Phylogenetics

Question 1

terminal nodes

Answer 1

currently extant (or extinct) organisms

Question 2

internal nodes

Answer 2

ancestral organisms

Question 3

monophyletic group

Answer 3

complete group of descendants from a common ancestor

Question 4

paraphyletic group

Answer 4

subset of all descendants from a common ancestor

Question 5

polyphyletic group

Answer 5

group that does not share a common ancestor

Question 6

sister

Answer 6

most closely related group of species

Question 7

taxon

Answer 7

generic word for a group of any size - could be a species

Question 8

clade

Answer 8

generic word for a monophyletic group of any size

Question 9

what type of group is invertebrates?

Answer 9

paraphyletic

Question 10

axes of phylogenetic trees

Answer 10

only 1 axis - time - must be in relative units

Question 11

longer branches indicate…

Answer 11

more genetic differences, not necessarily more time elapsed

Question 12

maximum parsimony

Answer 12

fewest transitions are required to explain the observed diversity

Question 13

outgroups

Answer 13

groups that branched off a long while ago - used to root trees

Question 14

neighbor joining

Answer 14

uses a distance matrix to determine neighbors, by finding groups that are the least distant

Question 15

homologs

Answer 15

distinct but closely related genes - similarities may be due to common ancestry

Question 16

paralogs

Answer 16

homologs due to gene duplication

Question 17

orthologs

Answer 17

homologs due to speciation

Question 18

gene families

Answer 18

groups of homologous genes

Question 19

horizontal gene transfer

Answer 19

DNA is not acquired from parents - can occur through bacteria, etc - makes it really hard to figure out bacteria phylogenies