NETVIEW P: a network visualization tool to unravel complex population structure using genome-wide SNPs

Steinig, Eike J., Neuditschko, Markus, Khatkar, Mehar S., Raadsma, Herman W., and Zenger, Kyall R. (2016) NETVIEW P: a network visualization tool to unravel complex population structure using genome-wide SNPs. Molecular Ecology Resources, 16 (1). pp. 216-227.

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Abstract

Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in wild and captive populations. netview p combines data quality control with the construction of population networks through 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. The pipeline was used 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 grey wolves from North America (n = 239, SNPs = 78 255). 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.

Item ID: 43182
Item Type: Article (Research - C1)
ISSN: 1755-0998
Keywords: graph theory, NETVIEW, network analysis, population genetics, SNP, wild and captive populations
Date Deposited: 10 Mar 2016 00:07
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060405 Gene Expression (incl Microarray and other genome-wide approaches) @ 100%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970105 Expanding Knowledge in the Environmental Sciences @ 100%
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