Biology II Chapter 26

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Biology II Chapter 26
2011-10-06 18:40:57
Phylogeny Tree Life Biology

Chapter 26 of Campbell's Biology Textbook 8th - Phylogeny and the Tree of Life
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  1. Phylogeny
    The evolutionary history of a species of group of species. A phylogenetic tree indicates only patterns of descent.

    A phylogeny of lizards and snakes, for example, indicates that both the scaly foot and snakes evolved from lizards with legs - but they evolved from different lineages of legged lizards. Thus, it appears that their legless conditions evolved independently.
  2. Systematics
    A discipline focused on classifying organisms and determining their evolutionary relationships.

    Systematics use data ranging from fossils to molecules and genes to infer evolutionary relationships. This allows for biologiests to construct a comprehensive tree of life, which will continue to be refined as addional data is collected.
  3. (T/F) Organisms share mologous characteristics because of common ancestory.

    As a result, one can learn a great deal about a species if the evolutionary history is known. For example, an organism is likely to share many of its gene, metabolic pathways, and structural proteins with its close relatives.
  4. Taxonomy
    A scientific discipline concerned with naming and classifying the diverse forms of life.

    This deals with the practical applications of information from systematics.
  5. Binomial Nomenclature
    The two-part format of the scientific name of an organism with use of Latin scientific names.

    The first part of a binomial is the name of the genus (plural, genera) to which the species begins. The second part called the specific epithet, refers to one species within the genus.

    Examples include Homo sapiens or Panthera pardus.
  6. What are the categories for the hierarchical classification of an organism? The taxonomic system commonly used is known as the Linnaean system.

    • Domain
    • Kingdom
    • Phylum
    • Class
    • Order
    • Family
    • Genus
    • Species
  7. Taxon
    The named taxonomic unit at any level of the hierarchy is called a taxon (plural, taxa). The Doman, Kingdom, Phylum, Class, Order, Family, Genus, and Species are all known as taxons.
  8. Phylogenetic Tree
    A branching diagram that represents a hypothesis about the evolutionary history of a group of organisms. A phylogenetic tree indicates only patterns of descent.

    In some cases, the branching pattern matches the hierarchical classification of groups nested within more inclusive groups.

    However, in other situations, certain similarities amoung organisms may lead taxonomists to place a species within a group of organisms (for example, a genus or family) other than the group to which it is most closely related.
  9. (T/F) The categories within the Linnaean classification system may provide little information about phylogeny.

    There are difficulties in aligning Linnaean classifications with phylogeny thus leading systematists to propose that classification be based entirely on evolutionary relationships.

    An approach to address this is the use of PhyloCode, which only names groups that include a common ancestorr and all of its descendents. PhyloCode would change the way that taxa are defined and recognized but the taxonomic names of most species would remain the same. However, species would no longer have "ranks" attached to them, such as family, order or class and some commonly recgnized groups would become part of other groups previously of the same rank.
  10. PhyloCode
    System of classification of organisms based on evolutionary relationships: Only groups that include a common ancestor and all of its descendents are named.

    PhyloCode would change the way that taxa are defined and recognized but the taxonomic names of most species would remain the same. However, species would no longer have "ranks" attached to them, such as family, order or class and some commonly recgnized groups would become part of other groups previously of the same rank.
  11. (T/F) A phylogenetic tree is different for a Linnaean classification system or a PhyloCode classification system,.

    Whether groups are named according to PhyloCode or to Linnaean classification, a phylogenetic tree represents a hypothesis about evolutionary relationships.
  12. Branch point in a phylogenetic tree.
    The representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor. Most branch points are shown as dichotomies, in which a branch representing the ancestral lineage splits (at the branch point) into two branches, one for each of the two descendant taxa.
  13. Sister Taxa
    Groups of organisms that share an immediate common anceestor and, hence, are each other's closest relatives.
  14. (T/F) Rooted phylogogenetic trees indicate that there is another common ancestor for the taxa shown that is not included in the diagram.

    A phylogenetic tree that is rooted indicates the the branch point within the tree (typically the one farthest to the left) represents the last common ancestor of all the taxa in the tree.
  15. (T/F) A polytomy is the equivalent to a branch point where there are two branch points.

    A polytomy is a branch point from which more than two descendant groups emergy. It indicates that evolutionary relationships amount the descendant taxa are not yet clear.

    ie. Unresolved pattern of divergence.
  16. (T/F) The sequence of branching in a tree indicates the actual (absolute) ages of the particular species.

    The sequence of brancing does not always necessarily indicate the actual (absolute) ages of the particular species. It only shows that the two species share a common ancestor, even when one divergance has subsequent branch points before reaching the species that is present today.
  17. (T/F) Taxons on a phylogenetic tree do not indicate that the sister taxa evolved from it.

    ie Two taxons that shared a common ancestor does not indicate that one evolved from the other.

    We cannot assume that a taxon on a phylogenetic tree evolved from the taxon next to it.
  18. (T/F) To infer phylogeny, systematists gather as much information as possible about the morphology, genes and biochemistry of the relevant organisms. It is not important to focus on features that result from common ancestry, because it is not relavent.

    It is very important to focus on features that result from common ancestry as those features tend to reflect evolutionary relationships.

    It is also true that information gathered from morphology, genes and biochemistry of the relevant organisms but it is not what made the statement false.
  19. Organisms that share very similar morphologies or DNA sequences are likely to be more closely related than organisms with vastly different structures in sequences.

    (T/F) The structural changes between two organisms that differ greatly are always followed with great differences in genetic differences or divergence.
    • False.
    • The morphological divergence btween related species can be great and the genetic divergence may be small (or vice versa).

    For instance, consider that a phylogeny based on DNA reveals that animals (including humans) and fungi (including mushrooms) are more closely related to each other than either is to plants.
  20. Convergent Evolution
    (Analogy in phylogeny)
    The evolution of similar features in independent evolutionary lineages.

    Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

    ie. Bat and a bird wing have the same function but the development of the wing did not come from the same common ancestor.
  21. Homology
    Similarity in characteristics resulting from a shared ancestry.

    This is different than convergent evolution in which environmental pressures and natural selection produce similar adaptations in organism from different evolutionary lineages.
  22. Homoplasies
    -to mold in the same way

    Similar (analogous) structures or molecular sequences that have evolved independently in two species.
  23. Homologous Structures
    Structures in different species that are similar because of common ancestry.
  24. Homologous Chromosomes
    A pair of chromosomes of the same length, centromere position, and staining pattern that possess genes for the same characters at corresponding loci. One homologous chromosome is inherited from the organism's father, the other from the mother.

    Also called homologs, or a homologous pair.
  25. Ancstral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor. The ______ and _______ mutations _____ what been matching sequences in the two species.
    Insertion, Deletion, Shift

    This is what occurs as two species diverge from a common ancestor and it is difficult to compare segments of DNA to identify related species.

    The use of computer software to find and align similar sequences along DNA segments allow for one to identify the similarities of DNA.
  26. Molecular Systematics
    A scientific discipline that uses nucleic acids or other molecules in different species to infer evolutionary relationships.
  27. Cladistics
    An approach to systematics in which common descent is the primary criterion used to classify organisms by placing them into groups called clades.
  28. Clade
    A group of species that includes an ancestral species and all of its descendents.
  29. (T/F) Clades, like taxonomic ranks, are nested within larger clades.

    For example, the cat group replresents a clade within a large clade that also includes the dog group.
  30. A taxon is equivalent to a clade only if it is ___________, signifying that it consists of an ancestral species and all its descendants.
    Monophyletic ("single tribe")

  31. A ________ group consists of an ancestral species and some, but not all, of its descendants.
    Paraphyletic ("beside the tribe").

  32. A _________ group includes taxa with different ancestors.
    Polyphyletic ("many tribes").

  33. Descent with Modification
    Proposed by Darwin where organisms both share characteristics with their ancestors and differ from them.

    For example, all mammals have backbones, but the presence of a backbone does not distinguish mammals from other vertebrates because all vertebrates have backbones. The backbone predates the brancing of mammalian clade from other vertebrates.
  34. Shared Ancestral Character
    A character that originated in an acestor of the taxon.

    For instance, the backbone originated from the ancestor of mammals.

    This is in contrast to shared derived character, that is an evolutionary novelty unique to a particular clade.
  35. Shared Derived Character
    An evolutionary novelty unique to a particular clade.

    For instance, hair is a character shared by all mammals but not found in their ancestors.

    This is in contrast to shared ancestral character that originiated from the ancestor.
  36. Outgroup
    A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup).

    A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences.

  37. By comparing members of an ingroup to each other and to the outgroup, we can determine which characters were derived at the various branch points of vertebrate evolution.
    • For example, all of the vertebrates in the ingroup have backbones: This character was present in the ancestral vertebrate but not in the outgroup. Now note that hinged jaws are a character absent in lampreys but presnet in other members of the ingroup.
  38. Maximum Parsimony
    Also knowns as "Occam's razor"
    The simplest explanation that is consistent with the facts should be investigated first.

    In the case of trees based on morphology, the most parsimonious tree requires the fewest evolutionary events, as measured by the origin of shared derived morphological chracters. For phyogenies based on DNA, the most parsimonious tree requires the fewest base changes.
  39. Maximum Likelihood
    Given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.

    Tree 1 is more likely if it is assumed that DNA changes have occured at equal rates along all branches of the tree from the common ancestor. Tree 2 requires assuming that the rates of evolution slowed greatly in the mushroom lineage and sped up in the tulip lineage.

    Thus, assuming that equal rates are more common than than unequal rates, tree 1 is more likely.

  40. Phylogenetic Bracketing
    We can predict (by parsimony) that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendents, unless independent data indicate otherwise.
  41. What does the phylogenetic tree below indicate abou the evolutionary relationships of the leopard, badger, and wolf?
    The branching pattern of the tree indicates that the badger and the wolf share a common ancestor that is more recent than the ancestor that these two animals shared with the leopard.
  42. Decide whether each of the following pairs of structures more likely represents analogy or homology.

    a) A porcupine's quills and a cactus's spines
    b) a cat's paw and a human's hand
    c) an owl's wing and a hornet's wing
    • a) analogy - Porcupines and cacti are not closely related and since most other animals and plants do not have similar structures.
    • b) homology - Cats and humans are both mammals and have homologous forelimbs, of which the hand and paw are the lower part.
    • c) analogy - Owls and hornets are not closely related and since the structure of their wings are very different.
  43. To distinguish a particular clade of mammals within the larger clade that corresponds to class Mammalia, would hair be a useful character?

    Hair is a shared ancestral character common to all mammals and thus is not helpful in distinguishing different mammalian subgroups.
  44. Why might the most parsimonious tree not necessarily be the most accurate in representing evolutionary relationships for a particular group of species?
    The principle of maximum parsimony states that the hypothesis about nature we investigate first should be the simplest explanation found to be consistent with the facts. Actual evolutionary relationships may differ from those inferred by parsimony owing to complicating factors such as convergent evolution.
  45. Like homologous genes in different species, these duplicated genes have a common ancestor. We distinguish these types of homologous genes by different names: O__________ genes and P__________ genes.
    • Orthologous genes (orthos, straight) - Homologous genes that are found in different species because of speciation.
    • Paralogous genes (para, beside) - Resulting from gene duplication, so they are found in more than one copy in the same genome.

  46. Homologous genes that are found in different species because of speciation are known as ____________ genes.
    Orthologous genes - Homologous genes that are found in different species due to speciation.

  47. Paralogous genes - Resulting from gene duplication, these genes are found in more than one copy in the same genome. These genes are known as _________ genes.
    Paralogous genes.

    These genes can diverge within a species because they are present in more than one copy in the genome.

  48. Explain how comparisons between the proteins of two species can yield data about their evolutionary relationship.
    Proteins are gene products. Their amino acid sequences are determined by the nucleotide sequences of the DNA that codes for them. Thus, differences between comparable proteins in two species reflect underlying genetic differences.
  49. Molecular Clock
    A yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates.

    The assumption underlying the molecular clock is that the number of nucleotide substitutions in othologous genes is proportional to the time that has elapsed since the species branched from their common ancestor (divergence time).

    The assumption for paralogous genes are that the number of nucleotide subsitutions are proprtional to the time since the genes became duplicated.
  50. The assumption underlying the molecular clock is that the number of nucleotide substitutions in othologous genes is proportional to the time that has elapsed since

    a) the species branched from their common ancestor (divergence time).
    b) the genes became duplicated.
    a) Orthologous genes are based on the divergence from the common ancestral species.

    Paralogous genes are proporational to the time since the genes became duplicated.
  51. Neutral Theory
    Much of evolutionary change in genes and proteins have no effect on the firness and therefore is not influenced by Dawinian selection.

    Many new mutations are harmful and are removed quickly but if most of the rest are neutral and have little or no effect on fitness, then the rate of molecular change should indeed be like a regular clock.

    The difference in the clock rate for different genes are a function of how important a gene is.
  52. If the exact sequence of amino acids that a gene specifies is ______ to survival, most of the mutational changes will be harmful and only a few will be neutral. As a result, such genes change slowly.

    But, if the exact sequence of amino acids is less critical, few of the new mutations will be harmful and more will be neutral. Such genes change more quickly.

    Basically, if a mutation is harmful in an essential for survival gene, the new species with the mutation will quickly be erradicated due to natural selection. The gene change will occur slowly.

    However, if the mutation is on a less important gene,the gene change will occur quickly and will not be harmful to the species and will be mutual.
  53. What is a molecular clock? What assumption underlies the use of a molecular clock? What assumption is made concerning the rates?
    A molecular clock is a method of estimating the actual time of evolutionary events based on the number of base changes in orthologous genes. It is based on the assumption that the regions of genomes being compared evolve at constant rates.
  54. Explain how numerous base changes could occur in DNA, yet have no effect on an organism's fitness.
    There are many portions of the genome that do not code for genes; many base changes in these regions could accumulate through drift without affecting an organism's fitness. Even in coding regions of the genome, some mutations may not have a critical effect on genes or proteins.
  55. Genetic Drift
    A process in which chance events cause unpredictable fluctuations in allele frequencies from one generation to the next.

    Effects of genetic drift are most pronounced in small populations.
  56. What are the three domains used in taxonomy.
    Bacteria, Archaea, Eukarya
  57. What does the domain Bacteria consist of?
    The domain Bacteria contains most of the currently known prokaryotes, including the bacteria closely related to chloroplasts and mitochondria.
  58. What does the domain Archaea consist of?
    The domain Archaea consists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments. Some archaea use hydrogen as an energy source and others use natural gas deposits found throughout Earth's crust.

    Bacteria differ from arachaea in many structural, biochemical, and physiological characteristics.
  59. What does the domain Eukarya consist of?
    The domain Eukarya consists of all the organisms that have cells containing true nuclei. This domain includes many groups of single celled organisms as well as multicellular plants, fungi, and animals.
  60. Horizonal Gene Transfer
    Comparisons of complete genomes from the three domains show that there have been substantial movements of genes between organisms in the different domains. These took place through horizontal gene transfer, a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection and perhaps fusions of organisms.

  61. Why is the kingdom Monera no longer considered a valid taxon?
    The kingdom Monera included bacteria and archaea, but we now know that these organisms are in separate domains. Kingdoms are subsets of domains, so a single kingdom (like Monera) that includes taxa from different domains is not valid (it is polyphyletic).
  62. Explain why phylogenies based on different genes can yield different branching patterns for the universal tree of life.
    Because of horizontal gene transfer, some genes in eukaryotes are more closely related to bacteria, while others are more closely related to archaea; thus, depending on which genes are used, phylogenetic trees constructed from DNA data can yield conflicting results.
  63. In the following figure, which similarly inclusive taxon descended from the same common ancestor as Canidae?

    a) Felidae
    b) Mustelidae
    c) Carnivora
    d) Canis
    e) Lutra

  64. Distantly related species often have ________ genes. The small variation in gene number in organisms of varying complexity suggests that the genes are versatile and may have multiple functions.
    Orthologous genes.
  65. Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that includes species T, X, Y, and Z make up

    a) a valid taxon
    b) a monophyletic clade
    c) an ingroup, with species U as the outgroup
    d) a paraphyletic group
    e) a polyphyletic group
  66. In a comparison of birds and mammals, having four appendages is

    a) a shared ancestral character
    b) a shared derived character
    c) a character useful for distinguishing birds from mammals
    d) an example of analogy rather than homology
    e) a character useful for sorting bird species
  67. Based on the following figure, which statement is not correct.

    a) The lineage leading to the salamanders was the first to diverge from the other lineages.
    b) Salamanders are a sister group to the group containing lizards, goats and humans.
    c) Salamanders are as closely related to goats as to humans.
    d) Lizards are more closely related to salamanders than to humans.
    e) The group highlighted by shading is paraphyletic

  68. If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup?

    a) lion
    b) domestic cat
    c) wolf
    d) leopard
    e) tiger
  69. The relative lengths of the amphibian and mouse branches in the phylogeny below indicates that

    a) amphibians evolved before mice.
    b) mice evolved before amphibians
    c) the genes of amphibians and mice have only coincidental homoplasies
    d) the homologous gene has evolved more slowly in mice
    e) the homologous gene has evolved more rapidly in mice

  70. To apply parsimony to constructing a phylogenetic tree,

    a) choose the tree that assumes all evolutionary changes are equally probable.
    b) choose the tree in which the branch points are based on as many shared derived characters as possible.
    c) base phylogenetic trees only on the fossil record, as this provides the simplest explanation for evolution.
    d) choose the tree that represents the fewest evolutionary changes, either in DNA sequences or morphology.
    e) choose the tree with the fewest branch points.