Peter L. Ralph

Ecotypes, Wolbachia, and urbanization shape Culex pipiens population structure in a West Nile virus hotspot

The paper analyzes population structure in Culex pipiens using genomic data from a WNV hotspot, finding that ecotypes, Wolbachia infection, and habitat type drive genetic variation.

Genetic prediction with ARG-powered linear algebra

The paper develops a method to estimate variance components and predict genetic values using ancestral recombination graphs (ARGs) and linear mixed models on large datasets.

Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs

The paper develops a scalable method to estimate allele ages from large genomic datasets, revealing purifying selection and heterogeneity in ultra-rare variants.

SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes

SLiM 5 extends the simulation framework to support multiple chromosomes, enabling full-genome simulations with various chromosome types.

Simulation-based spatially explicit close-kin mark-recapture

The paper introduces a simulation-based CKMR method, CKMRnn, that improves population size estimation by accounting for spatial heterogeneity and demonstrates its accuracy using Ugandan elephant data.

On ARGs, pedigrees, and genetic relatedness matrices

This paper introduces branch relatedness and efficient algorithms for computing branch GRMs using tree sequences, enabling large-scale genomic analysis.

Bridging forward-in-time and coalescent simulations using pyslim

The paper introduces the use of tree sequences from the forwards simulator SLiM to enable interoperability between forward-in-time and coalescent simulations.

Accessible, realistic genome simulation with selection using stdpopsim

The paper extends the stdpopsim simulation framework to include realistic selection models, enabling studies of selection's impact on genetic variation across species.

A forest is more than its trees: haplotypes and inferred ARGs

The paper introduces a method to insert non-coalescing haplotypes into ancestral recombination graphs (ARGs) and proposes new metrics to compare ARGs based on haplotype relationships.

Quantitative Genetics of Microbiome Mediated Traits

The paper extends quantitative genetic theory to include host-associated microbes as factors influencing phenotypic variation and demonstrates how microbiome-mediated responses to selection can arise from various transmission modes.

Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae

The paper uses spatial simulations to detect selective sweeps in Anopheles gambiae and identifies new variants under selection.

Likelihoods for a general class of ARGs under the SMC

This paper presents a backwards-time formulation of the Sequentially Markov Coalescent (SMC) and derives a likelihood definition for a general class of Ancestral Recombination Graphs (ARGs) without requiring precise recombination event details.

Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes

This paper provides a guide to implementing individual-based simulations in continuous landscapes, focusing on population dynamics and ecological applications.

Estimation of spatial demographic maps from polymorphism data using a neural network

This paper introduces a neural network method to estimate spatial demographic maps from SNP data, showing it can infer population density and dispersal rates across landscapes.

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

The paper introduces slendr, an R package for simulating spatio-temporal population genomic data, and demonstrates its features through example workflows.

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

The paper expands the stdpopsim species catalog and improves genome simulations by adding non-crossover recombination and species-specific annotations, making simulations more realistic for non-model organisms.

link-ancestors: Fast simulation of local ancestry with tree sequence software

The paper introduces an algorithm to efficiently simulate local ancestry tracts from tree sequences, implemented in tskit and tspop.

Efficient ancestry and mutation simulation with msprime 1.0

The paper introduces msprime 1.0, a high-performance simulation tool for ancestry and mutation in population genetics, showing it is faster and more memory efficient than existing alternatives.

Predicting Geographic Location From Genetic Variation with Deep Neural Networks

The paper introduces a deep learning method called Locator to predict geographic locations from genetic variation, achieving high accuracy and speed across different species.

Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes

The paper introduces a framework to efficiently compute population genetic statistics using genealogical trees, showing significant computational improvements over traditional methods.

Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data

This study investigates how continuous spatial structure affects population genetic analysis, finding biases in summary statistics, demographic inference, and GWAS when using discrete models.

Local PCA shows how the effect of population structure differs along the genome

The paper applies local PCA to genomic data from three species, showing population structure effects vary across genomic regions, likely due to linked selection and chromosomal inversions.

Efficient pedigree recording for fast population genetics simulation

This paper introduces an efficient method for recording and simplifying genetic history in population genetics simulations, reducing storage and computational costs.

Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise

The paper uses genomic data from Mojave desert tortoises to infer demographic parameters in a spatially explicit ecological model, showing a simple statistical method can estimate population density and migration distance within 10% accuracy.