Lecture 10 - Phylogenetics & Macroevolution

Question 1

taxonomy

Answer 1

organizing diversity
- the theory and practice of classification & naming

Question 2

Systematics

Answer 2

the study of biodiversity and the evolutionary relationships among organisms

Question 3

phylogeny

Answer 3

describes how organisms in the past branched out from each other

Question 4

how are taxonomic species names assigned?

Answer 4

assigned such that they are consistent with our present understanding of evolutionary relationships

Question 5

What did Carolus Linnaeus do?

Answer 5

• considered the father of taxonomy
• came up with binomial nomenclature
• came up with hierarchical system of classification
• did not talk about evolutionary relationships

Question 6

Taxon

Answer 6

a single named taxonomic unit at any level

Question 7

Dear King Phillip Came Over For Good Soup

Answer 7

Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

Question 8

What is the purpose of a biological classification?

Answer 8

• effective global communication as consistent accross language etc
• enables interpretation of origins and evolutionary history

Question 9

a species is made of many populations linked by gene flow

Question 10

nodes in a phylogenetic tree

Answer 10

corresponds to historical lineage splitting events
- when one lineage splits into two
- there is always one less node in the three than there are species

Question 11

Branches in phylogenetic trees

Answer 11

corresponds to single ancestor-descendant lineages
- branches are connected by nodes
- evolution occurs in branches

Question 12

Tips in phylogenetic trees

Answer 12

• do not have represented descendants
• don’t give rise to anything else
• can be individuals, species, clades
  aka leaves, terminals, operational taxonomical unit (OTUS)

Question 13

what is an internal branch in a phylogenetic tree?

Answer 13

branches that connect two nodes

Question 14

what is an external branch in a phylogenetic tree?

Answer 14

branches that connect 1 node to a tip

Question 15

What are sister groups (sister taxa) in a phylogenetic tree?

Answer 15

those that are immediate descendants of the same ancestor
- chimps and humans are sister lineages
- sisters can be at any level of taxonomy

Question 16

Parents + & Daughters in phylogenetic trees

Answer 16

ancestor = parent
descendant = daughter
parent branches give rise to daughter branches

Question 17

root in a phylogenetic tree

Answer 17

a node representing the earliest time point in the diagram
- often represented by an unlabeled branch
- hypotheical ancestor to everything in the phylogeny

Question 18

an ingroup in a phylogenetic tree

Answer 18

the focal species in a phylogenetic study

Question 19

an outgroup in a phylogenetic tree

Answer 19

a more distant relative of the ingroup taxa
- helps provide context

Question 20

MRCA in a phylogenetic tree

Answer 20

most recent common ancestor
- youngest node that is ancestral to all lineages in a given group of taxa

Question 21

Clade in a phylogenetic tree

Answer 21

an ancestor + all descendants
- and piece of phylogenfy that includes and MRCA and all of its descendants

Question 22

monophyly

Answer 22

a group made up of an ancestor and all its descendants

Question 23

scissor test

Answer 23

if you can remove all the species in the clade with a single cut then it is a monophyletic group

Question 24

paraphyly

Answer 24

a group made up of an ancestory and some but not all of its descendants
aka grade
- does not pass the scissor test

Question 25

polyphyly

Answer 25

a group that does not contain the most recent common ancestor of all members - like reptiles + amphibeans, does not include MRCA

Question 26

what terms can be refered to the inheritance of traits

Answer 26

- ancestral - derived - character evolution

Question 27

a trait is ancestral if...

Answer 27

it was inherited in its present form from the MRCA of the clade

Question 28

a trait is derived if....

Answer 28

for a clade it originated within that clade

Question 29

a trait can be ancestral for a clade but derived within a ________clade

Answer 29

larger

Question 30

synapomorphy

Answer 30

- a shared, **derived** trait for a clade - a trait shared by all species in the clade - evolved on the branch leading to the clade

Question 31

homology

Answer 31

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

Question 32

homoplasy

Answer 32

when a character or state arises more than one on a phylogenetic tree, - sort of convergence - similar traits are evolved seperately

Question 33

what does conducting phylogenetic analysis help with?

Answer 33

- understanding history of life - understanding large-scale patterns of evolution - understand how many times traits have evolved, how fast, and under what conditions

Question 34

What are some practical applications of phylogenetic analysis?

Answer 34

- where/when parasites spread - which flu strain was most successful last year can predict the most successful flu strain this year

Question 35

what are 2 principal sources of macroevolutionary insights?

Answer 35

paleontology phylogenetics

Question 36

paleontology (desribe) (5)

Answer 36

- **direct** record of past evolutionary change - good for groups that fossilize well - provides only evidence for completely extinct clades - documents long-term patterns of global biodiversity - provides evidence for catastrophic extinctions during Earth's history

Question 37

phylogenetics - describe (3)

Answer 37

- **indirect** record of past evolutionary change - strongest for groups that have living representatives - provides evidence for explosive diversification following mass extinctions

Question 38

mass extinction

Answer 38

extinction of more than 75% of Earth's species in a geologically short period

Question 39

diversification rate

Answer 39

speciation rate - extinction rate (minus)

Question 40

features associated with increased diversification (5)

Answer 40

- herbivory - species with more sexual selection - animal pollination in plants - increased dispersal - increased range size