title: netview p: a network visualization tool to unravel complex population structure using genome-wide SNPs.
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.
authors.affiliation: College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.
authors.forename: Eike J
authors.initials: EJ
authors.lastname: Steinig
authors.affiliation: Reprogen - Animal Bioscience, Faculty of Veterinary Science, University of Sydney, Camden, NSW, Australia.
authors.forename: Markus
authors.initials: M
authors.lastname: Neuditschko
authors.affiliation: Reprogen - Animal Bioscience, Faculty of Veterinary Science, University of Sydney, Camden, NSW, Australia.|Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, Qld, Australia.
authors.forename: Mehar S
authors.initials: MS
authors.lastname: Khatkar
authors.affiliation: College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.|Reprogen - Animal Bioscience, Faculty of Veterinary Science, University of Sydney, Camden, NSW, Australia.|Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, Qld, Australia.
authors.forename: Herman W
authors.initials: HW
authors.lastname: Raadsma
authors.affiliation: College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.|Centre for Sustainable Tropical Fisheries and Aquaculture, Townsville, Qld, Australia.
authors.forename: Kyall R
authors.initials: KR
authors.lastname: Zenger
mesh_terms: D000818:Animals; D003198:Computer Simulation; D048388:Gadiformes / Q000145:classification / Q000235:genetics*; D016678:Genome; D010125:Ostreidae / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D019596:Wolves / Q000145:classification / Q000235:genetics*
keywords: SNP; graph theory; netview; network analysis; population genetics; wild and captive populations