gene GIS: Computational tools for spatial analyses of DNA profiles associated with photo-identification records of whales and dolphins
The Wildlife Society 19th Annual Conference
October 13-18, 2012, Portland, OR
A growing number of large-scale studies of long-lived species (e.g., whales
and dolphins) are collecting spatially explicit records linked through
individual identification to genetic samples, photo-identification and
telemetry. These spatio-temporal records have been used to track the
migration and life history parameters of individuals, to estimate the
abundance and trends of populations and, in the case of genetic markers, to
infer close kinship (e.g., parent/offspring relationships) and define
management units, or Distinct Population Segments. To date, however,
there has been a conspicuous absence of computational tools for integration
and spatial exploration of individual records, particularly the potential for
linking photo-identification to genetic information (e.g., DNA profiles) and
for
extending genetic identity to include close kinship. Here, we present
progress on implementing the software platform geneGIS – computational tools to
facilitate visual exploration and spatial analyses of individual-based records
from DNA profiles and photo-identification records. Tools implemented
within geneGIS provide the ability to browse, filter and summarize
spatially
selected subset of genetic records (e.g., frequencies of microsatellite
genotypes and mtDNA haplotype) and map the spatial or temporal
relationship of individual-based records (e.g., multiple locations from
matching genotypes or photographs). The program provides export spatially
selected data subsets in most standard formats (e.g. XLS, CSV), as well as
to specialized programs for statistical analyses of genetic diversity and
differentiation (e.g., Genepop and GenAlEx), capture-recapture estimates of
abundance (e.g., Capture and Mark). We demonstrate the utility
of geneGIS
using a collated database of occurrence records from humpback whales
(Megaptera novaeangliea) in the North Pacific, with more than 8,000
naturally marked individual and 2,700 associated DNA profiles.
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