week 2

Question 1

what is systematics?

Answer 1

making sense of biological diversity

Question 2

what is taxonomy?

Answer 2

one aspect of systematics - the naming of biological groups

Question 3

who is linnaeus?

Answer 3

swedish biologist who devised the binomial system still used today for naming organisms

Question 4

what are the main hierarchical groups we are interested in from animal taxonomy?

Answer 4

phylum
class
order
family
genus
species

Question 5

what are the three major schools of hierarchical classification?

Answer 5

phenetics
cladistics
evolutionart taxonomy

Question 6

what is phenetics?

Answer 6

also known as numerical taxonomy

builds hierarchies on the basis of physical similarities and therefore emphasises adaptation

Question 7

what is cladistics?

Answer 7

is concerned with relatedness or phylogenetics

classifying organimss based on shared evolutionary origin

Question 8

what is evolutionary history?

Answer 8

mixture of both cladistics and phenetics

Question 9

what is a clade?

Answer 9

a lineage within a tree containing the descendants of a common ancestor

Question 10

what is a phylogenetic or evolutionary tree?

Answer 10

branching diagram representing the history of a group of species

Question 11

what does cladistics reject?

Answer 11

groups that contain some but not all the descendants of a common ancestor e.g. birds and reptiles
PARAPHYLETIC groups

Question 12

what sort of features does cladistics use?

Answer 12

shared derived characteristics because of common ancestry

Question 13

what is homology?

Answer 13

similar structures inherited from a recent common ancestor e.g. vertebrate forearm

Question 14

what is analogy?

Answer 14

similar function evolved independently not from a common ancestor

Question 15

the utility of different character types in systematics =
character is analagous?
character is homologous and primitive?
character is homologous and derived?

Answer 15

no use
limited use
great use for systematics

Question 16

what are the three kinds of similarity in phylogenetics?

Answer 16

primitive
convergent
derived

Question 17

the character state convergent is also known as

Answer 17

homoplasy

Question 18

the character state primitive is also known as

Answer 18

plesiomorphy

Question 19

shared primitive characters are —

Answer 19

symplesiomorphies

Question 20

the character state derived is also known as

Answer 20

apomorphy

Question 21

shared derived characters are also known as

Answer 21

synapomorphies

Question 22

characters unique to a group are known as

Answer 22

autopomorphies

Question 23

what is dollos law?

Answer 23

loss of features is more likely

Question 24

what is the principle of parsimony?

Answer 24

take the simplest explination the tree with the least number of changes

Question 25

what is a monophyletic group?

Answer 25

group contains a common ancestor and all its descendants

Question 26

what is the main thing you need to be aware of when building a tree?

Answer 26

confounding effect of convergent evolution

Question 27

what is the most important source of information for systematics?

Answer 27

dna sequence data

Question 28

5 reasons molecular data is better than morphological data?

Answer 28

``` cheaper easier to obtain non invasice objective comparable across all living things ```

Question 29

why do you have to be specific about selecting the correct gene to work with in evolutionary studies?

Answer 29

appropriate rate to be informative | easy to work with in lab and analysis

Question 30

what would mitochondrial genes reveal?

Answer 30

maternal lineages

Question 31

do mitochondrial genes have a high or low mutation ratee?

Answer 31

high mutation rate so good for within species | no recombination

Question 32

what do y chromosome genes reveal?

Answer 32

paternal lineages | low mutation rate so good for looking far back

Question 33

austosomal genes can also be used for trees but what is a major problem?

Answer 33

complex to interpret as results can be influenced by recombination and lineage sorting processes

Question 34

what is the brief outline of methodology for obtaining moelcular data?

Answer 34

extract dna target and amplify region of interest using specific primers and the polymerase chain reaction sequence the target dna analyse sequence

Question 35

what do sequence differences arise from?

Answer 35

mutations (substitution, insertion or deletion of bases) accumulate over time

Question 36

what are the 3 character state methods of building trees?

Answer 36

maximum parsimony maximum likelihood baysian statistics

Question 37

what are the 2 distance based methods?

Answer 37

neighbour joining | UPGMA (unweighted pair group method with arithmetic averages)

Question 38

likelihood and bayesian methods often perform better than parsimony or distance methods why?

Answer 38

they involve building a mathematical model of the process of substitution and calculating the probability of observing particular sequences at the ends of particular branches

Question 39

what gives us a molecular clock to calculate divergence times?

Answer 39

calibrating sequences

Question 40

what is a stochastic clock?

Answer 40

where it is not linear, mutations may accumulate with time at different rates

Question 41

what is a metronomic clock?

Answer 41

the stochastic clock plotted linearly

Question 42

Rates of change along lineages can be constant but stochastic how so?

Answer 42

because the same amount fo mutations occur on the lineages but they do not occur at regular intervals. one lineage may have 3 mutations close to each other and the other lineage may have 3 mutations evenly spaced

Question 43

molecular phylogenetic may often disagree with morphological phylogenies why? (3)

Answer 43

homoplasy or misinterpretation of morphology incorrect analysis of molecular data overconfidence in molecular results

Question 44

what is a shared primitive character?

Answer 44

a character that is shared by two or more taxa within the group because it has been inherited from the common ancestor of the entire group

Question 45

what is a shared derived character?

Answer 45

a character shared by two or more taxa within the group that has evolved within the group

Question 46

2 reasons why mutations may not survive through many generations

Answer 46

selection | genetic drift

Question 47

what is one of the assumptions of the molecular method to build a tree?

Answer 47

the gene tree reflects the species tree or the deeper phylogeny (this is not always the case)

Question 48

very often when reconstructing evolutionary trees we look at mitochondrial DNA why?

Answer 48

because it is often passed through the mother line and is simple inheritance

Question 49

the rate of evolution vs level of detail

Answer 49

some genes change faster than others and this has a bearing on building our phylogenies rRNAs very slow evolving microsattelites very fast evolving

Question 50

still have to be aware of homoplasy in molecular building of phylogenetic trees, why?

Answer 50

it is even harder to filter out convergent evolution from shared derived when looking at dna sequences

Question 51

problem with multiple substitutions?

Answer 51

If we are looking at an ancestral sequence at the top there, if overtime look at what can happen in those 2 descendent DNA sequences, various things can happen including sequence substitution, but over time you could get multiple substitutions, if you pick a fast evolving gene then this sort of thing happens all the time e.g. an A goes to a C and then to a T. You will miss the changes as when you sequence it you see the T only and not the changes that occurred between them.

Question 52

problem with gene trees vs species tree

Answer 52

* when looking at gene trees one hope is that reflects the branching pattern of species but not always the case * look at this diagram to make that point * time scale * gene in species a and that gene starts to obtain some mutations when you make the tree you have 2 different lineages * what does that mean in reality? * It could just mean a different phenotype not species * Gene will start to diverge and you get differences in the molecular gene tree way before speciation events occur * at what point does genetic difference give you a different species not a polymorphism

Question 53

calibration of molecular clocks

Answer 53

* hypothesis over time mutations arise they get fixed and those differences get larger as time goes by * the more genetically different the further back in time it was that they shared a common ancestor or sequence * some how need to calibrate this - reliable way to calibrate this molecular clock * surely we know what the mutation rate is in DNA? We actually don’t it is a hard thing to calculate and it is going to differ between different organisms need to find another way to calibrate * also the mutation rate is different ot the observed substitution rate * are mutations constant with time * are they constant within lineages? Defo no