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Phylogeny and the
Tree of Life
The Science of Biology: Part IV
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Taxonomy, Phylogeny
and Systematics
Taxonomy: the study of naming and classifying organisms.
Phylogeny: the evolutionary history of a group or a species Based on common ancestries inferred from:
• Fossil records
• Structural and biochemical similarities
• Genetic evidence
Systematics: Combines the studies of taxonomy and phylogeny to study biological diversity. Involves the reconstruction of phylogenetic history and
Cladistics 2
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Taxonomy
Taxonomy is the science of naming and classifying organisms.
Uses a hierarchical system to divide organisms into categories based on characteristics.
Developed by Carolus Linnaeus to group species in increasingly broad categories
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
• Each level is a taxa (taxon singular)
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Taxon
A group of organisms in a classification system
• Each level is included in a larger more general level
• Organisms placed into a particular group are more similar to each other than they are to organisms in other groups
12/1/2012 Averett 4
Taxon
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Eight different taxa (from general to specific)
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
12/1/2012 Averett 5
Eight Taxa
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Species “kind” in Latin
Group of interbreeding organisms that do not ordinarily breed with members of other groups.
Represented by both the genus name and the specific epithet • Homo sapiens
12/1/2012 Averett 6
According to the WWF, in 2008
scientists discovered 100 new plant
species, 28 fish, 18 reptiles, 14
amphibians, two mammals and one
bird in the Mekong River region of
Southeast Asia. Cat Ba Leopard
Gecko
Species
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Binomial
Nomenclature
Binomial nomenclature is the naming system used by all biologist around the world
A standard naming system
Gives each species a two part scientific name using Latin words
• Dead language
Developed by Carolus Linnaeus (aka Karl von Linne)
Includes the genus name and the specific epithet
Both parts together create the species’ scientific name.
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Example of Scientific
Names
Panthera pardus – leopard
Homo sapiens – human
Panthera leo – African lion
Panthera tigris – tiger
Canis familiaris – dog
Breed – domesticated variety of
an organism that is a subgroup
of a species
Armidillidium vulgare – pill bug 8
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Binomial Nomenclature
Rules
The first part of the binomial is the
genus (genera)
Always capitalized
The second part of the binomial is the
specific epithet
Refers to one species within the genus
Never capitalized
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Binomial Nomenclature
Always write both names when
naming an organism
If handwritten underline each name
part separately
if typed use italics
•Do not do both
12/1/2012 Averett 10
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Binomial Nomenclature
Used to eliminate confusion caused by
common names
Multiple informal names given to same
type of organism • Felis concolor – puma
• Felis concolor – cougar
• Felis concolor – panther
• Felis concolor – mountain lion
12/1/2012 Averett 11
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Examples
Quercus alba
Tyto alba
12/1/2012 Averett 12
Example of Scientific
Names
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Systematics and
Phylogeny
Systematics is the science of classification
It includes phylogeny and cladistics
Cladistics is classification based on
common ancestry
In general, organisms that share very similar
morphological or similar DNA sequences are
likely to be more closely related than organisms
with vastly different structures or sequences.
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Phylogenetic Trees
(Cladograms)
Phylogenetic trees called cladograms are
made to show the hierarchical classification
of taxonomic groups nested within more
inclusive groups
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Cladogram
Cladograms are evolutionary trees that
propose how species may be related to each
other through common ancestors
Each branch point represents the divergence of
two species.
• “deeper” branch points represent progressively greater
amounts of divergence
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Example Cladogram
12/1/2012 Averett 16
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Clades
A group of species that includes an ancestral
species and all its descendants is called a clade.
A clade is a group of species that shares a common
ancestor
To be a valid clade, the group needs to consist of an
ancestor species and all its descendants.
One of these is correct, two are NOT!
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Proper Clades
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Cladistics
Cladistics is a phylogenetic system of classification
used to infer and construct cladograms based on
shared and derived traits.
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Node:
- Each place where a
branch of a cladogram
splits off.
- Represents the most
common ancestor
shared by a clade.
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Cladistics and
Taxonomy
Cladistics
overlaps
with
taxonomy
12/1/2012 Averett 20
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Cladogram
Characteristics
The term “character” refers to any feature that a particular taxon possesses.
2 Types: Primitive Characters: The characteristic(s)
shared with common ancestor
Derived Characters: characteristic that appears in recent parts of a lineage, but not in older members • Traits that are shared to different degrees among species.
• Useful for determining evolutionary relationships among a group of species.
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12/1/2012
Through evolution, certain traits may change in some
species of a clade but stay the same in other species.
Therefore, in a clade each species has traits that have not
changed from its ancestry but may also have traits that have
changed over time.
Averett 22
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Shared and Derived
Characteristics
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Two groups have similar
characteristics.
Are they related?
Where do the similar characteristics
come from?
Analogy
Homology
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Homology and Analogy
A potential misconception in constructing a phylogeny is similarity due to convergent evolution, called analogy, rather than shared ancestry. It is important in phylogeny to sort HOMOLOGY
from ANALOGY.
HOMOLOGOUS structures INFER common ancestry. • “Home” Latin root means “same”
ANALOGOUS structures INFER convergent evolution by similar environmental pressures. • “alike” but not from the same “home”
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Homology
Similar in basic structure and development
Example: birds and bats – both have bones
• May or may not be similar in function
Indicates a close relationship and a
common ancestor
May end up looking different because
environmental pressures are different.
• This would be caused by adapting to different
conditions.
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Analogy
Produced by Convergent Evolution
Produced by adaptation to similar conditions.
Similar in function but not basic structure.
Example: ability to fly – birds and insects –
not closely related!
Not similar in basic structure or development.
• Birds have bones, insects do not!
Do not indicate a close relationship
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Convergent Evolution
Convergent evolution occurs when similar
environmental pressures and natural
selection produce similar (analogous)
adaptations in organisms from different
evolutionary lineages.
Analogous structures or molecular sequences
evolve independently
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Must analyze
characteristics
Do they indicate relationship.
Homologous?
Do they indicate convergent evolution.
Analogous?
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Homology vs. Analogy
Are these structures
analogous or
homologous?
12/1/2012 Averett 30
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Homology and Analogy
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Homology vs. Analogy
12/1/2012 Averett 32
Analogy: Bird and bat wings
When we examine bird wings
and bat wings closely, we see
that there are some major
differences. Bat wings consist of
flaps of skin stretched between
the bones of the fingers and
arm. Bird wings consist of
feathers extending all along the
arm. These structural
dissimilarities suggest that bird
wings and bat wings were not
inherited from a common
ancestor with wings.
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Domain Characteristics
3 Domains
12/1/2012 Averett 33
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Domains Bacteria and
Archaea
Domain Bacteria
Includes Kingdom
Eubacteria
Domain Archaea
Contains Kingdom
Archaebacteria
12/1/2012 Averett 34
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Domains Bacteria and
Archaea
Domains Bacteria and Arachaea
Prokaryotic
• No nucleus
• Have nucleoid region
• DNA molecules usually circular
• No protein associated with DNA
• No membrane-bound organelles
Three general shapes
Three general modes of movement
12/1/2012 Averett 35
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Domains Bacteria and
Archaea
12/1/2012 Averett 36
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Prokaryotic Shapes
Bacillus (pl. bacilli) rod-shaped
Coccus (pl. cocci) spherical
Spirillum (pl. spirilla)
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Prokaryotic Movement
Spiraling
Flagella (sg. Flagellum)
Gliding
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Eukaryotes
Domain Eukarya
Contains only eukaryotes
• Have nucleus
• Have membrane bound
organelles
Contains 4 kingdoms
• Kingdom Protista
• Kingdom Fungi
• Kingdom Plantae
• Kingdom Animalia 12/1/2012 Averett 39
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Kingdom Characteristics
12/1/2012 Averett 41
Eu bacteria
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Kingdom Characteristics
12/1/2012 Averett 42
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Kingdom Eubacteria
Prokaryotes
Unicellular
Cell walls contain peptidoglycan
Autotroph or heterotroph
• Photoautotrophic or chemoautotrophic
• Saprophytic – feed on dead substances
• Parasitic – obtain nutrients from living organisms
12/1/2012 Averett 43
Kingdom
Eubacteria
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Kingdom Archaebacteria
Prokaryotes
Unicellular
Cell walls do not contain peptidoglycan
Autotroph or heterotroph
• Photoautotrophic or chemoautotrophic
• Saprophytic – feed on dead substances
• Parasitic – obtain nutrients from living organisms
Live in extreme environments 12/1/2012 Averett 44
Kingdom
Archaebacteria
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Kingdom Fungi
Eukaryotic
Cell walls
• contain chitin
Unicellular or Multicellular
Heterotrophs
• Saprophytic or parasitic
Nonmotile
Yeast, mushrooms, mold
Reproduce by forming spores 12/1/2012 Averett 45
Kingdom
Fungi
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Kingdom Plantae
Eukaryotic
Cell walls with cellulose
Always multicellular
Photoautotrophs
Contain chloroplasts
Specialized tissues
Nonmotile
12/1/2012 Averett 46
Kingdom
Plantae
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Kingdom Animalia
Eukaryotic
No cell walls
Always Multicellular
Heterotrophs
Can move at some point in life cycle
12/1/2012 Averett 47
Kingdom
Animalia
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Kingdom Protista
Eukaryotes
• Fungus-like Ex: slime molds
• Plant-like Ex: algae, diatoms
• Animal-like Ex: protozoa
Unicellular, Multicellular or colonial
Photoautotroph or heterotroph
May have cell walls with cellulose
May have chloroplasts
12/1/2012 Averett 48
Kingdom
Protista
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• In kingdom Protista not because of what they have but because of what they don’t have!!! • They do not fit in any of the other eukaryotic kingdoms (Junk Drawer) •Fungus-like can move at some time
• True fungi cannot move
•Plant-like have cell walls and chloroplasts but no specialized tissues • True plants have tissues
•Animal-like can move but are single celled • True animals are multicellullar
12/1/2012 Averett 49
Kingdom Protista
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Dichotomous Keys
Dichotomous keys are tools used by
scientists to help identify already
discovered organisms or items
“Two part” key
• Each step requires you to choose between two
choices.
• Eventually leads you to the correct scientific
name of an organism
12/1/2012 Averett 50
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Dichotomous Key
1. Sex female---2
Sex male---5
2. Hair color red---Sally
Hair color not red---3
3. Hair color blonde---Julie
Hair color black---4
4. Glasses worn---Deanna
Glasses not worn---Leslie
5. Shoes high-top sneakers---Joseph
Shoes not high-tops---6
6. Hair color blonde--Michael
Hair color brown--David
12/1/2012 Averett 51
What is the name of the
male student with brown
hair wearing cowboy boots?
Imagine that you meet a
blonde male member of this
class wearing teva sandals.
Who is it?
Imagine that his girl
friend has black hair
but doesn't wear
glasses. Who is he
dating?