Inference and applications of ancestral recombination graphs

R Nielsen, AH Vaughn, Y Deng - Nature Reviews Genetics, 2025‏ - nature.com
Ancestral recombination graphs (ARGs) summarize the complex genealogical relationships
between individuals represented in a sample of DNA sequences. Their use is currently …

Thinking about the evolution of complex traits in the era of genome-wide association studies

G Sella, NH Barton - Annual review of genomics and human …, 2019‏ - annualreviews.org
Many traits of interest are highly heritable and genetically complex, meaning that much of
the variation they exhibit arises from differences at numerous loci in the genome. Complex …

Variable prediction accuracy of polygenic scores within an ancestry group

H Mostafavi, A Harpak, I Agarwal, D Conley… - elife, 2020‏ - elifesciences.org
Fields as diverse as human genetics and sociology are increasingly using polygenic scores
based on genome-wide association studies (GWAS) for phenotypic prediction. However …

A method for genome-wide genealogy estimation for thousands of samples

L Speidel, M Forest, S Shi, SR Myers - Nature genetics, 2019‏ - nature.com
Abstract Knowledge of genome-wide genealogies for thousands of individuals would
simplify most evolutionary analyses for humans and other species, but has remained …

The promise of inferring the past using the ancestral recombination graph

DYC Brandt, CD Huber, CWK Chiang… - Genome biology and …, 2024‏ - academic.oup.com
The ancestral recombination graph (ARG) is a structure that represents the history of
coalescent and recombination events connecting a set of sequences (Hudson RR. In …

An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

AJ Stern, PR Wilton, R Nielsen - PLoS Genetics, 2019‏ - journals.plos.org
Most current methods for detecting natural selection from DNA sequence data are limited in
that they are either based on summary statistics or a composite likelihood, and as a …

Landmarks in the history of selective sweeps

M Panigrahi, D Rajawat, SS Nayak, K Ghildiyal… - Animal …, 2023‏ - Wiley Online Library
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh
inaugurated the concept of the selection signature. Selective sweeps are characterised by …

[HTML][HTML] Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population

H Luo, P Zhang, W Zhang, Y Zheng, D Hao, Y Shi… - Science Bulletin, 2023‏ - Elsevier
Characterizing natural selection signatures and relationships with phenotype spectra is
important for understanding human evolution and both biological and pathological …

Disentangling selection on genetically correlated polygenic traits via whole-genome genealogies

AJ Stern, L Speidel, NA Zaitlen, R Nielsen - The American Journal of …, 2021‏ - cell.com
We present a full-likelihood method to infer polygenic adaptation from DNA sequence
variation and GWAS summary statistics to quantify recent transient directional selection …

Polygenic adaptation after a sudden change in environment

LK Hayward, G Sella - Elife, 2022‏ - elifesciences.org
Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we
model this process analytically, in the plausible setting of a highly polygenic, quantitative …