Consensus Trees, Ancestral reconstruction, Long Branch Attraction by xV43uA2v

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                                          Introduction to the Theory of Evolution:
                                                     Common Descent
                                                Classification: Linnaeus
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                                          Carl Linnaeus
                                           1707-1778
                                          Classification: Linnaeus


                                                          •   Hierarchical system
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                                                               –   Kingdom
                                                               –   Phylum
                                                               –   Class
                                                               –   Order
                                                               –   Family
                                                               –   Genus
                                                               –   Species
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                                          Classification depicted as a tree
                                                  Classification depicted as a tree



                                          Species Genus Family        Order           Class
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                                                 Theory of evolution
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                                          Charles Darwin
                                            1809-1882
                                                     Phylogenetic basis of systematics



                                          •   Linnaeus:
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                                              Ordering principle is God.

                                          •   Darwin:
                                              Ordering principle is shared descent from
                                              common ancestors.

                                          •   Today, systematics is explicitly based on
                                              phylogeny.
                                               Natural Selection: Darwin’s four postulates

                                          •   More young are produced each generation than can survive to reproduce.

                                          •   Individuals in a population vary in their characteristics.
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                                          •   Some differences among individuals are based on genetic differences.

                                          •   Individuals with favorable characteristics have higher rates of survival and
                                              reproduction.


                                          •   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
                                          Molecular Basis for Variation: DNA Mutation
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                                                               Other causes of evolution
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                                          • Sexual selection                 • Genetic drift (bottlenecks, founder effect,
                                                                             neutral evolution)
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                                          Introduction to the Theory of Evolution:
                                                The Evidence for Evolution
                                          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

                                          •   Science cannot prove or disprove the existence of God
                                          •   Evolutionary theory does not deny the existence of God, only a literal
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                                              interpretation of the first chapter of Genesis as an exact historical
                                              account.
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                                          Expected Gaps in Fossil Record
                                          Fossil Record, Distribution of Living and Extinct Animals

                                          •   Older geological strata contain extinct organisms

                                          •   Fossils in adjacent strata are typically more similar than fossils in non-adjacent
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                                              strata

                                          •   Fossils in the top (most recent) strata are very similar to contemporary species

                                          •   Fossils become progressively more different from contemporary species in
                                              progressively older (lower) strata.

                                          •   Fossils appear in the order which we would predict from the universal tree

                                          •   Fossils in a specific location are typically more closely related to local
                                              contemporary organisms.

                                          •   Closely related contemporary species are typically also close geographically,
                                              regardless of their habitat or specific adaptations.
                                                                 Fundamental Unity of Life
                                          •   All species use same genetic material (DNA/RNA)

                                          •   All species use catalysts (enzymes) based on protein molecules built from the
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                                              same set of 20 amino acids (from more than 390 naturally occurring)

                                          •   All species use extremely similar metabolic pathways and enzymes for their
                                              basic metabolism (e.g., glycolysis, the citric acid cycle, and oxidative
                                              phosphorylation).

                                          •   All species use the same genetic code (or minor variations)
                                          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
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                                                                       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
                                          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
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                                                                                       pelycosauria, therapsida, cynodonta, up
                                                                                       to primitive mammalia.




                                                                                       Interesting example: gradual evolution of
                                                                                       anvil and hammer in mammalian middle
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                                                                                       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.
                                          Fossilized Animals Should Conform to the Universal
                                                                Tree
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                                          Fossilized Animals Should Conform to the Universal
                                                                Tree
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                                                                    “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.
                                          Vestigial Structures


                                                        •   Vestige: a reduced and rudimentary
                                                            structure compared to the same
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                                                            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

                                                        •   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.
                                                                              Molecular Evidence
                                          •   Phylogenies based on DNA or protein sequences agree remarkably well with
                                              phylogenies based on morphology

                                          •   This is true regardless of whether functional or non-functional sequences are
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                                              used



                                                                                              For instance: endogenous
                                                                                              retroviruses (molecular remnants of a
                                                                                              past parasitic viral infection)

                                                                                              The arrows designate the relative
                                                                                              insertion times of the viral DNA into the
                                                                QuickTime™ and a
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                                                                                              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
                                              Molecular Evidence: Pseudogenes and Vitamin C



                                                                         GULO
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                                                                          gene         In most mammals
                                          Gene 1         Gene 2         Gene 3
                                                                                     Not so in primates…
                                          Enzyme 1       Enzyme 2       Enzyme 3
                                                                        Gulo Enz

                                      A              B              C              Vitamin C
                                                                                   D                       Vitamin C
                                            Portion of Working GULO Gene in Rat:




                                             Matching GULO Pseudogenes in 4 Primates                  Note Deletion
                                                                                Etc., etc., etc.

                                          •   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, ...).

                                          •   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).

                                          •   Extensive genetic change has repeatedly been observed in lab and wild populations of
                                              animals

                                          •   Numerous observations of morphological change in populations of living organisms
                                              (changes in color, size, length, width, and number of physical aspects of organisms)

                                          •   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.)

                                          •   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
                                                 Theory of evolution as the basis of biological
                                                                understanding
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                                          ”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
                                                                  Use of Animal Model Organisms

                                          •   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

                                          •   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 human-
                                              like 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

                                          Conserved features assumed to be important for functionality

                                          For instance: conserved pairs of cysteines indicate possible
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                                          disulphide bridge
                                                                    Sequences are related

                                          • Darwin: all organisms are related through descent with modification

                                          • Prediction: similar molecules have similar functions in different organisms
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                                                                                                Protein synthesis carried out by
                                                                                                very similar RNA-containing
                                                                                                molecular complexes
                                                                                                (ribosomes) that are present in
                                                                                                all known organisms
                                          Sequences are related, II
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                                                                 Related oxygen-
                                                                 binding proteins in
                                                                 humans
                                               Predicting Function from Sequence
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                                          Protein 1: binds oxygen
                                                                            •   Prediction of protein
                                                      Sequence similarity       function and structure
                                                                                (database searches).

                                          Protein 2: binds oxygen ?
                                                     Database searching
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                                              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
                                             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
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                                                                                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)

                                                    QuickTime™ and a
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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.
                                          Drug Resistance in Bacteria and Viruses
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                                                                        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
                                          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
                                               Sequence of 1918 Flu Provides Information About
                                              Important Adaptations for Human to Human Transfer
                                          •   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

                                          •   Several human isolates of 1997 Hong Kong H5N1 virus and 2004
                                              Vietnam H5N1 virus have one of these changes

                                          •   Other changes in other genes probably also necessary

                                          •   Would be interesting to find historical isolates of viruses predating 1918
                                              to fully reconstruct and understand the adaptation process

                                          •   Would be interesting to use mutational and epidemiological modeling to
                                              predict chance of virus adapting.

								
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