BIOEE1780 Week 2

  1. Phylogeny:
    • Is a visual representation of the evolutionary history of populations, genes or species. Phylogenetic trees represent the branching pattern of evolution over time.
    • They are most accurate when constructed using shared derived characters.
    • They are hypotheses that describe the relationships among taxa on the best available evidence.
  2. Tips:
    • The terminal ends of an evolutionary tree, representing species, molecules, or populations being compared.
    • The tips aren’t necessarily single species and may represent entire clades (based on what the tree aims to emphasize)
  3. Branches:
    • Are lineages evolving through time that connect successive speciation or other branching events.
    • They can be internal or terminal.
  4. Nodes:
    • Are points in the phylogeny where a lineage splits (a speciation event or another branching event such as the formation of a sub-species)
    • Occurs when individuals in two populations become subdivided to the point where they are no longer able to exchange genes.
    • Swiveling the nodes does not change the relationships.
    • Each node represents an actual organism or population that are or were alive at some point in the past.
    • They represent the most recent common ancestor between lineages. Thus, looking at nodes can tell us when certain taxa shared common ancestry. The more recent the MRCA, the closer the lineages.
  5. internal nodes:
    Nodes that occur within a phylogeny and represent ancestral populations or species.
  6. Monophyletic
    • Describes a group of organisms that form a clade.
    • Is composed of the most recent common ancestor and all of its descendants.
    • Modern taxonomists aim to create groups that represent monophyletic clades.
    • A piece of a larger tree that can be removed with a single cut.
    • Mammals are monophyletic.
  7. Clade:
    • Single branches in the tree of life that represent an organism and all of its descendants.
    • Used interchangeably with monophyletic group.
    • The number of clades is the number of nodes on the phylogenetic tree.
    • Smaller clades are within larger clades.
  8. Polyphyletic
    Describes a taxon that does not include the common ancestor of all members of the taxon. You need to cut the tree in two or more places to get all the species in a paraphyletic group.
  9. Paraphyletic
    • Describes a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor.
    • Reptilia is paraphyletic because it does not include the birds.
    • “Fish” is paraphyletic, so its divided into 4 monophyletic clades in modern taxonomy.
  10. Outgroup
    • Group of organisms that is outside the monophyletic group being considered.
    • Outgroups allow us to infer which character states are primitive (ancestral) or derived by helping us decide what traits looked like before they became specialized in a particular clade or lineage.
  11. taxon (taxa)
    • Groups of organisms that a taxonomist judges to be cohesive taxonomic units, such as species or order, genera or even genes.
    • The most closely related taxon to a monophyletic group is called the “sister taxon.”
  12. most recent common ancestor (MRCA)
    Is the node connecting all lineages in question.
  13. Character
    • Heritable aspects of an organism that can be compared across taxa. Each time we measure a character in a taxon, we “score” it.
    • Morphological or physiological characters (traits)
    • Molecular characteristics
  14. character state (ancestral state, derived state)
    • Relative terms that tell you when traits evolved in evolutionary time. Ancestral state is the historical state of the character.
    • Derived state refers to the more recently evolved state of the character.
    • 0 represents the ancestral state, whereas 1 represents the derived state.
  15. What is plesiomorphy?
    Ancestral character state
  16. What is apomorphy?
    Derived character state.
  17. Synapomorphy
    • Shared derived characters that evolved in the immediate common ancestor of the group and was inherited by all the descendants.
    • Synapomorphies are phylogenetically informative. Organisms that share more synapomorphies can be inferred to be closer relatives of each other.
    • Inherited from an ancestor for which the trait was an apomorphy and an autapomorphy.
  18. Symplesiomorphy:
    Pleisomorphy (ancestral character state) shared by 2 or more taxa.
  19. Autapomorphy:
    Distinct, derived trait specific to a taxon.
  20. Homoplasy
    Describes a character state similarity not due to shared descent, but due to convergent evolution or evolutionary reversal. (uncommon)
  21. convergent evolution
    The independent origin of similar traits in separate evolutionary lineages.
  22. evolutionary reversal (= character reversal)
    The reversal of a derived character state to a form resembling its ancestral state.
  23. Maximum Parsimony
    • Is a principle that guides the selection of alternative hypotheses; the alternative requiring the fewest assumptions or steps is usually (but not always) best.
    • In cladistics, scientists search for the tree topology with the least number of character state changes - the most parsimonious.
  24. Cladogram:
    • A phylogenetic tree that only shows the relationship between species.
    • The branches do not precisely measure the period of time it took between different speciation events.
    • Only relative timings of various speciation events can be inferred.
    • Note that derived and ancestral characters are relative to each other. A trait that is derived for one clade may be ancestral for another.
  25. It’s important not to interpret the sequence of species as a linear ancestor-descendant relationship. None of ABCD descend from each other. We can choose not to display certain species or collapse a clade into a single tip.
  26. Polytomy
    Describes an internal node of phylogeny with more than two branches. (the order in which the branchings occurred is not resolved in consensus trees)
  27. How do we know all life is related?
    • Homology: Different organisms share related structures. (homologous structures)
    • Ribosomes are universal. The extremely complex structures wouldn’t have evolved twice.
    • All life uses the same genetic code.
  28. Homoplasmy and Homology:
    • Homoplasmy is convergent evolution and analogous structures.
    • Homology is divergent evolution and homologous structures.
  29. What does the axis parallel to the phylogenetic tree represent?
  30. How do we determine how close two lineages are in time/ divergence time on a cladogram?
    • Determine the MRCA (the node connecting the two lineages).
    • Look at its position on the parallel axis to infer relative date.
    • “More distantly related to…” “more closely related to…”
  31. Why is there so much emphasis on monophyletic groups?
    • Classifications must be defined as evolutionary units aka monophyletic groups defined by nodes.
    • Reptiles and dinosaurs, because they’re missing birds, are paraphyletic groups. Birds are actually reptiles.
  32. Scientific Process:
    • Question to hypothesis
    • Experiment / observation
    • Data / fact
    • Inference (check if hypothesis is correct)
    • This is a cycle. Phylogenies are hypotheses. Phylogenetic trees are competing hypotheses.
  33. How do we select the best phylogenetic hypothesis?
    • Search algorithms: computational approaches.
    • It rapidly becomes difficult to compare all trees to choose the best one. There are often many trees that support your finite data.
    • Parsimony (fewest number of character state changes) This is the most common approach for morphological characters.
    • Select the tree that’s more probable (models of character evolution) based on probability estimates for different types of DNA mutations.
  34. Branch support metrics
    • The numbers on the branches of phylogenetic trees.
    • They represent statistical confidence given to branches.
    • “Bootstrap support” “posterior probabilities”
    • The closer you are to a 100, the more confident you are.
    • No number means that the confidence isn’t very high. There may be branches that conflict with this.
  35. Phylogenetics and similarity?
    • Trees are not a depiction of similarity.
    • Some lineages may have evolved very rapidly, with many character state changes (highly derived).
    • This would mean that these organisms are not similar to each other at all. (common theme in island biogeography)
  36. What can be done with phylogenetic trees?
    • Mapping characters to compare the evolution of different traits.
    • Trace the origin of epidemics.
    • Inform taxonomy. Naming conventions.
  37. Explain Phylograms
    • Branch lengths vary to represent the number of character state transitions on each branch (DNA mutations)
    • Useful for presenting the rate of evolution for various lineages.
  38. Explain neutral theory of molecular evolution
    • At the fine scale genetic level, most new mutations are not favored by natural selection or have no effect on fitness.
    • For example, many DNA nucleotide substitutions are synonymous (synonymous mutations), meaning they code for the same amino acid. This keeps the rate of mutation neutral. BACKGROUND MUTATION RATE (AVERAGE)
    • Neutral mutations arise at random and random factors (genetic drift) determine their fate in a population. They generally occur on the 3rd amino acid of the codon.
    • Can be used for dating the time of divergences.
    • Cytochrome C used due to strong selection against mutation (purifying selection)
  39. Molecular Clock
    • Use the rate of molecular change to deduce the divergence time between two lineages in phylogeny.
    • They work best when calibrated with other markers of time such as fossils.
    • Slow evolving genes like cytochrome C are preferred, as they’re likely to have accumulated less noise due to homoplasmy.
  40. polyphyletic
    a group that includes several descendants, but not the MRCA
  41. What kind of traits aren’t phylogenetically informative?
    • Autapomorphies. (derived traits in only one taxon)
    • They’re not useful because they do not group any taxa together.
  42. What are the different types of phylogenies?
    • Cladogram: Branch lengths are qualitative, not quantitative. Only relative dates, not absolute dates.
    • Phylogram: Branch lengths reflect amount of change in characters used to infer the tree.
    • Chronogram: Calibrated to real time: nodes indicate estimated ages of ancestors.
  43. What kind of characters are useful for reconstructing trees?
    • Morphological traits are the only option for fossils
    • DNA sequence is usually excellent for contemporary species. Base pairs are treated as the characters.
    • Remember that a character must be heritable in some sense to provide any insight!
  44. What kind of characters should we look at for distantly / closely related data?
    • For distantly related taxa, slowly evolving characters will minimize homoplasy.
    • For closely related taxa, rapidly evolving characters are needed to reveal relationships.
    • For both cases, ideal characters have low rates of convergence and reversal. This may lead to cases in which lineages appear to share characters, but the characters are not actually shared derived characters (homoplasies)!
    • For example, bird and bat wings are homoplasies and analogous structures.
  45. Vestigial
    • Character reversal leads to unused, extra traits.
    • Example: Vestigial hind limps and pelvis of boas and pythons.
  46. Not enough phylogenetically informative information means:
    The gene is evolving too slow.
  47. How can we use DNA sequences to build phylogenetic trees?
    • Align the DNA sequences from the species being examined.
    • Identify the positions that are variable. These are called phylogenetically informative characters.
    • Build the most parsimonious tree that requires the fewest number of evolutionary events (e.g. nucleotide substitutions) to explain the observed data.
  48. Explain detection and prevention through phylogenetic forensics:
    • Single outbreak: phylogeny used to date the origin of disease
    • Multiple infections: phylogeny used to determine the source.
    • Biogeography: Phylogeny used to explore disease spread.
  49. Explain phylogeny and method for single outbreak
    When viruses move from the source population to the recipient population, they only carry a subset of the viral diversity to the new location (founder effect). Through this, the source of the infection can be determined.
  50. Information about HIV:
    • Replicates and mutates very fast.
    • In 75% of all cases, infection happens with one virus from the source individual.
  51. How do we infer single infection?
    • Single infection event is inferred if the viruses within an individual form a monophyletic clade. Branching order gives clues about the movement of the HIV virus within the individual.
    • The viruses within the infected person are nested within the phylogeny of the source individual.
  52. Explain phylogeny and method for dating the date of the origin of disease
    • Viruses replicate fast and thus mutate rapidly. If this rate is constant, it can be used as a molecular clock.
    • Through this, virus epidemics can be tracked over time and space.
  53. What kind of evidence are we looking for in the case of HIV transmission?
    • Who was the index case? Can we prove that someone served as the ancestral population? We can prove this if the individual is paraphyletic.
    • How are the viral populations related? Can we demonstrate the directionality of the source to recipient? Yes, all infected were monophyletic and nested in the source individual’s phylogenetic tree.
    • When did it happen? Can we use molecular clock to corroborate timing of transmission? Branch lengths tell us about the timing of infection.
  54. Repeated paraphyly on the virus means
    Supports the hypothesis that the individual was the source rather than a recipient.
  55. Why are there multiple branches for each sample? Why does each sample form a clade?
    • Mutation leads to branching.
    • Infection occurs through a single source virus. A single infection event occurs (the individual wasn’t infected by anyone else)
  56. How can we tell how long ago the infection occurred?
    • Longer branch lengths mean that there is more time for mutations to accumulate.
    • In the phylogeny of infection, branch lengths matter more than branching events, as branching events don’t necessarily mean infection, but viral diversification does.
  57. What is an Ecomorph:
    • Species with the same structural habitat / niche, similar in morphology and behavior. Different species are grouped together based on their functional characteristics. Ecomorphs can be monophyletic or have evolved through convergent evolution in different clades.
    • If ecomorphs are not closely related, it can be inferred that they result from convergent evolution.
Card Set
BIOEE1780 Week 2
Phylogenetics 1, 2 and 3