Lecture 10

Question 1

what is taxonomy

Answer 1

the theory and practise of classification and naming

Question 2

what is systematics

Answer 2

the study of biodiversity and the evolutionary relationships among organisms

Question 3

what is a taxon

Answer 3

a single named taxonomic unit at any level

Question 4

who is the father of taxonomy

Answer 4

Carolus Linnaeus
- created binomial nomenclature and the hierarchical system of classification
Kingdoms, phyla, class, order, family, genus, species (KPCOFGS)

Question 5

what is the purpose of biological classification

Answer 5

• showing the shared information of an organism
• enables interpretation of origins and evolutionary history
• systematic research requires a robust and stable system for classifying organisms

Question 6

T/F phylogenetic trees show the history of species

Answer 6

true

Question 7

explain the node, tips, root and taxa components of a tree

Answer 7

nodes: when one lineage splits into 2
tips/leaves/terminals/OTU: do not have descendants - they can be individuals, species or clades
root: earliest time in the tree - showed by unlabeled branch
taxa: (sister groups): come from the same common ancestor = immediate descendants (sister clades, sister species, sister branches)

Question 8

explain all the types of branches on a phylogenetic tree

Answer 8

branches: the edges - all branches are connected by nodes - correspond to single ancestor-descendant lineages (its common ancestor)
external branches: connect a tip to a node
internal branches: connect 2 nodes
parent branches: the big branches that connect the smaller daughter branches together

Question 9

explain the ingroup of a tree

Answer 9

consists of the focal species in a phylogenetic study
- the more closely related species

Question 10

what is the outgroup in a tree

Answer 10

the more distantly related species of the ingroup taxa
- can help root the phylogeny and help determine what species is ancestral

Question 11

what is MRCA

Answer 11

• most recent common ancestor
  different MRCA for different taxa
• it is the youngest node that is ancestral to all lineages in a given group of taxa
  
  • there can be many MCRA for one tree (connecting the small taxa and bigger taxa)

Question 12

what is a clade

Answer 12

any piece of phylogeny that includes an MRCA and ALL of its descendants (one triangle)
- one tree = many clades

Question 13

how to determine the exact number of clades

Answer 13

n-1
n = the number of species
10 species = 9 clades

Question 14

what is a monophyly

Answer 14

describes a group made up of an ancestor and all of its descendants
- monophyletic group or clade
- scissor test –> if one cut separates the clade = monophyletic clade

Question 15

what is a paraphyly

Answer 15

a group made up of an ancestor and some (but not all) of its descendants
- fails the scissor test - cuts between a large clade

Question 16

what is a polyphyly

Answer 16

describes a group that does not contain the most recent common ancestor of all members
- multiple cuts in the phylogenetic tree

Question 17

what does it mean for a clade of species to be ancestral

Answer 17

the inheritance of traits for a given group of species
- it is ancestral if it was inherited in its present form from the MCRA of the clade

Question 18

what does it mean for a clade of species to be derived

Answer 18

a trait is derived if it originated within the clade
- all the descendants of the clades MRCA

Question 19

T/F the same trait can be ancestral for a clade but derived within a larger clade

Answer 19

true
- the ancestral group of species was cut and did not include the entire clade only a small MRCA of the bigger MRCA

Question 20

what is a synapomorphy

Answer 20

a shared, derived trait for a clade and it evolved on the branch leading to the clade
- a trait that all species in the clade share

Question 21

how does homology relate to phylogenetic trees

Answer 21

when structures observed in different taxa can be traced to a single structure present in a shared evolutionary ancestor
- homologous = common ancestor

Question 22

what is homoplasy

Answer 22

when a trait of a trait state arises more than once on a phylogenetic tree indicating convergent evolutionw

Question 23

why are phylogenetic analyses important

Answer 23

understand the history of life
understand large scale patterns
understand how traits evolve, how fast
where/when did a parasite spread
tracking flu strains

Question 24

T/F the data in the phylogenetic trees cannot be genetic

Answer 24

false
it can be genetic or phenotypic

Question 25

T/F if there is relatedness on a phenotypic phylogenetic tree is is inferred from homologous traits

Answer 25

true

Question 26

what are 2 principal sources of macroevolution

Answer 26

1. paleontology
2. phylogenetics

Question 27

what is paleontology

Answer 27

provides a direct record of past evolutionary change
good for groups that fossilized well
problem: a lot of species do not fossilize well

Question 28

what is phylogenetics

Answer 28

provides an indirect record of past evolutionary change
inference is strongest for groups that have living representatives - to make better connection and observe

Question 29

how can the fossil record relate to macroevolution

Answer 29

shows evidence for completely extinct clades
shows proof for long-term patterns of biodiversity
shows proof for catastrophic extinctions

Question 30

what is a mass extinction

Answer 30

when more than 75% of the earths species in a short period of time disappear

Question 31

what is the diversification rate

Answer 31

speciation rate - extinction rate

Question 32

what are some ways that increase diversification

Answer 32

herbivory
wider selection for mating
animal pollination for plants
increases dispersal
increases range size