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Protocols

IBDWS specifications

Information


Unique identifier OMICS_16713
Name IBDWS
Alternative name Isolation by Distance Web Service
Interface Web user interface
Restrictions to use None
Input data Some genetic data with or without corresponding geographical information.
Input format TXT,HTML
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Download


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Documentation


Maintainers


  • person_outline Jeffrey Jensen
  • person_outline Andrew Bonohak
  • person_outline Scott Kelley

Information


Unique identifier OMICS_16713
Name IBDWS
Alternative name Isolation by Distance Web Service
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Some genetic data with or without corresponding geographical information.
Input format TXT,HTML
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Medium
Version 2.1
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Jeffrey Jensen
  • person_outline Andrew Bonohak
  • person_outline Scott Kelley

Publication for Isolation by Distance Web Service

IBDWS citations

 (214)
library_books

Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations

2018
PLoS One
PMCID: 5919620
PMID: 29698411
DOI: 10.1371/journal.pone.0195833

[…] o localities) was evaluated using Reduced Major Axis (RMA) regression. The correlation between the two distances was assessed by the Mantel test [], implemented in the isolation-by-distance software (IBDWS v.3.23: http://ibdws.sdsu.edu/~ibdws/) [], with 20,000 randomizations. Long-term gene flow inference was estimated by Migrate-n v3.6 software []. Following a burn-in of 20,000, 2.0 x 106 genealo […]

library_books

Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China

2018
Sci Rep
PMCID: 5883011
PMID: 29615795
DOI: 10.1038/s41598-018-23986-z

[…] gnment; estimations were obtained from the 300,000 iterations that followed a burn-in period of 100,000 iterations. The correlation between genetic distance and geographic distance was assessed using IBDWS version 3.21. Additionally, the distribution of genetic variation was analyzed by AMOVA analysis using the Arlequin suite version 3.5. Principal components analysis (PCA) was performed using GCT […]

library_books

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish, Sebastes thompsoni (Pisces, Scorpaenoidei)

2018
Ecol Evol
PMCID: 5938445
PMID: 29760881
DOI: 10.1002/ece3.3993

[…] from 10,000 permutations in Arlequin 3.5.1.2 (Excoffier et al., ). Finally, isolation‐by‐distance (IBD) analysis was performed using a pairwise F ST matrix, with a Mantel test between populations in IBDWS (http://ibdws.sdsu.edu/~ibdws; Bohonak, ; Jensen, Bohonak, & Kelley, ), to test for correlation between genetic and geographic distances. […]

call_split

Role of oceanography in shaping the genetic structure in the North Pacific hake Merluccius productus

2018
PLoS One
PMCID: 5868808
PMID: 29579060
DOI: 10.1371/journal.pone.0194646
call_split See protocol

[…] ine distances (km) between sampled populations were estimated using Google Earth 4.3 and plotted against pairwise genetic distance []. IBD regressions were performed online using the IBD web service (IBDWS, http://phage.sdsu.edu/~jensen/) [] with 10,000 data randomizations. The extent of population differentiation among samples using microsatellites was visualized with discriminant analysis of pri […]

library_books

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae)

2018
PLoS One
PMCID: 5851647
PMID: 29538451
DOI: 10.1371/journal.pone.0194424

[…] l number of mutations (η), number of haplotypes (h) and the haplotype diversity (Hd). To test whether genetic divergence could be explained by isolation by distance, the Mantel test [] was applied in IBDWS 3.23 [], with (1000) replications. […]

library_books

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

2018
Front Plant Sci
PMCID: 5838013
PMID: 29545814
DOI: 10.3389/fpls.2018.00246

[…] v3.11.We tested for a correlation between pairwise population genetic distance (RST) and geographic distance among sampling locations (isolation-by-distance effect) using a Mantel test (Mantel, ) in IBDWS (Isolation by Distance Web Service) v3.21 (Jensen et al., ) with 10,000 permutations to determine the significance of IBD pattern. Additionally, we calculated the pollen/seed migration ratio (r) […]

Citations

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IBDWS institution(s)
High Tech High, San Diego, CA, USA; Department of Biology, San Diego State University, San Diego, CA, USA

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