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Download Key terms: Positional homology Homoplasy Reversal Parallelism
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BIOL 3046: Molecular evolution Key terms: Positional homology Parallelism Genetic co-option Pro-orthology Gametology Ancestral polymorphism LGT / HGT Review material Phylogenetic homology (Phylo_T2) Homoplasy Reversal Convergence Evolutionary dissociation Orthology Paralogy Semi-orthology Partial homology Xenology Sinology Reciprocal monophyly Birth-death evolution Non-phylogenetic lineage sorting Review questions: 1. Consider the difference between the statement that “a character is homologous” and the statement that “the character states are homologous”. Use the concept of positional homology in an alignment of DNA sequences to illustrate these concepts. 2. Assume you have several DNA sequences and that they are sufficiently divergent for multiple substitutions to have occurred at a given site. List and explain the possible sources of homoplasy at such sites. 3. Explain why a phylogenetic concept of homology is critical to correctly understanding cases of evolutionary dissociation. Are there possible problems with using the concepts of serial homology, functional homology, and biological homology? 4. What is meant by the phrase “trees within trees”. How are the concepts of mutation, polymorphism and substitution related to this way of thinking about molecular evolution? 5. Draw a tree for a gene family and illustrate the notions of orthology, paraology, pro-orthology, and semi-orthology. 6. List and explain four evolutionary processes that will cause the phylogeny of a particular gene to differ from the phylogeny of the organisms that carry the gene. [Do not include sources of error such as human error or statistical error.] 7. Define non-phylogenetic lineage sorting. Explain why this is sensitive to the effective size of a population. Make prediction about the frequency of genes that do not track with the species-phylogeny in cases where effective population size is very large, and where it is very small. 8. You inferred a phylogeny for a gene that differs substantially from the widely accepted species tree (say, inferred from morphology). Does this result argue against evolution from a common ancestor? Why?