2-Phylogenetic trees + HWE

Question 1

phylogenetic tree

Answer 1

(aka evolutionary tree)—diagram that depicts the hypothesized evolutionary relationships amongst species or other taxa (or DNA or proteins)

Question 2

where does time go?

Answer 2

from ROOT to TIP

Question 3

Tip of branches

Answer 3

taxa
- typically represent species, but not always
- can also represent populations, larger groups, genes, DNA, etc
- tips = youngest lineage

Question 4

root of branches

Answer 4

• oldest lineage on the tree
• lineage that is ancestral to all other organisms on the tree

Question 5

branches

Answer 5

• represents a lineage: ancestor to descendant
  
  • evolution is occuring along all the branches
  • length of branch is meaningless

Question 6

internal nodes

Answer 6

• last common ancestor of the two lineages descended from that node
• branching points in a tree represent an inferred speciation event where the ancestral lineage split into 2 or more descendant lineages
• take any 2 taxa and trace their lineage backwards in time, the node at which their two paths meet represents the point in which their common ancestor split into two lineages

Question 7

character states/marks

Answer 7

• placed on trees to show when a new character state (heritable trait) arose/was lost in a lineage
  • once a character state appears, assume that all descendents inherited that trait, unless the tree indicates taht the trait was lost in a certian lineage

Question 8

MONOPHYLETIC GROUPS (CLADES)

Answer 8

Part of the phylogeny that includes the ancestor (unique or common) and all of its descendants of that ancestor

Question 9

sister taxa

Answer 9

• pairs of terminal taxa and/or clades that branch from a common node
  
  • considered closely related

Question 10

snip test

Answer 10

if you cut a branch, anything that falls off is a clade or monophyletic group

Question 11

polyphyletic group

Answer 11

a group that does not include the most recent common ancestor (some descendants may also be missing)

Question 12

PRINCIPLE OF PARSIMONY

Answer 12

used to determine which tree represents the “best hypothesis”

• assumption that the simplest explanation is most likely to be true

tree with the fewest number of evolutionary changes is most likely to be correct

Question 13

HOMOLOGOUS TRAITS

Answer 13

traits shared by 2 or more taxa because the trait was inherited from a common ancestor

• use homologous traits to construct phylogenetic trees
  
  • indicate relatedness

Question 14

ANALOGOUS TRAITS (HOMOPLASIES)

Answer 14

not all traits that look the same were necessarily inherited from a common ancestor

• arise due to convergent evolution
  
  • independent solution to an environmental demand
  • not from a common ancestor

Question 15

how to find the most closely related taxa to a particular taxon?

Answer 15

LOOK AT WHO SHARES THE MORE RECENT COMMON ANCESTOR

Question 16

how to tell if two trees for the same taxa show the same pattern of relationships among taxa?

Answer 16

LOOK AT THE MONOPHYLETIC GROUPS—ARE THEY THE SAME OR NOT?

Question 17

4 COMMON MISTAKES IN READING TREES

Answer 17

• thinking proximity of tips as an indication OF RELATEDNESS
• Thinking that degree of relatedness is indicated by the number of nodes separating taxa
• thinking taxa at the tips are ancestors to other taxa on the tree
• thinking taxa that appear on the top right of the tree have been evolving for longer (or are more) evolved than other taxa on the tree

Question 18

how to determine if a population is in HWE for a specific gene or not?

Answer 18

compare observed genotypes frequencies and expected genotype frequencies!

Question 19

assumptions that HWE makes

Answer 19

• Random fusion of gametes (random mating)
  
  • organisms do not select mates with respect to this gene
• the population is infinitely Large
  
  • no changes in allele frequencies due to sampling error
  • no genetic drift
• no Natural selection
• no Gene flow
• no Mutation

Really
Let
No one
Get
More

if a population is not in HWE for a gene… at least one of these assumptions has been violated

Question 20

how close does the expected frequencies have to be to the observed frequencies to be in HWE?

Answer 20

0.010

Question 21

paraphyletic group

Answer 21

a group that contains the common ancestor, but not all descendants