The Genome-Wide Effect of Drift and Selection over a Single Generation

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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Coalescent-Based Time-Stratified Statistics Reveal Population Structure Dynamics using the Ancestral Recombination Graph

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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Joint dog and wolf genealogies reveal the evolution of the canine genome

Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close ...

biorxiv.org

Joint dog and wolf genealogies reveal the evolution of the canine genome

Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close ...

biorxiv.org

Research Associate in Population Genetics Modelling and Environmental DNA (Fixed Term) - Job Opportunities - University of Cambridge

Research Associate in Population Genetics Modelling and Environmental DNA (Fixed Term) in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.

jobs.cam.ac.uk

Rapid adaptive increase of amylase gene copy number in Indigenous Andeans - Nature Communications

The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...

doi.org

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biorxiv.org

Seeking a few Senior Research Scientists, Research Scientists, Postdoctoral Researchers at Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical...

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Seeking a few Postdoctoral Researchers at Mathematical Genomics RIKEN ECL Research Unit (25-695)

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Senior Research Associate in Population Genomics (RA2327) in University of East Anglia | UEA

View details and apply for this Senior Research Associate in Population Genomics (RA2327) vacancy in University of East Anglia. Faculty of Science School of Biological Sciences Senior Research A...

vacancies.uea.ac.uk

Not Just $N_e$ $N_e$-more: New Applications for SMC from Ecology to Phylogenies

Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Ma...

arxiv.org

Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever

Several bacterial pathogens have transitioned from tick-borne to louse-borne transmission, which often involves genome reduction and increasing virulence. However, the timing of such transitions remai...

science.org

A structured coalescent model reveals deep ancestral structure shared by all modern humans - Nature Genetics

The cobraa model extends the pairwise sequentially Markovian coalescent to identify structured population history by examination of the model transition matrix. Applied to human polymorphism data, cob...

nature.com

Assistant/Associate Professor in Computational Biology - Job Opportunities - University of Cambridge

Assistant/Associate Professor in Computational Biology in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.

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Cephalopod sex determination and its ancient evolutionary origin

Octopuses, squids, and cuttlefishes—the coleoid cephalopods—are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisti…

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Ancient genomics and the origin, dispersal, and development of domestic sheep

The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Ge...

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A putative ecocline in Klebsiella pneumoniae

Are quantitative traits important for bacteriology? The quantitative trait models used in animal and plant genetics assume that the trait takes continuous values and is influenced by many variants cir...

biorxiv.org