Category Archives: HC207

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome (Fierer, et al. 2012)

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The two essays on microorganisms were concerned with very similar ideas with very different applications. While Martiny’s essay considered that the properties effecting macroorganisms may be helpful in understanding the dispersal of microorganisms globally, Fierer posits that perhaps those same properties may effect microorganisms on a much smaller scale, within each human being.

Fierer puts forth some interesting ideas such as succession among microbiome communities which could be initiated by disturbances such as treatment with antibiotics (Fig 3). I can’t quite figure out how to square that idea with any sort of climax, especially given the rapid and constant changes in the human microbiome. He also states that taxa of microorganisms may fit into biological niches within the body.

That having been said, I am hesitant to agree entirely with Fierer. As I mentioned in my discussion question last week, the conditions that determine behavior of one species or in one region don’t necessarily do the same to other populations. They may be useful as a guide as to what to study, though there can be no promise as to whether those studies would be fruitful. One particular hurdle facing this line of inquiry is the difficulty inherent in conducting studies given the diversity of microbiomes among individuals. How accurate is a control when abundances of taxa even within family members can vary by up to two orders of magnitude (Turnbaugh et al. 2009a)?

Experimental Zoogeography of Islands: The Colonization of Empty Islands. Daniel Simberloff and E.O. Wilson (1968)

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This study was of the events following a defaunation event on six islands of the coast of the Florida Keys, each island consisting of one or several mangroves. Simberloff and Wilson suggest that given time the population of species on each island will reach a predictable dynamic equilibrium consisting of a similar but constantly changing cast of species.

The issues I found with this research were several. The authors conducted only a single survey of each island plus two controls before the experiment began and used this is an assumed average species number on each island, a sample size far too small from which to draw any conclusions. Beginning from this survey, any information they glean about average species numbers may match up to an anomalous “average” and wrongfully confirm their theories. Throughout the experiment, the collection of data was too infrequent given the ephemeral nature of many of the species involved. The experiment also ended before any of the islands populations were found to have arrived at a dynamic equilibrium, so any similarity between the pre-defaunation survey and the final survey could be a case of a broken clock being “right” twice a day, in this case, right meaning supporting the theory put forward in the paper. Finally, there is no indication that the two control islands were surveyed more than once before and once after the experiment, which would have given a much clearer view of the properties and typical variance of a dynamic equilibrium.

Aside from the conduct of the experiment, I found the writing to be a bit lacking. I would have found technical details on how the surveys were conducted, and where each island was located relative to a source and each other to be helpful in filling out my understanding of the theory.

My feeling toward this essay isn’t that the authors’ theory is incorrect, it’s that the way the experiment was conducted left didn’t find conclusive enough evidence to confirm it.

Landscape Ecology: The Effect of Pattern on Process. Monica G Turner (1989)

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Landscape ecology differs from most other ecological theories we’ve read in class in the way it approaches seeing a region. Where Clements would see a climax, or succession toward a climax, or Gleason would see millions of individual organisms vying for space to spread their seeds and germinate, or where Paine, Connell, or MacArthur or others may be studying a single species or a narrow portion of an ecosystem, Turner is taking a wider view. When I imagine the map of a region a landscape ecologist would use, I imagine many overhead transparencies that were used in school when I was younger; one would have the type of vegetation growing in a region drawn on it, another would be a topographical map, another shows drainage, another soil nutrient content, and so on. Layering these transparencies atop one another, one would begin to see patterns emerge where certain types of vegetation always grew near a stream but only in regions where another type of vegetation grew upstream, or perhaps the probability of a hectacre of land succeeding from one phase to the next in a given number of years is increased in proximity to a certain type of soil nutrient.

One of the points I appreciated about the essay is that, while it didn’t address the topic directly, I saw it as something of an answer to Gleason’s issue with the definition of a plant association. I see landscape ecology, when employed on a mass scale, as able to show the overarching trends in vegetational growth that would satisfy Clements’ and other’s definition of an association, while also having the nuance to address smaller regions that were anomalous to the general trend.

A few of the issues I found with this theory were that the more data one collected, the more variables were involved. In order to account for those variables more data still would need to be collected and so on and so on. In addition, there is an issue of scale. Turner writes on page 175, “Landscape complexity has not been shown to be constant across a wide range of a spatial scales… Applying predictions made at one scale to other scales may be difficult if landscape structure varies with scale.” On page 180 she also says, “Elucidating the relationship between landscape pattern and ecological processes is a primary goal of ecological research on landscapes… achieving this goal may require the extrapolation of results obtained from small-scale experiments to broad scales.” The issue here is that at each scale the variables involved will fluctuate. The scales aren’t just small or broad scale either; every scale, while similar will have slightly different considerations. What this leaves one with are more unknown unknowns the more one extrapolates from data extracted from a different scale. However, this is unavoidable because a thorough survey of all variables at every scale in every region of the earth is impossible, a point the author also addresses.

Once I began to understand the process of landscape ecology the utility quickly became clear. Being able to predict the behavior of a plot of land based on how it can be expected to interact with surrounding plots of lands could be extremely useful and paint a more accurate image of the future. The author points out that this form of fortune telling could and should be used by conservationists in planning preserves among other uses. I largely agree with the theory and the author’s closing statement that through experimentation and testing of the theory it could develop to an even more powerful tool.

Metapopulation Dynamics. Illka Hanski (1998)

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Metapopulation Dynamics is different in both form and function from all the previous readings we’ve done in Ecological Thought and Practice. Rather than perform an experiment and explain the results, as Paine, Connell, Lubchenco and Menge, and MacArthur did, or speak to the ideas and terms used in ecological thought as Clements, Tansley, and Gleason did, Hanski instead provided arguments for a way of predicting the behavior and trends of species in a region.

While I was reading Metapopulation Dynamics I had to revise the way I thought about a metapopulation. Initially, I thought of fish in ponds; the same species may be in several ponds. While each pond has its own population, they could also be observed as a whole and studied as a metapopulation. This conceptualization fell apart when Hanski began speaking about colonization. A species of fish colonizing a pond that wasn’t already connected to their own pond wasn’t helpful to me. Hanski also mentions pathogens as an example. If I have the flu, I have a population of influenza virus cells in my body. Considered with others with the same virus, the virus could be studied as a metapopulation. Colonization would take place, for example, if I sneezed and the virus landed on a surface. The virus cells may get into a healthy person and infect them, thereby colonizing another suitable space, or it might die before it colonizes, a risk of migration. Ultimately, after working through both of these, it helped me understand the example Hanski used, the Glanville Fritillary butterfly.

Hanski spends a good deal of time explaining how metapopulation dynamics can be used to predict a species’ persistence. I can’t explain any of the equations used, but when factoring the area of separate “patches” of populations, distance of the patches from one another, time, population density of patches, total number of patches, and other factors, one ought to be able to predict the persistence or tendency toward extinction of a metapopulation.  In this essay, I take patch to be a region of what MacArthur would call “suitable space”

There are a few, perhaps pedantic, issues I had with this essay. I don’t understand why, as Hanski says on page 42, why “for long-term metapopulation persistence the expected number of new populations generated by one existing population during its lifetime in an otherwise empty patch network must be greater than one.” Would replacement not be persistence? I understand that stochasticity leads to unforeseen events which could lead to the destruction of a single population, but if that group has already replaced itself with another colony elsewhere, the species should persist.  This sort of made me think of Zeno’s arrow, but I’m not sure how useful of a tool that is, considering Zeno was a philosopher and Hanski was using math.

In the last few paragraphs of the article, Hanski advocates for conservation in what seemed to me to be an emotional appeal to others. I highlighted the sentences, “We do not know which fraction of currently endangered populations and species are already committed to metapopulation extinction in their present environments. A real worry is that such ‘living dead’ populations and species are numerous, especially because the delay in reaching the new equilibrium is particularly ling in just those cases that matter most, where the new equilibrium is metapopulation extinction.” This type of appeal is new to me in academic writing. I appreciate that he voiced it though. Studying and understanding the environment is interesting but ultimately useless if that information isn’t applied to the preservation of life on earth.

Impact of Food and Predation on the Snowshoe Hare Cycle. Charles Krebs, et al. (1995)

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This essay opens up with the declaration that there is a 10-year cycle in the population of snowshoe hares. The experiment conducted was to determine if that 10-year cycle could be effected by manipulation of predation and prevalence of food in the populated region.

To conduct this experiment, the authors manipulated the environment in several ways during the cycle that was taking place from 1987 to 1994. After partitioning the region into nine 1km-square blocks. In two blocks, fertilizer was spread to promote the growth of vegetation and provide a more ample source of food to the hares. In two blocks, food was made more abundant directly. One block was fenced off to prevent mammalian predation. One block both was fenced off to prevent mammalian predation, as well as had supplemental food introduced. The last three blocks were used as controls. It is important to note that in the two regions with fences, the fences were permeable to snowshoe hares, and that predation from avian predators was not restricted.

To avoid this summary becoming too long, I’m going to be brief in getting to the results. The fertilizer had a very slim effect on the overall trend of the growth, peak, and decline of the hare population. Supplemental food had a positive effect during the decline, increasing hare density anywhere from 1.5 to 6-fold during the decline. Predator exclosure had almost no effect until late decline when it increased hare density by up a similar 1.4 to 6-fold. Supplemental food and mammalian predator exclosure had the greatest effect; from the peak onward, it increased hare density by up to 11-fold.

Even with the two most successful manipulations in place, the decline in population was still incredibly pronounced. Several factors could contribute to this, for example, the predator exclosures were permeable by the hares, meaning they could leave the exclosures and be eaten by the predators. This does not explain why the hares in the block with additional food as well as predator exclusion would have left. Additionally, the exclosures were not protected from avian predators, which may have had a profound undocumented effect on hare population, particularly when not in competition for food with land-based predators.

The results of this show that there is at least one more factor other than food and mammalian predation causing the 10-year cycle in snowshoe hare population. A follow up study restricting both land-based and avian predators from entering a habitat with additional food would help to determine the effect of avian predation. Another experiment excluding mammalian predators with an electric fence permeable to the hares around a region with supplemental food where additionally the behaviors of the hares were tracked when they left the exclosure may help determine what led them to expose themselves to predation.

Ecology of Some Warblers of Northeastern Coniferous Forests. Robert H. MacArthur (1958)

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Ecology of Some Warblers of Northeastern Coniferous Forests asks one central question, how is it that five species of warblers with similar needs and similar capabilities are able to live in the same region without one species out-competing the others and all but the dominant one being eliminated. MacArthur hypothesized that the species were in balance with one another because the factor limiting each species growth was intraspecific competition rather than interspecific competition.

To determine which factors governed the competition among species and among individuals of a single species, MacArthur observed the behavior of the species to discover their feeding habits and zones, nesting, and territoriality.

Observations showed each of the five species had preferences in their feeding habits and nesting locations. The species-wide preference in feeding locations largely meant that when a particular species was hunting for food, it was more likely that another individual from its own species had been there than an individual of any other species. The preference in feeding zone directly correlated to preference in nesting zone and territoriality as well, given that each warbler tended to build their nest in their preferred feeding ground and defend just enough space as they needed to eat and provide for young.

Further evidence that most competition was intraspecific is that each species nested as slightly different times of the year, meaning that the need for food was greatest among a single species at a time rather than among all species at once. When considered along with the preference for a single feeding area, the likelihood of a particular zone being over-hunted, thereby leading to the mortality of fledglings, was due to the behavior of others of the same species. There were several times when new parents of fledglings would feed only one or two of their young.  This was shown to be the most common cause of mortality among fledglings.

To close the essay, MacArthur succinctly states that differences in feeding position, behavior, and nesting date reduce competition among species and instead focuses competition among individuals of each species.

Community Development and Persistence in a Low Rocky Intertidal Zone. Jane Lubchenco and Bruce Menge (1978)

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Though I had to read through Community Development in a Low Rocky Intertidal Zone, in part or in full, several times before I feel I came to approach understanding, I feel the central idea is one of the more useful ones I’ve yet to read about for Ecological Thought and Practice. In the essay’s introduction the authors state that while communities have several characteristics, it is a mistake to study them as separate phenomena when in reality they are interconnected. In my notes, I wrote the following in order to clarify for myself what I was reading about: “Succession depends on competition (Connell) but also predation (Paine), dispersal rates and reproductive output (Gleason), life histories and persistence (Clements).

I think that due to their more holistic approach Lubchenco and Menge were able to add to ecological thought of the day by confirming and documenting the interactions among the ideas that their predecessors had proven. Though their results stated that “the role of consumers in determining the pattern followed during community development, or succession, seemed of overriding importance” which primarily confirms Paine’s 1966 essay, but predation, they found was largely inversely proportional to wave energy. They also documented, through denudation of patched of the rocks, the importance of dispersal and growth rates in determining which species became dominant, but because their study took place over several years, they were able to show the persistence of the communities and how quickly those patches returned to the state at which they had been before the experiment. This persistence supports Clements theory of a tendency toward climactic climax.

Today in class we were asked whether or not Connell and Paine’s studies contradicted one another, here Lubchenco and Menge showed that at least in some communities, the two ideas are both valid. I thought the reading was helpful in understanding other ideas we’ve already covered in class. The use of so many variables and controls including not only the exclusion of predators but the enclosure of predators were useful in illuminating the authors’ points.

The Influence of Interspecific Competition and Other Factors on the Distribution of the Barnacle Chthamalus Stellatus. Joseph Connell (1961)

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Upon witnessing that two species of barnacles seemed to have the adults of their species segregated into horizontal bands on a rocky intertidal shore but that the youth of the higher species could be found in the lower band with the other species, Connell set out to study the primary reason for that segregation. His theory was that the completion for space between the two species bore at least some responsibility for the separation. This theory was supported by the following studies; two species will either compete for resources with one species becoming more dominant in an area (Beauchamp and Ullyott 1932) (Kenny and Stevenson 1956), equal distribution of one species is due to that species competing primarily with itself (Holme 1950) (Clark and Evans 1954), and if two species with similar needs are living in the same area it is because they are not competing for resources (Lack 1954) (MacArthur 1958).

The method Connell used to test this theory was to map the locations of the barnacle species Chthamalus Stellatus, hereafter referred to at C.S., in the period of the year before what he hypothesized to be C.S.’s competitor Balanus Balanoides, hereafter referred to as B.B.. After mapping the locations of C.S. it was possible to control the height above or below mean tide level so that the effects of competition could be seen in environments where both C.S. and B.B. were primarily observed. One half of all clusters of C.S.  growth were kept from being interfered with by B.B.. The growth and mortality rates in each case were recorded.

The results showed that C.S. was fully capable of growing to maturity at the levels on which B.B. was typically dominant, implying that the competition for space is what was preventing C.S.’s proliferation at the lower levels. In fact, while the hypothesis was that competition was at least somewhat responsible for the distribution of the two species, the study found that predation by carnivorous aquatic snails, battery by waves, and intraspecies crowding combined were not much more likely to be responsible for the death of an individual C.S. than was crowding of some sort by B.B..

I read this essay about two hours ago and have been idly trying to come up with an example of competitors coexisting. None come to mind except in the case of lions and tigers and bears coexisting in Oz. Given this, I can’t find fault in Connell’s reasoning. His experiment took into account as many variables as I could think of and the information gained fulfilled his hypothesis without assumption. In the case of this essay the limited resource in question was space, but it is easy to imagine that if the same experiment were performed on species competing for water or a nutrient source like meat the results would show that at least some of the reason for animal dispersion was due to interspecific competition. As a follow up to this study, I would be interested to see if there were more studies done on intraspecific competition and what its causes may be.

Food Web Complexity and Species Diversity. Robert T. Paine (1966)

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In one of the most easy to interpret essays I’ve ever read, Paine states in quotes the hypothesis to be “local species diversity is directly related to the efficiency with which predators prevent the monopolization of the major environmental requisites by one species.” He goes on to say that the study he performed was on rocky, intertidal marine organisms, though the results may have wider applications.

To test his theory, Paine observed undisturbed portions of intertidal seashore rock to establish a baseline of the eating habits and caloric intake of the represented carnivorous life. In doing this, he identified what he considered to be the “terminal carnivore” or as other people might know it, the top of the food chain. The idea of the terminal carnivore is that, in each local environment, there is one animal that kills and eats without being killed and eaten. After determining the average eating habits within this environment and illustrating the food web, the environment was kept free of the terminal carnivore for a period of time, while all other factors remained natural. In the case of this study, the terminal carnivore was a species of starfish. Also represented in the food web were mollusks, carnivorous aquatic snails, herbivorous aquatic snails, and barnacles. The information on specific ratios and species may be found within the publication itself and henceforth I will be writing about the ideas and conclusions of the paper more so than data.

The results of the removal of the terminal carnivore was that within four months 60-80% of the surface area of the rock face was covered in a particular species of barnacle, six months after that that species was being crowded out by another. The system itself had decreased in diversity from a 15 species environment to an eight species environment.

The interpretation of this data was that the removal of the most efficient predator had a negative effect on the number of species living in an environment. The presence of the second most efficient carnivore, even taking into account an increase in density of up to 2,000%, did not seem to be sufficient to prevent the monopolization of space by one of the represented species, at the expense of the presence of others. In the absence of a complicating factor, in this study predation, the competition for space can be “won” by a particular species. The removal of the top predator has an outsized effect on the simplification of an environment.

The author later suggests two follow up studies. The first is to determine if resource monopolies are less frequent in areas with diversity than in similar environments with fewer represented species (an attempt to observe the results of this experiment without the human interference of artificially removing the top predator, if I understand) and to study more thoroughly the food subwebs.

When I was in AmeriCorps, one of the projects my team worked on brought us to Raccoon Creek State Park near Pittsburg, PA. While we were there, one of the park rangers gave the team a class on the local wildlife. After the class, because she was going to be working closely with us, the ranger began asking us questions about what we enjoyed doing outdoors, including asking about whom among us was a hunter. After one of the team members expressed objection to the hunting of deer, the ranger explained population control to us. Human beings had disrupted the food chain in the region three hundred years previously by hunting local wolf populations to near extinction. The wolves were competition for hunting game as well as being predacious of livestock. The result of the vast reduction in wolf population was a boom in the population of the wolves main prey, deer. As the deer population boomed, wildflower populations plummeted because they were being consumed by deer. The decline in wildflower population effected bees, which effected pollination among all sorts of vegetation, etc. As a result of all of this, the State of Pennsylvania, to this day, must release hunting licenses to keep in check the deer population.

I don’t know whether or not that park ranger ever read Robert Paine’s “Food Web Complexity and Species Diversity”, but once I realized the parallels between the two stories, I immediately understood much better what Paine was hypothesizing. I largely agree with Paine’s hypothesis and conclusions, though I’m still somewhat hesitant to agree that “in the absence of a complicating factor (predation), there is a “winner” in the competition for space, and the local system tends toward simplicity.” In this essay he admits that the area under study never reached equilibrium in the time it was under observation. My instinct leads me to believe that if the observation were extended until such a time that equilibrium were again reached the diversity may have climbed again to levels near where they were at the start of the experiment.

Nature and Structure of the Climax. Fredric Clements (1936)

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Clements’ Nature and Structure of the Climax was concerned, as one might expect, with the state of climax of vegetation. Clements initially explains what a climax is, followed by issuing a series of questions one would ask when determining whether or not a region constitutes a climax. He goes on to argue in favor of the theory that there is only one real climax and multiple proclimaxes leading up to it. Finally explaining the structure of a climax and the roles of those species involved play.

Having not read a great deal of ecological literature previous to this, I have always imagined climax as a flash in the pan, however, in the case of ecological studies, a climax is when vegetation (over a vast area, in this reading at least) reaches a state of equilibrium. For example, a climax may be the entirety of the Great Plains in North America; every year the same plant life is dominant throughout the entirety of that area. The term biome is used instead when one is referring not only to vegetation but also animal life in a region.

Clements lays out at least four “tests” of a climax. To qualify as a climax a region must be characterized by the same form in the dominants i.e. to be considered part of a grassland climax, the dominant type of vegetation must be grass throughout. No region in which trees are dominant can be considered a portion of the grassland dominant. A region also must have the presence of the same dominant species in all or nearly all of the associations (a subdivision of a climax). Subdominants are used to link associations together, and some animals may be used as indicators too, particularly smaller, less mobile animals.

The essay goes on to argue that contrary to what Tansley said in my previous reading, there is only one kind of climax. Climax can only be used to define an area if it is one in which a community is “capable of maintaining itself under a particular climate, except where a disturbance enters.” Meaning that except in the case of the addition of a variable such as human interference, forest fire, or mass migration, a region is in a state of dynamic equilibrium. Anything appearing to be a climax that does not fit this criteria should be considered a “proclimax” defined as resembling the climax in one or more respects but gradually replaced by the latter. Of proclimaxes there are four types; subclimax, dis-, pre-, and post-. The definitions of disclimax and subclimax are clearest and best address arguments made by Tansley in 1935. Tansley referred to a “mowing” or “grazing” climax, one in which the interaction of an outside force such as a human cutting down grass or a herd eating it, reaches a sort of equilibrium with the plant life. Clements would refer to this as a disclimax, a subversion of the typical climax or succession to the climax. A preclimax is an apparent climax before the climatic climax, perhaps the climax of a particular phase of succession, or the climax of vegetation shortly after a fire, before the typical dominant again matures in the area.

Having thoroughly argued for how a climax should be described, Clements goes on to explain the structure and rolls within a climax. A dominant is the most abundant and controlling species in a climax, by which, it seems, a climax is defined. A subdominant is any species that is not the dominant. The influents are the animal species of a biome, so called because of their influence on vegetational life. The units of a climax, in descending order of importance, are, association, consociation, faciation, lociation, society, and clan. I won’t here define each, but suffice it to say that each is smaller in size than the one before and with each grade the degree of diversity allowed is greater. A more full explanation is in my notes from this reading and the most complete explanation is the text itself.

I am glad to have read this and to have more of the terms I expect to find useful defined. I agree with Gleason’s (1926) arguments as to the difficulty in defining an association or climax, though, as I mentioned in my writing about that essay I understand the utility of these definitions. If these terms are the ones we are going to be using in class, I will need to take place in a discussion about them before I feel confident enough in their meanings to use them. Regarding Clements specific argument as to the only type of climax being that of climatic climax, I disagree somewhat, as it seems to entirely ignore human interaction with the environment. I would argue that when it comes to growing crops or grazing a herd, there is an equilibrium, though a more curated one than exists in nature.

Regarding the writing in this essay, it was far more confusing than Tansley (1935) and Gleason(1926). The multitude times Clements gave examples of his theories in nature including species names may have been very helpful to someone with more information regarding those species and regions, but to me they were only confusing. Having enjoyed reading the essays by Tansley and Gleason which both refuted some of the ideas Clements had previously written, I had hoped this essay would have addressed them somewhat. Instead, Clements references The Use and Abuse Vegetational Concepts and Terms only one time, and not in any too meaningful capacity, and Gleason not at all. Of the 36 works referenced in this essay a full 11 of them are works that Clements himself is author or coauthor of. Not being well versed in ecological thought of the time I may be mistaken, but I find this absence of debate somewhat disappointing.