Efficient ancestry and mutation simulation with msprime 1.0

F Baumdicker, G Bisschop, D Goldstein, G Gower… - Genetics, 2022 - academic.oup.com
Stochastic simulation is a key tool in population genetics, since the models involved are
often analytically intractable and simulation is usually the only way of obtaining ground-truth …

[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 …

On the importance of skewed offspring distributions and background selection in virus population genetics

KK Irwin, S Laurent, S Matuszewski, S Vuilleumier… - Heredity, 2016 - nature.com
Many features of virus populations make them excellent candidates for population genetic
study, including a very high rate of mutation, high levels of nucleotide diversity, exceptionally …

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

E Árnason, J Koskela, K Halldórsdóttir, B Eldon - Elife, 2023 - elifesciences.org
Highly fecund natural populations characterized by high early mortality abound, yet our
knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap …

Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner

DLJ Vendrami, LS Peck, MS Clark, B Eldon… - Science …, 2021 - science.org
A long-standing paradox of marine populations is chaotic genetic patchiness (CGP),
temporally unstable patterns of genetic differentiation that occur below the geographic scale …

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

F Freund, E Kerdoncuff, S Matuszewski… - PLoS …, 2023 - journals.plos.org
The standard neutral model of molecular evolution has traditionally been used as the null
model for population genomics. We gathered a collection of 45 genome-wide site frequency …

Inferring demography and selection in organisms characterized by skewed offspring distributions

AM Sackman, RB Harris, JD Jensen - Genetics, 2019 - academic.oup.com
The recent increase in time-series population genomic data from experimental, natural, and
ancient populations has been accompanied by a promising growth in methodologies for …

Bursts of coalescence within population pedigrees whenever big families occur

D Diamantidis, WT Fan, M Birkner, J Wakeley - Genetics, 2024 - academic.oup.com
We consider a simple diploid population-genetic model with potentially high variability of
offspring numbers among individuals. Specifically, against a backdrop of Wright–Fisher …

The site frequency spectrum for general coalescents

JP Spence, JA Kamm, YS Song - Genetics, 2016 - academic.oup.com
General genealogical processes such as Λ-and Ξ-coalescents, which respectively model
multiple and simultaneous mergers, have important applications in studying marine species …

Sweepstakes reproduction facilitates rapid adaptation in highly fecund populations

B Eldon, W Stephan - Molecular Ecology, 2024 - Wiley Online Library
Adaptation enables natural populations to survive in a changing environment.
Understanding the mechanics of adaptation is therefore crucial for learning about the …