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 …

From molecules to populations: appreciating and estimating recombination rate variation

JV Peñalba, JBW Wolf - Nature Reviews Genetics, 2020 - nature.com
Recombination is a central biological process with implications for many areas in the life
sciences. Yet we are only beginning to appreciate variation in the recombination rate along …

Genome-wide analyses of introgression between two sympatric Asian oak species

R Fu, Y Zhu, Y Liu, Y Feng, RS Lu, Y Li, P Li… - Nature Ecology & …, 2022 - nature.com
Introgression can be an important source of new alleles for adaption under rapidly changing
environments, perhaps even more important than standing variation. Though introgression …

Contrasting signatures of genomic divergence during sympatric speciation

AF Kautt, CF Kratochwil, A Nater… - Nature, 2020 - nature.com
The transition from 'well-marked varieties' of a single species into 'well-defined species'—
especially in the absence of geographic barriers to gene flow (sympatric speciation)—has …

Resequencing of 145 landmark cultivars reveals asymmetric sub-genome selection and strong founder genotype effects on wheat breeding in China

C Hao, C Jiao, J Hou, T Li, H Liu, Y Wang, J Zheng… - Molecular plant, 2020 - cell.com
Controlled pedigrees and the multi-decade timescale of national crop plant breeding
programs offer a unique experimental context for examining how selection affects plant …

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

JL Legras, V Galeote, F Bigey… - Molecular biology …, 2018 - academic.oup.com
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also
frequently associated with human activities. Despite recent insights into the phylogeny of this …

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 …

Whole-genome resequencing of a worldwide collection of rapeseed accessions reveals the genetic basis of ecotype divergence

D Wu, Z Liang, T Yan, Y Xu, L Xuan, J Tang, G Zhou… - Molecular plant, 2019 - cell.com
Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate
zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and …

Hybrid speciation via inheritance of alternate alleles of parental isolating genes

Z Wang, Y Jiang, H Bi, Z Lu, Y Ma, X Yang, N Chen… - Molecular plant, 2021 - cell.com
It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change
in chromosome number, is an important mechanism of speciation. HHS will likely increase in …

The origin of domestication genes in goats

Z Zheng, X Wang, M Li, Y Li, Z Yang, X Wang… - Science …, 2020 - science.org
Goat domestication was critical for agriculture and civilization, but its underlying genetic
changes and selection regimes remain unclear. Here, we analyze the genomes of …