Genegis: Computational Tools for Spatial Analyses of DNA Profiles with Associated Photo-Identification and Telemetry Records of Marine Mammals

• Main Authors: Baker, C S, Wright, Dawn, Calambokidis, John
• Other Authors: OREGON STATE UNIV NEWPORT HATFIELD MARINE SCIENCE CENTER
• Format: Text
• Language: English
• Published: 2013
• Subjects: Biology; Medicine and Medical Research; *DEOXYRIBONUCLEIC ACIDS; *ECOLOGY; *MAMMALS; *MARINE BIOLOGY; *NORTH PACIFIC OCEAN; ARCHITECTURE; COMPUTATIONS; COMPUTER PROGRAMS; DATA BASES; DATA MANAGEMENT; DOGS; INTEGRATED SYSTEMS; ONLINE SYSTEMS; PROFILES; STABLE ISOTOPES; TELEMETER SYSTEMS; TOOLS; VISION; WHALES; EUBALAENA GLACIALIS; RIGHT WHALES; HECTOR S DOLPHINS; CEPHALORHYNCHUS HECTORI; MEGAPTERA NOVAEANGLIAE; Hector; Pacific; Eubalaena glacialis; Megaptera novaeangliae
• Online Access: http://www.dtic.mil/docs/citations/ADA599184; http://oai.dtic.mil/oai/oai?&verb=getRecord&metadataPrefix=html&identifier=ADA599184

We are developing a suite of computational tools for improved visual exploration and spatial analysis of DNA profiles, with accompanying photo-identification records or telemetry tracks of marine mammals. Referred to as geneGIS, the tools provide the ability to display, browse, select, filter and summarize spatio-temporal relationships of these individual-based records and associated data from molecular markers and ecomarkers (e.g., stable isotopes). We have implemented geneGIS features on two platforms: 1) as programmatic enhancements of the web-based software, Wildbook, formerly the Shepherd Project (http://www.wildme.org/wildbook/); and, 2) as a toolbox in the desktop version of ArcGIS 10.1 or greater (http://genegis.org/). The software application and toolbox allow basic summaries of spatially selected data and export of data in standard tabular and database formats, as well as specialized formats required for programs commonly used in molecular ecology and capture mark- recapture. The data export format complies with OBIS standards and the database architecture is compatible with the Arc Marine data model (Wright et al. 2007), providing a link with other datasets and tools needed for an integrated description of the genetic and environmental seascape of cetaceans. The Wildbook implementation now includes online access to an integrated database of DNA profiles and photo-identification records derived from the SPLASH ocean-wide survey of humpback whales Megaptera novaeangliae in the North Pacific (Baker et al. in press, Barlow et al. 2011, Calambokidis et al. 2008).