Supervised machine learning for population genetics: a new paradigm

DR Schrider, AD Kern - Trends in Genetics, 2018 - cell.com
As population genomic datasets grow in size, researchers are faced with the daunting task
of making sense of a flood of information. To keep pace with this explosion of data …

Effects of selection at linked sites on patterns of genetic variability

B Charlesworth, JD Jensen - Annual review of ecology …, 2021 - annualreviews.org
Patterns of variation and evolution at a given site in a genome can be strongly influenced by
the effects of selection at genetically linked sites. In particular, the recombination rates of …

Going global by adapting local: A review of recent human adaptation

S Fan, MEB Hansen, Y Lo, SA Tishkoff - Science, 2016 - science.org
The spread of modern humans across the globe has led to genetic adaptations to diverse
local environments. Recent developments in genomic technologies, statistical analyses, and …

Deep learning for population genetic inference

S Sheehan, YS Song - PLoS computational biology, 2016 - journals.plos.org
Given genomic variation data from multiple individuals, computing the likelihood of complex
population genetic models is often infeasible. To circumvent this problem, we introduce a …

The unreasonable effectiveness of convolutional neural networks in population genetic inference

L Flagel, Y Brandvain… - Molecular biology and …, 2019 - academic.oup.com
Population-scale genomic data sets have given researchers incredible amounts of
information from which to infer evolutionary histories. Concomitant with this flood of data …

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

PA Gagnaire, T Broquet, D Aurelle… - Evolutionary …, 2015 - Wiley Online Library
Estimating the rate of exchange of individuals among populations is a central concern to
evolutionary ecology and its applications to conservation and management. For instance …

Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation

J Hermisson, PS Pennings - Methods in Ecology and Evolution, 2017 - Wiley Online Library
The tempo and mode of adaptive evolution determine how natural selection shapes patterns
of genetic diversity in DNA polymorphism data. While slow mutation‐limited adaptation …

Soft sweeps are the dominant mode of adaptation in the human genome

DR Schrider, AD Kern - Molecular biology and evolution, 2017 - academic.oup.com
The degree to which adaptation in recent human evolution shapes genetic variation remains
controversial. This is in part due to the limited evidence in humans for classic “hard selective …

S/HIC: robust identification of soft and hard sweeps using machine learning

DR Schrider, AD Kern - PLoS genetics, 2016 - journals.plos.org
Detecting the targets of adaptive natural selection from whole genome sequencing data is a
central problem for population genetics. However, to date most methods have shown sub …

[PDF][PDF] Predicting the landscape of recombination using deep learning

JR Adrion, JG Galloway, AD Kern - Molecular biology and …, 2020 - academic.oup.com
Accurately inferring the genome-wide landscape of recombination rates in natural
populations is a central aim in genomics, as patterns of linkage influence everything from …