6.1 Composition and diversity #
6.1.1 What a community description contains #
A community description states the scale, the taxon included, and the abundances. Composition is the list. Relative abundance is how even the list is. Physiognomy is the structure of the vegetation: canopy height, layers, the proportion of grasses and woody plants. Trophic structure is who eats whom. Interaction structure is the signs from Chapter 5, including indirect effects. None of these is a climax organism. Clements’s picture lost the argument in Chapter 1. It remains the mistake to avoid when a textbook draws an arrow labelled “the community develops.”
A rankโabundance diagram plots abundance against rank from commonest to rarest. A steep curve is a community dominated by a few species. A shallow curve is more even. Preston’s log-normal is a common shape for large samples and is a description of that shape. These notes do not fit a curve to a pretend forest.
6.1.2 Richness, evenness, and the indices that hide them #
Richness is the number of species. Evenness is how equal their abundances are. An index combines them and can rise because either one changed. Shannon’s index is Hโฒ = โฮฃ p_i ln p_i. Simpson’s concentration is ฮป = ฮฃ p_iยฒ, and 1 โ ฮป is a common diversity form. High ฮป means the community is dominated.
Invented proportions, for the arithmetic only. Two species at 0.5 and 0.5: Hโฒ = ln 2, about 0.69, and ฮป = 0.5. Two species at 0.9 and 0.1: Hโฒ is about 0.33, and ฮป = 0.81 + 0.01 = 0.82. Richness is 2 in both. The indices moved because evenness moved. A paper that reports only “diversity increased” has not said which.
Larger samples find more species. Comparing raw richness between a large sample and a small one measures effort. Rarefaction, or a coverage-based standardisation, asks what richness would have been at a common sample size or a common coverage. Until that is done, “site A is richer” is unfinished.
Whittaker’s three terms partition diversity in space. Alpha is local richness. Gamma is regional richness. Beta is turnover among sites. A landscape of different patches can have a high gamma and a modest alpha. Conserving one rich patch and losing the rest then loses the beta. The arithmetic relation depends on which beta formula is chosen. The idea does not: regional richness is local richness plus turnover.
Functional diversity uses traits rather than species names. Phylogenetic diversity uses evolutionary distance. Two communities with the same richness can differ in both. The species concept underneath the count is Evolutionary Biology. A richness number is only as good as the taxonomy and the sampling.
6.1.3 Food webs and the pyramids #
A food chain is one path. A food web is the set of paths. Connectance is the fraction of possible links that exist. Omnivory and intraguild predation, in which a predator eats both a consumer and that consumer’s prey, make “trophic level” a fraction. A fox that eats mice and berries is not an integer.
Food Web
Elton’s pyramid of numbers can invert: one tree, many insects. A pyramid of biomass can invert in water, where phytoplankton turn over fast and a small standing stock supports a larger standing stock of zooplankton. A pyramid of energy, production per unit time integrated long enough, does not invert. It records flux, not stock. Chapter 7 is why. A diagram that does not say which pyramid it is has not said anything about efficiency.
The JanzenโConnell effect is a spatial mechanism for tree diversity. Seeds and seedlings of a species suffer higher mortality from specialist enemies near the parent. Local recruitment of that species is suppressed where it is already common, which leaves space for others. It is a frequency-dependent enemy effect from Chapter 5, applied to a forest. It is well supported in some tropical and temperate studies and is not the only reason a forest is mixed.
6.2 Membership #
6.2.1 Filters #
A local community is a regional pool that has passed filters. Dispersal decides who arrives. Abiotic conditions decide who can tolerate the site. Interactions decide who is excluded or who is facilitated. The order is a checklist for hypotheses. In a given patch, a competitor can exclude a species that would have tolerated the climate, so the filters are not a sequence the species experiences one at a time in a fixed order.
6.2.2 Keystone, dominant, foundation, engineer #
A dominant changes the community when removed because there was a great deal of it. A keystone has an effect large relative to its abundance. Power and colleagues formalised the comparison as a ratio of impact to abundance. Paine’s seastar Pisaster ochraceus, removed from a rocky shore in Washington, is the type case. Mussels (Mytilus californianus) then occupied the rock and the diversity of the sessile community fell. The seastar was not the most abundant animal. Its effect was to suppress the competitive dominant. Calling every important species a keystone empties the word.
A foundation species, in Dayton’s sense, creates the structure others use: kelp, a reef-building coral, a canopy tree. An ecosystem engineer (Jones, Lawton, and Shachak) changes the physical state of the site. Beavers flood a valley. Burrowing animals turn soil. Earthworms, where they are introduced outside their historical range, change litter and nutrient cycles and are then both engineers and, often, invasive. One species can be more than one of these. A canopy tree can be dominant, foundation, and, by its shade and its litter, an engineer.
6.2.3 Indirect effects and two cascades #
A trophic cascade is an effect that runs down the web. Suppress a predator and the herbivore increases and the plants decrease. Add a fourth level and the signs alternate. Hairston, Smith, and Slobodkin’s green-world hypothesis is a predicted cascade: predators limit herbivores, so plants are green. Tests differ by system. Cascades are well documented in some lakes, where removing piscivorous fish increases smaller fish, decreases grazing zooplankton, and increases phytoplankton, and on some rocky shores. They are often weaker, not absent, on land, where herbivores face defended, poor-quality food and predators are themselves diverse.
Sea otters, sea urchins, and kelp along the North Pacific coast are a classic cascade: otters suppress urchins, and kelp forests persist. Later work added killer whales eating otters in some areas, which shows a fourth level rather than a cancellation of the first result. The Yellowstone story, wolves reintroduced in the mid-1990s, elk, and riverside vegetation, is more contested. Elk numbers and behaviour changed, and so did hunting, drought, and other predators. These notes will not say that wolves by themselves restored the rivers. A cascade is a measured chain of effects. A popular diagram is not the measurement.
Indirect mutualism and apparent competition are the Chapter 5 signs once more than two species are in the picture. A predator that suppresses a dominant competitor raises the subordinate. The subordinate and the predator are then linked by an indirect benefit, without being mutualists.
6.2.4 Neutrality again, at the community scale #
Niche assembly says differences stabilise coexistence, as in Chapter 5. Neutral assembly says that among similar species, drift and dispersal explain abundances. Most empirical answers are “both, depending on the guild and the scale.” A null model that preserves the number of species per site and the number of sites per species is the honest comparison. These notes keep the method from Chapter 1 and do not declare a winner for every taxon.
6.3 Succession and disturbance #
The study of Succession and disturbance provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
Ap Biology – Primary Succession
6.3.1 Primary, secondary, and the word “climax” #
Succession is directional community change after a disturbance or on a new surface. Primary succession starts without a developed soil and without a local seed bank: new lava, a retreating glacier, a bare dune. Secondary succession starts where soil, a seed bank, or living roots remain: a fire, a fallow field, a treefall. Plant Biology describes the change in plant form, including the tendency of early colonists to have small dispersible seeds and later woody species to be more shade-tolerant. The mechanisms are here.
Climax means a late stage set by climate and soil if disturbance is rare enough for it to be reached. It is not a goal, and it is not one composition for a climate. In many systems disturbance is frequent enough that the late stage is rarely occupied. A fire-maintained grassland is a state under its disturbance regime, not a failed forest. Gleason’s individualistic species explain why the sequence is a shifting overlap of tolerances rather than the development of an organism. Clements was right that the change can be directional and repeatable. He was wrong about the organism.
6.3.2 Facilitation, inhibition, tolerance #
Connell and Slatyer named three mechanisms. Facilitation: early species make the site more suitable for later ones. Inhibition: early species hold the site, and later ones enter when the early ones die or are damaged. Tolerance: later species are those that can grow despite the early ones, because they live longer or use a scarce resource more efficiently, and no help is required. All three occur, sometimes in one sequence.
Glacier Bay, in Alaska, is the classic primary sequence taught with a mechanism. After retreat of the ice, nitrogen accumulates with alder, which fixes nitrogen, and Sitka spruce then establishes. Later work showed spruce also suppressing alder. Facilitation through nitrogen is real there. It is not the mechanism of every succession. An old field follows whatever is in the seed bank and whatever can disperse in. Memorising one universal order of named species is the Clementsian habit without Clements’s excuse. Inhibition is common in marine fouling communities, where the first occupant holds the space.
6.3.3 Disturbance and the intermediate-disturbance hypothesis #
A disturbance, following White and Pickett, is a discrete event that removes biomass or opens space. A stress is chronic: cold, drought, a toxic soil. The regime is the frequency, intensity, extent, and timing of disturbance. A regime is not a list of accidents. Fire every decade is a property of some vegetation in the same sense that rainfall is.
Connell’s intermediate disturbance hypothesis says richness peaks at intermediate frequency or intensity. When disturbance is rare, competition goes to exclusion. When it is constant, few species tolerate it. In between, both colonists and competitors are present. The hypothesis is widely taught. The evidence is mixed, and Fox argued that both the logic and the empirical support are weaker than the textbook status. Huston’s related idea is more careful: richness depends on the rate of competitive displacement and the rate of disturbance together, and also on productivity, because productive sites can be competed over faster. These notes state the hypothesis and the doubt. A student answer that quotes it as a law has not read the tests.
Gap dynamics in a forest are succession at the scale of one treefall. Light-demanding species use the gap. Shade-tolerant species persist under the canopy and often take the gap later. The photosynthetic basis of shade tolerance is Plant Physiology. The coexistence is a spatial and temporal partition of one resource, light, and it is Chapter 5 applied to a canopy.
6.4 Change that is not one successional arrow #
The study of Change that is not one successional arrow provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
Aquatic Succession Or Hydrosere
6.4.1 Zonation #
Zonation is a spatial sequence. Succession is a temporal one. They can share mechanisms and they are not the same word. Connell’s barnacles on a Scottish shore are the clean separation of physiology from competition. Adult Chthamalus survived lower on the shore when Semibalanus (then called Balanus balanoides) was removed. The lower limit of Chthamalus was competition. The upper limit of Semibalanus was the time it could tolerate emersion. The upper species’ fundamental niche included the lower shore. Its realised niche did not. That is the Chapter 3 vocabulary with an experimental answer.
6.4.2 Alternative stable states #
Some systems have two equilibria under the same external conditions. A shock moves the system from one to the other. Shallow lakes are the best-established case (Scheffer): a clear state with aquatic plants, and a turbid state with phytoplankton. Plants stabilise the clear state by holding sediment and housing grazers. Algae stabilise the turbid state by shading the plants. Hysteresis means the path back is not the path out. Nutrient loading must fall below the level that caused the switch before the clear state returns, because the internal feedbacks have moved. The same logic applies to some grasslandโshrubland shifts under grazing and fire, where it has been demonstrated, and it should not be declared for every gradual trend. A smooth response to a driver is still the null. “Tipping point” means a threshold with a positive feedback beyond it. It is not a synonym for “a large change.”
Seasonal succession in plankton is a regular sequence inside a year, driven by light, nutrients, grazing, and mixing. It is succession in the broad sense and it resets. It does not produce a climax forest, and the word should not be asked to.
Key terms. Richness; evenness; alpha, beta, and gamma diversity; rarefaction; trophic cascade; keystone species; foundation species; ecosystem engineer; primary and secondary succession; facilitation; inhibition; tolerance; intermediate disturbance hypothesis; hysteresis; alternative stable states.
Summary. A community is a list, a set of abundances, and a set of interactions at a stated scale. Indices mix richness and evenness, so an invented two-species contrast can change Hโฒ with richness held at 2. Beta diversity is why the region is more than one plot. Energy pyramids do not invert; biomass pyramids can. A keystone’s effect is large for its abundance, as with Pisaster; a dominant’s effect is large because it is abundant. Succession is directional change by facilitation, inhibition, tolerance, or a mixture, and a climax is a late stage under a regime, not an organism. Intermediate disturbance is a hypothesis with mixed support. Alternative stable states and hysteresis are established for some lakes and are a special claim, not a description of every gradient.
Self-check.
1. Two samples have the same richness and different Shannon indices. What must differ, and why is a larger sample’s higher raw richness not yet evidence of a richer site?
2. Why can a pyramid of biomass invert in the plankton when a pyramid of energy does not?
3. In Paine’s experiment, which species was the keystone, which was the competitive dominant, and why is abundance the difference between those words?
4. At Glacier Bay, what did alder do for spruce, and why does that not make facilitation the mechanism of every succession?
5. What is hysteresis in a shallow lake, and why does returning nutrients to the level at which the lake switched sometimes fail to clear it?
