Chap 2.1, 2.2, 2.3 Community Structure Vocabulary

Measuring Ecological Diversity: Richness, Relative Abundance, and Rank-Abundance Diagrams

• Species Richness ($S$):

  • Defined as the total number of distinct species present within a specified area or sample.

  • Serves as a fundamental measure of biodiversity but does not take into account species evenness (how individuals are distributed among species).

• Relative Abundance ($P_i$):

  • The proportion of all sampled individuals in a community belonging to a specific species $i$.

  • Formula for relative abundance:         $\text{Relative Abundance} (P_i) = \frac{n_i}{N}$         where $n_i$ is the number of individuals of species $i$, and $N$ is the total number of individuals of all species sampled.

  • Boundaries and extremes:

    • Smallest possible value: $0$ (indicates that the species is absent from the community).

    • Largest possible value: $1$ (indicates a monoculture, where every single individual belongs to the exact same species).

• Ranked-Abundance Diagram:

  • A plot showing species relative abundance ordered from greatest rank ($1$) to least rank ($S$).

  • The vertical axis ($y$ axis) displays relative abundance on a logarithmic scale (e.g., $\log_{10}$ scale from $0.001$ to $1.0$), while the horizontal axis ($x$ axis) displays species rank abundance.

  • Interpretation of curve shape:

    • Slope: Represents species evenness. A flatter curve indicates greater evenness across species; a steep curve indicates severe dominance by a few species.

    • Line length along the $x$ axis: Represents species richness ($S$).

  • Comparison example (Garden/Meadow vs. Backyard):

    • A meadow/garden curve exhibits a shallower slope and extends across rank positions, demonstrating greater overall abundance and evenness.

    • A backyard lawn curve drops off steeply at rank $1$ due to extreme domination by a single grass species.

Mathematical Frameworks for Species Diversity: Simpson's and Shannon Indexes

• Diversity Index:

  • A summary value that takes into account both species richness ($S$) and species evenness.

• Product Rule of Probability:

  • The joint probability of two events occurring simultaneously or sequentially is equal to the product of their individual probabilities.

  • If $P(A)$ represents the probability or frequency of selecting species $A$ ($P(A) = \frac{n_A}{N}$), then the probability of selecting two individuals of species $A$ in succession is:         $P(A \text{ twice}) = P(A) \times P(A) = \left(\frac{n_A}{N}\right)^2$

• Simpson's Index Metrics:

Simpson's Index (D)**:
    *   Defined as the probability that two randomly collected individuals from a community belong to the exact same species.
    *   Formula:

            $D = \sum_{i=1}^{S} \left(\frac{n_i}{N}\right)^2 = \sum_{i=1}^{S} P_i^2$ * Range: $D$ is bounded between $0$ and $1$ ($0 \le D \le 1$). * Interpretation: As $D$ gets smaller, community diversity increases. A larger $D$ value indicates that larger populations of one or few species dominate the ecosystem (less diverse). * Simpson's Index of Diversity: * Formula:             $\text{Simpson's Index of Diversity} = 1 - D$ * Range: Values range between $0$ and $1$. Higher values reflect higher diversity. * Simpson's Reciprocal Diversity Index: * Formula:             $\text{Simpson's Diversity Index} = \frac{1}{D}$ * Range: Values are greater than or equal to $1$. As this metric increases, species diversity increases. * Simpson's Finite Population Dominance Index: * Used when sampling finite populations without replacement:             $\text{Dominance} = \frac{\sum_{i=1}^{S} n_i (n_i - 1)}{N (N - 1)}$ * Ranges from $0$ to $1$: $0$ indicates all taxa are equally present; $1$ indicates one taxon dominates the community completely.

• Shannon Index of Diversity ($H$):

  • Measures diversity based on information theory, placing greater weight on rare species.

  • Formulas:         $H = -1 \times \sum_{i=1}^{S} P_i \log_2(P_i)$         or         $H = -\sum_{i=1}^{S} P_i \ln(P_i)$         where $P_i = \frac{n_i}{N}$.

  • Interpretation: A larger calculated value of $H$ represents higher species diversity and greater evenness.

• Detailed Empirical Calculation Example: Backyard (Community A) vs. Meadow (Community B):

  • Community A (Backyard): Total individuals sampled $N = 1000$, Richness $S_1 = 13$.

    • Grass: $n_1 = 900$, $P_1 = 0.900$, $P_1^2 = 0.8100$, $n_1(n_1-1) = 809\,100$

    • Lilly: $n_2 = 50$, $P_2 = 0.050$, $P_2^2 = 0.0025$, $n_2(n_2-1) = 2\,450$

    • Geranium: $n_3 = 30$, $P_3 = 0.030$, $P_3^2 = 0.0009$, $n_3(n_3-1) = 870$

    • Violets: $n_4 = 10$, $P_4 = 0.010$, $P_4^2 = 0.0001$, $n_4(n_4-1) = 90$

    • Species A: $n_5 = 2$, $P_5 = 0.002$, $P_5^2 = 0.0000$, $n_5(n_5-1) = 2$

    • Species X, B, C, D, E, F, G, H: $n_i = 1$ each ($P_i = 0.001$ each), $P_i^2 = 0.0000$, $n_i(n_i-1) = 0$

    • Summary Calculations:

      • $D = \sum P_i^2 = 0.8135$

      • $\text{Simpson's Index of Diversity } (1 - D) = 0.1865$

      • $\text{Simpson's Reciprocal Index } \left(\frac{1}{D}\right) = 1.2292$

      • $\text{Finite Dominance} = \frac{812\,512}{999\,000} = 0.81333$

      • $\text{Shannon Index } H = 0.66876$

  • Community B (Meadow): Total individuals sampled $N = 1000$, Richness $S_2 = 7$.

    • Lupine: $n_1 = 400$, $P_1 = 0.400$, $P_1^2 = 0.1600$, $n_1(n_1-1) = 159\,600$

    • Grass: $n_2 = 200$, $P_2 = 0.200$, $P_2^2 = 0.0400$, $n_2(n_2-1) = 39\,800$

    • Daisies: $n_3 = 200$, $P_3 = 0.200$, $P_3^2 = 0.0400$, $n_3(n_3-1) = 39\,800$

    • Violets: $n_4 = 50$, $P_4 = 0.050$, $P_4^2 = 0.0025$, $n_4(n_4-1) = 2\,450$

    • Species A: $n_5 = 50$, $P_5 = 0.050$, $P_5^2 = 0.0025$, $n_5(n_5-1) = 2\,450$

    • Species B: $n_6 = 50$, $P_6 = 0.050$, $P_6^2 = 0.0025$, $n_6(n_6-1) = 2\,450$

    • Species C: $n_7 = 50$, $P_7 = 0.050$, $P_7^2 = 0.0025$, $n_7(n_7-1) = 2\,450$

    • Summary Calculations:

      • $D = \sum P_i^2 = 0.2500$

      • $\text{Simpson's Index of Diversity } (1 - D) = 0.7500$

      • $\text{Simpson's Reciprocal Index } \left(\frac{1}{D}\right) = 4.0000$

      • $\text{Finite Dominance} = \frac{249\,000}{999\,000} = 0.24925$

      • $\text{Shannon Index } H = 2.32193$

  • Core Ecological Takeaway: Even though Community A has 6 more species than Community B ($13$ species vs $7$ species), Community A has a significantly lower diversity index because it is overwhelmingly dominated by a single species (grass at $90\%$). Community B has higher overall diversity because its species abundance is distributed much more uniformly.

Dominance and Importance Values in Community Analysis

• Dominant Species:

  • Occurs when one or a few species predominate within a biological community.

  • Dominant species achieve dominance primarily by controlling critical resources (e.g., space, light, water, nutrients), thereby competitively excluding or suppressing other species.

  • Dominance can be evaluated within specific taxonomic or functional subgroups (e.g., dominant canopy trees, dominant understory shrubs).

• Importance Value:

  • A comprehensive quantitative metric measuring the degree of influence or structural dominance a species exerts on a community.

• Field Sampling Formulations and Equations:

  • Density:         $\text{Density} = \frac{\text{Number of individuals}}{\text{Area sampled}}$

  • Relative Density:         $\text{Relative Density} = \frac{\text{Density for a species}}{\text{Total density for all species}} \times 100$

  • Dominance:         $\text{Dominance} = \frac{\text{Total basal area or areal coverage}}{\text{Area sampled}}$

  • Relative Dominance:         $\text{Relative Dominance} = \frac{\text{Dominance for a species}}{\text{Total dominance for all species}} \times 100$

  • Frequency:         $\text{Frequency} = \frac{\text{Number of plots in which species occurs}}{\text{Total number of plots sampled}}$

  • Relative Frequency:         $\text{Relative Frequency} = \frac{\text{Frequency value for a species}}{\text{Total frequency values for all species}} \times 100$

  • Importance Value Formula:         $\text{Importance Value} = \text{Relative Density} + \text{Relative Dominance} + \text{Relative Frequency}$

  • Averaged Importance Value Index (used in tree community surveys):         $\text{Importance Value} = \frac{\text{Relative Basal Area} + \text{Relative Density}}{2.0}$

• Steps for Field Calculations (e.g., Mojave Desert Sampling):

  1. Choose RANDOM sample plots (utilizing random number generators).

  2. Survey and record every individual organism located within the plot boundaries.

  3. Perform calculations for density, dominance, frequency, and importance values.

• Comparative Field Case Study: Hilltop vs. Bottomland Forest Trees:

  • White Oak (Quercus alba): Hilltop Importance Value = $55.12$; Bottomland = $0.00$

  • Scarlet Oak: Hilltop = $9.35$; Bottomland = $0.00$

  • Yellow-poplar: Hilltop = $11.14$; Bottomland = $9.87$

  • Red Maple: Hilltop = $15.08$; Bottomland = $14.08$

  • Virginia Pine: Hilltop = $2.51$; Bottomland = $0.00$

  • Mockernut Hickory: Hilltop = $2.59$; Bottomland = $0.00$

  • Dogwood: Hilltop = $1.39$; Bottomland = $0.71$

  • Ironwood: Hilltop = $0.00$; Bottomland = $29.29$

  • Sweet Gum: Hilltop = $0.00$; Bottomland = $36.27$

  • Sycamore: Hilltop = $0.00$; Bottomland = $8.35$

  • Black Gum: Hilltop = $4.52$; Bottomland = $0.75$

  • Eastern Red Cedar: Hilltop = $0.00$; Bottomland = $0.68$

  • Overall Shannon Diversity Index ($H$): Hilltop = $1.69$; Bottomland = $1.72$

Trophic Interactions, Food Webs, and Keystone Species

• Keystone Species:

  • Definition: A species that exerts a disproportionately large impact on community structure relative to its abundance or biomass.

*   Key Principle: Species that control the greatest resources or biomass are NOT necessarily the species with the greatest influence on community integrity.
*   Keystone Predators: Regulate herbivore or primary competitor populations, preventing competitive exclusion by dominant prey species (e.g., coyotes, wolves, sea otters).
*   Ecosystem Engineers: Structurally modify or create habitat for other organisms (e.g., beavers constructing dams to transform running stream habitats into wetland pond communities).

• Food Webs and Trophic Architecture:

  • Food webs present a realistic depiction of feeding interactions across multiple levels, replacing simplistic linear food chains.

*   **Trophic Level**: The feeding position of an organism within a food web.
*   **Producers (Autotrophs)**: Occupy the base of the food web; possess the highest total energy.
*   **Primary Consumers (Herbivores)**: Organisms that feed directly on producers.
    *   Specific Example: Tobacco hornworms (*Manduca sexta*) feeding on tobacco leaves are classified as **Primary Consumers**.
    *   Grassland Examples: Cutworms, grasshoppers, prairie voles, pocket gophers, ground squirrels.
*   **Secondary Consumers (Carnivores)**: Organisms that feed on primary consumers (e.g., spiders, meadow frogs, garter snakes).
*   **Tertiary Consumers (Apex Predators)**: Carnivores at the top of the food web that feed on secondary consumers; possess the least available energy in the food web (e.g., marsh hawks, coyotes, badgers, weasels).
*   **Omnivores**: Organisms that feed across multiple trophic levels simultaneously (e.g., crows feeding on primary consumer insects and producer seeds).
*   **Decomposers**: Organisms that consume dead organic matter and break down nutrients for primary producers.

Ecological Guilds and Functional Types

• Guilds:

  • Groups of species within a trophic level that exploit common environmental resources in a similar manner (e.g., sap-feeding insects, seed-eating birds).

  • Because guild members rely on the exact same resource pool, interspecific competition among them is exceptionally strong and drives community structuring.

• Functional Types:

  • Groups of species that share a common morphological, physiological, or behavioral response to the environment, regardless of taxonomic relationship.

  • Example: Shade-tolerant understory plants (e.g., dogwood, rhododendron) form a functional type adapted to low-light regimes created by dense canopy trees.

Physical Structure and Vertical Stratification in Communities

• Vertical Stratification in Terrestrial Ecosystems:

  • Terrestrial vertical structure is determined primarily by plant growth forms and vertical light gradients.

*   **Canopy**: Main site of solar energy capture and photosynthesis.
    *   Open Canopy: Allows light penetration, encouraging robust understory and shrub growth.
    *   Closed Canopy: Restricts light penetration, limiting understory development.
*   **Lower Canopy / Understory Trees**: Composed of tall shrubs and short trees (e.g., dogwood); characterized by adaptation and selection for shade tolerance.
*   **Shrub Layer**: Composed of woody plants branching near the ground (e.g., rhododendron).
*   **Herbaceous Layer**: Non-woody ground vegetation, ferns, and mosses.
*   **Organic Layer / Forest Floor**: Site of fallen leaf litter accumulation, organic decomposition, and active nutrient cycling.

• Vertical Stratification in Aquatic Ecosystems (Lakes):

  • Aquatic vertical stratification is driven by physical environmental gradients.

  • Physical Gradients:

    1. Light intensity is inversely proportional to depth: $\text{Light Intensity}^{-1} \propto \text{Depth}$.

    2. Temperature is inversely proportional to depth during summer: $\text{Temperature}^{-1} \propto \text{Depth}$.

    3. Dissolved oxygen: Governed by a complex relationship involving depth, temperature, and respiration/decomposition.

    4. Hydrostatic pressure is directly proportional to depth: $\text{Pressure} \propto \text{Depth}$.

*   **Thermal Stratification Layers (Summer)**:
    *   **Epilimnion**: Upper layer of warm, freely circulating water receiving abundant light; dominated by phytoplankton (main primary producers).
    *   **Metalimnion / Thermocline**: Middle water stratum characterized by a rapid, steep decrease in temperature with depth.
    *   **Hypolimnion**: Deep, cold bottom water stratum; dark and low in dissolved oxygen due to bacterial decomposition.
*   **Light Stratification Zones**:
    *   **Photic (Euphotic) Zone**: Upper layer receiving sufficient solar illumination for net photosynthesis.
    *   **Aphotic Zone**: Deep water region where light penetration is insufficient for net photosynthesis.
    *   **Benthic Zone**: Bottom sediments where organic decomposition takes place.

Horizontal Structure and Spatial Zonation

• Horizontal Structure in Aquatic Environments (Lakes):

*   **Littoral Zone**: Shallow, near-shore water region where light reaches the sediment bottom; inhabited by emergent plants (e.g., cattails), floating plants (e.g., water lilies), and submerged plants.
*   **Limnetic Zone**: Open water region extending away from the shoreline down to the depth of effective light penetration (euphotic zone).

• Spatial Zonation:

  • Refers to spatial changes in biological community structure and physical architecture across environmental gradients.

  • Driven by changes in abiotic environmental factors (e.g., elevation, moisture, temperature, soil pH, salinity).

  • Most pronounced where physical environmental gradients are sharp or steep.

  • Universal phenomenon occurring across all terrestrial, freshwater, and marine habitats.

*   Elevation Example: Spatial zonation in Rocky Mountain National Park (elevation 11,000 ft) shows transitions from montane forests to subalpine coniferous belts and alpine tundra above the tree line.

Defining Ecological Community Boundaries

• Ecological community boundaries are frequently difficult to delineate due to three main factors:

  1. Extreme size variation: Communities range from tiny micro-habitats (e.g., a rotting log within a forest) to vast continuous biomes.

  2. Lack of precise boundaries (Gradation): Species turn over gradually across environmental gradients rather than stopping at sharp lines.

  3. Lack of complete isolation: Communities overlap extensively and are frequently nested within larger ecosystems (e.g., a rotting log community nested inside a forest ecosystem).

Theoretical Models of Community Organization: Clements vs. Gleason

• Frederic Clements' Organismic / Organic Concept (1874–1945):

  • Premise: Communities function as tightly integrated super-organisms whose constituent species have co-evolved interdependent relationships.

  • Key Features:

    • Species form distinct, highly repeatable "associations" that show clear spatial clustering.

    • Similar physical habitats produce consistent, predictable species groupings (e.g., beaver bogs in Maine and Michigan consistently harbour wild azalea, conifers, pitcher plants, and sundews due to adaptations to waterlogged, acidic soils).

    • Transitions between adjacent associations (ecotones) are sharp and distinct.

• Henry A. Gleason's Individualistic / Continuum Concept (1882–1975):

  • Premise: Coexisting species occur together as a result of overlapping individual physiological tolerances to abiotic conditions, not due to obligate co-evolution.

  • Key Features:

    • Species distributions along environmental gradients do not form discrete clusters or associations.

    • Species abundance curves vary independently along environmental or temporal continua, producing overlapping individualistic distributions.

  • Practice Question Insight: When an ecologist samples plant abundance over time and finds no discrete species clusters, but rather independent abundance peaks spaced along a temporal continuum, this observation directly supports the Individualistic or Continuum Concept of a Community.

• Modern Ecological Consensus:

  • Modern ecologists synthesize both concepts: individual species respond independently to physical gradients according to physiological limits (Gleasonian continuum), while strong localized biotic interactions (competition, predation, facilitation) can generate distinct species associations and localized boundaries (Clementsian clusters).

Quantitative Metrics of Community Similarity and Beta Diversity

• Sørensen's Coefficient of Community ($CC$):

  • A binary qualitative metric measuring species overlap based on presence/absence.

*   Formula:

        $CC = \frac{2c}{S_1 + S_2}$         where $c$ is the number of species common to both communities, $S_1$ is the total species richness in community 1, and $S_2$ is the total species richness in community 2. * Critical Limitation: Does NOT take species abundance or evenness into account! * Worked Example Calculation (Backyard vs. Meadow): * Shared species $c = 5$ (Grass, Violets, Species A, Species B, Species C) * Backyard richness $S_1 = 13$ * Meadow richness $S_2 = 7$ * Calculation:             $CC = \frac{2 \times 5}{13 + 7} = \frac{10}{20} = 0.50 \quad (50\% \text{ qualitative similarity})$

• Percent Similarity ($PS$):

  • A quantitative similarity metric that incorporates species relative abundances.

  • Formula:         $PS = \sum_{i=1}^{c} \min(P_{1i}, P_{2i})$         Sum of the lower relative abundance percentages for each species shared between the two communities.

  • Worked Example Calculation (Backyard vs. Meadow):

    • Grass: Backyard $90.0\%$ vs. Meadow $20.0\%$ $\rightarrow \min = 20.0\%$

    • Violets: Backyard $1.0\%$ vs. Meadow $5.0\%$ $\rightarrow \min = 1.0\%$

    • Species A: Backyard $0.2\%$ vs. Meadow $5.0\%$ $\rightarrow \min = 0.2\%$

    • Species B: Backyard $0.1\%$ vs. Meadow $5.0\%$ $\rightarrow \min = 0.1\%$

    • Species C: Backyard $0.1\%$ vs. Meadow $5.0\%$ $\rightarrow \min = 0.1\%$

    • Sum: $PS = 20.0\% + 1.0\% + 0.2\% + 0.1\% + 0.1\% = 21.3\%$

  • Comparison: Percent Similarity ($21.3\%$) is significantly lower than Sørensen's Coefficient ($50.0\%$) because $PS$ accounts for the extreme dominance of grass in the Backyard community.

• Bray-Curtis Dissimilarity:

  • Formula:         $\text{Bray-Curtis Dissimilarity} = 1 - \frac{2w}{a + b}$         where $w$ is the sum of the lesser abundance scores for species present in both communities, $a$ is the sum of abundances in community 1, and $b$ is the sum of abundances in community 2.

• Jaccard Index:

  • Computed as:         $\text{Jaccard Index} = \frac{2B}{1 + B}$         where $B$ is the Bray-Curtis dissimilarity value.

• UniFrac Distances:

  • Phylogenetic beta-diversity metrics based on shared versus unique branch lengths on a phylogenetic tree among samples.

  • Unweighted UniFrac: Considers strictly the presence or absence of species across phylogenetic lineages.

  • Weighted UniFrac: Incorporates the relative abundance of species along phylogenetic lineages.