Isolation by distance, web service

By J. L. Jensen, Andrew J. Bohonak, Scott T. Kelley. BMC Genetics, 2005

1,516 citations recorded by the source corpus.

BackgroundThe population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly.ResultsWe have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, population geneticists can perform a variety of powerful statistical tests including Mantel tests, Reduced Major Axis (RMA) regression analysis, as well as calculate FSTbetween all pairs of populations and perform basic summary statistics (e.g., heterozygosity). All statistical results, including publication-quality scatter plots in Postscript format, are returned rapidly to the user and can be easily downloaded.ConclusionIBDWS population genetics analysis software is hosted at http://phage.sdsu.edu/~jensen/ and documentation is available at http://www.bio.sdsu.edu/pub/andy/IBD.html. The source code has been made available on Source Forge at http://sourceforge.net/projects/ibdws/.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/1b7d6d3f0893be1a9076494765ea056c97c1bcae

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Citations in the corpus

• Introgression between invasive saltcedars (Tamarix chinensis and T. ramosissima) in the USA (2009, methodology): “Mantel r correlations were calculated with the program ‘‘Isolation by Distance, on the Web’’ (Jensen et al. 2005), comparing matrices of the pairwise geographic distances and pairwise similarity coefficients.”
• Multiple introductions determine the genetic structure of an invasive species population: American mink Neovison vison in Poland (2010, methodology): “The Mantel test, performed in the Isolation by Distance Web Service (Jensen et al., 2005), with significance based on 10,000 matrix permutations, was used for this correlation analysis.”
• The Marine Viromes of Four Oceanic Regions (2006, methodology): “Genetic Isolation by Distance of the Phage Assemblages Isolation by Distance Web Service (IBDWS) ([26]; http:// biome.”
• Genetic diversity and population structure of the invasive alien red swamp crayfish (2010, methodology): “Correlation between genetic distance and geographic distance was assessed using IBDWS version 3.08 (Jensen et al. 2005).”
• Population genetic structure reveals terrestrial affinities for a headwater stream insect (2007, methodology): “This result is expected of low-dispersal terrestrial species in the adjacent habitat and would provide evidence for the HM. We used IBDWS ( Jensen, Bohonak & Kelley, 2005 ) to perform a Mantel test of IBD using Slatkin’s (1995) linearized FST versus log (geographic distance) for all pairs of Chirica”
• Phylogeny and phylogeography of Atlantic oyster species: evolutionary history, limited genetic connectivity and isolation by distance (2011, methodology): “…between genetic and geographic distances in Crassostrea rhizophorae and C. brasiliana populations, we used the web service IBDWS version 3.11 (Jensen et al. 2005, http://ibdws.sdsu.edu), testing the significance of pairwise correlations between ΦST (or FST, for allozyme data) and geographic…”
• Hybridization between a native and introduced predator of Adelgidae: an unintended result of classical biological control. (2012, methodology): “To test for isolation by distance, IBDWS 3.23 (Jensen et al., 2005) was used to perform Mantel tests (with 1000 permutations) of the correlation between genetic differentiation and geographic distance among populations for each species.”
• Highly restricted gene flow and deep evolutionary lineages in the giant clam Tridacna maxima (2009, methodology): “Significance of the correlation was tested by a Mantel test with the isolation by distance web service (IBDWS 3.13), applying 30,000 permutations ( Jensen et al. 2005; http://ibdws.sdsu.edu).”