lecture presentations for biology - amborella … · class: mammalia phylum: chordata kingdom:...
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Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
PowerPoint® Lecture Presentations for
BiologyEighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Chapter 26Chapter 26
Phylogeny and the Tree of Life
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Fig. 26-1
A legless lizard instead of a snake!Common name: scaly-foot
• Characteristics for snakes:1) Fused eyelid2) Highly mobile jaw3) Short tail posterior to the anus
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Overview: Investigating the Tree of Life
• Phylogeny is the evolutionary history of a species or group of related species
• The discipline of systematics classifies organisms and determines their evolutionary relationships
How can we address “Phylogeny”?
Systematists use fossil, molecular, and genetic data to infer evolutionary relationships
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Fig. 26-2
Relationships among human, fungus, and tulip?
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Fig. 26-2
An unexpected phylogenetic relationships
Animals and fungi are more closely related to each other than either is to plants!
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Concept 26.1: Phylogenies show evolutionary relationships
• Taxonomy is the ordered division and naming of organisms
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Binomial Nomenclature
• In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
• Two key features of his system remain useful today:
- two-part (binomial) names for species
- hierarchical classification
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• The two-part scientific name of a species is called a binomial
• The first part of the name is the genus
• The second part, called the specific epithet, is unique for each species within the genus
• The first letter of the genus is capitalized, and the entire species name is italicized
• Both parts together name the species (not the specific epithet alone)
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Hierarchical Classification
• Linnaeus introduced a system for grouping species in increasingly broad categories
• The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
• A taxonomic unit at any level of hierarchy is called a taxon
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Fig. 26-3Species:Pantherapardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
ArchaeaDomain: EukaryaBacteria
At each level of the Linnaean classification system species are placed into groups belong to more comprehensive groups
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Linking Classification and Phylogeny
• Systematists depict evolutionary relationships in branching phylogenetic trees
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Fig. 26-4 Species
Canislupus
Pantherapardus
Taxideataxus
Lutra lutra
Canislatrans
Order Family Genus
Carnivora
FelidaeM
ustelidaeC
anidae
Canis
LutraTaxidea
Panthera
Let’s discuss about the problems in the Linnean system at the phylogenetic point of view.
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• Linnaean classification and phylogeny can differ from each other
• Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents
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• A phylogenetic tree represents a hypothesis about evolutionary relationships
• Each branch point represents the divergence of two species
• Sister taxa are groups that share an immediate common ancestor
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• A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
• A polytomy is a branch from which more than two groups emerge
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Fig. 26-5
Sistertaxa
ANCESTRALLINEAGE
Taxon A
Polytomy: unresolved pattern of divergence
The most recent common ancestor oftaxa A–F
Branch point(node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
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What We Can and Cannot Learn from Phylogenetic Trees (CLADOGRAM!)
• Phylogenetic trees do show patterns of descent
• Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage
• It shouldn’t be assumed that a taxon evolved from the taxon next to it
Phenogram vs. Cladogram vs. Phylogram
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Applying Phylogenies
• Phylogeny provides important information about similar characteristics in closely related species
• A phylogeny was used to identify the species of whale from which “whale meat” originated
DNA barcoding!!!
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Fig. 26-6
Fin(Mediterranean)Fin (Iceland)
RESULTS
Unknown #10,11, 12Unknown #13
Blue(North Pacific)
Blue(North Atlantic)
Gray
Unknown #1b
Humpback(North Atlantic)Humpback(North Pacific)
Unknown #9
Minke(North Atlantic)
Minke(Antarctica)Minke(Australia)Unknown #1a,2, 3, 4, 5, 6, 7, 8
What are some potential sources of error in this study?
How might the chances of reaching an erroneous conclusion be reduced?
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• Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax
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Fig. 26-UN1
A
B
A A
B
B
C
CC
D
D
D
(a) (b) (c)
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Concept 26.2: Phylogenies are inferred from morphological and molecular data
• To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
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Morphological and Molecular Homologies
• Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences
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Sorting Homology from Analogy
• When constructing a phylogeny, systematistsneed to distinguish whether a similarity is the result of homology or analogy
• Homology상동 is similarity due to shared ancestry
• Analogy상사 is similarity due to convergent evolution
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Fig. 26-7
Convergent evolution of analogous burrowing characteristicsMarsupial Australian mole and mammalian North American mole
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• Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
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• Bat and bird wings are homologous as forelimbs, but analogous as functional wings
• Analogous structures or molecular sequences that evolved independently are also called homoplasies (동류형성; 불계적유사성)
• 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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Evaluating Molecular Homologies
• Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms
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Fig. 26-8
Deletion
Insertion
1
2
3
4
Alignment!
Aligning segments of DNA
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• It is also important to distinguish homology from analogy in molecular similarities
• Mathematical tools help to identify molecular homoplasies, or coincidences
• Molecular systematics uses DNA and other molecular data to determine evolutionary relationships
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Fig. 26-9
A molecular homoplasy:These two DNA sequences from organism that are closely related coincidentally share 25% of their bases. Statistical tools have been developed to determine whether DNA sequences that share more than 25% of their bases do so because they are homologous.
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Concept 26.3: Shared characters are used to construct phylogenetic trees
• Once homologous characters have been identified, they can be used to infer a phylogeny
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Cladistics
• Cladistics분지론분계론 groups organisms by common descent
• A clade분계조, 분기군, 절 is a group of species that includes an ancestral species and all its descendants
• Clades can be nested in larger clades, but not all groupings of organisms qualify as clades
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• A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
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Fig. 26-10
A A A
BBB
C C C
DDD
E E E
FFF
G G G
Group IIIGroup II
Group I
(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group
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Fig. 26-10a
A
B
C
D
E
F
G
Group I
(a) Monophyletic group (clade)
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• A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
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Fig. 26-10b
A
B
C
D
E
F
G
Group II
(b) Paraphyletic group
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• A polyphyletic grouping consists of various species that lack a common ancestor
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Fig. 26-10c
A
B
C
D
E
F
G
Group III
(c) Polyphyletic group
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Shared Ancestral and Shared Derived Characters
• In comparison with its ancestor, an organism has both shared and different characteristics
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• A shared ancestral character is a character that originated in an ancestor of the taxon
• A shared derived character is an evolutionary novelty unique to a particular clade
• A character can be both ancestral and derived, depending on the context
= Symplesiomorphy
= Synapomorphy
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Inferring Phylogenies Using Derived Characters
• When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared
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Fig. 26-11
TAXA
Leop
ard
Tuna
Vertebral column(backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg
Hair
(a) Character table
Hair
Hinged jaws
Vertebralcolumn
Four walking legs
Amniotic egg
(b) Phylogenetic tree
Salamander
Leopard
Turtle
Lamprey
Tuna
Lancelet(outgroup)
0
0 0
0
0
0
0 0
0
0
0 0
0 0 0 1
11
111
1
11
1
1
11
11
창고기
칠성장어
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• An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
• Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics
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• Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor
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Phylogenetic Trees with Proportional Branch Lengths (Phylogram)
• 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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Fig. 26-12
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
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• In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record
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Fig. 26-13
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
CENOZOIC
Present65.5
MESOZOIC
251Millions of years ago
PALEOZOIC
542
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Mich. cavaleri
M.dawsoniana
M.cylindrica
M.sinica
M.nitida
Mich.baillonii
M.denudata
M.acuminata
P.praecalva
M.panamensisM.virginiana
K.duperreana
Mang.grandis
Mang.conifera
M.tamaulipana
M.guatemalensis
K.septentrionalis
Mang.aromatica
Mang.glaucaM.officinalis
M.sieboldii
M.macrophylla
M. fraseri var. fraseri
M.coco
M.tripetala
M.wilsonii
M.dealbata
M. fraseri var.pyramidata
M.gigantifoliaM.liliifera
M.pterocarpaM.splendens
M.dodecapetala
L.tulipifera
M.henryi
M.mexicana
L.chinense
Asimina trilobaEupomatia bennettiiDegeneria roseiflora
M.elegans
M.campbellii
M.kobus
Mich.figo
M.pealiana
M.biondii
Mich.odoraMich.champ
E.ovalisM.cathcartii
M.grandiflora
Galbulimima belgraveana
MY0.0
65.0
0
1.64
56.5
35.4
23.3
5.20
97.0
0
Late
C
reta
ceou
s
Ear
lyC
reta
ceou
s
Pal
eoce
ne
Eoc
ene
Olig
ocen
e
Mio
cene
Plio
cene
Qur
tana
ry
100.0 75.0 50.0 25.0125.0
Fossil Archaeanthus >93 MYMACROPHYLLA
GWILLIMIA
MICHELIA
YULANIA
GYNOPODIUM
FRASERI
KMERIA
Mich.
AlArBuBuYuYuYuCyTuMt
Gy
GwBlBl
GwLi
RyRyRyRy
THEORHODON
ThMaThThTh
Mich.
MiMich.Mich.Mich.Elme.
Pach.
Kmer.Kmer.
MANGLIETIA Mang.Mang.Mang.Mang.
TALAUMASpTaTa
RYTIDOSPERMUMRyRyOyOy
In case of Magnoliaceae
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Maximum Parsimony and Maximum Likelihood최대단순성법 and 최대개연성법(최대가능성법)
• Systematists can never be sure of finding the best tree in a large data set
• They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood
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• Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely
• The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events
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• Computer programs are used to search for trees that are parsimonious and likely
Maximum Parsimony
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Fig. 26-15-1
Species I
Three phylogenetic hypotheses:
Species II Species III
I
II
III
I
III
IIIII
III
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Fig. 26-15-2
Species I
Site
Species II
Species III
I
II
III
I
III
IIIII
III
Ancestralsequence
1/C1/C
1/C
1/C
1/C
4321
C
C C
C
T
T
T
T
T
T A
AA
A G
G
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Fig. 26-15-3
Species I
Site
Species II
Species III
I
II
III
I
III
IIIII
III
Ancestralsequence
1/C1/C
1/C
1/C
1/C
4321
C
C C
C
T
T
T
T
T
T A
AA
A G
G
I I
I
II
II
II
III
III
III3/A
3/A
3/A3/A
3/A
2/T2/T
2/T 2/T
2/T4/C
4/C
4/C
4/C
4/C
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Fig. 26-15-4
Species I
Site
Species II
Species III
I
II
III
I
III
IIIII
III
Ancestralsequence
1/C1/C
1/C
1/C
1/C
4321
C
C C
C
T
T
T
T
T
T A
AA
A G
G
I I
I
II
II
II
III
III
III3/A
3/A
3/A3/A
3/A
2/T2/T
2/T 2/T
2/T4/C
4/C
4/C
4/C
4/C
I I
I
II
II
II
III
III
III
7 events7 events6 events
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Fig. 26-14
Human
15%
Tree 1: More likely Tree 2: Less likely(b) Comparison of possible trees
15% 15%
5%
5%
10%
25%20%
40%
40%
30%0
0
0
(a) Percentage differences between sequences
Human Mushroom
Mushroom
Tulip
Tulip
Maximum Likelihood
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Gene Duplications and Gene Families
• Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
• Like homologous genes, duplicated genes can be traced to a common ancestor
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• Orthologous genes are found in a single copy in the genome and are homologous between species
• They can diverge only after speciation occurs
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• Paralogous genes result from gene duplication, so are found in more than one copy in the genome
• They can diverge within the clade that carries them and often evolve new functions
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Fig. 26-18
(b) Paralogous genes
(a) Orthologous genes
Ancestral gene
Paralogous genes
Ancestral species
Speciation withdivergence of gene
Gene duplication and divergence
Species A after many generations
Species A Species B
Species A
Orthologous genes
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Homologous 상동Orthologous genes: originated from speciationParalogous genes: originated from gene duplications
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Molecular Clocks
• A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
• In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor
• In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated
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• Molecular clocks are calibrated against branches whose dates are known from the fossil record
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Fig. 26-19
Divergence time (millions of years)120
90
90
60
60
30
300
0
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Mich. cavaleri
M.dawsoniana
M.cylindrica
M.sinica
M.nitida
Mich.baillonii
M.denudata
M.acuminata
P.praecalva
M.panamensisM.virginiana
K.duperreana
Mang.grandis
Mang.conifera
M.tamaulipana
M.guatemalensis
K.septentrionalis
Mang.aromatica
Mang.glaucaM.officinalis
M.sieboldii
M.macrophylla
M. fraseri var. fraseri
M.coco
M.tripetala
M.wilsonii
M.dealbata
M. fraseri var.pyramidata
M.gigantifoliaM.liliifera
M.pterocarpaM.splendens
M.dodecapetala
L.tulipifera
M.henryi
M.mexicana
L.chinense
Asimina trilobaEupomatia bennettiiDegeneria roseiflora
M.elegans
M.campbellii
M.kobus
Mich.figo
M.pealiana
M.biondii
Mich.odoraMich.champ
E.ovalisM.cathcartii
M.grandiflora
Galbulimima belgraveana
MY0.0
65.0
0
1.64
56.5
35.4
23.3
5.20
97.0
0
Late
C
reta
ceou
s
Ear
lyC
reta
ceou
s
Pal
eoce
ne
Eoc
ene
Olig
ocen
e
Mio
cene
Plio
cene
Qur
tana
ry
100.0 75.0 50.0 25.0125.0
Fossil Archaeanthus >93 MYMACROPHYLLA
GWILLIMIA
MICHELIA
YULANIA
GYNOPODIUM
FRASERI
KMERIA
Mich.
AlArBuBuYuYuYuCyTuMt
Gy
GwBlBl
GwLi
RyRyRyRy
THEORHODON
ThMaThThTh
Mich.
MiMich.Mich.Mich.Elme.
Pach.
Kmer.Kmer.
MANGLIETIA Mang.Mang.Mang.Mang.
TALAUMASpTaTa
RYTIDOSPERMUMRyRyOyOy
In case of Magnoliaceae
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• There have been substantial interchanges of genes between organisms in different domains
• Horizontal gene transfer (HGT) is the movement of genes from one genome to another
• Horizontal gene transfer complicates efforts to build a tree of life
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Fig. 26-22
3
Archaea
Bacteria
Eukarya
Billions of years ago4 2 1 0
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You should now be able to:
1. Explain the justification for taxonomy based on a PhyloCode
2. Explain the importance of distinguishing between homology and analogy
3. Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes
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4. Define horizontal gene transfer and explain how it complicates phylogenetic trees
5. Explain molecular clocks and discuss their limitations