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
Population	• A group of individuals of the same species living in the same area at the same time.
Community	• Populations of different species living and interacting in the same area
Ecosystem	• A community and its interacting abiotic environment
Biosphere	• Sum of all global ecosystems • The regions of Earth where life exists

B. Species

Species (biological species concept): A group of organisms whose members can interbreed naturally to produce viable, fertile offspring and are reproductively isolated from other such groups. This concept has limitations for asexual organisms. Species is a taxonomic category, not a structural ecological level.

1. Historic biologists

a. Aristotle (384 – 322 B.C.)

Scale of nature – Aristotle arranged living forms by increasing complexity; this was a historical view, not modern evolutionary theory.
Aristotle regarded species as fixed rather than evolving.

b. Carolus Linnaeus (1707 – 1778)

Binomial nomenclature: each species has a two-part name (genus and specific epithet).
Linnaeus grouped organisms by shared characteristics; his classification was not originally based on evolutionary ancestry.

c. Georges Cuvier (1769 – 1832)

Paleontology – the study of fossils.
Catastrophism – sudden geological events can cause extinctions and help explain changes seen among fossil-bearing rock strata.

d. James Hutton (1726 – 1797)

Gradualism – substantial geological change can accumulate through slow, continuous processes.

e. Charles Lyell (1797 – 1875)

Uniformitarianism – geological processes operating today also operated in the past.

f. Jean Lamarck (1744 – 1829)

Lamarck proposed inheritance of acquired characteristics; this is not the general mechanism of adaptive evolution.
Lamarck proposed that use and disuse altered traits and that these acquired changes were inherited.

g. Charles Darwin (1809 – 1882)

Voyage of HMS Beagle, including observations in the Galápagos Islands.

– Observations from the Galápagos Islands contributed to Darwin’s ideas about evolution.

Origin of species

– descent with modification from ancestral populations.

– species evolve through natural selection.

Natural selection

– Individuals with heritable traits that increase reproductive success tend to contribute more offspring to the next generation.

Artificial selection

– Selective breeding by humans increases the frequency of chosen heritable traits.

2. Evolution and structure

Evolution: change in heritable characteristics, including allele frequencies, in a population across generations.
Divergent and convergent evolution.

3. Geographic separation

Allopatric speciation

– Speciation following geographic isolation and the evolution of reproductive isolation.

Sympatric speciation

– Speciation through reproductive isolation without geographic separation.

– The diverging populations occupy the same geographic region.

C. Population

1. Sources of genetic variation

a. Mutation – the ultimate source of new alleles and new genetic variation.

b. Sexual recombination – reshuffles existing alleles into new genotype combinations.

2. Alteration of genetic composition

a. Genetic drift

: Random changes in allele frequencies, especially strong in small populations; drift can reduce genetic variation.

Bottleneck effect

– A sudden reduction in population size may leave an unrepresentative sample of alleles.

Founder effect

– A new population founded by a few individuals may have allele frequencies different from the source population.

b. Gene flow

Movement of alleles into or out of a population through migration of individuals or gametes.

c. Natural selection

: main source of adaptive evolution

Geographic variation

– A cline is a gradual geographic change in phenotype or allele frequency across an environmental gradient.

Evolutionary fitness: relative reproductive success

– stabilizing selection: favors intermediate phenotypes and selects against extremes.

– disruptive selection: favors both extreme phenotypes over intermediate phenotypes.

– directional selection: favors one extreme phenotype, shifting the trait distribution toward it.

3. Population dynamics

a. Exponential growth

Population size increases exponentially.
Under ideal conditions, constant positive per capita growth produces a J-shaped curve.

b. Logistic Growth

Sigmoid curve or S-curve.
As population size approaches carrying capacity (K), net growth decreases toward zero in the logistic model; real populations can fluctuate as conditions change.
Carrying capacity: Maximum population size that environment can sustain.
Life histories.

Life histories	Features
K-selection	• Traits favor survival and competitive success near carrying capacity (K) • Traditionally associated with relatively stable environments • Low reproductive rate • Slow growth • Small number of offspring • Population size may fluctuate around carrying capacity • Long life span • e.g., Human
r-selection	• Traits favor a high intrinsic rate of population increase (r) • Traditionally associated with variable or disturbed environments • High reproductive rate • Rapid growth • Numerous offspring • Short life span • e.g., Bacteria

D. Communities

1. Niche and habitat

Niche: the resources, conditions, and ecological interactions that characterize how a species lives.
Habitat: the place where an organism lives.

2. Species interactions

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 • e.g., 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	Commensalism	• One species is positively affected and another species is not affected • e.g., Cattle egrets and water buffalo, remora and shark
+ / +	Mutualism	• Both species benefit • Some endosymbiotic relationships are mutualistic • e.g., Acacia trees and protective ants; lichens (fungus with an alga or cyanobacterium); nitrogen-fixing bacteria in legume root nodules

3. Defensive adaptation

: defensive methods from predation.

Defensive adaptation	Classification	Features
Coloration	Aposematic coloration	• Conspicuous warning coloration signals defenses to predators; the coloration itself is not a chemical defense. • e.g., 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	Müllerian 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)

An innate, stereotyped behavioral sequence triggered by a sign stimulus; once initiated, it usually continues to completion.
E.g., a greylag goose rolls a displaced egg back toward its nest.

b. Imprinting

Learning during a sensitive period.
Combines an innate predisposition with experience during the sensitive period.
In filial imprinting, young birds learn to recognize and follow a parent or another moving object.
e.g., Young geese following their mother, flying imprinted cranes with an ultralight plane.

c. Habituation

Decreased response to a repeated, harmless stimulus.
e.g., Baby is no longer startled by sound of a car horn after repeated exposure.

d. Spatial learning

Learning and remembering spatial relationships, landmarks, routes, or locations.

e. Associative learning

: Learning that forms an association between two stimuli or between a behavior and its consequence.

Associative learning	Summary
Classical conditioning	• Learning by associating a previously neutral stimulus with an unconditioned stimulus, producing a conditioned response. • Conditioned stimulus → conditioned response after repeated or strong association. • e.g., A dog salivates in response to a conditioned bell sound
Operant conditioning	• Behavior changes because of its consequences: reinforcement increases a behavior, while punishment decreases it. • Voluntary behaviors → experience errors → learning • Trial and error learning • E.g., a rat learns to press a lever because pressing it delivers food.

f. Extinction

Extinction: a conditioned response weakens when the conditioned stimulus is repeatedly presented without the unconditioned stimulus; operant behavior can also weaken when reinforcement stops.

5. Ecological succession

: community composition changes over time as organisms colonize and modify an area, including after disturbance.

a. Primary succession

Succession begins on a substrate where soil has not formed.
Examples: fresh lava or land exposed by a retreating glacier.
Pioneers on bare substrates may include microbes, lichens, and mosses; the sequence depends on local conditions.
Communities

Communities	Features
Pioneering community	• Early colonizing organisms; composition varies by substrate • E.g., lichens and mosses on some bare substrates; herbs and grasses where soil remains
Climax community	• Late successional community • Many ecosystems remain dynamic because disturbance and climate prevent a single permanently stable “climax” state. • E.g., shade-tolerant trees in some forest successions

b. Secondary succession

Succession after disturbance where soil remains.
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.

– e.g., water, temperature, sunlight, wind, nutrients.

2. Energy flow in ecosystem

a. Food chain

Biomagnification: persistent toxins can become more concentrated at successively higher trophic levels.

Trophic structures	Features and examples
Producer	• Autotrophs make organic matter using light or chemical energy • Green plants, algae, phytoplankton
Herbivores	• Primary consumers • Animals that eat producers; herbivorous zooplankton
Primary carnivores	• Secondary consumers • Animals that eat primary consumers, including herbivorous 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 • e.g., Bacteria, fungi
Detritivores	• Organisms that eat nonliving organic materials • e.g., worms, arthropods

3. Nutrient cycles

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

a. Water cycle

Essential to all living organisms.
Evaporation and transpiration → condensation → precipitation → runoff, infiltration, and return to surface waters.

b. Phosphorus cycle

Components of ATP, nucleic acids, and phospholipids in living organisms.
Plants absorb phosphate from soil or water → consumers obtain it by feeding → decomposition returns phosphate.

c. Carbon cycle

Essential to all living organisms as organic structures.
Photosynthesis removes CO₂ from air or water; respiration, decomposition, and combustion return CO₂ to the environment.

d. Nitrogen cycle

Components of amino acids, nucleic acids in living organisms.
Nitrogen fixation: N₂ → NH₃/NH₄⁺; assimilation: inorganic nitrogen → organic nitrogen in biomass; ammonification: organic nitrogen → NH₃/NH₄⁺; nitrification: NH₄⁺ → NO₂⁻ → NO₃⁻; denitrification: NO₃⁻ → N₂.

Process and microorganisms	Functions
Nitrogen fixation (bacteria and archaea)	• Reduction of N₂ by nitrogen-fixing microbes • N₂ → NH₃, which can form NH₄⁺ in water
Ammonification (decomposer bacteria and fungi)	• Decomposers convert organic nitrogen from wastes and dead organisms into ammonia (NH₃) and ammonium (NH₄⁺).
Nitrification (bacteria and archaea)	• Oxidation of reduced inorganic nitrogen • NH₄⁺ → NO₂⁻ → NO₃⁻
Denitrification (mainly bacteria)	• Reduction of nitrate under low-oxygen conditions • NO₃⁻ → N₂ (through intermediates)

Nitrogen cycle

4. Temperature relation

a. Climate

Microclimate

– Local atmospheric conditions near the ground or around organisms that can differ from the broader regional climate.

– important to individuals of a species.

Macroclimate

– global or broad regional climate.

– important to distribution patterns of species.

b. Thermoregulation

Homeothermic animals

– maintaining a relatively stable body temperature.

– e.g., most mammals and birds. Endothermy refers to internal heat production; homeothermy refers to temperature stability.

Poikilothermic animals

– having a body temperature that varies substantially; this differs from ectothermy (reliance mainly on environmental heat).

– e.g., many reptiles and amphibians, whose temperatures often vary with their surroundings.

5. Water and salt regulation

a. Freshwater fish

Freshwater fish are hyperosmotic to their surroundings: water enters by osmosis. They excrete abundant dilute urine and actively absorb ions through their gills.

b. Saltwater fish

Marine bony fish are hypoosmotic to seawater: they lose water by osmosis, drink seawater, excrete excess salts through the gills, and produce relatively little urine.

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 • The euphotic zone has sufficient light for net photosynthesis; greater turbidity reduces light penetration and makes this zone shallower.
Aphotic zone	• Insufficient light for net photosynthesis
Benthic zone	• Bottom substrate of a lake or other body of water

b. Marine zones

Marine Zones		Features
Littoral zone	Intertidal zone	• Alternately exposed to air and submerged by tides • Many different types of organisms • Important area for study of ecology
Neritic zone		• Coastal ocean waters over the continental shelf, generally extending to depths of about 200 m. • Extends seaward from the low-tide line to the continental shelf edge • Often productive; oxygen and salinity vary with local conditions
Photic zone	Epipelagic zone	• Approximately 0–200 m; the light boundary varies with water clarity • Most photosynthesis takes place
Aphotic zone	Mesopelagic zone	• About 200–1,000 m; dim twilight, generally insufficient light for net photosynthesis
	Bathypelagic zone	• 1000-4000m depth
	Abyssopelagic zone	• 4000-6000m depth
	Hadalpelagic zone	• Deepest area of marine environment • Below 6000m depth

2. Water relations

a. Rain shadow

Moist air rises on the windward side of a mountain, expands and cools, causing condensation and precipitation.
Drier air descends on the leeward side, compresses and warms, lowering relative humidity and creating a rain-shadow region.
e.g., Death Valley (Sierra Nevada)

b. Seasonal turnover

: in many temperate lakes, spring and autumn mixing redistributes oxygen and nutrients through the water column.

Seasonal temperature changes weaken stratification, allowing wind-driven mixing.
Spring turnover

– Surface water warms toward about 4°C, approaches the density of deeper water, and the lake mixes.

Fall turnover

– Surface water cools toward about 4°C, becomes denser, and wind-driven mixing circulates the lake.

3. Terrestrial biomes

Terrestrial biomes	Main features
Tropical rain forest	• Very high terrestrial biodiversity; warm temperatures and abundant rainfall • Around region of equator
Savanna	• Tropical grassland with scattered trees and distinct wet and dry seasons • Seasonal drought and fire help maintain grass-dominated vegetation
Desert	• Dry places with low precipitation • Water conservation for plants and animals • Succulent plants of shrubs and cacti
Chaparral	• Hot, dry summers and mild, wet winters • Drought-tolerant evergreen shrubs and small trees
Temperate grassland	• Seasonal climate; typically cold winters and warm or hot summers • Grasses and herbaceous flowering plants; drought and fire limit trees • Many farmlands
Temperate deciduous forest	• Hardwood and broad-leaved deciduous forests • Precipitation throughout the year; cold winters and warm summers
Coniferous forest (Taiga)	• Coniferous trees with needle-like or scale-like leaves • Moderate precipitation, with snow common and summer rainfall in many regions • 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 • Generally low precipitation; polar regions are often cold deserts • Limited life of organisms