Chaudhuri - phylogenetics Flashcards
What does phylogenetics do?
- uses similarity of particular characteristics to assess the relatedness between species
How was what phylogenetics is based on changed?
- originally used morphological characteristics
- not uses DNA or protein seqs
What is convergent evo?
- indep evo of similar features in species of diff lineages
- creates analogous structures that have similar form or function, but that were not present in last common ancestor of these groups
- can obscure evo relationships so is problematic for phylogenetics
Why are DNA seqs useful for phylogenetic trees?
- although convergent evo can be problem for indiv base/AA, it’s highly unlikely to occur over longer seqs
- can be obtained easily, cheaply and accurately –> as discrete and unambiguous
Why is morphological seqs not as good as DNA seqs?
- can be difficult or expensive to obtain
- often ambiguous
- highly susceptible to convergence
What are the 4 major features of phylogenetic trees?
- topology –> branching order of tree, indicates relative relationships between taxa, joined at nodes
- branch lengths –> indicate degree of divergence
- root –> most ancient point on the tree
- bootstrap scores (or other stats) –> indicate confidence
What are phylogenetic trees used to indicate?
- relationships between particular groups, or “operational taxonomic units” (OTUs or taxa)
What do diff nodes represent?
- internal nodes represent inferred ancestral state
- external nodes represent observation (know seq here)
What is a clade?
- group of taxa clustered together
Does topology vary between graphically diff trees?
- can have same topology
What is the only meaningful axis of a tree?
- one that represents seq divergence (analogous to time)
- separation on other axis is only for clarity
How do you determine relationship between 2 diff taxa?
- identify node representing most recent common ancestor (MRCA)
Does rotation around node affect meaning of tree?
- no
What is the diff between bifurcation and multifurcation?
- most phylogenetic methods prod fully resolved bifurcating tree, where every node clusters 2 taxa
- multifunctions indicate ambiguity in branching order
What are monophyletic groups?
- groups which consist of all descendants of single common ancestor (represent single clade, w/ no exceptions)
- eg. birds, mammals
What are paraphyletic groups?
- groups defined by single clade, w/ exception of some descendant taxa, but look like common ancestor
- were at some point monophyletic but some members diverged, so not considered part of group anymore
- eg. reptiles, fish
What are polyphyletic groups?
- groups which consist of multiple distinct clades
- convergent evo, members occur sporadically w/in tree, not evo related
- eg. flightless birds, marine mammals
What do branch lengths req for tree?
- drawn to scale and scale bar added
- scale usually represents no. base/AA substitutions per site –> so prop to how much evo happened
Do all phylogenetic methods prod rooted trees?
- no, most unrooted, w/ no indication of direction of evo
How can a root be defined, instead of having an unrooted network?
- using external info (eg. known outgroup)
- or assumption (eg. assume all lineages are evolving at around same rate, and place root at midpoint)
Can circular trees be rooted?
- yes
What are bootstrap scores a measure of?
- confidence in particular internal branch
Does bootstrap scares equal confidence level?
- no, 95% score isn’t the same as 95% confidence
How do you distinguish between paraphyletic and polyphyletic groups?
- both result in clades w/ mix of species in the group and species not in the group
- need to consider MRCA –> is it likely it was a member of that group?
- paraphyletic groups share defining characteristics due to shared evo history, so MRCA will too
- polyphyletic groups share defining characteristics due to convergent evo, so are unlike MRCA
What is the mol clock?
- common assumption that rate of substitution is uniform over time
What are some distance matrix methods for drawing a phylogenetic tree?
- UPGMA
- Fitch and Margoliash
- Neighbor-joining
What are some optimality criterion methods for drawing a phylogenetic tree?
- maximum parsimony (simplest true)
- maximum likelihood
- Bayesian
What methods for drawing a phylogenetic are the best/used the most?
- max likelihood and Bayesian regarded as most reliable
- but neighbor-joining still freq used for “quick and dirty” analysis
If an animal has a shorter gen time how does this affect mol clock assumption?
- shorter gen time means likely to evolve faster
- so would violate assumption of mol clock
