#+hugo_base_dir: ../

#+hugo_section: ecology

Setup

no exams
groups of 4
group assignment in exam period
Read the entire textbook
4 field-trips
august 31 lake
9-14, 9-15 zoo
forest lab
october 26 UC field center
learning outcomes determine quiz questions.

Chapter 1

Terms

Ecology

The study of the interactions between an organism and its biological and physical environment.

Trait

A combination of characteristics in an individual. A trait that increases evolutionary fitness is an adaptation.

Hair color
resistance to antibiotics.

Population

All of the organisms of a particular species in a particular area.

The population of snow hares in the Himalayas.

Fitness

The degree to which an organism is likely to survive in an environment. The fitter the organism, the more likely they are to survive in an environment suited to their adaptations. This is more useful in the context of the population.

Levels of Ecological organization

organism
population
community
ecosystem

Proximate Vs Ultimate

Proximate Factors

Direct or Immediate causes/effects on the organism. The How.

Changes in photoperiod
Temperature changes

Ultimate Factors

The Indirect reason for an effect on the organism. The Why.

Scientific Method and Hypothesis testing

Good hypothesis lead to testable predictions. It is also falsifiable.

Observation
Hypothesis
Measurements
Results
Conclusion

Predictions

A prediction is an observation or a result that is expected if the hypothesis is true.

Hypotheses and tests

Focus on a population
Why does the population exist?
What unique challenges does it face?
Are circumstances changing?
Will the population grow, shrink, disturbed

Resources
- reproduction
- Survival
- Mate
- Food
- Shelter

Chapter 2

review

mutation
allele
gene frequencies
genotype
phenotype

Important terms for the course

Evolution is the change of populations (species) over time due to heritable changes.
Natural Selection is the "selection" of heritable traits due to their fitness
Adaptation is the tendency for natural selection to select changes most well suited to the environment.
Fitness is the likelihood that an organism will survive (pass its genes down) in its current environment.

Mechanisms for evolutionary change

Natural Selection
Genetic drift
Gene Flow
Mutation pressure

Natural section, genetic drift, gene flow

genetic drift

The random change of allele frequency based on non-random mating. Only affects populations with limited populations (non-random mating)

Gene flow

Individuals can move from population to population, or form a new population. These fluctuations can change the allele frequencies in a population.

Isolation

Differentiation is affected by Isolation. Isolation prevents gene flow.

Hardy Weinberg

\(P^2 + 2PQ + Q^2\)

Adaptation is an undirected process

Traits are not created to adapt to the environment. Traits instead are randomly generated (through mutation) and the traits that are well suited to the environment are selected for.

Phenotypic Plasticity

Development of physiological variation among phenotypes induced directly by the environment.

Occurs during the development of an individual.
Himalayan Rabbits are a good example, they have areas of black fur if born in a cold environment.

Adaptive landscape

An adaptive landscape is a three dimensional plot, where the x and y axis refer to allele frequency and the z axis refers to fitness. "Peaks" and "Valleys" show how different allele frequencies affect fitness and why genetic drift can be helpful for adaptation.

Red Queen Hypothesis

Increased fitness in the short term does not always end well for the species. This discrepancy of fitness between two related organisms (parasites/hosts, predators/prey) is related to generational rate. One of the species in the relationship cannot keep up evolutionarily with its pair species. This may result in extinction of prey or predator or both.

Chapter 3

Adaptation to environmental factors

Change factors that limit growth (amount of food, composition of air)
Change Tolerance Range (Temperature tolerance, ph tolerance )
Change Behavior to adapt beyond Range ( avoid cold areas )

Limiting environmental factors

physical factors (strength, ability to fly)
Physical resources
Tolerance bounds

optimality and `Principle of allocation`

Adaptation to one challenge may decrease for another. The more an organism adapts to a stable environment (optimality), the less able it is to adapt to new environments that pose new challenges (moving from hot to cold, fresh water to salt water or vice versa)

Large beaks make it easier to break large nuts, but harder to eat insects out of trees.
Homeostasis allows humans to survive in a variety of environmental conditions, but requires more (is limited by) food.

Normal Distribution and measures of variation

Many biological factors rely on modifications to the normal distribution.

quantified as a probability or confidence interval (95% of samples fall within this range of values)
\(\text{Sample Variance} = \frac{\sum_1^n (\bar x - x_i)^2}{n-1} = s^2\)
\(\text{Sample Mean} = \frac{\sum_1^n}{n} = \bar x\)
\(\text{confidence statistic (percentage)} = 1-\alpha\)
\(\text{confidence interval} = \bar x \pm t_{1-\alpha} * s/\sqrt n\)
\(\text{Standard Error (Estimate of the mean)} = \frac{s^2}{n}\)

Description of the plots used in ecology

y axis refers to the frequency of individuals (higher is more)
x axis refers to some limiting factor (food, temperature)
Peak refers to the mean of the sample

P Value

The P value is the probability that the Null hypothesis is true. This value is calculated with a statistical test (t test when using a sample).

Example
- \(H_0 = \text{Cancer is randomly occuring}\)
- \(H_a = \text{Cancer is caused by radiation damage}\)
- \(P < 0.05\)
- There is less than a 5 percent chance that cancer is randomly occurring.

behavioral Thermoregulation.

Animals will move to areas that are conducive to their optimal temperature range.

Snakes bask in the sun to warm up (ectotherms)
Humans will go inside (or put on clothes) to warm up (endotherms)
Monkeys will bathe in hot springs in cold climates. (endotherms)

Adaptive radiation

The tendency for species to diversify to fill open ecological niches.

Early Plants
Finches

Osmoregulation (water stress) and photosynthesis

Organisms alter their internal concentration of solute (or consume water) to regulate their internal water content.

Skin and scales prevent unintended evaporation of water
C3 pathway is shared by all plants (the calvin cycle)
C4 pathway allows plants to save water by closing the stomata when necessary.

Adaptation vs Plasticity

Some animals have larger optimal ranges of physical resources than others (plasticity)

Evolution through natural selection adapts organisms to their environments
Plasticity refers to the ability of an organism to survive in different environments
Humans could be said to have high plasticity due to our tool making
Octopi make extensive use of RNA editing sites to alter their expression Octopus RNA editing sites (plasticity?)

Chapter 4

8 Major Biomes

Tundra

Conifer and Evergreen Forest

Temperate Deciduous Forest

Temperate Grassland

Mediterranean Shrubland

Desert

Tropical Savanna

Tropical Rainforest

Adaptations of plants to different biomes

Chapter 5

Basic Aquatic Environments

Salt vs freshwater systems

Ice
Oceans
Lakes
Rivers
Ponds
groundwater
soil
atmosphere

Lentic System (freshwater)

Water Movement (air, land, water)

Hydrologic cycle
Transpiration (plants return water to air in photosynthesis)
Infiltration, water moves into soil (between particles)
Sheet flow, water directly moves to bodies of water
Aquifer (underground water reservoir)

Oxygen, Carbon, salt, nutrients move through aquatic environments

River Continuum hypothesis

Ecological changes that occur from first order to high-order streams

Species type concentration can be determined from this
CPOM -> Shredders
FPOM -> Collectors
Algae -> Grazers

Regression and correlation plots

Island Biogeography

Habitat islands
equilibrium = rate of arrival of new species vs Extinction rate
- Large islands have lower extinction rates
- Large islands have higher immigration rates.
change over time

Meta-population

Interconnected populations. Lots of movement between population fragments.

Theoretical models

Doesn't account for all real-world issues. Prevalence of natural disasters can be an example.

Island biogeography vs evolutionary divergence

Less Species = larger opportunity for divergence

Chapter 6

Sexual Reproduction

Increases genetic variation
Environmental stress can cause massive sexual reproduction (to increase variation)

Darwin-fisher

Balance vs Truth in advertising (Darwin Fisher)

Balance
- male traits are exaggerated by female choice (increases cost)
- Natural selection culls high cost male traits
- Male traits get "optimized" to a balance of excessive male traits, and functional survival traits
Truth in advertising
- Male traits indicate natural fitness
- Males can have excessive traits and still survive better

Mating Systems

Plants

outcrossing (mating among different individuals)
autogamy (self fertilization)
apomixix (asexual reproduction)

Territoriality

When resources are divided in a way that males can defend them
Females choose males that provide access to resources
Polygny is a mating system in which each female mates with more than one male

Leks

Males demonstrate at predetermined (traditional) sites.

Vocab

Relatedness: A measure of how many genes are shared between individuals
Inbreeding: When an individual mates with a close relative, eventually causing side effects.
kin selection: Individuals may increase fitness by helping a close relative (honeybees)
Inclusive Fitness: cooperation increases fitness (humans)
Social Systems: group size and composition, cooperation, mating system

CH 7

Evolutionary stable strategy, frequency-dependent selection and hypothesis of the evolution of sexual reproduction

Evolutionary stable strategy

Adaptation increases in frequency when rare (beneficial for the survival of a species)

Frequency dependent selection

Fitness is determined by frequency in population (sickle cell)

Evolution of sexual reproduction

Related to the red-queen hypothesis. Host had to find a way to evolve at same rate as parasite.

Genetic distance among populations

Number of differences or mutations between two sets of DNA.

Genetic bottlenecks, conservation genetics of small popululations

SMall populations have increased effects due to change. Allele frequency from generation to generation is much more random.

Genetic bottlenecks

Reduction in diversity of alleles because of some event (excessive predation, natural disaster, etc)

Design a common garden experiment to disentangle phenotypici plasticity verses evolutionary divergencce

Grow plants in the same garden (with different phenotypes)
If phenotypes persist, it is a genetically controlled phenotype
If phenotypes change, it is phenotypic plasticity

CH 8

Compare and contrast different life tables to infer different life history strategies.

Interpret differences in survivorship curves

Understand r, the intrinsic growth rate of a population

age structure pyramids in terms of population growth and reproduction

CH 9

Logistic Growth
- \(dN/dt = rN (1 - N/K)\)
Population regulation
Top-down
- Predators
Bottom-up
- food resources
K (carrying capacity)

ecology