Abstract
Our understanding of the effects of plant biodiversity on ecosystem function rests in large part on experiments that have disentangled environmental variables from local diversity. Yet phylogenetic diversity (PD) effects can be confounded by phylogenetic identity effects in such experiments if assemblages with low or high PD tend to be dominated by a single clade. We illustrate this problem in a 127-species experiment designed to test the effects of angiosperm PD and trait diversity on tallgrass prairie restoration outcomes. In this experiment, the taxon pool exhibits a phylogenetic bias: if species were randomly assigned to experimental assemblages, low PD plots would frequently be dominated by a single clade (the sunflower or daisy family, Asteraceae). We present a visualization tool for examining phylogenetic experiments for this bias and propose a taxonomically constrained experimental design to reduce the most egregious causes of bias. We then present the experimental design we developed using the constrained approach and summarize initial findings from this large-scale restoration experiment. Entanglement of phylogenetic diversity and phylogenetic identity is an underappreciated and likely widespread challenge for PD experiments, particularly those that draw upon a large number of candidate species. By recognizing, quantifying, and counteracting this bias, researchers can better differentiate the effects of PD per se from phylogenetic identity effects.
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Acknowledgments
The authors are grateful to staff, volunteers, and colleagues too numerous to mention by name at The Morton Arboretum and Chicago Botanic Gardens who made this work possible. Natural resources and facilities staff at the Arboretum—in particular Spencer Campbell, Kurt Dreisilker, and P.J. Smith—were especially instrumental. Donald Waller and colleagues at University of Wisconsin-Madison generously provided access to prepublication trait data for 74 species, supported by US National Science Foundation Award DEB 1046355 to DW and collaborators. Carri LeRoy, Will Pearse, Grégory Sonnier, Daniel Spalink, Donald Waller, and Lindsey Worcester provided valuable comments on an early draft of this manuscript. Collaborators at Pizzo and Associates and Prairie Moon Nursery—in particular Kyle Banas, Jack Pizzo, and Bill Carter—were closely involved in species selection and production and went above and beyond in making room for us in their facilities, even at the busiest of times. Lane Scher took pains to get excellent drone photos of the experiment. This work was supported by US National Science Foundation Awards to ALH (NSF-DEB 1354551) and DJM (NSF-DEB 1354426).
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Fig. 10.S1
Plot of mean phylogenetic diversity (PD) of all random 15 species assemblages including each of the species in the experimental design as a function of phylogenetic distinctiveness, ln(w), with species sampling weights a function of w. In an effort to reduce or eliminate the correlation between phylogenetic distinctiveness and mean PD of the plots in which each species occurs, we used w (Box 10.1) as a weight vector in our sampling rather than sampling species with equal probabilities; ln(w) was not utilized because it would result in negative sampling weights. A set of 5 × 105 assemblages of 15 species each were sampled for assemblages ranging from 0 to 1 in exponential and geometric scalings of w. Shown here is the result of using unscaled w as the weight vector, and the effect of all weightings was essentially the same: while the Asteraceae are no longer limited to the lowest PD plots (in fact, the highest mean PD is now occupied by one of the Asteraceae), and the dicots appear to have a sharply reduced correlation between ln(w) and mean PD, the monocots oddly show no reduction in the correlation. We did not use this sampling strategy for the final experiment (PDF 8 kb)
Fig. 10.S2
Plot of mean phylogenetic diversity (PD) of all random 15 species assemblages including each of the species in the experiment as a function of phylogenetic distinctiveness, ln(w), including only assemblages in which Asteraceae are constrained to a maximum of three species each. The experiment as planted utilized the original set of 2 × 106 assemblages of 15 species each, limited to just those assemblages in which Asteraceae are constrained to have a maximum of 3 species. The result is a reduced correlation between mean PD and phylogenetic distinctiveness, but not an elimination of this correlation (PDF 8 kb)
Fig. 10.S3
Ordinations of species included in experiment in trait space. Ordinations include (a) only species for which all data were present (n = 15 species); (b) species for which a maximum of five data observations were missing (n = 70 species); (c) all species, using both observed and MICE-imputed data; and (d) all species, treating missing data as missing. Ordinations were conducted using nonmetric multidimensional scaling on a Gower distance matrix (PDF 15 kb)
Fig. 10.S4
Aerial photo of site, end of first year. Photo is oriented with the north to the right; the road on the left side runs along the south edge of the site. (Photo by Lane Scher, 2017-08-02) (PDF 14244 kb)
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Hipp, A.L. et al. (2018). Effects of Phylogenetic Diversity and Phylogenetic Identity in a Restoration Ecology Experiment. In: Scherson, R., Faith, D. (eds) Phylogenetic Diversity. Springer, Cham. https://doi.org/10.1007/978-3-319-93145-6_10
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