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 …

Sequencing pools of individuals—mining genome-wide polymorphism data without big funding

C Schlötterer, R Tobler, R Kofler, V Nolte - Nature Reviews Genetics, 2014 - nature.com
The analysis of polymorphism data is becoming increasingly important as a complementary
tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs …

Genome sequencing and population genomics in non-model organisms

H Ellegren - Trends in ecology & evolution, 2014 - cell.com
High-throughput sequencing technologies are revolutionizing the life sciences. The past 12
months have seen a burst of genome sequences from non-model organisms, in each case …

Ten years of landscape genetics

S Manel, R Holderegger - Trends in ecology & evolution, 2013 - cell.com
Landscape genetics is now ten years old. It has stimulated research into the effect of
landscapes on evolutionary processes. This review describes the main topics that have …

Exploring population size changes using SNP frequency spectra

X Liu, YX Fu - Nature genetics, 2015 - nature.com
Inferring demographic history is an important task in population genetics. Many existing
inference methods are based on predefined simplified population models, which are more …

Robust identification of local adaptation from allele frequencies

T Günther, G Coop - Genetics, 2013 - academic.oup.com
Comparing allele frequencies among populations that differ in environment has long been a
tool for detecting loci involved in local adaptation. However, such analyses are complicated …

Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping

M Gautier, J Foucaud, K Gharbi, T Cézard… - Molecular …, 2013 - Wiley Online Library
Molecular markers produced by next‐generation sequencing (NGS) technologies are
revolutionizing genetic research. However, the costs of analysing large numbers of …

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA …

M Kapun, MG Barrón, F Staubach… - Molecular Biology …, 2020 - academic.oup.com
Genetic variation is the fuel of evolution, with standing genetic variation especially important
for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of …

Population genomics from pool sequencing

L Ferretti, SE Ramos‐Onsins… - Molecular …, 2013 - Wiley Online Library
Next generation sequencing of pooled samples is an effective approach for studies of
variability and differentiation in populations. In this paper we provide a comprehensive set of …

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

D Liu, Z Chen, W Zhao, L Guo, H Sun, K Zhu, G Liu… - BMC genomics, 2021 - Springer
Background Over several decades, a wide range of natural and artificial selection events in
response to subtropical environments, intensive pasture and intensive feedlot systems have …