SYSTEMA

(Fundamentals of Systematics)
Summer Term 2022
MEETING 1

Introduction
Systematics & Taxonomy
[Classification, Nomenclature]
 Taxonomy & Systematics
Taxonomy
 Science dealing with the
description, classification,
identification and
nomenclature of extinct and
extant organisms and
viruses
Systematics
 Science dealing with the
“taxonomy” of biological
diversity and the
determination of their
phylogenetic or evolutionary
relationships
 Taxonomy + biodiversity +
phylogenetic relationships
Taxonomy
 In the 18th century, Carolus Linnaeus (1707-1778) published a
system of taxonomy based on resemblances (=morphological
similarity)
Carolus Linnaeus (Carl von Linne) - Father of Modern
Taxonomy

Two key features of his system remain useful today:

1. binomial nomenclature)
(Linnaeus, Species Plantarum, 1753)
2. hierarchical classification (7 taxa / categories)
(Linnaeus, Systema Naturae, 1735)
Binomial Nomenclature
 The two-part scientific name of a species is called a binomial
▪ First part of the name = genus
▪ Second part = specific epithet [unique for each species within the genus]

 The proper way of writing the scientific name :

 First letter of genus always CAPITALIZED
 Specific epithet always in lower case
 Must be underlined when handwritten; italicized when typewritten
 Include author of the name
 Example: Corn: Zea mays Linnaeus or Zea mays Linn. or Zea mays L.
 Both parts together name the species (not the specific epithet alone)
 Uses Latin or Latinized words
 Rules for naming established and regulated by international
organizations of taxonomists
 INTERNATIONAL CODES OF NOMENCLATURE
1. International Code of Nomenclature of Prokaryotes (ICNP, 2019)

2. International Code of Nomenclature for Algae, Fungi, and Plants

(ICN) (=Shenzhen Code, 2017)

3. International Code of Zoological Nomenclature (ICZN) (2012)

4. The International Code of Virus Classification and Nomenclature
(ICTV 2018)
5. International Code of Nomenclature for Cultivated Plants (ICNCP,
2016)

Winston J. 2018. Twenty-First Century Biological Nomenclature—The Enduring Power of

Names. https://academic.oup.com/icb/article/58/6/1122/5064904?rss=1
 International Code of Nomenclature for algae, fungi, and plants
(ICN) (=Shenzhen Code, 2017)
 The nomenclature of algae, fungi, and plants is independent of
zoological and prokaryotic nomenclature. This Code applies equally to names of
taxonomic groups treated as algae, fungi, or plants, whether or not these groups were
originally so treated (see Pre. 8).
 The application of names of taxonomic groups is determined by means of
nomenclatural types.
 The nomenclature of a taxonomic group is based upon priority of publication.
 Each taxonomic group with a particular circumscription, position, and rank can bear
only one correct name, the earliest that is in accordance with the rules, except in specified cases.
 Scientific names of taxonomic groups are treated as Latin regardless of their
derivation.
 The rules of nomenclature are retroactive unless expressly limited.

https://www.iapt-taxon.org/nomen/main.php
 International Code of Zoological Nomenclature
(ICZN) (2012)

 Article 1. Definition and scope

 1.1. Definition
Zoological nomenclature is the system of scientific
names applied to taxonomic units (taxa; singular: taxon) of
extant or extinct animals.
 1.1.1. For the purposes of this Code the term "animals" refers
to the Metazoa and also to protistan taxa when workers
treat them as animals for the purposes of nomenclature (see
also Article 2).

https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/
 International Code of Nomenclature of Prokaryotes
(ICNP) (2019)
This Code of Nomenclature of Prokaryotes applies to all Prokaryotes.
The nomenclature of eukaryotic microbial groups is provided for by other
Codes:
fungi and algae by the International Code of Nomenclature for algae, fungi and plants;
protozoa by the International Code of Zoological Nomenclature.
The nomenclature of viruses is provided for by the International Code of Virus
Classification and Nomenclature.

 “Prokaryotes” covers those organisms that are variously recognized as

e.g. Schizomycetes, Bacteria, Eubacteria, Archaebacteria, Archaeobacteria,
Archaea, Schizophycetes, Cyanophyceae and Cyanobacteria.
https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000778
The International Code of Virus Classification and
Nomenclature (ICTV 2018)
 Scope of the classification
 3.3 The ICTV is not responsible for classification and nomenclature of virus
taxa below the rank of species. The classification and naming of serotypes,
genotypes, strains, variants and isolates of virus species is the responsibility
of acknowledged international specialist groups.
 3.4 Artificially created viruses and laboratory hybrid viruses will not be
given taxonomic consideration. Their classification will be the responsibility
of acknowledged international specialist groups.
 3.5 Taxa will be established only when representative member viruses are
sufficiently well characterized and described in the published literature so
as to allow them to be identified unambiguously and the taxon to be
distinguished from other similar taxa.

https://talk.ictvonline.org/information/w/ictv-information/383/ictv-code
 Hierarchical Species: Zea mays

classification
Panthera pardus

Genus: Zea
Panthera

Family:
Carl Linnaeus - (1735) Felidae Poaceae

- 7 taxa (taxon, sing.) / ranks / Order:

Poales
Carnivora
categories = K,P,C,O,F,G,S
Class:
Mammalia Liliopsida
Carl Woese - Domain (1990)
Phylum:
Magnoliophyta
Chordata

Domain: Kingdom:
Plantae
Bacteria Animalia
Domain:
Archaea
Domain: Eukarya
Eukarya
Linking Classification and Phylogeny

▪ Phylogeny - the evolutionary history of

a species or group of organisms

▪ The evolutionary history of a group of

organisms can be shown in a branching
phylogenetic tree (=cladogram).
Figure 26.4
Order Family Genus Species

Panthera
Felidae
Panthera
pardus
(leopard)

Taxidea
Carnivora
Taxidea

Mustelidae
taxus
(American
badger)

Lutra
Lutra lutra
(European
1 otter)

Canis
latrans
Canidae

Canis (coyote)
2

Canis
lupus
(gray wolf)
© 2014 Pearson Education, Inc.
Linnaean classification and phylogeny can differ from
each other
Linnaean Class Aves and Class Reptilia
Phylogeny indicates birds as a subgroup of reptiles

Systematists have proposed a classification system

that would recognize only groups that include a
common ancestor and all its descendants
 Figure 26.5

Branch point:
How to read a phylogenetic tree.
where lineages diverge Taxon A

3
Taxon B
Sister
4 taxa
Taxon C
2
Taxon D

5 Taxon E
ANCESTRAL 1
LINEAGE Taxon F
Basal
Taxon G
taxon
This branch point This branch point forms
represents the a polytomy: an
common ancestor of unresolved pattern of
taxa A–G. divergence.
© 2014 Pearson Education, Inc.
Phylogenetic trees
 A phylogenetic tree represents a hypothesis about evolutionary
relationships
 Each branch point represents the divergence of two species
 Tree branches can be rotated around a branch point without
changing the evolutionary relationships
 Sister taxa are groups that share an immediate common ancestor
 A rooted tree includes a branch to represent the last common
ancestor of all taxa in the tree
 A basal taxon diverges early in the history of a group and originates
near the common ancestor of the group
 A polytomy is a branch from which more than two groups emerge
More Terms to know!

Pre-existing feature?
Plesiomorphy (ancestral feature)
Symplesiomorphy (shared ancestral feature)

New feature?
Apomorphy (derived feature)
Synapomorphy (shared derived feature)
How do systematists infer phylogeny?
 Systematists gather morphological and molecular data (genes and
biochemistry) of living organisms and analyze fossil records.

 They seek morphological and molecular homologies

 Phenotypic and genetic similarities due to shared ancestry are called
homologies
 Organisms with similar morphologies or DNA sequences are likely to be more
closely related than organisms with different structures or sequences
 Is the similarity a result of homology or analogy?
 Homology is similarity due to shared ancestry
 Analogy is similarity due to convergent evolution
Morphological homologies

• Homologies are similarities due to common ancestry

• E.g. arms, forelegs, wings and flippers of mammals
• Carpels and leaves in flowering plants
Convergence - Stem succulence and “spines” in
Cactaceae and Euphorbia spp.

Convergent evolution occurs when similar environmental

pressures and natural selection produce similar
(analogous) adaptations in organisms from different
evolutionary lineages.
 Primary tenet of phylogenetic systematics?

Taxa (OperationalTaxonomic Units) can be grouped by apomorphies

because these represent unique evolutionary events.

Recency of common ancestry?

Premise: All forms of life share a common ancestor.

Taxa which share a common ancestor more recent in time are more
closely related to one another than they are to a taxon whose
common ancestor is further back in time.
Is C most closely related to D or to F?
Is C most closely related to E or to B?

Is C most closely related to A or to B?

Molecular homologies
 DNA and RNA sequences of nucleic acids

 Each change in a nucleic acid = one evolutionary event!

• The more events, the more distantly related are the species.
• Fewer events means that a species is more closely related

• Systematists use computer programs and mathematical tools

when analyzing comparable DNA segments from different
organisms
 Cell
1 CCATCA GAGT CC
division
2 CCATCA GAG T CC
error

Deletion
1 CCA T CAGAG T CC
2 CCA T CAGAG T CC
G T A Insertion

1 CCA T CAAGT CC
2 CCA TGTA CAG AGT CC

1 CCAT CA AG T CC
2 CCA TGTA CAG AGT CC
© 2014 Pearson Education, Inc.
A phylogenetic tree is also called a cladogram.

➢ Each branch in the tree is called a clade.

➢ A clade is a group of species that includes a

common ancestor and all its descendants.

• The analysis of how species may be grouped

into clades is called cladistics.
(Willi Hennig, Phylogenetic Systematics, 1966)
 Types of CLADES OR GROUPINGS

1. Monophyletic clade consists

of a common ancestor and
all its descendants.
– “single tribe”
– Only monophyletic groups
qualify as legitimate taxa
derived from cladistics.
Clades or groupings

2. Paraphyletic clade
consists of an ancestor
and some but not all of
the descendants.
➢ does not meet the cladistic
criterion
 Clades or groupings

3. Polyphyletic clade
consists of various species
with different ancestors;
lacks a common ancestor

➢ Fails the cladistic test

Types of clades
 Paraphyletic group
Common
ancestor of
even-toed Other even-toed
ungulates ungulates

Examples of a Hippopotamuses
paraphyletic
and a
Cetaceans
polyphyletic
group.
Seals

Bears

Other
carnivores
Polyphyletic group
© 2014 Pearson Education, Inc.
 Constructing cladograms

1. Identify homologies → shared characteristics derived

from one ancestor.
2. When constructing a cladogram, the greater the number
of homologous parts between two organisms, the more
closely related they are.
3. The classification scheme must reflect these similarities.
These similarities can either be :
a. Shared primitive characters, i.e. homologous
characters that are shared by more than one
taxon, e.g. backbone is shared by mammals
and reptiles.
b. Shared derived characters, i.e. an
evolutionary novelty that is unique for a
particular clade.
• The more derived characters that a species
has, the more evolutionarily unique it is.
STEPS TO CONSTRUCT A CLADOGRAM:

1. Select your species for which you want to make a

cladogram. These are called the ingroup. They have
shared primitive and derived characters.
2. Select an outgroup → a species that is closely related to the
species under study, the outgroup has a shared primitive
character that is common to all species.
3. Construct a character table and tabulate the data. → The
more shared characters, the more closely related are the
species.
4. Construct a cladogram based on the number of shared
characters.
Building a Cladogram
 Characters

TAXON VASCULAR TISSUES SEEDS FLOWERS

Moss A A A

Fern P A A

Pine P P A

Daisy P P P

Fig. 18-7 (1), p. 358

 Daisy
Moss

Fern

Pine
Common ancestor
with vascular tissues
Node
1

Common plant
ancestor

(a) All of the plant groups shown here except mosses

have vascular
Fig. 18-7a, p. 358
 Daisy
Moss

Fern

Pine
Node
2

Common ancestor
Node with vascular tissues
1

Common plant
ancestor

(b) Seeds are a shared character for all plant groups

shown here except mosses and ferns.
Fig. 18-7b, p. 358
 Daisy
Moss

Fern

Pine
Node
3

Common
seed-
Node
producing
2
ancestor
Common ancestor
Node with vascular tissues
1

Common plant
ancestor

(c) Of the plant groups shown here, only the daisy

produces flowers.
Fig. 18-7c, p. 358
Classification Schemes
1. Classical /Artificial – based on few observable characters e.g.
Linnaeus Sexual System and Theophrastus form system of plant
classification

2. Phenetics / Natural – Constructs phenograms based on overall

similarity, largely phenotypic, without regard to evolutionary history; all
characters are given equal weights
• Sneath and Sokal Numerical Taxonomy (1973)

3. Cladistics – constructs cladograms anchored on assumed

phylogenetic relationships
• Willi Hennig Phylogenetic Systematics (1966)
 Plant Classification Systems

287 BC
systems
Phylogenetic
Dawning of
Phylogenetic
classifications
Phylogenetic classifications
• Charles Bessey (1845-1915)
– Proposed the Phylogenetic
Taxonomy of Flowering Plants
– Based classification on 28
guiding dicta to determine level
of being simple/complex,
primitive/advanced
The cactus-tree
of Charles
Bessey (1915)

Ranales most primitive; Asteridae most derived

His ideas are greatly influential for twentieth century evolutionary thought…
Development of Plant Classification System

• Premolecular • Molecular • Postmolecular

classification classifications classifications
• Artificial • Phylogenetic • Phylogenetic based
• Natural on a wide array of
• Phylogenetic characters including
the molecular and
micromorphological
level (based on the
Angiosperm
Phylogeny Group
[APG])
 Classification of Living Organisms
2 - Kingdom 3- kingdom 4-kingdom 5-kingdom 6-kingdom 3-Domain
system system system system system system
(Linnaeus, (Haeckel, (Copeland, (Whittaker, (Woese, 1977) (Woese,
1735) 1866) 1938) 1969) 1990)
Vegetabilia Protista Monera Monera Eubacteria Bacteria
Animalia Plantae Protista Protista Archaebacteria Archaea
Animalia Plantae Fungi Protista Eukarya
Animalia Plantae Fungi
Animalia Plantae
Animalia
Classification of Life: The Five-Kingdom System
(R. Whittaker & L. Margulis 1969)
Classification of Life: The Three-Domain System (Woese, 1990)

Microbiologist Carl Woese

 Table 4. Classification of Life: The Three-Domain/ Eight Kingdom System
(Campbell, 1996)

Domain Bacteria
Kingdom Eubacteria
Domain Archaea
Kingdom Archaebacteria
Domain Eukarya
Kingdom Archezoa: the Archaeamoebae, Metamonada, and Microsporidia.
Kingdom Protista: the Kinetoplastida, Actinopoda, Alveolata, Choano-
flagellates and Opalozoans, and Mycetozoa.
Kingdom Chromista: the diatoms, brown and golden-brown algae, and the
water molds (oomycetes)
Kingdom Fungi: the molds, yeasts and fungi, excepting the water molds
Kingdom Plantae: the red algae, green algae, and land plants.
Kingdom Animalia: invertebrates and vertebrates
Table 5. Classification of Life: The Two-Empire/Eight-Kingdom System
(Mayr 1997)

Empire Prokaryota (Monera)

Kingdom Eubacteria
Kingdom Archaebacteria
Empire Eukaryota
Kingdom Archezoa
Kingdom Protozoa
Kingdom Chromista
Kingdom Metaphyta (plants)
Kingdom Fungi
Kingdom Metazoa (animals)
 Six-Kingdom Classification
(Woese, 1977)

• Kingdom Eubacteria (domain Bacteria)

• Kingdom Archaebacteria (domain Archaea)
• Kingdom Protista (domain Eukarya)
• Kingdom Fungi (domain Eukarya)
• Kingdom Plantae (domain Eukarya)
• Kingdom Animalia (domain Eukarya)
Thank you for your attention!