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The second scenario was used to simulate the hypothesis that satellite data cannot capture the full range of variance of forest structure due to the insensitivity of satellite measurements to vertical vegetation structure.
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The test uses a permutation approach [ 76] to simulate the null hypothesis that there is no phylogenetic signal.
The significance of the results can be determined by permutation tests [ 24] which involves a repeated application of the functional mapping model on the data where the phenotype and marker associations are broken to simulate the null hypothesis of no QTL.
To simulate the null hypothesis, we modeled the test scores of two models as a bivariate binormal distribution with a common covariance matrix [ 1, ρ; ρ,1] and means of [ 0,0] and for the actually negative class and the actually positive class respectively.
This simulates the null hypothesis of neutrality: the site was not subject to selection.
The phylogenetic signal was tested simulating the null hypothesis of the complete absence of a phylogenetic signal by randomly permuting the phenotypic data using 10,000 iterations [ 48].
Our method obtains locus specific standard deviations of iHS in simulating the null hypothesis and contrasting against an expectation of zero.
This test simulated the null hypothesis of the complete absence of a phylogenetic signal by randomly permuting SShD vectors among the terminal nodes of the phylogenetic tree and evaluated the resulting tree length for each permutation.
The phylogenetic signal in the shape data was tested by a permutation approach using the MorphoJ software [ 50], which simulated the null hypothesis of a complete absence of phylogenetic structure by randomly reassigning the phenotypic data to the terminal nodes [ 56].
We also simulated the null-hypothesis of no conservation by randomizing the ortholog pairs (see Methods).
Therefore, two replicate data-sets were simulated under the hypothesis that either topology Ta or Tb applies to the full set of genes using a parametric bootstrap approach [ 31].
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