Evolutionary Trees

Question 1

define phylogeny

Answer 1

the evolutionary history of a species or group of species

Question 2

define phylogenetic tree

Answer 2

a branching diagram representing a hypothesis about the evolutionary history of a group of organisms

Question 3

define transitions (evolutionary modifications)

Answer 3

• hatch marks on the tree
• indicates the evolution of a trait at a particular point in an evolutionary lineage

Question 4

what is the principle of parsimony

Answer 4

• used to determine which branching pattern is most likely
• parsimony = fewest steps or changes

Question 5

define sister species

Answer 5

• species that share a more recent last common ancestor with each other than either shares with any other species
• they are each other’s closest living relatives

Question 6

nuances on reading a tree - does adding a relationship change how the other’s are read?

Answer 6

no

Question 7

nuances on reading a tree - how do you read time?

Answer 7

through branch length

Question 8

nuances on reading a tree - how do you know if one species is more closely related to another?

Answer 8

• look at time
• not at branching points

Question 9

define monophyletic clade

Answer 9

consists of an ancestral species and ALL of its descendants

Question 10

define paraphyletic grouping

Answer 10

consists of an ancestral species and some NOT ALL of its descendants

Question 11

define polyphyletic grouping

Answer 11

common ancestor of members is NOT part of the group

Question 12

define polytomy

Answer 12

unresolved grouping where we do not know the correct relationships, so we cannot get the tree down to sister taxa

Question 13

where would you see a sister taxon’s unique evolutionary history on a tree?

Answer 13

the branch after the node to the particular species

Question 14

where would you see a sister taxon’s shared evolutionary history on a tree?

Answer 14

the branch before the node

Question 15

where is a speciation event of a taxa located

Answer 15

the node connecting the taxa

Question 16

where is the ancestral lineage of a taxa located

Answer 16

the line under the node that connects the taxa

Question 17

what is the goal of phylogenetic reconstruction

Answer 17

identify monophyletic groups

Question 18

explain the logic of a phylogeny inference under ideal conditions

Answer 18

• traits of the common ancestor are known
• evolutionary novelties evolve only once and are never lost in a lineage
• therefore, novelties can be interpreted as evidence of common ancestry

Question 19

phylogeny inference under ideal conditions - what are the steps

Answer 19

1. determine which novel traits are unique to a species and which novel traits are shared
2. start drawing the tree from the tips and work back in time
3. keep working back in time until all traits are nested

Question 20

what do homologous characteristics form on a tree and why?

Answer 20

• nested pattern
• bc all life shares some traits and each successive smaller group of descendant organisms adds its own homologies to those it shares with larger groups

Question 21

what is the outgroup comparison

Answer 21

used by systematics to differentiate between shared derived and shared primitive characteristics

Question 22

what is an outgroup

Answer 22

• a species or group of species that is closely related to the ingroup (species we wish to infer)
• should be relatives of the ingroup but less closely related to them than the ingroup are to each other
• ensures that group will be monophyletic

Question 23

outgroup comparison - what assumption is it based on

Answer 23

the assumption that homologies present in both the outgroup and the ingroup must be primitive characters

Question 24

define homoplasies

Answer 24

• similarity in character states due to convergence and/or reversal
• aka analogous (opposite of homology)
• misleading info when estimating phylogenies

Question 25

homoplasies - why do they occur

Answer 25

- convergent evolution - when similar environmental conditions and natural selection produce similar adaptations in organisms from different evolutionary lineages

Question 26

define apomorphies

Answer 26

an evolutionary novelty, or derived character

Question 27

define pleisiomorphies

Answer 27

a preexisting, or ancestral character

Question 28

define synapomorphies

Answer 28

- homologous traits that are shared and derived - reliable info when estimating phylogenies

Question 29

how can we maximize the use of reliable info when estimating phylogenies

Answer 29

using outgroups and parsimony

Question 30

how do we reconstruct evolutionary history using sequence data?

Answer 30

- align the sequences - then treat each site within a DNA sequence as a homologous character

Question 31

reconstructing evolutionary history using sequence data - what does 'treat each site as a homologous character' mean

Answer 31

shifting to account for any insertions or deletions that have occurred in some lineages but not in others

Question 32

reconstructing evolutionary history using sequence data - how to estimate evolutionary trees

Answer 32

- treat each site in a sequence as an independent character and look for synapomorphies that identify monophyletic groups - then build trees using the variable location in the genome - then identify transitions

Question 33

reconstructing evolutionary history using sequence data - maximum likelihood

Answer 33

uses mathematical models of base pair substitutions to assess the probability of a given tree

Question 34

reconstructing evolutionary history using sequence data: maximum likelihood - explain the branch length

Answer 34

- branch length is proportional to the number of nucleotide substitutions per site estimated to have occurred on each branch (not time) - branch length and expected number of substitutions are based on the models of sequence evolution and the actual DNA sequence data

Question 35

reconstructing evolutionary history using sequence data: maximum likelihood - how do you determine which is the maximum likelihood

Answer 35

- sum the probabilities at every nucleotide for every tree - max one is maximum likelihood

Question 36

reconstructing evolutionary history using sequence data - bootstrapping

Answer 36

- used after using maximum likelihood method to measure sure you're confident that you are correct - it generates random data sets by random sampling

Question 37

reconstructing evolutionary history using sequence data: bootstrapping - how does it work?

Answer 37

- it randomly choses numbers 1-6 representing nucleotides - it will then randomly pick a site and does this repeatedly to make a bootstrap replicate and make a tree - it will calculate a majority rule consensus