J. P. Spence

Scaling the Discrete-time Wright Fisher model to biobank-scale datasets

This paper introduces an algorithm to scale the Discrete-Time Wright Fisher model to large datasets, enabling efficient and accurate population genetic inference at biobank scale.

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

This paper validates pool-sequencing for tracking rapid plant population evolution and introduces tools to accelerate population genetic analysis.

Genetic diversity loss in the Anthropocene

The paper introduces a mathematical framework to estimate genetic diversity loss due to habitat reduction and shows that over 10% of genetic diversity may already be lost globally.

Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

The paper infers population-specific recombination maps across 26 human populations, revealing demographic and genetic factors influencing recombination rates.

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks

This paper introduces an exchangeable neural network framework for likelihood-free inference in population genetics, demonstrating superior performance on recombination hotspot testing.

Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans

This study introduces a model-based method to detect Neanderthal introgression in modern humans and finds weak selection against Neanderthal ancestry, possibly due to higher genetic load in Neanderthals.

Inference of complex population histories using whole-genome sequences from multiple populations

The paper introduces diCal2, a statistical method to infer complex population histories from whole-genome sequences, finding that Australian and Papuan populations diverged from East Asians and Europeans around 100,000 years ago with ongoing gene flow.