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Tag Archives: Ecosystem Function
Without a Seaweed Meadow
Ascophyllum nodosum is a brown seaweed and a ubiquitous member of intertidal communities throughout the temperate North Atlantic. This cold- and calm-water loving species has long strappy branches and air bladders along its axis. It grows in dense stands that are up to a meter tall – forming beautiful floating meadows at high tide and thick, floppy mats of seaweed at low tide. Ascophyllum’s high abundance, canopy formation, and place at the bottom of the food-chain makes it an important foundation species for intertidal rocky shore communities. So what would happen if Ascophyllum was suddenly gone tomorrow?
An aerial view of an Ascophyllum dominated intertidal community at low tide. Eager phycology students head down to survey the diversity at Quoddy Head State Park, Maine, USA. (C) Kylla Benes
Fortunately, there have been a few classic and long-term studies* that have addressed this question. Clearly, the removal of any foundation species would result in an immediate decline in associated and dependent species. But what about the long-term changes in intertidal communities?
First a little lesson on intertidal community organization. For sessile (attached and non-mobile) organisms, competition for space is a key driver of diversity on rocky substrate. Recruitment rates, growth rates, longevity, and position in the food-chain can determine which species are most abundant. Ascophyllum is not very good at recruiting. But its density, height, long life-span (up to 100 years), and low palatability mean that this species can out-compete many other sessile seaweeds and invertebrates. Large disturbances—such as strong waves or ice scour — that can remove Ascophyllum and/or high recruitment of other sessile species can lead to other seaweed and invertebrate species becoming dominant. Importantly, the identity of the dominant species can have major impacts on the associated community.
At locations where there is little recruitment, such as the northern-most reaches of the Gulf of Maine, the removal and absence of Ascophyllum could result in a mostly barren landscape or a sparse and low diversity community at best. At locations where there is high recruitment of invertebrates, barnacles and mussels can form near monoculture beds that provide little habitat for the intertidal community that is characteristically associated with Ascophyllum. Although, micro-invertebrates that can live in the interstices between mussels and predators of barnacles and mussels would be happy. In particular, mussels can become so dominant and persistent, that they can form stable and alternative intertidal communities to the Ascophyllum-based versions communities. At locations where predatory pressure from whelks and crabs is high enough to keep these invertebrates in-check, other brown seaweeds in the genus Fucus can be dominant space holders. As close relative to Ascophyllum, these species can play a similar role in intertidal communities, but they are not as long-lived and are more susceptible to damage from waves and herbivores. In the long-run, Fucus-dominated locations may be less stable compared to Ascophyllum-dominated intertidal communities.
The rocky intertidal at Mill Pond, Swans Island, Maine USA. From the 1980’s to 1990’s mussels and barnacles dominated this site (left). Beginning in 2000, disturbances from ice scour opened up space, allowing for a shift to a seaweed dominated community (right). Arrows indicate reference points at the site. Photos: (C) Steve Dudgeon and (C) Peter Petraitis – To see other photographs and learn more about the long-term studies of alternative stable states in the Gulf of Maine, visit the LTERB website.
The above, are all direct effects of the loss of Ascophyllum on the structure intertidal communities but there would also be some indirect effects. Many birds, fish, and invertebrates use Ascophyllum meadows as temporary habitat during migration or as juveniles. Further, seasonal release of gametes and senesce of Ascophyllum may be a large source of nutrients and carbon for intertidal animals or may even be exported to other ecosystems such as the deep subtidal. With Ascophyllum gone, these animals and ecosystems may suffer. These indirect, but potentially important, effects of Ascophyllum are much less well known and studied than direct effects.
Example seaweeds (A-C) and invertebrates (D-I) commonly associated with Asocphyllum. A) Palmaria palmata, B) Corallina officinallis, C) Ulva lactuca, D) Littorina littorea, E) Testudinium testudinalia, F) Littorina obtusata, G) Botryllus sp., H) Mytilus edulis, I) Semibalanus balanoides.
Photos: (C) Kylla Benes
Lastly, the disappearance of Ascophyllum would result in a loss of many ecosystem services that we humans are reliant upon. Lobster, cod, and several other fisheries species use seaweed meadows as nursery habitat for their young. The sudden disappearance of Ascophyllum would result in a reduction of these species, and ultimately income from these fisheries. And this would result in less of the surf, in your surf and turf dinners. Ascophyllum itself is harvested for use in fertilizer, nutritional and beauty products, and even as packaging to ship lobsters to distant restaurants (leading to a small temporary population in the San Francisco bay area). Last year, over 15 million pounds of seaweed were harvested from the coast of Maine, USA and the products of the seaweed industry are valued at about $20 million per year. In addition to its importance in fisheries, Ascophyllum is a foundation species of biodiversity hot spots (e.g., Cobscook Bay) and may be an important carbon sink, which could help mitigate the effects of ocean acidification.
Whether you’re an ecologist interested in community dynamics, think protecting the Earth’s biodiversity is important, or simply love a lobster dinner, we all have a reason to care about Ascophyllum.
*References on Intertidal Community Organization in the Gulf of Maine
Menge, B. A. 1976. Organization of the New England Rocky Intertidal Community: Role of Predation, Competition, and Environmental Heterogeneity. Ecological Monographs 46:355-393.
Petraitis, P. S. & S. R. Dudgeon. 1999. Experimental evidence for the origin of alternative communities on rocky intertidal shores. Oikos:239-245.
Bryson, E. S., G. C. Trussell, & P. J. Ewanchuk. 2014. Broad-scale geographic variation in the organization of rocky intertidal communities in the Gulf of Maine. Ecological Monographs 84:579-597.
May 31, 2016
Even deleting the chestnut blight won’t necessarily bring the chestnut tree back*
Degrading Forests and Extinction Debts
When I ask my introductory biology or ecology students what they think the biggest threat to Earth’s biodiversity is, climate change or pollution typically get the most votes. Perhaps the (much warranted) public attention and debate on these issues leads students to focus on these particular problems, but in fact, habitat loss and degradation have the largest impact on biodiversity. Further, many of the other major threats to biodiversity (e.g., climate change, pollution, etc.) can be directly or indirectly linked to habitat loss.
It is easy to connect complete habitat loss to loss of biodiversity – if a forest is cleared of trees, the diversity and abundance of associated flora and fauna will likely be reduced. But what about fragmented habitat? How does the size and shape of patches of forest or grassland influence remnant communities and ecosystems? The theory of island biogeography gives us hypotheses of how fragment size and isolation might influence populations and diversity. However, habitat fragments are embedded in an anthropogenically-influenced landscape and just how much that landscape influences the structure and function of the remaining habitat is an important question for conservation.
Nick Haddad and colleagues recently reported on the state of the world’s fragmented habitats; including a meta-analysis of long-term experiments specifically designed to test how area, isolation, and edge (distance to perimeter) of fragments effect the remaining communities and ecosystems. High-resolution satellite data revealed that 20% of the world’s forests were within 100 meters of a forest edge and 70% were within 1 kilometer, meaning most forests today are in close proximity of human activity.
A series of long-term (20+ years) habitat fragmentation experiments (see below), spanning multiple continents and biomes, have provided a data set of 76 studies testing how this proximity to human activity influences ecosystems. Specifically, this synthesis enabled Haddad et al. to test the effects of reduced habitat area, increased isolation, and increased habitat edge on a variety of community and ecosystem variables. Not surprisingly, all three treatment variables had negative effects on processes such as organismal abundance, species richness, pollination, nutrient retention, etc. and reduced habitat area and increased isolation appear to have the strongest effects.
Most striking however, was the accumulated long-term consequences of habitat fragmentation. By comparing changes in species richness, immigration, and ecosystem functions (e.g., biomass, total organic carbon, etc.) over time, a delayed effect of fragmentation appeared. That is, the proportional (negative) change in community structure and function increased over time. The negative effects of habitat fragmentation are not necessarily seen immediately after deforestation, and those effects may get worse over time – extinction and ecosystem function debts yet to be realized.
Large, expanses of forest still exist in South America, Africa, and boreal regions. Given that biodiversity loss itself can have strong detrimental effects on ecosystems, that climate change will likely exacerbate effects of fragmentation, and our economic incentives for protecting habitat, the analysis by Haddad et al. present a strong argument for maintaining these large stretches of uninterrupted forest.
Long-term experiments included the meta-analysis:
Biological Dynamics of Forest Fragments (Brazil, in Portuguese)
Kansas Fragmentation Experiment (USA)
Wog Wog Fragmentation Experiment (Australia)
SRS Corridor Experiment (USA)
Moss Fragmentation (UK, Canada)
Newly established experiments:
Metatron (France)
S.A.F.E. Project (Borneo)
April 1, 2015
Even Better than Gold: The Value of Protected Areas
The implementation of protected areas (PAs) is considered the backbone strategy of efforts towards the conservation of biodiversity and natural resources. Currently, the global network of PAs covers approximately 18.8% of the planet (15.4% of terrestrial and inland water and 3.4% of marine and coastal areas, see Fig. 1), safeguarding millions of species and providing a series of important ecosystem services such as water regulation, carbon neutralization, food, climate change mitigation and adaptation, as well as cultural and aesthetic services. Although many countries have committed themselves to increment the coverage of PAs in the upcoming years through international agreements, such as the Convention on Biological Diversity (which aims to assure that by 2020, at least 17% of terrestrial and inland water and 10% of coastal and marine areas are covered by PAs), they never been so threatened as now! A current, and overlooked, practice known as protected area downgrading, downsizing, and degazettement (PADDD) has become widespread in many countries, threatening and dismantling PAs everywhere due to economic interests such as mining, new power plant projects, etc. (for more information and a global map see here; Also, a while ago, I wrote a post about PADDD in Brazil here). Thus, estimating the economic relevance of PAs and bringing this information to political and socioeconomic discussions has become an urgent task.
Protected areas of the World. Extracted from: Juffe-Bignoli et. al. (2014).
In a pioneering study, Andrew Balmford and colleagues have attempted to estimate annual numbers associated with PA visitation and their local and global economic impact. They compiled data from more than 500 terrestrial PAs from 51 countries and built regional and global models to estimate, among other things, the number of visitors, direct expenditure by visitors (calculated from expenditures with fees, travel, accommodation, etc.), consumer surplus (defined as the difference between what visitors would be prepared to pay for a visit and what they actually spend) and the effect of some explanatory variables, such as PA size, remoteness and national income, that might affect visitation rates. Based on these explanatory variables they could predict visit rates for roughly 100,000 PAs.
Their results demonstrate that PAs receive approximately 8 billion visits/yr. Visitation rates are predicted to be higher in Europe, where PAs would receive a combined total of 3.8 billion visits/yr, and lower in Africa (69 million visit/yr). Associations with individual explanatory variables varied regionally in their effect, but as one might expect, national income is a common factor affecting visitation rates in every region. PAs generate approximately US $600 billion/yr in direct expenditure and US $250 billion/yr in consumer surplus. An older estimative shows that less than U$10 billion/yr is spent in protecting and managing PAs, so if this number still roughly valid, for each dollar spent in maintaining them, we would profit ~ U$60, which makes it a hell of a good deal! It is important to note that, although this study seems to be the most comprehensive representation of the global economic significance of tourism associated with PAs, the authors themselves recognize that this number is likely to be an underestimate, so the direct economic return of investing in PAs might be much higher than that!
Now, consider that the economic value of PAs is much, much, higher if we take into account the value of other ecosystem services. A recent study published by Costanza et al. 2014 shows that the global annual economic value of services provided by natural ecosystems is ~U$125 trillion. The same study shows that in less than 15 yrs, changes in land use has promoted an annual loss of U$4.3–20.2 trillion in ecosystem services. Although I could not find a global indicator of the economic participation of PAs as providers of ecosystem services, it seems an obvious conclusion that in a time where natural landscapes are being altered, destroyed and fragmented at very fast rates, PAs will have an even greater importance in protecting the natural and economic wealth of the planet.
So even under the economic development argument, one is left to wonder how governments, politicians and some other sectors of society can consider PAs a “waste of land” and endorse practices such as PADDD?! I don’t really have an answer to this question, but studies like Balmford et al. will surely help conservation biologists to make their discipline more effective and guide society to take batter informed decisions.
References
Costanza, R., et al. 2014. Changes in the global value of ecosystem services. Global Environmental Change 26: 152-158. DOI: 10.1016/j.gloenvcha.2014.04.002
Juffe-Bignoli, D., et. al. 2014. Protected Planet Report 2014. UNEP-WCMC. Available at <http://www.unep-wcmc.org/resources-and-data/protected-planet-report-2014>
Mascia, M. & Pailler, S. 2011. Protected area downgrading, downsizing, and degazettement (PADDD) and its conservation implications. Conservation Letters 4(1): 9–20. DOI: 10.1111/j.1755-263X.2010.00147.x
March 11, 2015
A mechanistic model of the S-shaped population growth
The main idea of this note is to show the most basic and purely mechanistic model of population growth, which has been used by us to create models of interspecific competition for verification of the competitive exclusion principle (1, 2). Our logical deterministic individual-based cellular automata model demonstrates a spatio-temporal mechanism of the S-shaped population growth.
A classical model of the S-shaped population growth is the Verhulst model. Unfortunately, this model is completely non-mechanistic (black-box) as the internal structure of the complex system and mechanisms remain hidden (previous post). Here I show a completely mechanistic ‘white-box’ model of the S-shaped population growth (Fig. 1).
Figure 1. S-shaped population growth. A logical deterministic individual-based cellular automata model of single species population dynamics.
A biological prototype of the model is aggressive vegetative propagation of rhizomatous lawn grasses – e.g. Festuca rubra trichophylla (Slender creeping red fescue). One individual corresponds to one tiller (Fig. 2). A tiller is a minimal semi-autonomous grass shoot that sprouts from the base. Rhizomes are horizontal creeping underground shoots using which plants vegetatively (asexually) propagate. Unlike a root, rhizomes have buds and scaly leaves. One tiller may have a maximum of six rhizomes in the model. A tiller with roots and leaves develops from a bud on the end of the rhizome. A populated microhabitat goes into the regeneration state after an individual’s death. The regeneration state of the site corresponds to the regeneration of the microhabitat’s resources including recycling of a dead individual (Fig. 2b). All individuals are identical. Propagation of offspring of one individual leads to colonization of the uniform, homogeneous and limited habitat. Finite size of the habitat and intraspecific competition are the limiting factors of the population’s growth. The maximum possible number of offspring of one individual is six (Fig. 2a). An individual may propagate in all nearest microhabitats according to the logical rules (Figs 2 and 3).
Figure 2. Biological interpretations of the model. a, Identical offspring of the one parental individual occupy all nearest microhabitats what corresponds to aggressive vegetative propagation of plants. The maximum number of offsprings per one individual equals six. The neighbourhood defines fecundity and spatial positioning of offsprings. b, A biological interpretation of the graph of transitions between the states of a lattice site. The graph represents a birth-death-regeneration process.
A mathematical description of the model. A cellular automata model is defined by the 5-tuple:
- a lattice of sites;
- a set of possible states of a lattice site;
- a neighborhood;
- rules of transitions between the states of a lattice site;
- an initial pattern.
Rules of the cellular automata model are presented in Fig. 3 and in the following text.
Figure 3. Rules of the cellular automata model. a, Hexagonal neighborhood. Coordinates i and j are integer numbers. b, Directed graph of transitions between the states of a lattice site.
The lattice consists of 25×25 sites and it is closed on the torus to avoid boundary effects (Fig. 1). Each site may be in one of the three states 0, 1 or 2, where:
0 – a free microhabitat which can be occupied by an individual of the species;
1 – a microhabitat is occupied by a living individual of the species;
2 – a regeneration state of a microhabitat after death of an individual of the species.
A free microhabitat is the intrinsic part of environmental resources per one individual and it contains all necessary resources and conditions for an individual’s life. A microhabitat is modeled by a lattice site. The cause-effects relations are logical rules of transitions between the states of a lattice site (Fig. 3):
0→0, a microhabitat remains free if there is no one living individual in its neighborhood;
0→1, a microhabitat will be occupied by an individual of the species if there is at least one individual in its neighborhood;
1→2, after death of an individual of the species its microhabitat goes into the regeneration state;
2→0, after the regeneration state a microhabitat becomes free if there is no one living individual in its neighborhood;
2→1, after the regeneration state a microhabitat is occupied by an individual of the species if there is at least one individual in its neighborhood.
Physically speaking this is the simplest model of active (excitable) media with autowaves (travelling waves, self-sustaining waves) (1, 3, 4). An active medium is a medium that contains distributed resources for maintenance of autowave. An autowave is a self-organizing dissipative structure. An active medium may be able to regenerate its properties after local dissipation of resources. In our model, reproduction of individuals occurs in the form of population waves (Fig. 1). We use the axiomatic formalism of Wiener and Rosenblueth for simulation of excitation propagation in active media (5). In accordance with this formalism rest, excitation and refractoriness are the three successive states of a site. In our model the rest state corresponds to the free state of a microhabitat, the excitation state corresponds to the life activity of an individual in a microhabitat and the refractory state corresponds to the regeneration state of a microhabitat. All states have identical duration. If the refractory period will be much longer than the active period, then such a model may be interpreted, for example, as propagation of the single wave of fire on the dry grass. Time duration of the basic states can be easily varied using additional states of the lattice sites.
According to Alexander Watt, a plant community may be considered ‘as a working mechanism’ which ‘maintains and regenerates itself’ (6). This logical model of the single-species population dynamics shows such mechanism in the direct and most simplified form. We consider the white-box modeling by logical deterministic cellular automata as a perspective way for investigation not only of population dynamics but also of all complex systems (1, previous post). The main feature of this approach is the use of cellular automata as a way of linking semantics (ontology) and logic of the subject area. Apparently, the effectiveness of this approach is provided by the fact that cellular automata are an ideal model of time and space.
Acknowledgements
I thank Vyacheslav L. Kalmykov for useful discussions and suggestions.
References
- L. V. Kalmykov, V. L. Kalmykov, Verification and reformulation of the competitive exclusion principle. Chaos, Solitons & Fractals 56, (2013). doi: http://dx.doi.org/10.1016/j.chaos.2013.07.006
- L. V. Kalmykov, V. L. Kalmykov, Deterministic individual-based cellular automata modelling of single species population dynamics. Available from Nature Precedings, (2011). doi: http://dx.doi.org/10.1038/npre.2011.6661.1
- A. N. Zaikin, A. M. Zhabotinsky, Concentration Wave Propagation in Two-dimensional Liquid-phase Self-oscillating System. Nature 225, (1970). doi: http://dx.doi.org/10.1038/225535b0
- V. I. Krinsky, in Autowaves: Results, problems, outlooks in Self-Organization: Autowaves and Structures Far from Equilibrium V. I. Krinsky, Ed. (Springer-Verlag, Berlin, 1984), pp. 9-19.
- N. Wiener, A. Rosenblueth, The mathematical formulation of the problem of conduction of impulses in a network of connected excitable elements, specifically in cardiac muscle. Archivos del Instituto de Cardiologia de Mexico 16, (Jul, 1946).
- A. S. Watt, Pattern and Process in the Plant Community. Journal of Ecology 35, (1947). doi: http://dx.doi.org/10.2307/2256497
December 10, 2014
Why Conservation? Communicating Applied Biodiversity Science
Applied Biodiversity Science Program – Texas A&M University
You might have a favorite science writer. Mine are David Quammen, Bill Bryson, Carl Sagan, and Tim Flannery. Others may be more inclined to read Pulitzer Prize-winning and nominated authors like Jonathan Weiner, Siddhartha Mukherjee, or James Gleick, MacArthur-fellow Atul Gawande, or consummate greats like E. O. Wilson, Richard Dawkins, Stephen J. Gould, and Oliver Sacks. Or perhaps books aren’t all you’re interested in. In that case you may be a fan of Carl Zimmer’s blogging or the stories and editorials from journalists/authors Malcolm Gladwell or Stephen J. Dubner.
It’s likely you’ve read at least one of these authors. Like most readers you were probably impressed by how well they articulated the complexities and subtleties of their topic: everything from astrophysics to evolution, cancer, neurology, chaos theory, economics, and psychology. If you find an author who draws you into a topic that wouldn’t otherwise gain your attention, particularly an unfamiliar scientific discipline, take notice. Take stock of what they have accomplished by gaining your interest and curiosity. As George Gopen and Judith Swan stated in their 1990 for American Scientific, “the fundamental purpose of scientific discourse is not the mere presentation of information and thought, but rather its actual communication.” Good communication requires gaining the reader’s attention. Attention requires garnering interest and curiosity.
In our ever-connected world with vast communication and social networking ability, we have the ability to do just that. We possess the tools to communicate science to a diversity of people in a diversity of ways.
As a member of the Applied Biodiversity Science Program (ABS) at Texas A&M University I find myself in a position where communicating science is an imperative for success. The ABS program is graduate program originally funded by the National Science Foundation as part of their Integrative Graduate Education and Research Traineeship (IGERT) program. The principle mission of ABS at Texas A&M is to achieve integration between biodiversity research in the social and natural sciences with on-the-ground conservation practices and stakeholders.
To that end, a foundational component of ABS is to communicate across scientific disciplines with various institutional actors to facilitate broader impacts across the realm of conservation. In essence, the ABS Program seeks to produce applied scientists who can communicate effectively across disciplines. A natural corollary of this goal is the ability to communicate science outside the realm of science. In this respect, our ABS Perspectives Series is intended to communicate more broadly and inclusively who applied biodiversity conservationists are, what we study, where we conduct research, how we conduct research, and why we are doing it. The current issue of the ABS Perspectives Series, features experiences from the Caribbean, the United States, Sénégal, Ecuador, Nicaragua, and Costa Rica. Contributions cover topics ranging from captive parrot re-wilding with pirates to blogging in the Nicaraguan forest with limited Internet access.
Perhaps more importantly, the ABS Perspective Series wants to reach out and share ABS student and faculty experiences with a diverse readership to raise awareness of biodiversity conservation issues. Outreach is an important axiom of actionable science, especially outreach that informs, improves and influences management and policy. I consider both the ABS Perspectives Series and BioDiverse Perspectives outreach initiatives to communicate the biodiversity conservation mission to the general public, communities where our research has been conducted, fellow academics and practitioners, and institutions that can provide logistics, infrastructure, and support. We must intend to make and practice making our research accessible and intriguing to everyone.
November 18, 2014
The dark side of theoretical ecology
Figure 1. Three types of mathematical models of complex dynamic systems.
Dedicated to the memory of Sir John Maddox (1)
Good science must be transparent in its theories, models and experiments. In my own research I often remember David Tilman’s great article which draws attention to the fact that ecologists investigate interspecific competition phenomenologically, rather than mechanistically (2). The article was published in 1987, however it is relevant for biodiversity science and mathematical modeling of complex systems even today. It discusses a problem among field experiments designed to test for the existence of interspecific competition in natural communities. Tilman suggests, ‘The design of the experiments, though, is a memorial to the extent to which the often-criticized Lotka-Volterra competition equations still pervade ecological thought. The experiments used a nonmechanistic, Lotka-Volterra-based, phenomenological definition of competition: two species compete when an increase in the density of one species leads to a decrease in the density of the other, and vice versa. … With a few notable exceptions, most ecologists have studied competition by asking if an increase in the density of one species leads to a decrease in the density of another, without asking how this might occur. … Experiments that concentrate on the phenomenon of interspecific interactions, but ignore the underlying mechanisms, are difficult to interpret and thus are of limited usefulness.’(2) To design an adequate field experiment we should have a mechanistic model based on a mechanistic definition of interspecific competition. Otherwise, we will not be able to overcome the limitations of phenomenological approach which hides from us internal functional mechanisms of ecosystems. Only a mechanistic approach will allow us not only to constate the loss of biodiversity, but to understand what needs to be done to save it. How to create such a mechanistic model? First, we need to know how to mechanistically model a complex dynamic system. A complex dynamic system may be considered as consisting of subsystems that interact. Interactions between subsystems lead to the emergence of new properties, e.g. of a new pattern formation. Therefore we should define these subsystems and logically describe their interactions in order to create and investigate a mechanistic model. If we want to understand how a complex dynamic system works, we must understand cause-effect relations and part-whole relations in this system. The causes should be sufficient to understand their effects and the parts should be sufficient to understand the whole. There are three types of possible models for complex dynamic systems: black-, grey-, and white-box models (Figure 1).
Black-box models are completely nonmechanistic. We cannot investigate interactions of subsystems of such a non-transparent model. A white-box model of complex dynamic systems has ‘transparent walls’ and directly shows underlying mechanisms – all events at micro-, meso- and macro-levels of a modeled dynamic system are directly visible at all stages. Logical deterministic cellular automata is the only known approach, which allows to create white-box models of complex dynamic systems (3). A micro-level is modeled by a lattice site (cellular automata cell). A meso-level of local interactions of micro-objects is modeled by a cellular automata neighbourhood. A macro-level is modeled by the entire cellular automata lattice. Unfortunately, this simple approach is commonly used in the overloaded form, what makes it less transparent. This is achieved by adding differential equations and stochasticity. Grey-box models are intermediate and combine black-box and white-box approaches. Basic ecological models are of black-box type, e.g. Malthusian, Verhulst, Lotka-Volterra models. These models are not individual-based and cannot show features of local interactions of individuals of competing species. That is why they principally cannot provide a mechanistic insight into interspecific competition.
A white-box model of a complex system is completely mechanistic. A white-box modelling is axiomatic modelling. To begin to create a white-box model we need to formulate an intrinsic axiomatic system based on a general physical understanding of the subject area under study. Axioms are first principles of the subject. René Descartes proposed that axiomatic inference is universal for any science on condition that a system of axioms is complete and provided that axioms are unquestionably true, clear and distinct (4). Descartes was inspired by Euclidean geometry which investigates the relations between ideal spatial figures. When scientists verify a theory first of all they should strictly verify its axioms. If at least one axiom is inadequate or an axiomatic system is incomplete, then the theory is inadequate too (5). Let’s consider an example of the inadequacy of ecological models in result of incompleteness of their axiomatic system. There are many models of population dynamics that do not take into account what happens with individuals after their death. Dead individuals instantly disappear with roots, stubs, etc. ‘One reason for the lack of understanding on the part of most botanists results from their failure to take into account the phenomenon of regeneration in plant communities, which was first discussed in general terms by A. S. Watt in 1947.’ (6)
Stephen Hubbell in his Unified Neutral Theory of Biodiversity (UNTB) in fact refuses a mechanistic understanding of interspecific competition: ‘We no longer need better theories of species coexistence; we need better theories for species presence-absence, relative abundance and persistence times in communities that can be confronted with real data. In short, it is long past time for us to get over our myopic preoccupation with coexistence’ (7). However, he admits that ‘the real world is not neutral’ (8). Since the basic postulate (axiom) of the UNTB about ecological neutrality of similar species is wrong, this theory cannot be true. In addition, local interactions of individuals are absent in the neutral models in principle. That is why neutral models cannot provide a mechanistic insight into biodiversity. The UNTB models are of black-box and dark grey-box types only – Fig.1. I agree with James Clark, that the dramatic shift in ecological research to focus on neutrality distracts environmentalists from the study of real biodiversity mechanisms and threats (9). Within the last decade, the neutral theory has become a dominant part of biodiversity science, emerging as one of the concepts most often tested with field data and evaluated with models (9). Neutralists are focused on considering unclear points of the neutral theory – the ecological drift, the link between pattern and process, relations of simplicity and complexity in modelling, the role of stochasticity and others, but not the real biodiversity problems themselves (8). Attempts to understand neutrality instead of biodiversity understanding look like attempts to explain the obscure by the more obscure. Nonmechanistic models make it difficult to answer basic ecological questions, e.g. Why are there so many closely allied species? (10) An example of the difficult ecological discussion is the debates ‘Ecological neutral theory: useful model or statement of ignorance?’ on the forum Cell Press Discussions (11).
Understanding of mechanisms of interspecific coexistence is a global research priority. These mechanisms can allow us to efficiently operate in the field of biodiversity conservation. Obviously, such knowledge must be based on mechanistic models of species coexistence. In order to create a practically useful theory of biodiversity, it is necessary to renew attempts to create a basic mechanistic model of species coexistence. But the question arises: Why do ecological modelers prefer to use the heaviest black-box mathematical methods, which cannot produce mechanistic models of complex dynamic systems in principle, and not use simple and long-known pure logical deterministic cellular automata, which easily can produce white-box models and directly obtain clear mechanistic insights into dynamics of complex systems?
Acknowledgements
I thank Vyacheslav L. Kalmykov for useful discussions and suggestions.
I thank Kylla M. Benes for helpful suggestions and edits.
References
1. J. Maddox, The dark side of molecular biology. Nature 363, 13 (1993). doi: http://dx.doi.org/10.1038/363013a0
2. D. Tilman, The importance of the mechanisms of interspecific competition. The American Naturalist 129, 769 (1987). doi: http://dx.doi.org/10.1086/284672
3. L. V. Kalmykov, V. L. Kalmykov, Verification and reformulation of the competitive exclusion principle. Chaos, Solitons & Fractals 56, 124 (2013). doi: http://dx.doi.org/10.1016/j.chaos.2013.07.006
4. R. Descartes, Discourse on the method of rightly conducting one’s reason and of seeking truth in the sciences. D. A. Cress, Ed., (Hackett Pub. Co., Indianapolis, 1637/1980), pp. xiii, 42 p.
5. B. Spinoza, Principles of Cartesian Philosophy: And, Metaphysical Thoughts. (Hackett Pub. Co., 1998).
6. P. J. Grubb, The maintenance of species-richness in plant communities: the importance of the regeneration niche. Biological Reviews 52, 107 (1977). doi: http://dx.doi.org/10.1111/j.1469-185X.1977.tb01347.x
7. S. P. Hubbell, The unified neutral theory of biodiversity and biogeography. Monographs in population biology ; 32 (Princeton University Press, Princeton, N.J. ; Oxford, 2001), pp. xiv, 375 p.
8. J. Rosindell, S. P. Hubbell, F. He, L. J. Harmon, R. S. Etienne, The case for ecological neutral theory. Trends in Ecology & Evolution 27, 203 (2012). doi: http://dx.doi.org/10.1016/j.tree.2012.01.004
9. J. S. Clark, Beyond neutral science. Trends in Ecology & Evolution 24, 8 (Jan, 2009). doi: http://dx.doi.org/10.1016/j.tree.2008.09.004
10. Anonymous. British Ecological Society: Easter Meeting 1944: Symposium on “The Ecology of Closely Allied Species”. Journal of Animal Ecology 13, 176 (1944). Stable URL: http://www.jstor.org/stable/1450
11. P. Craze, Ecological neutral theory: useful model or statement of ignorance? Available from Cell Press Discussions: < http://news.cell.com/discussions/trends-in-ecology-and-evolution/ecological-neutral-theory-useful-model-or-statement-of-ignorance > (2012).
October 7, 2014
FLUMP – Ancient ecologial networks, climatic niche evolution, functional diversity
It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!
The latest issue of the PNAS features a very interesting study, led by Justin Yeakel, “Collapse of an ecological network in Ancient Egypt”. The Authors studied the ecological effects of the extinction of mammalian species in Egypt, taking a very creative and remarkable approach in order to gather the data; they used artistic records found in tombs and in decorative objects produced over the past 6,000 years by the Egyptians in order to infer species extinctions and ecological dynamics. Their findings suggest that mammalian extinctions were non random and that large changes in the organization of these ecological systems coincide with periods of extreme drought and with the densification of the Egyptian population. Moreover, the decrease of diversity has led to an increase in the fragility of these ecological systems due to the loss of functional redundancy.
Adam M. Lawson and Jason T. Weir tested whether the rate of climatic-niche evolution of bird species varies with latitude, in a new preprint in Ecology Letters titled “Latitudinal gradients in climatic-niche evolution accelerate trait evolution at high latitudes“. The authors found a positive relationship between latitude and the rates of climatic-niche evolution and that climatic differentiation is often associated with divergence in traits indicative of ecological differentiation and reproductive isolation.
At last, I am happy to announce a new article, I co-authored with Jon Lefcheck and John Griffin, titled “Choosing and using multiple traits in functional diversity research”. In this commentary, we provide a brief discussion on choosing and using functional traits and some recommendations for best practice. We also explored, superficially, the behavior of some of the most used functional diversity indices, in terms of trait correlation, number of traits and species richness. If you are interested, check out the appendices to see the complete result of our simulation study and the R code for implementing it.
– Vinicius Bastazini.
September 11, 2014
