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High-throughput directed evolution produces longitudinal sequence libraries that are ideal for probing local fitness neighborhoods but often underpowered for global inference tasks such as contact pre...

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Pedigree and crossing experiments can measure crossovers directly and provide the gold standard for recombination mapping, but their cost restricts fine-scale recombination mapping to only a few speci...

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Abstract. Population genomics has transformed our understanding of how natural selection shapes plant genomes. The explosion of whole-genome resequencing d

Flexible, scalable, QTL analyses using generalized linear models implemented in JAX - mancusolab/jaxqtl

Nature Human Behaviour, Published online: 17 August 2026; doi:10.1038/s41562-026-02556-8Reconstructing parental haplotypes for up to 440,209 UK and Estonian Biobank participants, the authors estimate genetic assortative mating across 69 traits and find that assortment for height and education has intensified in recent generations.

Mathematically integrating genetics, development, and evolution is a longstanding challenge. A prevalent approach is quantitative genetics underpinned by the infinitesimal model, which considers a sim...

The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations)...

Many questions in population genetics are concerned with reconstructing evolutionary history through time, such as inferring how population structure has changed throughout the past. Yet, many existing approaches have only an implicit temporal component, using quantities such as allele frequency or haplotype length as rough proxies for age. Recent advances in the inference of Ancestral Recombination Graphs (ARGs) have made it possible to estimate the entire sequence of local genealogies along the genome. These genealogies explicitly encode how samples are related to each other at different time points in the past, enabling the inference of how population structure has changed over time. To this end, recent work has used ARGs to define time-stratified versions of widely-used population genetics summary statistics in an attempt to capture the population structure present within a particular time window. Here, we show that naive approaches result in statistics that cannot be interpreted solely in terms of the population structure present within the time window they are targeting. To address this problem, we introduce a framework of coalescent-based time-stratified statistics, which use coalescence probabilities to partition classical summary statistics into interval-specific contributions. Using coalescent simulations, we demonstrate that these statistics accurately isolate population structure at different temporal depths and avoid spurious signals. Our results highlight the necessity of integrating coalescent theory into ARG-based temporal analyses and provide a principled and practical foundation for studying the dynamics of population structure through time. ### Competing Interest Statement The authors have declared no competing interest. National Human Genome Research Institute, https://ror.org/00baak391, R01HG014005

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The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations)...

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Abstract. Standard methods for estimating the population recombination parameter, ρ, are dependent on sampling individual genotypes and calculating various

Genotype matrix IO for Python.

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