Lecture 10

Question 1

Define taxonomy

Answer 1

the theory and practice of classification and naming

Question 2

define systematics

Answer 2

the study of biodiversity and the evolutionary relationships among organisms

Question 3

Carolus Linnaeus

Answer 3

1707-1778
- father of taxonomy
- binomial nomenclature
- hierarchical system of classification

Question 4

define a taxon

Answer 4

a single named taxonomic unit at any level (plural = taxa)

Question 5

7 taxa

Answer 5

kingdom (kingdoms)
phylum (phyla)
class (classes)
order (orders)
family (families)
genus (genera)
species (species)

Question 6

what is the purpose of a biological classification?

Answer 6

• a name is key to shared information on an organism (eg scientific literature, field guides)
• therefore has predictive power
• enables interpretation of origins and evolutionary history

Question 7

systematics research requires

Answer 7

a robust and stable system for classifying organisms (i.e. taxonomy)

Question 8

describe how phylogenies arise/what they are made up of

Answer 8

1. individual organisms within a population
2. parents produce offspring
3. lines of descent persist across generations
4. a population is an aggregation of the genetic lineages of the individuals they contain
5. a species is made of many populations, linked by gene flow
6. individual species split to give rise to multiple species
7. a phylogeny shows the relationships and evolutionary histories of species

Question 9

node

Answer 9

corresponds to historical lineage splitting events, when one lineage splits into two

Question 10

branches/ edges

Answer 10

correspond to single ancestor-descendant lineages. All branches are connected by nodes

Question 11

tips/leaves/terminals/OTUs

Answer 11

tips do not have represented descendants. can be individuals, species, clades

Question 12

internal vs external branches

Answer 12

external branches (aka terminal branches) connect a tip and a node. internal branches connect two nodes

Question 13

root

Answer 13

• a node representing earliest time point in the diagram
• often represented by an unlabelled branch

Question 14

sister groups/taxa

Answer 14

those that are immediate descendants of the same ancestor, eg sister species, sister branches, sister clades

Question 15

parents and daughters

Answer 15

parent branches give rise to daughter branches

Question 16

ingroup

Answer 16

consists of the focal species in a phylogenetic study

Question 17

outgroup

Answer 17

a more distant relative of the in-group taxa; can help to root the phylogeny and determine what character states are ancestral

Question 18

MRCA

Answer 18

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

Question 19

clade

Answer 19

• any piece of a phylogeny that includes a MRCA and all of its descendants
• i.e. any piece of a phylogeny that exhibits monophyly

Question 20

monophyly

Answer 20

• describes a group made up of an ancestor and all its descendants
• ie a monophyletic group or clade

Question 21

paraphyly

Answer 21

• describes a group made up of an ancestor and some (but not all) of its descendants
• ie a paraphyletic group or grade

Question 22

polyphyly

Answer 22

• describes a group that does not contain the most recent common ancestor of all members
• ie. a polyphyletic group

Question 23

for the species in a clade a trait is ancestral if

Answer 23

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

Question 24

for the species in a clade, a trait is derived if

Answer 24

it originated within the clade, ie in a descendant of the clade’s MRCA

Question 25

relationship between ancestral and derived clades

Answer 25

the same trait can be ancestral for a clade, but derived within a larger clade

Question 26

define a synapomorphy

Answer 26

a shared, derived trait for a clade. it is a trait that all species in the clade share, and that evolved on the branch leading to the clade (ie its derived within the context of more inclusive clades)

Question 27

homology

Answer 27

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

Question 28

homoplasy

Answer 28

when a character or character state arises more than once on a phylogenetic tree (convergence is one kind)

Question 29

why conduct a phylogenetic analysis?

Answer 29

• understand history of life
• understand large scale patterns of evolution
• understand how many times traits have evolved how fast, under what conditions
• practical: where/when did parasites spread? which fly strain is most successful? what are the driver mutations as covid evolves?

Question 30

why is phylogenetic relatedness inferred from homologous traits and not homoplasy?

Answer 30

homoplasy (eg convergent trait evolution) can mislead phylogenetic inference

Question 31

2 principal sources of macroevolutionary insights?

Answer 31

palaeontology
- provides a direct record of past evolutionary change
- inference is strongest for groups that fossilise well
phylogenetics
- provides an indirect record of past evolutionary change
- inference is strongest for groups that have living representatives

Question 32

mass extinction

Answer 32

extinction of >75% of earth’s species in a geologically short period

Question 33

uses of fossil record

Answer 33

• provides only evidence for completely extinct clades
• documents long-term patterns of biodiversity
• provides evidence for catastrophic extinctions during earth’s history

Question 34

diversification rate

Answer 34

speciation rate minus extinction rate

Question 35

what happens after mass extinctions and how do we know?

Answer 35

explosive diversification; phylogenetic provides evidence for this

Question 36

features associated with increased diversification

Answer 36

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