Open research questions in Evolution and Genetic Dynamics
133 unresolved questions extracted from the limitations and future-work sections of 581 Evolution and Genetic Dynamics papers in our library. Each links back to the study that raised it.
What the literature leaves open
The exception is a variant in MUTYH, which is more common than predicted under plausible parameters, for reasons that remain unclear.
These results provide limited evidence for a general relationship between epidemic size and host-parasite (co)-evolution and instead suggest that evolutionary responses depend on the host-parasite system and broader ecological and temporal context.
The size of an epidemic can influence the strength of selection acting on hosts and parasites, but whether epidemic size consistently shapes host-parasite (co)-evolution remains unclear.
While the ecological roles and beneficial function of plant microbiomes are increasingly well understood, the evolutionary dynamics that shape them over time remain unclear.
Continental-scale understanding of such compound locust risks and underlying climatic drivers is crucial to designing coordinated and predictive control strategies but remains elusive.
Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multigenerational series of patterns of selection on a genome-wide scale in natural populations.
Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate-as a trait-remains to be accurately described.
Reproducing such correlations through appropriate population models remains an open challenge.
Sparse species interactions reproduce abundance correlation patterns in microbial communities · 2024 · DOIHowever, bacterial evolution experiments for testing these predictions are lacking.
However, the impact of surface irregularities on the population dynamics of biofilms remains elusive, as most experiments are conducted on flat surfaces.
When multiple resources are scarce, as frequently occurs in nature, microbes may experience resource colimitation in which more than one resource simultaneously limits growth.
Methods that jointly estimate the reproduction number R and the dispersion parameter k have however mainly remained limited to the analysis of epidemiological clusters or contact tracing data, whose collection often proves difficult.
Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences · 2024 · DOIAlthough adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence.
Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes · 2024 · DOIHowever, how this "developmental bias" can influence micro- and macroevolution is poorly understood.
The proof assumes specific equilibrium conditions (coexistence conditions like Coex2,3) hold, but the sensitivity analysis of how violations or perturbations to these conditions affect the emergence of dormancy is not addressed.
The proof relies on standard Freidlin–Wentzell type large-deviation arguments originating from prior work (Champagnat 2006; Coron et al. 2021), but the construction of coupling and adaptation to this specific multi-type model with viral lysis-induced death requires further detailed verification beyond what is presented.
The application of Deep Learning methods for population genomics inference. The integration of several types of genetic and epigenetic markers for evolutionary inference. The study of eco-evo feedback processes in multi-species systems.
Genomic perspectives on the inference of evolutionary changes in ecological life-history traits · 2026 · DOIMost theories and methods remain based on human life-history traits and genome characteristics. There is a need for new methods that can account for life-history traits in non-human species.
Genomic perspectives on the inference of evolutionary changes in ecological life-history traits · 2026 · DOITraditional thinking has treated lethal mutagenesis as a mean-field phenomenon, assuming that descendant genome copies incur similar numbers of errors. This assumption may not hold true.
Rethinking viral evolution: How BIAS mechanisms and Gamma-Poisson overdispersion redefine lethal mutagenesis · 2026 · DOIThe study only examined the effects of temperature on host-parasite interactions in a single host species. The study did not examine the effects of other environmental factors on host-parasite interactions. The study used a limited number of parasite species.
The impacts of coinfecting parasites on disease in the presence of environmental change, such as temperature, are unclear. There is a need to investigate the effects of temperature on host-parasite interactions in the presence of coinfections.
The emergence and spread of insecticide resistance in mosquito populations. The need for sustainable vector control strategies. The complexity of modeling the evolutionary mechanisms driving insecticide resistance.
Modelling the evolutionary dynamics of insecticide quantitative resistance in mosquito populations · 2026 · DOIThe emergence of insecticide resistance in mosquito populations threatens the gains made in reducing malaria incidence. There is a need for a novel mathematical framework to investigate the emergence and spread of insecticide resistance in mosquito populations.
Modelling the evolutionary dynamics of insecticide quantitative resistance in mosquito populations · 2026 · DOIThe importance and generality of mutation-biased adaptation remain unclear due to a lack of empirical tests. There is a lack of understanding of how mutation-biased adaptation scales with population size.
The model assumes a one-dimensional habitat. The model assumes reflecting boundary conditions. The paper does not address the effect of strong disturbances such as rapid high-amplitude climate changes.
Environmental “knees” and “wiggles” as strong stabilizers of species’ range limits set by interspecific competition · 2026 · DOI
Most-cited papers in Evolution and Genetic Dynamics
- The Evolutionary Fate and Consequences of Duplicate Genes · Science · 2000 · 3,887 citations
- Evolutionary Rate at the Molecular Level · Nature · 1968 · 2,732 citations
- Metapopulation dynamics · Nature · 1998 · 2,500 citations
- What Is Migration? · BioScience · 2007 · 987 citations
- The Evolutionary Significance of Phenotypic Plasticity · BioScience · 1989 · 940 citations
- New Computer Models Unify Ecological Theory · BioScience · 1988 · 546 citations
- Probabilistic epigenesis · Developmental Science · 2006 · 516 citations
- Quantifying the local adaptive landscape of a nascent bacterial community · Nature Communications · 2023 · 472 citations
- Developmental Systems and Evolutionary Explanation · The Journal of Philosophy · 1994 · 436 citations
- Mutation bias reflects natural selection in Arabidopsis thaliana · Nature · 2022 · 361 citations
Most recent work
- Replaying germinal center evolution on a quantified affinity landscape · bioRxiv · 2026
- Sex-specific dominance and its effects on allelic diversity in sexually antagonistic loci · bioRxiv · 2026
- Frequency-dependent fitness effects are ubiquitous in rapidly adapting microbial populations · bioRxiv · 2026
- Generative continuous time model reveals epistatic signatures in protein evolution · bioRxiv · 2026
- Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics · bioRxiv · 2026
- Loci under balancing selection facilitate the emergence of pseudo-overdominance and recombination suppression · bioRxiv · 2026
- Patterns of diversity under loose genetic draft · bioRxiv · 2026
- Overestimating zero-shot fitness prediction: Broad benchmarks mask local failures and practical limitations · bioRxiv · 2026
- Beyond adaptive gene transfers: a primer on horizontal gene transfer across scales · Integrative And Comparative Biology · 2026
- Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations · bioRxiv · 2026
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