Phylogeny Flashcards
midterm 1
How many percent are undiscovered species
86%
Phylogenies
- diagrams that represent ancestor-descendant relationships among organisms (evolutionary process)
- make prediction about evolution
- testable hypothesis
3 styles of phylogenetic tree
horizontal (box test), vertical(triangle test), circular
speciation (definition and represented as ___ on tree)
an ancestral lineage splits into two descendants
represented by node
taxa / taxon
-taxa = plural
-the tips
taxon can be anything from lineaen hierarchy (KPCOFGS)
what does a node represent?
node represents the MRCA and the speciation event
root node vs. internal node
root node is the MCRA of all the taxa in the phylogeny
internal node is all the other node except root node
sister taxa
share a node
by definition arise at the same time
How is time represented in phylogeny
preceding nodes represent earlier speciation events
branches
represent evolution overtime
root branch
root branch lead to root node
give examples of how phylogenetic trees are oversimplified
1) populations within species are not shown. There populations are from the speciation event.
2) some taxa not included (extinct)`
monophyly
MRCA and ALL descendants
clade
monophyly
mathematical relationship to find how many monophyletic groups in a tree
count the nodes
the two (artificial) nonmonophyletic group
1) paraphyletic : includes MRCA but excludes at least one descendant
2) polyphyletic : no MRCA : has a most common ancestor but not most recent (usually the root)
the science of systematics : relationship between phylogeny and taxonomy
systematics combines taxonomy and phylogenetics to produce classifications that reflect the evolutionary history of organisms
(KPCOFGS) species is italicized
polytomy
uncertain in branching
two kinds of polytomy
soft : polytomy can be resolved with more data
hard : speciation happened so fast that there is no way of fixing it
3 different types of phylogeny tree and difference in the information they give
cladogram : only order of branching is shown ; branch lengths have no meaning
phylogram : branch lengths are proportional to amount of character change
chronogram : branch lengths are proportional to absolute time
character vs. character state
character : a heritable feature (character trait)
character state: the form that a character takes
character: wings …. character state : present/absent
4 factors that causes speciation
mutation, drift, recombination, selection
synamorphy
a monophyletic group that shares a derived state
ancestral state vs. derived state
same character from ancestor group vs. different character from ancestor group
homoplasy vs. homologous
homoplasy : similarity not due to common ancestry caused by independent evolution
homology : similarity due to common ancestor
Trees are hypothesis. They are inferred from (3 factors)?
morphology, genetics, behavior
how are tree hypothesis tested?
by adding more data, taxa or using different analytical data
what’s a data matrix and what are the basic elements of it
a data matrix summarizes data for taxa understudy.
consists of character, character state, and code
unrooted tree
phylogenetic tree where the location of the root node is unknown
how many possible unrooted tree for four taxa
3
are there more ways to draw rooted or unrooted
rooted. increases exponentially
why use unrooted trees?
too many rooted trees possibility. we it for mathematical expediency
parsimony
the tree with the least amount of changes is the best tree
limitations of unrooted tree
-do not completely specify relationships but exclude some possibilities
outgroup vs. ingroup
outgroup = earliest species... connected to root branch in-group = everything else
limitations of parsimony
-all cost change are weighted the same though some happen more easily than others
Transitions vs. Transversion
Transition : change of purine to purine (A,G) and change of pyrimidine to pyrimidine (C,T)
Transversion : change of purine to pyrimidine and vice versa
Transition is more likely to happen due to molecular shape
wobble base
- third position may change without changing amino acid
- genetic code is redundant because an amino acid can be encoded by multiple codons
how do model-based (statistical) approaches to phylogengenetic inference differ from parsimony
model based use probability rather than just number of changes
