Python based GIS Tools for Landscape Genetics: Visualising Genetic Relatedness and Measuring Landscape Connectivity
Methods in Ecology and Evolution, Volume 2, Issue 1, pages 52–55, January 2011
Thomas R. Etherington
“Summary
“1. Landscape genetics is an area of research that can help to understand many spatial ecological processes, but requires significant interdisciplinary collaboration. Use of geographic information system (GIS) software is essential, but requires a degree of customisation that is often beyond the non-specialist.
“2. To help address this, a series of Python script based GIS tools have been developed for use in landscape genetics studies.
The test data supplied with the ArcToolbox can be used with a) the Kinship links tool to create lines between sample points which can be symbolised based on the strength of each pair-wise kinship value. This allows for the spatial visualisation of pair-wise relatedness to try and identify genetic patterns in relation to the landscape. From interpretation of the kinship links it is possible to b) assign sensible friction values to the landscape and use the Least-cost path tool to generate a least-cost pathway (LCP) between each pair-wise combination of sample points to see if variation in LCP is correlated to variation in genetic relatedness.
“3. The scripts convert files, visualise genetic relatedness, and measure landscape connectivity using least-cost path analysis. The scripts are housed in an ArcToolbox that is freely available along with the underlying Python code.
“4. The Python scripts allow researchers to use more current software, provide the option of further development by the user community, and reduce the amount of time that would be spent developing common solutions.”
