Post on 30-Dec-2015
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Systematics,Phylogenies,
and Comparative Biology Chapter 23
Sec. 23.1 - SystematicsIntroduction:All organisms share many characteristics Ex:
Composed of one or more cellsCarry out metabolismTransfer energy with ATPEncode hereditary information in DNA
There is a tremendous diversity of lifeEx:
Bacteria, whales, sequoia treesBiologists group organisms based on shared characteristics and newer molecular sequence data
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Since fossil records are not complete, scientists rely on other types of evidence to establish the best hypothesis of evolutionary relationships
SystematicsReconstruction and study of evolutionary
relationships through phylogenyPhylogeny
Hypothesis about patterns of relationship among species using cladograms
CladogramA branching, treelike diagram in which the
endpoints of the branches represent specific species of organisms. It is used to illustrate phylogenetic relationships and show points at which various species have diverged from common ancestral forms.
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Variations of a Cladogram
Gibbon Human Chimp Gorilla Orangutan Gibbon Orangutan Gorilla Human Chimp
Chimp
Human
Gorilla
Orangutan
Gibbon
1
3
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2
2
3
3
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1
Version 1 Version 2
Version 3
Darwin envisioned that all species were descended from a single common ancestor
He depicted this history of life as a branching tree
“Descent with modification”
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a.Reproduced by kind permission of the Syndics of Cambridge University Library, Darwin’s Notebook ‘B’,
‘Tree of Life’ Sketch, p. 36 from DAR.121 D312
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• Key to interpreting a phylogeny – look at how recently species share a common ancestor
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Variations of a Cladogram
Gibbon Human Chimp Gorilla Orangutan Gibbon Orangutan Gorilla Human Chimp
Chimp
Human
Gorilla
Orangutan
Gibbon
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Version 1 Version 2
b.
Version 3
Similarity may not accurately predict evolutionary relationshipsEarly systematists relied on the
expectation that the greater the time two species diverged from a common ancestor, the more different they would be Problems:
1. Rates of evolution varyEvolution may not be unidirectional
2. Evolution is not always divergentConvergent evolution
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CladisticsTechnique used for creating hierarchies of
organisms that represent true phylogenetic relationship and descent
Derived characteristicSimilarity that is inherited from the most
recent common ancestor of an entire groupAncestral
Similarity that arose prior to the common ancestor of the group
In cladistics, only shared derived characters are considered informative about evolutionary relationships
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When using cladistics the character variation needs to be identified as ancestral or derived
When creating cladistics, data needs to be collected on various Characters for ex:Morphology – PhysiologyBehavior – DNA
Characters should exist in recognizable character statesEx: Character: “teeth” in amniote vertebrates
has two states, present in most mammals and reptiles, and absent in birds and turtles
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“1” = possession of derived character state“0” = possession of ancestral character state
Cladistics (cont.)
To create a cladistics you need:1.Number of taxa (species or higher level groups)2.Determine the states for each character
Ex: Ancestral Vs. Derived Characters
Presence of hair is a shared derived feature of mammals
Presence of lungs in mammals is an ancestral feature; also present in amphibians and reptiles
Shared, derived feature of hair suggests that all mammal species share a common ancestor that existed more recently than the common ancestor of mammals, amphibians, and reptiles
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Examples of Ancestral Vs. Derived Characteristics
Determination of ancestral Vs. Derived1. Polarize the characters –
determine if states are ancestral or derived
2. Determine which state was exhibited by the most recent ancestor of the group
a) Outgroup comparison is used to assign character polarity.
b) If Outgroup, closely related but not a member, shares multiple character states, then state is considered to be ancestral, but outgroups also evolve from their ancestors, so outgroup will not always exhibit the ancestral condition.
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Polarity assignments are most reliable when using several different outgroups.
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The derived characters between the cladogram branch points are shared by all organisms above the branch points and are not
present in any below them. The outgroup (in this case, the lamprey) does not possess any of the derived characters.
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Lamprey Shark Salamander Lizard Tiger Gorilla Human
Jaws
Lungs
Amnioticmembrane
Hair
Tail loss
Bipedal
b.
Cladogram Clade - a group of
species that share a common ancestor as indicated by the possession of shared derived characters Evolutionary units
and refer to a common ancestor and all descendants
Synapomorphy – derived character shared by clade members
Plesiomorphies – ancestral states
Symplesiomorphies – shared ancestral states
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Simple cladogram is a nested set of clades, each characterized by its own synapomorphies
Amniotes are a clade for which the evolution of an amniotic membrane is a synapomorphy
Within that clade, mammals are a clade, with hair as a synapomorphy
Character state: “presence of a tail”Exhibited by
lampreys, sharks, salamanders, lizards, and tigers
Are tigers more closely related to lizards and sharks than apes and humans?
Symplesiomorphies reflect character states inherited from a distant ancestor, they do not imply that species exhibiting that state are closely related
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Bipedal
Tail loss
Hair
Amnioticmembrane
Lungs
Jaws
No.
Homoplasy – a shared character state that has not been inherited from a common ancestor. It can result from:Convergent evolution – independent
development of similar structures in organisms that are not related
Evolutionary reversal Systematists rely on the principle of
parsimony, which favors the hypothesis that requires the fewest assumptions
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Based on the principle of parsimony, the cladogram that requires the fewest number of evolutionary changes is favored; in this case the cladogram in (a) requires four changes, whereas that in (b) requires five
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Traits:Organism
Jaws Lungs AmnioticMembrane
Hair No Tail Bipedal Lamprey Shark Salamander Lizard Tiger Gorilla Human
Lamprey
Shark
Salamander
Lizard
Tiger
Gorilla
Human
0 0 0 0 0 0
1
1
1
1
1
1
0
1
1
1
1
1
0
0
1
1
1
1
1 1 1
1 1 0
1 0 0
0 0 0
0
0 0 0
0 0
Jaws
Lungs
Amnioticmembrane
Hair
Tail loss
Bipedal
Systematists increasingly use DNA sequence data to construct phylogenies because of the large number of characters that can be obtained through sequencing
Character states are polarized by reference to the sequence of an outgroup
Cladogram is constructed that minimizes the amount of character evolution required
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Other Phylogenetic MethodsSome characters evolve rapidly and
principle of parsimony may be misleadingFor example: parts of DNA that appear to have
no function. Can result in mutations and are not eliminated by
natural selection will thus have high rates of evolution of new character states as result of genetic drift
Because only 4 character states are possible (A, T, G,C), there is a high probability that two species will independently evolve the same derived character state at any particular base position
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1. Statistical approachRapid evolutionStart with an assumption about the rate at which
characters evolve and then Fit the data to these models to derive the phylogeny that best accords (i.e., “maximally likely”) with these assumptions
Advantage is that different assumptions of rate can be used for different models of evolution for different characters.
2. Molecular clockStates that the rate of evolution of a
molecule is constant through timeIn this model, Divergence in DNA can be
used to calculate the times at which branching events have occurred
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Systematics and ClassificationClassification
species and higher groups are placed into the taxonomic hierarchy
Genus, family, class, etc.
Monophyletic groupIncludes the most recent common ancestor of
the group and all of its descendants (clade)
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Monophyletic Group
Archosaurs
Systematics and ClassificationParaphyletic group
Includes the most recent common ancestor of the group, but not all its descendants
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Paraphyletic Group
Dinosaurs
Polyphyletic groupDoes not include the most recent common
ancestor of all members of the group
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Polyphyletic Group
Flying Vertebrates
Bats and birds could be classified in the same group, but their similarities reflect convergent evolution, not common ancestry.
Taxonomic hierarchies are based on shared traits, and should reflect evolutionary relationships, but do not fit the new understanding of phylogenetic relationships
Good example are BirdsTraditionally they were in the class Aves,
and dinosaurs in the class Reptilia but recent phylogenetic advances make clear that birds evolved from dinosaurs.
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Traditionally three major groups were recognized: green algae, bryophytes, and vascular plants
Recent research reveals that the green algae and bryophytes are not monophyletic:
Rather Bryophytes and are more closely related to vascular plants
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Red Algae Green Algae
Chlorophytes Charophytes Liverworts
Bryophytes
Hornworts Mosses
Vascular Plants
Biological species concept (BSC) Defines species as groups of
interbreeding populations that are reproductively isolated
Phylogenetic species concept (PSC)Species is a population or set of
populations characterized by one or more shared derived characters
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Species concepts
PSC solves 2 BSC problemsBSC cannot be applied to allopatric
populations – would they interbreed?PSC looks to the past to see if they have
been separated long enough to develop their own derived characters
BSC can be applied only to sexual speciesPSC can be applied to both sexual
and asexual species
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PSC still controversial Critics contend it will lead to the
recognition of even slightly different populations as distinct species
Paraphyly problem
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A B C D E
PhylogeneticsBasis for all comparative biologyHomologous structures
Derived from the same ancestral sourceDolphin flipper and horse leg
Homoplastic structures are notWings of birds and dragonflies
Phylogenetic analysis can help determine which a structure is
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Parental care in dinosaurs initially treated as unexpected
Examination of phylogenetic comparison of dinosaurs indicates they are most closely related to crocodiles and birds – both show parental care
Parental care in 3 groups not convergent but homologous behaviors
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a.a: Image #5789, photo by D. Finnin/American Museum of Natural History
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b.b: © Roger De La Harpe/Animals Animals
Homoplastic convergence: saber teeth Evolved independently in different
clades of extinct carnivoresSimilar body proportions (cat)Similar predatory lifestyleMost likely evolved independently at
least 3 times
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Monotremes
MarsupialsPlacentals
Phylogeny of Mammals
Car
niv
ore
s
Sab
er-t
oo
thed
m
arsu
pia
l
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Nimravids are a now-extinct group of catlike carnivores
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Carnivores
Felines
Nimravids
Sab
er-t
oo
thed
cat
Hye
nas
Civ
ets
Mo
ng
oo
ses
Sab
er-t
oo
thed
n
imra
vid
Phylogeny of CarnivoresB
ears
, se
als
,w
ease
ls,
can
ids
,an
d r
acco
on
s
Sab
er-t
oo
thed
nim
rav
id
Homoplastic convergence: plant conducting tubesSieve tubes facilitate long-distance
transport of food and other substances in tracheophytesEssential to the survival of tall plants on
landBrown algae also have sieve elementsClosest ancestor a single-celled
organism that could not have had a multicellular transport system
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µm 2 µm
Stramenopiles Alveolates Red Algae Chlorophytes Chlorophytes Liverworts Hornworts Mosses Tracheophytes
Brown Alga
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Angiosperms
(left): © Lee W. Wilcox; (right): © Dr. Richard Kessel & Dr. Gene Shih/Visuals Unlimited
Comparative BiologyMost complex characters do not evolve in one
stepEvolve through a sequence of evolutionary
changesModern-day birds exquisite flying machines
Wings, feathers, light bones, breastboneInitial stages of a character evolved as an
adaptation to some environmental selective pressure
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First featherlike structure evolved in theropod phylogenyInsulation or perhaps decoration
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Other dinosaurs Coelophysis Tyrannosaurus Sinosauropteryx Velociraptor Caudipteryx Archaeopteryx Modern Birds
Light bones
Wishbone, breastbone,loss of fingers 4 and 5
Downy feathers
Long arms, highly mobile wrist, featherswith vanes, shafts, and barbs
Long, aerodynamicfeathers
Arms longer than legs
Loss of teeth andreduction of tail
Phylogenetic methods can be used to distinguish between competing hypotheses
Larval dispersal in marine snailsSome snails produce microscopic larvae
that drift in the ocean currentsSome species have larvae that settle to
the ocean bottom and do not disperse
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• Fossils show increase in nondispersing snails
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Eocene
Percentage of species withnondispersing larvae
40 MYA
45 MYA
50 MYA
55 MYA
60 MYA
65 MYA
0 10050
Two processes could produce an increase in nondispersing larvaeEvolutionary change from dispersing to
nondispersing occurs more often than change in the opposite direction
Species that are nondispersing speciate more frequently, or become extinct less frequently than dispersing species
The two processes would result in different phylogenetic patterns
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In this hypothetical example, the evolutionary transition from dispersing to nondispersing larvae occurs more frequently (four times) than the converse (once)
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a.
Dispersing larvae
Nondispersing larvae
By contrast, clades that have nondispersing larvae diversify to a greater extent due to higher rates of speciation or lower rates of extinction (assuming that extinct forms are not shown)
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b.
Dispersing larvae
Nondispersing larvae
Phylogeny for Conus, a genus of marine snails. Nondispersing larvae have evolved eight separate times from dispersing larvae, with no instances of evolution in the reverse direction. This phylogeny does not show all species, however; nondispersing clades contain on average 3.5 times as many species as dispersing clades.
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c.
Dispersing larvaeNondispersing larvae
Dispersing larvae
Nondispersing larvae
Analysis indicates:Evolutionary increase in nondispersing
larvae through time may be a result of both a bias in the evolutionary direction and an increase in rate of diversification
Lack of evolutionary reversal not surprising – evolution of non-dispersing larvae a one-way street
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Loss of larval stage in marine invertebratesEggs develop directly into adultsNonreversible evolutionary changeMarine limpets: show direct development
has evolved many times3 cases where evolution reversed and larval
stage re-evolved
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a.
Larval stage
Direct development
Less parsimonious interpretation of evolution in the clade in the light blue box is that, rather than two evolutionary reversals, six instances of the evolution of development occurred without any evolutionary reversal
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b.
Larval stage
Direct development
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Phylogenetics helps explain species diversification
Use phylogenetic analysis to suggest and test hypotheses
Insight into beetle diversificationCorrespondence between phylogenetic
position and timing of plant origins suggests beetles are remarkably conservative in their diet
Beetle families that specialize on conifers have the deepest branches
Beetles specialize on Angiosperms have shorter branches
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Tertiary
Cretaceous
Jurassic
Triassic AngiospermCycadConifer
Number of Species
85 2000
24 1500
41,6
02
10 20 750
78 25,0
00
3 400
8 18 33,4
00
Phylogenetic explanations for beetle diversificationNot the evolution of herbivorySpecialization on angiosperms a
prerequisite for diversificationRisen 5 times independently within
herbivorous beetlesAngiosperm specializing clade is more
species-rich than the clade most closely related
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Disease EvolutionAIDS first recognized in 1980sCurrent estimate: > 33 million people
infected with human immunodeficiency virus (HIV); > 2 million die each year
Simian immunodeficiency virus (SIV) found in 36 species of primatesDoes not usually cause illness in
monkeysAround for more than a million years as SIV
in primates
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Phylogenetic analysis of HIV and SIV1. HIV descended from SIV
All strains of HIV are nested within clades of SIV
2. Number of different strains of HIV exitIndependent transfers from different
primate speciesEach human strain is more closely related
to a strain of SIV than to other HIV strainsSeparate origins for HIV strains
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3. Humans have acquired HIV from different host species
HIV-1, which is the virus responsible for the global epidemic, has three subtypesEach of these subtypes is most closely related
to a different strain of chimpanzee SIV, indicating that the transfer occurred from chimps to humans
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Subtypes of HIV-2, which is much less widespread, are related to SIV found in West African monkeys, primarily the sooty mangabey (Cercocebus atys) Moreover, the subtypes of HIV-2 also
appear to represent several independent cross-species transmissions to humans
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HIV
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Indicatestransmissionto humans
HIV mutates so rapidly that a single HIV-infected individual often contains multiple genotypes in his or her body
As a result, it is possible to create a phylogeny of HIV strains and to identify the source of infection of a particular individual
In this case, the HIV strains of the victim (V) clearly are derived from strains in the body of another individual, the patient
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