proposes a unified mathematical framework for understanding multiple stable states in ecological systems, synthesizing empirical and theoretical approaches.
The Origin of Life in the Light of Evolution
This paper argues that origin-of-life research must shift focus from how life began to how it evolved from pre-biological systems.
Chapter 2: Geometry of the Fitness Surface and Trajectory Dynamics of Replicator Systems
This paper analyzes the geometry of fitness surfaces in replicator systems, showing trajectories often miss fitness peaks and linking equilibria to evolutionary stability.
Direct From Darwin: Deriving Advanced Optimizers From Evolutionary First Principles
This paper unifies Fisher's and Wright's evolutionary theories to derive advanced gradient optimizers, showing many existing algorithms are evolutionarily compliant.
A process-based dynamic occupancy model to study range dynamics under non-equilibrium conditions
This paper introduces a process-based dynamic occupancy model using dispersal-pressure and sparse matrices to study species range dynamics at large scales.
Algorithmic bottlenecks in evolution: Genetic code, symbolic language, and the Great Filter hypothesis
This paper proposes that the origins of genetic code and symbolic language are algorithmic bottlenecks explaining the Great Filter hypothesis.
Genotype specificity and spatial arrangement govern the direction and magnitude of selection in variable environments
This paper presents a unified framework showing how genotype specificity and spatial arrangement govern selection in variable environments.
Catastrophe-dispersion models in random and varying environments across generations
This paper analyzes branching processes with catastrophe and dispersal in varying environments, showing survival is tied to the log-mean process.
Inferring Phylogenetic Networks from Allowed and Forbidden LCA-Constraints
This paper introduces polynomial-time algorithms to infer phylogenetic networks from both required and forbidden least common ancestor (LCA) constraints.
Tree-Conditioned Edit Flows for Ancestral Sequence Reconstruction
A new tree-conditioned edit-flow model reconstructs ancestral protein sequences, effectively handling insertions and deletions, unlike classical ASR methods.
From Individual-Based Models to Macroscopic Dynamics of Antimicrobial Resistance
This paper introduces a kinetic framework using Boltzmann and Fokker-Planck equations to model and quantify antimicrobial resistance spread.
Connecting IBD tracts and runs of homozygosity: A coalescent framework for inferring effective population size
This paper unifies IBD tracts and runs of homozygosity (ROH) within a coalescent framework to infer effective population size, accounting for various genetic factors.
A temperature-driven diffusion model of Usutu virus spread in Germany with spillover into neighbouring countries
A temperature-driven reaction-diffusion model accurately simulates the unique clockwise spread of Usutu virus in Germany and neighboring countries.
Epistatic strength, modularity, and locus heterogeneity shape the number of local optima in fitness landscapes
This paper reveals how epistatic strength, modularity, and locus heterogeneity determine the number of local optima in fitness landscapes.
Genealogical structures under interactive neutral reproduction: factorial moment duality via a Frankenstein process
This paper introduces a 'Frankenstein process' to genealogically explain moment duality in a novel interactive Moran model.
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