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Mammals and evolution > week 2 > Flashcards

week 2 Flashcards

1
Q

what is systematics?

A

making sense of biological diversity

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2
Q

what is taxonomy?

A

one aspect of systematics - the naming of biological groups

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3
Q

who is linnaeus?

A

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

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4
Q

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

A 
phylum
class
order
family
genus
species
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5
Q

what are the three major schools of hierarchical classification?

A

phenetics
cladistics
evolutionart taxonomy

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6
Q

what is phenetics?

A

also known as numerical taxonomy

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

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7
Q

what is cladistics?

A

is concerned with relatedness or phylogenetics

classifying organimss based on shared evolutionary origin

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8
Q

what is evolutionary history?

A

mixture of both cladistics and phenetics

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9
Q

what is a clade?

A

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

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10
Q

what is a phylogenetic or evolutionary tree?

A

branching diagram representing the history of a group of species

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11
Q

what does cladistics reject?

A

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

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12
Q

what sort of features does cladistics use?

A

shared derived characteristics because of common ancestry

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13
Q

what is homology?

A

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

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14
Q

what is analogy?

A

similar function evolved independently not from a common ancestor

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15
Q

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

A

no use
limited use
great use for systematics

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16
Q

what are the three kinds of similarity in phylogenetics?

A

primitive
convergent
derived

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17
Q

the character state convergent is also known as

A

homoplasy

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18
Q

the character state primitive is also known as

A

plesiomorphy

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19
Q

shared primitive characters are —

A

symplesiomorphies

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20
Q

the character state derived is also known as

A

apomorphy

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21
Q

shared derived characters are also known as

A

synapomorphies

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22
Q

characters unique to a group are known as

A

autopomorphies

23
Q

what is dollos law?

A

loss of features is more likely

24
Q

what is the principle of parsimony?

A

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

25
Q

what is a monophyletic group?

A

group contains a common ancestor and all its descendants

26
Q

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

A

confounding effect of convergent evolution

27
Q

what is the most important source of information for systematics?

A

dna sequence data

28
Q

5 reasons molecular data is better than morphological data?

A 
cheaper
easier to obtain
non invasice
objective
comparable across all living things
29
Q

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

A

appropriate rate to be informative

easy to work with in lab and analysis

30
Q

what would mitochondrial genes reveal?

A

maternal lineages

31
Q

do mitochondrial genes have a high or low mutation ratee?

A

high mutation rate so good for within species

no recombination

32
Q

what do y chromosome genes reveal?

A

paternal lineages

low mutation rate so good for looking far back

33
Q

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

A

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

34
Q

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

A

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

35
Q

what do sequence differences arise from?

A

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

36
Q

what are the 3 character state methods of building trees?

A

maximum parsimony
maximum likelihood
baysian statistics

37
Q

what are the 2 distance based methods?

A

neighbour joining

UPGMA (unweighted pair group method with arithmetic averages)

38
Q

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

A

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

39
Q

what gives us a molecular clock to calculate divergence times?

A

calibrating sequences

40
Q

what is a stochastic clock?

A

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

41
Q

what is a metronomic clock?

A

the stochastic clock plotted linearly

42
Q

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

A

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

43
Q

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

A

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

44
Q

what is a shared primitive character?

A

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

45
Q

what is a shared derived character?

A

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

46
Q

2 reasons why mutations may not survive through many generations

A

selection

genetic drift

47
Q

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

A

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

48
Q

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

A

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

49
Q

the rate of evolution vs level of detail

A

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

50
Q

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

A

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

51
Q

problem with multiple substitutions?

A

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.

52
Q

problem with gene trees vs species tree

A
  • 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
53
Q

calibration of molecular clocks

A
  • 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

Mammals and evolution (6 decks)

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