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Taxonomy and
Systematics

Ch. 25

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 Chapter 25

Taxonomy and Systematics

Key Concepts:
• Taxonomy
• Phylogenetic Trees
• Cladistics
• Molecular Clocks
• Horizontal Gene Transfer

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 Taxonomy
• Taxonomy
Science of describing, naming, and classifying living
and extinct organisms and viruses
• Systematics
Study of biological diversity and the evolutionary
relationships among organisms, both extinct and
modern
• Taxonomic groups are based on hypotheses regarding
evolutionary relationships derived from systematics

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 Taxonomy
• Hierarchical system involving successive levels
• Each group at any level is called a taxon
• Highest level is Domain
All of life belongs to one of 3 domains
Bacteria, Archaea, and Eukarya
• Previously kingdom was the highest (Linnaeus)

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 Table 25.1

Distinguishing Cellular and Molecular Features of 3 Domains

Characteristic Bacteria Archaea Eukarya
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Chromosomes Usually circular Circular Usually linear
Nucleosome structure No No Yes
Chromosome segregation/cell Binary fission Binary fission Mitosis/meiosis
division
Introns in genes Rarely Rarely Commonly
Ribosomes 70S 70S 80S
Initiator tRNA Formylmethionine Methionine Methionine
Operons Yes Yes No
Capping of mRNA No No Yes
RNA polymerases One Several Three
Promoters of structural genes −35 and −10 sequences TATA box TATA box

Cell compartmentalization No No Yes

Membrane lipids Ester-linked Ether-linked Ester-linked

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 A classification System for Living and
Extinct Organisms Figure 25.1

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 Taxonomic hierarchy
Supergroup between a domain and a kingdom
• 7 eukaryotic supergroups
Below domain and supergroup is Kingdom
Phyla
Class
Order
Family
Genus
Species

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 Taxonomic classification of grey wolf
Figure 25.2

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 Binomial nomenclature
• Every species has genus name and species
epithet
• Example: Homo sapiens
• Genus name always Capitalized
• Species epithet never capitalized
• Both names are italicized
• Rules for naming established and regulated by
international associations
• International Commission on Zoological Nomenclature (ICZN)
• International Code of Botanical Nomenclature (ICBN)
• International Committee on Systematics of Prokaryotes (ICSP)
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 Phylogeny
• Phylogeny – evolutionary history of a species
or group of species
• To propose a phylogeny, biologists use the
tools of systematics
• Trees are usually based on morphological or
genetic data

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 Phylogenetic trees
• Diagram that describes phylogeny
• A hypothesis of evolutionary relationships among
various species
• Based on available information
• New species can be formed by
Anagenesis – single species evolves into a different
species
Cladogenesis – a species diverges into two or more
species

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 How to read a phylogenetic tree Fig 25.3

Access the text alternative for slide images.

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 Phylogenetic trees
Branch point in a phylogenetic tree are called
nodes
• Times when cladogenesis has occurred
• Group species according to common ancestry

Clade consists of a common ancestral species

and all of its descendant species

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 Schematic relationship between phylogenetic tree and and
taxonomy Figure 25.4

Shaded areas represent taxonomic position of species 43

Which taxon has more recent common ancestor, a phylum or order?

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 Taxonomic groups are based on
evolutionary relationships
PBQL
Monophyletic group
• Taxon that is a clade
• Includes an ancestral species and all of its
descendants
Smaller and more recent clades are nested
within larger clades that have older common
ancestors

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 Taxonomic groups are based on
evolutionary relationships
Paraphyletic group
• Contains a common ancestor and some, but not
all, of its descendents
• Over time, taxonomic groups will be reorganized
so only monophyletic groups are recognized
Polyphyletic group
• Consists of members of several evolutionary lines and not
the most recent common ancestor
Reptiles were a paraphyletic group because birds
were excluded
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 Comparison of different taxonomic groups Figure 25.5

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An Example of Taxon which is not monophyletic
Figure 25.6

Reptilia

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 Homology
• Similarities among various species that occur
because they are derived from a common
ancestor
• Example: Bat wing, human arm and cat front leg
• Genes can also be homologous if they are
derived from the same ancestral gene

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 Morphological analysis
• First systematic studies focused on
morphological features of extinct and modern
species
• Many traits have to be analyzed to identify
similarities and differences
• Trees are based on morphological features
that change over many generations

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 Evolution of Modern Horse based on fossilized bones
Figure 25.7

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 Molecular systematics
• Analysis of genetic data, such as DNA and
amino acid sequences, to identify and study
genetic homologies and propose phylogenetic
trees
• DNA and amino acid sequences from closely
related species are more similar to each other
than to sequences from more distantly related
species

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 Cladistics
• Study and classification of species based on
evolutionary relationships
• Cladistic approach constructs phylogenetic
trees by considering the possible pathways of
evolutionary change
• These phylogenetic trees are called
cladograms

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 Cladistics
Cladistic approach compares homologous traits, also called
characters, which may exist in two or more character states
Shared primitive character or symplesiomorphy
• Shared by two or more different taxa and inherited from
ancestors older than their last common ancestor

Shared derived character or synapomorphy

• Shared by two or more species or taxa and has originated in
their most recent common ancestor
• Basis of the cladistic approach is to analyze many shared derived
characters to deduce the pathwaythat gave rise to those species

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 Primitive vs Derived Characters Figure 25.8

What is paraphyletic
in this context?

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 Cladogram
• Branch point – two species differ in shared
derived characters
• Ingroup – group we are interested in
understanding evolutionary relationship
• Outgroup – species or group of species that is
assumed to have diverged before the species in
the ingroup
• An outgroup will lack one or more shared derived
characters that are found in the ingroup

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 Cladogram based on shared primitive and derived characters
Figure 25.9

a) Characters among species

What is shared derieved chracter

in salmon, lizard, and rabbit?

Access the text alternative for slide images.

b) Cladogram based on morphological traits

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 Cladogram 2

• Cladogram can also be 12345678910

constructed with gene
sequences A: GATAGTACCC
• 7 species called A-G
B: GATAGTTCCC
C: GATAGTTCCG
• A mutation that changes D: GGTATTACCC
the DNA sequence is
E: GGTATAACCC
analogous to a change
of a characteristic F: GGTAGTACCA
G: GGTAGTACCC

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 Cladogram from shared genetics Figure 25.10

Access the text alternative for slide images.

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 Principle of parsimony
Preferred hypothesis is the one that is the
simplest for all the characters and their states
For example: If two species possess a tail,
assume that a tail arose once during evolution
and both species descended from a common
ancestor with a tail

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 Cooper and Colleagues Compared DNA from Extinct Flightless Birds
and Existing Species to Propose a New Phylogenetic Tree
PBQL
• Ancient DNA analysis or molecular paleontology
• Under certain conditions DNA samples may be stable as long
as 50,000 to 100,000 years
• Discovery-based science – gather data to propose a
hypothesis
• Sequences are very similar
• New Zealand colonized twice by the ancestors of flightless
birds
First by moa ancestor, then by kiwi ancestor

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 Cooper Experiment Figure 25.11

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 Revised Phylogeny of flightless birds Figure 25.12

What is surprisng with

regard to geography?

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 Molecular Clocks
• Favorable mutations are rare, detrimental mutations are
quickly eliminated – so most mutations are neutral
• If neutral mutations occur at a constant rate they can be used
to measure evolutionary time
• Not perfectly linear over long periods of time
Not all organisms evolve at the same rate
Differences in generation times

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 A Molecular Clock Figure 25.13

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