Author: Anna

Metrics to compare communities in space and time

To finish out the course, we selected two papers on the topic of diversity metrics. First was the 2005 paper by Chao et al., as well as the recent 2017 paper by Hillebrand et al. Both papers proposed improvements to more traditional diversity metrics like the Jaccard index through more comprehensive inclusion of either unseen species or species composition. I think strikingly, these two papers address very different audiences. Chao et al. published in Ecology Letters target ecologists who may adopt this new metric in their own scientific research. Hillebrand et al. rather utilize their new species diversity metric as a way to inform land and biological monitoring program managers on the nuances of stable local richness levels.

I think the adoption of the Chao’s statistical approach to beta diversity has largely been accepted (with >1000 citations). Yet by reading the paper, we began to understand the importance of choosing metrics that best test your questions. Especially with measures as contentious as beta diversity, being clear on the benefits and limitations of certain measures can lead to better selection of complementary metric choices (similar to model stacking). The primary goal of Chao et al. was to draw attention that almost all richness measures will be undersampled, comparisons between sites are rarely equal in sampling sizes, and species occurrence is uneven. The authors compare their revised metric (that incorporates both composition and abundance) to existing frameworks on empirical data and simulations of uneven and incomplete sampling. I think parasite systems fit nicely into datasets that the authors suggest for use of their updated metric.

In many ways the Hillebrand paper seemed to reference key themes we had discussed with island biogeography, though now comparable or connected sites are the islands with various immigration and emmigration rates. While their adoption of species composition as a main reason for mismatches between global and local biodiversity trends, I did not find their results particularly compelling. Also, they fail to fully reach into how the species composition of  local sites with stable species richness values may influence the function of these communities. I think by using available datasets that certainly have trait data such as biomass this would have been a simple calculation that could have really hammered home their point. I do think this paper forced me to gain a deeper understanding of immigration credit and extinction debt, and perhaps how quasi-equilibriums from island biogeography may be misleading as to the equilibrium of certain sites. I did appreciate the conceptual diagram given in Figure 1 that shows how both richness and evenness may change in a system, and then the use of their metrics on already established datasets. I’m not sure how much the Dutch phytoplankton added to the analysis, and would have perhaps wanted a more diverse dataset to complement the Iowa phytoplankton or grasslands example.

I think these papers may be best referenced when researching a specific problem with a dataset we are using or when designing a diversity study. I appreciate the recognition of imperfect data but using statistics to overcome imperfect data in logical and repeatable ways. Whenever explaining species richness and its importance, walking through the sampling and analysis approach iteratively, as well as showing alternatives through validated datasets or simulations, strengthens the interpretations and importance of richness measures. 

Chao A, Chazdon RL, Colwell RK, Shen TJ. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology letters. 2005 Feb;8(2):148-59.

Hillebrand H, Blasius B, Borer ET, Chase JM, Downing JA, Eriksson BK, Filstrup CT, Harpole WS, Hodapp D, Larsen S, Lewandowska AM. Biodiversity change is uncoupled from species richness trends: Consequences for conservation and monitoring. Journal of Applied Ecology. 2018 Jan;55(1):169-84

The continuing development of the theory of island biogeography

Focusing on the theme of island biogeography, we read an experimental paper by Simberloff & Wilson as well as a synthesis paper from Patiño et al. that came out of working group discussions at the 2016 Island Biology Conference. Together, these two works span the wide breadth of topics foundational to island biogeography including dispersal dynamics, colonization patterns, and extinction rates. As my research may deal with thinking of patch dynamics between different habitats of various resources, clarification of island biogeography theory and its translatable application to non-island systems such as fragmented landscapes will be important.

Simberloff & Wilson’s goal is to test theory put forth by McArthur & Wilson’s Monograph in Population in Biology series. By fumigating mangrove islands off the coast of Florida, the authors are able to observe colonization and competition dynamics in action, until the islands reach equilibrium arthropod species richness levels. I was particularly impressed with the speed in which this equilibrium was reached, in less than a year. I think this may be in some ways do the methodology of the eradication, as resources and habitat were maintained unlike many natural experiments of island colonization after volcanic eruptions. However, this method may be appropriate for more targeted disturbances such as an invasive species or an epidemic that wipes out the arthropod community. With large scale manipulative projects like this, it seems inevitable that sampling and replication are issues. Across the six islands, the authors were not able to support that distance from the faunal source was indicative of time to equilibrium, despite clear distance patterns pre-defaunation on species compositions of islands. While species richness equilibriums were achieved, population abundances were not comparable to pre-defaunation. I think this exemplifies the more recent term of “immigration credit”, where colonizers can be counted for richness values before they are functionally fixed.

Patiño et al. ask 50 new questions from the context of island biogeography to drive future work. This genre of a “horizon scan” is an appealing synthesis piece that acts as a concrete product from conference discussions. To coordinate pre-conference surveys, during conference discussions, and post-conference editing certainly was a challenge, yet this paper exemplifies a model the type of planning necessary to optimize conference-based collaborations. I think in contrast to the methods used in the paper that spurred this reading group (Courchamp and Bradshaw 2018), this process seemed more iterative and with strategic inclusion of multiple perspectives. I also appreciated the ten questions that are heavily related to how island biogeography theory can inform conservation and management policies. This field seems to especially be influenced by cross-disciplines such as genetics, paleobiology, climatology and geology. I think similar to other areas of ecology, island biology studies will move to an increasingly ecosystem-level and function studies of multiple trophic level interactions, community dynamics, and global change.

Simberloff DS, Wilson EO. (1969) Experimental zoogeography of islands: the colonization of empty islands. Ecology 50, 278–296.

Patiño J, Whittaker RJ, Borges PA, Fernández‐Palacios JM, Ah‐Peng C, Araújo MB, Ávila SP, Cardoso P, Cornuault J, de Boer EJ, de Nascimento L. (2017) A roadmap for island biology: 50 fundamental questions after 50 years of The Theory of Island Biogeography. Journal of Biogeography 44(5):963-83.

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.

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.

Biodiversity: origins and obstructions

Following John Weins‘ seminar “Understanding the Origin and Future of Biodiversity Patterns” this week, we are well poised to pursue our first theme: biodiversity. His talk centered on the interplay of phylogeny, ecology, and species richness. In particular, he focused on clade diversity addressing if variation across the clades of life is determined by clade-age hypothesis or the diversification-rate hypothesis. We, however, will take a step back in our papers to look a much earlier perspective of biodiversity in Hutchinson and a contemporary look at changes in biodiversity through a field study by Uchida & Ushimaru.

Biodiversity didn’t surface as a term until the 1980s, with Thomas Lovejoy named as the “Father of Biodiversity”. At this time, the term was often synonymous with species diversity. Of course, ecologists now take a view of several axes of biodiversity: taxonomic, phylogenetic, and functional. Also, the early thought of biodiversity limited to primarily animals and plants, with parasites dynamics often unexplored in this context.

Hutchinson’s perspective of biodiversity stems from the hypothesis that resource heterogeneity drive biodiversity patterns. In his “Homage to Santa Rosalia”, he focuses largely on food webs and the mosaic structure of the world. He begins to link life-history traits to diversity patterns, showcasing animal size and habitat range as drivers of diversification (i.e. the more microhabitats an animal population is exposed to the more opportunities for divergence). This agrees with some of the contemporary work Wein’s presented on the importance of microhabitats for clade diversity. That an emergent process (in this case environmental exposures) produce different (more or less diverse) systems. Further, Hutchinson’s talk propels some early though on the yet-unnamed process of autocatalysis in evolution: diversity promotes diversity. This likely leads acts as a natural precursor and inspiration for E.O. Wilson’s theory of biophilia. Ultimately, Hutchinson talk is both grounded in theory as well as promoting the continued exploration of life’s mysteries.

An experimental approach to biodiversity, Uchida and Ushimaru test how agriculture practices in Japan impact plant and insect diversity. Their study supports the intermediate disturbance hypothesis, with the traditionally-managed plots showcasing certain rare species that are lost in both intensively-managed and abandoned plots. Uchida’s study is unique in looking at multiple trophic levels, as well as various relevant agricultural practices in the area. It would be interesting if there are historical records of plant and insect to couple these agriculture practices with pristine areas. With the growing anthropogenic change across the globe, it will become impossible to decouple natural patterns of diversity with the dynamic impacts of change due to agriculture, invasive species, and climate change (to name a few).

Tackling the 100 must-read papers in ecology

Entering my first year of grad school has been intimidating. Returning to school, entering a new department, and moving away from my comfortable circle of friends and co-workers has forced me into a state of unease. Most of all, I feel as I am playing a constant game of catch-up to understand what the field of ecology is. Then couple nearly a hundred years of historical papers with the perpetual flow of new scientific articles and comprehending it all is impossible. So when Courchamp and Bradshaw published their “100 articles every ecologist should read” it seemed another insurmountable feat that I would never accomplish. 

Despite the infeasibility, lists like theirs seem important. And more important than the content of their list, is the discussion it sparked in the ecological community and in my community now at UGA. Clearly, building a strong foundation of ecological theory and being able to recognize seminal and diverse work that has moved the field forward is valuable knowledge to both new and seasoned ecologists.

And that’s what has sparked this reading group. We all come from different academic backgrounds: biology, anthropology, and mathematics, and now ecology has brought us together. We aren’t cemented to the list composed by Courchamp and Bradshaw, but are excited by the challenge to build our own lists and share the ideas, authors, and themes that might inspire and guide our own future work. Most of all, we are encouraged that these lists are dynamic. Ideas change, new eyes on historical works may uncover underappreciated authors, and paired contemporary papers keep us on the edge of ongoing scientific breakthroughs. 

This semester we won’t read 100 papers, but we will:

  1. Engage with a wide range of literature, both historical and current, to develop a broad understanding of ecology 
  2. Consider classic papers not only in the context of the time in which they were written, but also in terms of how the field and their ideas have changed
  3. Develop a common language with our peers for discussing ecological theories