Bio3132
Terms
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- homoplasy
- similarity in species of different ancestry, which is a result of convergent evolution
- plesiomorphy
- an ancestral character state
- apomorphy
- a derived character state
- synapomorphy
- a shared derived character state
- symplesiomorphy
- a shared ancestral character trait
- automorphy
- a unique derived character state
- cladistic
- tre is reconstructed by considering all possible pathways of evolution and choosing the best tree among them
- phenetic
- the trees are constructed considering the phenotypic similarities of species w/o looking at the evolutionary pathways
- UPGMA
- cluster algorithm; distance method Unweighted Pair Group Method Using Arithmetic Averages
- bifurcating tree
- has exactly two descendants from it\'s interior nodes
- paralogs
- homology by duplication
- orthologs
- separated by speciation event
- xenologs
- homology by lateral gene transfer
- convergence + due to..
- non related organisms evolve similar traits independently due to env pressure
- reversion
- return of a character back to its ancestral state
- OTU
- operational taxonomic unit
- paraphyletic
- species share a common ancestors but aren\'t part of a natural clade
- monophyletic
- species sharing a common ancestor + members of a natural clade
- polyphyletic
- group derived from 2+ common ancestors
- outgroup
- sequences related to the groups of seq being compared but are not part of this group
- unrooted tree
- no info abt directionality giver + only displays relationship btw nodes
- rooted tree
- a single node is designated as the common ancestor
- List two types of strand symmetry + give eg
- - Replication (lagging = muts) - Transcriptional (non-template strand = muts)
- Simple Sequence Repeats
- repeats of amino acids
- branch and bound
- consider all trees in a systematic manner but limit the search using a bound on ans
- Heuristic
- sequential addition + local rearrangements
- Bootstrap
- relies on the assumption that you have repeated seq (w/ replacement) to produce an accurate distribution of data
- Jackknife
- Boostrap w/o replacement --> each time you resample, an obs is removed
- consensus trees (2) + eg
- 1. >50% majority rule 2. strict consensus eg PHYLIP
- isochore
- large region of DNA (>3kb) with a homogeneous base composition
- Isochore are a result of .. (3)
- 1. mutation bias 2. biased gene conversion 3. natural selection
- Isochores: detection of patches
- purines (A/G): +1 pyramidines (C/T): -1 Result of walk is compared to the shuffled seq
- Dinucleotide composition formula=
- Pxy = fxy/fx/fy
- Pxy >1 = Pxy <1 =
- over representation of XY under representation of XY
- Why do you want to avoid CpG?
- - deamination occurs at C (changed to U or T)
- What is Chargaff\'s rule?
- DNA has 1:1 ratio of purines/pyramidines C=G A=T
- Shannon\'s Entropy Eqn?
- H= -LSUM plog2p
- Entropy
- measures the loss of info in a transmitted msg
- what are the units of entropy?
- bits
- If H/L=0 If H/L=2
- min complexity max complexity