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Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics
USDA Forest Service, Rocky Mountain Research Station, 800 E Beckwith, Missoula, MT 59801, USA
School of Forestry, Northern Arizona University, P.O. Box 1508, Flagstaff, AZ 86011, USA
Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
Climate Impacts Group, University of Washington, Seattle, WA 98109, USA
* Author to whom correspondence should be addressed.
Received: 30 November 2012; in revised form: 18 January 2013 / Accepted: 1 February 2013 / Published: 18 February 2013
Abstract: The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high correlation among alternative resistance models results in a high risk of spurious correlations using simple Mantel tests. Several refinements, including causal modeling, have been developed to reduce the risk of affirming spurious correlations and to assist model selection. However, the evaluation of these approaches has been incomplete in several respects. To demonstrate the general reliability of the causal modeling approach with Mantel tests, it must be shown to be able to correctly identify a wide range of landscape resistance models as the correct drivers relative to alternative hypotheses. The objectives of this study were to (1) evaluate the effectiveness of the originally published causal modeling framework to support the correct model and reject alternative hypotheses of isolation by distance and isolation by barriers and to (2) evaluate the effectiveness of causal modeling involving direct competition of all hypotheses to support the correct model and reject all alternative landscape resistance models. We found that partial Mantel tests have very low Type II error rates, but elevated Type I error rates. This leads to frequent identification of support for spurious correlations between alternative resistance hypotheses and genetic distance, independent of the true resistance model. The frequency in which this occurs is directly related to the degree of correlation between true and alternative resistance models. We propose an improvement based on the relative support of the causal modeling diagnostic tests.
Keywords: landscape genetics; mantel test; causal modeling; simulation; CDPOP
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Cushman, S.A.; Wasserman, T.N.; Landguth, E.L.; Shirk, A.J. Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics. Diversity 2013, 5, 51-72.
Cushman SA, Wasserman TN, Landguth EL, Shirk AJ. Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics. Diversity. 2013; 5(1):51-72.
Cushman, Samuel A.; Wasserman, Tzeidle N.; Landguth, Erin L.; Shirk, Andrew J. 2013. "Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics." Diversity 5, no. 1: 51-72.