Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

ZN Kamvar, JF Tabima, NJ Grünwald - PeerJ, 2014 - peerj.com
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic
analysis because these populations are clonal, admixed, partially clonal, and/or sexual …

An overview of population genetic data simulation

X Yuan, DJ Miller, J Zhang, D Herrington… - Journal of …, 2012 - liebertpub.com
Simulation studies in population genetics play an important role in helping to better
understand the impact of various evolutionary and demographic scenarios on sequence …

Effects of overlapping generations on linkage disequilibrium estimates of effective population size

RS Waples, T Antao, G Luikart - Genetics, 2014 - academic.oup.com
Use of single-sample genetic methods to estimate effective population size has skyrocketed
in recent years. Although the underlying models assume discrete generations, they are …

A review on methods for detecting SNP interactions in high-dimensional genomic data

S Uppu, A Krishna, RP Gopalan - IEEE/ACM transactions on …, 2016 - ieeexplore.ieee.org
In this era of genome-wide association studies (GWAS), the quest for understanding the
genetic architecture of complex diseases is rapidly increasing more than ever before. The …

[HTML][HTML] A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries

SU Ahmad, BH Kiani, M Abrar, Z Jan, I Zafar… - Journal of infection and …, 2022 - Elsevier
Background With the rapid development of the genomic sequence data for the Severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants Delta (B. 1.617. 2) and …

Detection of selective sweeps in structured populations: a comparison of recent methods

AI Vatsiou, E Bazin, OE Gaggiotti - Molecular ecology, 2016 - Wiley Online Library
Identifying genomic regions targeted by positive selection has been a long‐standing interest
of evolutionary biologists. This objective was difficult to achieve until the recent emergence …

High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability

PF Palamara, J Terhorst, YS Song, AL Price - Nature Genetics, 2018 - nature.com
Interest in reconstructing demographic histories has motivated the development of methods
to estimate locus-specific pairwise coalescence times from whole-genome sequencing data …

Large‐scale genetic panmixia in the blue shark (Prionace glauca): A single worldwide population, or a genetic lag‐time effect of the “grey zone” of differentiation?

D Bailleul, A Mackenzie, O Sacchi… - Evolutionary …, 2018 - Wiley Online Library
The blue shark Prionace glauca, among the most common and widely studied pelagic
sharks, is a top predator, exhibiting the widest distribution range. However, little is known …

Developing approaches for linear mixed modeling in landscape genetics through landscape‐directed dispersal simulations

JR Row, ST Knick, SJ Oyler‐McCance… - Ecology and …, 2017 - Wiley Online Library
Dispersal can impact population dynamics and geographic variation, and thus, genetic
approaches that can establish which landscape factors influence population connectivity …

Detecting population declines via monitoring the effective number of breeders (Nb)

G Luikart, T Antao, BK Hand… - Molecular Ecology …, 2021 - Wiley Online Library
Estimating the effective population size and effective number of breeders per year (Nb) can
facilitate early detection of population declines. We used computer simulations to quantify …