Transcript Chapter 26 Phylogeny and the Tree of Life (working

Chapter 26
Phylogeny and the Tree of Life
PowerPoint® Lecture Presentations for
Biology
Eighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-1
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
•
Systematists use fossil,
molecular, and genetic data,
geographical distribution,
behavior, and life history to
infer evolutionary relationships
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Concept 26.1: Phylogenies show evolutionary
relationships
•
Taxonomy is the ordered division and naming of organisms
•
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 names
for species and hierarchical classification
•
The two-part scientific name of a species is called a binomial
nomenclature
•
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)
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-3
Species:
Panthera
pardus
• 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
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea
Linking Classification and Phylogeny
•
Systematists depict evolutionary relationships in branching
phylogenetic trees
•
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
•
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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-4
Order
Family Genus
Species
Taxidea
Taxidea
taxus
Lutra
Mustelidae
Panthera
Felidae
Carnivora
Panthera
pardus
Lutra lutra
Canis
Canidae
Canis
latrans
Canis
lupus
Fig. 26-5
Branch point
(node)
Taxon A
Taxon B
Taxon C
ANCESTRAL
LINEAGE
Taxon D
Taxon E
Taxon F
Common ancestor of
taxa A–F
Polytomy
Redraw this tree, rotating the branches around
branch points “2” & “4”. Does your new version
tell a different story about the evolutionary relationships?
Sister
taxa
What We Can and Cannot Learn from
Phylogenetic Trees
•
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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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
• 13 samples of “whale meat” from Japanese fish markets
where sequenced.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-6
RESULTS
Minke
(Antarctica)
Minke
(Australia)
Unknown #1a,
2, 3, 4, 5, 6, 7, 8
Minke
(North Atlantic)
Unknown #9
This analysis indicated
that DNA sequences of
six of the unknown
samples
(in red) were most closely
related to DNA sequences
of whales that are not
legal to harvest.
Humpback
(North Atlantic)
Humpback
(North Pacific)
Unknown #1b
Gray
Blue
(North Atlantic)
Blue
(North Pacific)
Unknown #10,
11, 12
Unknown #13
Fin
(Mediterranean)
Fin (Iceland)
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-UN1
(a)
A
B
D
B
D
C
C
C
B
D
A
A
(b)
(c)
Which of the trees shown below depicts a different evolutionary history for taxa
A – D than the other two tress? Explain
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Sorting Homology from Analogy
•
When constructing a phylogeny, systematists need to distinguish
whether a similarity is the result of homology or analogy
•
Homology is similarity due to shared ancestry
•
Analogy is similarity due to convergent evolution
•
Convergent evolution occurs when similar environmental pressures
and natural selection produce similar (analogous) adaptations in
organisms from different evolutionary lineages
•
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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-7
Convergent evolution of analogous burrowing characteristics
Evaluating Molecular Homologies
• Systematists use computer programs and
mathematical tools when analyzing comparable
DNA segments from different organisms
1
Ancestral homologous DNA
segments are identical as
species 1 and species 2 begin
to diverge
from their common ancestor.
Deletion
2
Insertion
Of the three homologous
3
regions, two (shaded orange)
do not align because of these
mutations.
Homologous regions realign 4
after a computer program adds
gaps in sequence 1.
Deletion and insertion
mutations shift what had been
matching sequences in the two
species.
Concept 26.3: Shared characters are used to
construct phylogenetic trees
•
Cladistics groups organisms by common descent
•
A clade is a group of species that includes an ancestral species and all
its descendants
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-10
• A paraphyletic
grouping consists of
an ancestral species
and some, but not
all, of the
descendants
A
A
A
B
B
C
C
C
D
D
D
E
E
F
F
F
G
G
G
B
Group I
(a) Monophyletic group (clade)
• A clade is
monophyletic,
signifying that it
consists of the
ancestor species and
all its descendants
Group II
(b) Paraphyletic group
E
Group III
(c) Polyphyletic group
• A polyphyletic
grouping consists
of various species
that lack a
common ancestor
Shared Ancestral and Shared Derived Characters
•
In comparison with its ancestor, an organism has both shared and
different characteristics
•
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
•
When inferring evolutionary relationships, it is useful to know in which
clade a shared derived character first appeared
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-11a
Tuna
(a) Character table - A 0
indicates that a character is
absent, a 1 indicates that a
character is present
Leopard
TAXA
Vertebral column
(backbone)
0
1
1
1
1
1
Hinged jaws
0
0
1
1
1
1
Four walking legs
0
0
0
1
1
1
Amniotic (shelled) egg
0
0
0
0
1
1
Hair
0
0
0
0
0
1
(b) Phylogenetic tree – Analyzing the
distribution of these derived characters
can provide insight into vertebrate
phylogeny
Lancelet
(outgroup)
Lamprey
Tuna
Vertebral
column
Salamander
Hinged jaws
Turtle
Four walking legs
Amniotic egg
Leopard
Hair
Fig. 26-15-1
Species I
Species III
Species II
Three phylogenetic hypotheses:
I
I
III
II
III
II
III
II
I
Fig. 26-15-2
Site
1
2
3
4
Species I
C
T
A
T
Species II
C
T
T
C
Species III
A
G
A
C
Ancestral
sequence
A
G
T
T
1/C
I
1/C
II
I
III
III
II
1/C
II
III
1/C
I
1/C
Tabulate the molecular data for the species. The data represent a DNA sequence
Consisting of just four nucleotide bases.
Now focus on site 1 in the DNA sequence. In the tree on the left, a single base
Change event, represented by the purple hatchmark on the branch leading to
Species I and II is sufficient to account for the site 1 data. In the other two trees,
Two base-change events are necessary
Fig. 26-15-3
Site
1
2
3
4
Species I
C
T
A
T
Species II
C
T
T
C
Species III
A
G
A
C
Ancestral
sequence
A
G
T
T
1/C
I
1/C
II
I
III
III
II
1/C
II
III
I
1/C
3/A
2/T
I
2/T
3/A
3/A
4/C
II
II
2/T 4/C
III
2/T
4/C
III
3/A 4/C
I
III
II
4/C
1/C
I
2/T 3/A
Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of the
three trees requires a total of five additional base change events.
Fig. 26-15-4
Site
1
2
3
4
Species I
C
T
A
T
Species II
C
T
T
C
Species III
A
G
A
C
Ancestral
sequence
A
G
T
T
1/C
I
1/C
II
I
III
III
II
1/C
II
III
I
1/C
3/A
2/T
I
2/T
3/A
3/A 4/C
6 events
3/A
4/C
III
II
2/T
4/C
II
III
To identify the most parsimonious
tree (simplest), we total all of the
base change events. Conclusion
is the first tree is the most
parsimonious.
I
III
II
4/C
1/C
I
2/T 3/A
2/T 4/C
I
I
III
II
III
II
III
II
I
7 events
7 events
Concept 26.5: Molecular clocks help track
evolutionary time
•
To extend molecular phylogenies beyond the fossil record, we must
make an assumption about how change occurs over time
•
When inferring evolutionary relationships, it is useful to know in which
clade a shared derived character first appeared
•
Molecular clocks are calibrated against branches whose dates are
known from the fossil record
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Use the clock to estimate the divergence time for a mammal with a total of
30 mutations in the seven proteins.
90
60
30
0
0
30
60
90
Divergence time (millions of years)
120
Applying a Molecular Clock: The Origin of HIV
•
Phylogenetic analysis shows that HIV is descended from viruses that
infect chimpanzees and other primates
•
Comparison of HIV samples throughout the epidemic shows that the
virus evolved in a very clocklike way
•
Application of a molecular clock to one strain of HIV suggests that that
strain spread to humans during the 1930s
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-20
0.20
0.15
0.10
Computer model
of HIV
Range
0.05
0
1900
1920
1940
1960
Year
The points in
the corner
are based on
DNA
sequences
for a specific
HIV gene
collected
from patients
at different
know times.
If we project
the rate at
which
changes
occurred
back in time,
we intersect
1980 2000 the x-axis in
the 1930’s
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 three-domain system has been adopted: Bacteria,
Archaea, and Eukarya
•
The three-domain system is supported by data from many sequenced
genomes. The domain taxonomic level contains a single ancestor
for all its members, the five kingdom system does not.
•
The tree of life suggests that eukaryotes and archaea are more closely
related to each other than to bacteria
•
The tree of life is based largely on rRNA genes, as these have evolved
slowly
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-21
EUKARYA
Dinoflagellates
Forams
Ciliates Diatoms
Red algae
Land plants
Green algae
Cellular slime molds
Amoebas
Euglena
Trypanosomes
Leishmania
Animals
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
Halophiles
(Mitochondrion)
COMMON
ANCESTOR
OF ALL
LIFE
Methanobacterium
ARCHAEA
Spirochetes
Chlamydia
Green
sulfur bacteria
BACTERIA
Cyanobacteria
(Plastids, including
chloroplasts)
•
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 complicates efforts to build a tree of life
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
1 – Most recent common ancestor of all living things
2 – Gene transfer between mitochondrial ancestor and ancestor of eukaryotes
3 – Gene transfer between chloroplast ancestor and ancestor of green algae
Bacteria
2
3
1
Eukarya
Archaea
4
3
2
Billions of years ago
1
0
Fig. 26-23
Eukarya
Bacteria
Archaea
• Some researchers suggest that eukaryotes arose as an
endosymbiosis between a bacterium and archaean
• If so, early evolutionary relationships might be better depicted by
a ring of life instead of a tree of life
Fig. 26-UN9
Fig. 26-UN10
Fig. 26-UN10a
Fig. 26-UN10b
You should now be able to:
1.
Explain the importance of distinguishing between homology and
analogy
2.
Distinguish between the following terms: monophyletic, paraphyletic,
and polyphyletic groups; shared ancestral and shared derived
characters
4.
Define horizontal gene transfer and explain how it complicates
phylogenetic trees
5.
Explain molecular clocks and discuss their limitations
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings