Detecting positive selection in the genome

TR Booker, BC Jackson, PD Keightley - BMC biology, 2017 - Springer
Population geneticists have long sought to understand the contribution of natural selection
to molecular evolution. A variety of approaches have been proposed that use population …

Molecular population genetics

S Casillas, A Barbadilla - Genetics, 2017 - academic.oup.com
Molecular population genetics aims to explain genetic variation and molecular evolution
from population genetics principles. The field was born 50 years ago with the first measures …

The population genetics of structural variants in grapevine domestication

Y Zhou, A Minio, M Massonnet, E Solares, Y Lv… - Nature plants, 2019 - nature.com
Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known
about the type and size of SVs, their distribution among individuals and, especially, their …

Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data

P Tataru, M Mollion, S Glémin, T Bataillon - Genetics, 2017 - academic.oup.com
The distribution of fitness effects (DFE) encompasses the fraction of deleterious, neutral, and
beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the …

On the prospect of achieving accurate joint estimation of selection with population history

P Johri, A Eyre-Walker, RN Gutenkunst… - Genome biology and …, 2022 - academic.oup.com
As both natural selection and population history can affect genome-wide patterns of
variation, disentangling the contributions of each has remained as a major challenge in …

Ape origins of human malaria

PM Sharp, LJ Plenderleith… - Annual review of …, 2020 - annualreviews.org
African apes harbor at least twelve Plasmodium species, some of which have been a source
of human infection. It is now well established that Plasmodium falciparum emerged following …

Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site

PD Keightley, BC Jackson - Genetics, 2018 - academic.oup.com
It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned
with certainty, and that the most frequently used method to assign the ancestral state …

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development

H Zhang, S Dou, F He, J Luo, L Wei, J Lu - PLoS biology, 2018 - journals.plos.org
Upstream open reading frames (uORFs) play important roles in regulating the main coding
DNA sequences (CDSs) via translational repression. Despite their prevalence in the …

Deleterious variants in Asian rice and the potential cost of domestication

Q Liu, Y Zhou, PL Morrell, BS Gaut - Molecular Biology and …, 2017 - academic.oup.com
Many SNPs are predicted to encode deleterious amino acid variants. These slightly
deleterious mutations can provide unique insights into population history, the dynamics of …

Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites

DE Loy, LJ Plenderleith… - Proceedings of the …, 2018 - National Acad Sciences
Wild-living African apes are endemically infected with parasites that are closely related to
human Plasmodium vivax, a leading cause of malaria outside Africa. This finding suggests …