Community ecology

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PARASITISM CONTINUED:
What are the major steps in the life cycle of the HIV virus?
 Attachment to the Lymphocyte Membrane,
 Entry and release of genetic material.
 Reverse Transcription: Converting viral RNA into DNA
 Integration: the DNA can then be integrated (inserted) into the DNA of the
lymphocyte. The virus has its own enzyme called "integrase" that facilitates
incorporation of the viral DNA into the host cells DNA. The integrated DNA is
called a provirus.
 Transcription: Back to RNA
 Translation:RNA to proteins
 Viral protease, assembly and budding
War against the HIV virus
1a. Natural resistance to HIV
 Entry of the HIV virus into a T cell requires attachment to a CD4 receptor and a
CCR-5 or CXCR4 receptor (special proteins on cell surface)
 People with natural resistance to HIV have mutations in their chromosomes, thus
the CCR-5 is either absent or defective
 Fifteen to 20% of caucasians in Western Europe are heterozygous; i.e. +-CCR-5
(partial protection)
1% are homozygous --CCR-5 (Nature 382, 1996, page 668)
NOTE: the CD4 count is used as an indicator to help physicians decide when to
begin treatment in HIV-infected patients.
28. Natural resistance to HIV
 Certain HLA-B antigens have been associated with lack of progression to AIDS.
 WAR against the HIV virus
 Interrupting the point where HIV's genetic material is reversed transcribed into
DNA
Where are CCR5 and HLA-B genes found?
1c. Blocking the point of attachment
 R5, X4 and R5/X4 are strains of the HIV virus
 AMD3110 and SCH-C are cpds. with potent antiviral activity
 R5 isolates completely blocked by CCR5 antagonist SCH-C.
 X4 isolate was completely inhibited by AMD3100 CXCR4 antagonist
 A combination of AMD3110 + SCH-C blocked replication of all strains of the
virus
2. Target rev which transports RNA from nucleus to cytoplasm. HIV needs high
levels of this protein. Producing a drug that would lead to rev reduction will
reduce replication of the virus.
3. Target HIV protease which cuts up long protein strands into small pieces to
make new virus particles. Without this enzyme the HIV virus is malformed and
non infectious.
4. develop a vaccine
 http://www.youtube.com/watch?v=RO8MP3wMvqg&feature=related
Resistance to drugs in Africa
 20% of those treated with AZT had evidence of resistance, and
 50% of patients treated with a protease inhibitor had resistant virus.
 The 333 mutation, associated with dual AZT/3TC resistance present
 http://www.youtube.com/watch?v=TvNOmwRh0I0&feature=related
Some Emerging diseases
 Sars
 West Nile
 Yellow fever
 Dengue fever
 Ebola
Eradicated Diseases
 Rinderpest, an infectious disease that has decimated cattle and devastated their
keepers for millennia, is gone. (science magazine, October 22 2010)
 Small pox
COMMUNITY ECOLOGY
Main goals
 definition of a community
 characteristics of a community
 The main types of communities (chapter 4)
 Global patterns in species richness (chapter 10)
 direct and indirect effects on a community; direct effects can have + or consequences on the community (chapter 9:page 317-327)
 Species diversity (chapter 10)
 factors affecting species diversity
 diversity indices
 Cluster analysis
 Succession (chapter 18)
 Three models of succession
 What is a community?
 It is an assemblage of species populations which occur together in space and time
 What are the main characteristics of a community?
o species composition (unique for every community)
o temporal changes (daily, seasonal, and annual cycles of activity)
o trophic (energy transfer and nutrient recycling, unique)
o guilds and niches

Fundamental and realized niches

the fundamental niche of a species is when a niche has an infinite number of
dimensions.(Hutchinson 1957)

the realized niche of a species describes the more realistic spectrum of abiotic
factors which allows a species to maintain a viable population even in the
presence of predators and competitors (biotic factors).

The realized niche is generally smaller than the fundamental niche.
TERRESTRIAL and AQUATIC COMMUNITIES
 Seven terrestrial systems
 Tropical forests
 Temperate forests deciduous
 Temperate forests coniferous
 Tropical grasslands
 Temperate grasslands
 Desert and tundra
 Tropical forests and oceanic islands have the highest percentage of
threatened species
In communities we find
a) examples of direct negative interactions
 inhibition of recruitment
 inhibition of feeding
o an established occupant of a habitat, reduces feeding activity or the rate of
successful recruitment of the habitat by recruiting stages of another
species.
b) Examples of direct positive interactions

enhancement of recruitment

a prior occupant of a habitat, whether mobile or sessile, increases the rate of
successful recruitment by offering favored attachment sites. This is an interaction
between juvenile stages and established individuals
Provision of habitat or shelter

c) Indirect positive interactions
 Keystone predation: By reducing prey population densities, a predator can reduce
competition among prey species and promote their coexistence
 (chitons,limpets,goose necked barnacles,bivalves, and acorn barnacle,whelk)
Figure 10.7
 c) Indirect positive interactions

Habitat facilitation: occurs when one species indirectly improves the habitat of a
second species by altering the abundance of a third interactor.


Cascading trophic interactions: predatory effects at one trophic level affect
community structure, at trophic levels below the one affected directly
Example: in the salt marsh environment

Factors affecting species diversity
o
o
o
o
o
disturbance*
harsh environments
climatic stability
resources
predation*
Diversity indices: Measures of heterogeneity
 Why are diversity indices important?
Two categories of diversity indices
 Type I indices are most sensitive to changes in
the rare species in the community example
(Shannon Wiener index)

Type II indices are most sensitive to changes in
the more abundant species example (Simpson's
index)
Question: Are you more interested in
emphasizing the dominant or the rare species in
your community?
 Simpson's index (D) Simpson suggested that
diversity is inversely related to the probability
that two individuals picked at random belong to
the same species.
D =  p2i

 D = Simpson's index
 pi = proportion of species i in the community
 the reciprocal of Simpsons index =1/D,



Shannon-Wiener index (H)
H = -PilnPi
H increases with the number of species in the community to a maximum of
approx. 5
Community Similarity
 Diversity among areas can be compared using
 Diversity indices
Similarity coefficients
 Comparison involve a simple presence-absence matrix for two areas, A and B
 a = number of species common to both sites
 b = number of species in site B, but not in A
 c = number of species in site A, but not in B
 d = number of species absent in both samples
How do we know a species is absent in two sites?
 Is "‘d"’, meaningful?
 d is a measure of the negative matches, potentially biologically meaningful
 In reality, it is almost impossible to know
 Most similarity coefficients rely only on a, b, and c
Jaccard coefficient
 Jaccard coefficient is calculated from
Sorensen coefficient
 Number of species common to both sites is stressed
 Sorensen coefficient is calculated from
 Cs = 2a / (2a + b + c)

What is another coefficient used?
Cluster analysis
term applied to techniques used to build classifications.
 Useful when there are a very few sites and you simple want to determine which
sites are the most similar
Types of clustering
1. Single linkage clustering (nearest neighbor method) simplest
2. Complete linkage clustering (farthest neighbor method)
3. Average linkage clustering (avoids extremes introduced by single and complete
linkage clustering)
Cluster Analysis using similarity coefficients
 Using single linkage clustering technique
 Start by calculating the similarity coefficients for the two sites in the oak wood
habitat and for the 3 sites in the conifer habitat
 Then arrange the similarity coefficients in a table or matrix
 To build a dendogram, start by finding the greatest similarity coefficient
 The greatest similarity coefficient is between the conifer sites 2 and 3 = 0.7
 The next highest similarity coefficient is between the Oakwood sites 1 and 2 =
0.65
 The next highest similarity coefficient is 0.47 for the conifer sites 1 and 2 etc.
Problem: You are responsible for a large nature preserve: Calculate the Simpson’s
and Shannon Weiner index for the data below on large trees from two sites in
Pennsylvania. Comment on your results
 Simpson’s index
 D = 1/  p2i varies from 1 to S
 Shannon Wiener index
H = -PilnPi

 Find the total for each column (Table 3.2A)
 Calculate the proportion of individuals for each species (Pi , relative density,
Table 3.2B, lab book)
 Make sure proportions add up to 1 for each column (Table 3.2B)
 Square Pi values for each species (Pi 2) (Table 3.2C)
 Sum up the the Pi 2 values for each plate (Pi2) (Table 3.2C)
Find the inverse = Simpson’s index (D= 1/Pi2) (Table 3.3)

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