Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking

HD Daetwyler, MPL Calus, R Pong-Wong… - Genetics, 2013 - academic.oup.com
The genomic prediction of phenotypes and breeding values in animals and plants has
developed rapidly into its own research field. Results of genomic prediction studies are often …

Identification of management units using population genetic data

PJ Palsbøll, M Berube, FW Allendorf - Trends in ecology & evolution, 2007 - cell.com
The identification of management units (MUs) is central to the management of natural
populations and is crucial for monitoring the effects of human activity upon species …

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 …

pcadapt: an R package to perform genome scans for selection based on principal component analysis

K Luu, E Bazin, MGB Blum - Molecular ecology resources, 2017 - Wiley Online Library
The r package pcadapt performs genome scans to detect genes under selection based on
population genomic data. It assumes that candidate markers are outliers with respect to how …

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

T Mock, RP Otillar, J Strauss, M McMullan, P Paajanen… - Nature, 2017 - nature.com
Abstract The Southern Ocean houses a diverse and productive community of organisms,.
Unicellular eukaryotic diatoms are the main primary producers in this environment, where …

Genome-wide scan for adaptive divergence and association with population-specific covariates

M Gautier - Genetics, 2015 - academic.oup.com
In population genomics studies, accounting for the neutral covariance structure across
population allele frequencies is critical to improve the robustness of genome-wide scan …

Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests

KE Lotterhos, MC Whitlock - Molecular ecology, 2014 - Wiley Online Library
FST outlier tests are a potentially powerful way to detect genetic loci under spatially
divergent selection. Unfortunately, the extent to which these tests are robust to …

Effects of overlapping generations on linkage disequilibrium estimates of effective population size

RS Waples, T Antao, G Luikart - Genetics, 2014 - academic.oup.com
Use of single-sample genetic methods to estimate effective population size has skyrocketed
in recent years. Although the underlying models assume discrete generations, they are …

Detection of human adaptation during the past 2000 years

Y Field, EA Boyle, N Telis, Z Gao, KJ Gaulton, D Golan… - Science, 2016 - science.org
Detection of recent natural selection is a challenging problem in population genetics. Here
we introduce the singleton density score (SDS), a method to infer very recent changes in …

Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

RK Waples, WA Larson, RS Waples - Heredity, 2016 - nature.com
Contemporary effective population size (N e) can be estimated using linkage disequilibrium
(LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This …