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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
2
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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4
5
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
6
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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10
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
12
Domain Eukarya
4 traditional kingdoms
Protista
Fungi
Plantae
Animalia
13
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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
15
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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
21
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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
23
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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27
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
28
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
29
30
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
31
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
32
33
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
35
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
36
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
37
38
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
39
40
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
41
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
42
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
43
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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45
Cooper and Colleagues Extracted DNA from Extinct
Flightless Birds and Then Compared It with DNA from
Modern Species to Reconstruct Their Phylogeny
49
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
50
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