Tree of Life and Classification

Tree of Life and Classification

1. Kingdoms of life

   • Highest (most) inclusive rank of classifiction
   • Two kingdoms: plants and animals
   • Six lineages: Bacteria, Archaea, Protista, Plantae, Fungi and Animalia
     • Things are always changing classification

2. Tree of Life

   • Visual representation of Evolution

3. Theory of Evolution

   • Strong and well supported theory that has become the central unifying concept of biology
     • Evolution: depends on variation of trait (must be heritable, influenced by genetic differences)
       • Differential reproduction will carry the varying trait across generations
   • Evolution: Continuous process that produces genetic changes in a population
   • Tree of Life depicts evolutionary patterns, the products that evolution has produced over time

4. Why is TOL possible

   • Cells look alike
   • Cells function the same
   • DNA has same dictionary for all living things

5. Terminology

   • Phylogeny: Evolutionary history of species or a group of organisms
   • Systematics: science that classifies organisms and determines their evolutionary relationships
   • Taxonomy: Discipline that determines how organisms are named and classified; uses hierarchial system of clasification
   • Species: Basic Unit of taxonomy
     • Different concepts on how species taxon is defined
       • Biological species concept
         • Based on reproductive isolation between species
       • Morphological species concept
         • Based on phenotypic difference between species
       • Phylogenetic species concept
         • Based on relationships identified through cladistic analysis
   • Classification: How we group organisms
     • 8.74 +/- 1.3 million species (85% undescribed)

6. TOL = phylogeny

   • Phylogeny depicts hypothesis about evolutionary relationships among individuals or groups of organisms

7. Data used to reconstruct TOL

   • Data from any heritable trait that shows variaiton
     • Morphological (including fossil)
     • Molecular (DNA, RNA)

8. Troublesome Terminology

   • ANCESTRAL vs primitive: arose early in evolutionary history
   • DERIVED vs evolved: (derived) undergone recent change

9. Misconceptions about TOL and Evolution

   • Trees (phylogenies) should represent evolutionary progress and increasing complexity
   • 'Non-primitive' or 'advanced' organisms are somehow better and more complex
   • Trees (Phylogenies) should show increased diversity with time
   • Trees (Phylogenies) should show similar shape and structure

10. Phylogeny

    • Evolutionary relationships depicted in a branching diagram
      • Phylogenetic tree
      • Cladogram
      • Pattern of relationships uncovered using cladistics
        • An analysis that groups taxa by shared derived characters (synapomorphies)
    • Structure of phylogeny
      • Sorted into clades: groups that contain evolutionary ancestor and all species descended from that ancestor

11. Characters

    • Ancestral character
      • plesiomorphic chracter (simlar in form)
    • Shared plesiomorphies
      • Symplesiomorphies
        • E.g. platypus, koala, dingo: Hair, internal fertilisation, suckle young
        • These characters are symplesiomorphies: shared among all members so do not show pattern of relationships between taxa
    • Derived character
      • Apomorphy
      • Shared apomorphies - shared derived characters
        • Synapomorphies
          • Example: Koala and dingo: Anal and urogenital openings separate, mammary glands with teats
          • Each branch of a cladogram is supported by one or more synapomorphies
            • Each species has one or more unique characters that distinguish it from other species
              • Autapomorphy
              • No information about relationships

12. Comparing morphology

    • Anatomy
      • Comparison of body form
        • Example: pentadactyl limb of vertebrates
    • Embryology
      • Comparison of developmental patterns
        • Example: protosome vs deuterosome
      • Comparison of embryonic form
        • Example: notochord in chordates
    • Vestigial organs
      • Rudimentary (poorly developed) organ without functions
    • Evolutionary remnants of structures that were functional in ancestral species
      • E.g. phythons possess cloacal spurs - vestigial hind limbs: descended from limbed ancestors
    • Fossils
      • Preserved remains of organisms
    • Comparative morphology + geological time
      • Indicate minimum age of taxa
    • Reduced range of characters because of fossilisation process
      • Usually bones, teeth, shells, wood

13. Divergent evolution

    • Pattern of evolution is divergence from a common ancestral form
      • Example: crocodile, bird, bat and whale differ but are all descended from a common ancestral form
    • Change in form
      • Example: Crocodile, bird, bat and whale forelimbs differ in external appearance but have same basic structure
    • Homologous characters
      • Same plan, different function - indicate common ancestry

14. Convergent evolution

    • Convergence in form in unrelated organisms
      • Example: cacti, euphorbs etc are in similar form but descended from DIFFERENT ancestral forms
    • Similarity due to similar environments
      • Example: Succulent plants inhabit arid areas
    • Analogous characters
      • Different plan, same function - DO NOT indicate common ancestry

15. Reconstructing phylogenies

    • Homologous characters
      • Provide information for examining phylogeny
    • Analogous characters
      • do not provide information for examinig phylogeny

16. Parallel Evolution

    • Closely related organisms may evolve similar features because they face similar environments
      • Features are ANALOGOUS not homologous

17. Adaptive Radiation

    • New adaptation that allows organisms to us resource or niche that would have been unavailable without the adaption
    • Key innovations allows a species to access many new and different niches, which make it easier for a lineage to speciate

18. Flight/Wings

    • Insects, birds, pterosuars and bats all have wings and fly
    • Similar structure, same function - INDEPENDENT EVOLUTIONARY ORIGIN

19. Comparing molecules

    • Proteins
      • Comparison of amino acid sequences
        • E.g. chimpanzees and humans have identical sequences in proteins
    • DNA
      • Comparison of nucleotide sequences
        • E.g. phylogeny of apes reconstructed using mitochondrial DNA

20. DNA and RNA Sequences

    • Rates of change differ between sequences
    • Nuclear-encoded RNA
      • Ribosomal RNA
      • Highly conserved (slow to change)
      • Used to reconstruct phylogenies back to the origin of life
    • Mitochondrial DNA, chloroplast DNA
      • Variable rates of change
      • Can be used for more closely related taxa

21. Molecular clocks and measuring evolutionary time

    • DNA works like a timer as every mutation
      • Adverse mutations (affect function of critical gene) are eliminated by natural selection
      • Neural changes accumulate (constant rate) - act as a MOLECULAR CLOCK

22. Measuring evolutionary time based on DNA

    • No single molecular clock - different segments accumulate mutations at different rates
    • Regions of DNA where base substitutions accumulate rapidly (high rate of mutations) are useful for studying phylogeny of closely related organisms

23. Parismony

    • Observations as the explanation

24. Binomial system

    • Codes of nomenclature set rules for naming ranks of raxa
    • Identified by two words: GENUS + SPECIFIC EPITHET
      • GENUS name (Capitalized)
      • Specific epithet (never capitalised)

25. Monophyly

    • Hierarchial classification reflects phylogeny
      • Expresses the branching pattern of cladograms
    • Each named group should be monophyletic - should be a clade
      • Containing all descendants of a common ancestor
      • Non-monophyletic groups: paraphyly, polyphyly
        • Paraphyletic group
          • Does not include descendants of a common ancestor
        • Polyphyletic group
          • Includes descendants from unrelated groups
          • Based on convergent evolution
    • Traditional classifications often include non-monophyletic groups

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