NCBI Literature Search MCP Server

Recent Papers on Fitness Effects Inference (2023-2025)
Based on my search across the four strategies you specified, here are the most recent papers from 2023-2025:
Strategy 1: "Selective forces site frequency spectrum"
No papers from 2023-2025 in top results.
Strategy 2: "Mutation fitness effects inference"
2023-2025 Papers:

Soni et al. (2024) - "The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects"

Genome Biology and Evolution, 2024-Feb
PMID: 38207127
Examines how unaccounted rate heterogeneity impacts DFE and demographic inference using tools like DFE-alpha, Grapes, and polyDFE


Crombie et al. (2024) - "Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred Caenorhabditis elegans mutation accumulation lines"

Genetics, 2024-Oct
PMID: 39139098
Uses recombinant inbred lines to reduce linkage disequilibrium and infer DFE, finding conventional wisdom about mostly neutral/negative effects is likely correct


Weinstock et al. (2023) - "Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis"

Nature, 2023-Apr
PMID: 37046083
Studies mutations that increase HSC fitness leading to clonal hematopoiesis


Soni et al. (2023) - "The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects" [Preprint]

bioRxiv, 2023-Nov
PMID: 38014252
Earlier preprint version of the above study



Strategy 3: "Site frequency ratio fitness"
2023-2025 Papers:

Hey & Pavinato (2025) - "Isolating selective from non-selective forces using site frequency ratios"

PLoS Genetics, 2025-Apr (in press)
PMID: 40258089
Novel method using site frequency ratios to estimate DFE while avoiding non-selective demographic effects


Onerup et al. (2023) - "Associations between cardiorespiratory fitness in youth and the incidence of site-specific cancer in men: a cohort study with register linkage"

British Journal of Sports Medicine, 2023-Oct
PMID: 37582636
Epidemiological study on fitness and cancer risk


Onerup et al. (2023) - "Cardiorespiratory fitness and BMI measured in youth and 5-year mortality after site-specific cancer diagnoses in men"

Cancer Medicine, 2023-Oct
PMID: 37732468
Follow-up study on fitness measures and cancer outcomes


Zatloukal et al. (2024) - "The Association Between C24:0/C16:0 Ceramide Ratio and Cardiorespiratory Fitness is Robust to Effect Modifications by Age and Sex"

Advanced Biology, 2024-Apr
PMID: 38342586
Biochemical study of ceramides and fitness associations



Strategy 4: "DFE population genomics"
No papers from 2023-2025 in top results.
Key Recent Methodological Advances (2023-2025):

Site Frequency Ratios Method (Hey & Pavinato 2025): Novel approach using ratios of selected to neutral sites to avoid demographic confounding effects when estimating DFE.
Accounting for Rate Heterogeneity (Soni et al. 2024): Demonstrates how unmodeled mutation and recombination rate variation can bias DFE inference, emphasizing need for better parameter modeling.
Linkage Disequilibrium Effects (Crombie et al. 2024): Uses recombinant inbred lines to show how LD between mutations can lead to overestimation of positive fitness effects in DFE inference.

These recent papers highlight ongoing challenges in DFE inference, particularly around demographic confounding, rate heterogeneity, and linkage effects, while proposing new methodological solutions.