In the 1920s
1. A. I. Oparin of Russia
2. John B.S Haldane of England
Proposed a hypothesis on the probable origin of life.
a. Atmosphere of early Earth must have contained methane
(CH4), ammonia (NH4), Hydrogen (H2) and water vapor.
b. Chemical reactions in said mixture of gases must have
produced organic molecules and this could have given rise of
the first living cells.
30 years layer
1. Harold C. Urey
Proposed a model of the atmosphere of early Earth similar to Oparin
and Haldane hypothesis on the probable origin of life.
a. In 1952, he suggested an experiment to explore the origin of
life under the conditions of his model of Earth’s primordial
atmosphere.
1953
1. Stanley Lloyd Miller (American Chemist)
Miller – Urey Experiment
Theory of Chemical Evolution
a. Source of Energy for the formation of the first organic
molecules must have been gigantic fishes of lighting that must
have constantly agitated the atmosphere of early earth.
b. Source of energy must have been the abundant supply of
ultraviolet radiation that could have reached Earth without an
ozone shield to stop it.
Theories and Hypothesis on how life started on Earth
1. Divine Creation – life forms may have been placed on Earth by
supernatural or divine forces. The hypothesis that a divine God
created life is at the core of most religion.
2. Extraterrestrial Origin – also referred as “panspermia”,
proposes that meteors or cosmic dusts may have carried
significant amounts of complex organic molecules to Earth,
kicking off the evolution of life. It is hypothesized that an early
source of carbonaceous material is extraterrestrial, although
not proven yet.
3. Spontaneous origin – life evolved from inanimate matter as
associations among molecules become more and more
complex. As changes in molecules increased their stability
initiate more and more complex associations, culminating in
the evolution of cells.
Many ideas have been developed based on the Spontaneous
Origin
a. At the ocean’s ridge – life may arise from the constantly
forming bubbles at the edge of the ocean as suggested by
some scientists.
b. Deep in the earth’s crust – life may formed as by-product
of volcanic activity where sulfuric minerals, iron and nickel
recombine.
Gunther Wachtershauser in 1988 and fellow scientist
shows that these chemical combinations can form
precursors of amino acid which can be later linked to
peptides.
c. Under frozen areas – just like Jupiter’s moon, Europa. It is
hypothesized that life originated under a frozen ocean.
d. Within clay – the silicate surface chemistry was
hypothesized by some researchers emphasizing the positive
charges of clay surface that may attract organic molecules
and providing potential catalytic surface where life
chemistry may have occurred.
e. At the deep sea vent – another hypothesis that life
originated at deep sea vents where the necessary prebiotic
molecules are synthesized by metal sulfides in the vents.
The positive charge of sulfides may have attracted the
negative charge of biological molecules
What is the age of the Earth – 4.6 billion years.
What is the age of life on Earth – 3.5 billion years.
Man could have first appeared about 100-150 thousand years ago as
shown by artefactual evidences in various site.
Periods under Paleozoic; Cambrian-Ordovician-Silurian-Devonian-
What was earth like million years ago?
Periods under the Mesozoic; Triassic-Jurassic-Cretaceous
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
Earth is covered with thick blanket of ice.
Lots of volcanoes and high mountains
Large organism roamed the land
The atmosphere did not have high oxygen content
Asteroids/meteors frequently hit the surface.
The lands moved a lot or the continents were a little closer to
each other
Volcanic eruptions
A little bit warmer
Plants were bigger
Humans were not yet around
Geologic Time Scale – is a tabular presentation of the history of life
based on geologists’ study of rocks and the fossils they contain. All the
pieces of information about earth are arranged chronologically from
the oldest (at the bottom of the table) to the most recent (at the top of
the table).
Eon – the largest division of the geologic time scale, spans hundreds to
thousands of years ago (mya).
Era – division in an Era that span time period of tens to hundreds of
millions of years.
Period – a division of geologic history that spans no more than one
hundred million years.
Epoch – the smallest division of the geologic time scale characterized
by distinctive organism.
Geologic Time Record – a tabular representation of the major divisions
of the earth’s history. The time intervals are divided and described
from the longest to the shortest; Eons-Eras-Periods-Epochs. Each
period has an approximated time frame and characterized by
distinctive features (event and organisms)
4 eras – Precambrian-Paleozoic-Mesozoic-Cenozoic
Carboniferous-Permian
Period under Cenozoic; Tertiary-Quaternary
The Geologic time is divided into:
The four largest segments called Eons; Hadean-Archaean-Proterozoic-
Phanerozoic
The Phanerozoic is divided into eras; Paleozoic-Mesozoic-Cenozoic
Extinction events and appearance of new life forms
characterized by division among eras.
Smaller division called periods characterized by a single type of rock
system, make up each era.
Some period are further divided into smaller time frame called epochs.
Quaternary
Tertiary
Cretaceous
Jurassic
Triassic
Permian
Carboniferous
Devonian
Silurian
Ordovician
Cambrian
Permian
Devonian
Ordovician-Cambrian
Hadean
Human evolution
Mammals diversify
Extinction of dinosaurs; first
primates; first flowering plants
First birds; dinosaurs diversify
First mammals; dinosaurs
Major
extinction;
reptiles
diversify; pangea
First reptiles; trees, seed ferns
First amphibians; fish diversify
First vascular plants
Major diversification of animal
life
First fish; chordates (animal w/
backbone)
Age of amphibians
Age of fishes
Age of Invertebrates
Priscoan; atmosphere and ocean
Charles Darwin – Western England, After graduation he joined the
crew of the survey ship HMS Beagle as ship naturalist and
conversation companion to Captain Robert Fitzroy.
Voyage of the Beage – Dec. 1831; 22-year old, he left England as
naturalist aboard the HMS Beagle for 5 year voyage around the world.
Mission: Chart the South American Coastline
-
Freedom to explore on shore; Collected thousands of specimens
of the exotic and diverse flora and fauna of South America; He
noted that plants and animals of South America were very
different from those of Europe; While on the beagle, he read
the Lyell’s Principle of Geology
During the 5-year voyage of the Beagle:
Darwin’s observations challenged his belief that species do not
change overtime. His observation of geological formation and species
variation led him to propose by which species arise and change. – This
process is known as Evolution.
Aristotle (384-322 BCE) – arranged life forms on a scale on increasing
complexity scala naturae – “scale of nature”. He observed that
organisms vary in complexity and can be arranged based on their
order of increasing complexity.
He proposed that genetic change occurs in a species over time, which
leads to their genetic and phylogenetic differences. The process is due
to natural, not supernatural forces.
Greek Philosopher – Father of Biology; Organized all things according
to their Psyche [ a kind of soul]; Vegetative Psyche [lowest, you exist];
Animate Psyche [middle, you move]; Rational Psyche [Highest, you
think]; Problems: Anthropocentric, Subjective, unable to prove
existence of these psyches.
EVOLUTION – as descent with modification. Proposing that Earth’s
many species are descendants of ancestral species that were very
different from those alive today. Can also be define as a change in the
genetic composition of a population overtime.
Is both pattern and a process
Pattern of evolutionary change is revealed in observations
about the natural world; Process of evolution consists of the
mechanisms that have produced the diversity and unity of living
things.
Carolus Linnaeus: May 23, 1707- Swedish botanist, father of
taxonomy. Widely known for two contributions – classification of
binomial nomenclature of organisms. Classified nature into kingdoms,
classes, orders, genera & species, which exist till today with some
changes. Named 4,400 animal species & 7,700 plant species through
his binomial nomenclature, a two-part scientific name in Latin for
every species. He classified them in his book “Systema Naturae”. Was
appointed Chief Royal Physician in 1747 & Knighted by King of
Sweden in 1758.
Binomial Nomenclature: Naming system that gives organisms a twopart scientific name – Genus species and classifying species into a
hierarchy of increasingly complex categories.
Dating Fossils – knowing the age of fossil can help a scientist establish
its position in the geologic time scale and find its relationship with the
other fossils.
2 ways to measure the age of a fossil
a. Relative dating
b. Absolute dating
1. Relative Dating – based upon the study of layer of rocks; does
not tell the exact age; only compare fossil as older or younger,
depends on their position in rock layer; fossil in the uppermost
rock layer/strata are younger while those in the lowermost
deposition are oldest.
I.
Law of Superposition – if a layer of rock is undisturbed, the
fossil found on upper layers are younger than those found
in lower layer of rocks. However, because the earth is
active, rocks move and may disturb the layer making this;
process not highly accurate; sedimental layer are deposited
in a specific time – youngest rocks on top – oldest rocks at
the bottom.
II.
III.
Law of Original Horizontality – deposition of rocks happen
horizontally-tilting, folding or breaking recently happened
Law of Cross-Cutting Relationships – if an igneous
intrusion or a fault cuts through existing rocks, the
intrusion/fault is younger than the rock it cuts through.
Index Fossils (guide fossils/indicator fossils/zone fossils): fossils
from short-lived organism that lived in many places; used to define
and identify geologic periods.
Paleontology – the study of the remains of organisms of the past.
Fossils – evidences of organism that lived in the past; they can be actual
remains like bones, teeth, shells, leaves, seeds, spores or traces of past
activities such as animal burrows, nests and dinosaur footprints or
even the ripples created on a prehistoric shores.
2. Absolute Dating – determines the actual age of the fossil
through radiometric dating, using the radioactive isotopes
carbon-14 and potassium-40; considers the half-life or the
time it takes for half of the atom of the radioactive element to
decay; the decay products of radioactive isotopes are stable
atoms.
Radioactive Dating – dating organic matter up to around 70,000 years
old.
C-14 – it is based on the radioactive isotope of carbon; meaning its
mass is 14 atomic mass units, or a.m.u. is produced in nature by
cosmic ray bombardment of nitrogen atoms in the atmosphere.
C-14 decays’ with a half-life, +40 years; examination of the amount
of C-14, remaining today in a given organic material gives a fairly safe
estimate of the age of said material.
Radiocarbon dating has flaws; scientist discovered that the production
of C-14 in nature is not exactly constant; thus some correction in the
age of fossil remains had to be made.
Types of Fossil
Types of Fossil
Description
Examples
Molds
Impression made in
a
substrate
=
negative image of an
organism.
When a mold is filled
Organic material is
converted into stone
Shells
Casts
Petrified
Original remains
Carbon film
Trace/Ichnofossils
Preserved
wholly
(frozen
in
ice,
trapped in tar pits)
Carbon impression
in sedimentary rocks
Record
the
movements
and
behaviors of the
organism
Per mineralization / The organic contents of bone and wood
petrification
are replaced with silica, calcite or silica
pyrite, forming a rock-like fossils.
Replacement
Hard parts are dissolved and replaced by
the other minerals like calcite, silica pyrite
and iron.
Carbonization
or The other elements are removed and only
coalification
the carbon remained.
Recrystallization
Hard parts are converted to more stable
minerals or small crystal turn into larger
crystal.
Authigenic
Molds and casts are formed after most of
preservation
the organisms have been destroyed or
dissolved.
The theory that all organisms share a common ancestors is
supported by many lines of evidences.
Bones and teeth
Petrified trees; coal
balls
(fossilized
plants and their
tissues, in round ball
shape.
Woolly mammoth;
amber from Baltic
sea region
Leaf impression on
the rock
Trackways,
toothmarks, glizzard
rocks,
corpolites
(fossilized dungs),
burrows and nests.
-
Fossils – are the remains and traces of past life or any other direct
evidences of past life.
Fossil Record – provides evidences that organisms have changed
over time.
-
Ways of Fossilization
Unaltered preservation
Description
Small organism or part trapped in amber,
hardened plant sap.
Fossil Record, Biogeographic Distribution, Anatomical
Evidences,
Biochemical
Evidences,
Evidence
from
Developmental Biology, Molecular Homologies. Artificial
Selection
-
The remains of ancient life found in the oldest rocks are
fewer and more primitive than those found in younger rocks.
[Example: Earliest Fossils: Prokaryotes {blue-green
bacteria}, 3.4-3.6 billion years ago.
Findings: very simple forms of life lived in the past and over
millions of year, probably gave rise to many kinds of
organism with more complex body structures.
The remains of many ancient plants and animals show
structural similarities to certain organisms that lived today.
Although none is exactly the same as the living species, also,
-
fossils found in younger rocks are not found much in older
rocks.
Findings: imply that ancestral forms gradually evolved over
millions of years ang gave rise to offspring that are no longer
exactly like themselves.
In 2004, Paleontologist discovered fossilized remains of Tiktaalik
roseae, nicknamed the “fishapod” because it is the transitional form
between fish and four-legged animals, the tetrapods. Mix of fishlike
tetrapod-like features.
-
Fossils such as Tiktaalik roseae provide evidences that the
evolution of new groups involves the modification of
preexisting features in older groups. The evolutionary
transition from one form to another.
Anatomical transitions during the evolution of whales.
Transitional fossils, such as Ambulocetus and Basilosaurus,
support the hypothesis that modern whales evolved from
terrestrial ancestors that walked on four limbs. These fossils show
a gradual reduction in the hand limb and a movement of the nasal
opening from the tip of the nose of the head – both adaptations to
living in water.
Biogeography
Each type of marsupial in Australia is adopted to a different
way of life. All the marsupials in Australia presumably evolved from
a common ancestors that entered Australia some 60 million years
ago.
Divergent Evolution = Adaptive Radiation
Tortoises adapted to different habitats as they spread from
the mainland to the different islands.
Adapted to similar environments,
independently from different ancestors.
but
evolved
Sugar Glider

In Australia is a marsupial more closely
related to Kangaroos that North American
Flying Squirrels

Because its ancestors were marsupials.
Convergent Evolution
Whales and sharks have a similar body design even though
they are very different organisms [one is a fish; the other, a
mammal] because they have independently adapted to living in a
similar environment.
Biogeographical Evidence
Biogeographical differences; provided evidence that
variability in a single, ancestral population can lead to adaptation to
different environments through the forces of natural selection.
Competition for resources appears to provide some of the pressure
that leads to diversification.
Anatomical Evidence
Similarities in Structure
Homologous Structure
Structures that are similar because of common
ancestry | Organisms which undergo similar structures have close
evolutionary ties. [Limbs of human-cat-whale-bat]. Forelimbs of all
mammals share some arrangement of bones that can be traced to
same embryological origin.
Amnion – bag of waters; the extraembryonic membrane of
birds, reptiles and mammals, which lines the chorion and contains
the fetus and the amniotic fluid.
Vestigial Organs – some homologous structures are
vestigial and have no useful function even though they are still
present. [Example: Hipbones and pelvis in whales and boa
constrictors. Cecum {appendix} in human. Skink legs
Embryology – development of vertebrate embryos follow
the same path. [Fish-salamander-tortoise-chicken-rabbit-human].
Series of changes in body structure that an animal goes through
from egg to adult. Same groups of undifferentiated cells developed
in the same order to produce the same tissues and organs of all
vertebrates, suggesting that they all evolved from a common
ancestors.
Why grow a tail and then lose it?
Human embryo has a tail at 4 weeks which disappears at 8
weeks. Pharyngeal pouches become gills in fish, part of throat/ears
in humans.
Biochemical Evidences
All living organisms use the same basic biochemical
molecules, including DNA (deoxyribonucleic acid), RNA
(ribonucleic acid) and ATP (adenosine triphosphate). Organism use
a triplet nucleic-acid code in their DNA to encode for 1 of 20 amino
acids that will form their proteins. The sequence of amino acids of
some proteins is similar across the tree of life. The sequence of
amino acids in the human version of cytochrome c, a protein
essential to cellular respiration, is remarkably similar of that of
yeast.
Evidences from Developmental Biology
Many developmental genes are shared among all animals
ranging from worms to humans. It appears that life’s vast diversity
has come about by a set of regulatory genes that control the activity
of other genes involved in development. Hax, or homeobox, genes
orchestrated the development of the body plan in all animals, from
invertebrates (such as sea anemones and fruit flies) to humans.
Function of Hax Gene
A change in the timing and duration of the
expressions of hax genes that control the number and type of
vertebrae can produce the spinal column of a chicken or the longer
spinal column of a snake.
Molecular Homologies
All life forms share same genetic machinery (DNA & RNA).
Universal Genetic code. Important genes share highly conserved
sequences. Similarities in DNA and protein sequences suggested
relatedness. Similarities in karyotypes suggest an evolutionary
relationship.
Even differences show relatedness
Chimpanzees have 2 smaller chromosomes pairs we
don’t have
Humans have 1 larger chromosome pair [#2] they
don’t have.
Protective
chromosomes.
telomere
sequences
found
at
ends
of
Telomeres in Middle
Human chromosomes is only human chromosome that has
telomere sequences at the ends but also in the middle… suggesting
it was made by joining two other chromosomes together.
Extra Centromere
Chromosome #2 has a second inactive
centromere region… suggesting it was made by
joining two other chromosomes together.
Allele Frequency – portion of specific allele in the
population. The percentage of each allele in a population’s gene
pool.
Artificial Selection
Gene Pool – the allele of all genes in all individuals in a
population.
Works nature provides the variation through
mutation and sexual reproduction and
humans select those traits that they find useful. [Ex. We have
selected for and bred cows to produce more milk, turkeys with
more breast milk ect.]
Theodosius Dobzhansky, March 1973/ Geneticist, Columbia
University 1900-1975
“Nothing in Biology makes sense except in the light of evolution”.
Hardy-Weinberg Principle
p2 + 2pq + q2 = 1 [can measure the genotype frequencies of
a non-evolving population]
The frequency of the D and d alleles in each gametes
[sperm and egg] in this population would be the same as the allele
frequencies, so that 20% of alleles in eggs and sperm will be D, and
80% of alleles in eggs and sperm will be d.
Charles Darwin Theory of Evolution
Darwin observed that populations, not individuals, evolve.
But he could not explain how traits change overtime. Now we
know that genes interact with the environment to determine traits
– the diversity of individuals within that population.
Because genes and traits are linked, evolution is really
about genetic change – or more specifically, evolution is the
change in allele frequencies in a population over time.
Genes Population Evolution
Microevolution – evolutionary change within populations.
Populations – a group of organisms of a single species living
together in the same geographic area.
Compute the change in gene frequency from one generation to
another generation.
Allele – genes governing variation of the same character
that occupy corresponding positions on homologous
chromosomes.
Change in p and q from generation 1 to 2:
∆𝑝 = 𝑝1 − 𝑝1 = 0.37 − 0.34 = 0.03: ∆𝑞 = 𝑞2 − 𝑞1 = 0.63 − 0.66
= −0.03
This means that there is increase in the frequency of p by 0.03 and
a corresponding decrease in q after one generation of selection
against the white phenotype.
Hardy-Weinberg Equilibrium
A population in which allele frequencies do not change over
time. A stable, non-evolving state. The Hardy-Weinberg equilibrium
is a constancy of gene-pool allele frequencies that remains stable
from generation to generation if certain conditions are met.
1. No mutation: no new alleles can arise by mutation.
2. No migration: no new members [and their alleles] can
join the population, and no existing members can leave
the population.
No gene-flow, random mating, no
genetic drift, and no selection.
When gene-pool frequencies change,
microevolution occurs.
Deviations from Hardy-Weinberg
equilibrium allows us to detect microevolutionary shifts. Mutations occurs
when the DNA sequence has changed.
Which can serve as a source of new
genetic variation.
Migration
Gene flow is the movement of alleles between populations.
Occurs when plant and animals migrate, or more specifically their
gametes move, between populations. When gene flows brings a new
or rare allele into a population, the allele frequency in the next
generation changes. Gene flow in plants may result when pollen
from one plant fertilizes plant in another population.
Small Population Size
Genetic drift is when chance events cause allele frequencies
to change. Both the bottleneck effect and founder effect result from
the loss of genetic variation within the population. Genetic drift
refers to changes in allele frequencies of a gene pool due to chance
events. Such events remove individuals, and their genes, from a
population at random – without regard for phenotype or genotype.
Genetic drift occurs when, by chance, only certain members
of a population, [green frogs] reproduce and pass on their alleles to
the next generation. A natural disaster can cause the allele
frequencies of the next generation’s gene pool to be different form
those of the previous generation. Genetic drift can be a powerful
force for evolutionary change, especially in small populations. The
smaller the population, the more genetic drift impacts in the allele
frequencies.
A large population can suddenly become very small,
A bottleneck effect is a type of genetic drift in which the loss
pf genetic diversity is due to natural disasters [e.g. hurricane,
earthquakes, or fire], disease, overhunting, overharvesting or
habitat loss.
A founder effect, another type of genetic drift, is similar to a
bottleneck effect except that genetic variation is lost when a few
individuals break away from a large population to found a new
population.
Consequences of bottleneck and founder effect.
a. The gene pool of a large population contains four different
alleles, represented by colored marbles in a bottle, each with
a different frequency.
b. A population bottleneck occurs. The marbles, or alleles, that
exit the bottle must pass through the narrow neck into the
cup. The new gene pool will have a fraction of the alleles
from the original population.
c. The gene pool of the new population has changed from the
original. Some alleles are in high frequency, while some are
not present.
Nonrandom Mating
Nonrandom mating alone does not cause allele frequencies
to change. Nonrandom mating however, does affect how alleles in
the gene pool assort into genotypes, thus affecting the phenotypes
in a population. In a randomly mating population, the alleles in the
gene pool assort at random. When mating is nonrandom, gametes,
and thus alleles, assort according to mating behavior. Type of
nonrandom mating, called assortative mating, occurs when
individuals choose a mate with a preferred trait, such as a particular
coat color, feather length or body size. Assortative mating brings
together alleles for these traits more often than would happen by
chance.
Natural Selection
A population in Hardy-Weinberg equilibrium has
phenotypes that are equally likely to survive and reproduce. One
genotype does not have an advantage over another. But in nature,
some phenotypes do have a reproductive advantage. Individuals
who have an advantageous phenotype often pass on the allele for
this trait to their offspring. Over time, selection for this
advantageous trait increases the frequency of the alleles associated
with it, while other alleles decrease. Most of the traits of
evolutionary significance are polygenic, controlled by many genes.
Natural selection favors the most adaptive variant for a given
environment.
Three types of natural selections;
1. Stabilizing selection – the intermediate variation is the most
adaptive, and is found in human birth weight.
2. Directional selection – either of the extreme phenotypes is
favored, as when body size increases overtime
3. Disruptive selection – two or more extreme phenotypes are
adaptive, the curve forms two peaks, as when british land
snails have one of two different banding patterns of shell
color.
Sexual selection is about reproductive success, or fitness.
Males produce many sperm and compete in inseminate females.
Females produce few eggs and are selective about their mates.
Traits that promote reproductive success, such as sexual
dimorphism, are shaped by sexual selection. A cost benefit
analysis helps a male determine if it is worth competing for
mates.
Dominance hierarchy provide dominant males greater
reproductive opportunities than lower-ranking males.
A territory is defended with specific behaviors known as
territoriality.
Biological differences between the sexes may promote
certain mating behaviors because they increase fitness.
Maintenance of Diversity
Despite constant natural selection, genetic diversity is
maintained. Mutations and recombination still occur, gene flow
among small populations can introduce new alleles, and natural
selection itself sometimes results in variation. In sexually
reproducing diploid organisms, the heterozygote acts as a
repository for recessive alleles whose frequency is low. In regard
to sickle-cell disease, the heterozygote is more fit in areas where
malaria occurs; this is known as the heterozygote advantage.
a. Genes - The basic unit of heredity passed from parent to
b.
c.
d.
e.
f.
g.
child. Genes are made up of sequences of DNA and are
arranged, one after another, at specific locations on
chromosomes in the nucleus of cells.
Population - Population is a group of organisms of one
species that interbreed and live in the same place at the same
time. A group of individuals of the same species within a
community. The nature of a population is determined by
such factors as density, sex ratio, birth and death rates,
emigration, and immigration.
Allele Frequency - Allele frequency refers to how common
an allele is in a population. It is determined by counting how
many times the allele appears in the population then
dividing by the total number of copies of the gene. [p + q = 1]
Genotype Frequency - Genotype frequency in a population
is the number of individuals with a given genotype divided
by the total number of individuals in the population. In
population genetics, the genotype frequency is the
frequency or proportion (i.e., 0 < f < 1) of genotypes in a
population. [𝑝2 + 2𝑝𝑞 + 𝑞2 ]
Population Genetics - Population genetics is a field of
biology that studies the genetic composition of biological
populations, and the changes in genetic composition that
result from the operation of various factors, including
natural selection.
Gene Pool - A gene pool refers to the combination of all the
genes (including alleles) present in a reproducing
population or species. A large gene pool has extensive
genomic diversity and is better able to withstand
environmental challenges.
Gene Flow - Gene flow, the successful transfer of alleles
from one population to another, is now known to vary
considerably among species, populations, and individuals as
well as over time.
h. Genetic Drift - Genetic drift is the change in frequency of an
existing gene variant in the population due to random
chance. Genetic drift may cause gene variants to disappear
completely and thereby reduce genetic variation. It could
also cause initially rare alleles to become much more
frequent, and even fixed.
i. Mutation - A Mutation occurs when a DNA gene is
damaged or changed in such a way as to alter the genetic
message carried by that gene. A Mutagen is an agent of
substance that can bring about a permanent alteration to
the physical composition of a DNA gene such that the
genetic message is changed.
j. Bottleneck Effect - Population bottlenecks occur when a
population's size is reduced for at least one generation. A
population bottleneck or genetic bottleneck is a sharp
reduction in the size of a population due to environmental
events such as famines, earthquakes, floods, fires, disease,
and droughts; or human activities such as specicide,
widespread violence or intentional culling, and human
population planning.
k. Founder Effect - In population genetics, the founder effect
is the loss of genetic variation that occurs when a new
population is established by a very small number of
individuals from a larger population. It was first fully
outlined by Ernst Mayr in 1942, using existing theoretical
work by those such as Sewall Wright. Founder effect, as
related to genetics, refers to the reduction in genomic
variability that occurs when a small group of individuals
becomes separated from a larger population.
l. Nonrandom Mating - Nonrandom mating occurs when the
probability that two individuals in a population will mate is
not the same for all possible pairs of individuals.
m. Assertive Mating - assortative mating, in human
genetics, a form of nonrandom mating in which pair bonds
are established on the basis of phenotype (observable
characteristics). For example, a person may choose a mate
according to religious, cultural, or ethnic preferences,
professional interests, or physical traits.
Systematics: [study of the kinds and diversity of organisms and of
any and all relationships among them]
Taxonomy
Identification
Description
Nomenclature
Classification of Organisms
Goal of Systematics
1. Tracing phylogeny [the study of biological diversity in an evolutionary
context]
2. Use data ranging from fossils to molecules and genes to infer
evolutionary relationships. [information enable biologist to construct a
comprehensive tree of life that will continue to be refined as additional
data are collected]
Taxonomy – theory and practice of classifying organisms.
Modern Taxonomy – now based on evolutionary relationships.
Taxonomical study:
Structural similarities
Chromosomal Structures [karyotypes]
Reproductive potential
Biochemical similarities
Comparing DNA & Amino Acids
Embryology/Development
Breeding behavior
Geographic distribution
Classification – method of grouping organisms; arranging entities into some
type of order to provide a system for sorting and expressing relationships
between these entities.
Nomenclature – formal naming of taxa according to some standardized
system. For plants, fungi and algae, rules for naming are provided by the
International Code of Botanical Nomenclature. For animals, rules on naming are
based of the International Code of Zoological Nomenclature.
Identification – is the process of associating an unknown taxon with a known
one
Description – is the assignment of features or attributes [characters] to a
taxon.
Hierarchy – a system of organizing groups into ranks according to status;
putting groups at various levels according to importance
Carolus Linnaeus [1707-1778]
Swedish botanist and made the greatest contribution to taxonomy. He decided
that organisms should be grouped based on similarities in body structure.
Established binomial nomenclature: two part system to name and classify
organisms.
Kingdom
Phylum
Class
Order
Family
Genus
Species
Hierarchical Classification - Taxonomic system named after Linnaeus.
Linnaean System – places related genera in the same family, families into
orders, orders into classes, classes into phyla [singular, phylum], phyla into
kingdoms ad more recently kingdoms into domains.
Species: Panthera pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Domain: Bacteria; Kingdom: Animalia; Domain: Archaea
Domain: Eukarya
Taxon – named after taxonomic unit at any level of hierarchy.
Andrea Cesalpino [1524-1603] – Italian physician. Published De plantis
[1583]. He classified plants according to their fruits and seeds rather than
alphabetically or by medicinal properties. He helped establish botany as an
independent science and also made contributions to medical science and
physiology.
John Ray – in 1682, he had published a Methodus Plantarum Nova [revised in
1703 as the Methodus Plantarum Emendata]; his contribution to classification, which
insisted on the taxonomic importance of the distinction between monocotyledons
and dicotyledons, plants whose seeds germinate with one leaf and those with two,
respectively; Ray’s enduring legacy to botany was the establishment of species as
the ultimate unit of taxonomy; on the basis of the Methodus, he constructed his
masterwork, the Historia Plantarum, three huge volumes that appeared between
1686 and 1704.
Augustus Quirinus Rivinius [1652-1723] – his Introductio generalis in rem
herbariam [Leipzig, 1690]; divided plants into eighteen classes, based on the
regularity and number of petals and also on the fruit as whether the fruit was
bare or surrounded by a dry or fleshy pericarp [the main part of the fruit
excluding the seeds which develops from the wall of the ovary, Webb [2012].
Joseph Pitton de Tournefort – Elements de Botanique [1694]; placed primary
emphasis on the classification of genera, basing his classification entirely upon
the structure of the flower and fruit; he excelled in observation and description,
and some of his generic descriptions are still acceptable; he was less innovative
in theory, however, for he denied the sexuality of plants, and the classifications
that he put forward above the level of the genus were often artificial.
Phylogeny – a family tree for the evolutionary history of a species; the
evolutionary history of a species or a group of species
The root of the tree represents the ancestral lineage
Tips of the branches represent descendents of the ancestor
Movement upward shows forward motion through time
Speciation – a split in the lineage.
Shown as a branching of the tree.
Robert Whittaker – American plant ecologist, active in 1950s to the 1970s;
he was the first to propose the five kingdom taxonomic classification of the
world’s biota into the Animalia, Plantae, Fungi, Protista and Monera in 1969.
Carl Woese (Evolutionary Biologist) – microbiologist who revolutionized
the field of phylogenic taxonomy; the tree of life originally included two
domains, prokaryotic and eukaryotic, until Woese disproved this hypothesis
through the use of ribosomal RNA [rRNA]; he sequenced and compared the 16S
rRNA [a component of the small subunit of a prokaryotic ribosome] of bacteria
and elucidated that Archaea had evolved separately from the universal ancestor
of all life, simultaneously setting the standard for determining evolutionary
relatedness among organisms; these studies allowed him to propose the idea that
RNA was the precursor of life on Earth because of its catalytic tendencies,
stability and ability to store genetic.
Phylogenetic systematics [cladistics] – branch of the systematics
concerned with the inferring phylogeny.
Cladogram/Phylogenetic Tree – branching diagram that conceptually
represents the best estimate of phylogeny.
Polytomy – branch point from which more than two descendants groups
emerge. Signifies that evolutionary relationship among the taxa are not yet clear.
Taxa D-F
A branching diagram to show the evolutionary history of a species; helps
scientists understand how one lineage branched from another in the course of
evolution.
The connection between classification and phylogeny.
Hierarchical classification can reflect the branching patterns of phylogenetic
trees. Tree traces possible evolutionary relationship between some of the taxa
within order Carnivora, itself a branch of class Mammalia.
Branch point [3] represent the common ancestor of taxa A, B, and C; The
position of branch point [4] to the right of branch [3] indicates that taxa B and C
diverged after their shared lineage split from that of Taxon A; The taxa B and C
are sister taxa, groups of organisms that share an immediate common ancestors
[4] and others closest relatives.
Rooted – which means that a branch point within the tree represent the most
recent common ancestor of all taxa in the tree.
Basal Taxon – refers to a lineage that diverges early in the history of a group
and hence like taxon G lies on a branch that originates near the common ancestor
of the group.
The branch point [2] represent the most recent common ancestors of coyotes
and gray wolves.
Shared characters are used to contstruct phylogenetic trees.
In reconstructing phylogenies:
1. Distinguish homologous features from analogous ones.
2. Choose a method of inferring phylogeny from these homologous
characters.
Cladistics – a system of classification based on phylogeny; derived
characteristics/traits: appear in recent parts of a lineage but not in older
members.
Clades – are the lines of a cladogram; these represents sequences of ancestraldescendant populations through time, ultimately denoting a descent; includes
an ancestral species and all the descendants; like a taxonomic ranks, are nested
within the larger clades.
3. Polyphyletic ‘many tribes’ Includes taxa with different ancestor.
Node – point of divergence of one clade into two different clades.
Internode – region between two nodes.
Taxon is equivalent of a clade only if it is:
1. Monophyletic ‘single tribe’ Signifies that it consists of an ancestral
species and all of its descendants.
Shared ancestral character – a character that originated in an ancestor of
the taxon.
Shared derived character – an evolutionary novelty unique to a clade.
Unique to particular clades.
Out group – a species or group of species from an evolutionary lineage
In group – that is known to have diverged before the lineage that includes the
species.
2. Paraphyletic ‘beside the tribe’ Consists of an ancestral species and some
but not all of its descendants.
The tree was constructed by comparing the sequences of homologs of the gene
that play a role in development. Drosophila was used as an out group.
The branch length are proportional to the amount of genetic change in each
lineage; varying branch lengths indicate that the gene has evolved at different
rates in different lineage.
This tree is based on the same molecular data, but here the branch points are
mapped to dates based on fossils evidence. Thus, the branch lengths are
proportional to time. Each lineage has the same total length from the base of the
tree to the branch tip, indicating that all the lineages have diverged from the
common ancestor for equal amounts of time.
Classification is linked to Phylogeny
In certain similarities among organisms may lead taxonomist to place a species
within a group of organisms [genus/family] other than the group to which it is
closely related; If systematists conclude that such mistakes has occurred, the
organisms may be reclassified [that is placed in a different genus/family] to
accurately reflect its evolutionary history.
Lines of evidence that to infer evolutionary relationships
1. Fossil Evidences
2. Homologies – similar characters due to relatedness [shared ancestry];
homologies can be revealed by comparing anatomies of different living
things, looking at cellular similarities and differences, studying
embryological development, and studying vestigial structures within
individual organisms; organisms that are closely related to one another
share many anatomical similarities.
3. Biogeography – the geographic distribution of species in time and
space as influenced by many factors, including Continental Drift and log
distance dispersal
4. Molecular clocks help track evolutionary time – the base
sequences of some regions of DNA change at a rate consistent enough
to allow dating of episodes in past evolution. Other genes change in a
less predictable way.
Molecular Clock – a yardstick for measuring absolute time of evolutionary
change based on the observation that some genes and other regions of genomes
appear to evolve at constant rates.