Ecological communities

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.font200[
Even though I have separate sections on Competition and Predation in the course, I don't have one on Mutualism. Mutualism is important ecologically, but often each mutualism is important for a different reason. Mutualisms are often very specific for the types of organisms that are involved. .cyan[Because mutualism is caused by co-evolution, a lot of them have their own idiosyncrasies that don't generalize easily to a way of explaining the overall things that are common to mutualisms]. This is a contrast to Competition and Predation where there are a lot of features common to the interactions between very different pairs of species.
]

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# Levels of organization in Ecology

![](../01_whatIsEcology/figs/ecologicalOrganization.png)

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# What is an ecological community?

Community – collection of species that occur at the same place & time, circumscribed by natural (e.g., serpentine soil), arbitrary, or artificial (e.g., 1-m2 quadrat) boundaries

![:scale 85%](figs/community.png)

???

An ecological community is a set of interacting species which utilize the same environment.

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# What is an ecological community?

Community – an association of .blue[interacting] species inhabiting a defined area whose interactions can be + or - & direct or indirect.

![:scale 90%](figs/comm2.png)

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# Community Ecology

## Major focus

- How are these groupings explained by the environment and the interactions between and among species?
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# Biodiversity

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# Calculating Biodiversity

### There are multiple ways to calculate biodiversity:

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# Species diversity

![:scale 88%](figs/alpha_beta.png)

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# Measuring alpha species diversity

.font150[One of the most common measurement is .blue[species richness], the number of species in a community]

![](figs/comm_ab.png)

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# Species Richness

Richness depends on number of samples	collected

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# Species Richness

![](figs/sp_accum.png)

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# Species Richness

![:scale 60%](figs/sp_accum.png)

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- Want to predict the asymptote
- Try to collect as few samples as possible
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???

- with a few samples, you collect mostly common species
- with more samples, you start to collect some of the rarer species
- only with intensive sampling do you start to collect all species
- unless you’ve sampled enough to reach this plateau, beyond which no new species are added, you will miss species
- biological inventories conducted by Nature Conservancy and others rely on extrapolation
- try to predict the asymptote. Also try to collect as few samples as possible to achieve that asymptote

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# Rarefaction

.font200[Individual-based and sample-based  
Procedures of individual-based rarefaction  
Use rarefaction to compare diversity between two sites with different sampling effort
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# Rarefaction Assumptions

+  well-mixed community (spatial distribution of each species is random)

+  individuals are sampled at random (brighter colored individuals aren't sampled more often than others)

+ sampling with identical methods (if used to compare two communities)
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# Approximation

`$$E(S_{m}) \approx S - \sum_{i=1}^{S}(1-p_{i})^{m}$$`

where `$S$` is the number of species, `$m$` is the total number of individuals in the sample, and `$p_i$` is the proportion of species `$i$` in the original sample. 
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# Species richness estimators for extrapolation

## Chao1 index

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.font200[
If a sample of an ecological community results in the following abundances of species, what is the estimated overall richness of the community? Sp A (200 individuals), Sp B (140 individuals), Sp C (98 individuals), Sp D (30 individuals), Sp E (2 individuals), Sp F (2 individuals), Sp G (1 individual), Sp H (1 individual).

A. 8  
B. 9  
C. 10  
D. 11
]

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# Problem of Species Richness

![](figs/comm_ab.png)

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# Commonness vs. Rarity in communities

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# Species abundance

![:scale 80%](figs/moth_abund.png)

.font150[
- Moth data from England
- x-axis on log2 scale; 
- Partial bell-shaped curve -- .blue[log-normal distribution]
- .red[Very common pattern in nature]
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# Species Diversity

![](figs/comm_ab.png)

.pull-left[
.font150[
Two different things going on:
- Species Richness (number of species)
- Species Abundance (relative evenness)
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# Shannon Index

`$$H' = - \sum_{i=1}^{S}p_i\ln p_i$$`
Where: `$p_i$` = proportion of the total sample	represented by species `$i$`, `$\ln$` = log base `$e$`, `$S$` = the number of species in the community 
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# Shannon Index

![](figs/comm_ab.png)

.pull-left[
| Species | Abundance | Pi | ln(Pi) | Pi x ln(Pi) |
|---------|-----------|----|--------|-------------|
| Yellow  | 17        |    |        |             |
| Orange  | 1         |    |        |             |
| Purple  | 1         |    |        |             |
| Brown   | 1         |    |        |             |
| Total   | 20        | 1  |        |             |

.pull-right[
| Species | Abundance | Pi | ln(Pi) | Pi x ln(Pi) |
|---------|-----------|----|--------|-------------|
| Yellow  | 5         |    |        |             |
| Orange  | 5         |    |        |             |
| Purple  | 5         |    |        |             |
| Brown   | 5         |    |        |             |
| Total   | 20        | 1  |        |             |

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![:scale 80%](figs/shannon2.png)
.font150[

What is the Shannon Index of Diversity for the following community?  
A. 0  
B. 1  
C. 2.83  
D. 17  
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???

Prop = 1, and ln1 = 0. Therefore, it’s 0.

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# Shannon Index

- Can’t tell if differences in measurements are due to richness or evenness (or can you?)

- Difference between 0.58 & 1.39. What does it mean?

When all species are equally abundant: `$H' = \ln (4) = 1.39$`: Community B has max diversity

Evenness E = H'/H'max
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# Rank-Abundance Curve

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# Rank-Abundance Curve

.font150[Slope ≈ evenness; Length ≈ richness.   
.blue[Most species are moderately abundant; few are very abundant or extremely rare]]

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# Beta diversity

## To compare diversity between communities

Jaccard similarity:

$$ J(A,B) =  \frac{| A \cap	 B |}{| A \cup B|} $$

`$| A \cap	 B |$` is the shared species between communities `$A$` and `$B$`, while `$| A \cup B |$` is the total number of shared and non-shared species. 
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# Beta diversity

## There are many other beta diversity indices

.font200[
[Measuring beta diversity for presence–absence data](https://besjournals.onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2003.00710.x)

It reviewed 24 such measures!

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# Distance-decay in community similarity

.font150[
A common observation: communities which are farther apart tend to be more dissimilar than two communities which are close together
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# How have alpha and beta diversity changed over time?

.font200[
[Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss](https://www.science.org/doi/10.1126/science.1248484)
]

![](figs/dorenelas.jpeg)

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# How have alpha and beta diversity changed over time?

.font150[[Changes in taxonomic and phylogenetic diversity in the Anthropocene](https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0777)]

![](figs/figS2_all_taxa.png)

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# Community composition

.font200[Community composition describes the **diversity and identity** of species within a given community

.blue[_keystone species_] is a species that has a large impact on community structure relative to it's abundance / biomass in the community (e.g., top predator)

.blue[_foundation species_] is a species that can play a substantial role in determining what species can exist within the community (e.g., beavers, earthworms). Usually, this is a species that defines much of the structure of a community through e.g., habitat-forming

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# Community assembly

.font150[Whereas the figure is drawn as if these processes occur sequentially, in reality they occur more-or-less simultaneously or in any order]
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# Succession, Disturbance & Stress

.font150[
**Succession** – directional change in community composition at a site (as opposed to simple fluctuations), initiated by natural or anthropogenic disturbance, stress, or the creation of a new site

Some biologists restrict the definition to directional replacement of species after disturbance

**Disturbance** – a discrete event that damages or kills residents on a site (and potentially creates opportunities for other individuals to grow or reproduce); either catastrophic or non-catastrophic (Platt & Connell 2003 Ecological Monographs)

**Stress** – factor that reduces growth, reproduction, or survival of individuals (and potentially creates opportunities for other individuals)

]

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# Scales of Disturbance

.font150[Intensity & Severity (how much damage & death?); Frequency (how often?); Extent (how much  area was affected?)]

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# Disturbance & Succession

.font150[Primary Succession – succession that occurs after the creation of a “blank slate,” either through catastrophic disturbance or _de novo_ creation of a new site]

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# Disturbance & Succession

.font150[Secondary Succession – succession that occurs after non-catastrophic disturbance (including “old fields”)]

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# Primary successsion example

.font150[
One of the world’s most rapid and extensive glacial retreats in modern times 
(so far); eliminated ~2500 km2 of ice in ~200 yr, exposing large 
expanses of nutrient-poor boulder till to biotic colonization
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# Primary succession along the Glacier Bay chronosequence

intensively analyzed tree-rings
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# Primary succession along the Glacier Bay chronosequence

![](figs/glacier5.png)

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# Primary succession along the Glacier Bay chronosequence

.font200[
Species richness generally increased with successional age
(a common pattern in succession studies, even though at times a mid-succession peak is observed)
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# Primary succession along the Glacier Bay chronosequence

![](figs/glacier4.png)

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# Secondary succession

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# Disturbance & Succession

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# Disturbance & Succession

Lake Michigan sand dunes – late 1800s

Concluded that sites on the dunes were older further inland, i.e., formed a “chronosequence” (also space-for-time substitution) from which temporal change could be inferred

Referred to distinct plant assemblages as “societies” 
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# Succession: superorganism or individualism?

.font200[
Radical, “.blue[superorganism]” view of communities; species interact and act _en masse_ to promote a directed pattern of community development through “seral” (intermediate) stages, ending in a “climax” community
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]

.font200[
“.blue[individualistic view of succession]” in which “every species is a law unto itself”
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.font200[Our modern population-biology view derives primarily from Gleason’s conceptual model, even though Clementsian ideas of deterministic progression through seral to climax stages dominated ecological theory well into the 20th century]

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# Why aren't all communities predictable?

## Historical contingency or priority effects

## Stochasticity