Detecting natural selection in genomic data

JJ Vitti, SR Grossman, PC Sabeti - Annual review of genetics, 2013 - annualreviews.org
The past fifty years have seen the development and application of numerous statistical
methods to identify genomic regions that appear to be shaped by natural selection. These …

The search for loci under selection: trends, biases and progress

CW Ahrens, PD Rymer, A Stow, J Bragg… - Molecular …, 2018 - Wiley Online Library
Detecting genetic variants under selection using FST outlier analysis (OA) and
environmental association analyses (EAAs) are popular approaches that provide insight into …

Ecological genomics meets community‐level modelling of biodiversity: Mapping the genomic landscape of current and future environmental adaptation

MC Fitzpatrick, SR Keller - Ecology letters, 2015 - Wiley Online Library
Local adaptation is a central feature of most species occupying spatially heterogeneous
environments, and may factor critically in responses to environmental change. However …

Evaluating the use of ABBA–BABA statistics to locate introgressed loci

SH Martin, JW Davey, CD Jiggins - Molecular biology and …, 2015 - academic.oup.com
Several methods have been proposed to test for introgression across genomes. One method
tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D …

[HTML][HTML] Genotyping-by-sequencing in ecological and conservation genomics

SR Narum, CA Buerkle, JW Davey, MR Miller… - Molecular …, 2013 - ncbi.nlm.nih.gov
The fields of ecological and conservation genetics have developed greatly in recent
decades through the use of molecular markers to investigate organisms in their natural …

Deep learning for population genetic inference

S Sheehan, YS Song - PLoS computational biology, 2016 - journals.plos.org
Given genomic variation data from multiple individuals, computing the likelihood of complex
population genetic models is often infeasible. To circumvent this problem, we introduce a …

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 …

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 …

On the population dynamics of junk: a review on the population genomics of transposable elements

Y Bourgeois, S Boissinot - Genes, 2019 - mdpi.com
Transposable elements (TEs) play an important role in shaping genomic organization and
structure, and may cause dramatic changes in phenotypes. Despite the genetic load they …

Conservation genomics of threatened animal species

CC Steiner, AS Putnam, PEA Hoeck… - Annu. Rev. Anim …, 2013 - annualreviews.org
The genomics era has opened up exciting possibilities in the field of conservation biology by
enabling genomic analyses of threatened species that previously were limited to model …