1. Biology Sylvia S. Mader Michael Windelspecht
Chapter 19
Taxonomy, Systematics, and Phylogeny
Lecture Outline
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2. Biology, 9th ed,Sylvia Mader
Chapter 20
Outline
Classification of Living Things
19.1 Systematic Biology
19.2 The Three-Domain System
19.3 Phylogeny

3. Biology, 9th ed,Sylvia Mader
19.1 Systematic Biology
Chapter 20
Classification of Living Things
Taxonomy is the branch of biology that identifies, names, and organizes biodiversity into related categories.
A natural system of classification reflects the evolutionary history of organisms.
Naming and identifying organisms began with the Greeks and Romans.
Aristotle classified organisms into groups such as horses, birds, and oaks.
In the Middle Ages, organisms were described using Latin names.

4. Classifying Organisms
Biology, 9th ed,Sylvia Mader
Classifying Organisms
Chapter 20
Classification of Living Things
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© Sylvia S. Mader

5. Biology, 9th ed,Sylvia Mader
Chapter 20
Systematic Biology
Classification of Living Things
In the mid-eighteenth century, Carolus Linnaeus developed the system of binomial nomenclature.
First word is the genus name.
Second word is the specific epithet.
It refers to one species (of potentially many) within its genus.
Example: Lilium bulbiferum and Lilium canadense are different species of lily.
A species is referred to by the full binomial name (Genus species).
Genus name can be used alone to refer to a group of related species.

6. Biology, 9th ed,Sylvia Mader
Chapter 20
Carolus Linnaeus
Classification of Living Things

7. Biology, 9th ed,Sylvia Mader
Chapter 20
Systematic Biology
Classification of Living Things
Modern taxonomists use the following classification:
Species
Genus – one or more species
Family – one or more genera
Order – one or more families
Class – one or more orders
Phylum – one or more classes
Kingdom – one or more phyla
Domain – one or more kingdoms

8. The Classification System
Biology, 9th ed,Sylvia Mader
The Classification System
Chapter 20
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
DOMAIN Eukarya
Kingdom Animalia
PHYLUM Chordata
CLASS Mammalia
CLASS Amphibia
ORDER Rodentia
ORDER
ORDER
ORDER Anura
GENUS Mus
FAMILY Muridae
FAMILY
FAMILY
FAMILY Ranidae
ORDER
SPECIES
FAMILY
FAMILY
FAMILY
Mus musculus
house mouse
GENUS Rana
SPECIES
Rana catesbeiana
North America bullfrog

9. Biology, 9th ed,Sylvia Mader
Chapter 20
Systematic Biology
Classification of Living Things
The higher the category, the more inclusive it is.
Organisms in the same domain have general characteristics in common.
Members of a species share very specific characteristics.
The species is the most exclusive of categories since it contains only a single type of organism.
The task of creating standardized rules of nomenclature is difficult and has, most recently, been aided by the process of DNA barcoding.
It compares a short fragment of DNA sequence from an unknown organism to a large database of sequences from known organisms.

10. Biology, 9th ed,Sylvia Mader
Chapter 20
DNA Bar Coding of Life
Classification of Living Things
Traditionally, taxonomists relied on anatomical data.
Consortium for the Barcode of Life (CBOL) proposes that all scientists will be able to identify a species with the flick of a handheld scanner.
Like the 11-digit Universal Product Code (UPC) used in a supermarket,
DNA is the UPC of organisms on Earth
A DNA–bar-coding device would provide a fast and inexpensive way to catalog organisms.
DNA bar coding has been criticized as being too simplistic but it is a powerful way to catalogue a portion of the world’s biodiversity.

11. Biology, 9th ed,Sylvia Mader
Chapter 20
19.2 Three-Domain System
Classification of Living Things
The research of scientist Carl Woese, comparing the nucleotide sequences of rRNA of prokaryotes and eukaryotes, suggests that all organisms evolved along three distinct lineages:
Domain Bacteria
Prokaryotic unicellular organisms that reproduce asexually.
Cyanobacteria are photosynthetic.
Most are heterotrophic.
Important in ecosystems; keep chemical cycling going.
Parasitic bacteria cause disease.
Domain Archaea
Live in extreme environments
Cell wall is diverse but different from bacterial cell wall.
Bacteria and archaea differ in rRNA nucleotide sequences.

12. Biology, 9th ed,Sylvia Mader
Chapter 20
Three-Domain System
Classification of Living Things
Domain Eukarya
Unicellular and multicellular organisms
Cells with a membrane-bounded nucleus
Sexual reproduction common
Contains four kingdoms
Kingdom Protista
Kingdom Fungi
Kingdom Plantae
Kingdom Animalia
There has been considerable recent debate over the classification of protists; they are presently placed in six supergroups within the domain Eukarya.

13. Tree of Life Showing the Three Domains
Biology, 9th ed,Sylvia Mader
Tree of Life Showing the Three Domains
Chapter 20
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
fungi
animals
plants
EUKARYA
protists
protists
heterotrophic
bacteria
cyanobacteria
BACTERIA
ARCHAEA
common ancestor

14. Major Distinctions Among the Three Domains of Life
Biology, 9th ed,Sylvia Mader
Chapter 20
Major Distinctions Among the Three Domains of Life
Classification of Living Things

15. Biology, 9th ed,Sylvia Mader
Chapter 20
19.3 Phylogeny
Classification of Living Things
Systematic biology is a quantitative science that compares traits of living and fossil organisms to infer relationships over time.
Characters from the fossil record, comparative anatomy and development, and the sequence, structure, and function of RNA and DNA molecules are used to construct a phylogeny.
A phylogeny is the evolutionary history of a group.
Phylogeny is often represented as a phylogenetic tree.
A diagram indicating lines of descent
Each branching point:
Is a divergence from a common ancestor
Represents an organism that gives rise to two or more new groups

16. Biology, 9th ed,Sylvia Mader
Phylogeny
Chapter 20
Classification of Living Things
Classification lists the unique characters of each taxon and is intended to reflect phylogeny.
Ancestral traits:
Present in all members of a group, and
Present in the common ancestor
Are not useful for determining the evolutionary relationships of an ancestor’s descendents
Derived traits:
Present in some members of a group, but absent in the common ancestor
Are the most important traits for clarifying evolutionary relationships
An opposable thumb, not present in the common ancestor of all mammals, is an ancestral trait of primates.

17. The Relationships Among Phylogeny, Classification, and Traits
Biology, 9th ed,Sylvia Mader
The Relationships Among Phylogeny, Classification, and Traits
Chapter 20
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Phylogeny
Common ancestors
deer 1
artiodactyl common ancestor 2
cattle
mammal common ancestor
monkeys 3
primate common ancestor 4
apes

18. The Relationships Among Phylogeny, Classification, and Traits
Biology, 9th ed,Sylvia Mader
Chapter 20
Slide #18
Classification of Living Things 18

19. The Relationships Among Phylogeny, Classification, and Traits
Biology, 9th ed,Sylvia Mader
Chapter 20
Slide #19
Classification of Living Things 19

20. Biology, 9th ed,Sylvia Mader
Chapter 20
Phylogeny
Classification of Living Things
Cladistics is method that uses shared, derived traits to develop a hypothesis of evolutionary history.
This evolutionary history of derived traits is interpreted into a type of phylogeny called a cladogram.
A cladogram is a special type of phylogenetic tree.
A clade is an evolutionary branch that includes:
A common ancestor, together with
All its descendent species
It traces the evolutionary history of the group being studied.
A cladogram is a working hypothesis.
It may change when new traits are discovered and incorporated into the cladogram.
Cladistics is a hypothesis-based, quantitative science subject to testing.

21. Biology, 9th ed,Sylvia Mader
Chapter 20
Phylogeny
Classification of Living Things
Cladists are guided by the principle of parsimony—the minimum number of assumptions is most logical.
The best cladogram is one in which the fewest number of shared derived characters are left unexplained or that minimizes the number of assumed evolutionary changes.
Reliability of cladograms is dependent on the knowledge and skill of an investigator.

22. Constructing a Cladogram: The Data
Biology, 9th ed,Sylvia Mader
Chapter 20
Constructing a Cladogram: The Data
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Species
ingroup
lancelet (outgroup)
chimpanzee
crocodile
dog
finch
lizard
frog
tuna
mammary glands
hair
gizzard
epidermal scales
Traits
amniotic egg
four limbs
vertebrae
notochord in
embryo

23. Constructing a Cladogram: The Phylogenetic Tree
Biology, 9th ed,Sylvia Mader
Chapter 20
Constructing a Cladogram: The Phylogenetic Tree
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
enlarged brain
common ancestor
hair, mammary glands
chimpanzee
Amniotic
egg
long canine teeth
terrier
feathers
gizzard
finch
four limbs
crocodile
epidermal
scales
lizard
vertebrae
frog
common
ancestor
tuna
lancelet (outgroup)

24. Biology, 9th ed,Sylvia Mader
Chapter 20
Phylogeny
Classification of Living Things
Tracing Phylogeny
Fossil Traits
Fossil record is incomplete.
It is often difficult to determine the phylogeny of a fossil.
Homology
It refers to structures that stem from a common ancestor.
Homologous structures are related to each other through common descent.
Forelimbs of vertebrates contain the same bones organized as they were in a common ancestor.
Analogy
The similarity is due to convergent evolution.
Analogous structures have the same function in different groups but do not have a common ancestry.
Structures look similar due to adaptation to similar environments.
Wings of insects and bats are analogous.

25. Biology, 9th ed,Sylvia Mader
Chapter 20
Ancestral Angiosperm
Classification of Living Things
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fruits
paired stamens
© David Dilcher and Ge Sun

26. Biology, 9th ed,Sylvia Mader
Chapter 20
Phylogeny
Classification of Living Things
Tracing Phylogeny
Behavioral Traits
Parental care, mating calls, etc.
Molecular Traits
Systematics assumes:
Two species with similar base-pair sequences are assumed to be closely related.
Two species with differing base-pair sequences are assumed to be only distantly related.

27. DNA Sequence Alignment
Biology, 9th ed,Sylvia Mader
Chapter 20
DNA Sequence Alignment
Classification of Living Things

28. Biology, 9th ed,Sylvia Mader
Chapter 20
Phylogeny
Classification of Living Things
Tracing phylogeny through molecular traits
Protein Comparisons
Immunological techniques
The degree of cross reaction is used to judge relationship.
Amino acid sequencing
Similar sequence in the same protein indicates a close relationship.
Molecular Clock
Use neutral (non-adaptive) nucleotide sequences
Assumes a constant rate of mutation over time
Researchers doing comparative mtDNA sequencing used their data as a molecular clock
They equated a 5.1% nucleic acid difference among songbird species to 2.5 MYA.

29. A Phylogeny Determined from Molecular Data
Biology, 9th ed,Sylvia Mader
Chapter 20
A Phylogeny Determined from Molecular Data
Classification of Living Things
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
human
common
chimpanzee
white-handed
gibbon
rhesus
monkey
green
monkey
capuchin
monkey 60 50 40 30 20 10
PRESENT
Million years ago (MYA)
Increased difference in DNA