Community Ecology
Biodiversity
Outline:
1. How many species are there on Earth?
2. Definition of biodiversity (richness + evenness)
I. Diversity indices are easy but flawed measures of biodiversity
II. Species identity important
3. Scales of diversity
4. Four well-studied patterns of diversity: intermediate disturbance hypothesis, latitudinal
gradients, species-area relationship, diversity-productivity relationship
Terms/people:
biodiversity (diversity)
richness
evenness
rarefaction
abundance
J. Connell
intermediate disturbance hypothesis
latitudinal gradient
species-area relationship
species accumulation curve
diversity-productivity relationship
alpha, beta, gamma, delta, epsilon diversity (Whittaker)
diversity indices (Shannon-Wiener, Simpson, inverse Simpson, Shannon evenness, Simpson
evenness)
Question for the class to answer (have your answer ready before coming to class, and be
prepared to be called upon): approximately how many species are there on earth?
Why don’t we know exactly how many species there are? Dr. McIntyre’s $0.02:
1) Most studies have focused on “charismatic megafauna,” game, commercially valuable,
or pest species rather than the bulk of living organisms.
2) Most studies have taken place in small study areas.
3) Most studies have taken place over short time periods (only ~2% of studies last longer
than 5 years).
4) Most survey methods were designed to document common species and miss rare
species because emphasis has been placed on mapping and describing communities based on
dominant species, not rare ones.
5) There is little scientific reward for observational studies and surveys (compared to
studies using experiments/scientific method). Consequently, surveys are not funded much (pool
of money goes to experiments).
6) Lack of funding means that there is reduced emphasis on training taxonomists.
7) Lack of funding also means that museum specimen collections are not computerized
(not enough funds to hire programmers). Therefore, few specimen collections are able to be
cross-checked with other collections/surveys.
Basically, biodiversity inventories are lower priority than are projects with “deliverables” that
directly benefit humans (e.g. medical research, ag research, pest control, etc.).
So what can we do about this?
1) Make the best of existing information. Let’s get collections computerized,
standardized, and cross-checked.
2) Fund surveys! Find ways to make surveys appealing to funding agencies and
taxpayers. Emphasize small and rare species and the linkage from genetic to species to
community diversity, not just species of economical concern. Debunk the myth that experiments
are the only truly scientific and rigorous studies.
3) Train, reward, recruit, and maintain taxonomists.
These are easier said than done.
We are losing species at an unprecedented rate:
Extinction - loss of biodiversity.
There have been 5 major extinctions in history (due to climate change stemming from
asteroid impact, and natural ice age/interglacial cycles), involving the loss of ~96-99% of all
species that ever existed. However, we are now in the midst of "The Sixth Extinction," one that
is due to anthropogenic causes: for birds and mammals, there have been ~200 extinctions in the
past 400 years, which is 66x higher than the previous 2 million years. These losses are ones that
are often preventable and thus the focus of so much attention, conservation effort, etc. Only
~12% of the Earth is set aside for conservation, compared to rates of deforestation (e.g. Brazilian
Amazon: 1.4 km2/hr) or urbanization (e.g. PHX: acre/hr).
"This is the folly that our descendants are least likely to forgive us." - E.O. Wilson, 1985
Biodiversity (a.k.a. diversity)
diversity = richness + evenness
"diversity" should be used only to refer to richness + evenness and not as a synonym for
richness (Hurlbert 1971)
Example:
number of species
community 1
10
community 2
10
So the two communities have the same diversity, right? Wrong! Look at the communities in
more detail:
species 1
2
3
4
5
6
7
8
9
10
community 1
100 individuals
1
1
1
1
1
1
1
1
1
community 2
4 individuals
3
1
1
2
4
2
2
3
1
Community 2 is much more even and therefore more diverse, relatively speaking. But is it fair to
compare two communities if they have different numbers of individuals (since community 1 has
109 individuals whereas community 2 has only 23)? Rarefaction (from rarify = “to thin”)
standardizes by sample size (number of individuals) to compare communities with different
numbers of individuals (Sanders 1968 [who had wrong formula, corrected independently by
Hurlbert 1971 and Simberloff 1972], James and Rathbun 1981):
E(S)n = expected number of species in a sample of size n
S

( N  ni )!
N! 
E ( S ) n   {1  

}
 (n!)([ N  ni ]  n)! n!( N  n)!
i 1
where N = number of individuals in larger sample, n = number of individuals in subsample, ni =
number of individuals of species i; the ! (factorial) notation indicates a product of all previous
terms in a series (e.g. 5! = 5x4x3x2x1 = 120)
Example of rarefaction: two communities (A and B), with more species being found in
community B but also more individuals, so it really may not be a fair comparison without
rarefaction:
number of individuals in: community A
community B
species 1
5
10
species 2
5
20
species 3
6
10
species 4
0
20
species 5
0
2
total N
16
62
So you found 3 species in community A but 5 species in community B. But how many species
would you expect in community B if only 16 individuals were sampled there?
N = 62, n = 16, ni = {10,20,10,20,2}, E(S)n = 0.962+0.999+0.962+0.999+0.453=4.376
(interpretation: you’d expect to find between 4-5 species in community B if you only sampled 16
individuals, so community B is still slightly more speciose than community A). Ask Dr.
McIntyre if you have any questions about how this answer was obtained!
Rarefaction best to use when NA/NB >10 or <0.1. Rarefaction is computationally demanding; one
program that can be used is Ecosim (http://homepages.together.net/~gentsmin/ecosim.htm).
Caveat: Rarefaction assumes that individuals are randomly distributed, meaning that richness is
likely overestimated by rarefaction since most individuals in nature are typically clumped.
Gotelli (2008) gives a good, plain-language explanation of rarefaction.
For alternatives to rarefaction, see Ch. 13 in Southwood and Henderson (2000).
Not just numbers of species and individuals that are important: species identity also critically
important (e.g. native vs. exotic spp.).
Diversity indices: THE benchmark for evaluating management efficacy, disturbance, and other
factors. There are many:
- Shannon-Wiener (a.k.a. Shannon, incorrectly as Shannon-Weaver; was independently derived
by Shannon and by Wiener) Index, H’ = - (pi)(ln(pi)), where pi = proportion of individuals
belonging to the ith of S species
-One of the most commonly used indices, yet fraught with problems! (Highly sensitive
to n, highly influenced by rarity, difficult to interpret.) Simpson's Index is preferred:
- Simpson's Index (esp. useful for communities where all individuals are counted, which is rare),
lambda = (pi2) because this index, as written, is counterintuitive in that it ranges from 0 (high
diversity) to 1 (low), the inverse Simpson's Index is often used: D = 1/lambda
Evenness also has indices:
- Shannon evenness = H'/ln(S), ranges from 0 (not even) to 1 (completely even)
- Simpson evenness = D/S, ranges from 0 (not even) to 1 (completely even)
- Berger-Parker (dominance index), d = Nmax/N where Nmax = number of individuals of the
most abundance species, N = total number of individuals over all species
There are many other diversity and evenness indices: see Magurran (1988, 2004) for a thorough
exposition of diversity indices.
Because different diversity indices weight species’ abundances differently (i.e., treat rare species
differently), the conclusion of whether one community is more diversity than another can depend
on the diversity measure used.
Example of calculating diversity indices:
Suppose you survey a community and find 5 species, called A-E. Below is the abundance
(number of individuals) belonging to each species.
A = 100
B = 50
C = 98
D=7
E=2
Sum = 257 individuals
Using these data, calculate the Shannon, Simpson’s, and Shannon and Simpson evenness indices
of diversity for this community.
Answer:
Shannon-Wiener Index = 1.191
inverse Simpson's Index (D) = 2.981
Shannon evenness = 0.74
Simpson evenness = 0.59
Ask Dr. McIntyre if you have any questions about how these numbers were obtained!
There are MANY online pages that can be used to calculate various diversity indices, such as:
http://www.alyoung.com/labs/biodiversity_calculator.html
Diversity is invoked to quantify and to compare communities. But diversity is a function of area
sampled (topic of the next lecture), sampling effort, and species-specific traits such as crypsis.
So how do you know if you've adequately sampled a community's diversity? Since there is a
tradeoff between sampling effort (e.g. cost and time to sample) and diversity, and since
communities are constantly in flux (remember the lectures on equilibrium and on succession?),
you need to know when to stop ("stopping rule" of Magurran 2004). One easy way is to produce
a species accumulation curve (S vs. # of samples taken, or # of new species per sample vs. # of
individuals) and determine its asymptote. (There are also more recent and more rigorous ways to
determine whether you've adequately sampled a community, using nonparametric estimators of
richness as developed independently by Anne Chao and Robert Colwell; see Magurran 2004.)
Note how a species accumulation curve is similar to a rarefaction curve, but the SAC is based on
empirical data whereas rarefaction curves are based on smoothed models.
Scales of diversity (Whittaker 1960, 1972, 1977) to distinguish between diversity of species and
diversity of habitats; alpha and beta most commonly used:
alpha = within sample/habitat
diversity indices
beta = between habitats
similarity indices (Jaccard's or Sørensen’s [for presence-absence data], Morisita's [for
abundance data])
gamma = within landscapes
delta = between landscapes
epsilon = within biomes (biogeographic provinces)
and others (e.g. Ricklefs 1987 - local vs. regional scales of diversity)
4 well-studied patterns of diversity:
1) intermediate disturbance hypothesis (Connell 1961, 1978; but see Mackey and Currie 2001)
2) latitudinal gradient in diversity: more species in tropics than at poles (see Figs. 2.1, 2.2 in
Mittelbach text)
“The verdant carpet which a luxuriant Flora spreads over the surface of the earth is not woven
equally in all parts…[O]rganic development and abundance of vitality gradually increase from
the poles towards the equator.” (Alexander von Humboldt 1850)
Some proposed explanations for latitudinal gradient are given below (Pianka 1988, Rosenzweig
1995, Körner 2000), falling roughly into 4 categories:
1) null models (e.g. greater area in the tropics - “mid-domain effect” in Fig. 2.4)
2) resource limitations (i.e., an area’s carrying capacity) with respect to
climate/productivity (“species-energy hypothesis”) (MacArthur and MacArthur 1961, Brown et
al. 2004)
3) geologic history (tropics are older, glaciation refugia idea of Haffer 1969)
4) evolutionary time, speciation higher because of energy/metabolism, extinction lower
because of climate stability
Some researchers (e.g. Mannion et al. 2014) take a different approach to the lat. grad. and instead
view the tropics as either “cradles” of biodiversity or “museums” of biodiversity (cradles
generate new species with speciation rates that are higher in the tropics and extinction rates that
do not vary by latitude, museums preserve species with speciation rates that are constant with
latitude but with lower extinction rates in the tropics). It is also possible that the tropics support
both higher speciation and lower extinction rates (combination of cradle and museum).
3) species-area relationship (topic of a future lecture)
4) diversity-productivity relationships (see pp. 29- 31 in Mittelbach text)
Next lecture: why does biodiversity matter? (In other words, so what if biodiversity is
declining?)
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