10.5061/DRYAD.P3B3F
Steinig, Eike J.
James Cook University
Neuditschko, Markus
University of Sydney
Khatkar, Mehar S.
University of Sydney
Raadsma, Herman W.
James Cook University
University of Sydney
Zenger, Kyall R.
James Cook University
Data from: NetView P: a network visualization tool to unravel complex
population structure using genome-wide SNPs
Dryad
dataset
2015
Captive Populations
Pinctada maxima
Genomics/Proteomics
Bioinfomatics/Phyloinfomatics
Merluccius merluccius
Canis lupus
Wildlife Management
2015-07-01T19:05:37Z
2015-07-01T19:05:37Z
en
https://doi.org/10.1111/1755-0998.12442
50053060 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Network-based approaches are emerging as valuable tools for the analysis
of complex genetic structure in both wild and captive populations. NetView
P combines data quality control with the construction of population
networks based on mutual k-nearest-neighbours thresholds applied to
genome-wide SNPs. The program is cross-platform compatible, open-source
and efficiently operates on data ranging from hundreds to hundreds of
thousands of SNPs through multiprocessing in Python. We used the pipeline
for the analysis of pedigree data from simulated (n = 750, SNPs = 1279)
and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild
populations of the European Hake from the Atlantic and Mediterranean (n =
834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs =
86,103). The population networks effectively visualize large- and
fine-scale genetic structure within and between populations, including
family-level structure and relationships. NetView P comprises a
network-based addition to other population analysis tools and provides
user-friendly access to a complex network analysis pipeline through
implementation in Python.
Oyster DataArchive containing data for P. maxima analysis with NetView P,
including wild (n = 83, SNPs = 999), captive (n = 684, SNPs = 834) and
simulated (n = 3000, SNPs = 1271) genotypes, as well as input files
(PED/MAP), node attributes and networks for visualization in
Cytoscape.oyster_data.zip
Mediterranean
North America
Atlantic
Indonesia