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 …

Harnessing deep learning for population genetic inference

X Huang, A Rymbekova, O Dolgova, O Lao… - Nature Reviews …, 2024 - nature.com
In population genetics, the emergence of large-scale genomic data for various species and
populations has provided new opportunities to understand the evolutionary forces that drive …

SLiM 4: multispecies eco-evolutionary modeling

BC Haller, PW Messer - The American Naturalist, 2023 - journals.uchicago.edu
The SLiM software framework for genetically explicit forward simulation has been widely
used in population genetics. However, it has been largely restricted to modeling only a …

On the limits of fitting complex models of population history to f-statistics

R Maier, P Flegontov, O Flegontova, U Işıldak… - Elife, 2023 - elifesciences.org
Our understanding of population history in deep time has been assisted by fitting admixture
graphs (AGs) to data: models that specify the ordering of population splits and mixtures …

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

W Hu, Z Hao, P Du, F Di Vincenzo, G Manzi, J Cui… - Science, 2023 - science.org
Population size history is essential for studying human evolution. However, ancient
population size history during the Pleistocene is notoriously difficult to unravel. In this study …

A weakly structured stem for human origins in Africa

AP Ragsdale, TD Weaver, EG Atkinson, EG Hoal… - Nature, 2023 - nature.com
Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty
surrounds specific models of divergence and migration across the continent. Progress is …

The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes

C Sommer-Trembo, ME Santos, B Clark, M Werner… - Science, 2024 - science.org
Behavior is critical for animal survival and reproduction, and possibly for diversification and
evolutionary radiation. However, the genetics behind adaptive variation in behavior are …

The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics

AL Lewanski, MC Grundler, GS Bradburd - Plos Genetics, 2024 - journals.plos.org
In the presence of recombination, the evolutionary relationships between a set of sampled
genomes cannot be described by a single genealogical tree. Instead, the genomes are …

[PDF][PDF] Deep learning in population genetics

K Korfmann, OE Gaggiotti… - Genome Biology and …, 2023 - academic.oup.com
Population genetics is transitioning into a data-driven discipline thanks to the availability of
large-scale genomic data and the need to study increasingly complex evolutionary …

A general and efficient representation of ancestral recombination graphs

Y Wong, A Ignatieva, J Koskela, G Gorjanc… - Genetics, 2024 - academic.oup.com
As a result of recombination, adjacent nucleotides can have different paths of genetic
inheritance and therefore the genealogical trees for a sample of DNA sequences vary along …