The K = 2 conundrum

JK Janes, JM Miller, JR Dupuis… - Molecular …, 2017 - Wiley Online Library
Assessments of population genetic structure have become an increasing focus as they can
provide valuable insight into patterns of migration and gene flow. structure, the most highly …

Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives

M Govindaraj, M Vetriventhan… - Genetics research …, 2015 - Wiley Online Library
The importance of plant genetic diversity (PGD) is now being recognized as a specific area
since exploding population with urbanization and decreasing cultivable lands are the critical …

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

L Gao, I Gonda, H Sun, Q Ma, K Bao, DM Tieman… - Nature …, 2019 - nature.com
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We
present a tomato pan-genome constructed using genome sequences of 725 …

Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

X Sun, C Jiao, H Schwaninger, CT Chao, Y Ma… - Nature …, 2020 - nature.com
Domestication of the apple was mainly driven by interspecific hybridization. In the present
study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica …

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K

NM Kopelman, J Mayzel, M Jakobsson… - Molecular ecology …, 2015 - Wiley Online Library
The identification of the genetic structure of populations from multilocus genotype data has
become a central component of modern population‐genetic data analysis. Application of …

The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem

SJ Puechmaille - Molecular ecology resources, 2016 - Wiley Online Library
Inferences of population structure and more precisely the identification of genetically
homogeneous groups of individuals are essential to the fields of ecology, evolutionary …

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

N Duan, Y Bai, H Sun, N Wang, Y Ma, M Li… - Nature …, 2017 - nature.com
Human selection has reshaped crop genomes. Here we report an apple genome variation
map generated through genome sequencing of 117 diverse accessions. A comprehensive …

Stacks: an analysis tool set for population genomics

J Catchen, PA Hohenlohe, S Bassham… - Molecular …, 2013 - Wiley Online Library
Massively parallel short‐read sequencing technologies, coupled with powerful software
platforms, are enabling investigators to analyse tens of thousands of genetic markers. This …

fastSTRUCTURE: variational inference of population structure in large SNP data sets

A Raj, M Stephens, JK Pritchard - Genetics, 2014 - academic.oup.com
Tools for estimating population structure from genetic data are now used in a wide variety of
applications in population genetics. However, inferring population structure in large modern …

A genomic perspective on hybridization and speciation

BA Payseur, LH Rieseberg - Molecular ecology, 2016 - Wiley Online Library
Hybridization among diverging lineages is common in nature. Genomic data provide a
special opportunity to characterize the history of hybridization and the genetic basis of …