III. Ecology

Key focus of this chapter: population and communities.

This chapter focuses on population and communities and gives concise summaries of the important things about ecosystem and biosphere.

A. Hierarchical levels of organization

Hierarchical levels	Main features
Organism	• Individual living thing
Species	• A group of organisms that can interbreed • Similarity of gene pool
Population	• Collection of species
Community	• Group of interacting organisms sharing a geographic area
Ecosystem	• Biotic factors and abiotic factors
Biosphere	• Sum of all global ecosystems • Earth and atmosphere

B. Species

1. Historic biologists

a. Aristotle (384 – 322 B.C.)

Scale of nature – life forms ranked on a ladder by complexity from the most simple at the bottom to the most complex at the top as ordained by God during creation.
Species are perfect and do not evolve.

b. Carolus Linnaeus (1707 – 1778)

Binominal nomenclature system of taxonomy.
Similar species are not evolutionary kinship but follow the same pattern of creation.

c. Georges Cuvier (1769 – 1832)

Paleontology – the study of fossils.
Catastrophism – catastrophes (floods, drought, volcanoes) create stratum of rock eliminating species.

d. James Hutton (1726 – 1797)

Gradualism – profound change is slow accumulation and continuous processes.

e. Charles Lyell (1797 – 1875)

Uniformitarianism – uniform geological processes.

f. Jean Lamarck (1744 – 1829)

Inheritance of acquired characteristics.
A part of the body in frequent use becomes larger and stronger, while a part in disuse gradually deteriorates.

g. Charles Darwin (1809 – 1882)

Voyage of HMS beagle at Galapagos Islands.

– first proof of a new species from reproductive isolation.

Origin of species

– descendant species with modification from ancestral organisms.

– species evolve through natural selection.

Natural selection

– successfully adapted organisms with environment become successive generations in a population.

Artificial selection

– divergent results of intentional breeding by human selection.

2. Evolution and structure

Evolution: a change of the genetic composition in the population over time.
Divergent and convergent evolution.

3. Geographic separation

Allopatric speciation

– new species from population by geographic isolation

Sympatric speciation

– new species from population without geographic isolation

– new species share geographic region

C. Population

1. Variation of evolution

a. Mutation – making new genes and new alleles

b. Sexual recombination – making various traits

2. Alteration of genetic composition

a. Genetic drift

: reducing genetic variation from one generation to the next.

Bottleneck effect

– sudden disasters reduce the size of population.

Founder effect

– group isolated from a large population loses genetic variation and establishes new population.

b. Gene flow

Adding or losing alleles of population from fertilization

c. Natural selection

: main source of adaptive evolution

Geographic variation

– different plant sizes in common plant along with geographic altitudes (cline) have different genes.

Evolution Fitness

– stabilizing selection: shifting the overall population to favored middle values and removing extreme values.

– disruptive selection: shifting the overall population possessing favored values to both ends of the distribution.

– directional selection: shifting the overall population possessing favored values to one extreme end of the distribution.

3. Population dynamic

a. Exponential growth

Population size increases exponentially.
More birth rates than mortality rates.

b. Logistic Growth

Sigmoid curve or S-curve.
Initial stage is exponential growth but final stage is stopping growth.
Carrying capacity: Maximum population size that environment can sustain.
Life histories.

Life histories	Features
K-selection	• Maximize population size or carrying capacity (K) • Stable environments • Low reproductive rate • Slow growth • Small number of offspring • Roughly constant in size • Long life span • Eg/ Human
R-selection	• Maximize growth rate (R) of population • Unstable environments • High reproductive rate • Rapid growth • Numerous offspring • Short life span • Eg/ Bacteria

D. Communities

1. Niche and habitat

Niche: relational position or role of population in an ecosystem.
Habitat: environmental areas where organisms live.

2. Species community

Interaction	Classification	Main characteristics
- / -	Competition	• Two organisms in the same environment compete to get the same resource • Both species negatively affected
+/-	Herbivory	• Herbivore is positively affected and plant or alga is negatively affected
	Parasitism	• Parasite is positively affected and host is negatively affected • Eg/ Tapeworm living in the digestive tract and human, fungal agent (athlete’s foot) and human
	Predation	• Predator is positively affected and prey is negatively affected
+ / 0	Commensalisms	• One species is positively affected and another species is not affected • Eg/ Cattle egrets and water buffalo, remora and shark
+ / +	Mutualism	• Both species is positively affected • Endosymbiosis • Eg/ Tick bird and rhinoceros, acacia tree and ants, lichens (fungus & algae), nitrogen-fixing bacteria living in the root nodules of legumes

3. Defensive adaptation

: defensive methods from predation.

Defensive adaptation	Classification	Features
Coloration	Aposematic coloration	• Warning coloration to predator (Chemical defenses) • Eg/ Poison arrow frog
Coloration	Cryptic coloration	• Camouflage (Morphological defense)
Mimicry	Batesian mimicry	• Palatable species mimics an unpalatable species • Harmless species mimics a harmful species
Mimicry	Mullerian mimicry	• Two or more unpalatable species are similar to each other and have aposematic signals.

4. Innate and learned behaviors

a. Fixed action pattern (FAP)

Instinctive and unlearned behavioral acts by a sign stimulus.
Eg/ Characteristic movement of herd animals, mating dance in animal.

b. Imprinting

Sensitive phage learning.
Both instinctive and learning behavior.
Young animal or human learning a characteristic stimulus and influence their behavior later in their life.
Eg/ Young geese following their mother, flying imprinted cranes with an ultralight plane.

c. Habituation

Loss of behavior response to stimuli after repeated stimuli.
Eg/ Baby is no longer startled by sound of a car horn after repeated exposure.

d. Spatial learning

Memorizing for spatial environment including spatial orientation and any locations.

e. Associative learning

: learning process with pre occurring information.

Associative learning	Summary
Classical conditioning	• Learning from conditioning of respondent behaviors with reward or punishment • Arbitrary stimulus → conditioned response → learning • Eg/ Salivating mouth of a dog after ringing of a bell
Operant conditioning	• Learning from voluntary behaviors with reward or punishment • Voluntary behaviors → experience errors → learning • Trial and error learning • Eg/ Dog surviving from eating poisoned food does not eat the food again

f. Extinction

Conditioned response becomes lost from absence of stimulus.

5. Ecological succession

: disturbed areas from human activities or disasters are replaced by plant, animal, and microbial community

a. Primary succession

Succession with the lifeless area where soil is not formed
New area formed by volcano or retreating island
Pioneer species with algae, lichen, mosses, and fungus
Communities

Communities	Features
Pioneering community	• First colonizing plants • Eg/ horsetail, willows
Climax community	• Late successional community • Stable populations • Eg/ Shade trees

b. Secondary succession

Succession with the area where soil is already formed.
Disturbed area formed by forest fire.

E. Ecosystem

1. Biotic and Abiotic factors

Biotic factors: all living organisms in ecosystem
Abiotic factors

– nonliving physical and chemical factors.

– eg/ water, temperature, sunlight, wind, nutrients.

2. Energy flow in ecosystem

a. Food chain

Toxin becomes concentrated when it moves up from producer to tertiary carnivores.

Trophic structures	Features and examples
Producer	• Plants • Green plants, algae, phytoplankton
Herbivores	• Primary consumers • Animals that eat plants, zooplankton
Primary carnivores	• Secondary consumers • Animals that eat herbivores and zooplankton
Secondary carnivores	• Tertiary consumers • Animals that eat primary carnivores
Tertiary carnivores	• Quaternary consumers • Animals that eat secondary carnivores
Decomposers	• Organisms that break down nonliving organic materials • Eg/ Bacteria, fungi
Detritivores	• Organisms that eat nonliving organic materials • Eg/ worms, arthropods

3. Nutrient cycles

: pathway of biogeochemical elements through both abiotic and biotic factors.

a. Water cycle

Essential to all living organisms.
Evaporation of water by solar energy → concentration of water into clouds → precipitation

b. Phosphorus cycles

Components of ATP, nucleic acids, and phospholipids in living organisms.
Plant uptake phosphorus from soils → consumers → Decomposers

c. Carbon cycles

Essential to all living organisms as organic structures.
Cellular respiration by consumers → photosynthesis by plants

d. Nitrogen cycles

Components of amino acids, nucleic acids in living organisms.
Nitrogen gas (N₂) → ammonia (NH₃) → ammonium (NH₄⁺) → nitrites (NO₂^–) → nitrate (NO₃^–)

Bacteria for nitrogen cycles	Functions
Nitrogen fixing bacteria	• Adding hydrogen to nitrogen • Fixing nitrogen gas (N2) to ammonia (NH3)
Ammonification	• Changing ammonia (NH3) to ammonium (NH4+)
Nitrifying bacteria	• Adding oxygen to nitrogen • Converting ammonium (NH4+) to nitrites (NO2-) and nitrites (NO2-) to nitrate (NO3-)
Denitrifying bacteria	• Subtracting oxygen from nitrogen • Changing nitrate (NO3-) to nitrogen gas (N2)

Nitrogen cycles

4. Temperature relation

a. Climate

Microclimate

– climate of local zone surrounded by community of organisms.

– important to individuals of a species.

Macroclimate

– global or broad regional climate.

– important to distribution patterns of species.

b. Thermoregulation

Homeothermic animals

– keeping constant body temperature.

– eg/ Warm blood animals such as mammals and birds

Poikilothermic animals

– changing body temperature with environmental temperatures.

– eg/ Cold blood animals such as reptiles and amphibians

5. Water and salt regulation

a. Freshwater fish

Excreting large amount of water by kidney in the hypotonic environment.

b. Saltwater fish

Up taking large amount of salt ions and excreting small amount of salt ions in the hypertoinc environment.

F. Biosphere

1. Water structure

a. Lake zones

Lake zones	Features
Littoral zone	• Shoreline areas
Limnetic zone	• Open surface area away from littoral zone
Photic zone	• Area exposed to sunlight for photosynthesis • Euphotic zone (rich phytoplankton, shallow and murky water)
Aphotic zone	• Area of no sunlight
Benthic zone	• Lowest area of water

b. Marine zones

Marine Zones		Features
Littoral zone	Intertidal zone	• Exposed air and submerged area • Many different types of organisms • Important area for study of ecology
Neritic zone		• From coast to 200 m horizontally • Low tide mark area • Well-oxygenated water and stable salinity levels
Photic zone	Epipelagic zone	• Surface – 200 m depth • Most photosynthesis takes place
Aphotic zone	Mesopelagic zone	• 200-1000m depth
	Bathypelagic zone	• 1000-4000m depth
	Abyssal zone	• 4000-6000m depth
	Hadal zone	• Deepest area of marine environment • Below 6000m depth

2. Water relations

a. Rain shadow

When moist air passes the front side of the mountains, it becomes cool at high altitudes, and precipitation occurs by decreasing moisture-holding capacity.
When dry air moves down on back side of the mountains, it becomes warm at low altitudes and sucking up moisture occurs by increasing moisture-holding capacity.
Eg/ Death Valley (Sierra Nevada)

b. Seasonal turnover

: mixing water between oxygenated shallow water and nutrient-rich deep water during both spring and autumn seasons.

Breaking down thermal stratification of summer and winter seasons.
Spring turnover

– warm surface water sinks to bottom area.

Fall turnover

– cold surface water sinks to bottom area

3. Terrestrial biomes

Terrestrial biomes	Main features
Tropical rain forest	• The highest species of terrestrial plants and animals with richest ecosystem • Around region of equator
Savanna	• Dry tropical grassland with low precipitation • Transition between tropical forest and desert in the interiors of continents
Desert	• Dry places with low precipitation • Water conservation for plants and animals • Succulent plants of shrubs and cacti
Chaparral	• High temperature and dry summer and mid temperature and rainy winter. • Evergreen plants with spiny shrubs and small trees
Temperate grassland	• Dry and cold winter and humid and hot summer • Forb and grass plants • Many farmlands
Temperate deciduous forest	• Hardwood and broad-leaved deciduous forests • Summer rain and winter snow
Coniferous forest (Taiga)	• Coniferous tree with needle like leaves • Most limited precipitation during summer • Long and cold winter • Many large mammals
Tundra	• Found in far north with low precipitation • Small shrubs or vegetation • Long and cold winter and short and cool summer • Permafrost
Polar ice	• North and south pole • Almost no precipitation • Limited life of organisms