CHAPTER 8
Sea changes: structure and
functioning of emerging marine
communities
J. Emmett Duffy
8.1 Introduction
The earth is in the midst of a global-scale, uncon-
trolled experiment involving human alteration of
both the abiotic resources that support ecosystems
and the trophic linkages that control their structure
and function. Inputs of inorganic nutrients have
increased substantially worldwide, causing major
bottom-up shifts in ecosystems (Cloern 2001).
Abundances of large vertebrates have been sub-
stantially depleted both on land (Dirzo and Raven
2003; Cardilloet al. 2005) and at sea (Paulyet al.
1998; Steele and Schumacher 2000; Jacksonet al.
2001; Myers and Worm 2003; Hutchings and
Reynolds 2004), resulting in systematically altered
food web structure (‘trophic skew’; Duffy 2003;
Byrneset al. 2007), and exotic invasions are altering
community composition locally and homogenizing
communities globally (Sax et al. 2005). Finally,
rising CO2 inputs from fossil fuel combustion are
causing climate warming and acidification of the
surface oceans (Orret al. 2005); these and associated
changes in precipitation and circulation are shifting
species ranges, seasonal cycles and interactions
(e.g. Stachowiczet al. 2002b; Voigtet al. 2003; Schiel
et al. 2004; Winder and Schindler 2004; Hayset al.
2005; Perryet al. 2005; Parmesan 2006). Together,
these processes are producing novel or ‘emergent
ecosystems’ (Hobbset al. 2006) assembled in altered
habitats from species that may have had little or no
evolutionary history of interaction. The accelerating
pace and synergism of these changes create an
urgent need for rigorous applied community eco-
logy – we need to understand how complex inter-
actions within real ecological communities play
out on the large space and timescales relevant to
sustainable management, and how they mediate
stressor impacts on ecosystems and their provision
of services to humanity.
Much of our knowledge of the organization and
dynamics of communities comes from mathemati-
cal theory and controlled experiments. These ap-
proaches have advanced ecology tremendously
over the last 50 years or so. But there is also a widely
recognized trade-off between the clarity and ele-
gance of theory and experiments and the complexi-
ty of the real world (e.g. Carpenter 1996; Oksanen
2001). For example, the classical experiments of
community ecology are generally limited to small
spatial and temporal scales, and are logistically
prohibitive for the large mobile animals of special
conservation interest due to their status as strong
interactors (Souleet al. 2005). Thus, successfully
applying principles from academic community
ecology to real-world management and conserva-
tion remains a daunting challenge. The ultimate test
of ecological theory is its ability to explain, and to
forecast, community responses to environmental
change in the real world (e.g. Clarket al. 2001).
In this spirit, I focus here on one major human
impact, fishing, as a case study to evaluate the suc-
cess of fundamental principles of community eco-
logy in understanding impacts of environmental
change in marine ecosystems. I ask whether impacts95