Diadromy and the assembly and restoration of riverine fish communities: a downstream view

McDowall, RM. 1996. Diadromy and the assembly and restoration of riverine fish communities: a downstream view. Can. J. Fish Aquat. Sci. 53:219-236.

McDowall’s emphasizes the role of diadromous fish – species that migrate between fresh water and the sea, like salmon – in structuring freshwater fish communities. Because they disperse through the sea, diadromous fish are a “source” for natural restoration of existing rivers and colonization of new rivers (e.g. melting glaciers in Alaska). Freshwater fish communities should be viewed as more open to colonization and invasion that previously thought. McDowall documents high frequency of diadromous fish species in river systems with high disturbance and extirpation rates, e.g. volcanism in New Zealand and glaciation in North American. Human modification of drainage systems has altered fish communities, by allowing new access points to diadromous fish (Great Lakes canals) and by preventing access (Pacific Coast dams building). The implication for fisheries management and restoration is that diadromy provides a means of natural restoration which is rapid, cost-free, and results in well-adapted stocks.

I am fascinated by the dispersal abilities of fish and implications for freshwater fish community assemblies, as well as the idea of “natural” restoration. The paper’s weakness is that it underplays the variation among diadromous species’ ability to disperse and colonize new river systems, as well as the extent of human modification to rivers.

Landscape Assessment of the Degree of Protection of Alaska’s Terrestrial Biodiversity (SOURCE)

Duffy, D. C., Boggs, K., Hagenstein, R. H., Lipkin, R., & Michaelson, J. A. 

(1999, December). Landscape Assessment of the Degree of Protection

of Alaska’s Terrestrial Biodiversity. Conservation Biology, 13(6), 1332-1343. 

Ecological Theory and Community Restoration Ecology

Palmer, M.A., R.F. Ambrose, and N.L. Poff. 1997. Ecological Theory and Community Restoration Ecology. Restoration Ecology 5(4):291-300

Community ecological theory plays an important role in the development of restoration ecology. As one of the classic reviews, this paper discussed several major questions, including: What are our evaluation endpoints of restoration success? What is the relationship between biodiversity and community restoration? Is restoration of habitat a sufficient approach to reestablish species and function? What are the roles of natural disturbance regimes and successional processes (the roles of dispersal, colonization, and community assemble theory) in restoration?

Even though it was published in 1997, lots of the specific questions posted here are still popular or debated in recent studies and management. For instance, how do we define the restoration potential for community attributes? Are there critical thresholds of physical habitat restoration that will ensure restoration of species and ecological function? How do we assess the degree to which established exotic species will prevent successful restoration of a functioning community? In this paper, I found most interesting is the explanation of the utility of different community ecology restoration theories will vary depending on attributes of the natural communities. So it’s important to know the community attributes (relatively predictable or stochastic) for stored sites.

Based on the frameworks of this paper, we definitely need to explore more specific evidences and theory explanations to get deeper understandings on community restoration.

Landscape Assessment of the Degree of Protection of Alaska’s Terrestrial Biodiversity

The Bristol Bay region of AK is currently facing mining development pressures                    (photo credit: F. Cundy)

Even the last frontier has its ecological limits. The authors of this paper identify the threat Alaska faces as development pressures increase and the protection of biodiversity within it’s vast borders lack an evaluation for the conservation of species and systems. The hope of this paper is to identify and quantify the existing measures of protection throughout the 28 ecoregions with which they’ve identify. Their findings quantify that nearly 55% percent of Alaskan lands have what they categorize as the lowest level of protection and therefore convince us that there is an outstanding need to use a science-based approach to protect biodiversity during development decisions. 

Within the study, authors assess the amount of land necessary for the conservation of biodiversity with GIS, measuring three biotic-abiotic layers; advanced very high resolution radiometer (AVHRR) landcover maps, ecoregions of Alaska, and locations of globally rare vascular plant species that occur in Alaska. Assessments of species, communities, and landscape scale ecosystems benefit biodiversity in Alaska, providing information which will help identify natural features at risk and provide place specific sensitivities as a prevention of development.  

The authors convey that they are trying to nominate their literature’s direction as one that can be developed more thoroughly, and to a finer grain of detail for it to make any tangible contribution to ecosystem protection. While the authors clearly identified the lack of rigor this study takes on, I like it particularly for that reason. Alaska is an enormous territory and its lands and resources are managed by a multitude of organizations and owners. It would require an enormously complex system of regulation to manage for biodiversity protection and cannot, nor should not be preserved through the same. If you’re as big a fan of AK as I am, it’s a good read.

Duffy, D. C., Boggs, K., Hagenstein, R. H., Lipkin, R., & Michaelson, J. A. 

(1999, December). Landscape Assessment of the Degree of Protection

of Alaska’s Terrestrial Biodiversity. Conservation Biology, 13(6), 1332-1343. 

Ecological Theory and Community Restoration Ecology

Palmer, MA; Ambrose, RF; Poff, NL. 1997. Ecological theory and community restoration ecology. RESTORATION ECOLOGY 5 (4): 291-300.

In this very informative paper, the authors contend that ecological theory, specifically community ecological theory, should inform the science of restoration ecology. (This may be old news now, but the paper was written back in 1997). The article poses, and attempts to answer, a number of larger questions for the field of restoration from a community ecology perspective. These questions are some of the larger issues we've been struggling with in the class, eg: Is restoration of habitat alone sufficient? How do we set appropriate restoration goals? Do we focus on restoring function or structure? How does one recreate natural disturbance regimes? Can we use restoration as an experiment to test ecological hypotheses?

I found that the paper provides an excellent background of the basic ecological theories and frameworks that inform restoration ecology today. I think this paper would be an invaluable resource to those of use who are not trained ecologists. The questions and answers presented in the paper, while 13 years old, are still mostly relevant today. Indeed, many of the questions that they highlight as 'in need of research' remain largely unanswered today. Finally, the authors offer practical advice for focusing restoration efforts to achieve desired goals, eg: the protection of an endangered species vs. total ecosystem diversity.

The only downside of the paper is that it is a little dated, and this became an issue when authors suggested using Succession Theory to inform restoration efforts. From my understanding of last class' discussion, current theoretical thinking is that the succession model is outdated. However, it's often necessary to "read back in time" to find gems like this paper that offer a clear and comprehensive look at basic theoretical frameworks. Well worth the read.

Image: Bison grazing in a field. One of the examples used in the paper to demonstrate the role of low-level disturbance in promoting ecosystem diversity.

Viewing invasive species removal in a whole-ecosystem context

Erika S. Zavaleta, Richard J. Hobbs and Harold A. Mooney

This article makes clear the complications involved in invasive species removal. Namely that the removal of one species can have unforeseen consequences on other invaders, and thus on the system as a whole. If you take out an invasive herbivore, maybe thistle goes crazy; or if you take out an invasive predator (like cats), maybe an invasive herbivore (like rabbits) goes crazy; and there are many other examples used to show the inherent difficulties of invasive removal when complex relationships are involved. Each removal from the food web will have an impact both above and below that species, and when an ecosystem has been hit with multiple invaders, as is often the case, it becomes more and more necessary to take the implications of restoration decisions seriously. Within this context the authors argue for stricter and more careful management of ecosystem restoration. More time spent beforehand determining the likely impacts of removal, and more time spent afterward with careful monitoring of the system. This is an argument against knee-jerk invasive removal, and for holistic ecosystem-level awareness in restoration. Brings to mind a question: are there situations when a novel ecosystem with multiple invasives reaches a more stable state than what we could realistically hope to restore it to?

The logic of this article is hard to argue with, and the multiple brief case studies make it an interesting read. But if these ideas are common sense to you, and you’re already in agreement with the premise, it’s not a necessary read.

Ecological Theory and Community Restoration Ecology

Palmer, M.A., R.F. Ambrose, and N.L. Poff. 1997. Ecological Theory and Community Restoration Ecology. Restoration Ecology 5(4):291-300
It is easy to see the connection between the papers we read this week to the ideas that sprouted in this article, however it is yet another review paper, but at least it is a seminal one:
Palmer et al. (1997) pose numerous questions specifically pointing out areas where further research is need. They begin by addressing the intersection between community ecological theory and restoration ecology, then turn to posing questions about identifying appropriate endpoints and whether targeting specific species versus species diversity provides more resilience and stability. Specifically they review the importance of trophic interactions, community-level variability in space and time, and functional diversity.
The portion of this paper I found most interesting was their discussion of the need for restoration projects to incorporate dispersal corridors, and viewing projects as patches that may be part of a metapopulation structure. I would have liked them to dig deeper into landscape context; specifically they did not mention the influence of the penetrability of the landscape matrix that surrounds the corridors.

What's new about old fields? Land abandonment and ecosystem assembly.

Cramer, VA; Hobbs, RJ; Standish, RJ.
TRENDS IN ECOLOGY & EVOLUTION 23 (2): 104-112.

Cramer etal. survey the “biotic and abiotic legacies” of agricultural cultivation to identify three distinct scenarios of plant community assembly and restoration of abandoned fields: those that assemble along a broadly repeatable successional trajectory, those that assemble along a novel and/or delayed successional trajectory, and those that remain in a persistent degraded state, with little assembly towards an historiral or natural state.

The value of this article lies in the fact that, as the authors argue, “old fields provide not only interesting case studies for ecological theory and restoration ecology but an important challenge for the practice of ecological restoration now and into the future.” (104) Both aspects come as a consequence of “the growing trend of abandonment of agricultural land worldwide” (ibid.) that creates fertile ground for the activities of restoration ecologists and land managers (pun most definitely intended).

The fundamental weakness with this article is the complete neglect of the other side of the “abandonment” coin, viz., the global land grab that is currently taking place. Intensive agriculture is not diminishing its extension through abandonment, but in fact growing more extensive as more and more diversified small farmers are driven (by violent economic and political forces) to rural or urban wage labor instead. The “future challenge” that Cramer etal. recognize, therefore, cannot limit itself to the “restoration of old fields” but must encompass the entire agricultural production system and its shifting spatiality that acts as the fundamental determinant of what ecologists and land managers consider “proper objects” of management, conservation, and/or restoration.


Gustavo Oliveira

Viewing invasive species removal from a whole ecosystem context

Zavaleta, ES; Hobbs, RJ; Mooney, HA. 2001. TRENDS IN ECOLOGY & EVOLUTION 16 (8): 454-459.


This paper gives a good but brief introduction to the need for considering the potential complex effects of removing an invasive species from an ecosystem. While there have been many success stories of removing an exotic species followed by the recovery of native and endangered species, there have been numerous cases of unforeseen and unwanted effects from focusing too narrowly on the removal of a single exotic species from an invaded ecosystem. The authors provide many examples and outline the basic ideas behind trophic level interactions and trophic cascades in the context of restoration and species removal.
I would include this paper in the "seems obvious when you read about it but maybe not so obvious when you're actually doing a restoration project" category. So, a valuable topic to read about and understand.

Viewing invasive species removal in a whole-ecosystem context.

Zavaleta, ES; Hobbs, RJ; Mooney, HA. 2001. TRENDS IN ECOLOGY & EVOLUTION 16 (8): 454-459.

This paper is mostly geared toward restoration practitioners who are designing invasive species eradication projects. The authors highlighted the possibility of creating secondary impacts on and/or unexpected changes in the ecology of a place after eradication of an invasive plant or animal species. Examples of secondary impacts included trophic cascades in a multiple invader system in which the eradication of one invader may be to the unintended advantage of a different invader in the same landscape. A trophic cascade influencing secondary impacts could be the unintended increase of an invasive herbivore pressure by releasing the invasive them from the pressure of an invasive predator after eradicating the predator. The paper described several possible permutations of cascades at various trophic levels. The authors also included other unintended impacts of invasive eradication such as the removal of habitats niches which natives may have become dependent on if an invasive had been long established.

The paper was a very good overview of how “successful” invasive eradication projects may impact a system in sometimes unexpected and negative ways. In this way it served the purpose of illuminating the need for pre- and post assessment of sites for better identification of possible feedback loops and for adaptive management purposes. However, although the authors gave real world examples to illustrate different secondary impacts the paper discussed, they did not give details on time frames of monitoring or give specific recommendations that might help a practitioner design better projects. The take home message was purely that future projects should combine eradication methods with larger ecological principles and goals. If you don’t know much about eradication projects and possible secondary impacts this paper would be a good overview.

Dispersal and establishment limitation reduces the potential for successful restoration of semi-natural grassland communities on former arable fields

Oster, M; Ask, K; Cousins, SAO, et al. 2009. JOURNAL OF APPLIED ECOLOGY 46(6):1266-1274

Oster et al. compared species richness and individual species recruitment and persistence patterns in ex-arable Canadian grasslands of different ages, both observationally and in an experimental seeding trial. They found that species richness increased with time since abandonment in the observational plots, but that recruitment patterns did not vary between young and old fields in the seeded plots. This suggests that dispersal limitations may account for lower species richness in younger plots, and that the time scale for natural reassembly of communities may be long (>50 years). Recruitment was low in both unseeded plots and plots without herbicide, suggesting that restoration practitioners must address both dispersal and biotic (competition) filters to restore these lands.

Combining a space-for-time approach with experimental seeding allowed Oster et al. to make important statements about how dispersal and competition limit recruitment in this system. Their introduction hooked me, however, because it promised to relate these patterns to functional traits, and this analysis didn’t pan out at all. None of the traits they measured related to difference in species composition in any of the plots. This leaves me wondering whether they just measured the wrong traits, or if some stronger driver (climate variability, perhaps?) overwhelmed any pattern that was there.

Seeding of an old field restoration experiment in Western Australia. Credit: Lauren Hallett

Species divergence and trait convergence in experimental plant community assembly

Fukami, T., Bezemer, TM, Mortimer, SR & van der Putten, WH 2005. Species divergence and trait convergence in experimental plant community assembly. Ecol. Lett. 8:1283-1290.

This study takes an experimental approach to looking at the role of history in community assembly in a grassland system. At the outset of the study, plots were seeded with one of six different seed mixes (different species composition; there was also a non-seeded control). Species composition and functional trait composition were followed over a 9 year period. The authors found that species composition remained different between the different treatments over the study period while all treatments converged towards a similar composition of functional groups.

Pros: I thought this paper did a good job highlighting the importance of history in community assembly and was a nice complement to the core papers, espcially the Trowbridge paper. It also made me think about what a big difference it makes how functional groups are delineated (the groups in this study were fairly narrow and if they'd been broader the authors might not have seen significant results).

Cons: Focus on theory rather than practical application.

Photo Credit: John DiGregoria, NPS

On the Poverty of Theory II. Stochasticity and Determinism, or What About the Microbes?

Bever et al. (2010) - Rooting theories of plant community ecology in microbial interactions. Trends in Ecology and Evolution 25:468-478

“Moreover, the shift from stochastic to deterministic statements about the world can occur in changing from one level of explanation to another in either direction. Not only can the apparently random be explained as a result of deterministic forces in higher dimensionality with more specification, but a reduction in dimensionality by averaging also converts stochasticity into determination.” (Levins and Lewontin, 1980)

Is the “plant community” an appropriate level of analysis to determine whether a process, or a collection of complex processes, is stochastic or deterministic.

Bever et al. (2010) suggests that predominant theories of plant ecology have an above ground bias. They argue that it is this bias has resulted in the limited success that community ecologists have had in finding a mechanism to explain “the coexistence of competing plant species.” By neglecting the less visible aspects community structure and function, plant community ecologists fail to recognize the constraints and feedbacks that microbial structure and dynamics have on plant-plant interactions, diversity and competition. Bever et al. propose three conceptual models that incorporate plant-microbial feedbacks to help rectify these gaps. They conclude by suggesting that due to the role that microbial population dynamics play in the plant-plant competition and coexistence, incorporating microbial dynamics can help explain gaps in plant ecology theory.

And so I wonder if “plant community” is really the appropriate level of analysis to be asking the question of whether community (re)assembly will be stochastic or deterministic? As well, does of reliance on the niche concept obfuscate ecosystem processes that would allow us to answer some of these questions?

Zavaleta, ES; Hobbs, RJ; Mooney, HA. 2001. Viewing invasive species removal in a whole-ecosystem context. TRENDS IN ECOLOGY & EVOLUTION 16 (8): 454-45

This article discusses the unintended consequences of species eradication that have occurred when restoration projects lack sufficient contextual ecological understanding. As a remedy, the authors urge scientists to conduct amplified studies and plans related to inter-species dynamics in restoration projects; to conduct substantial monitoring of these dynamics after a project's completion; and to adopt an attitude that accepts the unavoidable unknowns (and consequential experimental nature) of restoration projects that involve species eradication and/or re-introduction. While this may seem like a given now, this article was written in 2001, and is notable for its range of specific historical examples.

The difficulty of establishing sufficient knowledge and understanding for a well-conceived restoration project seems daunting in terms of both time and money. But the effort to understand inter-species relationships, and the acknowledgement of the limits of one's knowledge, seem to be important ingredients for present-term conceptions of restoration.

Neutral Theory and the Evolution of Ecological Equivalence

Hubbell, SP. 2006. Neutral Theory and the Evolution of Ecological Equivalence. Ecology. 87 (6): 1387-1398.

This paper provides an excellent concise overview of neutral theory (although it is still a bit dense). Hubbell covers all of the major points of his seminal book (The Unified Neutral Theory of Biodiversity and Biogeography, 2001), but in a much briefer and more accessible way. If you'd like a basic understanding of neutral theory but don't want to make it a focus of your research, I highly recommend this paper. The cartoon I've included clearly takes neutral theory to a ridiculous extent... if you don't get it, you'll just have to read the paper!

Incorporating Positive Interactions in Aquatic Restoration and Conservation

Benjamin S. Halpern, Brian R. Silliman, Julian D. Olden, John P. Bruno, and Mark D. Bertness. 2007. Incorporating positive interactions in aquatic restoration and conservation. Frontiers in Ecology and the Environment 5: 153–160.

Negative interactions (competition, predation) commonly dominate ecological research over much of past century. This paper discusses the role of positive interactions in restoration and conservation, with a focus on aquatic environments. The authors clearly link the type of positive interaction; with where/when it important for restoration and conservation and with implications for the practice of restoration and conservation. The broad categories covered include: traditional interactions (facilitation, foundation species, mutualisms, succession), within-population interactions (Allee effects, density-dependent recruitment), and large scale interactions (resource subsidies between ecosystems, ontogenetic habitat shifts, protection of neighboring ecosystems). The authors conclude that two key interactions to consider in management plans include: (1) foundational species population size in order to avoid Allee effects and (2) spatial arrangement of different ecosystems and connections among those systems.

As a restoration practioner and land manager, I found the author’s approach to directly link ecological theory to on the ground restoration practice refreshing. I could clearly see what types of interactions should be considered in restoration planning. However, the authors acknowledge that it is not possible to prescribe how best to incorporate positive interactions across management plans. In addition, little is known between trade-offs and consequences between different types of interactions. For this reason it is crucial for managers to understand that the importance of different positive interactions is context dependent.

Using assembly rules to measure the resilience of riparian plant communities to beaver invasion in subantarctic forests

Wallem, P.K., C.R. Anderson, G. Martinez-Pastur, and M.V. Lencinas. 2010. Using assembly rules to measure the resilience of riparian plant communities to beaver invasion in subantarctic forests. Biological Invasions 12:325-335.

In the 1940s North American beavers were introduced to Tierra del Fuego, an area shared by Chile and Argentina. Their populations have increased dramatically with no natural predators and a plentiful food supply. Wallem et al compared sites in Chile and Argentina that a) are currently inhabited by beavers, b)were at one point inhabited by beavers, and c)never were inhabited by beavers to assess if any of these disturbed communities were resilient to the disturbance. They found that upon introduction, beavers set these communities on a different trajectory and even after 20 years of beaver removal a community did not return to its initial state.

This paper provides a good example of how researchers often use observational data along a natural gradient to infer an alternate state without empirically testing for it. While they didn’t actually test any of the assembly rules within this system (a little misleading given the title), they did use the theory to provide an explanation as to why these systems were not recovering after disturbance.

Toward the end of class last week, we began discussing the usefulness of resilience in restoration. By the end, it still wasn’t clear how it could be applied. This paper helped me realize that there is a multiple step process to enhancing the resilience of a community. We must first check to see if there is a community resilient to the disturbance, before we can identify the mechanisms that may contribute to this resilience and inform managers of potential active restoration programs.

Viewing invasive species removal in a whole-ecosystem context.

Zavaleta, Erika S., Richard J. Hobbs, and Harold A. Mooney. 2001. Viewing invasive species removal in a whole-ecosystem context. Trends in Ecology & Evolution 16 (8) (8/1): 454-9.

One of the main points of this paper is that many eradication efforts have unintended effects, even when they are successful in removing an invasive species. Another invasive species may then become more of a problem, or a native species may have come to depend on that invasive species. They suggest applying food web ideas to invaded systems, including concepts of trophic cascades and predator-prey/herbivore-plant interactions, and then give many clear examples of situations in which eradicating an exotic may have unintended negative consequences for native species and even to ecosystem functions. I admit that this seems obvious to me; why wouldn't you apply ecological theories like this to an invaded system to understand better what the consequences of potential restoration plans might be? But that seems to be one of the lessons of this class: we need better communication between scientists and planners/managers (also this paper is from 2001, and is highly cited, so that's a good sign). One thing I like about this paper is that again we do a little thinking about animals as well as plants and I believe that complements all the plant community ecology in the core papers. It's clearly written and presents a number of concrete examples of applications of the theories to invaded systems. I would be really curious to hear whether this approach of evaluating potential eradication plans has actually been adopted on the ground since the paper came out in 2001. Shortcomings of the paper include an emphasis on eradication as a method for restoration (how often is this really the strategy of choice, and when is it even practical other than on islands?) and a call for more monitoring and pre-evaluation but of course no suggestions for how to make this practicable.

Viewing Invasive Species Removal in a Whole-Ecosystem Context

Zavaleta, ES; Hobbs, RJ; Mooney, HA. 2001. Viewing invasive species removal in a whole-ecosystem context. TRENDS IN ECOLOGY & EVOLUTION 16 (8): 454-459.

The authors discuss the importance of considering the potential secondary effects of invasive species eradication efforts in ecosystems where multiple invaders interact or where exotics have eliminated native species and replaced their functional roles. These secondary effects are particularly likely when efforts are focused on non-island ecosystems. The paper goes on to describe a valuable conceptual framework for evaluating the risk of unintended secondary effects. Yet, something is missing—while the authors acknowledge that global change is altering systems, their framework does not include this temporal challenge. Instead, they focus on species interactions & current ecosystem functions. Adding climate change’s temporal impacts to this framework requires one not just to evaluate short-term secondary effects, but also to assess whether climate conditions will continue to support the ecosystem restoration being attempted. In other words, if one manages to eradicate an invasive without unintended consequences, is that ecosystem likely to be more resilient than it would have been had we not attempted the eradication at all? The authors note a dearth of data in existing literature on the long-term performance of ecosystems in which “successful” invasive extirpations have occurred—a major challenge for planners.

Photo Credit, Lori Oberhofer, National Park Service.