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Chapter 19Taxonomy, Systematics,

and Phylogeny Lecture Outline

BiologySylvia S. Mader

Michael Windelspecht

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Outline

• 19.1 Systematic Biology• 19.2 The Three-Domain System• 19.3 Phylogeny

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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.

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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.

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Carolus Linnaeus

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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

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The Classification System

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DOMAIN Eukarya

Kingdom Animalia

PHYLUM Chordata

CLASS AmphibiaCLASS Mammalia

GENUS Mus

GENUS Rana

ORDER

ORDER ORDER

FAMILY

FAMILYFAMILYFAMILY

FAMILY

ORDER AnuraORDER Rodentia

FAMILY Muridae

SPECIES

SPECIES

Rana catesbeianaNorth America bullfrog

Mus musculushouse mouse

FAMILY Ranidae

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 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.

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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

13common ancestor

ARCHAEABACTERIA

EUKARYA

animals

fungi

plants

cyanobacteria

protists protists

heterotrophicbacteria

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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 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.

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The Relationships Among Phylogeny, Classification, and Traits

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3

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Phylogeny

Common ancestors

artiodactyl commonancestor

mammal commonancestor

primate commonancestor

apes

deer

monkeys

cattle

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 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.

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Constructing a Cladogram: The Data

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chim

pan

zee

do

g

fin

ch

cro

cod

ile

liza

rd

fro

g

tun

a

lan

cele

t (o

utg

rou

p)

Species

Tra

its

mammary glands

gizzard

epidermal scales

amniotic egg

four limbs

vertebrae

hair

ingroup

notochord inembryo

Constructing a Cladogram: The Phylogenetic Tree

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vertebrae

four limbs

feathers

gizzard

hair, mammary glands

long canine teeth

enlarged brain

chimpanzee

tuna

frog

lizard

crocodile

finch

terrier

lancelet (outgroup)

common ancestor

epidermalscales

Amnioticegg

commonancestor

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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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© David Dilcher and Ge Sun

pairedstamens

fruits

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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

PRESENT

white-handedgibbon

rhesusmonkey

greenmonkey

capuchinmonkey

102030405060Million years ago (MYA)

Increased difference in DNA

commonchimpanzee