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Phylogenetics

Reconstructing the Tree of Life. Phylogenetics. Tree of Life Web Project. http://www.tolweb.org/tree/. Fig. 26-21. EUKARYA. Dinoflagellates. Land plants. Forams. Green algae. Ciliates. Diatoms. Red algae. Amoebas. Cellular slime molds. Euglena. Trypanosomes. Animals. Leishmania.

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Phylogenetics

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  1. Reconstructing the Tree of Life Phylogenetics

  2. Tree of Life Web Project http://www.tolweb.org/tree/

  3. Fig. 26-21 EUKARYA Dinoflagellates Land plants Forams Green algae Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Spirochetes Chlamydia Halophiles COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria (Plastids, including chloroplasts) ARCHAEA

  4. Outline What is a phylogeny? How do you construct a phylogeny? The Molecular Clock Statistical Methods

  5. Think about relationships among the major lineages of life and when they appeared in the fossil record Are Genetic Distances and fossil record roughly congruent?

  6. Fossil Record vs Molecular Clock • Molecular clock and fossil record are not always congruent • Fossil record is incomplete, and soft bodied species are usually not preserved • Mutation rates can vary among species (depending on generation time, replication error, mismatch repair) • But they provide complementary information • Fossil record contains extinct species, while molecular data is based on extant taxa • Major events in fossil record could be used to calibrate the molecular clock

  7. Evolutionary History of HIV HIV evolved multiple times from SIV (Simian Immunodeficiency Syndrome) Evolutionary Analysis Freeman& Herron, 2004 Time

  8. Charles Darwin (1809 -1882) On the Origin of Species (1859) • Living species are related by common ancestry • Change through time occurs at the population not the organism level • The main cause of adaptive evolution is natural selection

  9. Darwin envisaged evolution as a tree The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth…… …The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species….. ….the great Tree of Life….covers the earth with ever-branching and beautiful ramifications Charles Darwin, On the Origin of Species; pages 131-132

  10. Reconstructing the Tree of Life

  11. The only figure in The Origin of Species

  12. Past Future What did people believe before Darwin? Lamarck proposed a ladder of life

  13. Jean-Baptiste Lamarck • French Naturalist (1744-1829) • “Professor of Worms and Insects” in Paris • The first scientific theory of evolution (inheritance of acquired traits)

  14. Lamarck’s View of Evolution God Being • Continuum between physical and biological world (followed Aristotle) • Scala Naturae (“Ladder of Life” or “Great Chain of Being”) Angels Realm of Being Demons Man Animals Plants Realm of Becoming Minerals Non-Being

  15. What is wrong with a ladder? • Evolution is not linear but branching • Living organisms are not ancestors of one another • The ladder implies progress

  16. What is right with the tree? • Evolution is a branching process • If a mutation occurs, one species is not turning into another, but there is a split, and both lineages continue to evolve • So, evolution is not progressive - all living taxa are equally “successful” • Phylogenies (Trees) reflect the hierarchical structuring of relationships

  17. The only figure in The Origin of Species

  18. The Tree of Life is a Fractal http://tolweb.org/tree/phylogeny.html

  19. Genealogical structures • Phylogeny • A depiction of the ancestry relations between species (it includes speciation events) • Tree-like (divergent) • Pedigree • A depiction of the ancestry relations within populations • Net-like (reticulating)

  20. offspring parents Four butterflies connected to their parents

  21. future Individuals past Population

  22. Population Lineage/ Species What happened here? Phylogeny Lineage-branching Speciation

  23. What happened here? Extinction

  24. Representation of phylogenies? A B C A B C A simplified representation The True History

  25. Some terms used to describe a phylogenetic tree Taxon (taxa) Tip Internal branch Internode Node (Speciation event) Root

  26. Outline What is a phylogeny? How do you construct a phylogeny? The Molecular Clock Statistical Methods

  27. What is a Phylogeny? • A phylogenetic tree represents a hypothesis about evolutionary relationships • Each branch point represents the divergence of two taxa (e.g. species) • Sister taxa are groups that share an immediate common ancestor

  28. Molecular Clock • Mutations • On average, mutations occur at a given rate Example: Mitochondria: 1 mutation every ~2.2%/million years.

  29. Molecular Clock Faster if • Mutation rate is faster: • Shorter generation time (greater number of meiosis or mitosis events in a given time) • Replication Error (e.g. Sloppy DNA or RNA polymerase, inefficient mismatch repair)

  30. Phylogenetic Trees with Proportional Branch Lengths • In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage • So longer branches = greater evolutionary distance

  31. Phylogenetic Informative Characters(mutations) Neutral mutations: Mutations that are not subjected to selection Better for constructing phylogenies because selection could make unrelated taxa appear more similar or related taxa more different Examples: Noncoding regions of DNA, 3rd codon position in proteins, introns, microsatellites (“junk DNA”)

  32. Codon Bias • In the case of amino acids • Mutations in Position 1, 2 lead to change • Mutations in Position 3 don’t matter

  33. Species Order Family Genus Pantherapardus Panthera Felidae Taxidea taxus Taxidea Carnivora Mustelidae Lutra lutra Lutra Canis latrans Canidae Canis Canis lupus

  34. Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Taxon F Common ancestor of taxa A–F Polytomy (unresolved branching point)

  35. A monophyletic clade consists of an ancestral taxa and all its descendants A A A Group I B B B C C C D D D Group III Group II E E E F F F G G G (b) Paraphyletic group (c) Polyphyletic group (a) Monophyletic group (clade)

  36. Examples of Paraphyletic Groups

  37. A Group I B C D E F G (a) Monophyletic group (clade) (in the lecture on species concepts we discussed that the “smallest” monophyletic group is a “phylogenetic species”)

  38. Synapomorphies Synapomorphies are shared derived homologous traits They can be DNA nucleotides or other heritable traits They are used to group taxa that are more closely related to one another

  39. synapomorphies

  40. Sometimes similar looking traits are not homologous, and are not synapomorphies, but are the result of convergent evolution

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