CHAPTER 26

TAXONOMY
AND SYSTEMATICS

Prepared by
Brenda Leady, University of Toledo

1 reprod
Copyright (c) The McGraw-Hill Companies, Inc. Permission required for
Taxonomy and systematics
 Taxonomy
 Field of biology concerned with the theory,
practice, and rules of 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 now based on
hypotheses regarding evolutionary
relationships derived from systematics
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Taxonomy
 Hierarchical system involving successive
levels
 Each group called a taxon
 Domain
 Highest level
 All of life belongs to one of 3 domains
 Bacteria, Archaea, and Eukarya

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Binomial nomenclature
 Genus name and species epithet
 Genus name always capitalized
 Species epithet never capitalized
 Both names either italicized or underlined
 Rules for naming established and
regulated by international associations

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Domains similar but different
 Scientists think all life originated from
primordial prokaryotic cells between 4.0
and 3.5 bya
 Soon after, 2 prokaryotic domains,
Bacteria and Archaea, diverged
 2.5-2.0 bya first unicellular eukaryotic
species
 Multicellular eukaryotes arose about 1.5
bya 7
Similarities
 DNA is used as the genetic material
 All species use the same genetic code (with only
a few rare codon exceptions)
 Messenger RNA encodes the information to
produce proteins
 Transfer RNA and ribosomes are needed to
synthesize proteins, using mRNA as a source of
genetic information
 All living cells are surrounded by a plasma
membrane
 Certain metabolic pathways, such as glycolysis,
are found in all three domains 8
 These traits are universal because all 3
domains evolved from a common ancestor
 Dissimilarities exist because major
evolutionary changes have occurred since
the time that the three domains diverged

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 Domain Bacteria
 Diverse collection of many species
 So widespread only generalizations about
their ecology
 Key to success is metabolic diversity
 Come in a myriad of shapes and sizes
 Domain Archaea
 Less diverse than Bacteria
 Discovered in 1970s
 Many found in extreme environments
 Most are extreme halophiles, methanogens or
hyperthermophiles
 Not entirely restricted to extreme
environments 11
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Domain Eukarya
 4 traditional kingdoms
 Protista
 Fungi
 Plantae
 Animalia

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Kingdom Protista
 Simplest eukaryotes
 Most unicellular but some are colonial or
simple multicellular
 Some photosynthesize while others eat
bacterial or other protists
 Most live in aquatic habitats
 Leftover organisms not put in other 3
kingdoms
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Kingdom Fungi
 Yeasts, molds, mushrooms
 Present worldwide in aquatic and
terrestrial environments
 Many symbiotic with plants
 Cell walls contain chitin
 Most multicellular
 Mass of hyphae combine to make
mycelium
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Kingdom Plantae
 Multicellular
 Almost all capable of photosynthesis
 Mosses, ferns, conifers, flowering plants
 Cell wall made primarily of cellulose

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Kingdom Animalia
 Multicellular and eat others for food
 More than 1 million species
 Sponges, worms, insects, mollusks, fish, amphibians,
birds, reptiles, mammals
 Most ingest food and digest it in an internal
cavity
 Bodies composed of cells organized into tissues
(except sponges)
 Capable of complex and rapid movement
 Nervous system
 Lack a rigid cell wall
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Systematics
 Phylogeny – evolutionary history of a
species or group of species
 Gather morphological or molecular data
 Use mathematical strategies to analyze
data
 Construct evolutionary trees
 Molecular data has caused many revisions

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Phylogenetic tree
 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 2 or
more species
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 Monophyletic group or clade
 Group of species, taxon, consisting of the
most recent common ancestor and all of its
ancestors
 Smaller and more recent clades are
subsets of larger clades
 For larger taxa, common ancestor existed
a long time ago (kingdom)
 For smaller taxa, common ancestor more
recent (family or genus)
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Homology
 Similarities among various species that
occur because they are derived from a
common ancestor
 Bat wing, human arm and cat front leg
 Genes can also be homologous

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Morphological analysis
 First systematic studies focused on
morphological features of extinct and
modern species
 Convergent evolution (traits arise
independently due to adaptations to
similar environments) can cause problems

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Molecular systematics/clocks
 Analyzing genetic data to identify and
study genetic homology and reconstruct
phylogenetic trees
 DNA sequences from closely related
species are more similar to each other
than to sequences from more distantly
related species

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Molecular clock
 Favorable mutations rare and detrimental
mutations eliminated
 Most mutations are neutral
 If neutral mutations occur at a constant rate they
can be used to measure evolutionary time
 Longer periods of time since divergence allows
for a greater accumulation of mutations
 Not perfectly linear
 Not all organisms evolve at the same rate
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Primate evolution example
 Evolutionary relationships derived by comparing
DNA sequences in a mitochondrial gene
 3 branch points to examine (A,D, E)
 A- common ancestor diverges into siamangs
and other species
 Gene in siamangs more different than the gene in the
other 7 species
 Humans and siamangs have more differences
than humans and chimpanzees because there
has been more time for them to accumulate
differences
 2 chimp species diverged recently and have very
similar gene sequences 34
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Cladistic approach
 Reconstructs phylogenetic tree by
considering various possible pathways of
evolution and then proposing plausible
tree
 Phylogenetic trees or cladograms
 Compares traits shared or not shared
 Shared trait – shared primitive character or
symplesiomorphy
 Not shared – shared derived character or
synapomorphy
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 Branch point – 2 species differ in shared
derived characters
 Ingroup – monophyletic group we are
interested in
 Outgroup – species or group of species
that is most closely related to an ingroup
 All traits shared by the outgroup and the
ingroup must have arisen in a common
ancestor that predates the divergence of
the 2 groups
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 Cladogram can also
be constructed with
gene sequences
 7 species called A- G
 A mutation that
changes the DNA
sequence is
analogous to a
modification of a
characteristic

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Constructing a cladogram
1. Choose species
2. Choose characters
3. Determine order of character states
 primitive or derived?
4. Group species (or higher taxa) based on
shared derived characteristics

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1. Build a cladogram based on
 All species (or higher taxa) are placed on tips in the
phylogenetic tree, not at branch points
 Each cladogram branch point should have a list of
one or more shared derived characters that are
common to all species above the branch point unless
the character is later modified
 All shared derived characters appear together only
once in a cladogram unless they arose independently
during evolution more than once
2. Choose the most likely cladogram among
possible options

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Strategies for a likely cladogram
 Challenge in a cladistic approach is to determine the
correct order of events
 May not always be obvious which traits are ancestral
and came earlier, and which are derived and came later
in evolution
 Different approaches can be used to deduce the correct
order
 Analyze fossils and determine the relative dates that certain
traits arose
 Assume that the best hypothesis is the one that requires the
fewest number of evolutionary changes (principle of parsimony)
 Maximum likelihood and Bayesian analysis for gene sequence
data

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Example
 4 taxa (A-D)
 A is the outgroup
 Has all the primitive
states
 3 potential trees
 Tree 3 requires
fewest number of
mutations so is the
most parsimonous
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Cooper and Colleagues Extracted DNA from Extinct
Flightless Birds and Then Compared It with DNA from
Modern Species to Reconstruct Their Phylogeny

 Ancient DNA analysis or molecular

paleontology
 Under certain conditions DNA samples may
be stable as long as 50,000 – 100,000
years
 Discovery based sciences- 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
 Ideal goal of taxonomy to place organisms in
monophyletic groups

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 Many recent models propose several major
groups, supergroups, as a way to organize
eukaryotes into monophyletic groups
 Shows that protists played a key role in the
evolution of diverse eukaryote species

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Due to Horizontal Gene Transfer, the
Tree of Life Is Really a “Web of Life”
 Vertical evolution involves changes in species due
to descent from a common ancestor
 Horizontal gene transfer is the transfer of genes
between different species
 Significant role in phylogeny of all living species
 Still prevalent among prokaryotes but less common
in eukaryotes
 Horizontal gene transfer may have been so
prevalent that the universal ancestor may have
been a community of cell lineages