P. L. Ralph

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.

Genetic architecture, spatial heterogeneity, and the coevolutionary arms race between newts and snakes

The paper uses simulations to explore coevolutionary dynamics between newts and snakes, finding that ecological heterogeneity, not coevolution alone, produces observed spatial patterns of toxin and resistance levels.

Evidence for admixture and rapid evolution during glacial climate change in an alpine specialist

This study investigates the evolutionary history of alpine ground beetles, finding evidence of past admixture and rapid physiological evolution during glacial climate change.

Large effects and the infinitesimal model

The paper examines how the assumption of similar effect sizes in the infinitesimal model affects trait distribution, finding tail exponents between 1 and 2 in human disease-related traits and suggesting non-Gaussian models require explicit genetic tracking for large-effect loci.

Evaluating evidence for co-geography in the Anopheles Plasmodium host-parasite system

The paper evaluates whether spatial genetic correlation between Anopheles gambiae and Plasmodium falciparum indicates co-dispersal or spatial sampling bias.

Shared evolutionary processes shape landscapes of genomic variation in the great apes

This study shows strong correlations between genetic diversity and divergence in great apes, suggesting evolutionary processes like selection and mutation rate variation play a key role.

Dispersal inference from population genetic variation using a convolutional neural network

This paper introduces disperseNN, a convolutional neural network that estimates dispersal distance from genetic data without requiring geographic coordinates, outperforming existing methods in simulations and applied to 12 species.

Enabling inference for context-dependent models of mutation by bounding the propagation of dependency

This paper introduces a method to compute likelihoods for context-dependent mutation models by bounding dependency propagation, enabling phylogenetic inference and providing tools for analysis.

System drift and speciation

The paper models how genetic drift in molecular pathways can lead to speciation through system drift, explaining Haldane's rule and reproductive incompatibility.

Evaluating Human Autosomal Loci for Sexually Antagonistic Viability Selection in Two Large Biobanks

The paper evaluates evidence for sexually antagonistic viability selection on autosomal loci in humans using two large biobanks but finds no significant replication of associations, suggesting limited ongoing selection on single locus variation.

A community-maintained standard library of population genetic models

The paper introduces stdpopsim, a community-maintained library for population genetic models, to standardize simulations and facilitate benchmarking of inference tools.

Limits to Genomic Divergence Under Sexually Antagonistic Selection

This study shows that strong sexually antagonistic selection is needed for measurable sex-specific allelic divergence, and that small samples can falsely inflate male-female genetic differentiation.

A few stickleback suffice for the transport of alleles to new lakes

This study uses simulations to show that gene flow and migration-selection balance maintain adaptive alleles in marine stickleback populations, which are then used by freshwater populations for adaptation.

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

The paper uses whole-genome sequencing and simulations to show that differentiation landscapes in monkeyflowers are shaped by natural selection, adaptation, and gene flow rather than background selection.

Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method

The paper compares resistance distance and coalescence time models for inferring population movement and size, finding coalescence-based methods more accurate in realistic scenarios.

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

The paper implements tree-sequence recording in SLiM 3 to improve computational efficiency and enable new analyses of whole-genome simulations.