[PDF][PDF] How can we resolve Lewontin's paradox?

B Charlesworth, JD Jensen - Genome biology and evolution, 2022 - academic.oup.com
We discuss the genetic, demographic, and selective forces that are likely to be at play in
restricting observed levels of DNA sequence variation in natural populations to a much …

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 …

Codon usage bias in animals: disentangling the effects of natural selection, effective population size, and GC-biased gene conversion

N Galtier, C Roux, M Rousselle… - Molecular biology …, 2018 - academic.oup.com
Selection on codon usage bias is well documented in a number of microorganisms. Whether
codon usage is also generally shaped by natural selection in large organisms, despite their …

The determinants of genetic diversity in butterflies

A Mackintosh, DR Laetsch, A Hayward… - Nature …, 2019 - nature.com
Under the neutral theory, genetic diversity is expected to increase with population size.
While comparative analyses have consistently failed to find strong relationships between …

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 …

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 …

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 …

[PDF][PDF] Population Genomics on the Fly: Recent Advances in Drosophila

A Haudry, S Laurent, M Kapun - Statistical population genomics, 2020 - library.oapen.org
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-
studied model organisms. Early work in this system has uniquely shed light on the basic …

Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster

HE Machado, DS Lawrie, DA Petrov - Genetics, 2020 - academic.oup.com
Codon usage bias (CUB), where certain codons are used more frequently than expected by
chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant …

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

JL Campos, L Zhao… - Proceedings of the …, 2017 - National Acad Sciences
We used whole-genome resequencing data from a population of Drosophila melanogaster
to investigate the causes of the negative correlation between the within-population …