Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 19
Taxonomy, Systematics,
and Phylogeny
Lecture Outline
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Outline
19.1 Systematic Biology
19.2 The Three-Domain System
19.3 Phylogeny

19.1 Systematic Biology

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.

Classifying Organisms
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Sylvia S. Mader

Systematic Biology
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.

Carolus Linnaeus

Systematic Biology
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

The Classification System

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DOMAIN Eukarya
Kingdom Animalia
PHYLUM Chordata
CLASS Mammalia
GENUS Mus

SPECIES
Mus musculus
house mouse

CLASS Amphibia

ORDER Rodentia

ORDER

ORDER

ORDER Anura

FAMILY Muridae

FAMILY

FAMILY

FAMILY Ranidae

FAMILY

ORDER
FAMILY

FAMILY

GENUS Rana

SPECIES
Rana catesbeiana
North America bullfrog

Systematic Biology
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.
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DNA Bar Coding of Life

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 DNAbar-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 worlds biodiversity.
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19.2 Three-Domain System

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

Prokaryotic unicellular organisms that reproduce asexually.

Live in extreme environments
Cell wall is diverse but different from bacterial cell wall.
Bacteria and archaea differ in rRNA nucleotide sequences.

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Three-Domain System
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.
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Tree of Life Showing the Three Domains

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fungi
animals
plants

EUKARYA

protists

protists

heterotrophic
bacteria
cyanobacteria

BACTERIA

ARCHAEA

common ancestor

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Major Distinctions Among the

Three Domains of Life

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19.3 Phylogeny
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

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Phylogeny
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
ancestors 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.

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The Relationships Among

Phylogeny, Classification, and Traits
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Phylogeny
Common ancestors

deer
artiodactyl common
ancestor

2
cattle

mammal common
ancestor

monkeys
3

primate common
ancestor

4
apes

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The Relationships Among

Phylogeny, Classification, and Traits

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The Relationships Among

Phylogeny, Classification, and Traits

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Phylogeny

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.

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Phylogeny
Cladists are guided by the principle of
parsimonythe 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.
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Constructing a Cladogram:
The Data
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tuna

frog

lizard

crocodile

finch

dog

chimpanzee

ingroup

lancelet (outgroup)

Species

mammary glands

hair

gizzard

Traits

epidermal scales

amniotic egg

four limbs

vertebrae
notochord in
embryo

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Constructing a Cladogram:
The Phylogenetic Tree
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enlarged brain

common ancestor

hair, mammary glands

Amniotic
egg

chimpanzee

long canine teeth

terrier
feathers

gizzard

four limbs

finch

crocodile
epidermal
scales

lizard

vertebrae

frog
common
ancestor

tuna

lancelet (outgroup)

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Phylogeny
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.
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Ancestral Angiosperm
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fruits

paired
stamens

David Dilcher and Ge Sun

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Phylogeny
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.

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DNA Sequence Alignment

Phylogeny
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.
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A Phylogeny Determined from

Molecular Data
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human

common
chimpanzee

white-handed
gibbon

rhesus
monkey

green
monkey

capuchin
monkey

60

50
40
30
20
Million years ago (MYA)

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Increased difference in DNA

PRESENT

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