Cooper and colleagues extracted DNA from extinct flightless birds and modern species to propose a new phylogenetic tree. They found that DNA sequences were very similar, suggesting New Zealand was colonized twice by ancestors of flightless birds - first by moa ancestors, then by kiwi ancestors. This discovery was based on gathering genetic data to propose a new hypothesis about evolutionary relationships, showing how ancient DNA analysis can provide insight into phylogenetic relationships.

1. CHAPTER 26
LECTURE
SLIDES
Prepared by
Brenda Leady
University of Toledo
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2. Taxonomy and systematics
 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 now based on
hypotheses regarding evolutionary
relationships derived from systematics
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3. Taxonomy
 Hierarchical system involving successive
levels
 Each group at any level is called a taxon
 Domain
 Highest level
 All of life belongs to one of 3 domains
 Bacteria, Archaea, and Eukarya
3

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Domains: Bacteria Archaea Eukarya
Eukaryotic Excavata Land plants and algal relatives Alveolata Stramenopila Rhizaria Amoebozoa Opisthokonta
supergroups:
Large eukaryotic Plantae Fungi Animalia
kingdoms:
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Taxonomic Gray wolf Number of
group found in species
Domain Eukarya ~ 4– 10 million
Supergroup Opisthokonta >1 million
Kingdom Animalia >1 million
Phylum Chordata ~50,000
Class Mammalia ~5,000
Order Carnivora ~270
Family Canidae 34
Genus Canis 7
Species lupus 1
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6. 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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7. Phylogenetic trees
 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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8. 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
8

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Present F I G J H K
B E
Millions of years ago (mya)
5
C
Time
D
B
10
A
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10. 10

11.  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
nested within larger clades that have older
common ancestors
 Paraphyletic group
 Contains a common ancestor and some, but
not all, of its descendents
11

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H I J K L M N O H I J K L M N O H I J K L M N O
D E F G D E F G D E F G
B C B C B C
A A A
(a) Monophyletic (b) Paraphyletic (c) Polyphyletic
12

13.  Over time, taxonomic
groups will be
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KEY
reorganized so only Orders
Classes
monophyletic groups
and snakes
and snakes
Crocodiles
Crocodiles
are recognized
Lizards
Lizards
Turtles
Turtles
Birds
Birds
 Reptiles were a
paraphyletic groups
because birds were
excluded Reptiles
(a) Reptiles as a (b) Reptiles as a
Reptiles
paraphyletic taxon monophyletic taxon
13

14. 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 if they are
derived from the same ancestral gene
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15. 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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16. 16

17. 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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18. Cladistics
 Study and classification of species based on
evolutionary relationships
 Cladistic approach discriminates among
possible phylogenetic trees by considering the
various possible pathways of evolutionary
changes and then choosing the tree that
requires the least complex explanation for all of
the available data
 Phylogenetic trees or cladograms
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19.  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
19

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D E F G
B C
A
20

21.  Branch point – 2 species differ in shared
derived characters
 Ingroup – group we are interested in
 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
21

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Lancelet Lamprey Salmon Lizard Rabbit
Notochord Yes Yes Yes Yes Yes
Vertebrae No Yes Yes Yes Yes
Hinged jaw No No Yes Yes Yes
Tetrapod No No No Yes Yes
Mammary No No No No Yes
glands
(a) Characteristics among species
Lancelet Lamprey Salmon Lizard Rabbit
Mammary
glands
Tetrapod
Hinged jaw
Vertebrae
Notochord
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(b) Cladogram based on morphological traits

23.  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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24. 24

25. Constructing a cladogram
1. Choose species
2. Choose characters
3. Determine polarity of character states
 Primitive or derived?
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26. 4. Analyze 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
4. Choose the most likely cladogram among
possible options
5. Choose a noncontroversial outgroup as root
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27. Principle of parsimony
 Preferred hypothesis is the one that is the
simplest for all the characters and their states
 Challenge in a cladistic approach is to determine
the correct polarity of events
 Itmay not always be obvious which traits are primitive
and came earlier and which are derived and came
later in evolution
 Fossils may be analyzed
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28. 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
28

29. According to the principle
of parsimony, tree
number 3 is the
more likely choice
because it requires only
five mutations. 29

30. Molecular clocks
 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 over long periods of time
 Not all organisms evolve at the same rate
 Differences in generations times
30

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Nucleotide
differences in
a homologous
gene between
different pairs
of species
0
Evolutionary time since divergence of pairs of species
31
(millions of years)

32. Primate evolution example
 Evolutionary relationships derived by comparing
DNA sequences for cytochrome oxidase subunit
II
 Tends to change fairly rapidly on an evolutionary
timescale
 3 branch points to examine (A, D, E)
 Ancestor A
 Thisancestor diverged into two species that ultimately
gave rise to siamangs and the other five species
 23 million years for siamang genome to accumulate
changes different from other 5 species
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33.  Ancestor D
 This ancestor diverged into two species that
eventually gave rise to humans and chimpanzees
 Differences in gene sequences between humans and
chimpanzees are relatively moderate
 Ancestor E
 This ancestor diverged into two species of
chimpanzees
 Two modern species of chimpanzees have fewer
differences in their gene sequences
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34. 34

35. Cooper and Colleagues Extracted DNA from Extinct
Flightless Birds and Modern Species to Propose a New
Phylogenetic Tree
 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

38. Horizontal gene transfer
 Any process in which an organism
incorporates genetic material from another
organism without being the offspring of
that organism
 Vertical evolution
 Changes
in groups due to descent from a
common ancestor
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39. 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

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Bacteria Archaea Eukarya
Fungi Animals Plants
KEY
Vertical evolution
Horizontal gene transfer
Common ancestral community of primitive cells

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