Genes to ecosystems Flashcards
What is Ecology
The scientific study of the interactions
between organisms and their environment
that determines the distribution and
abundance of organisms
The environment includes other individuals of the same species as well as member of other
species BUT it also includes physical factors,
e.g. Temperature, rainfall, wind etc.
The 3 Basic Problems and Approaches to Ecology
Descriptive – natural history, e.g. describes the
vegetation groups of the world (temperate
deciduous forests, tropical rain forests, grasslands
etc.)
Functional – dynamics and relationships, energy
flow in ecosystems, populations and communities
as they exist and can be measured now
Evolutionary – the historical reasons why natural selection has favoured the particular adaptations we now see.
What is an individual?
-Genetically distinct unit.
-May be unicellular (e.g., bacterium, diatom, ciliate)
or multicellular (e.g., lizard, mouse, human).
- A bacterial colony (or diatom bloom) that arises by
binary fission from a single cell is a clonal
population. - A coral is a colony of hundreds or thousands of
individual, genetically identical polyps.
What are Unitary & Modular Organisms?
Unitary organisms come as individual units.
– Most animals are unitary organisms.
–Unitary organisms have determinate form.
– Individuals are usually genetically distinct
Modular organisms have indefinite growth
forms.
– Individuals are composed of an indefinite
number of genetically identical modules.
– Includes most plants and some animals such
as corals or sponges.
Can you provide examples of Modular
Organisms?
Many plants & some
animals show great
variation in size and
structure.
* e.g. blades of grass
are connected by
underground
rhizomes.
* Modular organisms
are often branched
What is a population?
A population is a group of individuals of the same species occupying a particular space at a particular time.
- Populations have attributes that
transcend those of individuals
–Age distribution
–Genetic composition
–Spatial distribution
–Temporal distribution
What is a community?
Any assemblage of populations of different
species in a prescribed area or habitat.
* e.g., the community of plants in a
deciduous forest, or the community of
animals in a rotting log
* May be of any size (NB interactions)
* May be restricted to
–a taxonomic group (e.g., bird community
of a forest) or
–include many different taxonomic groups
(plankton community)
What is an ecosystem?
An interacting complex of plant, animal,
and micro-organism communities and
their non-living environment (Arthur
Tansley, 1935)
* e.g., all of the living organisms together
with topography, soil, underlying geology,
hydrology and atmosphere
(weather/climate)
What is Biodiversity?
“Biodiversity is the genetic, taxonomic and ecosystem variety in living organisms of a given area, environment, ecosystem or the whole planet” (McAllister, 1991). It can be divided into genetic, organismal and ecological diversity (Harper and Hawksworth, 1994). Genetic diversity is defined as the variety of genes within a species, organismal diversity is the variety of species within a community, and ecological diversity is the variety of biomes within a geographic area (Harper and
Hawksworth, 1994).
What are the general patterns in
ecology (do we have laws)?
Species Area Relationships
Species Abundance Distributions
Latitudinal diversity gradient
Diversity-function relationship(s)
Mass-abundance relationship(s): Big sized species have lower population densities than small sized species.
What is meant by the term biodiversity?
The term biological diversity is used in at least four
different ways to indicate:
* genetic diversity within a species
* species diversity within a community
* community or ecosystem diversity within a region
* functional diversity within an assemblage of species
Species diversity: The number of species in a community, weighted by their relative abundance.
What are the 4 Components of Species Diversity?
Species richness?
– The number of species in a community
Species evenness (equitability)?
– The relative abundance of different species in a community.
Species heterogeneity?
– A concept that combines both the number of species and their relative abundance in a single metric.
Diversity index?
– A quantitative measure of species heterogeneity.
What do you need to know to be able to assess species diversity?
Taxonomic information: ability to assign individuals to the
appropriate species.
- A count of the number of species in the community.
- A measurement of the relative abundance of the species in
the community. - May be straightforward for some communities. (e.g., bird
community of a small woodland) - May be difficult for many invertebrate groups for which
there are a large number of species that have similar
morphologies.
Why is biodiversity declining?
Loss of habitat
– Logging
– Farming
– Urbanization
* Habitat modification
– Water extraction
– Flood control
* Overexploitation
– Overfishing
– Hunting (e.g., bushmeat)
* Introduced species
– Invasive species
* Pollution
* Climate change
Why does biodiversity matter?
Ecosystem functions (processes) and ecosystem services depend on biodiversity.
- Intergovernmental Science-Policy Platform for
Biodiversity and Ecosystem Services (IPBES) has been
established to
– assess change (loss) of biodiversity
– assess how these changes affect human wellbeing.
What is the difference between ecosystem functions and ecosystem services?
Ecosystem functions are
the biological, geochemical
and physical processes and
components that occur
within an ecosystem.
* Ecosystem functioning
affects nutrient cycles, the
water cycle and the carbon
cycles.
* Other ecosystem functions
affect population dynamics
(e.g., seed dispersal,
pollination).
—————————-
Ecosystem services are
ecosystem functions that
are directly beneficial to
humans.
* Provisioning services (e.g.,
food, fibre, fuel, minerals,
water)
* Regulating services (e.g.,
CO2
sequestration, waste
decomposition)
* Cultural services (e.g.,
ecotourism, heritage values)
Examples of ecosystem functions and
ecosystem services
Ecosystem functions:
Plants are primary
producers.
* Grazing and predation
balance plant and animal
populations.
* Plant seed dispersal.
* Animals find mates and
reproduce.
* Waste materials are
degraded and recycled back
into the soil.
Ecosystem services:
Bees pollinate crop plants.
* Animals provide protein for
human consumption.
* The watershed provides
water for human
consumption.
* Trees serve as buffers
against storms preventing
destruction of homes and
other structures.
DIVERSITY-PRODUCTIVITY
HYPOTHESIS
Niche Differentiation accounts for
increased productivity in more
diverse communities.
Habitat is heterogeneous.
* Different species have different
niches.
In the hypothetical case illustrated, each species has a circular radius in niche space
in which it is a good competitor.
* By occupying more of the habitat
space, diverse communities use
more of the available nutrients to
produce more total biomass.
What is ecological stability?
Response to change…
-Press perturbation: Sustained alteration to a system state variable, e.g. temp,
pH, or biological subsidy.
- Pulse perturbation: temporary change to a system state variable that can then
recover.
Four key aspects…
- Variability - the variation of community biomass over time
- Resistance - the degree to which community biomass is changed following a perturbation
- Resilience - how long it takes for community biomass to return to predisturbance or reference state levels following a perturbation
- Persistence - the length of time that biomass remains unchanged
Does diversity increase stability?
Charles Elton suggested that species diversity promoted
stability citing:
* Theoretical and laboratory experiments on 2-species systems
(Lotka-Volterra, Gause)
* Islands (which have lower biodiversity) are more vulnerable
to invading species than continents.
* Outbreaks of pests are found most often in simple
communities on cultivated or disturbed land.
* Tropical rain forests (which have very diverse plant
communities) do not have insect irruptions whereas
temperate forests do.
* Use of pesticides can lead to irruptions by eliminating insects
that are predators or parasites of “pest” species (by reducing
the biodiveristy of the predators).
DIVERSITY-STABILITY HYPOTHESIS:
Ecosystems that have more species
are more stable because diversity
promotes resistance to
disturbance.
* Species differ in their traits.
* More diverse communities
contain some species that can
thrive after a perturbation
(change in a biotic or abiotic
factor).
* These species can compensate
for competitors that are stressed
by the perturbation.
Latitudinal Diversity Gradient
Species diversity is greater in
tropics (23° N/S) than at high
latitudes.
* Tropical rainforests contain
>1,000 tree species. (around
800 species in 50ha)
* Northern Europe contains
only 50 tree species.
Latitudinal Diversity Gradients – Some
Exceptions
Exceptions to the typical
pattern.
* Puffins are more diverse at
higher latitudes in N.
hemisphere.
* Sea lions are more diverse at
high latitudes in both N. and
S. hemispheres.
Why are the tropics so diverse?
i.e. why does species richness increase towards the tropics and away from the poles across the majority of taxonomic groups?
- The time theory (tropics are old, more time for speciation)
- The theory of spatial heterogeneity (tropics are structurally
complex more niches) - The competition hypothesis (more competition drives
narrower niches) - The predation hypothesis (less competition via greater
predation) - The theory of climatic stability (easier to specialise)
- The productivity hypothesis (climate increases productivity)
Six factors have been advanced to account for
variations in species richness. These are:
Evolutionary speed
Geographic area
Interspecific interactions
Ambient energy
Productivity
Intermediate disturbance
More than one of the factors may be important – some
drivers and some maintainers.
* Importance varies amongst regions and/or taxonomic
groups.
Evolutionary Speed Hypothesis (1/3)
- Explanation for why so many species arise – not why so many can coexist
- Length of time tropics have existed, promoting speciation
- Stability of the tropics reducing extinction (difficult to text)
- Climate favours small bodied, fast generation time, taxa
- UV exposure higher, could (little evidence) increase
mutations
Evolutionary Speed Hypothesis (2/3)
Species diversity is the product of evolution.
Faunas and floras that have evolved for longer time
and/or at faster rate will be more diverse.
Tropics are more diverse because:
– Conditions are favourable
– Evolution has not been interrupted by glaciation.
Evolutionary Speed Hypothesis (3/3)
Species richness increases
over evolutionary time scales, unless interrupted by
catastrophes.
* Evolution brings new species into communities (and extinction removes extant
species).
* Ecological time scales are
much faster than evolutionary time scales, so
other processes must operate
as well.
Geographic Area Hypothesis
Hypothesis: More species can be supported in larger areas
because larger areas provide more niches.
Number of habitats may increase with area.
– more scope for speciation
Total population may increase with area.
– less likelihood of extinction
Diversity Hotspots
Hotspots are areas with high numbers of endemic
species.
* An endemic species is found in only one, relatively
small, geographic area.
* Species arise primarily by geographic isolation.
* On global scale, patterns of isolation are a
consequence of continental drift.
* Locally, topography can be important.
* Many, but not all, hotspots are in tropics.
Interspecific Interactions
Greater competition can increase diversity
Stronger predation may increase diversity.
Greater competition can increase diversity.
– More stable, less stressful environmental conditions may lead to greater competition.
– Greater competition leads to resource partitioning and
narrower niches (more specialist species).
– This leads to both greater habitat specificity (contributing to b-diversity) and within habitat diversity (a-diversity).
Stronger predation may increase diversity by
– reducing competition, allowing more species to share the same resource if predation controls prey abundance or
removes competitively superior species.
Interspecific Interactions: Competition
Competition in “equilibrium”
communities:
– the number of species that can
coexist is no greater than the
number of limiting resources.
* Where there is a range of
resource availability, species
can partition the resource to
avoid competitive exclusion.
* Species richness depends on
the average niche width and
extent of overlap.
Interspecific Interactions: Competition
Anolis are small, diurnal, insect eating lizards
* sit and wait predators that perch in trees or bushes
* food size is a critical niche dimension
* niche breadth decreases with increased species richness
Interspecific Interactions: Predation
Predation can lead to increased species richness by removing animals that are superior competitors,
because there is often a tradeoff between maximum
reproduction rate and ability to resist predation.
Removal of a keystone predator can lead to reduced diversity
Interspecific Interactions: Disease
Tropical forests have high tree diversity.
* Seed deposition is high, but
survival is low close to a mature
tree of the same species.
* Survival is reduced by host specific parasites or disease in
the immediate vicinity of
mature trees.
* Some seeds carried away from
the parent tree by fruitivores
are more likely to survive.
Ambient Energy Hypothesis
Hypothesis: Energy
availability generates and
maintains species richness
* because fewer species can
tolerate extreme
environments.
* Key variables are solar
radiation, temperature and
water availability.
* Annual evapotranspiration can
be used as an index of energy
balance.
Productivity Hypothesis
Hypothesis: greater
primary production results
in greater species diversity.
* In terrestrial systems, total
primary productivity
depends on
– area of habitat,
– sunlight and
– precipitation.
Counter examples to the Productivity
Hypothesis
Some of the most speciesrich plant communities
occur on nutrient poor
soils
– fynbos in South Africa
– heath scrublands in
south-eastern Australia
* Compare location of
biodiversity hotspots with
NPP map.
Intermediate Disturbance Hypothesis
Hypothesis: at local scales, competitive exclusion,
which should reduce species diversity, is prevented by
disturbance.
* Disturbance includes any event that disrupts
competition:
– fluctuations in physical/chemical factors
– catastrophes such as fires or erosion
– predation or herbivory
Species of low
competitive ability are
lost when disturbance is
infrequent.
* Species are lost
indiscriminately when
disturbance is severe.
* Maximum diversity
should occur at
intermediate disturbance.
Does Diversity Increase Productivity?
DIVERSITY-PRODUCTIVITY
HYPOTHESIS
Niche Differentiation accounts for increased productivity in more diverse communities.
Habitat is heterogeneous.
* Different species have different
niches.
In the hypothetical case illustrated, each
species has a circular radius in niche space
in which it is a good competitor.
* By occupying more of the habitat
space, diverse communities use
more of the available nutrients to
produce more total biomass.
Potential mechanisms (plant niche)
Below ground niche
complementarily due to resource
competition
The regulation of plant productivity
by soil microbiota
Potential mechanisms (plant niche)
Below ground niche
complementarily due to resource
competition
The regulation of plant productivity
by soil microbiota
Potential mechanisms (soil microbes)
Below ground niche
complementarily due to
resource competition
The regulation of plant
productivity by soil
microbiota
soil sterilisation treatments
also remove beneficial
organisms such as
saprotrophs and
mycorrhizae, and modify
nutrient availability
Diversity and Ecosystem Function.
Diversity-productivity hypothesis: Ecosystems containing more species are on average more productive or have greater total biomass because diversity allows more of the habitat space/resources to be occupied.
Diversity-stability hypothesis: Ecosystems that have more
species are more stable because more diverse communities
contain some species that can thrive after a disturbance
(change in a biotic or abiotic factor) and these can compensate
for competitors that are stressed by the disturbance.
What is ecological stability?
Response to change…
Press perturbation: Sustained alteration to a system state variable, e.g. temp,
pH, or biological subsidy.
* Pulse perturbation: temporary change to a system state variable that can then
recover.
Four key aspects…
Variability - the variation of community biomass over time
2. Resistance - the degree to which community biomass is changed following a
perturbation
3. Resilience - how long it takes for community biomass to return to predisturbance or reference state levels following a perturbation
4. Persistence - the length of time that biomass remains unchanged
Functional Traits
Examples of plant traits
– Phenology
– Height at maturity
– Root depth
– Seed size
– Maximum photosynthesis rate
– Water use efficiency
– Affinity for limiting nutrients
What is meant by the term functional diversity?
Functional diversity: the amount of trait variation in an assemblage.
* Species do not contribute equally to varied ecosystem
processes and delivery of services.
– Keystone predators
– Ecological engineers
Modern Molecular Ecology –
The Basic Method!
BIG ECOLOGICAL QUESTION FIRST!
Extract starting
material –
Nucleic Acids
DNA or RNA
-> Amplify
extracted DNA
or RNA material
via PCR
-> Downstream
processing of
product
-> Bioinformatics
and data
analysis
PCR Produces Large Amounts of
Nucleic Acid From Small Starting Templates
ds DNA separates into
ss DNA > ca. 94°C.
Causes DNA melting of
the DNA template by
disrupting the hydrogen
bonds between
complementary bases,
yielding single-stranded
DNA molecules
The reaction
temperature is lowered
to 50–65 °C for 20–40s.
Annealing of the
primers to the ss DNA
template.
annealing temperature
is ca 3-5 °C below the
Tm of the primers used.
Stable DNA-DNA
hydrogen bonds are
only formed when the
primer sequence very
closely matches the
template sequence. The
polymerase binds to
the primer-template
hybrid and begins DNA
synthesis.
The temperature
depends on the DNA
polymerase used
Taq polymerase has its
optimum activity
temperature at 75–80
°C (72 °C is used)
DNA polymerase
synthesizes new DNA
strand complementary
to template strand by
adding dNTPs in 5’ to 3’
direction
Extension time depends
both on the DNA
polymerase used and
length DNA fragment to
be amplified
DNA polymerase
synthesizes new DNA
strand complementary
to template strand by
adding dNTPs in 5’ to 3’
direction
≈1kb per min.
Quantitative PCR - qPCR
Used to quantify PCR product (commonly in real-time;
hence confusion with RT-PCR).
* Measures starting amounts of DNA, cDNA, or RNA.
* Used to determine whether a DNA sequence is present
in a sample and the number of its copies in the sample.
* Quantitative real-time PCR has a very high degree of
precision. One of the best methods for working out how
much DNA/RNA is in a sample.
Quantitative PCR – Basic Method
TaqMan probes:
A fluorophore is attached to the 5’
end of the probe (additional oligo to
primers) and a quencher to the 3’
end.
The fluorophore is excited by the
machine and passes its energy to
the quencher.
FAM as the fluorophore and TAMRA
as the quencher.
TaqMan probes:
FAM does not fluoresce as it passes
its energy onto TAMRA.
As TAMRA fluorescence is detected
at a different wavelength to FAM,
the background level of FAM is low.
The probe binds to the amplicon
during each annealing step of the
PCR.
TaqMan probes:
When the Taq polymerase extends
from the primer which is bound to
the amplicon, it displaces the 5’ end
of the probe, which is then
degraded by the 5’-3’ exonuclease
activity of the Taq polymerase.
Releases the fluorophore and
quencher into solution, leading to an
irreversible increase in fluorescence
from the FAM and a decrease in the
TAMRA.
ddPCR – Basic Method
qPCR: Inconsistent CT
* Data not comparable between
runs
* Nonspecific amplification
ddPCR: * No standard curve
* Data is comparable between
runs
* No replicate wells needed (?)
Uses for different PCR
Metagenetics: who is there? and number of species
qPCR: How many are there and abundance
Metagenomics: What can they do, abundance
Metatranscriptomics: What are they doing?, activity
Definitions in PCR practices (1/4)
Amplicon: The short DNA sequence products of polymerase chain
reaction (PCR) amplification using taxon- or gene-specific primers to target a particular region of the genome.
Biodiversity genomics: Biodiversity assessed using high-throughput
DNA-based methods or data from whole genomes integrated with a broad array of metadata describing biological and environmental
indicators.
Biomonitoring: Biodiversity analysis that is repeated across space and
time that may focus on a target organism such as invasive or at-risk
species, an assemblage such as the bioindicator groups (amphibians, birds, macroinvertebrates) as an indicator of ecosystem status.
