Download Key terms: Positional homology Homoplasy Reversal Parallelism

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?