Next Article in Journal
Fabrication of Porous Scaffolds with a Controllable Microstructure and Mechanical Properties by Porogen Fusion Technique
Next Article in Special Issue
An Unstructured Phylogeographic Pattern with Extensive Gene Flow in an Endemic Bird of South China: Collared Finchbill (Spizixos semitorques)
Previous Article in Journal
Identification of a Male-Specific Amplified Fragment Length Polymorphism (AFLP) and a Sequence Characterized Amplified Region (SCAR) Marker in Eucommia ulmoides Oliv.
Int. J. Mol. Sci. 2011, 12(2), 865-889; doi:10.3390/ijms12020865
Article

Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics

1,2
, 3,†
, 4
, 5
 and 1,6,*
1 Laboratory of Alpine Ecology, Equipe Population Genomics and Biodiversity, UMR CNRS 5553, BP 53, University Joseph Fourier, 38041 Grenoble Cedex 9, France 2 Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetosimunska 25, 10000 Zagreb, Croatia 3 Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84321, USA 4 The Nature Conservancy, 1917 1st Ave, Seattle, WA 98101, USA 5 Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, M6R 2R8, Canada 6 Laboratory of Population Environment Development, UMR 151 UP/IRD, University Aix-Marseille I, 3 place Victor Hugo, 13331 Marseille Cedex 03, France Present address: U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331, USA
* Author to whom correspondence should be addressed.
Received: 15 December 2010 / Revised: 18 January 2011 / Accepted: 19 January 2011 / Published: 25 January 2011
(This article belongs to the Special Issue Advances in Molecular Ecology)
View Full-Text   |   Download PDF [1290 KB, uploaded 19 June 2014]   |   Browse Figures

Abstract

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance.
Keywords: landscape genetics; genetic boundaries; spatial Bayesian clustering; edge detection methods landscape genetics; genetic boundaries; spatial Bayesian clustering; edge detection methods
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Share & Cite This Article

Export to BibTeX |
EndNote


MDPI and ACS Style

Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S. Comparison of Bayesian Clustering and Edge Detection Methods for Inferring Boundaries in Landscape Genetics. Int. J. Mol. Sci. 2011, 12, 865-889.

View more citation formats

Related Articles

Article Metrics

Comments

Citing Articles

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert