The effects of phylogenetic relatedness on invasion success and impact:
deconstructing Darwin’s naturalization conundrum
5
Shao-peng Li,1, 2, 3 Marc W. Cadotte,2,3* Scott J. Meiners,3 Zheng-shuang Hua,1 Hao-yue Shu,1 Jin-tian
Li1 and Wen-sheng Shu1*
Supporting Information
Materials and Methods
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Phylogenetic patterns across the phylogeny. To examine the distribution of species status across the
whole phylogeny, we classified the exotic species into different status groups according to whether they
could establish or dominate at least one plot in at least one time interval. Similarly, all the native
species were also classified into two status groups according to whether they could persist at least one
plot for the last observation in year 2009 (persistent versus extinct native species).
15
For exotic species, we calculated their mean phylogenetic distances to the all native species across
the tree (MPD), and the mean phylogenetic distances of each exotic species in the group to its nearest
native relative (MNND).To quantify the clustering of exotic species across the whole phylogeny, we
calculated the standardized effect size of MPD and MNND (hereafter SES.MPD and SES.MNND) as:
Standardized effect size = (χobs – χnull)/SDnull
20
where χobs is the observed MPD or MNND among exotics, χnull is the mean of the simulated values
according to the phylogeny tip labels shuffling null model, and SDnull is the standard deviation of the
simulated values. Similarly, we calculated the SES.MPD and SES.MNNPD of successfully established
and dominant exotic species to the native species, to assess whether these successful exotics were more
or less related to the natives than random expectations. Our null models were applied by swapping the
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exotics along the phylogenetic tree. Such randomization holds the number of successfully established
and dominant species fixed, but allows any exotic species to be the successfully established/dominant
one. This model has been suggested as a most appropriate null model to resolve Darwin’s naturalization
conundrum (Thuiller et al. 2010). A total of 10,000 random assemblages were generated, and positive
SES.MPD and SES.MNND indicate the exotic status group is more distantly related to natives than
30
would be expected by chance, whereas negative values indicate the opposite (Webb et al. 2002).
Further, we implemented generalized linear models (GLM) to assess the effect of phylogenetic
distances to native species on the probability of establishment and dominance of exotic species. We
independently modeled the effect of MPD and MNND on the binary response variable
“failure/success” assuming a binomial error distribution (link = logit).
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Results
Phylogenetic patterns across the phylogeny. Of the 319 species recorded in our 480 plots from 1966
to 2009, 116 species were classified as exotics, 41 of these exotics were able to maintain self-sustaining
populations in at least one plot for more than ten years (successfully established exotics), whereas the
remaining 75 were classified as exotics that failed to established. Among the 41 successfully
40
established exotics, 24 species became more abundant than any natives in at least one plot (successfully
dominant exotics), and the remaining 17 species were classified as established exotics that failed to
become dominant (Fig. S1). Of the 203 native species, 89 species could persist in at least one plot for
the last observation. For these persistent native species, the numbers of plots they persisted in 2009
were also show in Fig. S1.
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Considering all exotic species together at the whole-phylogeny scale, they were randomly
dispersed across the phylogeny (SES.MPD = -1.26, P = 0.11) but showed some clustering of the
terminal nodes (e.g., Poaceae, Fabaceae, Caryophyllaceae, Plantaginaceae, and Brassicaceae;
SES.MNND = -2.37, P = 0.016; Fig. S1). The establishment and dominance probabilities of the
introduced exotics were unaffected by their phylogenetic distances to the native species (GLM, P >
50
0.05 for all, Table S4), and successfully established and dominant species could be considered as
random samplings from the exotic species pool (for SES.MPD and SES.MNND, |SES| < 1.96, P >
0.05; Table S4).
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