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Evolution Flashcards

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Biology 101 flashcards
1
Q

what is evolution?

A
  • process by which different kinds of living organism have developed from earlier forms during the history of the earth
  • change in the gene pool of a population from generation to generation by such processes as mutation, natural selection and genetic drift
  • a change in allele or genotype frequencies
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2
Q

why is evolution important?

A
  • all forms of life an biodiversity exist due to evolutionary processes
  • an ongoing process, that will affect all populations
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3
Q

what is population genetics?

A
  • study of patterns of genetic variation and of the mechanism of evolution, i.e. of allele and genotype frequency
  • the process of evolution → how alleles and genotypes change over time
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4
Q

what are the 5 processes contributing to evolution?

A
  1. Mutation and recombination
  2. Genetic drift
  3. Selection
  4. Gene flow
  5. Non-random mating
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5
Q

how do we know if there is evolution and changes in allele frequencies?

A
  • we can see genetic variation in most populations

- we need a model to be able to describe this variation → find out if evolution is happening

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6
Q

what is an allele?

A

variant form of a gene

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7
Q

what is a gamete?

A

mature haploid or female germ cell

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8
Q

what is a genotype?

A

genetic constitution of an organism

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9
Q

why do we need the hardy weinberg equilibirum?

A

want to know how many people carry an allele

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10
Q

what do p and q stand for in the hardy weinberg equation?

A

Allele frequency = p, q

Genotype frequency = pxp (homozygous dominant), qxq (heterozygous recessive), 2pq (heterozygous)

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11
Q

what is the hardy weinbeerg equilibrium?

A

p + q = 1

p(^2) + 2pq + q(^2) = 1

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12
Q

what are the assumptions of the Hardy-Weinberg equilibrium?

A
  • no selection
  • no migration
  • large population size
  • random mating
  • no mutation
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13
Q

what is natural selection?

A

variation in average reproductive successes (including survival) among phenotypes

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14
Q

what was darwins theory of natural selection?

A
  • favourable variations would tend to be preserved and unfavourable ones to be destroyed
  • the result of this would be the formation of a new species
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15
Q

what are the requirements of natural selection?

A

Link between phenotypes and fitness
Link between genotype and phenotype
Link between genotype and fitness

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16
Q

what is adaptation?

A
  • a consequence of selection
  • feature that has a beneficial function and has become present or is maintained in a population or species because of natural selection
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17
Q

what is fitness?

A

the average relative chance of a genotype of leaving offspring

  • survival to maturity
  • fecundity
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18
Q

describe the results of artificial selection experiments

A

Selection can happen quite rapidly
Selection experiment since 1890s to test for limits of directional selection
Selected lines are outside initial variation
Complex trait >50 genes involved
Dramatically separated in a relatively short amount of time

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19
Q

what is the selection coefficient?

A

S = reduction in fitness

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20
Q

what would the fitess animals have?

A

relative fitness of 1 - reproduce the maximum amount

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21
Q

what does selection alter?

A

allele and genotype frequencies

- after selection a population is no longer in hardy-weinberg equilibrium

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22
Q

what are the different types of mutations

A

somatic or in the germline

advantageous, neutral or deleterious

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23
Q

describe population genetics and mutations

A
  • fate of mutations

- the mutations itself does not change allele frequencies to a significant degree, other processes need to act

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24
Q

why do we need mutations?

A
  • wouldn’t have evolution without them
  • any one mutation occurring leads to a minimum allele change
  • in a large population a mutation is tiny
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25
Q

what is neutral drift?

A
  • chances are the mutation will be lost
  • by neutral processes because its rare
  • if the individual is reproducing more than average the mutation could increase in a population
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26
Q

what is fixation?

A
  • over a long period time if theres not selection
  • one allele could be lost an another could fixed
  • could be the original or could be mutated thats fixed
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27
Q

what is negative selection?

A
  • negative mutation wouldn’t be selected for

- would happen faster than neutral drift

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28
Q

what is positive selection?

A
  • might be beneficial and positively selected for
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29
Q

what is a population bottleneck?

A

population is reduced to a few individuals

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30
Q

what are the consequences of a population bottleneck?

A

Rare alleles are lost
Change of allele frequencies by chance
Allele frequencies will therefore change
Surviving population will have quite a different make up to the original population

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31
Q

what is an example of a population bottleneck

A

cheetahs
- Genetically uniform because there haven’t been enough mutations to recreate the genetic diversity they would have had in the first place

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32
Q

what is genetically uniform?

A

not the diversity for selection to be able to act upon

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33
Q

what is the founder effect?

A

a few individuals start a new population

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34
Q

what is an example of the founder effect?

A

colonisation of an island
The great human expansion → serial founder effect
Original population disperse → new population would have a different genetic makeup

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35
Q

what is the neutral theory?

A

Much DNA variation appears to have no effects on fitness and is therefore neutral
No selection acts on this variation
Genetic drift acts on these alleles and is therefore important molecular evolution

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36
Q

what is gene flow?

A

movement of alleles from one population to another

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37
Q

what are the consequences of gene flow?

A
  • Increases genetic diversity in the receiving population
  • Homogenises connected populations
  • Can be maladaptive → Some alleles introduced to the resident population could be bad for that environment and become less adapted
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38
Q

what could happen in migration?

A

individual moves it could be that there is already another population there → would have different genetic makeups
If migrants mate with the resident population it increases genetic diversity in the receiving population
Might introduce some alleles → eg if there are similar environment one of the populations might have an allele that copes better in an environment

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39
Q

what is non-random mating?

A
  • when individuals do not mate randomly

- could be a preference for the same or a different genotype

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40
Q

what could be the consequences of non-random mating?

A
  • if each is homozygous, there will be a deficit of heterozygous
  • with a different partner leads to heterozygous
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41
Q

why is species difficult to define?

A

species change due to evolutionary process and may give rise to new species

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42
Q

what are features that define a species?

A
  • Reproductive isolation form other species
  • Species form morphological and/or genetic clusters are distinct from other such clusters
  • Members of a species share a common ancestor
  • Group that is adapted to a particular ecological niche
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43
Q

what is the biological species concept?

A

A species is a group of actually or potentially interbreeding natural populations that are reproductively isolated from other such groups

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44
Q

what are the issues with the biological species concept?

A
  • Difficult to test for reproductive isolation
  • Cannot apply to asexual organisms
  • Cannot be tested in extinct groups
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45
Q

what is the genotypic cluster concept?

A

A species is a (morphologically or genetically) distinguishable group of individuals that has few or no intermediates when in contact with other such clusters

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46
Q

how do new species form?

A

speciation requires the evolution of reproductive isolation

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47
Q

what is pre-zygotic reproductive isolation?

A

behavioural isolation (not mating), incompatibility of reproductive organs

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48
Q

what is post-zygotic reproductive isolation?

A

some type of genetic incompatibility

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49
Q

how does the evolution of reproductive isolation occur?

A
  • population splits
  • see 2 groups emerging
  • random mutations happening separately
  • overtime genetic drift and selection will happen
  • genetic divergence → no longer able to interbreed
  • call them different species
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50
Q

what is a cladogenesis?

A

evolutionary splitting event where a parent species splits into two distinct species, forming a clade (speciation)

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51
Q

what is allopatric speciation?

A

geographically isolated

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52
Q

what is paraptric speciation?

A

adjacent

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53
Q

what is sympatric speciation?

A

without spatial separation

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54
Q

what is anagenesis?

A

cumulative change within lineage

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55
Q

what is the process of allopatric speciation?

A

Physical geographical barrier
Parental species splits into population A and population B
Populations evolve independently
Become species A and species B
Reproductive isolation gradually evolves
On renewed contact new species do not interbreed

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56
Q

what are the features of allopatric speciation?

A

Genetic drift acting independently in separate geographic areas
Divergent selection if environment conditions differ
Different mutations occur

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57
Q

why does allopatry occur?

A
  • dispersal

- vicariance (geographical barrier arises)

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58
Q

what is the process of parapatric speciation?

A

No geographic barrier but extreme change in environmental conditions
Parental range limited by environmental conditions
Range expansion with adaptation to new conditions
Few hybrids between the parental and derived → separate

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59
Q

what is the process of sympatric speciation?

A

Speciation occurring without physical barriers
Need strong disruptive selection
Overtime these populations differentiate sufficiently to become a new species
Has been controversial whether it can occur because gene flow in homogenises populations

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60
Q

what is adaptive radiation?

A

usually rapid evolutionary diversification, accelerated by natural selection

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61
Q

what is cospeciation?

A

Two groups of organism speciate in response to each other at the same time

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62
Q

what is direct selection?

A

selection leading to assortative mating

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63
Q

what happened 3.8 billion years ago?

A

life starts to emerge

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64
Q

what was earth like 3.8 billion years ago?

A
  • mainly ocean
  • no ozone layer
  • UV radiation
  • volcanic activity
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65
Q

what is primordial soup?

A

solution rich in organic compounds in the primitive oceans of the earth from which life is though to have originated

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66
Q

what is the Miller-Urey experiment

A

mimicked early earth conditions to create amino acids from water, methane, ammonia and hydrogen

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67
Q

what were the criticisms of the Miller-Urey experiment?

A

early atmosphere hydrogen poor → not high enough concentrations

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68
Q

what is theory of how the chemical origin of life came about?

A

Life begins at submarine hydrothermal vents spewing key hydrogen-rich molecules
Tectonic plate → volcanic activity
Rich in molecules
Concentrated the precursors of amino acids
Their rocky nooks could have concentrated molecules together and provided mineral catalyses for critical reactions
Even now the vents are rich in chemical and thermal energy → sustain vibrant ecosystems
The energy was acquired through chemotrophic interactions → oxidising inorganic compounds

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69
Q

what were the simple beginnings 3.8 billion years ago?

A

Life might have begun with smaller molecules interacting with each other in cycles of reactions
Metabolism-first (didn’t first have genes, no way of storing or replicating information, birth of DNA and RNA came later) vs gene-first model

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70
Q

what is the panspermia theory?

A

Life brought here from elsewhere in space (bacterial spores)
Even if this is true how did life begin elsewhere in space
There have been experiments → shooting microbes up into space along with satellite

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71
Q

what happened 3.5 billion years ago?

A

first cells

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72
Q

what was the atmosphere like 3.5 billion years ago?

A

no oxygen, lots of UV radiation

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73
Q

what were the first cells though to be?

A

Archaea
- Extremophiles living in harsh environments, such as hot springs, salt lakes and cold environments
Also found in soils, oceans, marshlands and the human colon, oral cavity and skin
Archaea are particularly numerous in the oceans and the archaea in plankton may be one of the most abundant groups of organisms on the planet
Look like bacteria but metabolic pathways more similar to eukaryotes

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74
Q

what is the evidence of the first life 3.5 billion years ago?

A

Fossil records
Stromatolite → pillars of bacteria, see them in extreme environments so there is less predation
Lots of debate → people say they’re only chemical reactions

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75
Q

what happen 2.7 - 2.4 billion years ago?

A

cyanobacteria and the great oxidation event

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76
Q

where did photosynthesis occur 2.7 - 2.4 billion years ago?

A

in cyanobacteria

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77
Q

how was oxygen built in the atmosphere 2.7 - 2.4 billion years ago?

A
  • cyanobacteria = photosynthesis - able to produce oxygen

switch between cyanobacteria and methane producing bacteria

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78
Q

what changes were there to the earth 2.7 - 2.4 billion years ago?

A

Oxidised rocks rise on top of the mantle and reduce natural reduction
Birth of ozone layer that protects life from UV radiation → once there was a high enough concentration
Benefits → aerobic respiration more efficient than anaerobic respiration (supports longer food chains) → release energy more efficiently

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79
Q

what was the benefit of oxidising rock?

A

reacted with sea water - reacting with iron compounds

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80
Q

what was the oxygenation of the earth linked to?

A

diversity among organisms

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81
Q

why were cyanobacteria thought to be the most successful on earth?

A

Genetically diverse
Occupy a broad range of habitats including freshwater, marine and terrestrial ecosystems
Can survive in extreme niches
Photoautotrophic, oxygen producing cyanobacteria created the conditions in the planet’s atmosphere
Directed evolution
Debated whether they were responsible for oxygenated or allowed plants to move on earth to oxygenate the earth

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82
Q

what happened 2 billion years ago?

A

birth of the eukaryotic cell

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83
Q

what were the benefits of eukaryotic cells?

A

Prokaryotes are similar than eukaryotic cells → DNA in a nucleoid not in a proper structure
Eukaryotic cells are more complex and have cell organelles and enclosed nucleus
Eukaryotic cells will have a more efficient metabolism
Nucleus → DNA material enclosed, current theory suggests that its a more efficient expression of genes, produce mRNA

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84
Q

describe endosymbiosis 1

A
  1. one cell engulfs the other
  2. specialises later
    Early mitochondria was originally a bacteria that was engulfed by another prokaryotic
    Through evolution they became to benign to each
    Bacteria was at first a parasite
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85
Q

what is the evidence for endosymbiosis 1?

A

DNA sequencing, very similar to another bacteria (same common ancestor), mitochondria are dividing independently, have functions in the cell called porins (common in bacteria for transferring material)

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86
Q

describe endosymbiosis 2

A
  1. cells engulfed photosynthetic bacteria (cyanobacteria) that developed later into chloroplasts
    Cyanobacteria then used to gain energy
    Creating plant cells
    Chloroplasts → very similar to cyanobacteria
    Different lineages evolved chloroplasts independently at least three times → one lineage evolved to green algae and later to a plant
    The cyanobacterial origin of plastids is now supported by various pieces of phylogenetic, genomic, biochemical and structural evidence
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87
Q

what happened 1.5 billion years ago?

A

animals, plants and fungi

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88
Q

what is LUCA?

A

last universal common ancestor - all life emerges from one - share similarites

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89
Q

what is a phylogenetic tree?

A

branching diagram, shows evolutionary relationships based on similarities or differences in physical and genetic characteristics
All life on earth is part of a single phylogenetic tree, indicating common ancestry

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90
Q

how has sequencing formation changed the view of life?

A

most cases there are big gaps in fossil records
Makes it like a jigsaw puzzle with half the pieces missing
Phylogenies based on genome sequence similarities and differences much more accurate
Sequence based trees
Genome sequencing → more accurate

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91
Q

what are the key features of LUCA?

A
  • all descended from
  • estimated to have lived 3.5 - 3.8 billion years ago
  • can be studied by comparing genomes of descendants
92
Q

what genes could have been present in LUCA?

A
  • 355 genes
  • Had a gene for a revolving door protein that could swap sodium and hydrogen ions across this gradient
  • No genes involved in making amino acids, the building blocks of proteins
    LUCA may have depended on amino acids produced spontaneously at deep sea vents
93
Q

what happened 0.9 billion years ago?

A

multicellularity evolves

94
Q

what were the first multicellular cells?

A

red and green algae

95
Q

what are the advantages of multicellularity?

A
  • mroe efficient sharing of nutrients that are digested outside the cell
  • increased resistance predators, who attack by engulfing
  • ability to resist current by attaching to a firm surface
  • ability to reach upwards to filter feed or to obtain sunlight
  • ability to create an internal environment
  • behave intelligently
96
Q

what did multicelluarity trigger?

A

the diversity of life on earth

97
Q

what happened 0.7 billion years ago?

A

snowball earth and loss of diversity

98
Q

what is the snowball earth hypothessis?

A

proposes that earth’s surface became entirely or nearly entirely frozen at least once

99
Q

what are the 5 stages of the snowball earth?

A
  1. Extended cold spell oceans start freezing
  2. Lowered reflectively causes further cooling ending in ‘snowball earth’
  3. CO2 cycle in oceans stops; CO2 outgassing by volcanoes builds up
  4. Strong greenhouse effect melts snowball earth and results in hotball earth
  5. CO2 cycle restarts pulling CO2 back into oceans reducing greenhouse effects to normal
100
Q

what is the criticism of the snowball earth hypothesis?

A
  • difficult to ccreate with global climate models
  • the levels of CO2 needed to melt the glacier consdiered unrealistic
  • potentially triggered by cyanobacterial blooms and major oxygenation event
101
Q

what would have been the consequence of snowball earth?

A

mass extinctions

102
Q

what are the potential causes of snowball earth?

A

Asteroid impacts
Climate change
Volcanoes

103
Q

how many mass extinctions have there bee?

A

5

104
Q

what happened 0.5 billion years ago?

A

cambrian explosion and increase in diversity

105
Q

what is the cambrian explosion?

A

begins with many new body layouts appearing on the scene though the seeming rapiditiy of the appearance of new life forms may simply be an illusion by a lack of older fossils

106
Q

why was there the cambrian explosion?

A

potentially because oxygen availability enabled more effective release

107
Q

describe the increase in diveristy 0.5 billion years ago

A

When most animals are thought to arise
What drove this was the increase in oxygenation
Increase in food chains and trophic networks
This is again debated → what was the trigger? Are plants the most likely explanation

108
Q

what happened 0.4 billion years ago?

A

colonisation of land

109
Q

what was the colonisation of land?

A

Land was colonised by plants → which evolved from the green algae
Microbial mats and lichen creates soil
Mosses thought to be the first land plants → had to evolve

110
Q

what were the evolutionary challenges when colonising land?

A 
Desiccation resistance
Support (lignin)
Resistance to UV radiation
Resistance to oxidation
Reproduction in non-aquatic environment
111
Q

what were the benefits of colonising land?

A

Abundant sunlight
Abundant CO2
No predation (initially)
Predators followed 70-80 million years after which triggered the evolution of plant defenses: spines, thornes and chemicals

112
Q

what happened 0.2 billion years ago?

A

Brekaup of Pangea via continental drift

113
Q

what is contintental drift?

A

Drift of tectonic plates → did not have the same continent

114
Q

what evidence is there to support contintental drift?

A

an find fossils in different continents and therefore had to be moving in the past
If you look at maps → there are similarities between breakup points

115
Q

what happened 195,000 years ago?

A

humans evolve

116
Q

describe human evolution

A

Human history is relatively quite history
Closest relatives are chimpanzees if you compare the genomes → 95%
Human success attributed to be able to walk on 2 legs, increase in the size of the brain, cognition and speech → social interactions the driver of human success?

117
Q

what are the 8 major transitions?

A
  1. replicating molecules
  2. independent replicators
  3. RNA
  4. prokaryotes
  5. asexual reproduction
  6. protists
  7. solitary individuals
  8. primate societies
118
Q

what is replication molecules?

A

populations of molecules

- how chemical life ight have emerged

119
Q

where might have life started?

A

optimal conditions near deep sea vents

120
Q

what is a chemothon?

A

an abstract of protocells

121
Q

describe the chemothon

A
  • abstract model for the fundamental unit of life

- basic assumption is metabolism, self repication and lipid membrane

122
Q

what was the autocatalytic subsystem in the chemothon?

A

formed by the metabolic and replication functions together - necessary for the basic functions of life
- membrane encloses this subsystem

123
Q

what are independent replicators?

A

chromosomes

124
Q

what is the difference between prokaryotes and eukaryotes?

A

chromosomes - prokaryotes don’t have chromosomes or packaged DNA

125
Q

how is DNA organised in euakryotes?

A

DNA → nucleosomes → chromosomes → tightly wrapped DNA to better fit inside the cell

126
Q

what are the benefits of chromosomes?

A

storage of more information. Recombination and maintenance of genetic variation. Efficient packing of DNA

127
Q

how are chromosomes organised in humans?

A

organised into pairs → if there are deletions in the genes and you get a dysfunctional copy than the other chromosome will have a functional copy

128
Q

what came first proteins or DNA?

A

DNA needs proteins in order to form and prtoeins require DNA to form

129
Q

what is the RNA world hypothesis?

A

RNA is primordial, multifunctional molecules → they have a lot of roles and can carry out a lot of functions
Enzyme: self replicates, catalyzes simple chemical reactions, amino acid RNA ligation, peptide bond formation
Information storage: similar to DNA (but less table)
Regulation: riboswitches and RNA thermometers, regulates gene expression

130
Q

describe the hypothesis that RNA evolved into DNA

A

Taken place in intermediate stages
RNA is thought to have been replaced by the DNA through an intermediate stage of ribonucleoprotein enzymes
Can catalyze peptide ligation or amino acid polymerisation → DNA
DNA is thought to have taken over the role of data storage due to its increased stability (inherently less reactive)
Proteins replaced RNA’s role in specialised biocatalysis through a greater variety of monomers (amino acids)
RNA as both genes and enzymes → transition → DNA as genes; proteins as enzymes

131
Q

what were the benefits of endosymbiosis?

A

more efficient metabolism → mitochondria provides energy for the cell

132
Q

describe the secondary symbiosis in progress in Hatena arenicola

A

Flagella used for predation → filter bacteria
Happens between the flagellated cell and green algal symbiont
Able to culture these cells properly in the lab
Mitosis → one daughter cell retained the chloroplast (autotrophic) and the other lost the symbionts and became a predator which helps to engulf more bacteria
Symbiosis also changes: loses flagella, cytoskeleton and endomembrane system but plastid increases in size X10

133
Q

what are the advantages of sexual reproduction?

A

High genetic variability
Facilitates adaptation
Speeds up evolution

134
Q

what are the disadvantages of sexual reproduction?

A

Energy costly
Courtship time/resource consuming
Usually sacrifices the fitness of one sex to the other
For populations to stay the same size → need 2 offspring. For populations to grow → need 2 offspring
Only paying half of your genes to the next generation
One reproductive offspring
Men are costly
Reproduction breaks adaptive gene combination → can lower population fitness in constant environments

135
Q

what are the advantages of asexual reproduction?

A

Saves energy
Courtship is a non-issue
Greatest increase in fitness for each individual

136
Q

what are the disadvantages of asexual reproduction?

A

Low genetic variability
Adaptation to environment is difficult
‘Retards’ evolution

137
Q

what does recombination create?

A

creates genetic variation → raw material for selection

138
Q

hwo is there variation in prokaryotes if they reproduce clonally?

A

Mutations

Horizontal gene transfer (conjugation and transduction)

139
Q

what are mutations in prokaryotes?

A

mistakes in transcription or translation during cell division → will be some amount of error

140
Q

what is horizontal gene transfer in prokaryotes?

A

Can move DNA from one bacteria to another
Gene transfer is mediated by plasmids eg antibiotic resistance
Can get DNA from the environment
Also bacteriophages → they infect bacteria and replicate themselves using the cell machinery, they might also be getting DNA from the host cell and transfer it to a different cell

141
Q

why is genetic variation important for rapid bacterial evolution?

A
  • resistance genes can emerge as a result of mutations or horizontal gene transfer
  • antibiotic resistant bacteria wont be killed off and then they replicate and pass the genes on to susceptible bacteria
142
Q

how does genetic variation emerge through recombination?

A
  • half of genes acquired from each parent
  • more raw material for selection tha cna lead to faster adaptation
  • purging of delerious mutations from populations
143
Q

what is parthogenesis?

A

a natural form of asexual reproduction in which growth and development of embryos occur without fertilisation

144
Q

what are protsists?

A

very old - not bacteria or arachaea, they are very simple eukaryotes

145
Q

what are some examples of protists?

A
  • algae
  • amoebas
  • ciliates
146
Q

describe the evoluation of multicellualrity

A

Single cells
Clumped together → undifferentiated multicellularity
Division of labour → differentiated multicellularity
Ancestors of Volvox
Transitioned from single cells to form multicellular colonies at least 200 million years ago
An estimate using DNA sequences

147
Q

what does evolution favour?

A
  • mutations that increase the fitness of the individuals
148
Q

what is the main advantage of aggregation of cells leading to multicellualrity?

A

defence against predation

- example: protsits feed on bacteria so bacteria clump together

149
Q

explain how division of labour occurred?

A

Selection acts on the genetic information
If cell is more closely related to the other cells in its group than those of another group
Therefore natural selection can favour a cell with low reproductive potential as long as it increases to reproductive potential of its sister cells by a greater amount
Example → social amoebas

150
Q

what is eusociality?

A

evolved repeatedly in different order of animals particularly the hymenoptera (eg wasps)

151
Q

what are the four main criteria of eusociality?

A
  • Overlapping generations
  • Cooperative brood care (individuals other than parents assist in raising offspring)
  • Philopatry (individuals remain living in their birthplace)
  • Reproductive altruism (only subset of individuals reproduce)
152
Q

what are the theories of evolution of eusociality?

A
  • kin selection

- competing theory of group selection

153
Q

what is kin selection?

A
  • altruistic behaviour that favours the reproductive success of an organisms relatives
  • Even at the cost to the organisms own survival and reproduction
  • rB - C > 0
154
Q

what is group selection?

A
  • A proposed mechanism of evolution in which natural selection acts a the level of the group instead of at the level of the one individual
  • Selection favours individuals whose traits improve the survival of the associated group
155
Q

describe primate soceities (human societies)

A

Sociocultural evolution: language (code similar to DNA)
Communication
Storage of information
Various social uses such as signifying group identity, social stratification, social grooming and entertainment
Language enables memes (analogous to genes): an idea, behaviour, or style that spreads from person to person with a culture
Criticism: meme just a synonym to a concept

156
Q

describe gradual v rapid contemporary evolution

A

If evolution is slow and steady we would expect to see the entire transition from ancestor to descendant in the fossil record
However, fossil records are often incomplete and not all organisms form fossils
Use mone mitochondrial gene: cytochrome c oxidase subunit 1 → to compare the organisms → comparative genomic based on sequence data

157
Q

what esxpiermental evolution?

A

Experimental evolution → use of laboratory or controlled field manipulation to investigate processes
Usually make use of organisms with rapid generation times and small physical size
Often microbes → every 20 minutes → they are however asexual
Observe phenomena that in large multicellular organisms occur too slowly
Allows you to properly replicate → exclude any background noise

158
Q

what is phase 1 of experimental evolution?

A

selection experiment

159
Q

what are the stages of an selection experiment?

A
  1. genetically unofrm base population
  2. replicate in different lineages
  3. grow in media
  4. transfer a bit to a fresh tube
  5. repeat transfer with samples of lines every 100 generations
  6. every transfer take a subset - put in -80degrees
160
Q

what is the result of the selection experiment?

A
  • there are errors during replication, may be beneficial
  • sine lineages may become a larger proportion of the population
  • end up with a living fossil record
161
Q

what is phase 2 of experimental evolution?

A

comapre changes in fitness

162
Q

what are the stages of comparing changes in fitness?

A
  • measure adaptation
  • compare performance of evolved population to ancestral population
  • through direct competition
  • transfer to solid media
  • estimate frequency of each population
  • can sequence and find mutations
163
Q

what is the Long Term Evolution Experiment?

A
  • 12 replicate populations of E.coli bacteria
  • adapting to glucose
  • minimal medium
  • 1% transferred to fresh media every day
  • other samples stored
  • experiment has lasted 30 years
164
Q

how are the results of the Long Term Evolution Experiment measured?

A
  • fitness measured by direct competition with ancestral bacterial strain
  • followed by a genome sequence
165
Q

does evolution proceed with constant rate in a constant environment?

A

rate of adaptation is fast in the beginning but slows down through evolutionary time

166
Q

why does the rate of evolution change?

A
  • mutations with large fitness effects are selected first

- evolved bacteria bacteria are better at comparing and using glucose

167
Q

what does a power law model show about evolutionary rate?

A

an ever slowing increase in fitness that has no upper limit

168
Q

what does a hyperbolic model show about evolutionary rate?

A

there is a hard limit for adaptation

169
Q

what do the results of the long term evolutionary experiment show?

A

results suggest that adaptation and adaptive divergence can potentially increase indefinitely even in a constant environment

170
Q

what are examples of evolution being predictable and selection lines having similar evolutionary trajectories?

A

Yes bacteria with larger cell sizes were observed in all 12 replicate populations
E.coli is normally unable to grown aerobically on citrate due to the inability to express a citrate transporter when oxygen is present
However, E.coli has a complete citric acid cycle and therefore metabolizes citrate as an intermediate during aerobic growth on other substances including glucose
Bacteria evolve to utilize citrate in 1 replicate population

171
Q

what is an example of evolution not being predictable and no all selection liens following similar evolutionary trajectories?

A

Some key innovations rose only after fixation of of other mutations
Only 9 Cit+ genotypes found → one mutation per trillion cell divisions = 1 in 1,000,000,000,000
Before the Cit+ trait could evolve the population had to evolve a genetic background in which a new function was beneficial
Benefit of Cit+ mutation depend on other mutations (epistasis)

172
Q

what did the MEGA plate experiment look at?

A

rapid evolution of the antibiotic resistance

173
Q

how does a mutation become prominent?

A
  • big population with some resistant mutants
  • apply a big selection pressure
  • resistant mutants become prominant
174
Q

describe how the MEGA plate experiment worked

A

Used a petri dish which had swim agar on top → solid agar with ink and antibiotics) → antibiotics seep through → inoculate swim agar → looked at the antibiotic concentration and see how the bacteria reaction through time
The antibiotic concentration gets larger as you move towards the middle of the petri dish
Mutants move and compete with other mutants → repeated at each band
It’s a process of accumulating mutations

175
Q

what is the Red Queen Hypothesis?

A

Evolutionary hypothesis suggests that organisms must constantly adapt, evolve and proliferate not only to gain reproductive advantage but to survive
Evolutionary arms race → struggle between competing sets of co-evolving genes, traits or species → develop adaptations and counter adaptations against each other
The parasite needs to evolve along with its host to be able to survive

176
Q

what is an example of a coevolutionary arms race?

A

bacterial resistant and phage infectivity

177
Q

why are influenza viruses so infectious?

A

ability to rapidly evolve resistance to antibodies produced by our immune system

178
Q

what are the 3 main characteristics which contribute to the rapid evolution of these viruses?

A
  • Large populations
  • Short generation times
  • High mutation rates (made of unstable RNA)
179
Q

what are the two major surface glycoproteins?

A
  • Humeagglutinin

- Neuraminidase

180
Q

what is antigenic drift?

A

mutations that change the sruface glycoproteins can allow viral strains to evade pre-existing imminutiy by preventing antibodies binding to viral particles

181
Q

describe the viral genome in influenza

A

Viral genome consists of 8 discrete RNA segments that can combine when one cell gets coinfected with 2 different viruses resulting in progeny viruses contain gene segments of both parental viruses (antigenic shift)

182
Q

what are zoonoses?

A

when animal strains recombine with human strains can cause pandemics

183
Q

what are the features of seasonal influenza?

A
  • Public health problem each year
  • Usually some immunity built up from previous exposures
  • Result of antigenic drift
  • pre-treated with vaccination
184
Q

what are the features of pandemic influenza?

A
  • Appear in human population rarely and unpredictable
  • Lack immunity
  • Antigenic shift
  • emerge every 8-41 years, global outbreaks
185
Q

how is the vaccination for seasonal influenza developed?

A
  • WHO makes recommendation for which weakened virus strains to use every year
  • Contain 3-4 viral strains
  • Have to consider which strains are most likely responsible for next year’s outbreak
186
Q

how has the primate family tree been established?

A

comparative anatomy

187
Q

what evidence is the there to show chimpanzees and humans are closely related?

A
  • robust canine teeth
  • earlobes
  • delayed puberty
  • morphological evidence
188
Q

what is morphological evidence?

A

places humans in the taxonomic order of primates - most closely related to chimpanzee, bonop, gorilla and orangutan

189
Q

how can related pieces of DNA from different organisms be identified by DNA hybridisation?

A
  • double stranded DNA from 2 organisms
  • heat to separate
  • combine single strands
  • cool to allow reannealing
  • complementary attach
  • if DNA is similar you can make hybrid DNA
190
Q

what are the different degrees of hybridization?

A
  1. complete = organisms identical
  2. partial = organisms related
  3. none = organisms unrelated
191
Q

what are the results of hybridization?

A
  • can infer the relatedness between two organisms

- don’t need to sequence the DNA

192
Q

what happens when you have more mismatches between 2 single stranded molecules?

A
  • denature at lower temperatures
  • easier to break apart
  • can measure points where they come apart
193
Q

what temperature did human-chimpanzee molecules separate?

A
  • 1 degree less than human-human

- estimate there was a 1% difference

194
Q

when is the human-chimp split estimated to have happened?

A

last shared a common ancestor is about 5-7 Mya

195
Q

how can you estimate the time since human-chimpanzee split?

A
  • using fossils
  • looking at chromosomes
  • sequencing the genomes
196
Q

how can we use chromosomes to estimate the time since human-chimpanzee split?

A
  • karyotype
  • produce ideograms - banding patters
  • chimps and humans ahve similar chromosomes
  • match up the chromosomes
  • not identical
197
Q

what is karyotype?

A

the size and the number

198
Q

how can we sequence the genome to compare humans and chimpanzees?

A
  • inital sequence of the chimpanzee genome compared with the human genome
  • have a lot in common
  • molecular comparisons show that in two thirds of their DNA sequences humans and chimpanzees are more closely related than either one is to a gorilla
  • there are about 35 million nucleotide differences
199
Q

How do great apes differ from humans?

A
  • differ by gains
  • losses of genetic material
  • 53 functional human genes that are completely deleted or partially deleted in the chimpanzees
200
Q

where are some of the genetic losses in chimpanzees as compared to humans?

A
  • olfactor receptor (OR) genes
  • genes related to immunity or male fertility
  • not as good a vision
201
Q

what are the hominins?

A
  • modern humans
  • neanderthals
  • denisovans
202
Q

where is the evidence of humans and neanderthals taken from?

A
  • fossil record
  • but not complete
  • had to make inferences
203
Q

which continent was important for evolution?

A

Africa

204
Q

describe the discovery of Homo floresiensis

A
  • believed to be a long term isolated descended of javanese H erectus
  • but could also have been a recent divergence
  • relatively recent
205
Q

what is the brain expansion during human evolution?

A
  • expansion of the neocortex in humans
  • some of the increase in brain size is due to an increase in body size
  • brain size increased in homids much faster than body size
  • due to increased proliferative capacity of neural progenitor cells during cortical development
  • greater gyrification (folding) in modern humans to chimpanzees is particularly evident in the frontal lobe
206
Q

what is the geography of human ancestry?

A
  • humans evolved from ancestors in Africa

- contentious

207
Q

what is the multi regional hypothesis?

A
  • Proposed that H. erectus left africa 2 Mya and evolved independently into H. sapiens around the world
  • This theory has been disproved
208
Q

what is the out of africa hypothesis?

A

H. sapiens arose from H. heidelbergensis and left Africa and outcompete H. erectus everywhere

209
Q

what is the repeated migrations theory?

A

There were repeated migrations and some interbreeding with earlier migrants (more recent theory)

210
Q

what is the experiment to prove the out of africa hypothesis?

A
  • Mitochondrial DNA compared from 147 people around the world
  • disproves the multiregional hypothesis
  • purified the DNA and did a restriction test
  • mapped the different restriction sites
  • process the information and convert it into a phylogenetic tree
  • chimpanzees = outgroup, so you can predict an ancestral group
  • Look at the likelihood of restriction sites being lost or gained you can come up with a phylogeny
  • The first branch point separates an African individual to the other 3
211
Q

what is the conclusion of the experiment to disprove the multiregional theory?

A

Therefore the conclusion from this data is that humans originated from africa → most common ancestor

212
Q

how was human origin out of Africa proved?

A
  • Global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins
  • Most similar to african sequences → suggest an african origin
  • There are 6 individuals which represent 6 different groups → likely to be descendents of ancestors that left africa and populated the rest of the world
213
Q

when did neanderthals become extinct?

A

30,000 years ago

214
Q

how similar the neanderthal genome to the human genome?

A
  • 99.84% identical
215
Q

why were the findings of the neanderthal genome contreversial?

A
  • evidence demonstrates that there was gene flow between neanderthals and the ancestors of all non-Africans
  • based upon genome sequences every non-African is part Neanderthal
  • between 1-4% of each non-African human genome contains Neandethal sequences
  • about 1/3 of the neanderthal genome is represented in non-African humans
216
Q

what are denisovans?

A
  • archaic hominin
  • DNA from a finger bone 50,000 years old
  • genome sequenced
  • share a common origin with neanderthals
217
Q

what is special about the denisovans?

A
  • contribute between 1-6% of their genome to present day Melanesians
  • Tibetans have a gene which allows them to have extra RBA which is from Denisovans
  • molar is much bigger than neanderthals and humans
218
Q

how are neanderthals, denosavans and humans interlinked?

A
  • Modern humans encountered both neanderthals and denisovans
  • All three groups interbred
    Every non-african has inherited Neanderthal DNA and many non-Africans have alo inherited Denisovan DNA
  • There is also evidence for a fourth and unknown hominin group
219
Q

what does genomic DNA suggest?

A

Neanderthals and Denisovans were each other’s closest kin and that their lineage split from ours more than 600, 000 years ago

220
Q

what can we predict about the evolutionary relationships between homins?

A
  • In the recent evolution there was an event
  • One of the earliest migrants out of africa mated with a neanderthal male → there were much earlier interactions between humans leaving africa and neanderthals
  • Therefore a different set of neanderthals spread through the population as they inherited the human mitochondria - chances are they also acquired other bits of human DNA
  • This is only a theory at the moment → only evidence so far is from a shin bone
221
Q

what makes us human?

A 
Brain growth trajectory
Brain size
Descended larynx
Eccrine sweat gland density
Endurance running
Early onset of labour and longer duration of labour
Lacrimation (crying)
T cell function (enhanced immune function)
Longer and more extended thumb
222
Q

what else are people looking at as to what makes us human?

A

Protein evolution
Less is more
To be human do you need to lose the human traits
Are key amino acid changes found in rapidly evolving proteins
Phenotypic differences between humans and chimpanzees could arise from changes in gene-regulatory regions
Gene regulatory evolution

223
Q

Define adaption

A

Feature that has a beneficial adaptation and has become prevelant in a population

224
Q

What is nonsynonymous substitution?

A

DNA base change that alters the amino acid coded

225
Q

What are the main 4 criteria for eusociality?

A
  1. Overlapping generations
  2. Cooperative brood care
  3. Philopatry
  4. Reproductive altruism
226
Q

What are 2 key aspects of sociocultural evolution?

A
  1. Language in communication

2. Memes and concepts, spread complex ideas and behaviours

Genetics and Evolution (2 decks)

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