REVIEW AND
SYNTHESIS
The merging of community ecology and phylogenetic
biology
Jeannine Cavender-Bares,
1
*
Kenneth H. Kozak,
2
Paul V. A.
Fine
3
and Steven W. Kembel
3†
1
Department of Ecology,
Evolution and Behavior,
University of Minnesota, St.
Paul, MN 55108, USA
2
Bell Museum of Natural
History, and Department of
Fisheries, Wildlife, and
Conservation Biology, University
of Minnesota, St. Paul, MN,
55108, USA
3
Department of Integrative
Biology, University of California,
Berkeley, CA 94720, USA
†
Present address: Center for
Ecology and Evolutionary
Biology, University of Oregon,
Eugene, OR 97403, USA.
*Correspondence: E-mail:
cavender@umn.edu
Abstract
The increasing availability of phylogenetic data, computing power and informatics tools
has facilitated a rapid expansion of studies that apply phylogenetic data and methods to
community ecology. Several key areas are reviewed in which phylogenetic information
helps to resolve long-standing controversies in community ecology, challenges previous
assumptions, and opens new areas of investigation. In particular, studies in phylogenetic
community ecology have helped to reveal the multitude of processes driving community
assembly and have demonstrated the importance of evolution in the assembly process.
Phylogenetic approaches have also increased understanding of the consequences of
community interactions for speciation, adaptation and extinction. Finally, phylogenetic
community structure and composition holds promise for predicting ecosystem processes
and impacts of global change. Major challenges to advancing these areas remain. In
particular, determining the extent to which ecologically relevant traits are phylogeneti-
cally conserved or convergent, and over what temporal scale, is critical to understanding
the causes of community phylogenetic structure and its evolutionary and ecosystem
consequences. Harnessing phylogenetic information to understand and forecast changes
in diversity and dynamics of communities is a critical step in managing and restoring the
Earths biota in a time of rapid global change.
Keywords
Community assembly, deterministic vs. neutral processes, ecosystem processes,
experimental approaches, functional traits, phylogenetic community ecology, phylo-
genetic diversity, spatial and phylogenetic scale.
Ecology Letters (2009) 12: 693–715
INTRODUCTION
Community ecology investigates the nature of organismal
interactions, their origins, and their ecological and evolu-
tionary consequences. Community dynamics form the link
between uniquely evolved species and ecosystem functions
that affect global processes. In the face of habitat
destruction worldwide, understanding how communities
assemble and the forces that influence their dynamics,
diversity and ecosystem function will prove critical to
managing and restoring the Earths biota. Consequently, the
study of communities is of paramount importance in the
21st century.
Recently, there has been a rapidly increasing effort to
bring information about the evolutionary history and
genealogical relationships of species to bear on questions
of community assembly and diversity (e.g. Webb et al. 2002;
Ackerly 2004; Cavender-Bares et al. 2004a; Gillespie 2004;
Fine et al. 2006; Strauss et al. 2006; Davies et al. 2007;
Vamosi et al. 2008). Such approaches now allow community
ecologists to link short-term local processes to continental
and global processes that occur over deep evolutionary time
scales (Losos 1996; Ackerly 2003; Ricklefs 2004; Pennington
et al. 2006; Mittelbach et al. 2007; Swenson et al. 2007;
Donoghue 2008; Emerson & Gillespie 2008; Graham &
Fine 2008). This effort has been facilitated by the rapid rise
in phylogenetic information, computing power and compu-
tational tools. Our goal here is to review how phylogenetic
information contributes to community ecology in terms of
the long-standing questions it helps answer, the assumptions
it challenges and the new questions it invites. In particular,
we focus on the insights gained from applying phylogenetic
approaches to explore the ecological and evolutionary
factors that underlie the assembly of communities, and
how the interactions among species within them ultimately
influence evolutionary and ecosystem processes.
Ecology Letters, (2009) 12: 693–715 doi: 10.1111/j.1461-0248.2009.01314.x
 2009 Blackwell Publishing Ltd/CNRS

There are three perspectives on the dominant factors
that influence community assembly, composition and
diversity. First is the classic perspective that communities
assemble according to niche-related processes, following
fundamental rules dictated by local environmental
filters and the principle of competitive exclusion (e.g.
Diamond 1975; Tilman 1982; Bazzaz 1991; Weiher &
Keddy 1999). An alternative perspective is that commu-
nity assembly is largely a neutral process in which species
are ecologically equivalent (e.g. Hubbell 2001). A third
perspective emphasizes the role of historical factors in
dictating how communities assemble (Ricklefs 1987;
Ricklefs & Schluter 1993). In the latter view, the starting
conditions and historical patterns of speciation and
dispersal matter more than local processes. The relative
influence of niche-related, neutral and historical processes
is at the core of current debates on the assembly of
communities and the coexistence of species (Hubbell
2001; Chase & Leibold 2003; Fargione et al. 2004;
Ricklefs 2004; Tilman 2004). This debate falls within
the larger historic controversy about the nature of
communities and the extent to which they represent
associations of tightly interconnected species shaped over
long periods of interaction or are the result of chance co-
occurrences of individually dispersed and distributed
organisms (Clements 1916; Gleason 1926; Davis 1981;
Brooks & McLennan 1991; Callaway 1997; DiMichele
et al. 2004; Ricklefs 2008).
Here we review how the merging of community
ecology and phylogenetic biology advances these debates
and allows new areas of enquiry to be addressed. First,
phylogenetics helps to resolve the long-standing contro-
versy about the relative roles of neutral vs. niche-related
processes in community assembly and facilitates identifi-
cation of the kinds of processes that underlie community
assembly. Second, insights from phylogenetic approaches
present strong challenges to the classical idea that the
species pool (and the traits of species within it) is static
on the time scale over which communities are assembled.
These approaches are also beginning to demonstrate that
community interactions might strongly influence how the
pool itself evolves and changes across space and time.
Finally, phylogenetic diversity and composition is relevant
to predicting ecosystem properties that impact global
processes.
We argue that ongoing efforts to integrate knowledge
of phylogenetic relationships of organisms with their
functional attributes will enhance understanding of the
distribution and function of the Earths biota at multiple
scales, increasing our ability to predict outcomes of
species interactions as well as the consequences of these
outcomes for ecosystem and evolutionary processes.
Progress towards this end will require consideration of
both phylogenetic and spatial scale in the interpretation of
ecological and evolutionary patterns (Box 1, Figs 1 and 2)
and cognizance of the multiplicity of processes that
underlie patterns. Observational, experimental and theo-
retical studies aimed at deciphering the mechanisms
involved in community assembly and how they shift with
scale are paving the way for phylogenetic approaches to
large-scale prediction of ecosystem dynamics in response
to global change.
We first discuss the historical origins of the classic
debates in community ecology that phylogenetics helps to
address. We then turn to specific examples in the general
areas highlighted above and review contributions made
possible by integrating community ecology and phyloge-
netic biology. In doing so, we discuss the challenges
involved in further progress. We close with a summary of
the major advances, challenges and prospects for the
emerging field of phylogenetic community ecology. We
include illustrative examples from animals, plants and
other organisms in discussing the contributions of
phylogenetic information to understanding community
assembly and the feedbacks to evolutionary processes.
However, we focus largely on the plant literature in
discussing the ecosystem and global consequences of
community assembly, reflecting the plant orientation of
much of the relevant literature.
HISTORICAL OVERVIEW
Niche-related processes and assembly rules
Early ecologists, including Darwin, recognized that specific
attributes of species could influence their interactions with
other species and with the environment in predictable ways.
In particular, Darwin noted a paradox inherent in
phenotypic similarity of species with shared ancestry. On
the one hand, if closely related species are ecologically
similar, they should share similar environmental
requirements and may thus be expected to co-occur. On
the other hand, closely related species should experience
strong competitive interactions due to their ecological
similarity, thereby limiting coexistence and thus driving
selection for divergent traits.
The idea that similar phenotypes should share habitat
affinities was championed by the Danish plant ecologist,
Eugenius Warming (1895), who emphasized differences in
the physiological abilities of plants to adjust to some
environments but not others. The core idea was that similar
physiological attributes would be selected for by similar
environments in different regions and that plant pheno-
types should match their environments in predictable ways
(Collins et al. 1986). These ideas were important in the
development of niche theory (e.g. Grinnell 1924; Elton
694 J. Cavender-Bares et al. Review and Synthesis
 2009 Blackwell Publishing Ltd/CNRS