A survey of methods and tools to detect recent and strong positive selection

P Pavlidis, N Alachiotis - Journal of Biological Research-Thessaloniki, 2017 - Springer
Positive selection occurs when an allele is favored by natural selection. The frequency of the
favored allele increases in the population and due to genetic hitchhiking the neighboring …

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

A Bissett, A Fitzgerald, T Meintjes, PM Mele, F Reith… - GigaScience, 2016 - Springer
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …

Inferring signatures of positive selection in whole-genome sequencing data: an overview of haplotype-based methods

P Abondio, E Cilli, D Luiselli - Genes, 2022 - mdpi.com
Signatures of positive selection in the genome are a characteristic mark of adaptation that
can reveal an ongoing, recent, or ancient response to environmental change throughout the …

Using population genomics to detect selection in natural populations: key concepts and methodological considerations

PA Hohenlohe, PC Phillips… - International journal of …, 2010 - journals.uchicago.edu
Natural selection shapes patterns of genetic variation among individuals, populations, and
species, and it does so differentially across genomes. The field of population genomics …

Assessing genomic selection prediction accuracy in a dynamic barley breeding population

AH Sallam, JB Endelman, JL Jannink… - The Plant …, 2015 - Wiley Online Library
Prediction accuracy of genomic selection (GS) has been previously evaluated through
simulation and cross‐validation; however, validation based on progeny performance in a …

Industrial melanism in British peppered moths has a singular and recent mutational origin

AE van't Hof, N Edmonds, M Dalíková, F Marec… - Science, 2011 - science.org
The rapid spread of a novel black form (known as carbonaria) of the peppered moth Biston
betularia in 19th-century Britain is a textbook example of how an altered environment may …

Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations

P Pavlidis, JD Jensen, W Stephan - Genetics, 2010 - academic.oup.com
A major goal of population genomics is to reconstruct the history of natural populations and
to infer the neutral and selective scenarios that can explain the present-day polymorphism …

Linkage disequilibrium between rare mutations

BH Good - Genetics, 2022 - academic.oup.com
The statistical associations between mutations, collectively known as linkage disequilibrium,
encode important information about the evolutionary forces acting within a population. Yet in …

Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

M Ben Hassen, TV Cao, J Bartholome… - Theoretical and Applied …, 2018 - Springer
Key message Rice breeding programs based on pedigree schemes can use a genomic
model trained with data from their working collection to predict performances of progenies …

Genomic signatures of reinforcement

AG Garner, BE Goulet, MC Farnitano… - Genes, 2018 - mdpi.com
Reinforcement is the process by which selection against hybridization increases
reproductive isolation between taxa. Much research has focused on demonstrating the …