Phylogenetic Perspectives on Plant Community Composition
Jeffrey E. Ott
Submitted to fulfill the written examination requirement for the PhD degree
Department of Biology, University of North Carolina at Chapel Hill
April 29, 2004
Abstract
Comparative studies of species composition in plant communities could benefit from a
phylogenetic perspective. Phylogenetic relationships between species are pertinent to
discussions of environmental filtering, historical contingency, spatial autocorrelation, and
scale dependency in plant community ecology. Related species are likely to occupy
similar environments because of phylogenetic niche conservatism, and are likely to have
non-random patterns of geographic distribution because they share a common ancestral
range. These phylogenetic implications are most applicable to studies of community
composition across large spatial scales. Phylogenetic information could be integrated
into community multivariate analyses (classification and ordination) through similarity
indices based on phylogenetic distance between species, although appropriate measures
of distance may be difficult to obtain. Alternatively, approaches based on the concept of
phylogenetic scale could be used to compare community patterns of different ranks or
lineages in a phylogenetic hierarchy. Phylogenetic scale can be described in terms of
grain (level of resolution of branch tips) and extent (phylogenetic bounds of study).
Groups at a grain above or below the species level might be found to be more informative
than species in plant community studies.
Introduction
Applications of phylogenetic information have generated considerable interest in
recent years, concurrent with the publication of increasingly well-resolved phylogenies
for many taxonomic groups. Many areas of comparative biology that have traditionally
ignored phylogenetic relationships between species have recently developed approaches
that set species in a phylogenetic context. Proponents of phylogenetic approaches have
argued that species are not statistically-independent units because of the differing degrees
to which they share common ancestry (Harvey and Pagel 1991, Harvey et al. 1995,
Freckleton et al. 2002). Hence the common practice of analyzing biotic assemblages
using species as units of comparison has been questioned, and alternatives incorporating
phylogenetic information have been proposed.
Webb et al. (2002) recently reviewed applications of phylogenetic information in
the field of community ecology, where topics such as community assembly, niche
structure, evolutionary development of communities, and community emergent properties
have been explored from a phylogenetic perspective. These authors concluded that
phylogeny has important implications for community ecology and described potential
directions for future work, including phylogenetic approaches to classification and
ordination. Standard approaches of the latter methods are commonly used to compare
species composition of sample communities at different locations. This is especially true
in plant community studies where there is an established tradition of describing,
classifying and interpreting patterns of plant species composition in natural or seminatural areas (Braun-Blanquet 1965, Daubenmire 1968, Mueller-Dombois and Ellenberg
1974, Kent and Coker 1992). Methods of data analysis used in this field (Kent and Coker
1992, McCune and Grace 2002) are typically based on metrics of compositional
similarity that either treat species equally, or weigh species according to their abundance
or dominance, but seldom consider phylogenetic relationships between species (but see
van der Maarel 1972, Dale and Clifford 1976, Dale et al. 1989).
The purpose of this paper is to examine the pertinence of a phylogeny in
comparative studies of plant community composition. I refer specifically to studies of
spatial variation in plant species composition, where “composition” can include
information on abundance as well as presence of species. A phylogenetic perspective
takes into account evolutionary relationships among taxa, whether modeled explicitly as a
phylogenetic tree or represented approximately by a taxonomic hierarchy. The first
section of this paper discusses conceptual implications of phylogeny in this field of study.
The second section then presents, in general terms, approaches for including phylogenetic
information in plant community analyses. To a large extent these ideas also pertain to
communities of other types of organisms, and to the related topics of spatial species
turnover and beta-diversity (Velland 2001); but I focus on terrestrial plant communities in
order to capture a specific research tradition and discuss advantages and limitations of
phylogenetic approaches within it.
Implications of phylogeny to plant community composition
In a recent discussion of vegetation classification, Jennings et al. (2002) identified
four conceptual threads (modified from Mueller-Dombois and Ellenberg 1974) that have
emerged from studies of plant community composition:
1.
Similar combinations of species recur from stand to stand under similar habitat conditions,
though similarity declines with geographic distance.
2.
No two stands (or sampling units) are exactly alike, owing to chance events of dispersal,
disturbance, extinction, and history.
3.
Species assemblages change more or less continuously if one samples a geographically
widespread community throughout its range.
4.
Stand similarity depends on the spatial and temporal scale of analysis.
Each of these concepts relates to one or more topics of continuing research in plant
community ecology. The first statement in (1) pertains to environmental filtering; (2)
describes historical contingency; (3) and the second statement of (1) fall under the topic
of spatial autocorrelation (or distance decay of similarity); and (4) can be stated as scale
dependency. Phylogenetic relationships between species have implications for each of
these topics, as discussed below.
Environmental filtering
Plant community comparative studies take advantage of non-random patterns of
species composition. Within a given set of community samples at least some species
tend to be distributed non-randomly, co-occurring with a degree of regularity that allows
community types to be identified (Mueller-Dombois and Ellenberg 1974). Furthermore,
the distribution of such species (or the community types they define) can often be
correlated with measurable environmental variables such as temperature, moisture, light,
substrate, or nutrient availability (Whittaker 1978, Allen and Peet 1990, Newell and Peet
1998, Pyke et al. 2001). Such environmental factors have been described as “filters” that
dictate which species can survive and compete at a given site (Keddy 1992, Belyea and
Landcaster 1999). Environmental filtering occurs because species differ in physiological
tolerances and ecological attributes that collectively characterize each species’ niche.
The niche concept can refer not only to attributes but also to the distribution of a species
across environmental gradients: either the potential distribution due to abiotic
environmental filtering (fundamental niche) or the actual distribution due to the
additional effects of competition and other biotic interactions (realized niche). The
realized niche is frequently inferred from a species’ occurrence or abundance relative to
one or more environmental variables (Whittaker et al. 1973).
Given that niche differences are ultimately the result of evolutionary divergence,
the effects of environmental filtering on a set of species would be expected to vary
according to the degree of phylogenetic relatedness among those species. Closely-related
species are likely to share more niche attributes than distantly-related species because of
evolutionary inertia and constraint, or what has been termed “phylogenetic niche
conservatism” (Harvey and Pagel 1991, Webb et al. 2002, Ackerly 2003). Consequently,
closely related species may have similar habitat requirements and might be expected to
be found together in community samples. A counteracting possibility is that closelyrelated species with similar niches may compete for resources, or otherwise adversely
affect each other’s performance, discouraging coexistence. Webb et al. (2002) referred to
these contrasting possibilities as phylogenetic attraction and phylogenetic repulsion,
respectively.
Phylogenetic niche conservatism implies that the niche concept applies not only
to species but also to other levels of a phylogenetic hierarchy. Several authors have
characterized niche parameters for genera, families, and other higher taxa of plants within
specific regions (Grime 1984, Peat and Fitter 1994, Silvertown et al. 2001, Webb and
Peart 2000, Prinzing et al. 2001). The widespread use of the ecotype concept (Briggs and
Walters 1997) implies that entities below the species level may also have niche identity.
Wilson (1994) noted that ecotype differentiation may explain cases of species with more
than a single mode of abundance along an environmental gradient. If each mode were to
correspond to a single ecotype with a distinct niche, the environmental correlation would
be sharpened by analyzing ecotypes rather than the entire species.
Historical contingency
While factors of the contemporary environment often appear to explain much of
the distribution of plant species in communities, they cannot account for all variability in
community composition. Plant community ecologists recognize that the presence of a
particular set of species at a particular place is partly an artifact of historical events that
may or may not be known. Historical evidence reveals changes in composition of
communities over time (Davis 1981, Cole 1990) as well as changes in the geographic
distribution of species (Brown et al. 1996, Davis and Shaw 2001). In this context, history
can be considered from the perspective of places or of species (or more broadly, lineages;
Brown et al. 1996). The history of a place may involve disturbance events and
environmental changes of varying magnitude and duration. The history of a species may
involve dispersal, colonization of new places, and extinction in others.
Ultimately, the history of a species involves the history of all its ancestors
including those that it shares in common with other species. This depth of history is
typically ignored in plant community studies although it plays a prominent role in
historical biogeography (Crisci et al. 2003). In the latter field, geographic ranges of
modern species are used in conjunction with phylogenetic information (and other
historical evidence) to infer the geographic ranges of ancestral species. The logic of this
approach is that modern geographic ranges of related species were once united as a single
ancestral range, but became independent following divergence. Thus the ranges of
recently-diverged species are likely to be associated in space—either overlaid or nearadjacent, depending on whether the mode of speciation was sympatric or allopatric
(Barraclough and Vogler 2000, Losos and Glor 2003). I refer to this association between
phylogenetic relatedness and geographical range as ancestral range dependence.
Ancestral range dependence has limited implications for community studies
spanning small spatial scales, beyond the recognition that it has affected the species pool
present in the study area (McPeek and Brown 2000). Plant community ecologists have
traditionally worked at spatial scales much smaller than the geographic ranges of most
species. However, plant community databases built from multiple field surveys are now
being used to compare communities across large regions spanning the boundaries of
species ranges (Bruelheide and Chytrý 2000, Jennings 2003). At this scale of study,
community composition is influenced not only by environmental filtering but also by
biogeographical phenomena such as vicariance and endemism (Crisci 2003). These
phenomena may be evident at the species level or at taxonomic levels above or below it.
Studies using phylogeographic approaches (Avise 2000, Tribsch and Schoenswetter
2003) have revealed widespread geographic differentiation of lineages within species.
Spatial autocorrelation (distance decay of similarity)
Plant community composition is typically spatially autocorrelated: sites in close
proximity are likely to have more species in common than distant sites. Nekola and
White (1999) referred to this phenomenon as “distance decay of similarity.” Distance is
not a factor in and of itself, but both environmental similarity and shared history decline
with distance, driving the corresponding decline in community similarity (Nekola and
White 1999, 2002). The exact nature of the relationship between community similarity
and distance depends of the spatial continuity of environmental gradients and historical
factors (e.g., dispersal barriers). The relationship also depends on the degree to which
species’ responses to these factors are similar, as reflected in how tightly they cluster
together in community samples. Since the time of Gleason (1926), plant community
ecologists have recognized the generally individualistic behavior of plant species in
communities: each species tends to be distributed differently (though not entirely
independently) from others. This may result in changes in community composition so
gradual that exact community boundaries cannot be delineated.
Patterns of distance decay and spatial continuity might differ, however, with the
inclusion of phylogenetic information. A phylogenetic perspective might reveal that
spatial compositional change is partly due to the replacement of species with close
relatives in similar environments. That is, related species may be segregated locally due
to competitive interactions or regionally due to historic events such as allopatric
speciation, but phylogenetic niche conservatism should cause these species to
nevertheless occupy similar habitats. Individualistic patterns of species distribution will
only occur to the extent that species have escaped the confines of phylogenetic niche
conservatism and ancestral range dependence.
Of course, many species have indeed ‘escaped’ to varying degrees, sometimes
abruptly through rapid evolution or long distance dispersal. Phylogenetic niche
conservatism, like spatial autocorrelation, is but a general pattern subject to variation:
niche is correlated with phylogenetic relatedness, but with variation due to discontinuities
in evolutionary rate and divergence. In a similar manner, the association between
relatedness and geographic range varies depending on differences in dispersability,
colonizing ability, and extinction susceptibility among lineages (Brown et al. 1996,
Edwards and Westoby 1996, Lloyd et al. 2003). Recent naturalization of species beyond
their historic range due to human introduction adds another complication to the generality
of ancestral range dependence. Species introductions may also result in modification of
niche context: rapid evolution of founder populations in a new environment may give rise
to new ecological traits, altering the fundamental niche of the population (Reznick and
Ghalambor 2001, Sakai et al. 2001, Hanfling and Khollmann 2002). Or, even if the
fundamental niche does not change, the realized niche of an introduced species may be
different in the absence of its historic competitors, predators or pathogens (Wilson et al.
1992, Maron and Villa 2001).
Scale dependency
The foregoing discussion of environmental filtering, historical contingency and
spatial autocorrelation hints at the importance of scale in determining observed patterns
of compositional similarity. Scale has become an important topic in community ecology
due to increased understanding of processes operating at different scales and
consequences of changing the scale of sampling and analysis (Allen and Starr 1982,
Weins 1989, Reed et al. 1993). Spatial scale (area) and temporal scale (time) are related
such that patterns at a given spatial scale can be used to infer processes and events
occurring at a corresponding temporal scale (Allen and Starr 1982). The processes of
competition, habitat filtering and speciation are evident at different spatial scales (small
to large, respectively), and as alluded to above, different patterns of phylogenetic
structure (repulsion or attraction) will be discernible at each scale (Webb et al. 2002).
The concept of scale includes the components grain and extent (Weins 1989,
Palmer and White 1994). Spatial grain refers to the size of individual sample units
(generally plots or quadrats in plant community studies), while spatial extent is the entire
area covered by a sampling scheme. Investigations have been undertaken to examine the
effects of changing these components of spatial scale in plant community studies (Reed et
al. 1993, Stolgren et al. 1997, Ohman and Spies 1998). A goal of finding optimal grain
(plot size) for plant community surveys has been expressed by some (Critchley and
Poulton 1998, Jonsson and Moen 1998).
The hierarchical character of phylogenetic relationships suggests that phylogeny,
like space and time, can be described in terms of scale. Thus the “phylogenetic scale”
(Ackerly 2003; or “taxonomic scale”, Farnsworth 1998) of a community study includes a
grain component corresponding to phylogenetic resolution (of the branch tips, e.g. the
species level) and extent corresponding to the phylogenetic bounds of study (e.g.,
vascular plants). In the same way that plot similarity in plant community studies is
dependent on the spatial and temporal scales of analysis (Jennings et al. 2002), it is also
likely to be dependent on the phylogenetic scale. Changing the phylogenetic grain of
community analysis could yield different patterns of plot similarity that could affect the
results and interpretation of multivariate analyses (Dale and Clifford 1976, Lasiak 2003).
For this reason I would argue that phylogenetic scale needs to be given attention
equivalent to that given spatial scale in studies of community composition.
Phylogenetic approaches to the study of plant community composition
The previous section presents a case for placing species in a phylogenetic context
in comparative studies of plant community composition. In this section I discuss two
categories of approaches for incorporating phylogenetic information into such studies,
one based on phylogenetic distance and the other on phylogenetic scale.
Phylogenetic distance approaches
One way of adding a phylogenetic dimension to community studies is by
quantifying the phylogenetic distance (or conversely, relatedness) between species.
Phylogenetic tree models typically offer estimates of evolutionary change within lineages
(branch lengths) as well as depicting the pattern of divergence between lineages
(topology of nodes) (Harvey and Pagel 1991). Within the framework of a specific
phylogenetic tree, the distance between two or more species can be inferred based on the
shortest path length connecting them, where length is measured as nodes crossed, branch
lengths spanned, or some weighted combination of the two (Faith 1992, Clarke and
Warwick 1999, Webb 2000, Webb et al. 2002). Much of the attention given to such
phylogenetic distance measures has centered on their use in indices of phylogenetic
diversity (Faith 1992) and community structure (Webb 2000), but their use in similarity
indices has also been demonstrated (Izsak and Price 2001). A phylogenetic similarity
index bases similarity between community samples on the shared phylogenetic legacy of
their species rather than simply their overlap in species composition. Phylogenetic
similarity values, once obtained, would be relatively easy to incorporate into the
classification or ordination algorithms commonly used in plant community studies
(McCune and Grace 2002).
Currently one of the challenges of such an approach lies in the acquisition of
quality phylogenetic data. Ideally phylogenetic distance should be based on branch
lengths, but these are not always available or consistent, especially for phylogenies built
using supertree methods (Giannini 2003, Sanderson and Driskell 2003). If nodal distance
is used the measure becomes much more dependent on the particular pool of species
under consideration. Unresolved branching patterns, including those depicted by
taxonomic hierarchies, add further ambiguity to the measurement of phylogenetic
distance (Clarke and Warwick 1999). Furthermore, phylogenetic distance as discussed
above is based on the assumption that evolutionary history is most accurately represented
by a cladistic, dichotomous divergence model. For plants this type of model may be
inaccurate, especially near the species level where introgression, hybridization, and
polyploidy events may lead to reticulate patterns of evolution (Briggs and Walters 1997).
How to infer phylogenetic distance from a reticulate phylogeny is unclear. An alternative
is to abandon explicit phylogenetic models and use gross similarity—whether genetic
(Crozier 1992) or morphological (Sneath and Sokal 1973)—as a proxy for phylogenetic
distance.
The phylogenetic distance approach is limited by the degree to which
phylogenetic relatedness actually corresponds with niche similarity and geographical
distribution (see previous section, “spatial autocorrelation”). There is no guarantee that
genetic markers or other characters used by systematists for phylogenetic reconstruction
will adequately represent ecologically-pertinent information (Giannini 2003). This has
led many plant community ecologists to prefer approaches that classify species based on
traits of known ecological importance, irregardless of phylogenetic origin (Westoby
1998, Pillar 1999, Duckworth et al. 2000). These approaches are well suited for studies
that focus on function or physiognomy, when the important axes of trait variation can be
easily identified and measured. Disadvantages include the difficulty of capturing all
important traits, and the potentially confounding effect of different combinations of traits
in different species. In this context phylogenetic approaches have the advantage of
predicting net trait similarity, and (for the user of phylogenetic information) do not
require a priori decisions of trait importance (Harvey and Pagel 1991).
Phylogenetic scale approaches
Phylogenetic scale, as described above (see “scale dependency”), refers to the
phylogenetic level of resolution (grain) and phylogenetic bounds (extent) of a dataset.
Given that these properties can be modified for a given plant community dataset, one way
of gaining a phylogenetic perspective on community composition is by examining the
effects of changing one or both of them. This type of approach differs from phylogenetic
distance approaches which require a fixed level of resolution (e.g. species) and
predetermined bounds. Phylogenetic scale approaches allow comparisons to be made at
different levels within a lineage as well as at comparable levels between lineages.
Several authors have explored the use of taxonomic ranks other than species in
plant community analyses (Webb et al. 1970, van der Maarel 1972, Dale and Clifford
1976, del Moral and Denton 1977, Dale 1989), effectively changing phylogenetic grain
within a fixed phylogenetic extent. Dale and Clifford (1976), for example, compared
plant community classifications at the level of species, subgenera, genera, subfamilies,
and families. Such comparisons could conceivably be expanded to include other clades
nested between taxonomic ranks, but as such phylogenetic detail is added the proper
correspondence of levels in different lineages is likely to become ambiguous. Taxonomic
ranks themselves can be criticized as being arbitrary constructs with little equivalence in
different groups (Harvey and Pagel 1991), although Dale and Clifford (1976) expressed
confidence that species, genera, and families of plants represent distinct levels of
ecological adaptation with characteristic geographic range sizes. The fact that genera and
families tend to have larger geographic ranges than species has favored their use in largescale biogeographical comparative studies (McLaughlin 1992, Qian 1999).
Another possible way to look at the effects of phylogenetic scale on community
patterns is by changing phylogenetic extent as well as grain. This would entail carrying
out an analysis for each individual taxon or node in a phylogenetic hierarchy. Such an
approach would highlight differences between levels within lineages at the expense of
comparisons between lineages. It could potentially yield large numbers comparisons that
might be difficult to interpret without a systematic strategy for identifying meaningful
patterns. However, if this approach were used to map the distribution of specific
environmental or spatial correlates onto a phylogenetic tree, it might reveal
discontinuities interpretable as breaks in niche conservatism or spatial distribution among
the taxa in a dataset.
An approach intermediate between those outlined above would consider the entire
plant community (fixed phylogenetic extent) but also take into account the nested
character of lineages. Nested Analysis of Variance and related phylogenetic comparative
methods (Harvey and Pagel 1991) assess the amount of variance present between
different levels of a phylogenetic hierarchy, e.g. species within genera, genera within
families, etc. This type of approach was used by Silvertown et al. (2001) and Prinzing et
al. (2001) to assess patterns of niche conservatism in plants across local and regional
environmental gradients, respectively. Giannini (2003) recently proposed a method,
canonical phylogenetic ordination, which identifies significant monophyletic groups
(accounting for high amounts of variance) in comparative datasets. This method holds
promise for the types of analyses discussed here because it requires neither phylogenetic
distances nor taxonomic ranks.
The recognition that certain phylogenetic groupings may be more informative
than others raises the possibility that an optimal set of groups could be obtained for a
given dataset. For example, species in a standard community dataset could be grouped
into higher taxa on a case by case basis according to degree to which such groupings
decrease sample variance, increase sample similarity, or meet some other optimality
criteria. This procedure could also involve the splitting of heterogeneous species into
subspecies, ecotypes, or populations. The net result would be a set of optimal groups,
some containing many related species that might be interpreted as being ecologically
redundant, others containing ecologically-unique single species or subspecific taxa. The
groups themselves could be interpreted as being more appropriate units of ecological
comparison than the species comprising them. The phylogenetic constraint on grouping
would differentiate this type of approach from analogous grouping algorithms such as Rmode clustering (McCune and Grace 2002).
The idea of adjusting taxonomic resolution for specific taxonomic groups is not
foreign to plant community studies because it is often employed for practical reasons. In
practice, plant ecologists often lump taxa that are difficult or costly to identify all the way
to the species level. The implications of lumping taxa of known identification difficulty
could be explored using the approaches outlined here. Phylogenetic approaches might
also prove useful for analyses integrating multiple datasets with inconsistent taxonomic
treatment and resolution.
Conclusion
Phylogenetic information offers insight into the species composition of
contemporary plant communities because of the influence of phylogenetic niche
conservatism and ancestral range dependence. These phenomena can be considered
broadly relevant, although their exact effect on plant community composition can be
expected to vary between places, for different lineages, and when viewed at different
spatial scales. The phylogenetic approaches presented in this paper can be interpreted
legitimately only within the context of the specific locations, taxa, and scale of study to
which they are applied. This, however, is no different from the typical case in this
spatially-explicit field of study. Comparative plant community ecology, like
phylogenetic systematics, has benefited from recent conceptual and quantitative advances
and continues to build its base of information and scientific understanding. The
integration of these two fields of study is a promising area for future research.
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