1. 20
Phylogeny

2. Phylogeny A phylogenetic tree is a reasoned hypothesis of the
evolutionary relationships of organisms.
Phylogeny: history of descent with
branching/modification and the
accumulation of change over time
Node: represents the common
ancestor from which the descendent
species divergent; can be rotated
without changing evolutionary relationships
The process of speciation can be depicted in a phylogenetic tree, where branches represent diverging populations. As species proliferate, their evolutionary relationships to one another unfold in a treelike pattern, with present-day species as the tips of branches and their last common ancestors at nodes from which they branched off.

3. Phylogeny of Vertebrates
The order of branches indicates the sequence of events in time
The branching order found in a phylogenetic tree hypothesizes the evolutionary relationship within a group.
This tree proposes that the closest living relatives of birds are crocodiles and alligators. It also proposes that the closest relatives of all tetrapod (four-legged) vertebrates are lungfish.

4. Classification & Phylogenetic Trees
Figure 20.4
Order
Family Genus
Species
Classification & Phylogenetic Trees
Panthera
Felidae
Panthera
pardus
(leopard)
Taxidea
Carnivora
Taxidea
taxus
(American
badger)
Mustelidae
Lutra
Lutra lutra
(European
otter)
Figure 20.4 The connection between classification and phylogeny
Canis
latrans
(coyote)
Canidae
Canis
Canis
lupus
(gray wolf)
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5. Concept 20.1: Phylogenies show evolutionary relationships
Organisms share many characteristics because of common ancestry
Taxonomy : the ordered division and naming of organisms; 8 taxons; Linnaeus: the Father of Taxonomy
Ranked from most general to most specific
Domain….Kingdom….Phyum….Class….Order…
.Family…..Genus…..Species
Binomial nomenclature: most specific; Genus & species
i.e. Homo sapien
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6. Domain: Bacteria Kingdom: Animalia Domain: Archaea Domain: Eukarya
Figure 20.3
Species: Panthera pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Figure 20.3 Linnaean classification
Phylum: Chordata
Domain: Bacteria
Kingdom:
Animalia
Domain:
Archaea
Domain:
Eukarya
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7. Classification Taxonomic classification: Domain (most general) Kingdom
Phylum
Class
Order
Family
Genus
Species (most specific; called binomial nomenclature)
Organisms are classified into domain, kingdom, phylum, class, order, family, genus, and species.
Closely related species are grouped into a genus. Closely related genera belong to a larger branch of the tree classified as a family. Closely related families form an order, orders form a class, classes form a phylum, and phyla form a kingdom.
Today, biologists refer to the three largest limbs of the entire tree of life as domains—Eukarya, Bacteria, and Archaea.
3 Domains (Superkingdoms) of life: Eukarya, Bacteria, Archae

8. where lineages diverge Taxon A
Figure 20.5
Branch point:
where lineages diverge
Taxon A
Taxon B
Sister
taxa
Taxon C
Taxon D
Taxon E
ANCESTRAL
LINEAGE
Taxon F
Figure 20.5 How to read a phylogenetic tree
Basal
taxon
Taxon G
This branch point
represents the common
ancestor of taxa A–G.
This branch point forms a
polytomy: an unresolved
pattern of divergence.
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9. Sister Groups
Two groups are considered to be each others’ closest relatives if they share a common ancestor not shared by any other group. Two groups that are each others’ closest relatives are called sister groups. The closeness of the relationship is determined by looking to see how recently two groups share a common ancestor. It’s important to understand that a node can be rotated without changing the evolutionary relationships of the groups.
Sister groups: 2 groups that share a common ancestor not shared by any other group

10. HOMOLOGOUS VS ANALOGOUS
Homologies: similarities based on shared common ancestor
Analogies: similarities based on independent adaptations

11. Homologous and Analogous Features
Shared derived characters:
Anatomical
Physiological
Molecular features
that are in common
Homologies: similarities based on
shared common ancestor
Analogies: similarities based on
independent adaptations
When constructing a phylogenetic tree, the anatomical, physiological, or molecular features that make up an organism are compared. These features, called character states, can be similar for one of two reasons between organisms:
Common descent from an ancestor that had the same character state
Convergent evolution, in which the character state evolved independently in two separate groups
Here, mammals and birds both produce amniotic eggs. Because amniotic eggs occur only in groups descended from the common ancestor at the node connecting the mammal and sauropsid branches of the tree, we accept that birds and mammals each inherited this character from a common ancestor in which the trait first evolved. Characters that are similar because of common descent are said to be homologous.
However, similarities due to independent adaptations by different species are said to be analogous. For instance, evidence supports the view that wings in both birds and bats do not reflect descent from a common winged ancestor, but, rather, evolved independently in the two groups.
A phylogenetic tree is built on the basis of shared
derived characters.

12. Convergent Evolution: Analogous Structures
Figure 20.2
Convergent Evolution: Analogous Structures
Legless lizards and snakes evolved from different lineages of lizards with legs
No limbs
Eastern glass lizard
Monitor lizard
Iguanas
ANCESTRAL
LIZARD
(with limbs)
Snakes
Figure 20.2 Convergent evolution of limbless bodies
No limbs
Geckos
Legless lizards have evolved independently in several different groups through adaptation to similar environments (analogies through convergent evolution)
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13. Convergent Evolution in Burrowers
Figure 20.7
Convergent Evolution in Burrowers
Australian marsupial mole
Figure 20.7 Convergent evolution in burrowers
North American eutherian mole
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14. Homologous versus Analogous Structures
Bat and bird wings are homologous as forelimbs, but analogous as functional wings
Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity
The more complex two similar structures are, the more likely it is that they are homologous
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15. Concept 20.3: Shared characters are used to construct phylogenetic trees
Once homologous characters have been identified, they can be used to infer a phylogeny
Cladistics: classifies organisms by common descent
A clade: a group of species that includes an ancestral species and all its descendants
A clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
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16. (a) Monophyletic group (clade)
Figure
Monophyletic Group (clade): it consists of the ancestor species and all its descendants
(a) Monophyletic group (clade) A B
Group I C D E
Figure Monophyletic, paraphyletic, and polyphyletic groups (part 1: monophyletic) F G
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17. (b) Paraphyletic group
Figure
A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
(b) Paraphyletic group A B C D E
Group II
Figure Monophyletic, paraphyletic, and polyphyletic groups (part 2: paraphyletic) F G
In a paraphyletic group, the most recent common ancestor of all members of the group is part of the group
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18. (c) Polyphyletic group
A polyphyletic grouping consists of various taxa with different ancestors
(c) Polyphyletic group A B
Group III C D E
Figure Monophyletic, paraphyletic, and polyphyletic groups (part 3: polyphyletic) F G
In a polyphyletic group, the most recent common ancestor is not part of the group
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19. (a) Monophyletic group (clade) (b) Paraphyletic group
Figure 20.10
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group A A A B
Group I B B
Group III C C C D D D E E
Group II E
Figure Monophyletic, paraphyletic, and polyphyletic groups F F F G G G
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20. Paraphyletic group Common ancestor of even-toed Other even-toed
Figure 20.11
Paraphyletic group
Common
ancestor of
even-toed
ungulates
Other even-toed
ungulates
Hippopotamuses
Cetaceans
Seals
Figure Paraphyletic vs. polyphyletic groups
Bears
Other
carnivores
Polyphyletic group
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21. Figure 20.12
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared
TAXA
Lancelet
(outgroup)
(outgroup)
Lancelet
Lamprey
Leopard
Bass
Turtle
Frog
Lamprey
Vertebral column
(backbone) 1 1 1 1 1
Bass
Vertebral
column
CHARACTERS
Hinged jaws 1 1 1 1
Frog
Hinged jaws
Four limbs 1 1 1
Turtle
Amnion 1 1
Four limbs
Figure Using derived characters to infer phylogeny
Hair 1
Amnion
Leopard
Hair
(a) Character table
(b) Phylogenetic tree
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22. Phylogenetic Trees with Proportional Branch Lengths
Figure 20.13
Phylogenetic Trees with Proportional Branch Lengths
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Figure Branch lengths can represent genetic change.
Human
Mouse
In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage
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23. In other trees, branch length can represent chronological time
Figure 20.14
In other trees, branch length can represent chronological time
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Figure Branch lengths can indicate time.
Human
Mouse
500
400
300
200
100
Present
Millions of years ago
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24. Figure 20.16
Birds and crocodiles share several features: four-chambered hearts, song, nest building, and egg brooding
Lizards
and snakes
Crocodilians
†Ornithischian
dinosaurs
Common
ancestor of
crocodilians,
dinosaurs,
and birds
†Saurischian dinosaurs other than birds
Figure A phylogenetic tree of birds and their close relatives
Birds
These characteristics likely evolved in a common ancestor and were shared by all of its descendants, including dinosaurs
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25. The fossil record supports nest building and brooding in dinosaurs
Figure 20.18
The fossil record supports nest building and brooding in dinosaurs
Front limb
Hind limb
Eggs
Figure Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs.
(a) Fossil remains of Oviraptor and eggs
(b) Artist’s reconstruction of the dinosaur’s posture based on the fossil findings
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26. From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
More recently, the 3-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes
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27. Euglenozoans Forams Diatoms Domain Eukarya Ciliates Red algae
Figure 20.21
Euglenozoans
Forams
Diatoms
Domain Eukarya
Ciliates
Red algae
Green algae
Plants
Amoebas
Fungi
Animals
Nanoarchaeotes
Archaea
Domain
Euryarcheotes
Crenarcheotes
COMMON
ANCESTOR
OF ALL LIFE
Figure The three domains of life
Proteobacteria
(Mitochondria)*
Domain Bacteria
Chlamydias
Spirochetes
Gram-positive
bacteria
Cyanobacteria
(Chloroplasts)*
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28. 3 Domain Classification System
The 3-domain system shows the importance of single-celled organisms in the history of life
Domains Bacteria and Archaea are single-celled prokaryotes
Only three lineages in the Domain Eukarya are dominated by multicellular organisms, kingdoms Plantae, Fungi, and Animalia
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29. The Important Role of Horizontal Gene Transfer
The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria (based on rRNA genes)
There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms
Horizontal gene transfer complicates efforts to build a tree of life ,
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30. Figure 20.22
Horizontal gene transfer may have been common enough that the early history of life is better depicted by a tangled web than a branching tree
Domain Eukarya
Ani
malia
Fungi
Plantae
Chloropl
asts
Archaea
Domain
Mitochondria
Methanogens
Ancestral cell
populations
Thermophiles
Figure A tangled web of life
Cyanobacteria
Domain Bacteria
Proteobacteria
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