Chaudhuri - phylogenetics

Question 1

What does phylogenetics do?

Answer 1

• uses similarity of particular characteristics to assess the relatedness between species

Question 2

How was what phylogenetics is based on changed?

Answer 2

• originally used morphological characteristics

- not uses DNA or protein seqs

Question 3

What is convergent evo?

Answer 3

• 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

Question 4

Why are DNA seqs useful for phylogenetic trees?

Answer 4

• 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

Question 5

Why is morphological seqs not as good as DNA seqs?

Answer 5

• can be difficult or expensive to obtain
• often ambiguous
• highly susceptible to convergence

Question 6

What are the 4 major features of phylogenetic trees?

Answer 6

• 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

Question 7

What are phylogenetic trees used to indicate?

Answer 7

• relationships between particular groups, or “operational taxonomic units” (OTUs or taxa)

Question 8

What do diff nodes represent?

Answer 8

• internal nodes represent inferred ancestral state

- external nodes represent observation (know seq here)

Question 9

What is a clade?

Answer 9

• group of taxa clustered together

Question 10

Does topology vary between graphically diff trees?

Answer 10

• can have same topology

Question 11

What is the only meaningful axis of a tree?

Answer 11

• one that represents seq divergence (analogous to time)

- separation on other axis is only for clarity

Question 12

How do you determine relationship between 2 diff taxa?

Answer 12

• identify node representing most recent common ancestor (MRCA)

Question 13

Does rotation around node affect meaning of tree?

Answer 13

• no

Question 14

What is the diff between bifurcation and multifurcation?

Answer 14

• most phylogenetic methods prod fully resolved bifurcating tree, where every node clusters 2 taxa
• multifunctions indicate ambiguity in branching order

Question 15

What are monophyletic groups?

Answer 15

• groups which consist of all descendants of single common ancestor (represent single clade, w/ no exceptions)
• eg. birds, mammals

Question 16

What are paraphyletic groups?

Answer 16

• 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

Question 17

What are polyphyletic groups?

Answer 17

• groups which consist of multiple distinct clades
• convergent evo, members occur sporadically w/in tree, not evo related
• eg. flightless birds, marine mammals

Question 18

What do branch lengths req for tree?

Answer 18

• drawn to scale and scale bar added

- scale usually represents no. base/AA substitutions per site –> so prop to how much evo happened

Question 19

Do all phylogenetic methods prod rooted trees?

Answer 19

• no, most unrooted, w/ no indication of direction of evo

Question 20

How can a root be defined, instead of having an unrooted network?

Answer 20

• using external info (eg. known outgroup)

- or assumption (eg. assume all lineages are evolving at around same rate, and place root at midpoint)

Question 21

Can circular trees be rooted?

Answer 21

• yes

Question 22

What are bootstrap scores a measure of?

Answer 22

• confidence in particular internal branch

Question 23

Does bootstrap scares equal confidence level?

Answer 23

• no, 95% score isn’t the same as 95% confidence

Question 24

How do you distinguish between paraphyletic and polyphyletic groups?

Answer 24

• 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

Question 25

What is the mol clock?

Answer 25

• common assumption that rate of substitution is uniform over time

Question 26

What are some distance matrix methods for drawing a phylogenetic tree?

Answer 26

• UPGMA
• Fitch and Margoliash
• Neighbor-joining

Question 27

What are some optimality criterion methods for drawing a phylogenetic tree?

Answer 27

• maximum parsimony (simplest true)
• maximum likelihood
• Bayesian

Question 28

What methods for drawing a phylogenetic are the best/used the most?

Answer 28

• max likelihood and Bayesian regarded as most reliable

- but neighbor-joining still freq used for “quick and dirty” analysis

Question 29

If an animal has a shorter gen time how does this affect mol clock assumption?

Answer 29

• shorter gen time means likely to evolve faster

- so would violate assumption of mol clock