Evolution, part 2!
Lesson 1: Cladistics
The Value of Natural Classification
(Clades)
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It is easier to identify specimens as
belonging to a species, information is more
coordinated and useful
It clarifies evolutionary relationships
between similar species and allows
predictions about new members of that
group
It gives a basis for studying change in
biodiversity
Universality of DNA and proteins
 All
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living things:
Use DNA to store their hereditary information
Translate DNA info into proteins using RNA
Use the same code of 3-base codons in
translations (e.g. AUG = start)
Use the same 20 amino acids (there are many
other possible R-groups)
Use the same form of amino acids (left-handed).
(Each amino acid has a mirror form called an
entantiomer).
 Suggets
that ALL current species evolved
from ONE common ancestor with the
above features established
Clade and Cladistics
 Cladistics:
classification of organisms based on
cladograms
 Cladogram: tree-shaped diagrams (made from
combinations of clades) showing the most
probable sequence of divergence
 Clade: a group that includes all species
evolved from a common ancestor
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Node: branching point on “tree” diagrams
Any ancestor species can be chosen (recent will
usually have a smaller clade than an ancient
ancestor)
Variations in Molecules Indicate
Phylogeny, Membership in a Clade

Phylogeny: (study of)
evolutionary relationships
 DNA, RNA and protein have
inherited sequences
 There may be variety within a
species (alleles) BUT
 When a species separates,
each group may randomly
(mutation, fertilization) acquire
differences (new alleles or
combinations of alleles) NOT
seen in the other group
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Differences in DNA and protein
gradually accumulate over time
The groups with more
differences between them have
probably been separated longer
Caution because mutations are
unpredictable events
However, mutations occur with
predictable frequency
There is a positive correlation
between the number of
differences between two
species and the time since they
diverged from a common
ancestor
Pop. 1
Pop. 2
Pop. 3
Populations 2 and 3 are
more closely related to
each other than either is to
population 1
PHYLOGENETIC TREE
Of LIFE
Which are valid clades
(monophlyetic)?
Yes
Yes
No
No
1. According to the cladogram on the left,
which is more closely related, crocodiles
and lizards or crocodiles and birds?
2. According to the bottom cladogram,
what is most closely related to fungi?
(Tricky!)
3. A new species is found that lays
amniotic eggs, but does not have
feathers or make milk. What can you
predict about this creature?
1. What node joins all dinosaurs?
2. What can you determine about S. American ungulates?
3. What group has four limbs but not watertight eggs?
4. Compare the degree of relatedness between Glires,
Carnivores, Cetaceans, and Sirenians.
What are cladograms based on?
IN THE PAST:
Structural Data
 Shared features such as
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Feathers
Bones/joints
Milk
Cell wall, etc.
Trouble with ANALOGOUS v.
HOMOLOGOUS features
(analogous features look
similar due to similar
environmental pressures
instead of ancestry)
Also called morphological data
CURRENTLY:
Biochemical Data
 Similarities in sequences of
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DNA
RNA
Protein
Sophisticated analysis of
millions of base-pairs done
by computer
Trouble because based on
probability (least possible
number of changes) BUT
sometimes the improbable
DOES happen
Cladogram
of primates
Does not include all
primates. For example,
there is more than one
species of chimpanzee:
Pan troglodytes (chimp)
Pan pansicus (bonobo)
Drawing shows bias for
humans.
Which is more closely
related for an old world
monkey; a new world
monkey or a gorilla?
Explain.
Figwort
Cladogram
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Ususally structural
classifications and
cladograms agree on
ancestry – but not always!
Ex. figworts were
classified on flower and
seed structures
DNA evidence showed
that some of the figworts
were only distantly related
In similar environments
they had developed
similar-looking structures
for similar strategies
Enrichment (not needed):
Biochemical Variations can be
used as an Evolutionary Clock
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Within a category, mutations are incorporated at a
relatively constant rate:
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Fast: silent mutations, non-coding DNA
Medium: coding DNA, proteins that can be functional with
a variety of general structures
Slow: Proteins that require a very specific shape in order
to be functional
Each mutation represents a given amount of time;
thus every genetic difference is like a “tick” of the
clock. An estimate can be made about how long
species have been separate.
Lesson 2: Speciation
Gene Pool and Allele Frequency
 Gene
pool: the sum of all genes, including all
forms of each gene (alleles) found in an
interbreeding population
 Allele frequency: the commonness of an allele
as a proportion of all the alleles for a gene
rr
rr
Rr
Rr
rr
RR
rr
rr
rr
rr
GENE POOL:
Face shape
Round face (R)
Oval face (r)
Face color
Dark (D)
Light (d)
Outline color
Blue (B)
Yellow (b)
ALLELE FREQ.:
Face shape
4/20 = 0.2
16/20 = 0.8
Micro-evolution:
change in allele frequency over time

Evolution involves
the change in allele
frequency in a
population’s gene
pool over a number of
generations

Since the introduction of
birth screening, the
frequency of the PKU
allele may become more
common
Species definition
IB definition: groups of organisms that can potentially
interbreed to produce fertile offspring.
Genetic definition: organisms that share a gene pool
Morphological definition: a group with common
characteristics that separate it from other such groups.
Common definition: Organisms that can produce fertile
offspring in nature.
Others (wikipedia)
Speciation: formation of a new species
 Isolation
of gene pools by reproductive isolation
of populations. Can be due to:
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Geographic barriers
Temporal barriers
Behavioural barriers
Geographic isolation

A population enters a new territory,
becomes isolated from the original
population
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May be a non-representative, small number
of founding individuals
May have new / different selective pressures
/ mutations providing variation
Geographic Isolation of Gene Pools
Kaibab squirrel on
The north rim.
Abert’s lives on the
south rim.
Temporal Isolation of Gene Pools
 Although
in the same location, two
populations may not breed at the
same time (of day, month, season)
 Ex. The tree frog and the leopard
frog could interbreed, but one
mates in early April and the other
in late April.
 Mating in mid April is a
disadvantage due to highly active
predators.
Behavioral Isolation of Gene Pools
 Apple-maggot
flies are one species, but
parasitize two types of fruit: apple and
hawthorn
 Since the fruits ripen at different times, the
two fly groups rarely mate and are
accumulating differences; may speciate
Results of selection
Giraffe neck
Human baby size
Oyster coloration
 Disruptive
selection: can
create new species in same
geographic location
Speciation can be sudden
 Polyploidy:
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extra copies of all chromosomes
Most plants and some animals have “doubling”
events in their past
can’t interbreed with parent plants (# of
chromosomes not compatible)
 Usually
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Instant speciation!
Speciation in
Allium
 Rumex
genus (100+
species) includes the
sorrels
 Standard number of
chromosomes is 20
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R. acetosa = 20
R. obtusifolius = 40
R. crispus = 60
R. hydrolapathum = 200
20
40
60
200
The Pace of Evolution:
Gradualism v. Punctuated Equilibrium
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Slow, continual
change
 Focus on
accumulation of
helpful alleles as they
emerge
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Long periods of stasis and
burests of rapid change
 Focus on times of extreme
selective pressure (plague,
meteor impact, rapid
climate change)
Both can
occur!
Gradualism v.
Punctuated Equilib.
 This
can be interpreted
as either
 Appears to be a gradual
trend, but also no
significant difference
between 411.9 and
406.7 MYA
 Scale is important (is 2
MYA a long or short
time?)
brachiopod Eocelia
Lesson 3: Classification
Binomial Nomenclature
 Using
a unique combination of TWO names to
identify a species
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Names MUST be written with the first letter of the
first name capitalized and the entire name in italics
The first name is the “genus” and the second name
is the “species”
Second name often descriptive
• Ardea alba: great (snowy) egret
• Quercus alba: white oak
• Quercus rubra: red oak
 Agreed
on by all biologists, universal system
 Taxonimists classify species using hierarchical
taxa
Domains: The fundamental split
 From
LUCA (the last universal common
ancestor) there are three distinct lineages
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Eubacteria (bacteria)
Archaea (archaeans)
Eukaryote (eukaryotes)
• Eukaryotes are classified principally in the
Linnaean system (7 levels after domain)
Classification by Taxa (Levels)
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(Domain)
Kingdom (King)
Phylum (Philip)
Class
(Came)
Order
(Over)
Family (For)
Genus (Great)
Species (Soup)
Ex: Animal
Eukaryote
Animalia
Chordata
Mammalia
Primata
Hominidae
Homo
Homo sapiens
Plant
Eukaryote
Plantae
Angiospermae
Magnoliolipsida
Asterales
Asteraceae
Helianthus
Helianthus annuus
Natural Classification

Natural classification:
each taxon contains al
the species evolved from
a common ancestral
species
 Natural classification is
when taxa = clades
 When new evidence is
found (usually DNA),
taxonomists may
reassign species to
different taxa for the sake
of natural classification
The Five Kingdom System
Name of
kingdom
Possess
nucleus
Prokaryotae N
Eubacteria – “standard” bacteria
Archaea – extremophiles, very unique
Ex. Bacteria,
streptococcus
Protocista
Y
Ex. Algae, amoeba
Fungi
Have Autotrophy Key features
tissues
No membrane bound organelles
N
Some
N
Some
Not genetically valid group, “leftovers”
usually N
Saprotrophic (absorb nutrients),
spores for reprod., cell wall
Y
Y
Y (almost
all)
Chlorophyll for autotrophy, most
on land unlike algae (protists),
closely related,cell wall
Y
Y
N
Often motile, ingestion of
nutrients, no cell wall
Ex. Moss, tree,
flower
Animalia
Ex. Fish, bird, ant
Not closely related, usually
unicellular or colonial, need wet
or damp, some motile, diverse!
Y
Ex. Mold, yeast
Plantae
metabolically diverse, often
considered two kingdoms /
domains, most w/ cell wall
Animal phylum:
Porifera
 Sponges
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No tissues
“early” animal
Sessile
Animal phylum:
Cnidaria
 Jellyfish
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and hydra
Some sessile,
some motile, some
alternate
Stinging cells
(nematocysts)
One opening into
body cavity
Tentacles
Soft-bodied
Animal phylum: Platyhelminthes
 Flatworms
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Ex. Flukes
(parasites),
tapeworms
(parasites),
Planaria
(free-living)
One
opening to
body cavity
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Animal phylum: Mollusca
Mollusks
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Snails, slugs, clams, octopi, squid
Muscular foot (usually for motion)
Visceral mass with internal
organs
Mantle that secretes shell (may
be very obvious, reduced,
internal, or absent)
Two openings to body cavity
Animal phylum:
Annelida
 Segmented
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worms
Earthworms, leeches
Segmented bodies, may have
bristles on each segment
Animal phylum:
Arthropoda
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Arthropods
 Insects, millipedes,
centipedes, arachnids
(spiders, scorpions),
crustaceans (lobsters, crabs)
 Hard exoskeleton
 Jointed appendages
 Segmented
 Most species
Animal phylum:
Chordata
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Chordates (including
vertebrates)
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Fish, sharks, tunicates,
reptiles, amphibians,
birds, mammals, turtles,
etc.
Internal bones and/or
cartilage
(Some) Major Animal Phyla
Phylum
Porifera
Cnidaria
Platyhelminths
Mollusca
Annelida
Arthropoda
Chordata
Common
name /
examples
Sponge
Jellyfish,
hydra,
corals
Flatworms,
Tapeworm,
planaria, fluke
Clam,
snail,
slug,
squid,
octopus,
Segmented
worms,
earthworm,
leech
Insects, spiders,
milli- and
centipedes,
crustaceanslobster, crab,
Mammals,
Reptiles,
Amphibians
, Fish, Birds
Symmetry none
radial
bilateral
bilateral
bilateral
bilateral
bilateral
Segments No
No
No
No/
Yes
Not visible
Yes
No / not
visible
Mouth
No
Yes
Yes
Yes
Yes
Yes
Yes
Anus
No
No
No
Yes
Yes
Yes
Yes
Other
Totipotent
cells,
filter
feeders,
sharp or
spongy
“skeleton”
immobile
Stinging
cells,
tentacles
to capture
prey, softbodied
Free-living planaria have
eyespots,
parasitic- with
suckers and / or
hooks, up to
20m
Muscular
foot
(move),
soft body,
mantle to
secrete
shell
Closed
circulation,
may have
bristles,
Hard
exoskeleton,
joints in
appendages,
huge variety,
million+ species
Dorsal
nerve cord,
backbone if
vertebrate,
pharyngeal
gill slits,
post-anal
tail
Chordates
NOT NEEDED FOR IB (but interesting!):
Can anyone think of a kind of animal not
included in the previous phyla?
This is the closest relative to chordates – the
other major deuterostome phylum!*
Chordates have:
• A dorsal nerve cord
• As an embryo, a
notochord (supports
nerve cord)
If animals have a complete digestive tract, they
make two openings during embryonic
development. One becomes the mouth, the
other becomes the anus. In deuterostomes the
second opening become the mouth (as opposed
to protostomes).
Fish
Amphibians
Reptiles
Birds
Mammals
Chordate Summary
Fish –
Amphibians
Reptiles
Birds
Mammals
Osteichthyes*
Skin
Scales
Moist,
permeable
Dry, scaly
(impermeable)
Feathers
Hairs / fun
Lungs /
Gills
Gills
Lungs (less
folding)
Lungs (more
folding)
Lungs
(parabronchi)
unidirectional
air flow
Lungs
(alveoli)
Fertilization Usually
external
Usually
external
Usually internal
Internal
Internal
Offspring
Egg with
(generally) moist
membrane
Egg with gel
and moist
membrane
Egg with
leathery or soft
shell
Egg with hard Birth live
shell
young
Locomotion Fins with
bony rays*
Pentdactyl –
leg in adult
Pentadactyl- leg Pentadactyl – Pentadactyl
– diverse
front limb
wing
Other
Aquatic as
larva, varied
adult
Generalized
teeth
Aquatic
Beak
Specialized
teeth, milk
Plants: Bryophyta
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Mosses, liverworts,
hornworts
 Small (up to 0.5 m, usually
smaller)
 No vascular tissue
 No true roots or leaves
 Spores
 Moist areas (sperm must
swim to egg)
Diploid
Haploid
Plants: Filicinophtya
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Ferns
“seedless vascular”,
spores (in sori on frond
back)
Moderate height, 15m
Heart shaped phase;
dominant frond phase
Plants:
Coniferophyta
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Conifers, evergreens, pines
Narrow or needle-like
leaves
Cones with seeds (no fruit)
Can be large (up to 100m)
Pollen (no flowers)
Plants: Angiospermatophyta

Flowering plants, up to
100 m
 Seeds in fruits
 Pollen in flowers (can be
very reduced or absent)
Plant Diversity
Type
Bryophytes
Filicinophytes
Coniferophytes
Angiospermatophytes
Common term
Mosses
Ferns
Conifers
Flowering plants
Roots
No* (rhizoid)
Yes* (rhizome)
Yes
Yes
Vascular
(veins)
No
Yes
Yes
Yes
Pollen
No
No
Yes
Yes
Reproduction
Spores
Spores
Seeds
Seeds
Flowers / fruit
No
No
No
Yes
~Max. height
0.5 m
15 m
100 m
100m
Likely to be
woody
No
No
Yes
Sometimes
Other
Needs
moisture,
spores from
capsule on
stalk, green
parts haploid
Heart-shaped
part haploid,
furled fronds
with leaflets on
either side,
spores in sori
Thick cuticle,
narrow leaves,
produce cones
with pollen
(male) and
seeds (fert.
female)
Flowers may attract
pollinators, seeds form
in or on fruit
What determines classification
levels?
 There
is no set rule, but the more specific the
level, the more the species have in common

Which trees would have more in common: those in
the same genus or those in the same class?
 Based
on similarities in DNA, fossil history,
etc.
 Before DNA sequencing, classification was
based more on similarities in structure,
adaptations, appearance
Dichotomous Keys
 Allow
a specimen to be identified using a
series of yes-or-no questions.
 One question may lead to another
question or the identification.
1. Has more than 5 petals
YES… go to #2
NO … go to #3
2. Yellow petals around a large center
YES… sunflower
NO … rose
3. Petal edges show an indentation
YES… dogwood
NO … go to #4
4. Grows on a tree
YES… plumeria
NO … buttercup
Dichotomous key practice
 Identify

this plant tree using this site:
http://www.for.msu.edu/extension/ExtDocs/Identkey/opening.htm
A
site to categorize major insect types:
http://www.projects.ex.ac.uk/bugclub/bugid.html
 Classroom practice!!