Lecture 6 - Origins and Evolution of Life Flashcards
cladograms
shows tree topology where lengths do not mean anything
ultrametric trees (time trees)
tips in trees are equidistant from roots but branch lengths could indicate time
polytomy
internal node in a phylogenetic tree with more than 2 descendants
phylogenetic analysis
- genes must be homologous
- aligned bps/a.a. residues must share positional homology
- multiple-sequence alignment must include positions that are informative for the method of analysis used
- single-gene alignments can be concatenated and analyzed
concatenated alignment
combining different gene alignments to form “mega alignment”
phylogenetic analysis methods
- clustering
- parsimony
- likelihood-based
clustering
calculate estimated evolutionary distance between all pairs of distance
pasimony
minimum number of character changes
maximum likelihood
possible trees are compared and given a score (score is based on how likely the tree was evolved given a.a. or nucleotide sub possibilties)
problems with trees
- long branch attraction
- homoplasy
long branch attraction (LBA)
- groups together taxa that are at the end of long branches but are not related
- parsimony can be misleading if true tree had long branches
- ## “parallel changes exceed informative nonparallel changes”
homoplasy
multiple mutations turn into convergence evolution and the tree can group it wrong
clustering and parsimony are susceptible to LBA
- parsimony can be misleading if true tree had long branches
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likelihood of phylogenetic tree
- likelihood of generating the observed data given that tree, where the tree compromises a topology and branch lengths
- measure of how well a model fits the data
log-likelihood
natural logarithm of likelihood values are used to make calculations easier
maximum likelihood
minimizes the amount of surprise at the observed data
elements of likelihood models
- model of substitution
- phylogram
model of substitution
- the assumptions regarding the process of sequence evaluation
- includes a substitution matrix
phylogram
- the topology and branch lengths
- each tree will represent a different hypothesis regarding evolution
simple nucleotide substitution models
usually GTR or simplifications of GTR
model simplicity
simple models can cause problems if they are too simplistic
simplifying assumptions
- independence of evolution
- equal rates of nucleotide substitution types
- reversibility substitutions
- BPS are the only types of mutations
- evolutionary process remain the same among different lineages
3-domain TOL (Woese’s Hypothesis)
archaea is monophyletic, therefore eukaryotes may not be a sister clade
2-domain TOL (eocyte hypothesis)
archaea is paraphyletic to eukaryotes
3-d vs 2-d TOL
2D is inferred when overly simplistic assumptions are avoided, therefore archaea is not monophyletic
