CHAPTER 26 STUDY GUIDE PHYLOGENY AND THE TREE OF LIFE Phylogenies Show Evolutionary Relationships

1. Distinguish between phylogeny and systematics.Phylogeny is evolutionary history of the 2.

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a species or a group of species. System atics is a discipline focused on classifying and organism s determ ining their evolutionary relationships. Explain the following characteristics of the Linnaean system of classification: a. Binomial nomenclatureThe first part of a binomial name is the name of the genus to which the species belongs, while the second part, called the specific epithet, is unique for each species within the genus. b. Hierarchical classificationThis consists of a hierarchy of increasingly inclusive categories (dom ain, kingdom , phyla, class, order, fam ily, genus, .species) Explain the justification for the proposal to replace Linnaean classification with PhyloCode designations for monophyletic taxa.This is an approach which only names groups that include a common ancestor and all of its descendants. While PhiloCode would change the way taxa are defined and recognized, the taxonomic names of most species would remain the same. But species would no longer have ranks attached to them, such as family, order, or class. Explain the statement: A phylogenetic tree represents a hypothesis about evolutionary relationships.These relationships are depicted as a series of dichotomies, or two-way branch points, each branch point representing the divergence of two evolutionary lineages from a common ancestor. Explain why it is crucial to distinguish between homology and analogy before selecting characters to use in the reconstruction of phylogeny. Describe how homology and analogy can be distinguished from each other.A potential red herring in constructing a phylogeny is similarity due to convergent evolutioncalled analogyrather than to shared ancestry. Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages. Distinguishing between homology and analogy is critical in reconstructing phylogenies. To see why, consider bats and birds, both of which have adaptations that enable flight. This superficial resemblance might imply that bats are more closely related to birds than they are to cats, which cannot fly. But a closer examination reveals that a bats wing is far more similar to the forelimbs of cats and other mammals than to a birds wing. Flight is enabled in different waysstretched membranes in the bat wing versus feathers in the bird wing. Explain why bird and bat wings are homologous as vertebrate forelimbs but analogous as wings.Explained above. Define molecular systematics. Explain some of the problems that systematists may face in carrying out molecular comparisons of nucleic acids.M olecular system atics is the discipline that uses DNA and other m olecular data to determ ine relationships. M olecular com parisons of nucleic acids often pose technical challenges for researchers. The first step after sequencing the m olecules is to align comparable sequences from the species being studied. If the species are very closely related, the sequences probably differ at only one or a few sites. In contrast, com parable nucleic acid sequences in distantly related species usually have different bases at m any sites and m ay have different lengths. This is because insertions and deletions accum ulate
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over long periods of tim e. Two sequences that resem ble each other at m any points along their length m ost likely are hom ologous. But in organism s that do not appear to be closely related, the bases that their otherwise very different sequences happen to share m ay sim ply be coincidental m atches, called m olecular oplasies hom . The Construction of Phylogenetic Trees 8. Define a clade. Distinguish between a monophyletic clade and paraphyletic and polyphyletic groupings of species.A clade is a group that includes an ancestral species and all of its descendants like taxonom ic ranks, are nested within larger clades. A monophyletic and clade consists of an ancestral species and all of its descendants. A paraphyletic clade consists of an ancestral species and som e, but not all, of its descendants. A polyphyletic clade includes taxa with different ancestors. 9. Distinguish between shared ancestral characters and shared derived characters.A shared ancestral character originated in an ancestor of the taxon, e.g., the backbone in mammals. A shared derived character is an evolutionary novelty unique to a particular clade. 10. Explain why shared derived characters are useful in establishing a phylogeny, while shared ancestral characters are not.Because, e.g., the backbone, a shared ancestral character, does not distinguish mammals from other vertebrates because all vertebrates have backbones, in other words, predating the branching of the mammalian clade from other vertebrates. But certain mammalian clades can have evolutionary novelties or shared derived characters which do help distinguish them and establish a phylogeny. 11. Distinguish an ingroup from an outgroup.An outgroup is a species or group of species from an evolutionary 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. 12. Explain how outgroup comparison can be used to differentiate shared ancestral characters from shared derived characters.By comparing members of the 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. 13. Discuss how systematists use the principles of maximum parsimony and maximum likelihood in reconstructing phylogenies.According to the principle of m ax parsim ony, we should first investigate the sim plest explanation that is consistent with the facts. In the case of trees based on m orphology, the m ost parsim onious tree requires the fewest evolutionary events, as m easured by the origin of shared derived m orphological characters. For phylogenies based on DNA, the m ost parsim onious tree requires the fewest base changes. The principle of m ax likelihood states that given certain rules about how DNA changes over tim e, a tree can be found that reflects the most likely sequence of evolutionary events. 14. Distinguish between orthologous and paralogous genes. Explain how gene duplication has led to families of paralogous genes.Orthologous genes refer to homologous genes that are found in different species because of speciation. Paralogous genes result from gene duplication, so they are found in more than one copy in the same genome. 15. Explain how molecular clocks are used to determine the approximate time of key evolutionary events. Explain how molecular clocks are calibrated in actual time.A m olecular clock is a yardstick for m easuring the absolute tim e of evolutionary change based on the
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observation that som e genes and other regions of genom es appear to evolve at constant rates. The num ber of nucleotide substitutions in orthologous genes is proportional to the tim e that has elapsed since the species branched from their com m on ancestor (divergence tim e). In the case of paralogous genes, the num ber of substitutions is proportional to the tim e since the genes becam e duplicated. W e can calibrate the m olecular clock of a gene that has a reliable average rate of evolution by graphing the num ber of genetic differences for exam ple, nucleotide, codon, or am ino acid differences against the dates of evolutionary branch points that are known from the fossil record. Such graphs can then be used to estim ate the dates of evolutionary episodes that cannot be discerned from the fossil record, such as the originsilverswords of the . 16. Describe some of the limitations of molecular clocks.Of course, no gene m arks tim e with com plete precision. In fact, som e portions of the genom e appear to have evolved in irregular fits and starts that are not at all clocklike. And even those genes that seem to have reliable m olecular clocks are accurate only in the statistical sense of showing a fairly sm ooth average rate of change. Over tim e, there m ay still be chance deviations above and below that average rate. Furtherm ore, the sam e gene m ay evolve at different rates in different groups of organism s. 17. Explain the neutral theory of evolutionary change.It states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection. Kimura pointed out that 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 regular like a clock. 18. Explain how scientists determined the approximate time when HIV-1 M first infected humans.Researchers used a molecular clock to date the origin of HIV infection in humans. Phylogenetic analysis shows that HIV, the virus that causes AIDS, is descended from viruses that infect chimpanzees and other primates. The multiple origins of HIV are reflected in the variety of strains (genetic types) of the virus. HIVs genetic material is made of RNA, and like other RNA viruses, it evolves quickly. The researchers compared samples of the virus from various times during the epidemic, including one sample from 1959. A comparison of gene sequences showed that the virus has evolved in a clocklike fashion since 1959. By extrapolating from their molecular clock, the researchers concluded that the HIV-1 strain first spread to humans during the 1930s. 19. Describe the evidence that suggests there is a universal tree of life.This reconstruction of the tree of life based largely on sequence com parisons of genes, which code for the is rRNA RNA parts of ribosom es. Because ribosom es are fundam ental to the workingsrRNA cell, of the genes have evolved so slowly that hom ologies between distantly related organism s can still be detected m aking these genes very useful for determ ining evolutionary relationships am ong deep branches in the history of life. There have been substantial m ovem ents of genes between organism s in the different dom ains. These took place through horizontal gene transfer, a process in which genes are transferred from one genom e to another through m echanism s such as exchange of transposable elem ents and plasm ids, viral infection, and perhaps fusions of organism s. 20. Explain why the occurrence of horizontal gene transfer has led to the suggestion that the history of life should be represented by a ring rather than a tree.Some scientists have argued that horizontal gene transfers were so common that the early history of life should be represented as a tangled network of connected branchesnot a simple, dichotomously branching tree. Other suggest a ring, hypothesizing that eukaryotes arose as an endosymbiosis between an early bacterium and an early archaean. That would mean that eukaryotes are simultaneously most closely related to
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bacteria and archaeaan evolutionary relationship that cannot be depicted in a tree of life, but can be depicted in a ring of life.