TopHat 4.2 Notes PDF

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TopHat 4.2 with questions...

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4.2 Determining Phylogenetic Connections Introduction • Homologous structures: they stem from developmental similarities that are based on evolution • More complex features are more likely of overlap due to evolutionary past Misleading Appearances • Some genetically related organisms can look quite different • Some unrelated organisms can look alike as they are in common environmental conditions which lead to similar adaptations • Analogous -characteristics bearing similar functions occur because of environmental constraints • EX: insects use wings to fly like birds and bats, but their wing structure and embryonic origin is very different • Homoplasy- characteristics just resemble each other • Some structures are both analogous and homologous, such as wings of birds and wings of bats • They share a common evolutionary pathway in wing bone structure • The mechanisms are different • Scientist must decipher the types of similarities between features to determine phylogeny of organisms • Structures between two individuals may be any combination of homologous, analogous, and homoplastic, to include all three • Characters that are similar because of descent from a common ancestor are homologous; characters that are similar due to convergent evolution are analogous Molecular Comparisons • DNA evolve from mutations being fixed in DNA and populations • In some situations, two closely related organisms can appear unrelated due to a mutation that causes a frameshift • This can also be caused by an insertion of deletion would move a nucleotide base making two similar codes appear unrelated • Two segments of DNA in distinctly related organism s randomly shares a higher percentage of bases in the same locations, the organisms appear closely related when they are not • Computer systems combined with the use of morphologic and molecular information is effective phylogeny Building Phylogenetic Trees • How to construct phylogenetic trees: • After homologous and analogous traits are sorted, homologous traits are organized using a system called cladistics

• A system to organizes organisms in to clades: groups of organisms that depend from a common ancestors

• EX: All organisms in yellow evolve from a common ancestor with amniotic eggs. Consequently, all organisms also have amniotic eggs and make a single cla also called a monophyletic group • Clades vary in size depending on which branch p being referenced • The important factor in all organism sis the clade or monophyletic group • Clade comes from a single point • Non-clade groups show branches that do not share a single point • Clades always contain all the members from a shared branch point. Depending on what branch point is chosen clades can be of different sizes (contain different numbers of groups) Shared Characteristics • Organisms evolve from common ancestors and then diversify • “Descent with modification” • The pattern of change occurs and the pattern repeats until one goes through the phylogenetic tree of life: 1. A change in the genetic makeup if an organism leads to a new trait that enhances fitness and as a result becomes more prevalent in the group 2. Many organisms descend from this point and have this trait 3. New variations may arise from branch point; some are adaptations and these persist become new traits 4. With new traits, the new branch point (go back to step 1 and repeat) • If characteristics are found in the ancestors of a group, it is considered a shared ancestral character, because all organisms in the taxon/ clade will likely inherit the trait • In image, having a vertebrae is a shared ancestral character, and amniotic egg is a characteristic of same phylogeny • Only come may have this trait, called shared derived character, as the trait is derived at some point but doesn’t include all ancestors in trait • Shared ancestral and shared derived characteristics help distinguish between clades to build phylogenetic trees • Ultimately, shared derived characters are the result of? MUTATIONS Choosing the Right Relationships • Maximum Parsimony- this concept predicts the pathway with least number of events that could have occurred is the most likely one • The pathway of evolution probably includes major events that coincide with the evidence • Why do scientists apply the concept of maximum parsimony? • To aid in figuring out the most likely evolutionary relationships...