Minor allele frequency thresholds strongly affect population structure inference with genomic data sets

E Linck, CJ Battey - Molecular Ecology Resources, 2019 - Wiley Online Library
A common method of minimizing errors in large DNA sequence data sets is to drop variable
sites with a minor allele frequency (MAF) below some specified threshold. Although …

Next-generation data filtering in the genomics era

W Hemstrom, JA Grummer, G Luikart… - Nature Reviews …, 2024 - nature.com
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology,
evolution and human health. However, these datasets often contain noise or errors and are …

Faster‐X evolution: Theory and evidence from Drosophila

B Charlesworth, JL Campos, BC Jackson - Molecular ecology, 2018 - Wiley Online Library
A faster rate of adaptive evolution of X‐linked genes compared with autosomal genes can
be caused by the fixation of recessive or partially recessive advantageous mutations, due to …

Evolutionary genomics of a subdivided species

T Maruki, Z Ye, M Lynch - Molecular biology and evolution, 2022 - academic.oup.com
The ways in which genetic variation is distributed within and among populations is a key
determinant of the evolutionary features of a species. However, most comprehensive studies …

The effect of balancing selection on population differentiation: a study with HLA genes

DYC Brandt, J César, J Goudet… - G3: Genes, Genomes …, 2018 - academic.oup.com
Balancing selection is defined as a class of selective regimes that maintain polymorphism
above what is expected under neutrality. Theory predicts that balancing selection reduces …

Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

KW Kim, BC Jackson, H Zhang, DPL Toews… - Nature …, 2019 - nature.com
Colour polymorphisms play a key role in sexual selection and speciation, yet the
mechanisms that generate and maintain them are not fully understood. Here, we use …

Genomic differentiation across the speciation continuum in three hummingbird species pairs

EC Henderson, A Brelsford - BMC Evolutionary Biology, 2020 - Springer
Background The study of speciation has expanded with the increasing availability and
affordability of high-resolution genomic data. How the genome evolves throughout the …

High nucleotide diversity accompanies differential DNA methylation in naturally diverging populations

J Ord, TI Gossmann… - Molecular biology and …, 2023 - academic.oup.com
Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an
invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic …

CYSTM, a Novel Non-Secreted Cysteine-Rich Peptide Family, Involved in Environmental Stresses in Arabidopsis thaliana

Y Xu, Z Yu, D Zhang, J Huang, C Wu… - Plant and Cell …, 2018 - academic.oup.com
The cysteine-rich transmembrane module (CYSTM) is comprised of a small molecular
protein family that is found in a diversity of tail-anchored membrane proteins across …

Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna

PD Fields, S McTaggart, CMO Reisser… - Molecular Biology …, 2022 - academic.oup.com
Daphnia are well-established ecological and evolutionary models, and the interaction
between D. magna and its microparasites is widely considered a paragon of the host …