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A Non-linear regression was also performed in XLstat using the least squares method and default functions.
We used the maximum likelihood method and default Nelder-Mead algorithm in the 'mle2' function of R (package 'bbmle' [44]) to estimate parameter values when fitting the three one-dimensional functions to the seed density vs. distance data for each of the four tree groups (SF, SM, LF, LM).
qPCR reactions were conducted using the StepOne Plus system and software (Applied Biosystems) using a relative standard curve method and default reaction parameters.
We used the family-wise error rate (fwer) for type I error adjustment, step-down max T (sd.maxT) for method and default values for others in MTP.
The resulting alignments were used to perform phylogenetic analysis conducted with the program MEGA version 3.1 [ 42] using the Neighbour-Joining method and default parameters.
The scaffold content of each cluster was aligned with Mafft 6.864 b, using the L-iNSI method and default parameters (Katoh et al. 2005).
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Recommendations on methods and default values for assessing carbon stocks and emissions are provided by the IPCC Good Practice Guidance [3] and Greenhouse Gas Inventory Guidelines [13].
An intra-specific phylogeny was produced using maximum likelihood (ML) methods and default settings in the program RAXML 7.2.7 [ 51].
Recommendations on methods and default values for assessing carbon stocks and emissions are provided by the IPCC Good Practice Guidance [ 3] and Greenhouse Gas Inventory Guidelines [ 13].
The "pca" method for "ord" (ordination method) function and default settings as from made4 introduction file were used.
The same method and parameters (default) were kept fixed during comparative analysis.
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