INTRODUCTION

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- Supplementary Material - Appendix S1 -
1
Less lineages – more trait variation: phylogenetically
clustered plant communities are functionally more
diverse
SUPPLEMENTARY MATERIAL
Appendix S1: Explanations and references for the 16 traits analysed
Traits related to the established phase (“persistence traits”) were
(1) Moisture demands under field conditions according to indicator values by Ellenberg
(1992). These values rank species distributions in the field in 12 steps along a moisture
gradient and were available for 1178 species. Although originally based on expert
knowledge accumulated from several thousand original studies, Ellenberg indicator
values for moisture have meanwhile extensively been validated (references in Prinzing
2001). The same applies to Ellenberg indicator values for nutrients or light (see below).
(2) Nutrient demands under field conditions (9 ranks) according to Ellenberg (1992;
available for 1122 species, see above).
(3) Light demands under field conditions (9 ranks) according to Ellenberg (1992;
available for 1122 species, see above).
(4) Plant height, related to vertical niche differentiation, calculated as the mean
between minimal and maximal heights given in Van der Meijden (1996).
(5) Growth-form categories according to Barkman (1988): 20 categories characterizing
rooting, stem and foliage patterns relating to vertical and horizontal differentiation of
occupation of habitat space.
(6) Life form according to Raunkiaer (1934): Nine categories, and various combinations
hereof, relating to differences in seasonal persistence and successional distribution, i.e.
to habitat use in time (information available for 1290 species, Klotz et al. 2002).
- Supplementary Material - Appendix S1 -
2
(7) Life-strategy categories according to Grime et al. (1987) related to differentiation in
the use of habitats and the speed and competitiveness in occupying them: competitive,
ruderal, stress tolerant and various combinations hereof, available for 1196 species.
(8) Lifespan (Klotz et al. 2002), i.e. the speed and permanence of establishment within
habitats: annual; biannual; perennial with a single generative reproduction and death
thereafter; truly perennial with multiple generative reproductions; ranked 1 to 4, in the
case of multiple assignments the mean between minimal and maximal values was
taken. Information was available for 1290 species.
Dispersal traits were
(1) Ln Seed weight, i.e. the amount of resources made available for the embryo and
seedling (available for 1080 species; Kleyer et al. in prep; Poschlod et al. 2003)
(2) and (3) Diaspore size and diaspore form, related in various ways to the mode and
distance of primary and secondary dispersal. We compiled information on length,
height and width of diaspores of 932 species from the literature; in case of multiple data
for a species we calculated means across minimal and maximal values (Poschlod et al.
2003; Kleyer et al. 2007). We calculated a principal component analysis across these
informations and extracted the first and second factor which accounted for a total of 93
% of the variation. The first factor was correlated to an increase in length, height and
width and we thus used scores along the first factor as a proxy for diaspore size. The
second factor corresponded to an increasingly slenderness of diaspores and we thus
used scores along this factor as a proxy of diaspore form.
(4) Extent of sexual reproduction, related to the capacity to occupy habitats rather by
short distance (vegetative) or long distance (sexual) dispersal: four ranks from 0, no
sexual reproduction to 4, exclusively sexual reproduction (Klotz et al. 2002)
(5) Morphological structures of vegetative reproduction, relating to the mode of
vegetative occupation of patches. Categories included runner, bulbil, bulb,
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3
fragmentation, rhizome, root shoot, shoot tuber, turio, various modifications and
combinations hereof, none (Klotz et al. 2002)
(6) Extent of clonal spread in space and time, related the pace of patch occupation
through dispersion, grouped into four categories: spatial clonal dispersion for < / > 10
cm combined with temporal clonal dispersion for < / > one year. (Kleyer et al. 2007)
(7) 7 abiotic dispersal modes, and combinations there of, related to the capacity to use
different vectors to spread out, and to arrive at different types of microsites (Bonn et al.
2000; Römermann & Tackenberg. 2005; Poschlod et al. 2005).
(8) 7 biotic dispersal modes, and combinations thereof; as above for abiotic dispersal
modes (Bonn et al. 2000; Römermann & Tackenberg. 2005; Poschlod et al. 2005).
References
Barkman, J.J. (1988). New systems of plant growth forms and phenological plant types.
In: Plant Form and Vegetation Structure (eds. Werger, M.J.A., van der Aart,
P.J.M., During, H.J., Verhoeven, J.T.A.) SPB Academic Publishing. The Hague,
pp 9-44.
Bonn, S., Poschlod, P. &Tackenberg O. (2000). "Diasporus" - a database for diaspore
dispersal - concept and applications in case studies for risk assessment.
Zeitschrift für Ökologie und Naturschutz, 9, 85-97.
Ellenberg, H., Weber, H.E., Düll, R., Wirth, V., Werner, W. & Paulißen, D. (1992).
Zeigerwerte von Pflanzen in Mitteleuropa. Scripta Geobotanica, 18, 1-248.
Grime, J.P., Hodgson, J.G. & Hunt, R. (1987). Comparative Plant Ecology, a functional
approach to common British species. Unit of Comparative Plant Ecology (NREC),
Department of Plant Sciences, University of Sheffield.
Kleyer, M., Bekker, R.M., Knevel, I.C., Bakker, J.P., Thompson, K., Sonnenschein, M.,
Poschlod, P., van Groenendael, J.M., Klimes, L., Klimesová, J., Klotz, S., Rusch,
G.M., Hermy, M., Adriaens, D., Boedeltje, G., Bossuyt, B., Endels, P.,
- Supplementary Material - Appendix S1 -
4
Götzenberger, L., Hodgson, J.G., Jackel, A.-K., Dannemann, A., Kühn, I.,
Kunzmann, D., Ozinga, W.A., Römermann, C., Stadler, M., Schlegelmilch, J.,
Steendam, H.J., Tackenberg, O., Wilmann, B., Cornelissen, J.H.C., Eriksson, O.,
Garnier, E., Fitter, A. & Peco, B. (2007 and in prep.). The LEDA Traitbase: A
database of plant life-history traits of North West Europe. (http://www.ledatraitbase.org/LEDAportal/).
Klotz, S., Kühn, I. & Durka, W. (2002). BIOFLOR: a database on biological and
ecological traits of the German flora, 27-40. Bundesamt für Naturschutz.
Poschlod, P., Kleyer, M., Jackel, A.K., Dannemann, A. & Tackenberg, O. (2003).
BIOPOP - a database of plant traits and Internet application for nature
conservation. Fol Geobot., 38, 263-271.
Poschlod, P., Tackenberg, O. & Bonn, S (2005). Plant dispersal potential and its
relation to species frequency and coexistence. in E. van der Maarel, editor.
Vegetation Ecology.
Prinzing, A., Durka, W., Klotz, S. & Brandl, R. (2001). The niche of higher plants:
evidence for phylogenetic conservatism. Proc. Roy. Soc., Ser. B, 268, 2383–
2389.
Raunkiaer, C. (1934) The Life Forms of Plants and Statistical Plant Geography.
(collected translated papers of C. Raunkiaer). 16 + 632 p. Clarendon Press.
Oxford.
Römermann, C. & Tackenberg, 0. (2005). Dispersability traits. In The LEDA Traitbase
Collecting and Measuring Standards. (eds. Knevel, I.C., Bekker, R.M.,
Kunzmann, D., Stadler, M. & Thompson K.). University of Groningen, Community
and Conversation Ecology Group/Scholma Druk B.V., Bedum, NL (2005), pp 8189.
Van der Meijden, R. (1996). Heukels’ flora van Nederland. 22e edition. WoltersNoordhoff, Groningen.
- Supplementary Material - Appendix S2 -
5
Appendix S2: Illustration of our parameter of dispersion across phylogenetic lineages and
exploration of possible biases
Numbers of species per node
in community
I
II
Node a:
b:
c:
d:
e:
f:
g:
h:
i:
j:
k:
l:
m:
n:
2
3
4
2
6
0
0
0
6
0
0
6
0
6
0
1
1
1
2
1
1
1
3
1
1
4
1
5
=> negative
standard deviation:
-2.62 -1.39
Community
I
II
c
b
a
e
d
i
g
f
h
l
n
k
j
m
Community I is clumped on the tree, hence some phylogenetic nodes carry many
species others few, resulting in a high standard deviation and a low negative standard
deviation of numbers of species per nodes. Community II, in contrast, is much more
equally scattered across phylogenetic lineages, resulting in a less negative value. Note
that the root of the tree was excluded because it is non-informative (it always carries all
species). Note also that phylogenetic dispersion finally needs to be standardized for a null
expectation, which may result also in positive values if observed values are less negative
than the null expectation, i.e. if a community is phylogenetically overdispersed (Methods).
We found that our parameter of phylogenetic dispersion reflected well the dispersion
across a taxonomic classification (Bremer et al. 2003), both at higher and at lower
taxonomic levels. For instance, among local communities with 5 species, the one with the
- Supplementary Material - Appendix S2 -
6
lowest phylogenetic dispersion recruited 4 out of 5 species from the same subfamily,
while in the community with the highest phylogenetic dispersion at most 2 species came
from the same subfamily (both communities were grasslands). Among communities with
15 species, the most clustered one (a forest field layer) was recruited from 11 families,
ten of which are clustered in the same subclass, while the most dispersed community (a
wetland) was dispersed across 13 families which are equally scattered across two
subclasses (7 vs. 6 families in each).
Measures of phylogenetic dispersion might relate to the clade rank of the component
species, i.e. whether species occupy rather basal or rather derived positions within the
phylogenetic tree. We indeed found the phylogenetic dispersion of communities to
increase with the average clade rank of species within communities (r=0.34). We thus
repeated our regressions of trait-state dispersions against phylogenetic dispersion with
clade rank as a co-variable (the number of nodes between the root and the species,
Prinzing et al 2004). We found that this changed the results only little or not at all: t values
of phylogenetic dispersion were highly correlated to the results without clade rank as a
co-variable (r>0.98, regression coefficient =1.1; n=16 traits). Note that in the analysis in
which we had accounted also for the habitat species-pool (‘Regresssion 2’, see
Methods), we had in fact already accounted for the presence of species with extremely
low clade ranks (such as Lemna species in floating communities) or with extremely high
clade ranks (such as Poaceae species in grasslands). We hence only present results of
the initial analyses without clade rank.
There is no evidence for a bias of the results due to the presence of particular
lineages. The most species rich and also highly derived lineage, throughout most of the
38 vegetation classes, is Poaceae. However, inclusion of percentage of Poaceae species
into “Regression 1” never changed the results (mean beta values across 16 traits
including and excluding, respectively, the percentage of Poaceae as covariable: -0.19
and -0.18, correlation between beta values obtained with both approaches: r=0.99). Less
species-rich lineages differ strongly among the vegetation classes (e.g. Nymphaceae in
- Supplementary Material - Appendix S2 -
7
aquatic vegetation, Dipsaceae in open, dry vegetation grasslands etc.). Nevertheless, the
overall relationship between phylogenetic dispersion and trait-state dispersions of the 16
traits was consistent across all vegetation classes (beta values of traits in “Regressions
1” obtained for different vegetation classes were highly correlated at r=0.92 to 1.0).
Recently, inclusion of regional species frequencies into null models has been
suggested for quantifications of phylogenetic diversity (Kembel & Hubbell 2006) but
turned out to have no effect on comparative analyses across multiple communities
(Kembel & Hubbell 2006). Moreover, already Colwell & Winkler (1984) caution that
regional frequency of species may well be the result of local processes and should thus
not be used to construct null models against which to test the existence of local
processes (“narcissus effect”, Colwell & Winkler 1984). In fact, we found that within
vegetation classes that are widespread across The Netherlands (across a 1832 cell grid)
species are not necessarily widespread, too (no correlation between frequencies of
vegetation classes and average frequencies of species within vegetation classes: r= 0.06, n= 38 vegetation classes). This suggests that local processes prevent species from
becoming as widespread as their environments. Local processes may be less important
only in the few widespread vegetation classes in which also most species are
widespread, i.e. the score [vegetation class frequency x average frequency of species
within class] is high, and in the few rare vegetation classes in which also most of the
species are rare (resulting in a low score). We hence selected the five classes with the
highest and the five classes with the lowest score. We found that local communities
belonging to the two groups did not differ in phylogenetic dispersion (means= -0.168 and
-0.139, respectively, F=0.60; p=0.29). Again, this is evidence that the frequency of
species in the species pool did not influence the ranking of communities in terms of
phylogenetic dispersion.
In an exploratory analysis of phylogenetic dispersion vs. trait-state dispersion we
included species richness as an additional independent variable (as well as its interaction
with phylogenetic dispersion). We found negative relationships between phylogenetic and
- Supplementary Material - Appendix S2 -
8
trait-state dispersion in 10 traits (instead of 12 traits without this co-variable). However, in
14 out of 16 traits we found that species richness was negatively related to trait-state
dispersion, while the relationship should be positive if species richness was a true
independent variable, i.e. if species richness leads to increased character displacement
and thus increased trait-state dispersion (Begon et al. 2006). In fact, species richness has
often been shown to be rather a dependent variable, notably species richness will
increase in communities in which species of the same trait states can co-exist (i.e.
communities of low trait dispersion, Begon et al. 2006), which may in turn be the result of
high phylogenetic dispersion (Introduction). Treating species richness as an independent
variable thus risks rendering the analysis highly circular and hiding the effect of true
independent variables, and we therefore refrained from further doing so.
References
Begon, M., Townsend C.R. & Harper, J.L. (2006) Ecology. Blackwell, Oxford.
Bremer, B. et al. (2003). An update of the Angiosperm Phylogeny Group classification for
the orders and families of flowering plants: APG II. Bot. J. Linn. Soc., 141, 399436.
Colwell, R.K. & Winkler, D.W. (1984). A null model for null models in biogeography. In
Ecological Communities: Conceptual Issues and the Evidence. (eds Strong DR,
Simberloff D, Abele LG, Thistle AB) Princeton University Press, pp 344–359.
Kembel, S.W. & Hubbell, S.P. (2006). The phylogenetic structure of a neotropical forest
tree community. Ecology, 87, S86-S99.
Prinzing, A., Ozinga, W. & Durka, W. (2004): The relationship between the global and
regional distribution of species changes during phylogeny. Evolution, 58, 2622–
2633.
- Supplementary Material - Appendix S3 -
9
Appendix S3: Comparison with a distance-based approach to phylogenetic diversity
Contrary to our measure of phylogenetic dispersion, existing measures do not
consider lineage membership, but phylogenetic distances, either based on distances
between species pairs, or on a phylogenetic minimum spanning tree connecting all the
species of a community (e.g. Faith 1992, Webb 2000). Essentially, such distancebased parameters test hypotheses on evolutionary time, and its range between species
across a community, i.e. they increase with the inclusion of highly derived species from
separate major lineages (examples in Faith et al. 1992), making the connecting
branches in between reach both far down and far up. Evolutionary time, however, often
shows only little correlation to changes in functional traits (Böhning-Gaese & Oberrath
1999, Böhning-Gaese et al. 2003, Cavender-Bares et al. 2004). In contrast, within
lineages, functional traits have been shown to be strongly conserved while they may be
highly labile between lineages, even those separated by short branch lengths
(Peterson et al. 1999, Prinzing et al. 2001, Maherali & Klironomos 2007). The explosive
diversification of major Angiosperm lineages, for instance, has resulted in a
diversification of many traits, which have to a large extent been conserved since then
(Peat & Fitter 1994, Prinzing et al. 2001, Maherali & Klironomos 2007).
Moreover, distance-based parameters are particularly dependent on a correct
assessment of branch lengths. This is further complicated by the fact that trait evolution
may not be linearly related to molecular clock branch lengths, with no correlation at all
in pure punctuated equilibrium mode of trait evolution. It has thus been suggested to
quantify branch lengths in terms of degrees of trait evolution (Diniz-Filho 2004) leading
to different estimates of phylogenetic dispersion of a given community for different traits
(and, in our case, to a circular analysis). In fact, the need for precise branch lengths
has largely limited the application of parameters based on phylogenetic distances to
relatively small clades (Carnivora as the largest one; Diniz-Filho 2004), for which a
- Supplementary Material - Appendix S3 -
10
single, comprehensive study of the species-level phylogeny is feasible, providing,
consistent branch length estimates across the entire phylogeny. This, however, may
not suffice to characterize entire communities of potentially competing species. The few
studies that did consider larger clades such as the entire Angiosperms could rely on
consistent branch length estimates only for the basal branches, up to family level (e.g.
Kembel & Hubbell 2006) i.e. branches spanning a short time window, and partly
suffering from relatively large confidence limits (Jansen & Bremer 2004; Magallon &
Sanders 2005). More peripheral branches, i.e. the vast majority of the branches,
covering a much larger time window, had been arbitrarily assigned to equal intervals
between ancient, dated nodes and the presence. Alternatively, all branches can be set
to unity.
Finally, and perhaps most importantly, distance-based parameters (in the absence
of branch lengths reflecting evolutionary advancement) do not identify whether or not
the lineages present in the species pool are evenly represented in the community which is exactly what our hypotheses refer to (Introduction). For instance, the below
illustration shows a case where two communities cover equal pairwise distances, but
one (squares) covers two major lineages, while the other (circles) covers only one. In
contrast, this difference is correctly reflected by our parameter of phylogenetic
dispersion (see also Mace et al. 2003)
- Supplementary Material - Appendix S3 -
11
We stress, however, that for other types of hypotheses, and with reliable branch
length estimates in studies across more restricted phylogenetic scales, distance-based
approaches might perform much better than outlined here. Also, distance-based and
lineage-based approaches converge and give qualitatively similar results if phylogenies
are symmetrical (long distances have to cover multiple nodes across multiple major
branches), while in asymmetric topologies the power of distance-based approaches to
detect phylogenetic clustering on few lineages may decrease (Kraft et al. 2007).
To explore the performance of a distance-based approach we applied the
particularly widely used average pairwise distance between species (-1 * Net
Relatedness Index as defined in Kraft et al. 2007, see also Webb 2000). We set all
branches to unity (Ackerly 2000). We then standardized the observed mean pairwise
distances for the means and the standard deviation across 1000 random communities
of the same species richness as described in the Methods section. However, we found
that the pairwise distances varied much less across communities than our measure of
phylogenetic dispersion making pairwise distances a poorer tool to differentiate
phylogenetic structure (standard deviations=0.4 vs. 2.9 for our parameter). Also the
correlation to clade rank was stronger (r=0.46 vs. 0.34 for our parameter). Accordingly,
pairwise distances showed an increase in phylogenetic dispersion with increasing
proportion of Poaceae in the community (r=0.201). However, in the sense of our
hypothesis an increasing proportion of Poaceae in fact represents rather the opposite:
an increasing clustering (as correctly indicated by our parameter which declined with
increasing proportion of Poaceae; r= -0.197). Interestingly, we found that pairwise
distances, just like our parameter, were negatively correlated to trait-state dispersions:
beta values in Regression 1 for the 16 traits ranged from -0.37 to 0.18, mean= -0.13
(for our parameter; -0.47 to 0.19, mean -0.18), and were correlated to those yielded by
our parameter at r=0.632 (p=0.0086, n=16 traits). We conclude that the two parameters
seem to portray complementary aspects of phylogenetic dispersion and suffer from
complementary weaknesses.
- Supplementary Material - Appendix S3 -
12
References
Ackerly, D.D. (2000). Taxon sampling, correlated evolution, and independent contrasts.
Evolution, 54, 1480-1492
Böhning-Gaese, K. & Oberrath, R. (1999). Phylogenetic effects on morphological, lifehistory, behavioural and ecological traits of birds. Evol. Ecol. Res., 1, 347-364.
Böhning-Gaese, K., Schuda, M.D. & Helbig, A.J. (2003). Weak phylogenetic effects on
ecological niches of Sylvia warblers. J. Evol. Biol., 16, 956-965.
Cavender-Bares, J., Ackerly, D.D., Baum, D.A. & Bazzaz, F.A. (2004). Phylogenetic
overdispersion in Floridian oak communities. Am. Nat., 163, 823–843.
Diniz-Filho, J.A.F. (2004). Phylogenetic diversity and conservation priorities under
distinct models of phenotypic evolution. Conserv. Biol., 18, 698-704.
Faith, D.P. (1992). Conservation evaluation and phylogenetic diversity. Biol. Cons., 61,
1-10.
Janssen, T. & Bremer, K. (2004). The age of major monocot groups inferred from
800+rbcL sequences. Bot. J. Linn. Soc., 146, 385-398.
Kembel, S.W. & Hubbell, S.P. (2006). The phylogenetic structure of a neotropical forest
tree community. Ecology, 87, S86-S99.
Kraft, N.J.B., Cornwell, W.K.,, Webb, C.O. &,Ackerly, D.D. (2007). Trait evolution,
community assembly, and the phylogenetic structure of ecological communities.
Am. Nat., 170, 271-283.
Mace, G.M., Gittleman, J.L. & Purvis, A (2003) Preserving the Tree of Life. Science
300, 1707-1709.
Magallon, S.A. & Sanderson, M.J. (2005) Angiosperm divergence times: The effect of
genes, codon positions, and time constraints. Evolution, 59, 1653-1670.
Maherali, H. & Klironomos, J.N. (2007). Influence of Phylogeny on fungal community
assembly and ecosystem functioning. Science, 316, 1746–1748.
- Supplementary Material - Appendix S3 -
13
Peat, H.J. & Fitter, A.H. (1994). Comparative analyses of ecological characteristics of
British angiosperms. Biol. Rev., 69, 95–115.
Peterson, A.T., Soberon, J. & Sanchez-Cordero, V. (1999). Conservatism of ecological
niches in evolutionary time. Science, 28, 1265–1267.
Prinzing, A., Durka, W., Klotz, S. & Brandl, R. (2001). The niche of higher plants:
evidence for phylogenetic conservatism. Proc. Roy. Soc., Ser. B, 268, 2383–
2389.
Webb, C.O. (2000). Exploring the phylogenetic structure of ecological communities: An
example for rain forest trees. Am. Nat., 156, 145-155.
- Supplementary Material - Appendix S4 -
14
Appendix S4: Accounting for spatial non-independence in the analysis of trait-state
dispersion versus phylogenetic dispersion of communities
In the analyses we found the residuals to be highly significant spatially autocorrelated, indicating spatial non-independence of the data points. We thus used a
spatial regression analysis, an approach that basically uses the spatial neighbors as a
co-variable (Insightful Corp. 2005). After exploring several neighborhood structures we
found that one including the 4 nearest neighbors and applying a simultaneous autoregression based covariance structure, was the most efficient to remove spatial
autocorrelation. To additionally remove large-scale spatial trends we included the X
and Y coordinates of the sampling points, which we found to be significant predictors of
the dispersion of most traits. Overall, the residuals of regressions of this structure were
independent of spatial position (-0.015 < Moran’s I < 0, permutation test p > 0.61). The
exact choice of the spatial model, however, was not important, as all models gave very
similar results. In fact, analysis with and without accounting for space gave very similar
results (beta values of phylogenetic dispersion in the Regression 1 models for
dispersions of 16 traits were correlated at r = 0.95 between models accounting for and
ignoring spatial position). For the various exploratory analyses presented in the other
appendixes we hence decided leave out this spatial standardization (increasing
computation speed by more than three orders of magnitude).
References
Insightful Corp. (2005). S+SpatialStats Version 1.5.7 for Microsoft Windows : 2005
- Supplementary Material - Appendix S5 -
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Appendix S5: Correlates of the relationships between phylogenetic dispersion and the
trait-state dispersion of different traits: Accounting for non-independence of data points
The goal of the analysis was to explain why some traits show strong relationships
between the trait-state dispersion and phylogenetic dispersion within communities,
while others do not. We for instance regressed the relationships between phylogenetic
dispersion and the state-dispersions of different traits to retention indices of these
traits. Such an analysis across traits begs the risk of a bias due to non-independence
of data points, i.e. traits. Some traits may be linked to each other and thus display
similar trait-state dispersions within communities and influence the above across-trait
regression in a similar way. We verified whether such a bias exists. We calculated a
matrix of pairwise correlations between the trait-state dispersions of different traits
across the local communities, indicating which traits tend to be overdispersed or
underdispersed in the same communities. We compared this to a second matrix
indicating which traits exert a similar influence on the above across-trait regression (a
matrix of pairwise distances between the residual values of traits in this regression).
We found the two matrices to be hardly correlated (R² < 0.01), indicating that there was
no bias. For instance, dispersion of moisture demands within communities was most
positively correlated to the dispersion of life strategies and most negatively to the
dispersion of plant height. This, however, did not correspond to particularly similar or
dissimilar influences of these traits on the regression [retention index of traits vs.
relationship between phylogenetic dispersion and trait-state dispersion]. The residual of
moisture demands in this across-trait regression was only moderately similar to that of
life form (residuals of three other traits were more similar) and it was not particularly
dissimilar from that of plant height (residuals of eight other traits were more dissimilar).
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