1 Ontological Taxonomy of Breast Cancer18th Lecture – November 10, 2016 -- Last assignment is posted. -- Read Gilbert on Blackboard Thursday, November 10, 4:00 pm, 1024 KING—BIOLOGICAL SCIENCE COLLOQUIUM, Ontological Taxonomy of Breast Cancer Dr. Tan A. Ince University of Miami.

2 food webs and trophic structureSo, here is the food web inside pitcher plants, with a mosquito that eats a rotifer and several protozoa species. All these, plus a mite, eat bacteria, and the bacteria feed on the dead bugs captured by the plants. And, there are some other species as well that directly consume the ants. How do we describe the complexity? food webs and trophic structure

3 A. What is community ecology? V. Community ecology A. What is community ecology? 1. What is a community - "An assemblage of populations of living organisms in a prescribed area or habitat that interact with one another, directly or indirectly” Similar terms: ecosystem: all the interacting parts of the physical and biological worlds. association: group of species living in the same place. guild: species in the same community utilizing resources in the same way, often competitors. Remember Populations? Association – not interacting spiders not interacting with our classroom is part of the association. Students, TA’s and Professors Students must know these terms

4 A. What is community ecology? V. Community ecology A. What is community ecology? 1. What is a community - "An assemblage of populations of living organisms in a prescribed area or habitat that interact with one another, directly or indirectly” A caution that ecologists use “community” to mean two different things: -- as described above, all the species in an area or -- what might more properly be called a guild, which is all the species that share a resource base (e.g., birds, rodents, or plants) -should refer to multiple trophic levels (entire food webs). -not within a single trophic level or a guild. Be careful

5 A. What is community ecology? 1. What is a community? V. Community ecology A. What is community ecology? 1. What is a community? 2. Approaches to studying communities a. Descriptions - associations between different species and between different species assemblages and climate. Biomes, Holdridge classification, now GIS. Phytosociology - the study of the composition and structure of plant communities. b. Population-based approaches - reductionist view, using individuals and species as building blocks and units. Stresses biotic interactions such as predation and competition. c. Ecosystem ecology - also can be reductionist, using energy and nutrients as units instead of individuals and populations. People love maps – explorers which types of communities are where. lots of different forms of these Biome – vegetation pattern => temperature and precipitation

6 Holdridge Classification SchemeThe Holdridge scheme defines habitat types by precipitation and, essentially, temperature (evapotranspiration is related to temperature)

7 Example of PhytosociologySome Floristic provinces of NA: I. Tundra II. Northern conifer III. Eastern deciduous IV. Coastal Plains V. West Indian VI. Grassland VII. Cordilleran Forest VIII. Great Basin IX. California X. Sonoran dominant vegetation types  “floristic provinces” just based on observation of patterns. Don’t say anything about forces which may have created these vegetation patterns.

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9 Habitats around TallahasseeThis underlying geology and geological history results in 3-4 major habitat types. Above the Cody Scarp is largely mixed forest, with long-leaf pine, magnolia, and oak.  Below the scarp is mostly Pine Flatwoods and Pine Sandhills, along with Swamp Forest along rivers, largely depending on elevation and the presence of old sand dunes.

10 A. What is community ecology? 1. What is a community? V. Community ecology A. What is community ecology? 1. What is a community? 2. Approaches to studying communities a. Descriptions - associations between different species and between different species assemblages and climate. Biomes, Holdridge classification, now GIS. b. Population-based approaches - reductionist view, using individuals and species as building blocks and units. Stresses biotic interactions such as predation and competition. c. Ecosystem ecology - also can be reductionist, using energy and nutrients as units instead of individuals and populations. Other two -> processed-based. Population-come from the niche concept – resource availability, competition, and predation how these same forces then help to determine the numbers and types of species in a given habitat. The “currency” is individual fitness or population growth rates. The other approach ignores species

11 The food web may be known.So, here is the food web inside pitcher plants, with a mosquito that eats a rotifer and several protozoa species. All these, plus a mite, eat bacteria, and the bacteria feed on the dead bugs captured by the plants. And, there are some other species as well that directly consume the ants. How do we describe the complexity? The food web may be known.

12 . . . or it may be more of an association.~19 cm Atrina rigida . . . or it may be more of an association. 12

13 A. What is community ecology? 1. What is a community? V. Community ecology A. What is community ecology? 1. What is a community? 2. Approaches to studying communities a. Descriptions - associations between different species and between different species assemblages and climate. Biomes, Holdridge classification, now GIS. b. Population-based approaches - reductionist view, using individuals and species as building blocks and units. Stresses biotic interactions such as predation and competition. c. Ecosystem ecology - also can be reductionist, using energy and nutrients as units instead of individuals and populations. population based approaches some ecosystem approaches > Combining is best, but it is rarely done.

14 c. Ecosystem ecology - also can be reductionist, using energy and nutrients as units instead of individuals and populations. Ignores numbers of individuals or species. energy or nutrient flow structure communities in trophic levels Light - > photosynthesis into biomass -> Herbivores -> carnivores important factors -> size of these boxes (biomass within trophic levels) and the arrows between them (nutrient and energy fluxes). Odum’s model of the Silver Springs ecosystem

15 A. What is community ecology? B. How do we quantify communities? IV. Community ecology A. What is community ecology? B. How do we quantify communities? 1. Tools of community ecology a. growth form and structure b. number of species vs. diversity of species c. dominance/ relative abundance: d. rank abundance curves e. food or trophic webs Broad categories of ways we might describe communities, -> from the most to the least detailed.

16 A. What is community ecology? B. How do we quantify communities? IV. Community ecology A. What is community ecology? B. How do we quantify communities? 1. Tools of community ecology a. growth form and structure prairie vs. forests, coral reef vs. sandy bottom b. number of species vs. diversity of species c. dominance/ relative abundance: d. rank abundance curves e. food or trophic webs Recall phytosociology – identifying communities by some dominant biotic or abiotic feature. Ignores the species and certainly doesn’t reveal much about species interactions.

17 A. What is community ecology? B. How do we quantify communities? S = 13 spp. IV. Community ecology A. What is community ecology? B. How do we quantify communities? 1. Tools of community ecology a. growth form and structure b. species number, diversity, or eveness c. dominance/ relative abundance d. rank abundance curves e. food or trophic webs similar numbers of species different members. So Diversity S = 12 spp.

18 a. growth form and structure (sedans, trucks, etc.) IV. Community ecology . . . a. growth form and structure (sedans, trucks, etc.) b. species number, diversity, or eveness (10 vs. 9 species) Car color (species) Faculty Student Blue 16 7 Grey/silver 13 5 Red 18 Tan/brown 8 Black 17 White 9 Green 4 Two-tone 3 2 Orange Purple/pink 1 Here is a list of car colors from FSU lots, which we can treat like “communities” and compare. Since students and faculty have a very similar number of species, are they really similar communities? Use species number to compare different communities Now we have very similar species and numbers of species. But, are these communities the same? What else is different? (push the students to think about the relative proportions of different species)..

19 a. growth form and structure (sedans, trucks, etc.) V. Community ecology . . . a. growth form and structure (sedans, trucks, etc.) b. species number, diversity, or eveness Shannon-Weiner diversity index: Car color (species) Faculty Proportion (%) = p ln(p) pln(p) Blue 16 0.21 -1.56 -0.33 Grey/silver 13 0.17 -1.77 -0.30 Red Tan/brown 8 0.11 -2.25 -0.24 Black White 7 0.09 -2.38 -0.22 Green 4 0.05 -2.94 -0.15 Two-tone 3 0.04 -3.23 -0.13 Orange 2 0.03 -3.64 -0.10 Purple/pink quantify the patterns of relative abundance for communities. SW – popular – weird – increases as either the number of species or their EVENESS goes up. Eveness is how similar their abundances are – remember classroom community perfectly even community has equal numbers -> higher shannon-weiner diversity. Excel – Remember the negative sign Whenever we say diversity, we mean some combination of the number of species and their relative abundances.

20 a. growth form and structure (sedans, trucks, etc.) V. Community ecology . . . a. growth form and structure (sedans, trucks, etc.) b. species number, diversity, or eveness Shannon-Weiner diversity index: Car color (species) Faculty Student Blue 16 7 Grey/silver 13 5 Red 18 Tan/brown 8 Black 17 White 9 Green 4 Two-tone 3 2 Orange Purple/pink 1 FACULTY = 2.10 The faculty have a somewhat more diverse set of car colors. But, it isn’t clear if this is because there is one more “species” or if this is due to greater eveness. STUDENT = 1.94

21 a. growth form and structure (sedans, trucks, etc.) V. Community ecology . . . a. growth form and structure (sedans, trucks, etc.) b. species number, diversity, or eveness Shannon-Weiner diversity index: Car color (species) Faculty Student Blue 16 7 Grey/silver 13 5 Red 18 Tan/brown 8 Black 17 White 9 Green 4 Two-tone 3 2 Orange Purple/pink 1 FACULTY = 2.10 Diversity indices allow comparisons but confound species number and eveness. STUDENT = 1.94 Indices are handy, but confound species number with eveness of abundance.

22 b. number of species (S) and diversity of species (H’) Both can also be measured at different spatial scales: -- alpha diversity is within-habitat diversity, number of species in local, small areas of uniform habitat -- beta diversity is between habitat diversity, the variation in species composition from one habitat to another within a region. This is really a measure of variation in diversity, not diversity directly. -- gamma diversity is regional diversity, number of species in a larger area of interest across habitats or local areas Alpha – local regional – gamma They are related but how? you would think if alpha diversity increases, gamma diversity must increase. Not necessarily. Beta - variation in diversity among local habitats example

23 Consider three different regional communities, each with five different local populations and maximum of five species: 1 A, B, C, D, E A A, B 2 B B, D 3 C E, A 4 D 5 E B, C High alpha low beta High gamma Now, you should be able to figure out the next one. What is alpha (local) diversity? What is gamma diversity? What is beta diversity? (take a show of hands, if necessary, for high vs. low).

24 Consider three different regional communities, each with five different local populations and maximum of five species: 1 A, B, C, D, E A A, B 2 B B, D 3 C E, A 4 D 5 E B, C High alpha low beta High gamma Low alpha high beta Now, consider a somewhat more mixed community. What is alpha (local) diversity? What is gamma diversity? What is beta diversity? This is a little bit harder, but should give you . . .

25 Consider three different regional communities, each with five different local populations and maximum of five species: 1 A, B, C, D, E A A, B 2 B B, D 3 C E, A 4 D 5 E B, C High alpha low beta High gamma Low alpha high beta Mod alpha mod beta Note that all these have high gamma diversity, but we cover the range of alpha and beta diversity. The use alpha, gamma, and beta diversity measures allows us to incorporate spatial scale and patterns into our understanding of diversity.

26 Consider three different regional communities, each with five different local populations and maximum of five species: 1 A, B, C, D, E A A, B 2 B B, D 3 C E, A 4 D 5 E B, C High alpha low beta High gamma Low alpha high beta Mod alpha mod beta Note that all these have high gamma diversity, but we cover the range of alpha and beta diversity. Allows us to incorporate spatial scale and patterns into our understanding of diversity. It may be helpful to think of the relationship between these measures as alpha * beta = gamma though this is not totally accurate.

27 a. growth form and structure (sedans, trucks, etc.) IV. Community ecology . . . a. growth form and structure (sedans, trucks, etc.) b. diversity or species number (10 vs. 9) c. dominance/ relative abundance (blue/grey vs. red/black) d. rank abundance curves. Car color (species) Faculty Student Blue 16 7 Grey/silver 13 5 Red 18 Tan/brown 8 Black 17 White 9 Green 4 Two-tone 3 2 Orange Purple/pink 1 Now, back to our list of car colors. Another way to describe these communities be based on the dominant species (in red). Even better would be to somehow describe the rankings of species in each community. We can do that with a graph. S and H are similar for both communities, but H’ is hard to interpret because it is confounded by S. But Sand H are similar for both communities! But they are obviously different! 3 dominant sp vs. 2 dominant sp. Looks more even- but can’t tell from SW because it could be due to more species! Look at change in the relative abundance of species with a graph! We are going to take the most abundant species and plot its abundance first, then the next most abundant, etc. This gives us:

28 Rank-abundance curves for faculty/staff car, based on abundanceRank vs. Abundance Since we want to compare communities we want relative abundance find proportion like you did for SW

29 Rank-abundance curves for faculty/staff car, based on proportionExactly the same shape! Proportional is directly related to abunbance just changed the scale on the y-axis…………not the patterns. In some communities like are classroom disproportionately common Gotta use the log scale or you wouldn’t even notice us So, using a log scale for the y-axis gives a better view of the patterns in species abundance. So, let’s take the log of our proportions. Log of fractions are negative multiply by a constant, - won’t affect the overall pattern Taking logs should make the smaller bars bigger relative to the larger bars. Here we go . . .

30 Rank-abundance curves for faculty/staff car, based on log (proportion)Look at that This is RANK-ABUNDANCE CURVE! Beautiful isn’t it and you have to make a similar one for Assignment 3. Good for comparisons

31 faculty/staff students Dark Bars – faculty light bars – studentspretty similar. We could connect the dots and make lines We will come back to this, but let’s consider some data from real communities . . .

32 --- Faculty --- StudentsSo, if we go back and look at the car data, what do we see? If I had to hazard a guess, I say that the faculty/staff cars fit the geometric series, while the student data fits the broken stick. This suggests that faculty/staff may choose cars colors for very different reasons than students. But, I’d like a lot more data before I’d say much about this! --- Faculty --- Students

33 Note the log scale! Here is data from different forests in North America, from Panama to Canada – note the log scale To the right – #species. The slope – eveness steep vs. flat tropics – more species and more evenness

34 Why? What do these curves tell us about communities?Rank abundance curves have been measured for lots of communities and seem to fall into several different sorts of shapes. Why? What do these curves tell us about communities? What makes the curve flat? – all species equal, equal competitive ability maybe? Steeper curve? - competitive dominance by some species? Let’s think more.

35 Rank abundance curves have been measured for lots of communities and seem to fall into several different sorts of shapes. Why? What do these curves tell us about communities? (Here is where Dr. Miller demonstrates his strength by breaking some sticks) What makes the curve flat? – all species equal, equal competitive ability maybe? Steeper curve? - competitive dominance by some species? Let’s think more.

36 Random (well, not really):Rank abundance curves have been measured for lots of communities and seem to fall into several different sorts of shapes. Random (well, not really): What makes the curve flat? – all species equal, equal competitive ability maybe? Steeper curve? - competitive dominance by some species? Let’s think more.

37 MacArthur fraction (more random, not really sequential):Rank abundance curves have been measured for lots of communities and seem to fall into several different sorts of shapes. MacArthur fraction (more random, not really sequential): What makes the curve flat? – all species equal, equal competitive ability maybe? Steeper curve? - competitive dominance by some species? Let’s think more.

38 Dominance-decay (sequential):Rank abundance curves have been measured for lots of communities and seem to fall into several different sorts of shapes. Dominance-decay (sequential): What makes the curve flat? – all species equal, equal competitive ability maybe? Steeper curve? - competitive dominance by some species? Let’s think more.

39 -- geometric assumes division of resource in regular, sequential way.-- broken stick model assumes division of a single resource, but random. -- log-normal distribution also. In this case, it is likely that multiple factors are affecting the distribution of species abundances (such as competing for multiple resources). Most communities fit a log-normal distribution. common patterns seen in natural communities. The main conclusion here is that rank abundance curves are a great way to compare communities, Getting at the same thing as Shannon Weiner- but better What can we say about our car species?

40 --- Faculty --- StudentsSo, if we go back and look at the car data, what do we see? If I had to hazard a guess, I say that the faculty/staff cars fit the geometric series, while the student data fits the broken stick. This suggests that faculty/staff may choose cars colors for very different reasons than students. But, I’d like a lot more data before I’d say much about this! --- Faculty --- Students

41 Example questions from past exams over this materialI think the answer can be found by going back to Paine’s different types of food webs. Polis built a connectedness web that shows all possible pathways, regardless of strength or importance. If he had instead restricted his analysis to energy flow webs or functional webs, he would have found a much simpler picture, that would be more readily quantified by the measures we have discussed in class.

42 Example questions from past exams over this materialI think the answer can be found by going back to Paine’s different types of food webs. Polis built a connectedness web that shows all possible pathways, regardless of strength or importance. If he had instead restricted his analysis to energy flow webs or functional webs, he would have found a much simpler picture, that would be more readily quantified by the measures we have discussed in class.

43 A. What is community ecology? B. How do we quantify communities? IV. Community ecology A. What is community ecology? B. How do we quantify communities? 1. Tools of community ecology a. growth form and structure b. diversity or species number c. dominance/ relative abundance: d. rank abundance curves Most of the above stuff is best for guilds, but may not be informative about entire communities. e. food or trophic webs Remind me: What is Community Ecology? We are awesome, and community ecologists… why? -Diversity! – a million named speces- estimates up to 10 mil. Species Interactions, niches ect. -Conservation… -restoration (sustainability) Tools etc.

44 In this food web of the community that occurs in the water filled leaves of pitcher plant, the top predator is a mosquito larvae (W. smithii) that eats rotifers (H. rosa) and protozoa. The rotifers and protozoa in turn eat bacteria, as do the mites (S. gibsoni). The bacteria are basal species, as they consumer dead ants in this brown food web. There are a couple of more species of flies, whose larvae also feed directly on the ants. So, here is the food web inside pitcher plants, -with a mosquito that eats a rotifer and several protozoa species. All these, plus a mite, eat bacteria, and the bacteria feed on the dead bugs captured by the plants. And, there are some other species as well that directly consume the ants. -whats the source of energy? How do we describe the complexity?

45 Omnivores -- species that feed at more than one trophic level Top predators -- species that get eaten by nothing else in the food web Basal species -- species that feed on nothing within the web (usually plants) Omnivores -- species that feed at more than one trophic level Trophic species -- groups of species that have the same predator and prey Cannibalism -- a cycle in which a species feeds upon itself Connectance -- number of actual interactions divided by the number of possible interactions Compartments -- suites of species with strong linkages among group members but weak linkages to other species Terms help – you will be responsible for them Hide your kids, hide your wife – they’re eating everyone up in here! compartments – GROUPS OF SPECIES that interact with each other and not others

46 top predator top predator predator herbivore herbivore plant resourcesSome simple expectations for factors controlling food webs. Trophic interactions are +/- Top-down effects of increasing predators (trophic cascade) top predator top predator top predator predator predator predator herbivore herbivore herbivore plant plant plant resources resources Bottom-up effects of increasing resources resources

47 IV. Community ecology Food web patterns: i. limits to complexity. linkage density: average number of links or interactions per species in the web. The linkage density remains constant with the number of species -- regardless if there are 5 or 50 species in the community.

48 IV. Community ecology Food web patterns: ii. food chains are short. In a survey of 113 food webs, the most common maximum length is 4 and virtually all have 5 or fewer. The energetic hypothesis doesn't hold here, as marine food chains in areas of high productivity are actually shorter. Dynamical hypothesis suggests that long chains are unstable because fluctuations at lower trophic levels are magnified at higher trophic levels. So, shorter food chains in unpredictable environments -- appears to be correct.

49 IV. Community ecology Food web patterns: iii. constant proportions of species at each trophic level. Ratio of number of prey to number of predators is about 2 to 3 prey species per predator.

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51 IV. Community ecology Food web patterns: iv. Omnivory is rare. One explanation comes from modeling, in which omnivores tend to destablize communities. Not so true in aquatic communities where fish are often omnivores.

52 Study Guide Items from Lecture 18Terms: Community -- ecosystem Guild -- association Alpha and beta diversity -- Brown and green food webs beta diversity -- omnivores gamma diversity -- top predators Top-down and bottom up -- basal species Trophic cascade -- connectance Linkage density Concepts: Different ways to describe a community Diversity indices, especially Shannon-Weiner Alpha, beta, and gamma diversity – different spatial scales Rank-abundance curves -- shapes of the rank-abundance curves may have biological meaning (e.g., broken stick model) Polis’ suggesting food webs are too complex and have no clear trophic levels Three different types of food webs, according to Paine (connectedness, energy flow, and functional) Case Studies: Tropical tree diversity patterns Paine’s intertidal food web 52