Systematics: An

Overview
Lecturer: E.M. Hortillosa
Biodiversity

•  Biological Scientists estimate that less than 10% of

bacteria,10% of fungi, 2% of nematodes, and 20% of insect
species have been identified

•  The variety of living organisms and the ecosystems they are

part of are referred to as biological diversity (biodiversity)

•  Unfortunately, human activity is seriously reducing

biodiversity, and species are becoming extinct faster than
researchers can study them
Classifying Organisms

•  Systematics
•  Scientific study of the diversity of organisms and their
evolutionary relationships

•  Taxonomy
•  Science of naming, describing, and classifying organisms

•  Classification
•  Arranging organisms into groups based on similarities that
reflect evolutionary relationships among lineages
The Binomial System

•  Carolus Linnaeus simplified scientific classification by

developing a binomial system of nomenclature in which
each species is assigned a unique two-part name

•  The first part designates the genus

•  The second part (specific epithet) designates the species

•  Example: Homo sapiens (human)

Taxonomic Levels

•  A taxon is a formal grouping of organisms at any given level

•  Linnaeus’ system assigns each species to a hierarchy of

increasingly broader groups (taxa)

Species > Genus > Family > Order >

Class > Phylum > Kingdom > Domain
Categories Used in Classification
DOMAIN
Eukarya

KINGDOM
Animalia

PHYLUM
Chordata

CLASS
Mammalia

ORDER
Carnivora

FAMILY
Felidae

GENUS
Felis

SPECIES 8
Stepped Art
Felis catus
Fig. 23-1, p. 484
DOMAIN
Eukarya

KINGDOM
Animalia

PHYLUM
Chordata

CLASS
Mammalia

ORDER
Carnivora

FAMILY
Felidae

GENUS
Felis

SPECIES 9
Felis catus
Fig. 23-1, p. 484
Classification of Corn

Table 23-1, p. 483

KEY CONCEPTS

•  Traditionally, biologists have named organisms using a

binomial system (in which each species has a genus name
followed by a specific epithet) and have classified organisms
in taxonomic categories arranged in a hierarchy from most
inclusive (domain) to least inclusive (species)
History of Systematics

•  From the time of Aristotle to the mid-19th century, biologists

divided organisms into two kingdoms: Plantae and Animalia

•  In 1866 Ernst Haeckel proposed that a third kingdom,

Protista, be established for bacteria and other
microorganisms
History of Systematics (cont.)

•  1969: R. H. Whittaker proposed a five-kingdom classification

based on cell structure and mode of nutrition

•  Kingdom Fungi was established for mushrooms, molds, and

yeasts

•  Kingdom Prokaryotae was established for bacteria

History of Systematics (cont.)

•  1970s: Carl Woese showed that there are two fundamentally

different groups of prokaryotes, so prokaryotes were divided
into two groups: Bacteria and Archaea

•  Today, many biologists have also abandoned kingdom

Protista (as well as a kingdom classification for plants and
animals) and now assign the eukaryotes to five
“supergroups” based on molecular data
KEY POINT: The Three Domains

•  Biologists now
classify organisms
in three domains:
Archaea, Bacteria,
and Eukarya
(eukaryotes)
Domain Domain Domain
Bacteria Archaea Eukarya

Common ancestor of
all living organisms 16
Fig. 23-2, p. 485
Domains and Kingdoms

Table 23-2, p. 486

Moving Away From
Linnaean Categories

•  Many systematists argue that Linnaean categories are limiting

and do not fit well with recent findings

•  Some systematists prefer classifying organisms into clades

classify them in one of the three domains

•  clade
•  A group of organisms that share characters
(characteristics) inherited from a common ancestor
PhyloCode

•  Some biologists use PhyloCode, in which organisms are

grouped into clades based on evolutionary relationships

•  A species is defined as a segment of a population lineage,

and taxonomic ranks are not required
Cladograms
•  Phylogenetic trees graphically represent hypothesized
evolutionary relationships
•  A cladogram is a type of phylogenetic tree in which each
branch represents a clade, a group of organisms with a
common ancestor
•  Each branching point (node) represents the divergence of two
or more new groups from a common ancestor
Cladograms (cont.)

•  Each branch of a cladogram represents one or more

characteristics shared by the clade, but not found in the
ancestors of the clade

•  The node at the base of the cladogram (root) represents the

most recent common ancestor of all clades in the tree

•  Cladograms depict evolutionary relationships of each group,

but not when a particular species evolved
The Tree of Life
 Proteobacteria
Cyanobacteria

Gram-positives
Chlamydias

Spirochetes
Domain Bacteria

Actinobacteria
Euryarchaeota

Crenarchaeota
Domain
Archaea

Excavates
Chromalveolates

Rhizarians

Red algae
Green algae

Land plants
Archaeplastids

Most recent common

Domain Eukarya

Fungi
ancestor of all living things

Choanoflagellates
Unikonts

23

Animals
Fig. 23-3, p. 487
Other Hypotheses

•  When we think of how organisms acquire their genes, we

think of vertical gene transfer in which genes are transmitted
from parent to offspring within the same species

•  Genes can also move from one species to another species in

the same generation – gene swapping between organisms in
one taxon and unrelated organisms in another taxon is called
horizontal gene transfer, or lateral gene transfer
Horizontal Gene Transfer

•  Horizontal gene transfer can occur by exchange of DNA

among different populations or species of bacteria, or by
interbreeding between closely related groups

•  In eukaryotes, horizontal gene transfer has occurred by

endosymbiosis – one organism living inside the cell of another

•  Some systematists argue that the common ancestor of all

living things may have been a community of species that
traded genes (ring of life)
Three-Domain Approach with
Horizontal Gene Transfer
 Bacteria Eukarya Archaea

Crenarchaeota
Euryarchaeota
Animalia
Cyanobacteria
Proteobacteria

(a) The three-domain approach drawn to show horizontal

gene transfer as a continuous process between domains
and also among groups within each domain. Only some
of the branches are labeled. The diagonal brown arrow
represents mitochondrial endosymbiosis; the diagonal 27
green arrow represents chloroplast endosymbiosis. Fig. 23-4a, p. 488
Ring of Life Approach
 Protists Plants Fungi Animals

First eukaryote

Bacteria Archaea

(b) The ring of life is based on the hypothesis that lateral

gene transfer between bacteria and archaea gave rise to 29
the eukaryotes. Fig. 23-4b, p. 488
KEY CONCEPTS

•  Based on current knowledge, the three main branches of the

tree of life are the three domains: Bacteria, Archaea, and
Eukarya
Phylogeny

•  Modern taxonomy reconstructs phylogeny – the evolutionary

history of a group of organisms from a common ancestor

•  Phylogenies help us understand evolutionary patterns, and to

predict characteristics of new species

•  Evolutionary relationships among species depend on the

degree of genetic divergence since their populations
branched from a common ancestor
Homologous Structures

•  Identifying homologous traits (structures derived from a

recent common ancestor) is important in inferring phylogeny

•  Not all similar traits are homologous – similar structures

sometimes evolve when unrelated species adapt to similar
environmental conditions (convergent evolution)

•  For example, bones in bat wings, dog paws, and human

hands are homologous – butterfly wings are not homologous
Homologous Structures (cont.)

•  Another challenge in identifying homology is reversal, in

which a trait reverts to its ancestral state (removes a similarity
that had evolved)

•  A characteristic that appears homologous but is acquired by

convergent evolution or reversal is said to exhibit homoplasy
Shared Ancestral Characters

•  Determining which traits indicate evolutionary relationships is

extremely important

•  shared ancestral characters (plesiomorphies)

•  Features that were present in an ancestral species and
remain present in all groups descended from that ancestor
•  Characteristics found in the largest group (such as phylum
or class) of organisms being studied, indicating the most
remote common ancestry
•  Example: Vertebral column in the subphylum Vertebrata
Shared Derived Characters

•  Systematists use shared derived characters to identify points

where groups diverged from one another

•  shared derived characters (synapomorphies)

•  Novel traits that evolve when two populations become
separated and begin to evolve independently
•  Characters that originate in a recent common ancestor
and are present in its descendants

•  Species that share derived characters form a clade

Choosing Taxonomic Criteria

•  A trait viewed as a derived character in a more inclusive

(broader) taxon may also be considered an ancestral
character in a less inclusive (narrower) taxon

•  Example:
•  Dolphins share important homologous derived characters
(synapomorphies) with humans (class Mammalia)
•  Dolphins and humans share ancestral characters
(plesiomorphies) with fish (phylum Chordata)
Choosing Taxonomic Criteria

•  Determining which traits best illustrate evolutionary

relationships can be challenging

•  Organisms are typically classified on the basis of a

combination of traits rather than on any single trait

•  Example:
•  The duck-billed platypus has many characteristics of birds:
beaks, absence of teeth, egg laying, and endothermy
Is this animal a bird?

Fig. 23-5, p. 490

Molecular Markers

•  Variations in structure of specific macromolecules, like

differences in anatomical structure, result from mutations

•  All living things can be identified by unique sequences of DNA

or RNA, like a genetic marker or barcode

•  This method can be used to distinguish among species that

look alike, for example, two species of African elephants
Molecular Homologies

•  The science of molecular systematics focuses on molecular

structure to clarify evolutionary relationships

•  Macromolecules that are functionally similar in two different

types of organisms are considered homologous if their subunit
sequence is similar

•  The more subunit sequences of two species correspond, the

more closely related the species are considered to be
Molecular Clocks

•  Macromolecules in which molecular changes occur at a

steady rate can be used as molecular clocks

•  The number of differences in certain DNA or RNA nucleotide

sequences or in amino acid sequences in two groups of
organisms may reflect how much time has passed since the
groups branched from a common ancestor
Examples of Molecular Systematics

•  Ribosomal RNAs have been extensively used to determine

evolutionary relationships among bacteria

•  Ribosomal RNA analysis also suggests that fungi are more

closely related to animals than to plants

•  Comparisons of nucleotide sequences in gene exons and

introns was used to produce a cladogram for canids
Molecular Phylogeny
 Side-striped jackal
(Canis adustus)

Black-backed jackal
(Canis mesomelas)

Golden jackal
(Canis aureus)
Dog
(Canis lupus familiaris)

Gray wolf
(Canis lupus)

Coyote
(Canis latrans)

Ethiopian wolf
(Canis simensis)

Dhole
(Cuon alpinus)

African wild dog

44

(Lycaon pictus)
Fig. 23-6, p. 491
Evolutionary Relationships

•  Cladograms show three types of taxonomic relationships:

monophyletic, paraphyletic, and polyphyletic

•  monophyletic group (clade)

•  Includes an ancestral species and all its descendants
•  Defined by shared derived characters
•  Sister taxa share the most recent common ancestor on a
cladogram
Evolutionary Relationships (cont.)

•  paraphyletic group
•  Contains a common ancestor and some, but not all, of its
descendants
•  Share ancestral characters

•  polyphyletic group
•  Consists of several evolutionary lines that do not share the
same recent common ancestor
•  Unnatural grouping that misrepresent evolutionary
relationships
KEY POINT: Evolutionary Relationships
 Group II

Group I

1 2 3 4 5 6

Common
C ancestor E
of groups
2 and 3
D Common
ancestor of
groups 4, 5,
and 6
B
Common
A ancestor of
all groups
shown

(a) Group I and group II are monophyletic groups, or

clades. Each includes a common ancestor and all its 48
descendants. Fig. 23-7a, p. 492
 Group III

1 2 3 4 5 6

C
E

Common
D ancestor of
groups 4, 5,
and 6
B

(b) Group III is paraphyletic. It includes some, but not all of

the descendants of the recent common ancestor indicated at
node D. 49
Fig. 23-7b, p. 492
 Group IV

1 2 3 4 5 6

Most recent
common ancestor of E
C
groups 2 and 3
Most recent
D common
ancestor of
groups 4, 5,
and 6
B

(c) Group IV is polyphyletic. Members of this group do not

50
share the same recent common ancestor.
Fig. 23-7c, p. 492
KEY CONCEPTS

•  Modern systematics seeks to reconstruct phylogeny

(evolutionary history of a group of species) based on common
ancestry inferred from shared characters (characteristics),
including structural, developmental, behavioral, and molecular
similarities, as well as from fossil evidence
Approaches to Systematics

•  Phenetic approach (numerical taxonomy)

•  Based on the number of shared characters
•  Does not distinguish between shared ancestral characters
and shared derived characters
•  Currently used with molecular data

•  Example: Species are placed at relative distances from one

another based on the number of differences in amino acid
sequence
Approaches to Systematics (cont.)

•  Cladistics (Phylogenetic Systematics)

•  Based on recent common ancestry (shared derived
characters that can be structural, behavioral, physiological,
or molecular)
•  Expressed in cladograms

•  Example: Crocodiles, dinosaurs, and birds constitute a

monophyletic group, or clade
Approaches to Systematics (cont.)

•  evolutionary systematic approach

•  Uses phenotypic similarity and a combination of shared
ancestral characters and shared derived characters to
establish evolutionary relationships and classifications
•  Recognizes both monophyletic and paraphyletic taxa

•  Example: Recognizes the class Reptilia (snakes, lizards,

crocodiles, dinosaurs, and turtles) as a valid group even
though is paraphyletic and does not include birds
Two Approaches to Classification
 REPTILES

Lizards, snakes

Flying reptiles

Ornithischian

Saurischian
Crocodiles,

dinosaurs

dinosaurs
alligators

Mammals
Tuataras

(extinct)

(extinct)

(extinct)
Turtles

Birds
C
G
F
(a) Cladists classify birds and reptiles E
together because they have a recent
common ancestor and are a monophyletic D
group. The cladogram shows the
branching points in the evolution of the
major groups of reptiles. Lizards, snakes,
and crocodiles are phenotypically most B
similar, but crocodiles, dinosaurs, and
birds are most closely related because A
they evolved most recently from a
common ancestor (node D). Node F
represents the branching of two clades of Most recent
dinosaurs from a common ancestor, and common ancestor 56
the subsequent branching of birds from
the dinosaurs.
of all groups shown Fig. 23-8a, p. 494
 REPTILES

Lizards, snakes

Flying reptiles

Saurischian
Crocodiles,

dinosaurs
alligators

Mammals
Tuataras

(extinct)

(extinct)

(extinct)
Turtles

Birds
C
G
F
(b) Evolutionary E
systematists recognize D
the common ancestry
of birds and reptiles,
but assign them to
B
different classes
because of their many A
unique adaptations. In
this approach, reptiles Most recent
are a paraphyletic common ancestor 57
group. of all groups shown
Fig. 23-8b, p. 494
Outgroup Analysis

•  Outgroup analysis is used to estimate which attributes are

shared derived characters in a given group of organisms

•  An outgroup is a taxon considered to have branched off

earlier than the taxa under investigation, the ingroups

•  An ideal outgroup is the closest relative of the group being

studied, its sister taxon
Constructing a Cladogram

•  Character states (present or absent) are organized into their

correct evolutionary order using outgroup analysis

•  The root, or base, of the cladogram represents the common

ancestor for all taxa being analyzed

•  To form a valid monophyletic group, all members must share

at least one derived character

•  The branching process continues, using all the characters,

until all clades are established
Constructing a Cladogram
 CHARACTERS
A = Absent

(backbones)

Opposable
Mammary
Vertebrae

Amniotic
Tetrapod
P = Present

(4 limbs)

thumb
glands

posture
Upright
Jaws

egg
TAXA

Lancelet (outgroup) A A A A A A A

Lamprey P A A A A A A

Sunfish P P A A A A A

Frog P P P A A A A

Lizard P P P P A A A

Bear P P P P P A A

Chimpanzee P P P P P P A

Human P P P P P P P
61
Fig. 23-9 (top), p. 495
Jaws
Absent Present

Chimpanzee
Lamprey
Lancelet

Sunfish

Human
Lizard

Bear
Frog
Common jawed
Node
B vertebrate ancestor
Node
Node C
A
Common vertebrate
ancestor
Common chordate
ancestor

(a) All of the seven vertebrate taxa shown here have jaws,
except the lamprey. Jaws are a shared derived character for 62
these six taxa. Fig. 23-9a, p. 495
 Tetrapod limbs
Absent Present

Chimpanzee
Lamprey
Lancelet

Sunfish

Human
Lizard
Frog

Bear
Node Common tetrapod
(b) Tetrapod limbs
C
are a shared derived Node ancestor
character for all B Common jawed
vertebrate taxa Node vertebrate ancestor
shown here except A
Common vertebrate
the lamprey and ancestor
sunfish.
Common chordate
ancestor 63
2 Fig. 23-9b, p. 495
 Amniotic egg
Absent Present

Chimpanzee
Lamprey
Lancelet

Sunfish

Human
Lizard
Frog

Bear
Node Common amniote
D
ancestor
Node
C Common tetrapod
Node ancestor
B Common jawed
Node
(c) The taxa vertebrate ancestor
A
represented by lizard, Common vertebrate
bear, chimpanzee, and ancestor
human are amniotes.
Common chordate
They share the derived
ancestor 64
character amniotic egg.
Fig. 23-9c, p. 495
Opposable thumb
Absent Present

Chimpanzee
Lamprey
Lancelet

Sunfish

Human
Lizard

Bear
Frog
Node
G
Node
F Common primate
Node ancestor
E Common mammal
Node ancestor
D
(d) Of the vertebrate Node Common amniote ancestor
taxa shown here, C Common tetrapod ancestor
only the chimpanzee Node
and human share the B Common jawed vertebrate
Node ancestor
derived character A
opposable thumb. Common vertebrate ancestor

Common chordate
ancestor 65
Fig. 23-9d, p. 495
Constructing a cladogram

66
Branch Points

•  As you trace the tree from root to tips, each branch reflects
the addition of one or more shared derived characters

•  The order of divergence (branching) is indicated by relative

distance from the base of the diagram

•  Relationships are determined by tracing along branches back

to the most recent common ancestor

•  The ancestor itself remains unspecified

Cladogram Styles
 69
Fig. 23-10a, p. 496
Opposable thumb
Absent Present

Chimpanzee
Lamprey
Lancelet

Sunfish

Human
Lizard
Frog

Bear
Node
G
Node Common primate ancestor
F
Node
E Common mammal ancestor
Node
D Common amniote ancestor
Node
C Common tetrapod ancestor
Node
B Common jawed vertebrate ancestor
Node
A
Common vertebrate ancestor

Common chordate
ancestor

(a) This cladogram, the style used in this book,

has diagonal branches. 70
Fig. 23-10a, p. 496
 71
Fig. 23-10b, p. 496
 Opposable thumb
Absent Present Absent

Chimpanzee

Lamprey
Lancelet

Sunfish

Human
Lizard

Frog
Bear
Node Node
G F
Node
E
Node
D
Node
C
Node
B
Node
A

Common chordate
ancestor

(b) This is another way to depict the same 72

relationship shown in (a). Fig. 23-10b, p. 496
 73
Fig. 23-10c, p. 496
 Opposable thumb
Lancelet
(outgroup)
Common
chordate Lamprey
ancestor

Sunfish
Vertebrae

Absent
Frog
Jaws
Lizard
Tetrapod

Bear
Amniotic egg

Present
Chimpanzee
Mammary glands
(c) This cladogram has Opposable thumb
rectangular branches and is Human
rotated 90 degrees. However, it Upright posture
illustrates the same relationships 74
as the cladograms in (a) and (b). Fig. 23-10c, p. 496
Principles of Parsimony

•  When choosing between multiple, competing cladograms, the

most common criterion is the principle of parsimony – the
simplest explanation to interpret the data

•  Parsimony requires that the cladogram with the fewest

changes in characters (the one with the fewest homoplasies)
be accepted as most probable
Using the Principle of Parsimony
 Amphibians

Terrestrial
mammals
Dolphins

Reptiles
Jawless

Sharks
fishes

fishes
Bony
A A
B B
C C

(a) Hypothesis 1:
Dolphins and bony
fishes are close
relatives. Common
ancestor 77
Fig. 23-11a, p. 497
 Amphibians

Terrestrial
mammals

Dolphins
Reptiles
Jawless

Sharks
fishes

fishes
Bony
A
B
C

(b) Hypothesis 2:
Dolphins and
terrestrial mammals
Common are close relatives.
ancestor 78
Fig. 23-11b, p. 497
Maximum Likelihood

•  maximum likelihood
•  A statistical method used to make decisions, especially
when analyzing molecular data
•  Complex computer programs analyze large data sets and
report the probability of a particular tree

•  Example: The probability that nucleotide sequences in DNA

and RNA change at a constant rate over time
KEY CONCEPTS

•  Cladograms (a type of phylogenetic tree) are diagrams of

hypothetical evolutionary relationships; they are constructed
by analyzing shared derived characters