Population Genetics 1 Flashcards

1
Q

facets of evolution (5)

A
  • speciation and extinction
  • origin and spread of new genetic variants
  • gradual change over a long period of time
  • rapid changes in response to changing conditions
  • changes in the genetic pool
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2
Q

what is evolution

A
  • CHANGE in the form/behaviour of organisms between generations
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3
Q

evolution

- described by Darwin

A
  • descent with modification
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4
Q

evolution

- described by Futuyma and Kirkpatrick (4)

A

origin and alteration over generations of:

  • ideas within society
  • frequencies of genotypes within populations
  • proportion of differentiated populations within species
  • proportion of species with different traits within a lineage
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5
Q

how can evolutionary change occur? (2)

A
  • chance bursts of reproduction, deaths or mutation

- natural selection

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6
Q

what does natural selection explain?

A
  • explains how undirected change can improve the match between an organism and its environment
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7
Q

natural selection

A
  • process whereby some individuals contribute more offspring to the next generation as a consequence of their carrying a trait(s) favourable to survival and reproduction
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8
Q

when does evolution by natural selection occur? (3)

A

occurs whenever

  • individuals vary in some trait (VARIANCE)
  • individuals with some trait values are more likely to live/reproduce (SELECTION)
  • parents have offspring with similar trait values (HERITABILITY)
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9
Q

Aristotle (3)

A
  • greek philosopher
  • examined natural world for evidence of divine order
  • created the Scale naturae (“Chain of Being”)
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10
Q

Scale naturae (“Chain of Being”) (3)

A
  • hierarchical arrangement of forms
  • species arranged linearly along a scale: god -> man -> mammals -> egg-laying animals -> insects -> plants -> non-living matter
  • formed the basis for the western belief in the fixity of species, each of which has a typical form
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11
Q

Carolus Linnaeus (4)

A
  • classified organisms according to binomial system, giving each a SPECIFIC and a GENERIC name (Genus species -> eg. Homo sapiens)
  • proposed a nested system of relationships (as opposed to the Scale naturae)
  • recognized fundamental difference between interbreeding (within species) and non-interbreeding organisms (non-interbreeding species)
  • believed in balance of nature
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12
Q

what are the facets of the modernized Linnaean system? (7)

- generally know

A
  • kingdom
  • phylum
  • class
  • order
  • family
  • genus
  • species
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13
Q

balance of nature (3)

- from Carolus Linnaeus

A
  • each species has its place in a divine plan
  • species would not chance or go extinct
  • eventually acknowledged LIMITED formation of new species by hybridization
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14
Q

Comte de Buffon (2)

- beliefs

A
  • believed Linnean hierarchy reflected common descent (dégéneration) with divergence over time
  • believed that change only happened within families
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15
Q

common descent/dégéneration (3)

- from Comte de Buffon

A
  • physical environment somehow changes organic particles
  • new species form when animals migrate to new environments
  • new environment then causes changes to the species
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16
Q

change only happens within families (2)

- from Comte de Buffon

A
  • each family conforms to an internal mold

- species can change over time but are limited to their original mold at the family level

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17
Q

Erasmus Darwin (4)

  • relation to Charles Darwin
  • wrote…
  • beliefs (2)
A
  • Charles Darwins’ Grandfather
  • Wrote Zoonomia/The Laws of Organic Life
  • believed organisms constantly attempted to improve themselves by adapting to their environments (transformism/transmutation) but did not know the mechanism
  • believed that all life consists of “one living filament” connecting all libing forms to a common ancestor
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18
Q

Jean-Baptiste Lamarck (3)

A
  • theory of “transformism”, which was incorrect
  • believed that at the base of hierarchy, “simple” organisms constantly arise by spontaneous generation
  • suggested a mechanism for organic progression in Philosophie zoologique
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19
Q

theory of “transformism”

A
  • organisms progress through a hierarchy of ever-more-advanced forms (almost a Scala naturae in reverse)
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20
Q

suggested mechanism for the theory of “transformism” (2)

A
  • first law: use or disuse of a structure within a structure leads to its development or diminishment
  • second law: these acquired characters can be passed on to offspring
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21
Q

suggested mechanism for the theory of “transformism” (2)

- example

A
  1. muscles shrink due to no use (diminish) OR muscles growing due to lots of us
  2. large/small muscles can be passed to offspring
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22
Q

Thomas Malthus (2)

A
  • principle of overproduction: wrote “An Essay on the Principle of Population
  • major of influence on Darwin and Wallace
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23
Q

principle of overproduction from “An Essay on the Principle of Population (3)
- from Thomas Malthus

A
  • most organisms produce far more offspring than can possibly survive
  • even when resources are plentiful, populations tend to grow geometrically until they outstrip their food supply
  • poverty, disease, and famine are inevitable, leading to a “struggle for existence”
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24
Q

Charles Lyell (3)

A
  • “uniformitarianism”
  • his Principles of Geology was a major influence on Darwin and Wallace
  • ideas on Earth was applied to his views on the living world
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25
Q

uniformitarianism (2)

- from Charles Lyell

A
  • earth is subject to gradual and continuous change, but without progress or development
  • earth remains in a steady state (slow building of volcanoes from earthquakes is also worn down by erosion at the same time)
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26
Q

Charles Darwin (3)

A
  • life’s work: development of the theory of evolution by natural evolution
  • used Lyell’s work to apply uniformitarianism to coral reef formation and developed appreciation for biogeographical patterns
  • travelled around the world on The Voyage of the Beagle observing biodiversity and biogeography
27
Q

biogeographical patterns (3)

A
  • how organisms are arranged over space
  • Darwin’s rhea
  • giant tortoises and finches on the Galapagos Islands
28
Q

niche

A
  • similar combination of environment and vegetation that animals can occupy
29
Q

biogeography (3)

- Darwin’s rhea

A
  • considered why species such as ostrich, rhea and emu all inhabited similar niches differed when found on different continents
  • noticed that two similar species often coexisted in a “boundary zone” where neither were better adapted than the other, and that these species must compete
  • found that species were not fixed
30
Q

biogeography

- giant tortoises

A
  • on the Galapagos Islands, Darwin found giant tortoises that were distinct from each other even though they were on islands close together
31
Q

biogeography (2)

- finches

A
  • found species were closely related between islands

- determined that species change over time and fill different niches

32
Q
natural selection (2)
- from Charles Darwin
A
  • recognized several critical facts about evolution by natural selection
  • concluded that some variants will be preserved over time more than others and that the composition of populations must change over time
33
Q

critical facts realized by Charles Darwin about natural selection (4)

A
  • variability exists within species
  • variant traits may be inherited
  • Malthus’ Principle of Overproduction implies that many individuals must die or fail to reproduce
  • therefore, individuals slightly better suited to their environment must be more likely to survive
34
Q

how did Darwin explain speciation (2)

A
  • as natural selection acts on geographically isolated populations, they become increasingly different from each other
  • leads to formation of first varieties within species, then separate species, then genera…etc, in an ever-branching process
35
Q

Alfred R. Wallace (3)

  • profession and work
  • who did he reference
  • connection to Darwin
A
  • English professional naturalist that travelled that world observing biodiversity and biogeography like Darwin
  • read Lyell and Malthus’ work to discover natural selection and survival of the fittest
  • sent letter to Darwin describing his independent discovery of natural selection
36
Q

evolution made public (2)

A
  • Darwin and Wallace’s views were co-presented at meetings in 1858
  • Darwin published “ The Origin of Species by Means of Natural Selection” that revolutionized science due to depth and breadth
37
Q

timeline of important figures of evolution (8)

A
  1. Aristotle
  2. Carolus Linneaus
  3. Comte de Buffon
  4. Erasmus Darwin
  5. Jean-Baptiste Lamarck
  6. Thomas Malthus
  7. Charles Lyell
  8. Charles Darwin and Alfred R. Wallace
38
Q

why is the brief history of evolutionary thought dominated by white males

A
  • many ideas and discoveries lost due to the denial of the privileges, education, and access to the records of history by non-white male demographics
39
Q

why is diversity needed in the study of evolution (3)

  • general reason
  • dangers
  • truth of evolution
A
  • need diversity of education to completely understand whole diversity of evolution itself
  • previous colonialism gave privilege to do research and publish books; created opportunity for biological racism that could incite harm to those targeted
  • truth: we are all closely related no matter our skin colour and all living things are equally evolved
40
Q

haploid

A
  • one copy of each gene
41
Q

diploid

A
  • two copies of each gene
42
Q

survival

A
  • differential survival and reproduction of different entities
43
Q

what are the steps in one generation cycle for a haploid organism (3)

A
  • gamete union forms diploid phase
  • meiosis forms haploid phase
  • selection occurs during the haploid phase
44
Q

how can we track two variant allele (A and a) frequencies after selection for a haploid organism? (3)
- generally know

A

after selection occurs in the haploid phase:

  • freq A = W(A)*p[t]
  • freq a = W(a)*q[t]

then the following occasion applies to find the frequencies of each allele; for the A allele:
W(A)p[t]/(W(A)p[t] + W(a)*q[t])

45
Q

fitness (3)

A
  • individuals haploids carrying varying alleles have different fitness
  • average contribution per parent to the next generation including survival and reproduction
  • symbol: W with subscript of allele
46
Q

how can we track two variant allele (A and a) frequencies between the diploid -> haploid phase in haploid organisms? (3)

A
  • fertilization brings alleles together (gamete union), followed by separation at meiosis; however there is no selection here so allele frequencies are expected to remain the same
  • nothing perturbs frequency during this phase; therefore, no selection
  • frequency remains the same from previous calculation, except that p[t] -> p[t+1]
47
Q

does evolution by natural selection depend on the absolute or relative fitness values of alleles? explain (2)

A
  • depends on their relative fitness values
  • if the relative fitness values are the same, then the resulting change in frequency of evolutions will also be the same, even if the absolute fitness values change
48
Q

how do we measure the fitness of each type of allele relative to W(a), relative to W(A), or relative to a standard W (3)

A
  • divide both fitness values by W(a), making the W(a) fitness value 1
  • divide both fitness values by W(A), making the W(A) fitness value 1
  • divide both fitness values by a standard and set W
49
Q

what happens to the allele A frequency if W(A) > W(a) during long term natural selection? (2)

A
  • the frequency will converge to 1, p[t] -> 1

- “directional selection” favouring A

50
Q

what happens to the allele A frequency if W(A) < W(a) during long term natural selection (2)

A
  • the frequency will converge to 0, p[t] -> 0

- “directional selection” favouring a

51
Q

how would you plot the change over time in the frequency of an allele A that increases fitness by 20%? (3)

A
  • plot a graph with “frequency A” on the y-axis and “time” on the x-axis
  • as W(A) is 1.2 and W(a) is 1, the frequency of allele A will converge to 1
  • plot the line starting from ~0 and show that it eventually reaches 1 with an S-shaped curved line
52
Q

how does variance affect the frequency change per generation within a haploid population? (4)

  • affects
  • how is this reflected on the plot
  • high variance vs low variance
  • section of formula affected
A
  • more variability will increase the frequency change per generation
  • this is reflected by a plot where the change is increasingly slow when the allele is rare and when it is common
  • highest variability: p[t]=0.5 and q[t]=0.5; lowest variability occurs when one allele frequency is 1 and the other is 0
  • in the per generation change formula: p[t]*q[t]
53
Q

how does selection (difference in relative fitness values) affect the frequency change per generation within a haploid population? (3)

  • affects
  • how is this reflected on the plot
  • section of formula affected
A
  • higher difference in relative fitness values will create faster evolutionary change/more evolutionary change per generation
  • plots with larger differences in relative fitness values will converge to 1 or 0 more quickly; the line will reach the top/bottom faster than a line with smaller difference
  • W(A) - W(a)
54
Q

how does selection (difference in relative fitness values) affect the frequency change per generation within a haploid population?

A
  • not an effect; more of a condition: A-bearing parents with frequency p[t0 must pass A allele to offspring
55
Q

what happens to the allele A frequency if W(A) = W(a) during long term natural selection (2)

A
  • then the frequency of allele A will not change, p[t] remains at p[0]
  • “neutral”
56
Q

when considering the spread of a new beneficial allele (A) in a population of wildtype alleles (a), how do we measure fitness?

A
  • measure fitness relative to wildtype using a selection coefficient
    W(a) = 1
    W(A) = 1 + s
57
Q

selection coefficient (3)

  • symbol
  • defintion
  • value limits
A
  • symbol = s
  • proportional increase in fitness caused by replacing a with A allele; larger |s| values will create larger evolutionary changes per generation
  • can be positive or negative
58
Q

how does the selection coefficient (s) change the # of generations it takes for allele A to rise from low frequency to high frequency (2)

A
  • is s is 10 times smaller, it takes ~10 times longer (10x the amount of generations) to observe the same amount of frequency change
  • is s=0.1 then it will take 100 generations; if s=0.01, then it will take 1000 generations
59
Q

how does evolutionary change by natural selection affect the match between an organism and its environment?

A
  • it increases the mean fitness of an organism
60
Q

mean fitness of an organism

A
  • symbol: Wbar[t]

- W(A)p[t] + W(a)q[t]

61
Q

how does the mean fitness change across one generation in haploid organisms?

A
  • the mean fitness rises (or stays the same) in the haploid model of evolutionary change cause the fit between organism and environment increases
62
Q

if evolution were so easy and effective, why isn’t everything the same and perfect? (4)

A
  • organisms vary
  • environments vary
  • the world is changing constantly
  • evolution NOT by natural selection is also occurring
63
Q

evolution NOT by natural selection (5)

A
  • mutations arise
  • chance plays a role
  • sex and recombination alter
  • alleles favoured for effects on some traits may affect other traits (pleiotropy and fitness trade-offs)
  • neighbouring alleles in the genome can be dragged with selected alleles (hitchhiking)