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UCR / Biology / BIOL 5C / How do biomes affect climate?

How do biomes affect climate?

How do biomes affect climate?


School: University of California Riverside
Department: Biology
Course: Introduction to Evolution and Ecology
Term: Fall 2018
Tags: Biology: Ecology and Evolution
Cost: 50
Name: BIO5C Ecology & Evolution Final Exam Study Guide
Description: This is a study guide for the BIO5C Final Exam (for Professors Rafferty & Nunney), it covers all topics mentioned on the "Topics to Know" documents from both professors.
Uploaded: 12/10/2018
24 Pages 145 Views 6 Unlocks

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BIOL005C Intro to Evolution & Ecology Final Study Guide

How do biomes affect climate?

I. Biomes & Climate

A. Key Characteristics of TERRESTRIAL Biomes

1. A biome is a major type of biological assemblage

2. What determines a biome? 

● On land…

○ Temperature and rainfall

● In water…

○ Temperature, depth, and salinity





Vegetation/Pr imary







Rain forests: constant

Dry forests:


High, minimal seasonal



layered, lots of


for light; High “pp”

Very high -

home to 70% of land

animals and plants

Temperate Broadleaf



High rainfall


Cool winters, hot & humid summers


layered trees, shrubs,





Coniferous Forest


North America & Eurasia








coastal areas are wet

Cold winters, hot summers

Conifers -

pine, spruce, fir, hemlock; low





Low rainfall

Cool & rainy winters, hot & dry summers

Many native plants

specific to

location; low





Seasonal w/ an extensive dry season


varying w/ the season

Fire- and



plants -


forbs, trees;



What are the 3 differences between weather and climate?

We also discuss several other topics like What is not usually a characteristic of the developed countries in the contemporary world?
We also discuss several other topics like What are the 3 tenets of the cell theory?

Temperate Grassland

Central North America

(prairie) &


Low, usually occurring in


Cold winters, hot summers

Grasses &

forbs are fire and drought tolerant;






gof equator & interiors of


Low - less

than 30cm a year

Varies from extremities - can be very

hot or very


Adapted for

extremely dry weather and low nutrition; low

Low but




Alpine tundra: high

mountaintops, all latitudes

Arctic tundra: low

Alpine tundra: high(er)

Very cold

winters, cool summers

-permafrost: overs the

ground so

that no plants may

penetrate/gro w



forbs, dwarf

shrubs and

trees, lichen; low


How does air circulation affect climate?

Don't forget about the age old question of What is the meaning of foodborne illness?

B. Key Characteristics of AQUATIC Biomes





Intertidal Zone

Area of the shore

covered at high tide, & exposed at low tide




Narrow &

meandering through mountains, toward ocean




Marshes or swamps




Individual bodies of water




Area where

rivers/streams meet the ocean



Coral Reef

Mid-/shallow ocean



Oceanic Pelagic

Open ocean



Oceanic Benthic

Deep ocean (ocean floor)



We also discuss several other topics like How do isotopes behave?

C. Climate

1. Climate vs. Weather?

● Climate: long-term weather conditions

● Weather: daily weather conditions

2. The SUN

● The sun drives the climate

● Latitude affects the intensity of the sunlight

○ More intense at the equator due to direct sunlight hitting

surface of earth

○ Less intense at North/South poles

3. Air Circulation

● The earth spins faster at the equator (1,670 km/hr), causing the

wind to bend

● Wind pushes water → ocean currents

4. Climate Change We also discuss several other topics like Attitude formation refers to what?

● Bodies of water moderate climates - coastal regions have less

fluctuations in temperature compared to areas like Riverside

● Greenhouse Effect: CO2 and other gases (mostly produced by car

emissions) trap heat from the sun, causing an increase in climate

temperature If you want to learn more check out Nonspontaneous process means what?

○ Consequences:

○ → Rising temperatures

○ → Loss of glaciers

○ → Loss of polar sea ice @ exponential rate

○ → Rising sea levels

○ → More severe storms

○ → Increase in ocean acidification

○ → Depletion of the ozone layer

II. Food Webs & Trophic Pyramids

A. Food chains: lists trophic levels of an ecosystem from producers (bottom) to carnivores (top)

1. Trophic levels always numbered starting w/ “1” (producers)

4 Tertiary Consumers

3 Secondary Consumers

2 Primary Consumers

1 Primary Producers

2. Decomposers: organisms that break down organic matter from ALL trophic levels

3. Green Food Web (Grazing): basal trophic level = primary producer

4. Brown Food Web (Decomposer): basal trophic level = dead plant/animal matter

B. Trophic Pyramids

1. Trophic transfers: transfer of energy b/w trophic levels

● Total energy available declines by 90% w/ each step up food


2. What’s controlling the food chain? 

● From BOTTOM-Up…

○ Producers

● From TOP-Down…

○ Predators - can cause “trophic cascade”, where predator

keeps suppressing prey until next trophic level below that

is freed of predation

III. Biogeochemical Cycles

A. Biogeochemical cycle: describes flux of atoms and molecules b/w biotic and abiotic reservoirs

1. Flux: rate of movement b/w reservoirs

2. Reservoir: place where types of atoms or molecules accumulate or are held for a relatively long period of time

● Lithosphere

● Hydrosphere

● Atmosphere

● Organisms

3. Earth is a closed system for elements and nutrients:

Inaccessible ⇄ Accessible ⇄ Organisms

B. Water Cycle

1. Water is primarily used in its liquid state

2. Reservoirs:

● Ocean = 97%

● Glaciers/Ice caps = 2%

● Lakes, rivers, groundwater = 1%

3. Movement by: evaporation, transpiration, condensation, precipitation, & surface/groundwater

C. Carbon Cycle

1. Plants convert CO₂ to organic molecules consumed by heterotrophs 2. Reservoirs:

● Fossil fuels

● Soil/sediment

● Atmosphere

3. Movement by: photosynthesis and cellular respiration

D. Nitrogen Cycle

1. N is component of amino acids, proteins, & nucleic acids

→ Often a limiting nutrient in terrestrial and aquatic ecosystems

2. Reservoir:

● Atmosphere (N₂)

→ N₂ must be converted to usable forms NH₄⁺ or NO₃⁻ in order

to be taken up by plant bacteria via nitrogen fixation

3. Nitrogen Pollution

● Human activities doubled rate of N entering biogeochemical cycles

due to: nitrogen fertilizers, fossil fuels (cars), over-cultivation of

legumes (which are useful for N fixation)

→ Consequences:

- Inc. in global concentration of nitrous & nitric oxide

- Contamination of drinking water

E. Phosphorus Cycle

1. Imp. for nucleic acids, phospholipids, & ATP

→ Most important inorganic form: PO₄³⁻

2. Reservoirs:

● Sedimentary rocks in ocean

● Soils

● Organisms

IV. Density, Dispersion, & Demographics

A. The Population and its Characteristics

1. Populations are dynamic

● Births & immigration => adding to population

● Deaths & emigration => subtracting from population

● 4 Properties of a Population:

→ Size (N): total # of individuals in population

→ Density: # individuals per unit area or volume

→ Dispersion: distribution of individuals in population over


→ Rate of change in size over time: growth, decline, or stability

2. How do you measure density? 

● Count standardized census methods (plots)

● Count subsamples & estimate (divide plot, count, multiply by #


● Use a proxy (nests, tracks)

● Mark - recapture (tag animals)

→ Use equation:

N = (n₁ - n₂)/m,


N = pop. size

n₁ = # captured and marked

n₂ = # captured in 2nd sample

m = # recaptured

3. Patterns of Dispersion 

● Random distributions: every point in space has equal and

independent probability of containing an individual

● Clumped distributions: Individuals more aggregated, more likely

to be found close to one another

● Uniform distributions: Individuals more evenly spaced, less

likely to be found near each other

B. Demographics

1. Demography: study of the vital stats of a population and how they vary w/ age

● Life Table: an age-specific summary of demographics

→ Data from life table can be used to graph survivorship curves

● Cohort: group of individuals in a population born around same


● Survivorship (Iₓ): proportion of individuals born that survive to

certain age (X)

● Reproductive Table: age-specific summary of reproductive rates

→ Only contains data for reproductive females & number of

female offspring produced

C. Life History Traits

1. Life History: the schedule of an organism’s life

● Age/size when ready for reproduction

● Allocation of energy for reproduction

● Size and # of offspring

→ Either produce more, smaller offspring (insects) or fewer, larger

offspring (bears)

● # of times of reproduction

→ Semelparous: reproduces once

→ Iteroparous: reproduces multiple times

● Life span

V. Population Growth & Age Structure

A. Regulated Population Growth

1. Logistic Population Growth

● Unregulated pop. growth cannot be sustained due to:

→ shortages in food & resources

→ greater aggression w/in the population

→ increased predation rates

→ higher risk of diseases

● More realistic growth model includes carrying capacity (K): the maximum population the environment can support

● Logistic Growth Model (CONTINUOUS MODEL)

dN/dt = rN x [(K - N)/K]


→ K - N = # of additional individuals that can still be supported

→ (K - N)/K = fraction of carrying capacity still available for

population growth

2. r-Selected vs. K-Selected 

● r-selection: life history traits that maximize reproductive success at times of low population density

→ “Live fast, die young”

● K-selection: life history traits that are advantageous at times of high population density

→ “Live long and prosper”

3. Density Dependence

● In populations that are density-dependent, birth/death rates are regulated by pop. density

→ Only density-dependent factors can influence pop. size 

→ Example of negative feedback that regulates pop. growth

● In density-independent populations, birth/death rates are

unaffected by pop. density

● Mechanisms to regulate growth of density-dependent populations: → Competition for resources: crowded populations intensify

competition for resources & lower birth rates

→ Territoriality: competition for space can disperse dense


→ Disease: pathogens spread quicker

→ Predation: large populations are easier to spot & prey on

→ Intrinsic Factors: physiological factors

→ Toxic Wastes

B. Age Structure

1. Age-Structure Diagrams

● Age structure: the relative # of individuals of each age in a


● Age structure diagrams (pyramids): predicts a population’s growth trends

→ Illuminates social conditions and helps us plan for future

2. Global Carrying Capacity

● Predicted 8.1-10.6 billion people will live on Earth in 2050

→ The carrying capacity is uncertain

● Ecological footprint concept summarizes aggregate land and

water are needed to sustain a person, city, or nation

● Potential limiting resources for carrying capacity are food, space,

nonrenewable resources, and waste buildup

→ Humans have the power to regulate population growth through

social change

VI. Interspecific Interactions

Def: Interactions b/w species; classified by the direction of effects (+ / - / 0) A. Antagonism (-/-) or (+/-)

1. Competition (-/-) 

● Occurs when species compete for limited resources that are

essential for survival and reproduction

● 2 mechanisms of competition:

○ exploitative: “first come, first serve” - individuals deplete

resources by using them up

○ interference: aggression b/w individuals

● Strong competition can lead to competitive exclusion: when 2

species competing for the same limited resources cannot coexist

permanently, and one is eventually eliminated from the local area

● Species can coexist if there are 1 or more significant differences in

their ecological niches...

→ fundamental niche: the niche that a species could potentially


→ realized niche: the niche that a species actually occupies

○ Resource partitioning: differentiation in ecological niches

that enables similar species to coexist in ONE community

→ spatial partitioning: different birds live in different parts

of the same tree

→ temporal partitioning: one species of mice looks for food

during the day, the other at night

2. Predation (+/-) 

● An interaction in which one species (the predator) kills and eats

the other (the prey)

○ predation: predators kill live prey

○ scavenging: scavengers eat dead organisms

● Both predator and prey have specialized adaptations



➢ Camouflage

➢ Sensory adaptations to

➢ Camouflage

➢ Sensory adaptations to

detect prey

➢ Adaptations for

handling prey

detect predators

➢ Adaptations for

escaping capture

● Presence of predators may result in slower growth rate of prey ● Defense Mechanisms:

○ Aposematic Coloration: prey exhibit bright colors as a

warning signal to predators that it is dangerous

○ Mimicry: close resemblance of an organism (the mimic) to

some different organism (the model); the mimic benefits

from the mistaken identity

→ Batesian: an unprotected species evolves to look like a

protected species (only one is dangerous)

→ Müllerian: a chemically protected species evolves to

look like another protected species (both are dangerous)

→ Predators also mimic other species to get closer to prey

3. Herbivory (+/-) 

● An interaction in which an herbivore eats part of a plant or alga ● Both the herbivore and the plant have adaptations



➢ Physiological

➢ Morphological

➢ Herbivore teeth

➢ Structural

➢ Chemical

4. Parasitism (+/-) 

● One organism (parasite) derives nourishment from another

organism (host), which is harmed in the process

○ Ectoparasite: external; on outside of host

○ Endoparasite: internal; lives inside host

○ Parasitoids:

→ Special type of parasitism

→ Always kills host

→ Lays eggs inside host

→ Adult stage is free-living

B. Mutualism (+/+): interaction that benefits both species

1. Obligate: necessary for survival and reproduction of one or both species; sometimes symbiotic

2. Facultative: not necessary for survival of either species

3. Reciprocal Exploitation

● ex) Plant-pollinator mutualisms

○ Service/resource mutualisms

○ → An insect provides service of pollination

○ → Flower provides resource of nectar

● Flowers can exploit pollinators by…

○ restricted access to nectar

○ deception: resembling a female insect

○ visible/UV light: insects are attracted to colorful flowers

● Pollinators can exploit flowers by…

○ nectar robbing: extracting the resource w/o providing


C. Commensalism (+/0): interaction in which one species benefits and the other is neither harmed nor helped

● Commensal interactions can sometimes be mutualistic

● It is difficult to prove/disprove that the host is always unaffected

Interaction Type

Species A

Species B

Antagonism: Predation/Herbivory/Parasitism



Antagonism: Competition









VII. Species Diversity

Def: variety of organisms that make up a community

A. Components of Species Diversity

1. Species richness: # of different species in a community

2. Relative abundance: the proportion each species represents of all

individuals in a community

B. Calculating Species Diversity

1. Species-Area Curve 

● The species-area curve quantifies the idea that a bigger

geographical area will have more species

S = cAz 

→ S = # of species

→ c is a constant

→ A = area

→ z = how many more species should be found as area increases

C. Trends in Species Diversity

1. Area - Island Equilibrium Model 

● Species richness represents a balance b/w immigration and

extinction, which in turn are affected by island size and distance

from mainland

○ Islands contain fewer species than a nearby mainland

○ Small islands contain less species than large islands

→ Immigration ↓, Extinction ↑

○ Islands closer to mainland contain more species than

similarly sized islands farther away

→ Immigration ↑, Extinction ↓

● Equilibrium: rate of immigration = rate of extinction

2. Latitude - Latitudinal Diversity Gradient 

● Species richness is high near equator and slowly declines

approaching the poles

→ Gradient is affected by evolutionary history and climate

○ Evolutionary History

→ “Tropics as Cradle” model: tropical environments may

have greater species richness b/c there has been more

time for speciation to occur

→ “Tropics as Museums” model: temperate and polar

communities have “started over” multiple times after


○ Climate

→ evapotranspiration: the evaporation of water from soil +

transpiration of water from plants (shaped by amounts

sunlight and precipitation)

→ Species richness is related to (potential)

evapotranspiration, which tends to be greater in tropics

VIII. Environmental Change and Selection

A. Directional Selection

1. Industrial Melanism in Peppered Moth

● Peppered moth, Biston betularia, sits on trees during the daytime

and is well camouflaged against lichen-covered bark

● ~1850: rapid increase of black (melanic) form of moth began

appearing in northern England

→ What caused change in color? 

○ Genetic change: peppered (typica) and melanic

(carbonaria) morphs determined by a polymorphic gene

(dark allele dominant)

○ Increase in carbonaria morph coincided w/ dramatic

increase in coal pollution due to Industrial Revolution

(centered around northern England)

→ coal pollution => kills lichens on trees, soot blackens

tree branches

B. Selection

1. Rapid Directional Selection 

● Types of Selection

○ Directional Selection: when distribution of seed size

changes (e.g. during drought)

○ Stabilizing Selection: when seed distribution remains fairly

constant, selection favors a fixed optimal beak depth

● Phenotypic selection of beak depth results in natural selection b/c

bill depth is highly heritable

● Heritability (h2) = slope of parent-offspring regression

○ Estimates the proportion of individual variation due to

genetic differences

2. Selection on an Environmental Gradient

● Selection on a gradient often results in a genetic polymorphism

that takes form of a gene frequency cline 

→ cline: directional change w/ distance

→ often associated w/ some environmental gradient

○ Mytilis edulis (a mussel): a cline in lap (leucine amino

peptidase) alleles in Long Island Sound is related to

changes in salinity

→ Mussels at the entrance of the Sound experience

changes in salinity w/ every tide => enzyme lap controls

osmotic environment w/in the mussel

○ Fundulus heterclitus (small fish found on coast of eastern

US): cline in heart-type Ldh (lactate dehydrogenase)

alleles related to latitude and - hence - water temperature

→ the different homozygotes have faster swimming

speeds at the temperature extremities - high (a/a) and low


C. Positive vs. Negative Selection

1. Terms & Definitions

● Directional natural selection: where one end of a genetically based

phenotypic distribution is favored over the other

○ Positive selection: results in spread of new advantageous

alleles in a population

→ industrial melanism in the 1800s

○ Negative selection: results in removal of rare,

disadvantageous alleles

→ such selection acts to prevent accumulation of

mutations that may result in genetic disorders or lower


IX. Drift, Inbreeding, Nonrandom Mating, & Mimicry

A. A Founder Event

1. Variegate Porphyria

● Variegate Porphyria: an inherited skin disease due to a dominant allele that is (unusually) common in South Africa

○ Symptoms: areas of skin exposed to sun develop severe

blisters, scars, & changes in pigmentation and become

fragile & easily damaged; no symptoms in ~40% of cases

○ Estimated to affect >20,000 people in So. Africa

→ Origin of mutant allele traced back to 1688 when Dutch

settlers Gerrit Jansz van Deventer married Adriaantje

Ariens in Cape Town

● High frequency of Variegate Porphyria allele is an example of a founder event during establishment of Afrikaaner population

○ In Netherlands, frequency of the allele is <1/10,000

○ In So. Africa, frequency of the allele is 1/300

→ the frequency of a rare allele can increase exponentially

by the random inclusion of just a single copy in a small


2. Retinitis Pigmentosa

● 1814: Tristan da Cunha settled in the mid Atlantic w/ 15 other settlers from the UK => 30 gene copies

○ Any allele must initially be at frequency of ≥1/30 or 3.3%

● Among the 15 settlers, there existed ≥1 copy of a recessive

mutant allele that causes retinitis pigmentosa: progressive


● Late 1960s: 4/240 people had the disease

B. Random Sampling and Evolution

1. Population Bottleneck

● During a population bottleneck, strong selection may act, but random sampling always alters some allele frequencies

○ Changes are retained as the population recovers

2. Random Genetic Drift 

● General term for the changes in gene frequency due to random sampling

● Random genetic drift occurs because…

○ If 2 individuals have same expected fitness, their actual

fitness may differ

→ one may die before reproducing while other may

successfully mate and produce offspring

○ Mendelian inheritance has a random element

● Genetic drift has biggest effect when 2 alleles give rise to

genotypes w/ same “wild-type” fitness (neutral alleles), but can

overcome selection and cause disadvantageous alleles to spread in very small populations

● Long-term effects of genetic drift are non-adaptive

→ Since genetic change isn’t caused by natural selection, it is

often called “neutral evolution”

C. Inbreeding & Hardy-Weinberg Ratios

1. Inbreeding

● Increased probability of mating b/w relatives

○ Can occur in small, isolated populations or through mate


○ Most extreme form is selfing (self fertilization), made

possible only in organisms w/ both male and female

reproductive organs (i.e. Mendel’s pea plants)

→ Some plant species have high frequency of selfing,

resulting in reduced flowers

● Selfing guarantees fertilization, but at a cost of some inbreeding depression in offspring (i.e. loss of fitness)

2. Inbreeding Depression 

● If there is more mating among relatives than expected, this is a form of non-random mating => population won’t be in H-W ratios ○ Inbreeding results in excess of homozygotes (relative to

H-W expectation)

○ Effect due to the fact that inbred families have higher freq.

of homozygotes than outbred (random mating) ones w/in

same population

→ Offspring of inbred matings more likely to be

homozygous for recessive deleterious alleles

3. Non-Random/Positive Assortative Mating 

● A non-random choice of mate based on similarity of a heritable phenotype will lead to an increase in homozygotes at the loci that determines that phenotype

→ ex) mating based on height: short/short => short offspring, vs. tall/tall => tall offspring

● Effect on genotype frequencies:

○ Inbreeding: increases frequency of homozygotes at all loci

○ Positive assortative mating: increases freq. of

homozygotes at the loci determining the target phenotype

○ Non-random mating (by itself) does not change gene

frequencies bc in general it does not change mating


● Heliconius cydno alithea (a butterfly from Ecuador) is a Müllerian mimic, but in Ecuador, populations are polymorphic

→ Müllerian mimic: protected by toxins and evolved to look like another protected species

● Positive assortative mating helps maintain the 2 forms since color and pattern loci are unlinked

→ ex) yellow males prefer yellow females

D. Mimicry

1. Müllerian Mimicry 

● 2 or more dangerous/toxic animals can coevolve to more closely

resemble each other if they share a common predator that learns

to avoid them, reducing fitness loss caused by naive predators

○ Often involves aposematic (warning) coloration

● Heliconius numata is a distasteful So. American butterfly that is

polymorphic and resembles other distasteful Melinaea species

○ The diff. forms often co-occur in one region and are

inherited as a “supergene” involving several polymorphic

genes inherited as a unit due to suppressed recombination

→ Intermediates are rare as a result

2. Batesian Mimicry - Evolutionary Cheating

● Harmless animal mimics/closely resembles a dangerous/toxic


→ Fitness is gained because of reduced predation

● Papilio dardanus (an unprotected African butterfly)

○ In a single geographic region, females will mimic 1 of 3

protected species

X. Sexual Selection, Pollination, Local Adaptation

A. Sexual Selection

1. Natural Selection for Mating Success

● Most commonly affects male characteristics

● Can trade off w/ other aspects of fitness

2. Intrasexual Selection

● Intrasexual selection (“mate choice”): competition amongst

individuals of one gender (usually males) for mates of the opposite


○ Occurs when individuals of one sex (usually the females)

are selective in choosing who they mate with

○ Usually results in sexual dimorphism for traits favored in

competition (e.g. color, sound, size, horns, etc)

● Lek mating: when males gather together at “leks” to display

○ Females visit leks, compare males, and choose one to

mate with

○ In lekking species (like grouse) there is no paternal care

3. “Runaway” Process

● In absence of parental care, females will likely choose mates that

have “good genes” - males that will produce high-fitness offspring

● This type of mate choice can lead to the “runaway” process

○ ex) If females favor mates w/ the longest tail: male

genotypes producing the longest tails are most successful

→ average tail length increases → females still favor

longest tails → average tail length continues to increase

4. Choosing “Good Genes”

● In lab tests, female gray tree frogs prefer long duration calls

○ Experimental crosses of frogs all caught in same vicinity

showed that offspring of long callers were (on avg) more fit

5. Experiments

● Long-tailed widow bird - Malte Andersson

○ Altered tail length in a natural population

→ Males w/ extra long tails had higher fitness

B. Pollination

1. Attracting Pollinators

● Flowering plants do not attract mates directly

→ they require an intermediary - a pollinator - unless they are

wind-pollinated like most grasses

○ Pollinators usually fly: moths, butterflies, birds, & bats

○ Plant provides a reward in return, usually nectar

● In some cases extreme coevolution may occur

○ ex) Darwin predicted existence of insect w/ extremely long

tongue that pollinated the Angraecum sesquipedale orchid

○ 1903: naturalists found Morgan’s sphinx moth Xanthopan


2. Pollinator Cues

● Plants provide different cues to attract different pollinators

○ Red tubular flowers = hummingbirds

○ Nocturnal flowers = bats and/or moths

○ Flowers that smell like rotting meat = carrion flies

● Generalist strategy: plant attracts a wide range of pollinators ● Specialist strategy: plants rely almost entirely on a single pollinator ● Each strategy has a trade-off for the plant 

○ Specialist system maximizes chance that the pollinator

takes pollen from one plant to another of same species,

but minimizes chances of being visited bc there is a lack of


○ Generalist has opposite problem

C. Local Adaptation

1. Disruptive Selection 

● Selection that favors the extremes of a distribution, and selects against intermediates

● How can disruptive selection maintain adaptation?

○ 3 examples of polymorphic mimicry show it can be

resolved by:

→ “supergenes”

→ a regulatory switch that shifts the phenotype from one

extreme to the other, avoiding intermediates

→ positive assortative mating, changing the distribution of

genotypes to increase the extremes

● Most commonly arises when 2 neighboring environments select

for different traits

○ ex) the snail Cepaea nemoralis is subject to bird predation

=> it is advantageous to be obscure

→ In areas of mixed beech woodland/grassland habitats in

England, yellow/banded genotypes are favored on

grassland but brown are favored in the woodland

2. Gene Flow vs. Local Adaptation

● Local adaptation can occur over small distances (i.e. boundary

b/w a wood and a grassy field) provided that gene flow across the

boundary is limited

● Gene flow: the distance that gene copies move per generation,

either by individuals moving or by movement of gametes (e.g.

pollen dispersal)

○ Gene flow across a habitat boundary reduces local

adaptation by introducing maladapted alleles every


XI. Species & Speciation (pt. 1)

A. What is a species?

1. Biological Species Concept 

● A species is a population or group of populations whose members

have the potential to interbreed w/ one another in nature to

produce healthy, fertile offspring, BUT cannot produce healthy,

fertile offspring w/ members of other groups

● Appropriate mating tests are often impossible/impractical to apply

w/ asexual species and fossils. Alternatives:

○ Morphological species concept - physical differences

○ Paleontological species concept - physical differences

○ Ecological species concept - habitat differences

○ Phylogenetic species concept - genetic differences

● Problems arise bc speciation is a process involving the

development of reproductive isolation => must maintain different

ecological adaptations

○ Divergence of allopatric (physically separated) populations

of the same species often builds up slowly over time

→ As allopatric divergence increases, we divide a species

into geographical subspecies which may ultimately

become distinct species

2. Ring Species 

● In CA, Ensatina eschscholtzii salamander found on both sides of central valley

○ Where the ring meets, the subspecies do not interbreed

● Greenish warbler Phylloscopus trochiloides is divided into

subspecies that differ in song; two Siberian subspecies do not


● 2 mechanisms that drive reproductive isolation:

○ Prezygotic barriers

→ Habitat isolation

→ Temporal isolation

→ Behavioral isolation

→ Mechanical isolation

→ Gametic isolation

○ Postzygotic barriers

→ Reduced hybrid viability

→ Reduced hybrid fertility

→ Hybrid breakdown

3. Types of Speciation

● Allopatric 

○ 2 populations of a single species are spatially separated,

preventing the 2 forms from mating

→ Allows the 2 populations to become genetically distinct,

often through local adaptation

● Sympatric 

○ Disruptive selection favors 2 forms w/in a single population

→ Active mate choice/other prezygotic separation that

limits mating b/w the 2 forms is critical in maintaining the

effects of disruptive selection

● Hybrid Zones: if 2 closely related, allopatric species meet through the range expansion of one or both (secondary contact) they


○ Fuse back together

○ Be so different that they already show prezygotic isolation

○ Form a hybrid zone at the point of contact

B. Hybridization & Isolation

1. Reinforcement: Strengthening Reproductive Barriers

● If hybrids have fitness disadvantage, there is selection for wider

range in of mating signals at zone of overlap

○ Selection can result in reinforcement of inter-specific

mating barriers => reduction in rate of hybridization

○ Reproductive barriers will be stronger in sympatric

populations, versus in allopatric populations

→ Pied and collared flycatcher males are more similar in

allopatric populations than sympatric populations

2. Pollinator-Mediated Prezygotic Isolation

● 2 closely related species of monkey flower have different

pollinators due to different flower shape & color

→ Pink Mimulus lewisii attract bumblebees

→ Red Mimulus cardinalis attract hummingbirds

○ In areas where they coexist, reproductive isolation is

maintained by this difference in pollinators

3. Adaptive Radiation on Island Chains

● Sequence of allopatric speciation events

○ ex) Drosophila fruit fly speciation in Hawaii

○ → Genetic data indicates that the 800+ species of

Drosophila-like flies on the islands are descended from

one invasion

XII. Speciation (pt. 2), Continental Drift, Fossils

A. Sympatric Speciation

1. Ecological Speciation 

● Apple-maggot fly Rhagoletis pomonella occurs in eastern US

○ Natural larval host - hawthorn berries

○ 200 yrs ago - started to colonize introduced apple trees

● Host “races” developed b/c...

○ Two fruits ripen at different times

○ Flies are attracted to their own host fruits => positive

assortative mating by niche preference

○ Strong disruptive selection against hybrids (not adapted to

either host fruit)

2. Chromosomal “Instant” Speciation 

● Autopolyploids: an increase in ploidy w/in a species

● Allopolyploids: arise by hybridization b/w species

● Polyploidy relatively common in agricultural crops

○ Often infertile (and still diploids) at first

○ Achieve chromosomal balance and fertility later by

diploidization of both chromosome sets

● Spartina anglica - fertile allotetraploid, a 4n hybrid of 2 different species

○ 1870 - originated as sterile hybrid (S. townsendii) that

reproduced asexually

→ Cross b/w the European native cordgrass S. maritima

and the introduced American species S. alterniflora

○ Common in so. England

○ Now an invasive species in western US marshes

● Interspecific hybridization in animals typically results in an asexual (i.e. parthenogenetic “unfertilized”) species

○ All-female whiptail lizard, Cnemidophorus neomexicanus

species, was formed by hybridization of C. inornatus and

C. tigris - two sexual species that have males

B. Allopatric Speciation

1. Vicariance & Continental Drift

● Vicariance: splitting of a species range by a geographical barrier ○ 9-13 MYA: 15 pairs of sibling species of Alpheus snapping

shrimp were separated by Isthmus of Panama, which

separates Atlantic and Pacific oceans

● Creation of the isthmus caused by slow movement of the

continents, joining North & South America

● Himalayas formed where India joined Eurasia

2. Plate Tectonics & Biogeography

● Earth’s crust is divided into plates

● Various forces like seafloor spreading cause plates to move ○ Subduction zone: where one plate goes under another;

location of volcanoes and earthquakes

● 65 mil yrs ago (MYA) - So. America, Antarctica & Australia all connected

○ Proof: Southern beech species are found in So. America

and Australia

→ Fossil impression of a southern beech leaf found in


3. Fossils

● Fossils record history of life on Earth

○ Formed in sedimentary rock: rock formed by deposition of

material over time

● How do we know age of fossils?

○ Stratigraphy: use layers (“strata”) of sedimentary and

volcanic rock

● Biostratigraphy: links strata in different areas based on

assemblage of fossils

○ This approach used in Darwin’s time

○ Seemingly no possible way to determine fossil age, but

possible to define geological time scale based on relative


XIII. Dating the Geological Record, Mass Extinctions

A. Dating the Fossil Record

1. Radiometric Dating

● Obtaining actual age of fossils was impossible before early 1900s

→ Methods for dating old rock do not work on sedimentary rock;

instead age is based on presence of volcanic rock b/w

sedimentary strata

● Radiometric dating: the ratio of a radioactive isotope to its

breakdown product

○ The ratio of isotope/product at time of formation must be


● Some important radiometric methods:

* First 2 methods can indirectly date fossils in sed. rock located

right below a volcanic layer *

○ Uranium-lead: U235 → Pb207 and U238 → Pb206for volcanic

(igneous) rock

→ Half-life = 700my and 4500 my, respectively

→ Good for rock >1my before present (bp)

○ Potassium-argon: K40 → Ar40 generally in volcanic rock

→ Half-life = 1300my

→ Good for rocks >100,000yrs

○ Carbon dating: C14, created in upper atmosphere

→ Half-life = 5,730yrs

→ Can date organic matter back to 75,000ybp

B. Timescale of Geological Record

1. Organic Compounds on Early Earth

● Earth formed ~4.6 billion yrs ago (bya)

● Bombardment of earth by rocks and ice likely vaporized water and

prevented formation of seas until about 4.2-3.9bya

● Earth’s early atmosphere probably contained water vapor and

chemicals released from volcanoes: N, NO, CO2, CH4, NH3, H,


2. Self-Replicating RNA, Protocells, Natural Selection

● First genetic material was probably RNA, not DNA, b/c RNA

molecules called ribozymes have been found to catalyze RNA


● Protocells: fluid-filled vesicles w/ membrane-like structure

○ Ultimately need protocells w/ RNA that code for functions

to be favored by selection

3. Earliest Evidence of Life

● Stromatolites: sedimentary particles that have been trapped,

bound, and cemented by the biofilms of microorganisms

○ Modern stromatolites found worldwide in lakes and

lagoons w/ high salinity

● Most atmospheric O2 created from photosynthesis of


● Oldest eukaryotic fossils date back to 2.1 bil. yrs

○ Eukaryotic cells have nuclear envelope, mitochondria, ER,

and a cytoskeleton

● Endosymbiont Theory: proposes that mitochondria and

chloroplasts were originally small prokaryotes living inside a larger

host cell

○ Endosymbiont: an organism that lives w/in host cell, and

critical support is given by DNA

● Wave of diversification occurred after complex body plans

appeared ~640mya, setting up “Cambrian explosion” about 100

mil. yrs later

4. Mass Extinctions

● # of species is a balance b/w formation of new species and

extinction of existing species

● Extinction typically caused by changes in a species’ environment

○ Average duration of a species = 1-15 million yrs

● Mass extinction: dramatic increase in rate of extinction as a result

of some disruptive global environmental change

● In each of the 5 mass extinction events, >50% of earth’s species

went extinct

○ Permian extinction: occurred 251mya, lasted <5 mil. yrs,

96% of marine animals and 70% of land vertebrates went


○ Cretaceous extinction: occurred 65.5mya, 75% of all

species went extinct due to asteroid impact that wiped out

dinosaurs; mammals & birds emerged as dominant land

vertebrates afterward

XIV. Radiation of Birds and Mammals, Phylogenetic Trees A. Extinctions

1. Consequences of Mass Extinctions

● Extinction events mark boundaries b/w eras of Phanerozoic eon, Paleozoic-Mesozoic, and Mesozoic-Cenozoic, and the ends of the Ordovician and Triassic periods

● Recovery of diversity after an extinction can take from 5-100 million yrs

● Mass extinctions allow for adaptive radiation

○ Permian period: reptile-like synapsids dominated


→ After Permian extinction: dinosaurs radiated in Triassic


→ Cretaceous extinction wiped out dinosaurs, birds

underwent major radiation

2. Origins of Birds

● Birds and predatory dinos share similar features

○ Skeleton: breast bone, collarbone, 4-toed foot supported

by 3 toes

○ Feathers: found in many dinos

○ Collagen: short amino acid sequences from T. rex match

closely w/ chickens

○ Egg shell microstructure

● Mammals existed when dinos were around, but radiated after Cretaceous extinction

○ Earliest known placental mammal dated to 160mybp

(middle of Mesozoic era & before Cretaceous extinction)

B. Phylogeny & Taxonomy

1. Taxonomy 

● The division and naming of organisms

● 18th century - Linnaeus published system of taxonomy based on resemblances

○ Binomial names: Genus + species (e.g. Homo sapiens)

○ Hierarchical classification: domain, kingdom, phylum,

class, order, family, genus, species (from broad to specific)

2. Phylogeny

● Systematists can show evolutionary relationships by making phylogenetic trees 

○ Branch lengths in phylogenetic trees can:

→ be arbitrary - mean nothing

→ represent time

→ represent genetic divergence

● Phylogenies are inferred from morphological and molecular data ○ Organisms w/ similar features or DNA are more closely

related than organisms w/ different features or sequences

● When comparing an organism w/ its ancestor, it will have both

shared and derived characteristics

○ Cladistics groups organisms based on shared derived


○ Maximum parsimony uses a cladistic approach to create a

tree w/ the fewest evolutionary divergences possible

○ Maximum likelihood uses DNA sequence data to create a


→ Bayesian method: computer-intensive approach based

on Bayes Theorem to create probability distribution of the

trees that best explain the data

XV. Phylogenetic Trees, Tree of Life, Human Ancestry

A. Tree of Life

1. Evidence of a Single Origin

● Genetic code is nearly identical for all known life forms

● All cells use ribosomes (rRNA) and tRNA to synthesize proteins

from polypeptide chains

● Biochemical processes only use L-amino acids

● Tree of Life can be rearranged as a molecular phylogeny using

very slowly evolving rRNA genes

○ Current position of the root suggests eukaryotes are more

similar to archaea than bacteria, or evolved from archaea

2. Primates

● Primates originated around 55mya, during early radiation of


○ Split b/w New World and Old World anthropoids occurred

35-40mya, a while after So. America separated from Africa

● Apes (Hominoids) originated 25mya

○ While most monkeys have tails, apes do not

○ Chimp-Human split occurred 7mya

● It is predicted that all modern humans have African ancestry

○ 1.8mya - Homo erectus was first ancestral humans to

leave Africa for Asia

○ Homo neanderthalensis have a Eurasian origin (350k-30k


→ Distinct Asian group of “Denisovans” based on DNA

○ Homo sapiens have African origin (200-300k yrs ago),

spread to Eurasia 100,000 yrs ago

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