25. sistematica campbell
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Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings
PowerPoint Lectures forBiology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Chapter 25
Phylogeny and Systematics
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Overview: Investigating the Tree of Life
Phylogeny is the evolutionary history of a speciesor group of related species
Biologists draw on the fossil record, which
provides information about ancient organisms
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Systematics is an analytical approach tounderstanding the diversity and relationships oforganisms, both present-day and extinct
Systematists use morphological, biochemical, andmolecular comparisons to infer evolutionaryrelationships
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Concept 25.1: Phylogenies are based on common ancestriesinferred from fossil, morphological, and molecular evidence
To infer phylogenies, systematists gatherinformation about morphologies, development,and biochemistry of living organisms
They also examine fossils to help establishrelationships between living organisms
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The Fossil Record
Sedimentary rocks are the richest source of fossils Sedimentary rocks are deposited into layers called
strata
Video: Grand Canyon
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LE 25-3
Rivers carry sediment to theocean. Sedimentary rock layerscontaining fossils form on theocean floor.
Over time, new strata aredeposited, containing fossilsfrom each time period.
As sea levels change and theseafloor is pushed upward,sedimentary rocks are exposed.Erosion reveals strata and fossils.
Younger stratumwith more recentfossils
Older stratum witholder fossils
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The fossil record is based on the sequence inwhich fossils have accumulated in such strata
Fossils reveal ancestral characteristics that may
have been lost over time
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Though sedimentary fossils are the most common,paleontologists study a wide variety of fossils
Animation: The Geologic Record
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Dinosaur bones beingexcavated from sandstone
Casts of ammonites, about375 million years old
Boy standing in a 150-million-year-old
dinosaur track in Colorado
Tusks of a 23,000-year-old mammoth, frozen whole
in Siberian ice
Petrified trees in Arizona, about 190million years old
Insects preserved whole in amber
Leaf fossil, about 40 millionyears ago
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Morphological and Molecular Homologies
In addition to fossils, phylogenetic history can beinferred from morphological and molecularsimilarities in living organisms
Organisms with very similar morphologies orsimilar DNA sequences are likely to be moreclosely related than organisms with vastly differentstructures or sequences
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Analogous structures or molecular sequences thatevolved independently are also calledhomoplasies
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Evaluating Molecular Homologies
Systematists use computer programs andmathematical tools when analyzing comparableDNA segments from different organisms
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Concept 25.2: Phylogenetic systematics connectsclassification with evolutionary history
Taxonomy is the ordered division of organismsinto categories based on characteristics used toassess similarities and differences
In 1748, Carolus Linnaeus published a system oftaxonomy based on resemblances.
Two key features of his system remain useful
today: two-part names for species and hierarchicalclassification
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Binomial Nomenclature
The two-part scientific name of a species is calleda binomial
The first part of the name is the genus
The second part, called the specific epithet, isunique for each species within the genus
The first letter of the genus is capitalized, and theentire species name is latinized
Both parts together name the species ( not thespecific epithet alone)
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Hierarchical Classification
Linnaeus introduced a system for groupingspecies in increasingly broad categories
Animation: Classification Schemes
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Species
Panthera pardus
Panthera Genus
FamilyFelidae
CarnivoraOrder
MammaliaClass
PhylumChordata
KingdomAnimalia
EukaryaDomain
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Linking Classification and Phylogeny
Systematists depict evolutionary relationships inbranching phylogenetic trees
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Carnivora
Panthera pardus
(leopard)
Mephitis mephitis
(striped skunk)
Lutra lutra (European
otter)
Canis familiaris
(domestic dog)
Canis lupus (wolf) S
p e c i e s
G e n u s
F a m
i l y
O r d e r
Felidae Mustelidae Canidae
Panthera Mephitis Lutra Canis
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Each branch point represents the divergence oftwo species
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LE 25 UN497
Leopard Domestic cat
Common ancestor
Leopard Domestic catWolf
Common ancestor
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Deeper branch points represent progressivelygreater amounts of divergence
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A valid clade is monophyletic, signifying that itconsists of the ancestor species and all itsdescendants
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Grouping 1
Monophyletic
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A paraphyletic grouping consists of an ancestralspecies and some, but not all, of the descendants
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Paraphyletic
Grouping 2
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A polyphyletic grouping consists of variousspecies that lack a common ancestor
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Polyphyletic
Grouping 3
Sh d P i iti d Sh d D i d Ch t i ti
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Shared Primitive and Shared Derived Characteristics
In cladistic analysis, clades are defined by theirevolutionary novelties
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A shared primitive character is a character that isshared beyond the taxon we are trying to define
A shared derived character is an evolutionarynovelty unique to a particular clade
Outgroups
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Outgroups
An outgroup is a species or group of species thatis closely related to the ingroup, the variousspecies being studied
Systematists compare each ingroup species withthe outgroup to differentiate between sharedderived and shared primitive characteristics
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LE 25-11TAXA
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Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column(backbone)
Character table
C H A R A C T E R S
TAXA
L a n c e
l e t
( o u
t g r o u p
)
L a m p r e y
T u n a
S a
l a m a n
d e r
T u r t
l e
L e o p a r d
Turtle Leopard
Hair
Amniotic egg
Four walking legs
Hinged jaws
Vertebral column
Salamander
Tuna
Lamprey
Lancelet (outgroup)
Cladogram
Phylogenetic Trees and Timing
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Phylogenetic Trees and Timing
Any chronology represented by the branching of aphylogenetic tree is relative rather than absolute inrepresenting timing of divergences
Phylograms
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Phylograms
In a phylogram, the length of a branch in acladogram reflects the number of genetic changesthat have taken place in a particular DNA or RNAsequence in that lineage
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Ultrametric Trees
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Ultrametric Trees
Branching in an ultrametric tree is the same as ina phylogram, but all branches traceable from thecommon ancestor to the present are equal length
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C e n o
z o i c
M e s o z o
i c
P a
l e o z o
i c
6 5
. 5
2 5 1
5 4 2
N e o p r o
t e r o z o
i c
M i l l i o n s o
f
y e a r s a g o
Maximum Parsimony and Maximum Likelihood
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Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the besttree in a large data set
They narrow possibilities by applying theprinciples of maximum parsimony and maximumlikelihood
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The most parsimonious tree requires the fewestevolutionary events to have occurred in the formof shared derived characters
The principle of maximum likelihood states that,given certain rules about how DNA changes overtime, a tree can be found that reflects the mostlikely sequence of evolutionary events
LE 25-14Human Mushroom Tulip
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0 30%
0
p
40%
40%
Human
Mushroom
0Tulip
Percentage differences between sequences
Comparison of possible trees
15% 15% 20%
5% 5%10%
15%
25%
Tree 1: More likely Tree 2: Less likely
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In considering possible phylogenies for a group ofspecies, systematists compare molecular data forthe species.
The most efficient way to study hypotheses is toconsider the most parsimonious hypothesis, theone requiring the fewest evolutionary events(molecular changes)
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Sites in DNA sequence
I
Species
1
Base-changeevent
Bases atsite 1 foreach species
2 3 4 5 6 7
II
III
IV
I II III IV
Phylogenetic Trees as Hypotheses
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Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit themost data: morphological, molecular, and fossil
Sometimes the best hypothesis is not the mostparsimonious
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Lizard Bird Mammal
Four-chamberedheart
Mammal-bird clade
Lizard Bird Mammal
Four-chamberedheart
Four-chamberedheart
Lizard-bird clade
Concept 25.4: Much of an organisms
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Concept 25.4: Much of an organism sevolutionary history is documented in its genome
Comparing nucleic acids or other molecules toinfer relatedness is a valuable tool for tracingorganisms evolutionary history
Gene Duplications and Gene Families
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Gene Duplications and Gene Families
Gene duplication increases the number of genesin the genome, providing more opportunities forevolutionary changes
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Orthologous genes are genes found in a singlecopy in the genome
They can diverge only after speciation occurs
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Ancestral gene
Speciation
Orthologous genes
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Ancestral gene
Gene duplication
Paralogous genes
Genome Evolution
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Orthologous genes are widespread and extendacross many widely varied species
The widespread consistency in total gene numberin organisms indicates genes in complexorganisms are very versatile and that each genecan perform many functions
Concept 25.5: Molecular clocks help track
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p pevolutionary time
To extend molecular phylogenies beyond thefossil record, we must make an assumption abouthow change occurs over time
Molecular Clocks
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The molecular clock is a yardstick for measuringabsolute time of evolutionary change based on theobservation that some genes and other regions ofgenomes seem to evolve at constant rates
Neutral Theory
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y
Neutral theory states that much evolutionarychange in genes and proteins has no effect onfitness and therefore is not influenced byDarwinian selection
It states that the rate of molecular change in thesegenes and proteins should be regular like a clock
Difficulties with Molecular Clocks
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The molecular clock does not run as smoothly asneutral theory predicts
Irregularities result from natural selection in whichsome DNA changes are favored over others
Estimates of evolutionary divergences older thanthe fossil record have a high degree of uncertainty
Applying a Molecular Clock: The Origin of HIV
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pp y g g
Phylogenetic analysis shows that HIV isdescended from viruses that infect chimpanzeesand other primates
Comparison of HIV samples throughout theepidemic shows that the virus evolved in a veryclocklike way
The Universal Tree of Life
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The tree of life is divided into three great cladescalled domains: Bacteria, Archaea, and Eukarya
The early history of these domains is not yet clear