Tag Archives: ecology

No surprise to Buzz Holling: Non-linear response of seabirds to forage fish depletion

Guest post from Henrik Österblom from the Stockholm Resilience Centre.

Basic ecology rests firmly on a number of basic assumptions.  Some of these assumptions, specifically how predators interaction with their prey, were developed by a key figure in the history of resilience – Buzz Holling. The Holling type I, II and III functional responses are standard material in many textbooks in ecology (here’s wikipedia on functional response).  The different functional responses reflect the prey consumption ratio as a function of food density.  I learned about these different types of functional response more than a decade before coming across anything related to resilience theory, which is perhaps not surprising as the first papers published by Holling on the topic came out in the late 1950s (Holling 1959).

The different functional responses reflect different ways in which predator consumption of prey varies  with changes in food density. The functional response is also related to the numerical response – the reproduction rate in relation to food abundance. If this is too technical, bear with me.

Different types of functional response.

As shown above, a type I functional response is linear – meaning that more prey means that more prey are consumed – straightforward and simple. A type II response is non-linear – the number of prey consumed/reproduction increases initially but reaches a plateau at a certain prey density, as the predator ability to consume prey is gradually saturated. A type III response is more complex and S shaped, with a slow increase in prey consumed/reproduction, due to difficulty in discovering  prey, followed by an increase and subsequent leveling off, as predators are saturated (for more background see here).

What has all this got to do with seabirds?

Seabirds are some of the most conspicuous components of the marine environment and are also well studied throughout the world. Many places where seabirds are studied also have monitoring programs for their prey. Seabirds prey on small pelagic, fat schooling fish – some of which are very important in the rapidly growing aquaculture and meat production sectors.

Recently, I was part of a large group of scientists who analyzed long-term data collected of seabird breeding success, for a range of seabird species breeding throughout the world, including puffins, murres, gulls and penguins. Several of these data sets had previously indicated a type I, or possibly a type II response in some instances, but the evidence were inconclusive. However – when putting all the data together, an interesting pattern emerged – the data indicated a clear type II response!What was even more interesting was that this response was consistent across ecosystems and species.  All ecosystems and species investigated had a very similar level of the threshold – regardless of latitude or foraging strategy. Although we assumed that there would be some nonlinear response in all ecosystems and species, we did not think the threshold would be so similar in where it was located (i.e., at one third of the maximum observed fish biomass).

The key figure from our paper is below.

Fig. 2 (A) Relationship between normalized annual breeding success of seabirds and normalized prey abundance. Each data point from all the time series was plotted with the predictions of a generalized additive model (GAM) (solid line). The gray area represents the 95% confidence interval of the fitted GAM. The threshold in the nonlinear relationship (black solid vertical line) and its 95% confidence interval (black dashed vertical lines) were detected from a change-point analysis. (B) Change in variance across the range of normalized food abundance ranging from –1.5 to 2 standard deviations in eight classes. Variance below the threshold was 1.8 times higher than above it. (C and D) Similar relationships were present when data were pooled (C) for species within ecosystems and (D) for species pooled among ecosystems using the best-fitting asymptotic model (table S2). The Arctic Tern (not shown) model fit was not significant (table S1). The colors in (A) and (C) represent the data set for each ecosystem and in (D) for each seabird species.

The findings, just published in Science (Cury et al. 2011), show that seabirds are unable to increase their breeding output over a certain prey abundance. However, if the amount of prey falls below a threshold – which we estimated at one third of the observed maximum prey abundance – breeding success drops dramatically. This non-linear response has potentially important implications for management: If forage fish stocks are maintained above the identified threshold – seabird breeding success is likely sustainable. However, if fish stocks are harvested to below this level for extended periods of time, we are likely to observe decreasing breeding success and decreasing seabird populations. The study suggests that the one-third rule of thumb can be used as a precautionary guiding principle for marine management. So, potentially, we can use some basic principles from ecology to arrive at some basic principles for marine resource use.

The study highlights the importance of curiosity driven research and long term monitoring program. These monitoring programs were not primarily intended to inform management of marine resources but were instead set up by individuals with a keen interest in basic seabird ecology The study also underlines the importance of multidisciplinary collaboration for producing fun and exciting syntheses. Most of all, it highlights how rewarding it is to work with seabirds – coolest critters on the planet.  Seabirds occupy some of the most remote and harsh habitats on the planet and are incredibly resilient – until critical thresholds are passed.


Cury, P.M., Boyd, I.L., Bonhommeau, S., Anker-Nilssen, T. Crawford, R. J. M., Furness, R.W., Mills, J.A., Murphy, E.J., Österblom, H., Paleczny, M., Piatt, J.F., Roux, J.-P., Shannon, L., Sydeman, W.J., 2011 Global Seabird Response to Forage Fish Depletion —One-Third for the Birds. Science 334 (6063), December 23. (DOI: 10.1126/science.1212928 )

Holling, C. S. 1959. The components of predation as revealed by a study of small-mammal predation of the European pine sawfly. Canadian Entomologist 91: 293-320

Biotic simplification and ecological reorganization

From a powerful review paper in Science on the Trophic Downgrading of Planet Earth (DOI: 10.1126/science.1205106) James A. Estes and many other ecological stars documents the strong role of apex consumers (i.e. big herbivores like elephants) and top predators (e.g. wolves).

Fig. 4. Examples of the indirect effects of apex consumers and top-down forcing on diverse ecosystem processes, including wildfires (30); disease (35); composition of atmosphere (37), soil (47), and fresh water (49); invadability by exotic species (55); and species diversity (60). Interaction web linkages by which these processes are connected to apex consumers are shown in the center. Magnitude of effect is shown in graphs on right. Blue bars are data from systems containing the apex consumer;brown bars are data from systems lacking the apex consumer. Data replotted from original sources (cited above), except raw data on native bird diversity in chaparral habitats provided by K. Crooks.

A new global database of plant traits – TRY

An ongoing research programme in ecology is to use species traits to model ecosystem dynamics and function.   Most of the effort on traits has focussed on plants.

Location of TRY sample sites

TRY is an exciting new global database of plant traits that has managed to combine many of these efforts – bring together 93 separate plant trait databases, and worked with 198 partners from 106 different scientific institutions, to produce a global database that contains 3 million trait records for about 69 000 plant species (of the world’s 3 00 000 plant species).  The database covers  about 1,500 different plant traits, including the morphological, anatomical, physiological, biochemical, and phenological – and ranging from leaf area, to fire tolerance, and nitrogen fixation capacity.  The project’s objectives are:

(1) The construction of a global-scale database of vascular plant traits. This database should gather under a single, easily accessible format data available in different existing datasets that cover a variety of biomes, geographic areas, and traits. The database construction is under the technical responsibility of the Organismic Biogeochemistry Group at the Max-Planck-Institute for Biogeochemistry.

(2) Make the trait data available for the ecological community. The TRY database is not public, but data are shared among participants of the TRY initiative upon request, respecting the intellectual property rights of data contributors.

(3) Support the design of a new generation of dynamic global vegetation models (DGVMs) which take into account the greater biological complexity, necessary for a more robust representation of ecosystem response to global environmental change.

A new paper from the project in Global Change Biology (DOI: 10.1111/j.1365-2486.2011.02451.x) presents the TRY database and an initial analysis of traits that shows:

  • most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits.
  • most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation.
  • Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation.

Hopefully we can expect much more progress in understanding ecological dynamics, as well as ecosystem function and services based on the further development and analysis of this database.

Seven Reflections on Disasters and resilience from around the web

1) The Boston Globe’s Big Picture photo blog has pictures of Japan one month after the quake & tsunami

2) Andy Revkin comments on DotEarth on the limits of Japan’s disaster memory in response to a fascinating Associated Press article by by Jay AlabasterTsunami-hit towns forgot warnings from ancestors.

3) And Andy Revkin also wonder’s whether nuclear power is simply too brittle to be a resilient power source.

4) Richard A. Kerr writes in Science Magazine article Long Road to U.S. Quake Resilience about recent NRC report that argues that it is underfunding programs to develop resilience to Earthquakes.

5) New York Times on how Danger Is Pent Up Behind Aging Dams. Apparently of the USA’s 85,000 dams, more than 4,400 are considered susceptible to failure, but governments cannot agree on who should pay for renovations.

6) Bob Costanza and others write in Solutions magazine on Solutions for Averting the Next Deepwater Horizon.  They argues that sensible resource development should require resource developers to purchase disaster bonds to capture true social costs of resource development

7) In New York Times Leslie Kaufman writes on complexity and resilience of Gulf of Mexico’s ecosystems response to BP Oil Spill.

Microbiological resilience

From Microbiology: The new germ theory in Nature news:

…collaborations are linking those exploring the human microbiota in the intestine, skin, mouth and other surfaces with microbial ecologists, such as Banfield, who have already made a career out of studying microbial universes in environments such as soil, ocean water and toxic waste sites.

The human microbiologists need the help. Although work by Relman and many others over the past five years has gone a long way to building up a genetic catalogue of human microbiota — what types of microbes live where — it has also revealed its staggering and previously unappreciated complexity. With hundreds of interacting, coevolving species living in and on every individual, and frustratingly little species overlap between each person’s microbial population, understanding the connection between microbes and health seems more daunting than ever. Researchers want to know what role the body’s microbial inhabitants have in immune function, nutrition, drug metabolism and conditions as diverse as obesity, cancer, autism and multiple sclerosis. But to do so, they have to sort through an avalanche of genetic sequence to find out what microbes are in the community, how they change over the course of a day, a lifetime or after a change in diet, and which functions are served by particular microbes, combinations of microbes or microbial metabolites (see ‘Exploring the superorganism’).

Microbial ecologists are supplying some of the expertise and bio-informatic tools to help make sense of the data mountain. They are also bringing to the human microbial field ecological principles such as colonization, succession, resilience to change, and competition and cooperation between community members. “It’s hard not to think about ecology when you enter the field,” says Jeff Gordon, a leader in gut microbiology at Washington University in St Louis, Missouri. In return, specialists in human microbiology are attracting funding and attention that ecologists have sometimes struggled to find. “The arbitrary and false barriers between environmental and medical microbiology are breaking down,” Gordon says.

Other collaborations are also exploring how human microbial ecosystems adjust during illness, shifts in diet or after antibiotics. “They’re probably changing all the time in response to all sorts of perturbations,” says Claire Fraser-Liggett, a microbiologist at the University of Maryland School of Medicine in Baltimore, who, in collaboration with Janet Jansson, a soil microbiologist at the University of California, Berkeley, is studying microbiomes associated with the intestinal disorder Crohn’s disease in identical Swedish twins. “Are these communities resilient enough to rebound to where they were before a perturbation like antibiotics? What should we be measuring in order to answer that question? What’s going on in the recovery period? It leads to all these questions that ecologists have been dealing with for decades.”

Ecological concepts are also helping to account for the substantial differences that most studies have found between the microbiota of individuals — even, to a lesser extent, between identical twins. Ecology offered a likely explanation in the form of redundancy. The idea now is that every person’s microbes provide a core set of genes or biological functions, regardless of the specific species encoding them. “If you look at grasslands in different parts of the planet, there’s a common morphology and function,” says Gordon, drawing parallels. “But in different locales, the component species are quite distinct.” Gordon and other researchers hope that more extensive sequencing and analysis of many individuals’ microbiomes will reveal what those core functions are. Relman, meanwhile, has become interested in finding ‘keystone species’, rare species that nevertheless have a vital role in a community, and he is working with a colleague at Stanford, bioengineer Stephen Quake, to sequence the genomes of single microbial cells from the gut.

Bridge building ecological theory

A new book from my former McGill colleague, Michel Loreau is lying on my desk.  I haven’t read From Populations to Ecosystems: Theoretical Foundations for a New Ecological Synthesis yet, but Tadashi Fukami has, and his review is in Science.  He writes:

… Michel Loreau argues that an effective way forward is to give up building a single unified theory of ecology altogether. Loreau (a theoretical ecologist at McGill University) believes that “a monolithic unified theory of ecology is neither feasible nor desirable.” As an alternative approach, he advocates theoretical merging of closely related, yet separately developed subdisciplines.

The merging (or bridge-laying) Loreau advocates involves translating different “languages” used in the mathematical models developed separately in various subdisciplines into a common language so that the subfields can talk to one another. Although this approach does not yield a truly unified theory, it helps, Loreau argues, to “generate new principles, perspectives, and questions at the interface between different subdisciplines and thereby contribute to the emergence of a new ecological synthesis that transcends traditional boundaries.” Taking this tack, one gets a sense that the problem with specialization in subdisciplines can be solved by theoretical bridging without having to trade specificity for generality.

An elegant example of the author’s approach can be seen in the work conducted by him and his colleagues over the past decade or so that merges two major subdisciplines of ecology, community ecology and ecosystem ecology. Loreau devotes much of the book to recounting this body of research. He starts by summarizing essential elements of the mathematical models developed in the two subdisciplines. He then discusses how the two sets of models, though developed separately and with apparently distinct sets of equations, can be merged by basing the two on a common currency: the mass and energy budgets of individual organisms. Once this translation is accomplished, new models that simultaneously consider the composition of coexisting species (the focus of traditional community ecology) and the flow of materials through functional compartments of ecosystems (the focus of traditional ecosystem ecology) can be built and analyzed. These allow one to study reciprocal influences between species composition and material flows in the ecosystem.

As Loreau acknowledges, his is not the first book to advocate this type of theoretical merging. In particular, the approach he presents resembles that laid out in an influential 1992 book by Donald DeAngelis (3). What makes Loreau’s contribution novel and creative is his successful application of the merging approach to understanding the functional consequences of biodiversity loss, the topic that has received perhaps greater attention than any other ecological issue over the past two decades because of its broad social implications.

Trends in Ecology and Ecosystem Services

In response to my recent post on the growth in research on Ecosystem Services, Mark Neff from the Consortium for Science, Policy & Outcomes at Arizona State University writes:

You’re right that there has been significant growth in number of publications about ecosystem services, and that is a noteworthy trend. Although it does not directly map onto the assessment you did, Elizabeth Corley and I recently conducted a study of recent trends in ecology based upon an analysis of ecology publications,

Neff, M. W., & Corley, E. (2009). 35 years and 160,000 articles: A bibliometric exploration of the evolution of ecology. Scientometrics, 80(3), 657-682. (DOI: 10.1007/s11192-008-2099-3)

so I felt compelled to offer my insights. The way you and I did our searches differed, but perhaps you’ll be interested in our findings.

The field of ecology (as defined by the ISI ‘ecology’ journal classification, which includes your top five ‘ecosystem service journals with the exception of PNAS) has grown significantly over the past couple of decades, from 914 articles in 1970 to 10,488 in 2005. Assuming you searched for those terms in the ‘Topic’ field of the ISI WOS database, the results identify all articles with those terms in the title, abstract, author keyword, and indexer assigned keywords. You would have to normalize by the total number of words in all of those things in indexed publications to identify an increase relative to the number and length of indexed publications generally (and the number of journals, publications per journal, and number of words in titles and abstracts are all increasing).

Just to give you an idea, the total number of words in titles of articles in ecology journals – which takes into account the increased number of articles and increased title length – grew over 300% between 1990 and 2005. Also, what ISI indexes (keywords, abstracts, etc) has changed over time and is not consistent across journals. All of these things really complicate attempts to see trends in ecology over time.

The most reliable way I found to analyze trends in the discipline using the publication record is to limit your search to article titles because ISI has been consistent in the way it indexes them (of course, this introduces a suite of problems itself). Then, you have to normalize by the total number of words in titles to get an idea of the relative growth in that area compared to the rest of ecology.

If you search only in titles and normalize for the total number of title words each year, the graph of trends for ‘ecosystem’ and ‘services is unremarkable compared to others. Most notable is the increase in molecular genetic terms and topics like climate change, tropical forestry, and biodiversity. I’ve included one graph comparing the normalized trends in ‘ecosystem’ and ‘services’ to molecular genetic terms show you how the growth in that topic compares.

Note that the y axis is not a number of publications, but rather is a ratio of title words to the total number of title words that year, with a multiplier to ease comparison of the various graphs in our study to one another.

Our 2009 paper  contains more graphs of recent trends in ecology.

Perhaps the biggest trend is the sheer growth in the field, but I have no idea how that compares to the growth of the scientific enterprise writ large.

Short Links: Gorillas, drunky shrews, and jellyfish

Three nature stories from the New York Times:

In the Congo Republic a survey has discovered a large population (125 000) of Western lowland gorillas.

Trove of Endangered Gorillas Found in Africa

The survey was conducted by the Wildlife Conservation Society and local researchers in largely unstudied terrain, including a swampy region nicknamed the “green abyss” by the first biologists to cross it. Dr. Steven E. Sanderson, the president of the society, marveled at the scope of what the survey revealed. “The message from our community is so often one of despair,” he said. “While we don’t want to relax our concern, it’s just great to discover that these animals are doing well.”

It’s Always Happy Hour for Several Species in Malaysian Rain Forest

German scientists have discovered that seven species of small mammals in the rain forests of western Malaysia drink fermented palm nectar on a regular basis. For several of the species, including the pen-tailed tree shrew, the nectar, which can have an alcohol content approaching that of beer, is the major food source — meaning they are chronic drinkers.

Oceanic food webs shifting to dominance by jellyfish, due to overfishing of top predators, and likely coastal eutrophication and climate change.

Stinging Tentacles Offer Hint of Oceans’ Decline

From Spain to New York, to Australia, Japan and Hawaii, jellyfish are becoming more numerous and more widespread, and they are showing up in places where they have rarely been seen before, scientists say. The faceless marauders are stinging children blithely bathing on summer vacations, forcing beaches to close and clogging fishing nets.

But while jellyfish invasions are a nuisance to tourists and a hardship to fishermen, for scientists they are a source of more profound alarm, a signal of the declining health of the world’s oceans.

“These jellyfish near shore are a message the sea is sending us saying, ‘Look how badly you are treating me,’ ” said Dr. Josep-María Gili, a leading jellyfish expert, who has studied them at the Institute of Marine Sciences of the Spanish National Research Council in Barcelona for more than 20 years.

A view of the RA’s research from Cultural Ecology

Lesley Head in her article Cultural ecology: the problematic human and the terms of engagement (Prog Hum Geogr 2007 31:837 DOI: 10.1177/0309132507080625) discusses the current ‘terms of engagement’ between the cultural and the ecological. She writes:

Although ecology would in theory claim a holistic remit that includes humans as part of earth’s biota, its usual practice has reinforced humans as different (Haila, 1999; 2000), with anthropologists more likely to consider humans within an explicitly biogeographical perspective (Terrell, 2006). A recent contents analysis of mainstream conservation biology journals shows a continued focus on relatively ‘intact’ habitats, with few studies ‘conducted entirely in areas under intense human pressure (agricultural landscapes, coastal and urban areas)’ (Fazey et al., 2005: 70).

Changes can be seen as part of the so-called ‘new ecology’, or ‘non-equilibrium’ ecology, in which change and contingency rather than stability is the norm, and ‘disturbances’ such as fire and human actions are understood as internal to the system rather than external.

She describes the Resilience Alliance as follows:

An integrative brand of ecology is practised by the Resilience Alliance, published mostly in their journal Ecology and Society. The Alliance works through interdisciplinary collaborations to explore the dynamics of social-ecological systems, using key concepts such as resilience, adaptability and transformability. The approach is avowedly integrative of ‘ecology’ and ‘society’ (eg, Gunderson et al., 2005) and acknowledges the pervasiveness of humans in ecosystems (Elmqvist et al., 2003; Folke et al., 2004; Trosper, 2005). Yet the assumption of separate systems remains curiously unexamined in this work. Further there is conceptual slippage between treating humans as different, and ultimately absorbing all human activities as part of ecosystems.