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Phylogenetics

Reconstructing the Tree of Life. Phylogenetics. In the Speciation lecture, I talked about a “ Phylogenetic Species Concept ” What is a “ Phylogeny? ” How do you construct one? Why on earth should I care?. Why you should care:.

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Phylogenetics

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  1. Reconstructing the Tree of Life Phylogenetics

  2. In the Speciation lecture, I talked about a “Phylogenetic Species Concept” • What is a “Phylogeny?” • How do you construct one? • Why on earth should I care?

  3. Why you should care: • All biological relationships can be determined by constructing phylogenies: Even if phylogenies are not always the best way to define species boundaries, they do tell you the genetic and evolutionary relationships among groups and individuals • Your ancestry • Diseases—figure out evolutionary origins and evolutionary pathways of disease, like HIV, Ebola, SARS, etc. • Crops and live stock (food security)—rescue from inbreeding, create new varieties • Endangered Species— figure out how endangered populations are related and how to perform genetic rescue

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

  5. Tree of Life 2016Hug et al. 2016 Nature Microbiology Bacteria Eukarya Archaea

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

  7. 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?

  8. 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

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

  10. 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

  11. 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

  12. Reconstructing the Tree of Life

  13. The only figure in The Origin of Species

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

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

  16. 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

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

  18. 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

  19. The only figure in The Origin of Species

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

  21. 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)

  22. offspring parents Four butterflies connected to their parents

  23. future Individuals past Population

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

  25. What happened here? Extinction

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

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

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

  29. 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

  30. Molecular Clock • Phylogenies rely on the “Molecular Clock,” namely the fact that Mutations on average, occur at a given rate • So, on average, more mutational differences between taxa means that they branched from a common ancestor longer ago • So longer branches on phylogeny often  greater evolutionary distance Example: Mitochondria: 1 mutation every ~2.2%/million years

  31. Phylogeny of 53 humans (Homo sapiens) just based on mtDNA • A different locus might yield a different tree • The horizontal branch lengths reflect genetic distance ≈ # of mutations

  32. Cladogram of mitochondrial cytochrome oxidase II alleles in humans and the African Great Apes (Ruvolo et al. 1994) This is not a phylogeny, but a cladogram. A cladogram shows the hierarchical relationships among the taxa, but the branch lengths do not reflect evolutionary time.

  33. Molecular Clock Problem: mutation rate can vary among species • 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; poor mismatch repair mechanisms)

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

  35. 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)

  36. 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)

  37. Examples of Paraphyletic Groups (not recognized as legitimate groups in the Phylogenetic Species Concept, which only recognizes monophyletic groups)

  38. 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”)

  39. 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

  40. synapomorphies

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

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