The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics
In the presence of recombination, the evolutionary relationships between a set of sampled
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
Insertions and deletions: Computational methods, evolutionary dynamics, and biological applications
Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …
Interpreting population-and family-based genome-wide association studies in the presence of confounding
A central aim of genome-wide association studies (GWASs) is to estimate direct genetic
effects: the causal effects on an individual's phenotype of the alleles that they carry …
effects: the causal effects on an individual's phenotype of the alleles that they carry …
Tree sequences as a general-purpose tool for population genetic inference
LS Whitehouse, DD Ray… - Molecular Biology and …, 2024 - academic.oup.com
As population genetic data increase in size, new methods have been developed to store
genetic information in efficient ways, such as tree sequences. These data structures are …
genetic information in efficient ways, such as tree sequences. These data structures are …
Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
In comments on our paper “Within-host genetic diversity of SARS-CoV-2 lineages in
unvaccinated and vaccinated individuals,” Soni et al. argue that the methods we employed …
unvaccinated and vaccinated individuals,” Soni et al. argue that the methods we employed …
Population suppression by release of insects carrying a dominant sterile homing gene drive targeting doublesex in Drosophila
W Chen, J Guo, Y Liu, J Champer - Nature Communications, 2024 - nature.com
CRISPR homing gene drives can suppress pest populations by targeting female fertility
genes, converting wild-type alleles into drive alleles in the germline of drive heterozygotes …
genes, converting wild-type alleles into drive alleles in the germline of drive heterozygotes …
Using computational simulations to model deleterious variation and genetic load in natural populations
CC Kyriazis, JA Robinson… - The American …, 2023 - journals.uchicago.edu
Deleterious genetic variation is abundant in wild populations, and understanding the
ecological and conservation implications of such variation is an area of active research …
ecological and conservation implications of such variation is an area of active research …
Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to …
The demographic history of a population, and the distribution of fitness effects (DFE) of
newly arising mutations in functional genomic regions, are fundamental factors dictating …
newly arising mutations in functional genomic regions, are fundamental factors dictating …
Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives
The extinction risk of the giant panda has been demoted from “endangered” to “vulnerable”
on the International Union for Conservation of Nature Red List, but its habitat is more …
on the International Union for Conservation of Nature Red List, but its habitat is more …
Temporal challenges in detecting balancing selection from population genomic data
The role of balancing selection in maintaining genetic variation remains an open question in
population genetics. Recent years have seen numerous studies identifying candidate loci …
population genetics. Recent years have seen numerous studies identifying candidate loci …