Phylogeny (Chapter 26)

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Phylogeny (Chapter 26)
2013-12-12 18:03:24

Biology 2009
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  1. What is phylogeny?
    the evolutionary history of species
  2. systematics
    the discipline of classifying organisms (important because allows us to build evolutionary trees to show life progression)
  3. Taxonomy
    how organisms are named and classified (goes along with systematics)
  4. Hierarchical classificaitons
    • There are rules: genus and species- capitalize genus and italicize both. 
    • (domain (bacteria, eukarya, and archaea)>kingdom> phylum>class>class>order>family>genus>species
  5. Taxon
    • a grouping of organisms at a given level (mammals at the class level)
    • How taxonomists group organisms
  6. what is the object of drawing a Phylogenetic tree?
    What do the branches represent?
    • Represents the evolutionary history of species
    • Branchpoints represent common ancestor species, possibly extinct.
  7. Why can drawing a phylogenetic tree be difficult?
    • The tree branches based on fossils cannot be certain because we cannot go back in the past. 
    • We are prejudiced by believing that we can tell by looking at organisms that they are related (and we can sometimes but sometimes we can't)
  8. What are the two approaches to drawing a tree?
    • Morphological homologies- shared characteristics
    • Molecular homologies- DNA identities
  9. Morphological homologies

    What leads to analogy?
    • We use visual characteristics. Works as long as we are systematic and cautious. (Mole rat looking thing is an example)
    • convergent evolution
  10. What are homoplasies?
    • analogous structures, like bird and bat wings
    •  (homology- bone changes structure by Hox gene)
  11. Taxon
    All the organisms within a phylogenetic level (example- all cat genera in the family felidae)
  12. clade
    • all the organisms, past and present, starting at an evolutionary branch point (ex- four walking legs) 
    • Monophyletic group
  13. What is cladistics a systematic approach to?
    Morphological homologies
  14. What is used to draw a tree?
    shared characteristics
  15. Shared ancestral characteristics
    originated before a branch point
  16. shared derived characteristic
    peculiar to the species after a branch point
  17. How are birds and dinosaurs similar?
    • Birds are the last of the dinosaurs
    • Fossils show that some dinosaurs brooded (protected eggs) as do birds
    • additional structure similarities include bone structure, which also suggests evolutionary relationship
  18. What makes for a good phylogenetic tree between birds and dinosaurs?
    the combination of shared characteristics (cladistics) and the fossil records. (they are in the same clade)
  19. What's the second approach to drawing a tree?
    How is it done?
    What's unique about it?
    • DNA identity
    • tally base pair differences for a orthologous gene
    • the branch lengths are proportional to evolutionary distance (assuming constant molecular clock)
  20. Ortholog
    • Same genes, within different organisms (a product of speciation)
    • We can use either the primary sequencee of amino acids with orthologous proteins or the base sequence of othologous genes
  21. Paralogs
    Duplication of genes within a particular organism (within a species two genes form)
  22. Molecular clocks (what does combining fossil dating and base pair difference give us?
    A decent straight line (7 protein average)
  23. Parsimony
    • Selecting from among competing hypotheses the one that makes the fewest new assumptions- a systematic approach
    • (plurality must never be posited without necessity) (for every complex problem there is an answer that is clear, simple, and wrong)
  24. Mushroom systematic approach to parsimony
    • Draw what makes the most sense based on the data
    • if the mutation rate is the same and constant for all organisms, then 1 makes more sense than 2 because the distance from the earliest common ancestor is the same (don't have to make an assumption for one of them)
    • (maybe read more into this, it's confusing)
  25. Maximum likelihood (systematic approach)
    • for data (like nucleotide differences between orthologous genes) statistical tests can be applied
    • max Likelihood is like say that you are using a stats tests that tests whether your data (evolutionary distances) fit a particular model.
    • Example= our last exam scores on a bell curve is a test of maximum likelihood
  26. How can you check a phlogenetic tree and DNA sequence tree?
    • They should agree, there will be small differences but will be remarkably similar (can tell differences when talking about molecular clock) 
    • Mutation rate doesn't have to be constant
  27. What's a problem with drawing trees using morphological homologies?
    Looks can be deceiving
  28. What's the problem with drawing trees by molecular homologies?
    the mutation rate may not be constant
  29. Anomaly
    The more DNA that gets sequenced, the better the power to identify evolutionary relationships among species. Unfortunately, DNA is not preserved in ancient fossils. We can get small DNA fragments from wooly mammoth carcasses and neanderthal bones from 50,000 years before present, but not further back. Recently a 700,000 year old horse carcass dug out of the canadian permafrost yielded DNA (this is an anomaly)
  30. What species does the molecular clock run slow in?
    • Primates
    • For reasons we don't quite understand, the rate of mutational change in primates is slower than the rate for comparison mammals
  31. What clade are humans?
    What is our closest living evolutionary relative?
    • Hominin
    • the chimpanzee, who diverged from a common ancestor 6-7 million years ago.
  32. What do we know from mitochondrial DNA in humans?
    • That our progenitor species evolved over millions of years ago
    • Our species developed over the last million years
    • Variation (base changes) found in mitochondrial DNA within humans decreases with the distance from Africa. Based on a molecular clock it is converted into 100,000 year intervals. (Mitochondrial DNA is only from mommy)
    • Fewer mean that there has been a founder effect and it is a younger population
  33. What does DNA diversity in a population say?
  34. Recently fossils of another homo species have been discovered, what are they called and where were they found?
    • Denisovans
    • siberia