Download Consensus Trees, Ancestral reconstruction, Long Branch

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Introduction to the Theory of Evolution:
Common Descent
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Classification: Linnaeus
Carl Linnaeus
1707-1778
Classification: Linnaeus
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Hierarchical system
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Kingdom
Phylum
Class
Order
Family
Genus
Species
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Classification depicted as a tree
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Classification depicted as a tree
Species Genus Family
Order
Class
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Theory of evolution
Charles Darwin
1809-1882
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Phylogenetic basis of systematics
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Linnaeus:
Ordering principle is God.
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Darwin:
Ordering principle is shared descent from
common ancestors.
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Today, systematics is explicitly based on
phylogeny.
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Natural Selection: Darwin’s four postulates
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More young are produced each generation than can survive to reproduce.
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Individuals in a population vary in their characteristics.
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Some differences among individuals are based on genetic differences.
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Individuals with favorable characteristics have higher rates of survival and
reproduction.
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Evolution by means of natural selection
Presence of ”design-like” features in organisms:
Quite often features are there “for a reason”
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Molecular Basis for Heredity: DNA
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Molecular Basis for Heredity: DNA
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Molecular Basis for Variation: DNA Mutation
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Other causes of evolution
• Sexual selection
• Genetic drift (bottlenecks, founder effect,
neutral evolution)
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Introduction to the Theory of Evolution:
The Evidence for Evolution
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The Evil Tree of Evolution
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Evolution Seen as Ungodly
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“Teach the Controversy”
…to help revitalize science education
Science and Religion are not Contradictory
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Science cannot prove or disprove the existence of God
Evolutionary theory does not deny the existence of God, only a literal
interpretation of the first chapter of Genesis as an exact historical
account.
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Expected Gaps in Fossil Record
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Fossil Record, Distribution of Living and Extinct Animals
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Older geological strata contain extinct organisms
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Fossils in adjacent strata are typically more similar than fossils in non-adjacent
strata
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Fossils in the top (most recent) strata are very similar to contemporary species
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Fossils become progressively more different from contemporary species in
progressively older (lower) strata.
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Fossils appear in the order which we would predict from the universal tree
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Fossils in a specific location are typically more closely related to local
contemporary organisms.
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Closely related contemporary species are typically also close geographically,
regardless of their habitat or specific adaptations.
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Fundamental Unity of Life
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All species use same genetic material (DNA/RNA)
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All species use catalysts (enzymes) based on protein molecules built from the
same set of 20 amino acids (from more than 390 naturally occurring)
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All species use extremely similar metabolic pathways and enzymes for their
basic metabolism (e.g., glycolysis, the citric acid cycle, and oxidative
phosphorylation).
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All species use the same genetic code (or minor variations)
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Fossilized Animals Should Conform to the Universal
Tree
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Fossilized Animals Should Conform to the Universal
Tree
We have found a quite complete set of
dinosaur-to-bird transitional fossils with no
morphological "gaps",
Represented by Eoraptor, Herrerasaurus,
Ceratosaurus, Allosaurus,
Compsognathus, Sinosauropteryx,
Protarchaeopteryx, Caudipteryx,
Velociraptor, Sinovenator, Beipiaosaurus,
Sinornithosaurus, Microraptor,
Archaeopteryx, Rahonavis,
Confuciusornis, Sinornis, Patagopteryx,
Hesperornis, Apsaravis, Ichthyornis, and
Columba, among many others
All have the expected possible
morphologies.
For instance: Archaeopteryx
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Fossilized Animals Should Conform to the Universal
Tree
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Fossilized Animals Should Conform to the Universal
Tree
We also have an exquisitely complete
series of fossils for the reptile-mammal
intermediates, ranging from the
pelycosauria, therapsida, cynodonta, up
to primitive mammalia.
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Interesting example: gradual evolution of
anvil and hammer in mammalian middle
ear from reptilian jawbones
In the reptilian fetus, two developing
bones from the head eventually form two
bones in the reptilian lower jaw, the
quadrate and the articular.
The corresponding developing bones in
the mammalian fetus eventually form the
anvil and hammer (incus and malleus) of
the mammalian middle ear.
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Fossilized Animals Should Conform to the Universal
Tree
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Fossilized Animals Should Conform to the Universal
Tree
“Finally, and most glaringly obvious, if random
evolution is true there must have been a large
number of transitional forms between the
mesonychid and the ancient whale: Where are
they? It seems like quite a coincidence that of all
the intermediate species that must have existed
between the mesonychid and whale, only species
that are very similar to the end species have been
found.”
(Behe 1994)
But: In recent years, we have found several
transitional forms of whales with legs, both capable
and incapable of terrestrial locomotion.
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Vestigial Structures
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Vestige: a reduced and rudimentary
structure compared to the same
complex structure in other organisms.
Vestigial characters, if functional,
perform relatively simple, minor, or
inessential functions using structures
that were clearly designed for other
complex purposes
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From common descent and the
constraint of gradualism, we predict
that many organisms should retain
vestigial structures as structural
remnants of lost functions. Note that
the exact evolutionary mechanism
which created a vestigial structure is
irrelevant as long as the mechanism is
a gradual one.
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Molecular Evidence
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Phylogenies based on DNA or protein sequences agree remarkably well with
phylogenies based on morphology
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This is true regardless of whether functional or non-functional sequences are
used
For instance: endogenous
retroviruses (molecular remnants of a
past parasitic viral infection)
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The arrows designate the relative
insertion times of the viral DNA into the
host genome.
All branches after the insertion point (to
the right) carry that retroviral DNA - a
reflection of the fact that once a retrovirus
has inserted into the germ-line DNA of a
given organism, it will be inherited by all
descendants of that organism
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Molecular Evidence: Pseudogenes and Vitamin C
A
Gene 1
Gene 2
GULO
gene 3
Gene
Enzyme 1
Enzyme 2
Gulo Enz3
Enzyme
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C
In most mammals
Not so in primates…
Vitamin
C
D
Vitamin C
Portion of Working GULO Gene in Rat:
Matching GULO Pseudogenes in 4 Primates
Note Deletion
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Etc., etc., etc.
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Ontogeny: often an organism’s evolutionary history is represented temporarily in its
development (hind limbs in whales and snake embryos, tails in human embryos, gill
pouches in mammal embryos, ...)
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Atavism: Occasionally contemporary animals are born with characters representative of
remote ancestors (living whales with hindlimbs, human babies born with tails, ...).
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Atavisms and vestiges are always found to be consistent with the universal tree (organisms
always have atavistic or vestigial characters that are predicted to have been present in an
ancestor).
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Extensive genetic change has repeatedly been observed in lab and wild populations of
animals
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Numerous observations of morphological change in populations of living organisms
(changes in color, size, length, width, and number of physical aspects of organisms)
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Many observations of newly acquired functions (bacteria that evolved to use nylon and
pentachlorophenol as their sole carbon source, bacteria that evolved to synthesize new
amino acids, crustaceans that evolve new defenses to predators, etc.)
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Experimental observations of speciation (according to the biological species concept): plants
(with and without polyploidization), fruit fly, house fly, apple maggot fly, gall former fly, flour
beetles, polychaete worm. (Major changes seen for asexual species also)
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The Role of Evolutionary Theory in Contemporary
Biomedical Research
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Theory of evolution as the basis of biological
understanding
”Nothing in biology makes sense, except in the light of evolution.
Without that light it becomes a pile of sundry facts - some of them
interesting or curious but making no meaningful picture as a
whole”
T. Dobzhansky
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Use of Animal Model Organisms
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Model organism: a species that is studied to understand biological phenomena, with the
expectation that discoveries made in the organism model will provide insight into the
workings of other organisms.
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This is only possible because fundamental biological principles such as metabolic,
regulatory, and developmental pathways, and the genes that code for them, are conserved
through evolution
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For instance: pre-clinical testing in animals (rodents often used, but species closer to
humans in the universal tree are preferred when it is important to test under more humanlike conditions)
• Very fundamental systems can be
examined in very distant species (e.g., cell
cycle regulation examined in yeast)
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Interpretation of Multiple Alignments
Interpretation of Multiple Alignments
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Conserved features assumed to be important for functionality
For instance: conserved pairs of cysteines indicate possible
disulphide bridge
Sequences are related
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• Darwin: all organisms are related through descent with modification
• Prediction: similar molecules have similar functions in different organisms
Protein synthesis carried out by
very similar RNA-containing
molecular complexes
(ribosomes) that are present in
all known organisms
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Sequences are related, II
Related oxygenbinding proteins in
humans
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Predicting Function from Sequence
Protein 1: binds oxygen
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Sequence similarity
Protein 2: binds oxygen ?
Prediction of protein
function and structure
(database searches).
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Database searching
Find similar sequences in database,
Predict function
Query sequence
Database
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BLAST database search on the web
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BLAST database search on the web
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Sequence and Function are not Necessarily Linked
• Proteins can retain function despite extensive changes (e.g., yeast and
human cytochrome c are 40% different, but yeast can live with human
cytochrome c if its own gene has been deleted)
• On average only 34% of random amino acid changes in a protein will
disrupt function (Guo et al., 2004, Protein tolerance to random amino acid
change. PNAS 101(25):9205-10)
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• Cytochrome c from various bacterial species have virtually no sequence
similarity but fold up into the same 3D structure and perform the same
function
• Different structure, same function. For instance: carbonic anhydrase in
mammals, plants, and methane-producing bacteria have no structural or
sequence similarity but perform same function.
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Drug Resistance in Bacteria and Viruses
Several types of antibiotics
inhibit protein synthesis by
binding to ribosomes
Antibiotic resistance often
involves point mutations in
the ribosome that disrupt
binding of the antibiotic
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Drug Resistance in Bacteria and Viruses
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Influenza Subtypes
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Reconstruction of 1918 Flu strain
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Influenza Pandemics and Bird Flu
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Sequence of 1918 Flu Provides Information About
Important Adaptations for Human to Human Transfer
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Sequence analysis has identified 10 amino acids that are found in
polymerase genes of human influenza viruses (including 1918 strain)
but not in avian viruses
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These could be important for adaptation to the human host
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Several human isolates of 1997 Hong Kong H5N1 virus and 2004
Vietnam H5N1 virus have one of these changes
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Other changes in other genes probably also necessary
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Would be interesting to find historical isolates of viruses predating 1918
to fully reconstruct and understand the adaptation process
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Would be interesting to use mutational and epidemiological modeling to
predict chance of virus adapting.