Toward an evolutionarily appropriate null model: jointly inferring demography and purifying selection

P Johri, B Charlesworth, JD Jensen - Genetics, 2020 - academic.oup.com
The relative evolutionary roles of adaptive and non-adaptive processes remain a central
question in population genetics. Resolution of this debate has been difficult as an …

The impact of purifying and background selection on the inference of population history: problems and prospects

P Johri, K Riall, H Becher, L Excoffier… - Molecular biology …, 2021 - academic.oup.com
Current procedures for inferring population history generally assume complete neutrality—
that is, they neglect both direct selection and the effects of selection on linked sites. We here …

Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements

DA Murphy, E Elyashiv, G Amster, G Sella - Elife, 2022 - elifesciences.org
Analyses of genetic variation in many taxa have established that neutral genetic diversity is
shaped by natural selection at linked sites. Whether the mode of selection is primarily the …

A quantitative genetic model of background selection in humans

V Buffalo, AD Kern - Plos Genetics, 2024 - journals.plos.org
Author summary Across the human genome, there are large-scale fluctuations in genetic
diversity caused by the indirect effects of selection. This “linked selection signal” reflects the …

Background selection does not mimic the patterns of genetic diversity produced by selective sweeps

DR Schrider - Genetics, 2020 - academic.oup.com
It is increasingly evident that natural selection plays a prominent role in shaping patterns of
diversity across the genome. The most commonly studied modes of natural selection are …

Comparison of the full distribution of fitness effects of new amino acid mutations across great apes

D Castellano, MC Macià, P Tataru, T Bataillon… - Genetics, 2019 - academic.oup.com
Castellano et al. provide the first comparison of the full distribution of fitness effects
(including deleterious, neutral but also beneficial mutations) in the great apes. The authors …

Beyond Equilibria: the neglected role of history in ecology and evolution

HG Spencer - The Quarterly Review of Biology, 2020 - journals.uchicago.edu
Research in ecology and evolution today often emphasizes an equilibrium view of
dynamical systems, to the point where historical explanations are largely ignored. Such …

From drift to draft: how much do beneficial mutations actually contribute to predictions of Ohta's slightly deleterious model of molecular evolution?

J Chen, S Glémin, M Lascoux - Genetics, 2020 - academic.oup.com
Since its inception in 1973, the slightly deleterious model of molecular evolution, also known
as the nearly neutral theory of molecular evolution, remains a central model to explain the …

Gene flow, linked selection, and divergent sorting of ancient polymorphism shape genomic divergence landscape in a group of edaphic specialists

F Ke, L Vasseur, H Yi, L Yang, X Wei, B Wang… - Molecular …, 2022 - Wiley Online Library
Interpreting the formation of genomic variation landscape, especially genomic regions with
elevated differentiation (ie islands), is fundamental to a better understanding of the genomic …

An efficient and robust ABC approach to infer the rate and strength of adaptation

J Murga-Moreno, S Casillas, A Barbadilla… - G3: Genes …, 2024 - academic.oup.com
Inferring the effects of positive selection on genomes remains a critical step in characterizing
the ultimate and proximate causes of adaptation across species, and quantifying positive …