Month: April 2019

How to study incremental and pervasive human impacts

The two papers presented this week were a poor pairing to address the topic of anthropogenic change. We had selected this theme in the context of global change and the ‘age of the Anthropocene’ – a time of unique human impact from urbanization, deforestation, agricultural intensification, and increased carbon emissions. The papers we selected did not directly measure or experiment these human-driven changes, instead only reviewing human impact studied in a separate paper or touching on deforestation/pesticide use tangentially. Further, both views exhibited a static before and after of human impact, rather than a more appropriate incremental shift of anthropogenic drivers.

Alessa & Chapin is an Update article in TREE that is basically a positive response to a conceptual review published in Frontiers in the same year by Ellis and Ramankutty, a paper now with over 1000 citations. Not only were we dissatisfied with this brief overview, but we found the land classifications incomplete due to the omission of marine systems. With global classification systems, as in Figure 1, I struggle to discern what is most important as a viewer and reader of the paper, rather than a user of spatial data. Certainly, the fine scale detail is necessary when inputting this layer into a future model to select sites, project a species’ habitat, or estimate nutrient cycling. As a figure in a paper, however, I argue that the authors would do better to focus on certain important regions of human impact, or to dilute their classification system to a smaller amount of bins (<= 7 to abide by color theory). We were unclear on the function of this type of work, though hypothesized that one or both of the authors had acted as a peer reviewer for the Ellis and Ramankutty paper.

Our historical paper, Likens et al. 1970  is a monumental study on how removing a component from an ecosystem can have consequences on nutrient flow. Their experiment, however, was not modeled after a standing logging practice. Instead, this study was an ecosystem science study rather than an explicit look at anthropogenic change. They provide an extensive look at all the ecosystem processes that can change due to a component in the nutrient cycle being disrupted, from specific elemental levels to hydrological function.

Recognizing these two papers did not complement each other nor excite us while reading, I think the best use of this blog post is to recommend a new pairing of papers that could be used in a future semester. For a current paper, I think Borer et al. 2017 in Nature Ecology & Evolution provides a cumulative approach to studying human impacts, specifically increased nutrient inputs, through comparative, observational, and experimental work. Not only is this paper does this work showcase the global, coordinated work of Nutrient Net, but it’s lead author, Elizabeth Borer, is a leading female ecologist in current ecosystems and disease ecology research.  For a classic work on ecological consequences of human impacts, I suggest Michael Soulé’s paper from 1985, “What Is Conservation Biology?”. In complement to the Borer et al., this work proposes a synthetic, multidisciplinary framework to study conservation biology and sets the stage for work documenting the “Anthropocene”.

References:

Alessa L, Chapin III FS. (2008). Anthropogenic biomes: a key contribution to earth-system science. Trends in Ecology & Evolution 23(10):529-31.

Borer ET, Grace JB, Harpole WS, MacDougall AS, & Seabloom EW. (2017). A decade of insights into grassland ecosystem responses to global environmental change. Nature Ecology & Evolution, 1(5), 0118.

Ellis EC, Ramankutty N. (2008), Putting people in the map: anthropogenic biomes of the world. Frontiers in Ecology and the Environment 6:439-447.

Likens GE, Bormann FR, Johnson NM, Fisher DW, Pierce RS. (1970). Effects of forest cutting and herbicide treatment on nutrient budgets in the Hubbard Brook watershed- ecosystem. Ecological Monographs 40, 23–47.

Soulé, M. E. (1985). What is conservation biology?. BioScience, 35(11), 727-734.

The dual axes of host-parasite systems

This week we read two disease ecology papers both in Nature: the classic Anderson & May (1979) paper that introduces the compartmental model foundational to most parasite population theory and a review from Keesing et al. (2010) on the multiple impacts biodiversity can have on infectious diseases, a continually debated topic in the study of emerging infectious diseases. Comparing the two papers was difficult. These works are different styles of articles (though both listed as reviews), written about two different scales, with different directionality of effects between hosts and parasites. Anderson & May focus on parasite trait affects on a single host species population through a modeling approach, while Keesing synthesized some case studies on host community traits that affect parasite populations. Inevitably disease ecology studies involve multiple species, which adds complexity to their dynamics. Taking perspectives from both reviews will allow us to apply to address the multiple different axes at play in host-parasite systems.

After working on disease ecology projects and in the midst of ECOL6150 Population Biology of Infectious Diseases, reading through Anderson & May’s work was particularly exciting. Most intriguing was their original use of standard variables, XYZ, (see Figure 3) rather than the now ubiquitous S-I-R compartmental model. I think Anderson & May allow simple adjustments to build to more complicated mathematical models, providing an interpretable framework to approach any population dynamics question. I appreciate that they isolate one variable, the number of hosts, and address this as dynamic in the context of parasite transmission factors. This trend has extended into other variables of focus in my labs, for instance, how the degree of provisioning or animal movement can also be dynamically scaled. Further, Anderson & May provided convincing evidence through their multipronged use of experimental, modeling, and comparative analysis. Lastly, I thought it was particularly intriguing to think about their point of modern vs. non-industrialized societies, in which infectious agents that are more epidemic wouldn’t survive due to low influx of susceptibles. Typically I think of infectious pathogens as more of undeveloped world issue, yet this view may emphasize intermediate levels of developement where there are large populations but poor public health access, as opposed to undeveloped and isolated communities. 

Unique to Keesing et al. is the authors’ motivation to influence policy, as evidenced by a current events-based opener rather than a scientific thesis. The authors elaborate on known issues regarding linkages between biodiversity and ecosystem services to include currently unknown consequences on the emergence and transmission of infectious diseases. While we agreed with the authors on many points, much of our discussion focused on the inadequate figures to argue the author’s points. In particular, Figure 1 and 2 suffer from poor data visualization techniques: awkward scaling, using non-interpretable colors and pie graphs. We discussed how the small sliver of green/yellow contrast on Fig. 1 did not hit home the main goal of this case study: that host behavior drives host competence. We thought that this could have been better addressed through bar graphs comparing hosts in a more straight forward way. Similarly, Fig. 2 was also disappointing in that there was too much information. I wish they had further synthesized trends based on continent or GDP of country, as on a map many of the pie charts were lost. I do think this paper set the stage for the classic disease systems used in biodiversity case studies: lyme and hantavirus. We did appreciate that they broke down the underlying mechanisms on how biodiversity loss can increase transmission through either changes in host/vector abundance or behavior. Despite these issues in figures, I think the overarching goal of the article to shed light on the urgency to study biodiversity’s role on infectious disease was effective in motivating science in the 2010s. 

References:

Anderson RM, May RM. (1979) Population biology of infectious diseases: part I. Nature 280: 361–367.

Keesing F, Belden LK, Daszak P, Dobson A, Harvell CD, Holt RD, Hudson P, Jolles A, Jones KE, Mitchell CE, Myers SS. (2010) Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature 468(7324): 647.

Niche Theory and the Empty Niche

This week we turned our discussion to the topic of ecological niches. That is, we discussed the variety of ways that a species’ ecological niche could be defined from its environmental tolerances, to the species interactions, to an n-dimensional hypervolume. We also discussed the concept of an “empty niche” and its role in speciation and invasion.

For our classic paper we read “Concluding Remarks” by G.E. Hutchinson,1 which he wrote to summarize the new ideas and thoughts from a recent Symposium on populations and demography. Hutchinson describes his quantitative approach to understanding niche theory, as pulling out the metaphorical vacuum cleaner to synthesize the “irrelevant litter” that has accumulated around niche theory. He starts by arguing that the applicability (or lack of) to human demography is not a reflection of a flaw in the theory, but instead demonstrates that we are not considering it on the right time scale or asking the right questions. He then uses an example of amphipods that don’t exist in seemingly suitable habitat to argue that the “suitable habitat” is based on our understanding and perception of the environment, which differs considerably from that of an amphipod species.  Our discussion of this long-winded paper ultimately led us to consider how variation in space/time can contribute significantly to the maintenance of species diversity.

We turned next to discuss the Sahney et al.2 and the concept of the empty niche contributing to the explosion of biodiversity with the expansion of species to terrestrial environments. Sahney used body size, diet and habitat to explore the potential modes of life that species could fill. The modes of life in some ways are similar to Hutchinson’s n-dimensional cube with 3 specific dimensions. In this case, Sahney argued that when species moved from sea to land there were countless niches waiting to be filled, which contributed to the rapid speciation and expansion of tetrapods. They also suggested that 64% of the terrestrial “modes of life” have yet to be filled and that tetrapod diversity may continue to increase as those modes are filled. While this suggestion will ultimately be difficult to verify, it seems plausible that empty niches may still play a vital role in understanding biodiversity.

Understanding the role of empty niche space can also help us better understand the vulnerability of systems to invasion. Recent anthropogenic disturbances to environments have led to major disruptions to ecosystems through both the extirpation of existing species and the introduction of novel players. These disruptions can lead to unexpected consequences like invader meltdown and community collapse. For that reason taking into account the amount of empty niche space in a habitat may help inform management decisions.

References:

  1. Hutchinson, G. E. Concluding Remarks. 117, 1937–1938 (1975).
  2. Sahney, S., Benton, M. J. & Ferry, P. A. Links between global taxonomic diversity , ecological diversity and the expansion of vertebrates on land. Biol. Lett. 6, 544–547 (2010).

Sessility: a model trait to study species interactions

For our week on competitive theory, we read two papers on the interactions between sessile (i.e. stationary, immobile) organisms. Almost 50 years apart, both Connell (1961) and Wulff (2008) utilize experimental manipulation in natural systems to assess species interactions. Competitive theory centers on similar species due to their diet, phylogenetic closeness or function fighting to utilize the same resource and can often lead to the exclusion of the less competitive species. Each of this week’s studies builds upon a profound amount of natural history to then test theory on which resource or phenomena may be lead sessile organisms to organize in space.

Connell explores the stark spatial segregation of two barnacle species, an upper resident Chthamalus stellatus and a lower resident Balanus balanoides along Scotland’s rocky intertidal shore. First, Connell removed barnacles to look at each single species along the full intertidal gradient. He found that  Chthamalus was able to survive in a much broader environmental area than observed (fundamental niche > realized niche). Balanus, the faster growing better crowd competitor, could not exist in upper bands of the zone due to environmental pressures (heat that led to desiccation). Interestingly, with the introduction of a predator or a parasite, these competitive interactions appeared to decrease.

Wulf’s study, however, observes collaborative interactions between sponges focusing on a poor competitor, Lissodendoryx colombiensis. Sponges uniquely form diverse assemblages that grow on top of each other, and seem to defy standard competitive theory. Wulf showed that crowding of sponges on and around Lissodendoryx deterred predation pressure from the starfish, Oreatus reticulatus.

A fascinating similarity between these two papers is they are both single-authored. Are there perceptions of a single-author? Does this show more initiative and independence of the scientist? Or does singularity in authorship show a lack of collaborative spirit, often necessary to link natural history and ecological mechanisms? Certainly both these projects took an immense amount of work beyond the author in data collection, processing and organization, and write-up. Yet, perhaps these tasks don’t seem to warrant authorship. I think this brings up a unique point about coordination vs. collaboration, and how lead authors may work with many, and yet be the sole driver of their research.

I was particularly struck, that not only is the Wulff paper single-authored, but the ten self-cited papers are single-authored as well. Standards of authorship operate differently among labs. For instance, dissertation work may be single-authored completely or be required to include the graduate advisors. In Dr. Wullf’s case, it seems to be the former, as her graduate students also produce single-authored work. I think this single-authorship, and perhaps the attitude behind it, maybe a component in how Dr. Wulff is so successful (R1 professor, Smithsonian fellow, and prolific publishing), despite the notorious leaky pipeline for women in her field.

References:

Connell, JH (1961). The influence of interspecific competition and other factors on the distribution of the barnacle Chthamalus stellatus. Ecology 42, 710–743 .

Wulff, JL (2008). Collaboration among sponge species increases sponge diversity and abundance in a seagrass meadow. Marine Ecology, 29(2):193-204.

Ecological Neutral Theory: From Concept to Tool

My first year of grad school has been a roller coaster. Developing my questions, taking classes, doing fieldwork, and so much reading. It has been a whirlwind learning about and discussing countless ecological theories, so I was really excited this week to read about one that admittedly has always confused me. Neutral theory is one of those “classic” theories that is taught in modern ecology classes and has always rubbed me the wrong way. The idea that there are no ecological differences between organisms or species seems like a non-starter, why would different species exist if all species were equal and the survival of a species was simply the result of stochastic processes?

To try to understand it, I went back and read some of Hubbell’s early papers on the topic including his work in Costa Rica and Tree Dispersal1 to try to understand why the concept of neutral theory seemed so at odds with my understanding of species interactions.  Of all of Hubbell’s papers, why was this one included on the penultimate list by Courchamp and Bradshaw? It was there in the very last paragraph that things started to make sense again.  Hubbell spends most of the paper discussing tree abundance and seed dispersal and how the tree community can be explained in simple terms by a stochastic model, but what caught my attention was the statement right at the end, so small I nearly missed it.

“Obviously this model is an oversimplified representation of the dynamics of natural communities, but it does provide a number of important lessons….”

There it was. Proof that even the author of the paper thinks neutral theory isn’t the full story. I turned next to a 2012 paper by Rosindell et al. that I hoped would hold all the answers. In The case for Ecological Neutral Theory2 the authors discuss some of the contentious debates surrounding neutral theory. They make a case that the concept of ‘neutral theory’ is not to treat all organisms as equal but to be used as a null model for comparison when species are not.  They point out that at some scales neutral theory may be the simplest explanation for the data, and it’s the job of the scientist to prove otherwise. Finally, a clear explanation for why Neutral theory is still relevant to modern ecology.

Perhaps, I missed the boat in my other ecology courses, but I can’t imagine presenting neutral theory in any other way but as a tool to be used. I’m left with more questions than answers about other “classic” theories and how they are taught in ecology courses, but at least on this topic I feel relatively satisfied.

The concluding thoughts of the Rosindell paper are a reminder to us all, that theories change and evolve, and we must recognize the limitations of our understanding.

References:

  1. Hubbell, S. P. Tree Dispersion, Abundance, and Diversity in a Tropical Dry Forest. Science (80-. ). 203, 1299–1309 (1979).
  2. Rosindell, J., Hubbell, S. P., He, F., Harmon, L. J. & Etienne, R. S. The case for ecological neutral theory. Trends Ecol. Evol. 27, 203–208 (2012).