Open research questions in Evolution and Genetic Dynamics
367 gap statements mined from Evolution and Genetic Dynamics papers in our 7.9M-paper local library, which holds 1,845 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.
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What the literature leaves open
The lack of understanding of the evolutionary and mechanistic aspects of prey escape from predation. The need to identify the genetic basis of putative resistance mechanisms. The gap in knowledge about the potential of predatory bacteria as a solution to combat AMR.
Such reciprocal phenotypic plasticity can shape the behaviour and evolution of ecological communities, but its genetic architecture remains elusive.
A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions · 2026 · DOIThe intraspecific evolutionary mechanisms of adaptation in blooming cyanobacteria, particularly those occurring on small spatial and temporal scales, remain poorly understood.
Microdiversity drives resilience and niche partitioning in the bloom forming cyanobacteria Limnospira platensis · 2026 · DOIBacterial species span orders of magnitude in growth rate, yet how its evolution is embedded within the broader evolutionary dynamics of other bacterial traits remains poorly understood.
Although non-coding regions play important roles in gene regulation and contribute to individual fitness, the precise distribution of fitness effects (DFE) of new mutations in these regions remains poorly understood.
The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome · 2026 · DOISummarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.
A Concept Using α‐Niche Evolution Within Bacterial Communities to Direct β‐Niche Evolution of Focal Species · 2026 · DOIHowever, the evolutionary repeatability of CS across different experimental conditions and its clinical relevance remain underexplored, hindering its potential for translation into clinical practice.
Large scale laboratory evolution uncovers clinically relevant collateral antibiotic sensitivity · 2025 · DOIHowever, frameworks utilizing these features have not yet been compared and benchmarked.
Population genetic simulation: Benchmarking frameworks for non‐standard models of natural selection · 2024 · DOISummary statement Epigenetic inheritance is hypothesized to lead to rapid adaptation, yet evidence is scarce, possibly because of the current experimental approaches.
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 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.
Finally, it should be noted that the present analysis evaluated migration fraction at a fixed carrying capacity; future work should examine how critical thresholds respond to variation in absolute population size and migrant number, particularly Author Contributions Andrew A.
The 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 lack of a comprehensive mathematical theory of selection by spatial sorting. The need to understand the biological conditions that drive selection at margins.
The permute-match test is limited by the number of replicates (n). The minimum p-value of the trial-swapping permutation test is 1/n!. The paper does not provide a comprehensive evaluation of the permute-match test on various datasets.
Permute-match tests detect significant correlations between time series despite nonstationarity and limited replicates · 2026 · DOIThe analysis assumes a haploid population that is large enough that genetic drift can be ignored. The simulations are limited to a specific model of selective interference. The paper does not consider the effects of other factors that may influence the evolution of recombination.
Future research should investigate the effects of recombination-associated mutation on the evolution of recombination in different species. The paper suggests that studies should examine the relationship between the number of crossovers per chromosome and the rate of recombination-associated mutation.
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.
Traditional 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 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 · DOITo investigate the effect of strong disturbances such as rapid high-amplitude climate changes on the stability of range limits. To study the interaction between environmental nonlinearities and other factors affecting range limits, such as Allee effects.
Environmental “knees” and “wiggles” as strong stabilizers of species’ range limits set by interspecific competition · 2026 · DOIAnswering questions about the entities under selection and how traits are linked to sorting fitness.
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 · DOITo evaluate the performance of the permute-match test on various datasets. To compare the performance of the permute-match test with other statistical tests. To apply the permute-match test to real-world problems in various fields.
Permute-match tests detect significant correlations between time series despite nonstationarity and limited replicates · 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
- Clinically relevant mutations in core metabolic genes confer antibiotic resistance · Science · 2021 · 365 citations
Most recent work
- Spatial structure: shaping the ecology and evolution of microbial communities · FEMS Microbiology Reviews · 2026
- Replaying germinal center evolution on a quantified affinity landscape · bioRxiv · 2026
- The effect of long-range linkage disequilibrium on allele-frequency dynamics under stabilizing selection · PLoS Genetics · 2026
- Additive genetic variance for fitness maintained by balancing selection · Evolution · 2026
- SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements · Bioinformatics · 2026
- Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics · Nature Microbiology · 2026
- Interspecies interaction alters the trajectory of antibiotic resistance evolution by amplifying negative fitness epistasis · The ISME Journal · 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
- Inference and Visualization of Complex Genotype–Phenotype Maps · Molecular Biology and Evolution · 2026
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