BIOL 410 Population and

Community Ecology

Community composition
 Ecological communities

Species richness (number of species)

 Questions of ecological communities
• For a given community, how many species are
present and what are their relative
abundances?
• How many species are rare?
• How many species are common?
• How can the species in the community be
grouped
• What type of interactions occur between the
species groups (guilds)?
 Community structure
• Diversity
– Does a community contain a divers range of species or few
• Relative Abundance
– What can we learn from the relative abundance of species
within a community?
• Dominance
– Is a community dominated (numerically of functionally) by
some species?
• Trophic structure
– How is the community organized and how does energy
(food) flow through it?
 Species diversity
• What determines the number and kinds of species that
occur in a particular place?
• Why do number and kinds of species vary from place
to place?
 Species diversity
• Species diversity consists of two
components

1. Species Richness
• The total number of species in an
area
• Simple summation

2. Species Evenness
• How evenly the species are
represented in the area
• E.g. do most of the individuals belong
to one species?
 Species richness
Just count the number of
species

– Detection bias between

species?
• Within habitat types?
• Between habitat types?

– Sample effort (size) bias?

 Species richness

Relationship between sampling area and bird species richness in North America
 Species richness
Margalef’s index
𝑆−1 S: total number of species in area sampled
𝐼𝑀𝑎𝑟𝑔𝑎𝑙𝑒𝑓 =
ln⁡(𝑁) N: total number of individuals observed

Menhinick’s index
𝑆
𝐼𝑀𝑒𝑛ℎ𝑖𝑛𝑖𝑐𝑘 =
𝑁

• Attempts to estimate species richness independent of sample size

• Index will be independent of the number of individuals in the

sample only if the relationship between S (or S-1) and ln(N) or
sqrt(N) is linear

– This is seldom the case

 Species Richness
Margalef’s and Menhinick’s index
• Interpretation
– The higher the index the greater the richness

– E.g.
• S = 6 and N = 50
– Margalef index = 1.28, Mehinick index = 0.85
• S = 6 and N = 20
– Margalef index = 1.67, Mehinick index = 1.34
 Species diversity
species diversity = f(species richness, species evenness)

• Many calculations use species proportions (not absolute numbers)

𝑠

𝑝𝑖 = 𝑥𝑖 𝑥𝑖
𝑖=1

• X is observed abundance of species I (numbers, biomass, cover etc.)

• S is the number of species
• Pi is the proportion of individuals belonging to species I

𝑠
Species richness
𝐷0 = ⁡ 𝑝𝑖 0
𝑖
 Simpson’s Index
• Edward Simpson, British Statistician
– Developed index to measure the degree of
concentration when individuals are classified by types
(i.e. a measure of the degree of dominance)

– Asked: “if I draw two individuals at random from this

community, what is the probability that they will
belong to the same species?“
• Probability of drawing species i is pi
• Probability of drawing species I twice is pi2
• Sum of the value for all species is the Simpson’s index of
dominance

𝐷𝑆𝑖𝑚𝑝𝑠𝑜𝑛 = 𝑝𝑖 2
 Simpson’s index of dominance
• In small samples, the probability of drawing species i
the second time is not the same as the first since there
are now fewer individuals

• In small populations the index is:

𝑛𝑖 𝑛𝑖 − 1
𝐷𝑆𝑖𝑚𝑝𝑠𝑜𝑛 =
𝑁(𝑁 − 1)

• n total number of organisms of a particular species

• N total number of organisms of all species
 Simpson’s index of diversity
• Species diversity is given as the counter to
dominance and calculated as either:
𝐼𝐶𝑜𝑚𝑝𝑆𝑖𝑚𝑝 = 1 − ⁡ 𝐷𝑆𝑖𝑚𝑝𝑠𝑜𝑛 Gini-Simpson index

𝐼𝐼𝑛𝑣𝑆𝑖𝑚𝑝 = 1/𝐷𝑆𝑖𝑚𝑝𝑠𝑜𝑛

• Range 0 to 1
• The higher the index the greater the diversity
 Simpson’s Index
n n(n - 1)
∑ n(n - 1) Species A 12 132
D= Species B 3 6
N(N - 1)
Species C 7 42
Species D 4 12
∑ n(n - 1) = 264 Species E 9 72
∑ n(n - 1) 264

N = total number of all individuals = 35

∑ n(n - 1)
D =
N(N - 1)

D = 264 = 0.22184
1190
 Shannon’s index
• Measure of the entropy (disorder) of a sample
– Measures the “information content” of a sample unit
• Field of information theory
• i.e. have a string of letters (r,e,f,r,f,f,e,a), and want to predict which
letter will be next in the string
– More letters = more difficult
– More even the letters = more difficult

– Degree of uncertainty associated with predicting the

species of an individual picked at random from a
community
• i.e. if diversity is high, you have a poor chance of correctly
predicting the species of the next randomly selected individual
– Increased species number reduces chance of correctly predicting species
– Decreased evenness reduces chance of correctly predicting species
 Shannon’s diversity index
Log 2, 10
• H or Hˈ 𝑆

𝐻ˈ = − 𝑝𝑖 ⁡ln⁡(𝑝𝑖 )
𝑖

• s = number of species
• pi = proportion of individuals belonging to species I

• Range usually between 1.5 and 3.5

• Low value indicates low diversity
• High information content
• High value indicates high diversity
• Large number of species
• Even distribution of species
 Shannon’s diversity index
Sp A Sp B pA pB
Plot 1 99 1 0.99 0.01
Plot 2 50 50 0.50 0.50

2
H '    pi log pi
For plot 1 i 1

H '  10.99  log(0.99)  0.01  log(0.01)  0.024

For plot 2

H'  1 0.5  log(0.5)  0.5  log( 0.5)  0.301

 Species evenness
• How equally abundant are each of the species?
• What is the structure of species relative abundance within
a community?
• Can we compare how evenly distributed two communities
are

• Rarely are all species equally abundant

– Some are better competitors, more fecund than others

• Are communities with high species evenness

– More resilient to disturbances?
– Harder to invade by a new species?

– High evenness is often viewed as a sign of ecosystem health

 Shannon’s index of evenness
• Calculated from the diversity index
• Value of H when all species are equally abundant
(i.e. perfect evenness) is ln(S)
𝐻
𝐸𝑆ℎ𝑎𝑛𝑛𝑜𝑛 =⁡
ln⁡(𝑆)

• When the proportions of all species are the same

evenness is one
• Value increases as evenness decreases
Simpson’s index of evenness
𝐼𝐼𝑛𝑣𝑆𝑖𝑚𝑝
𝐸𝑆𝑖𝑚𝑝𝑠𝑜𝑛 =
𝑆

S = number of species

𝐼𝐼𝑛𝑣𝑆𝑖𝑚𝑝 = 1/𝐷𝑆𝑖𝑚𝑝𝑠𝑜𝑛
Community diversity metrics
 Species and community diversity
• Estimates of species diversity are scale
dependent
– Species area curves

– Habitat type differences?

 Scales of diversity
• Alpha diversity
– Within patch diversity
• Beta diversity
– Between patch diversity
– Rate of species change between two areas
– Spatial (but calculation can also be applied to
temporal changes)
• Gama diversity
– Landscape level diversity
 Scales of diversity

Andres Baselga 2015

 Beta diversity
• R.H. Whittaker (1960)
– “the extent of change in community composition,
or degree of community differentiation, in relation
to a complex-gradient of environment, or a
pattern of environments”

• Why is beta diversity important?

– Biodiversity is not evenly distributed around the
world
– Quantifying the differences among biological
communities is often a first step towards
understanding how biodiversity is distributed
 Beta diversity
• Rate of change between two habitats
• Dissimilarity between habitats
– Normally based on species presence-absence data
– Dissimilarity indexes
Habitat Spec. A Spec. B Spec. C Spec. D
1 1 1 0 0
2 1 1 1 0
3 1 0 0 1
4 0 0 1 1
5 1 0 0 0

– Which habitats are most similar

– Which habitats are least similar
 Beta diversity
• Beta diversity can be quantified in a couple of
ways
1. Beta diversity defined as the ratio between
gamma diversity and alpha diversity
• Multiplicative beta diversity
• β = γ/α (γ=α β)
• α is the mean α diversity across all sites

https://methodsblog.wordpress.com/2015/05/27/beta_diversity/
 Beta diversity
• Evaluating “difference” in biological communities

α γ

4,4,4
8
4

8,3,1
8
4

6,3,3
8
4
Similarity, dissimilarity

a b

c d
Jacard’s dissimilarity index
𝑎
𝐷𝑗 = 1 − ⁡
𝑎+𝑏+𝑐

a = number of species common to both areas

b = number of species unique to the first area
c = number of species unique to the second area

2
𝐷𝑗12 = 1 −⁡ = 0.33
2+2+2
Sorensen dissimilarity index
2𝑎
𝐷𝑠 = 1 − ⁡
(2𝑎 + 𝑏 + 𝑐)

a = number of species common to both areas

b = number of species unique to the first area
c = number of species unique to the second area

2 2
𝐷𝑠12 = 1 −⁡ = 0.5
2 2 +2+2
 Beta diversity
• Evaluating “difference” in biological communities
 2𝑎
Beta diversity 𝐷𝑠 = 1 − ⁡
(2𝑎 + 𝑏 + 𝑐)

a b c Sorenson Jacard
A1-A2 2.00 2.00 2.00 0.50 0.33
A1-A3 2.00 2.00 2.00 0.50 0.33
A2-A3 2.00 2.00 2.00 0.50 0.33
0.50 0.33

a b c Sorenson Jacard
A1-A2 3.00 5.00 0.00 0.55 0.38
A1-A3 1.00 7.00 0.00 0.22 0.13
A2-A3 1.00 2.00 0.00 0.50 0.33
0.42 0.28

a b c Sorenson Jacard
A1-A2 3.00 3.00 0.00 0.67 0.50
A1-A3 1.00 5.00 2.00 0.22 0.13
A2-A3 1.00 1.00 1.00 0.50 0.33
0.46 0.32