An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes

YXC Bourgeois, BH Warren - Molecular Ecology, 2021 - Wiley Online Library
Characterizing the population history of a species and identifying loci underlying local
adaptation is crucial in functional ecology, evolutionary biology, conservation and …

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 …

abc: an R package for approximate Bayesian computation (ABC)

K Csilléry, O François, MGB Blum - Methods in ecology and …, 2012 - Wiley Online Library
Many recent statistical applications involve inference under complex models, where it is
computationally prohibitive to calculate likelihoods but possible to simulate data …

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

M Carneiro, CJ Rubin, F Di Palma, FW Albert, J Alföldi… - Science, 2014 - science.org
The genetic changes underlying the initial steps of animal domestication are still poorly
understood. We generated a high-quality reference genome for the rabbit and compared it to …

[HTML][HTML] Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

PY Novikova, N Hohmann, V Nizhynska… - Nature …, 2016 - nature.com
The notion of species as reproductively isolated units related through a bifurcating tree
implies that gene trees should generally agree with the species tree and that sister taxa …

Deep diversification and long-term persistence in the South American 'dry diagonal': integrating continent-wide phylogeography and distribution modeling of geckos

FP Werneck, T Gamble, GR Colli, MT Rodrigues… - …, 2012 - academic.oup.com
The relative influence of Neogene geomorphological events and Quaternary climatic
changes as causal mechanisms on Neotropical diversification remains largely speculative …

An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data

KR Veeramah, D Wegmann, A Woerner… - Molecular biology …, 2012 - academic.oup.com
Abstract Sub-Saharan Africa has consistently been shown to be the most genetically diverse
region in the world. Despite the fact that a substantial portion of this variation is partitioned …

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

P Duchen, D Živković, S Hutter, W Stephan… - Genetics, 2013 - academic.oup.com
Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing
new environments. Here, we modeled the joint demography of African (Zimbabwe) …

[HTML][HTML] The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression

M Ravinet, K Yoshida, S Shigenobu, A Toyoda… - PLoS …, 2018 - journals.plos.org
Speciation is a continuous process and analysis of species pairs at different stages of
divergence provides insight into how it unfolds. Previous genomic studies on young species …

[HTML][HTML] Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data

K Nadachowska-Brzyska, R Burri, PI Olason… - PLoS …, 2013 - journals.plos.org
Profound knowledge of demographic history is a prerequisite for the understanding and
inference of processes involved in the evolution of population differentiation and speciation …