General Biology BI 04 Summer School Lecture Notes



definition - change in gene frequencies in populations over time

single, unifying theory in biology,


origin of species,

diversity of organisms and their relationships,

similarities and differences among species,

adaptation to the environment


History of Evolutionary Theory

Ancient Greeks

Search for Natural Explanations


Essentialism, Eternal harmony, Soul, Supernatural Creation


Purpose for every organism, fixity of species, ladder of life (scala naturae)

St. Augstine

nature has the potential to produce and evolve

Middle Ages

Natural Theologians and Creationism

Bishop Usher

Protestant Reformation and Fundamentalism


Ray - catalogs/classifications of species of plants and birds


Linnean Hierarchy (Kingdom, Phylum, Class, Order ...)

Binomial epithet (genus species: Homo sapiens or Homo sapiens)

Physicists, Astronomers break with traditional beliefs (Galileo, Bacon, Descartes)

solar system debate - earth versus sun as center of the universe

Kant - first ideas about the Big Bang that created the solar system



dilemma of fossils, previous ideas: fossils are examples of organisms growing out of rocks, killed off by the Great flood

fossils, extinction, catastrophism

Rise of Geology

Smith (principles of stratification), Lyell and Hutton - uniformitarianism

Lamarck - introduces concept of change through acquired inheritance, les sentiments interieur


collected recent and extinct specimens of organisms from all over the world during voyages on the HMS Beagle

influenced by the fauna of the Galapagos islands - Galapagos Tortoise, Galapagos Mockingbird and Galapagos Finches

studied materials back in England

read Malthus' work on human populations and famine

noticed the results of artificial selection, sparked ideas about natural selection

Accumulated evidence for theory of evolution

geographic variation in species, comparative anatomy, comparative embryology, biogeography,

artificial selection, classic example of the use of scientific method and hypothetico-deductive method

1859 Linnean Society Meeting - co-presentations of famous papers on evolution by natural selection with Wallace


studied animals of Malaysia and surrounding archipelagos

read Malthus' work on human populations and famine while being struck with Malaria

1859 Linnean Society Meeting - co-authors famous paper on evolution by natural selection with Darwin

Darwin-Wallace theory of evolution - basic tenets

evolution is change in populations over time

mechanism of change is natural selection, selects for most fit individuals and against less fit

natural selection can occur when

there is variation among individuals

some individuals are better fit/adapted to their environment than others

there are differences in productivity, some individuals leave more offspring behind in future generations than others

evolution is gradual, takes a long time, can't be observed in one person's lifetime

Evidence for evolution

Emerging evidence - fossil record and discovery of Archaeopteryx by Von Meyer, missing link between birds and reptiles

Artificial selection

domesticated animals (e.g., dogs, cats, horses, cattle) and plants

comparative anatomy - homology and vestigial organs

comparative embryology



Early 1900's - leads to the New (neo-Darwinian) Synthesis



Neo-Darwinian Synthesis - Everyone gets together and explains how evolution supports their ideas


Hardy, Weinberg and the Hardy-Weinberg Equilibrium

Fisher, Haldane, Wright

Pearson and statistics

Geneticists - Fruit Fly Biologists

Morgan, Chetverikoff, Dobzhansky


Mayr and speciation

Paleontologists - Simpson

Botanists - Stebbins

Recent 1900's - leads to the "Unfinished Synthesis"

1953: Watson and Crick - discovery of DNA

Biochemical systematics

Immunology, Proteins, mtDNA, cl DNA, nuclear DNA

DNA-DNA hybridization

Nei and genetic distances

PCR and genetic sequencing

Debate over whether natural selection versus neutral evolution better explains change in populations and leads to speciation

Study of adaptation-using rigourous experimental testing versus idle-Darwininzing

Advances in paleontology - debate over punctuated versus gradual equilibrium

Study of ancient DNA - molecular paleontology

Hubble telescope and Big Bang

Advances in Embryology and Development, links with genetics (hox genes turn on and off developmental pathways)

New developments in systematics and theory of taxonomy

Evidence for Evolution - Microevolution

Artificial selection

dogs, cats, horses, cattle, etc.

Some Genetic Variation Maintained by Natural Selection

Sickle-Cell Anemia

Disease affects shape of hemoglobin molecule

Causes red blood cells to assume irregular, elongated shapes

Molecules form long, fibrous clumps that deform blood cell

Sickle-cell trait

Heterozygous, Ss individuals

Produce few sickle-shaped cells

Frequency of recessive allele in various populations - geographic distribution

Recessive allele maintained at unusually high levels

Heterozygotes less susceptible to malaria

Heterozygous women more fertile than homozygotes

Environment acts to maintain allele frequency

Selective force in Africa is presence of malaria

Maintenance of allele has adaptive value in Africa

No such selective force in US black population

Selection acts to eliminate allele in US

Peppered Moths and Industrial Melanism 

European moth that rests on trees during daytime

Prior to 1850 most had light-colored wings

After 1850 most had dark-colored wings

Possess dominant allele

Allele rare in populations until then

Observed dark tree trunks in industrial areas

Dark moths less conspicuous on their surfaces

Air pollution killed light-colored lichens

Kettlewell hypothesis: birds ate moths on trees

More dark moths survived in polluted areas

More light moths survived in unpolluted areas

Trends reversing due to pollution controls

Lead Tolerance

Bent grasses grow on lead mine refuse

Soils contain toxic chemicals

Few plants survive conditions

Comparison of plants in pasture and mine refuse areas

Mine plants in pasture soil survived but grew slowly

Mine plants in mine soil grew well

Most pasture plants in mine soil grew poorly if at all

Few exceptions that grew well

Were of same ancestral stock as mine plants

Genetic predisposition to lead tolerance

Population change is rapid when environment demands it


Documented cases of adaptation exist as indicated above

More medical examples

Darwinian medicine - antibiotic resistance (microorganisms, strains of the AIDS virus)

Environment dictates direction and extent of change

Evidence for Evolution - Macroevolution

The Fossil Record

Discovery of Archaeopteryx

Subsequent discoveries of bipedal ancestors

Formation of fossils

Organisms buried in sediment

Calcium in bone and hard tissue is mineralized

Imprints of dead organisms

Fossil bones

Example of sedimentary rocks - Grand Canyon and other Canyons of the western US

Date of rocks reflects age of fossils

Dating in Darwin`s day solely by relative position

Recent dating uses more accurate techniques

Measure rate of radioisotope decay

Example - radioisotopes and half-lives

Rate constant over time, not affected by temperature or pressure

Fossils arrayed from oldest to youngest

Provide evidence of progressive evolutionary change


Hoofed mammals

Horse evolution

Human evolution

The Molecular Record

Progressive evolutionary change implies a change within DNA

Result from accumulation of genetic changes

Distant relatives have greater number of differences

Comparison of DNA sequences between organisms

Greater time since divergence associated with more nucleotide changes

Example: cytochrome c

Example: hemoglobin

Phylogenetic tree

Pattern of genetic descent

Determined by comparing nucleotide sequences

Often similar to relationships predicted by anatomy


Structures derived from common form, but functions are variable

Example: forelimbs of mammals


Evolutionary history reflected in development of embryo

Embryo exhibits characteristics of its ancestors` embryos

Example: human development

Possess fish-like gill slits early in development

Exhibit tail, its vestige becomes coccyx

Possess fine fur during fifth month

Example:Other Vertebrate embryo comparisons

Vestigial Structures

Structures with no apparent function resembling those of presumed ancestors


Human ear muscles

Whale pelvic bones

Four-footed "missing link" whales

Human vermiform appendix

Convergent Evolution - Unlikely that similarities result from coincidence

Community level

Different areas may possess very distantly related communities with similar appearance

Species level

Pleiosaur - fusiform shape

Example: forms of Australian marsupials

Examples: albinism and blindness in cave-dwelling organisms

Systematics and Classification and Comparative Anatomy

Patterns of imilarities among organisms and their classification strongly suggests evolutionary origins

Patterns of Distribution

Continent - Island

Organisms on islands most closely resemble forms on nearest continent

Forms not identical, but diverged over time

Example: Galapagos Finches, Hawaiian Honeycreepers


Biogeographic realms

Interesting resources on Evolution versus Creationism debate

15 Answers to Creationist Nonsense

National Center for Science Education

Science and Creationism: A View from the National Academy of Sciences

Talk/Origins Archive

Pope John Paul II's Message to Pontifical Academy of Sciences on October 22, 1996


definition - evolution at the level of populations within species, changes in gene frequencies in populations

gene frequencies in populations

frequency of homozygote dominant individuals - f(AA) = number of homozygote dominant individuals/total population size

frequency of heterozygote individuals - f(Aa) = number of heterozygote individuals/total population size

frequency of homozygote recessive individuals - f (aa) = number of homozygote recessive individuals/total population size

frequency of dominant alleles - f(A) = total number of A alleles/total number of alleles

frequency of recessive alleles - f(a) = total number of a alleles/total number of alleles

Hardy - Weinberg Eaquilibrium

definition - no changes in gene frequencies when there are no agents (mutation, migration, natural selection, assortative mating, genetic drift) of evolution acting on a population

Derivation and some problems










AA x Aa






AA x aa






Aa x AA






Aa x Aa






Aa x aa







aa x AA






aa x Aa






aa x aa







f(AA) = p4 + 2p3q + p2q2= p2 (p2+ 2pq +q2)

f(Aa) = 2p3q + 4p2q2 + 2pq3 = 2pq (p2 + 2pq +q2)

f(aa) = p2q2 + 2pq3 + q4 = q2 (p2 + 2pq +q2)



f(A) = p

p + q = 1


f(AA) = p2

f(a) = q f(Aa) = 2pq

f(aa) = q2

(p2+ 2pq +q2 )= 1


Problems - Calculating gene frequencies (from Strickberger 2000, page 519)

What are the gene frequencies in the following population: p=freq of T=? and q=freq of t =?

90 TT, 60 Tt, 50 tt = 200 individuals and 400 total genes (200 x 2)

freq(T) = (90x2) + 60 (1) divided by 400 = (180+60)/400 = .60

freq(t) = (50x2) + 60 (1) divided by 400 = (100+60)/400 = .40


Problems - Calculating the HW Equilibrium frequencies


What are the HW EQ frequencies in a population where 25% of the population contains the recessive phenotype?

q2 = .25

q = .5

p = 1 - .5 = .5

Algebraic Frequencies

Expected Frequencies


.5 (.5) = .25


2 (.5)(.5) = .50


.5 (.5) = .25


Problems - Calculating the HW Equilibrium frequencies

What are the HW Eq frequencies for the following population of plants with different colored flowers?

Is the population in HW Equilibrium?

63 red (RR), 294 pink (Rr) and 343 white (rr) = 700 plants, 1400 genes or alleles


Genotype Number in RR Number in Rr Number in rr Total Frequency
R 2x63=126 294 0 420 420/1400 = 0.3
r 0 294 686 980 980/1400 = 0.7



Algebraic Frequencies

(see above)

Observed Frequencies

and numbers

Expected Frequencies

and numbers



63/700 = .09

p2 = (.3)(.3) = .09

.09 (700) = 63



294/700 = .42

2pq = 2(.3)(.7) = .42

.42 (700) = 294



343/700 = .49

q2= (.7)(.7)=.49

.49(700) = 343



Problems - Is a population in HW Equilibrium

Is the population below in HW Equlibrium?

50 individuals (AA), 50 individuals (Aa), 50 individuals (aa), 300 alleles


Genotype Number in RR Number in Rr Number in rr Total Frequency
A 2x50=100 50 0 150 150/300 = 0.5
a 0 50 2x50=100 150 150/300 = 0.5



Algebraic Frequencies

(see above)

Observed Frequencies

and numbers

Expected Frequencies

and numbers



50/150 = .33

p2 = (.5)(.5) = .25

.25 (150) = 37.5



50/150 = .33

2pq = 2(.5)(.5) = .50

.50 (150) = 75



50/150 = .33

q2 = (.5)(.5) = .25

.25 (150) = 37.5

Agents of evolution

Genetic Drift - random fluctuations of genes in populations,

What causes drift

Factors - founder population - small sample of population leaves and colonizes new area

Example: Founder effect - plant seeds on seabirds

Other Founder Examples

Afrikaner Population in South Africa (Dean 1972, Hayden 1981) 20 families are descendants of current populationhigh incidence of porphyria (problems with barbiturates) and Huntington's disease

Human populations on Islands of Tristan de Cunha - founded by 15 individuals - high incidence of retinitis pigmentosa (leads to blindness)

Kidd and Cavalli-Sforza (1974) - cattle in Iceland versus mainland Europe, brought over by the Vikings, exhibit different frequencies

Buri (1956) - brown alleles in Fruit Flies changed over a few generations, each new generation was started by a founder of 8 males and 8 females, lead to elimination and fixation in different lines of flies

Factors - bottleneck effect - population size is reduced by external factors

Example: Bottleneck effect

Cheetah in Africa

Bonnel and Selander (1974) - Northern Elephant Seal populations depleted by overhunting, exacerbated by harem system of mating, leads to lack of genetic variation in today's population

Migration - gene flow between populations

Effects on populations

changes gene frequencieshomogenizes populations (makes different populations more similar to each other)

Examples from the literature

Glass and Li (1953) - studied Rh alleles in humans (white and African-Americans)

Mutation - old alleles change into new alleles

Occurs at 2 levels - genic level and chromosomal level

Chromosomal level mutations

Deletion - loss of a segment

Fusion - addition of a segmentInversion - reversal of a segment

Aneuploidy - loss or addition of chromosomes due to non-disjunction during meiosis

Genic level mutations - exchanges or substitutions of nitrogenous bases (Purines - A, G; Pyrimidines - C, T)


substitution of purine for a purine - see bold text (G for A)


substitution of pyrimidine for a pyrimidine - see bold text (C for T)



substitution of pyrimidine for a purine or vice-versa - see bold text


Frameshift mutation - loss or addition of a nitrogenous base in a gene sequence

addition - ATCG - AATCGloss - ATCG - ACG, lost T

Consequences of mutations

Silent mutation - change does not affect amino acid sequence of protein production

Missense mutation - alters amino acid sequence

Nonsense mutation - turns off protein production

Summary of Examples from the literature

3 Types of Studies of Mutation in the Literature

1) Neutral mutations2) Deleterious mutations3) Adaptive mutation

Assortative mating - non-random mating


+ Assortative Mating: Inbreeding - like x like individuals

- Assortative Mating: Outbreeding - like x unlike individuals

Consequences of Inbreeding

1) Harmful - increase the chances of 2 deleterious or lethal alleles coming together

2) Harmless - occurs in many species of plants that undergo selfing

Examples of Inbreeding from the literature

Stone (1963), Dobzhansky (1963), Mettler et al. (1963) - inbreeding depression in Fruit Flies, numbers are % survival rates

Species Distant cousins Closely related Sibling
1 90 75 65.5
2 90.2 83.2 80.5
3 84.3   63.5

Crow et al. (1956) - incidence of problems in human births

Problem 1st cousin 2nd cousin unrelated
still birth .09 .06 .03
infant death .14 .09 .07

Spuhler (1968) - human mating preferences (tall females preferred tall males)

Anderson (1982) - widow birds females showed preferences for males with longer tails

Moller (1989) - similar pattern in Barn Swallows

Natural Selection

Natural Selection - survival of the fittest

Conditions under which natural selection can occur

genetic variation among individualsdifferential survivaldifferential reproductive success

Non-evolutionary variation

seasonal, age, sexual

Examples of genetic variation among individuals

Individual variation - birds (Harris' Sparrows, Ruddy Turnstones)

Polymorphism - Map butterflies

Balanced Polymorphism

Heterozygote advantage and sickle-cell anemia

Geographic variation

Well defined subspecies or races - Fox Sparrows, Song Sparrows, Northern Juncos

Clinal variation

Bergmann's rule - animals in colder climates tend to be larger, decrease ratio of surface to

body mass (volume) and conserves heat

Allen's rule - animals in colder climates tend to have smaller extremities, decrease ratio of

surface to body mass (volume) and conserves heat

Gloger's rule - animals in the tropics tend to be more colorful while organisms in colder environments tend to be paler

Maintaining variation in populations

recombination - mixing of chromosomes and genes during meiosis

crossing over - eschange of chromosome pieces during meiosis I (prophase I)

mutation - chromosome and genic level mutations

heterosis - heterozygote advantage as in sickle-cell anemia

What is the struggle in the environment against?

Abiotic factors - physical aspects of the environment

Climate - precipitation, wind, humidity, temperature, etc.

Other - altitude, daylength, water depth, water chemistry, tides, etc.

Biotic factors - biological aspects of the environment

parasitism, predation, competition, etc.

Types of selection

Directional Selection - selection for a particular genotype

Examples from the literature

Ricker (1981) - Pink Salmon decrease in size over time with fishing

Kettlewell (1954) - Pepper Moths

Wood (1981) - DDT resistance and insects

Antonovics (1971) - plants and heavy metal resistance near mines

Hirschberg and McIntosh (1983) - weed resistance to herbicides (triazine)

Boag and Grant (1981) - Galapagos Finches (during drought, body size of birds increased)

Stabilizing Selection - selection against extreme individuals and for the average phenotype

Examples from the literature

Bumpus (1899) - House Sparrows near Woods Hole, MA

Karn and Penrose (1951) - birth weight in human babies

Rendel (1953) - duck eggs parallel human birth weight results

Hecht (1952) - lizard size affected by predation versus territorial defense

Mason (1964) - milkweed butterflies (less variable males performed most of the matings)

Disruptive Selection - selection for extreme phenotypes and agains the average phenotype

Examples from the literature

All cases of Batesian mimicry

Ford (1975) - multiple phenotypes of the Swallowtail Butterfly

Thoday and Gibson (1962) - laboratory example, selected for extreme Fruit Flies

Remington (1954) - field study of the Sulfur Butterfly (orange-winged versus white-winged morphs)

Other Types of Natural Selection

Frequency Dependent

All cases of Batesian mimicry - too many mimics spoils the program and predators find outAll cases of Mullerian mimicry - the more the merrier, more toxic mimics of each other - the faster the predators find out

Clark (1962) - when morphs reach a certain level in the population they are selected against by fish predation

Ehrman (1968) - rare male Fruit Fly achieves the most matings

Sexual selection

first described by Darwin as a mechanism that leads to sexual dimorphism in a speciescould be due to female mate choicecould be due to result of male versus male interactionsother (e.g., exploitation of different feeding niches)

Species and Speciation

Species concepts

Biological Species Concept: Species are groups of interbreeding natural populations that are reproductively isolated from other such populations.

emphasis: reproductive isolation

problems: universal application - unisexual species, paleospecies and the temporal dimension

Ecological Species Concept: A species is a lineage (or closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all otherlineages outside its range.

emphasis: natural selection, co-adapted genes and ecological niche

problems: ignores other agents responsible for evolution

Cladistic/Phylogenetic Species Concept: A species is the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent.

emphasis: diagnostic characters

problems: elevating too many subspecies to species level

Pluralistic Concept - combination of the above, criteria are applied differently to different species' situations

Speciation - origin of new species

Allopatric speciation: differentiation of geographically isolated populations into species

Geographical or Continental Speciation

Example: North American Orioles

Mengel's (1964) species groups of North American Warblers

Nashville Group

Nashville Warbler Disjunct Range: Rocky Mountains

and Eastern Boreal Forest

Virginia's Warbler southwestern US
Lucy's Warbler southwestern US

Connecticut Group

Connecticut Warbler boreal Canada and n. US
Mourning Warbler boreal Canada and n. US
MacGillivray's Warbler Rocky Mountains

Black-throated Green Group

Black-throated Green Warbler boreal Canada
Hermit Warbler coastal nw US
Golden-cheeked Warbler central Texas
Townsend's Warbler coastal British Columbia

and Alaska

Black-throated Gray Warbler Rocky Mountains

Yellow-rumped Group

Yellow-rumped Warbler -

Audubon's Warbler

Rocky Mountains
Yellow-rumped Warbler -

Myrtle Warbler

boreal US and Canada
Grace's Warbler sw US
Virginia's Warbler se US

Rising (1983)


Eastern Meadowlark grasslands of eastern

North America

Western Meadowlark grasslands of western

North America


Baltimore Oriole eastern North America
Bullock's Oriole western North America

Northern Flickers

Yellow-shafted Flicker eastern North America
Red-shafted Flicker western North America


Indigo Bunting eastern North America
Lazuli Bunting western North America


Rose-breasted Grosbeak eastern North America
Black-headed Grosbeak western North America

Salamanders in California - invasion of species into California from Oregon, split by mountain ranges to form ring species, southern populations are incapable of breeding with northern populations and are considered separate species

Quantum Model - peripheral isolates become founder populations

Archipelago = Island Speciation

Bock (1970) - Hawaiian Honeycreepers

Darwin (1859) - Darwin's Finches

Carson (1992) - Hawaiian Drosophila

Sympatric speciation: splitting of populations in a common area into species



autopolyploidy - results from members of the same species

failure of chromosomes to separate during meiosis in males and females, results in tetraploid (4N) individuals

allopolyploidy - results from members of different speciesExample: plant hybridization

Lewis and Lewis (1955) - plant genus Clarkia primitive species, 2N are 7 and 8 chromosomesadvanced species, 2N are 18, 16, 15 chromosomes (probably 4N)

In each case, polyploid individuals are capable of breeding with each other but not backcrossing with parents -due to chromosome # problems

Other examples

Tragopgon weeds in the Pacific northwestern US

Wheat used for bread - allopolyploid between cultivated wheat and wild grass

Gradual model - multiple niche polymorphism

Boiler and Bush (1973) - host switching by parasites

Tauber and Tauber (1989) - lacewing insects: C. carnea feeds on deciduous trees, C. downsei feeds on conifers

Bush (1969) - Rhagoletis Fruit Fly species - rapid host shift from Hawthorn trees to Apple, Cherry, Pear, etc. occurred over last 100 years

Isolating Mechanisms - keep species apart

Prezygotic Isolating Mechanisms

Ecological isolation - Same area, but different habits and habitats

Thamnophis garter snakes separated by habitat preferences

aquatic species

terrestrial species

Temporal isolation - Breeding periods at different times

Spotted Skunks

Eastern species breeds in late winter

Western species breeds in late summer

Three species of Dendrobium orchids breed in rainforest on different days

Behavioral or Ethological isolation - Species specific mating rituals

Stein (1960's) - Empidonax flycatchers

Trail's Flycatcher divided into Willow and Alder Flycatchers based on song differences also includes Acadian, Least, Yellow-bellied Flycatchers

Fish Crow and American Crow

Lanyon (1957, 1962) - Eastern and Western Meadowlarks in the United States

Pitocchelli (1990) - Mourning and MacGillivray's Warblers

Sex Pheromones in insects and mammals

Hawaiian Drosophila

Fireflies - different signal patterns for different species

Cricket song and female choice

Mechanical isolation - General structural differences in genitalia or other structures prevent interbreeding

Dufour (1844) - lock and key relationship of male and female genitalia in some insects

Dodson (1967) - orchid species: flowers of some species mimic female insects of certain bees and wasps, encourages pseudo-copulation and pollination

Gametic Isolation - Prevention of gamete fusion, Sperm not attracted to eggs of other species, Sperm incapable of penetrating eggs

Postzygotic Isolating Mechanisms

3 types

Hybrid inviability - embryos die early

Hybrid sterility - adults are somatically vigorous but can not reproduce

Hybrid breakdown - adults are somatically vigorous and can reproduce but future offspring fail to reproduce

Macroevolution - evolution above the species level

How do higher taxa (categories above the species level - genera, families, orders, phyla, et.) evolve?

Timing - tempo of evolution above the species level

Gradualism - long time

Punctuated equilibrium - short spurts of evolution followed by stasis

Origin of evolutionary novelties - how do new features evolve

Allometry - different parts of the body have different growth rates, leads to shape changes

Heterochrony - timing of growth changes in different parts of the body, some parts grow while others do not or grow later:

Example: Ground-dwelling versus tree-dwelling salamanders, Tree-dwelling species have shorter feet, growth of the feet was controlled by turning off genes involved in growth

Example: Paedomorphosis - incorporation of adult sexual features into larval or immature forms, sexual organs continue to develop while the rest of the body does not

Example:Neoteny - retain traits of immature stages in the adult

Homeotic changes or mutations - gross aberrations in development and growth patterns, growth of body parts and position of body parts found inHox genes, mutations could result where cells lose positional information

Example - antennapedia mutation in Drosophila - leg grows in place of an antenna

Interesting trends in macroevolution

Horse Evolution: woodland browser to grazer on the open savanna

4 toes and clipping teeth to one toe and grinding teeth

Human Evoltuion: arboreal tree climber - edge species (knuckle walker) - bipedal movement on the savanna

Evoltuion of the vetebrate jaw - from gill arches

Evolution of the mammalian ear - from jaw and skull bones

Evolution of size - titanotheres

All of the above examples - due to chance, random changes in the environment, not goal-directed

Fossil - term coined by Agricola in the 16th century, derived from fossilis - to dig up

Modern Definition of fossils

Stahl (1985) - "Every trace of the physical existence of an extinct organism is considered a fossil and

regarded as potentially helpful in determining the history of an ancestral line."

Examples of fossils

fossilized bone, animal body parts, plant parts, etc.

imprints of organisms or their body parts



corprolites - fossil feces

eggshells and nest imprints

wounds or other damage caused by predators are left on some organisms

fossil remains in the intestines of organisms

gastroliths - fossil gizzard stones in some reptiles

fossil insects in amber

Processes of fossil formation

sedimentation - organisms die near shorelines or wet areas, become buried in mud and covered by silt and sediments

cold storage: frozen fossils - frozen in ice (Wooly Mammoth, ICE MAN)


mineralization - minerals seep into tissues or hollow spaces of bones (silica or calcium carbonate

amber = chemically altered resin of ancient trees

bogs - aseptic preservation in water hostile to bacteria and other organisms

tar pits - organisms caught and drown in tar pits, become covered over

waxy hydrocarbon covering caused by oil flows


lava flow catches an organism

dessication or sandstorms in the desert

Limitations of the fossil record

bias towards organism preserved by sedimentation, living near water

Dating Fossils

Radiometric dating - decay of radioactive materials (decay at a constant rate)

Carbon 14 method - ratio of C14/C12, c14 has a half life of approximately 5,600 years, used for rocks approximately 50,000 years old

Uranium (U238 isotope) -Lead (PB 206) method - calculate the ratio of lead/uranium, 1/2 life of 4.5 billion

years, used to age rocks in billions of years

The moving crust - plate tectonics

crust floats/moves over the mantle

lava floats up to the surface and moves plates/continents apart

2 adjoining plates slides past each other (Pacific plate carrying section of California northward along the San Andreas fault)

2 plates collide, one plates goes under the other (Pacific plate plunges into the mantle where it meets the North American

plate at the Aleutian Islands, causes volcanic activity and uplifting or mountain building - Aleutian Islands, Andes

Mountains where Pacific plate meets and plunges under the American plate in South America)

Major land masses

Pangea - oldest, all continents connected

Laurasia - split of Pangea, this contained the northern continents

Gondwanaland - split of Pangea, this contained the southern continents

Systematics -study of evolutionary relationships of organisms

Taxonomy - Science of biological classification of organisms

Goals of Taxonomists

1) Reveal evolutionary relationships between organisms

2) Describe pattern of evolutionary relationships from primitive to advanced

3) Find ancestors along with input from paleontology

4) Constantly re-evaluate previous classifications

Current System: The Taxonomic/Linnaen Hierarchy for a Biological Classification

Characteristics of the system

System Is Hierarchical

Binomial Classification

What is a classification?

Classification is a system with categories that contain similar organisms which descended from a common ancestor, reflects a phylogeny or genealogy, reconstruction of relationships among taxa and groups they belong to

A classification is also considered to be a monophyletic group of taxa

Composed of Categories


Kingdom, Phylum, Class, Order, Family, Genus, Species

Categories are arranged into a hierarchy with most inclusive group at top and least inclusive at the bottom, For each category there are many taxa (in parentheses) that organisms belong to, Below is an example of the classification for humans)


Kingdom (Animalia)

Phylum (Chordata)

Class (Mammalia)

Order (Primates)

Family (Hominidae)

Genus (Homo)

Species (Homo sapiens)

Taxon - formal name for each category


Animalia, Chordata, Mammalia, Primates, Hominidae, Homo, Homo sapiens

Printing conventions

Genus capitalized, species not capitalized

Both genus and species italicized or underlined

All other taxonomic unit names capitalized, but no distinctive print style

How are classifications produced


Fundamental concept to evolution and classification

Definition - a structure possessed by members of 2 or more taxa that was shared by a common ancestor


Individual bones of the vertebrate forelimb - humerus, radius, ulna, carpals, metacarpals, digits (or phalanges) - each are homologous structures found in many vertebrates

bones of the pelvic girdle of vertebrates (illium, ischium, pubis)

Chitinous exoskeleton of arthropods

Feathers of birds

Hair and mammary glands of mammals

Types of characters used in taxonomic research

Qualitative characters (qualities of an organism's phenotype)

Behavioral characters

Quantitative characters (measurements)

Biochemical genetics

Immune responses (antigenic distances), allozymes, nuclear DNA, mtDNA, clDNA, other

Assess character state

primitive - reveals evidence of the ancestral condition

derived - reveals evidence of recent modification

Schools of Taxonomy


use of mathematical measures of similarity - produces a similarity matrix between taxa

Taxa A B C
A - .7 .2
B   - .2
C     -

uses as many characters as possible (don't worry about convergence)

produce dendrogram depicting relationships, uses various clustering algorithms, based on the similarity matrix

Example - Schnell (1970) produced classification of Charadriiform birds based on external and skeletal measurements

problems - too much emphasis on total similarity, can not handle convergent or parallel traits

Cladistics or Phylogenetic Systematics

uses homologous characters and rigorous character analysis

primitive characters = pleisiomorphic

derived characters - apomorphic

determined by character polarization - finding out which one is primitive versus derived

Methods - compare with the fossil record, outgroup comparisons, other

use of shared, derived characters (synapomorphies) that define groups, produce cladograms

Example - vertebrate evolution

Evolutionary classification (being replaced with Cladistics)

mix of both philosophies, use homologous characters and emphasize overall similarity, emphasizes the amount of morphological change during construction of phylogenetic relationships

uses shared derived characters, uses overall similarity in assessing taxonomic rank

problems - character weighting plays an influential role in defining taxa



Summary of major events

Timing Event
11 - 20 BYA Big bang
4.5 BYA Origin of the earth
3.5 BYA Appearance of the first prokaryotic organisms
2.1 BYA Appearance of the first eukaryotic organisms
540 MYA Cambrian Explosion
5 MYA Ape-like ancestors of humans

Origin of the Universe

Cosmology - study of the origin of the universe

Big Bang - Big Bang - single origin, expanding universe, time has a single beginning and the universe will eventually end in a single collapse, 11 - 20 BYA - big bang (all matter is condensed into a small area, followed by an explosion Immediately after explosion - fusions of small atoms into larger atoms 10 BYA - galaxies form, stars are formed and are burning, some explode into supernova Hale-Bopp - one example of a piece of the big bang floating around the universe

Oscillating Universe - series of big bangs, time has no beginning and no end, time is infinite, universe oscillates between expansions contractions (big crunch), contractions caused by gravity which can reverse expansion of matter

Steady State - unchanging universe except that as hydrogen diminishes in supply it is replaced by hydrogen from an unknown source, at higher levels - old galaxies are replaced by new galaxies

Origin of the Planets and Solar Systems

Collision theory - a second star nearly collided with our sun and its gravity pulled out materials from the sun which eventually became the protoplanets Dust cloud or condensation theory - large condensing mass of material in the center of a cloud became the sun, peripheral masses never reached critical temperatures to becomes suns, instead became protoplanets

Earth Formed 4.5 Billion Years Ago

5 BYA - origin of our solar system and the Milky Way Galaxy

Particles revolve around a proto-sun

Dust condenses

asteroid belts

planetessimals - collide and compress

4 BYA - planets form and revolve around the sun

Earth's atmosphere - dominated by hydrogen, methane, water, ammonia, nitrogen, carbon monoxide

Where did oxygen come from?

  1. UV irradiation of water in the upper atmosphere, split water into hydrogen and oxygen
  2. 2 - 3 BYA, appearance of first autotrophs - blue-green algae

Earth as it is today


The moving crust - plate tectonics

crust floats/moves over the mantle

lava floats up to the surface and moves plates/continents apart

2 adjoining plates slides past each other (Pacific plate carrying section of California northward along the San Andreas fault)

2 plates collide, one plates goes under the other (Pacific plate plunges into the mantle where it meets the North American plate at the Aleutian Islands, causes volcanic activity and uplifting or mountain building - Aleutian Islands, Andes Mountains where Pacific plate meets and plunges under the American plate in South America)

Major land masses
Pangea - oldest, all continents connected
Laurasia - split of Pangea, this contained the northern continents
Gondwanaland - split of Pangea, this contained the southern continents


Origin of Life - Early Ideas

1) Spontaneous generation - life from inanimate materials

2) Experimentation

Redi - showed that animals could not arise from inanimate materials using dead fish

Pasteur - showed that microorganisms could not arise from inanimate materials

Origin of Life 5 Hypothetical Stages - Hypothetical Sequence

1) Formation of organic molecules from inorganic materials - abiotic synthesis of organic compounds

(Oparin - Haldane model, confirmed by Miller-Urey experiments)

reducing atmosphere, energy, water = environment

Panspermia - organic molecules could have come from outer space, Murchison meteorite contained amino acids that did not originate on earth, all amino acids were very similar to ones produced in the Miller-Ureyexperiments

2) Polymerization of organic molecules to make more complex compounds

dehydration synthesis needs energy and concentrating organic compounds - cyanic condensing agents (cyanamide, cyanogen, cyanic acid, etc..) produce peptide bonds in aqueous solutions, could have occurred on clays

anhydrous production - heat can remove water in the absence of condensing agents

3) Formation of a barrier to separate inside of proto-cell from outside, could have formed through membranous droplets or vesicles


coacervates - colloidal particles separate out of solution into droplets under certain conditions (temperature, pH, etc.), electrically charged water molecules become tightly bound to charged molecules and or charged particles, water molecules form a film-like barrier, separates internal chemistry of the droplet from the outside (Oparin 1957, 1971)

proteinoids - dry amino acids can be polymerized, forming protein-like molecules (proteinoids) when heated and allowed to cool in water, coolling water can produce microspheres which separate out of solution, microspheres have two-layered boundary which is osmotically active, are gram - when stained, internal chemistry of the droplet from the outside, can undergo processes similar to fission and budding under certain conditions (Fox 1965, 1980)

liposomes - protocells with a phospholipid bilayer membrane, under certain conditions (addition of proteins, etc.) boundary becomes increasingly selectively permeable

Importance to evolution of life

selective permeability

isolation of external and internal environment

small size increases probability of chain reactions inside the cell (products of one reaction can be the reactants of another)

membranes could have incorporated peptides which acted as channels or pumps for other molecules, moving them in and out of the droplet

4) Production of enzymes necessary for energy in chemical reactions that take place inside a cell but proteins are made from instructions from RNA which receive instructions from DNA (transcription and translation) - where did the catalysts come from? First - need a self-replicating system

Probable answers: 1) rRNA replicates itself and controls chemical reactions without help of other proteins, RNA world, based on work by Cech (1987), found that rRNA could make copies of itself without the help from proteins

Probable answers: 2) proteins or protein-nucleic acid combinations

5) Evolution of metabolism

pattern, based on comparative studies, indicates that anaerobic metabolism preceded aerobic metabolism,

reactions that break down high energy carbon compounds similar to anaerobic glycolysis may have been primitive percursors, had to occur under anaerobic conditions because there was little oxygen in the atmosphere, predetermined by the abundance of small molecules available, later pathways evolved to handle larger molecules, eventually gave rise to the Krebs cycle

some protocells switched to reduction reactions with CO2 using H2S and later H2O as electron sources, released them from a dependence on organic compounds as a source of energy, although still heterotrophs - this transition could have lead to the evolution of photosynthesis, photosynthesis creates an aerobic environment and organisms that have produced their own sugars which could be made available to other organisms, provides opportunity for evolution of the Krebs cycle and create more energy from the breakdown of glucose in advanced heterotrophs

Experimental Recreation of Origins

Miller and Urey hypothetically repeated process

Miller and Urey Apparatus

Similar atmosphere over liquid water
Temperature 100%C with sparks of energy
Methane formed carbon compounds
Formaldehyde, hydrogen cyanide
Further combined into formic acid, urea

Later experiments produced carbon compounds
Amino acids: glycine, alanine, valine, proline, glutamic, aspartic acids
Adenine produced, one of the bases found in DNA and RNA


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Copyright 2001 Jay Pitocchelli. All rights reserved. The contents of this page are the intellectual property of Dr. Jay Pitocchelli for distribution to students enrolled in General Biology BI 04 at Saint Anselm College. These pages may not be copied, photocopied, reproduced, translated, or published in any electronic or machine-readable form in whole or in part without prior written approval of Jay Pitocchelli. Students enrolled in General Biology BI 04 at Saint Anselm College have permission to print this material for their lecture notes.