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 …

[HTML][HTML] The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

JM Miller, CI Cullingham, RM Peery - Heredity, 2020 - nature.com
Inference of genetic clusters is a key aim of population genetics, sparking development of
numerous analytical methods. Within these, there is a conceptual divide between finding de …

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 …

An introduction to Docker for reproducible research

C Boettiger - ACM SIGOPS Operating Systems Review, 2015 - dl.acm.org
As computational work becomes more and more integral to many aspects of scientific
research, computational reproducibility has become an issue of increasing importance to …

An empirical analysis of journal policy effectiveness for computational reproducibility

V Stodden, J Seiler, Z Ma - Proceedings of the National …, 2018 - National Acad Sciences
A key component of scientific communication is sufficient information for other researchers in
the field to reproduce published findings. For computational and data-enabled research, this …

Examining the generalizability of research findings from archival data

A Delios, EG Clemente, T Wu, H Tan… - Proceedings of the …, 2022 - National Acad Sciences
This initiative examined systematically the extent to which a large set of archival research
findings generalizes across contexts. We repeated the key analyses for 29 original strategic …

Challenges in analysis and interpretation of microsatellite data for population genetic studies

AI Putman, I Carbone - Ecology and evolution, 2014 - Wiley Online Library
Advancing technologies have facilitated the ever‐widening application of genetic markers
such as microsatellites into new systems and research questions in biology. In light of the …

Nonindependence and sensitivity analyses in ecological and evolutionary meta‐analyses

DWA Noble, M Lagisz, RE O'dea, S Nakagawa - 2017 - Wiley Online Library
Meta‐analysis is an important tool for synthesizing research on a variety of topics in ecology
and evolution, including molecular ecology, but can be susceptible to nonindependence …

[HTML][HTML] StrAuto: automation and parallelization of STRUCTURE analysis

VE Chhatre, KJ Emerson - BMC bioinformatics, 2017 - Springer
Background Population structure inference using the software STRUCTURE has become an
integral part of population genetic studies covering a broad spectrum of taxa including …

Genome-wide association in tomato reveals 44 candidate loci for fruit metabolic traits

C Sauvage, V Segura, G Bauchet, R Stevens… - Plant …, 2014 - academic.oup.com
Genome-wide association studies have been successful in identifying genes involved in
polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a …