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Evolution > Population Genetics - Genetic Variation > Flashcards

Population Genetics - Genetic Variation Flashcards

1
Q

What is population genetics?

A

the study of naturally occurring genetic differences among organisms

the study of polymorphism and divergence

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2
Q

What is polymorphism?

A

genetic variation within species (ie., microevolution - ex. variety of domestic dog breeds)

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3
Q

What is divergence?

A

Genetic variation between species (ie., macroevolution)

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4
Q

Why are the spandrels a good metaphor for evolution? / What is the major message of Gould + Lewontin’s classic paper of the spandrels?

A

interpretations of spandrels can be misdirected because people think they are the purpose of the structure because they’re painted so nicely, but really they’re just filler for the architecture

G & L argue that we need to be cautious when trying to describe WHY we see certain patterns and that it’s common for us to think that everything we see must has a beneficial reason (natural selections acts to be beneficially adaptive) but there are MANY NON-ADAPTIVE EXPLANATIONS FOR THINGS

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5
Q

What was the famous example of a ‘molecular spandrel’?

A

Microcephalin & ASPM - the ‘common’ microcephalin haplotype

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6
Q

Why was the microcephalin study controversial?

A

there are many ways to interpret the data showing the distribution of the most common haplotype globally = data shows it’s very common in some, but not all parts of the world (not Africa), but the authors claimed the frequency was due to natural selection

there is still no evidence linking the derived, common haplotype to natural selection (any phenotypic difference)

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7
Q

What have follow up studies shown about the derived microcephalin and ASPM alleles?

A

a study measured 7 different phenotypes/characteristics across over 5000 individuals and there was no statistically significant phenotypic difference between individuals with either the derived or ancestral alleles

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8
Q

Who won the 2022 Nobel Prize in Physiology or Medicine? What for?

A

Svante Paabo for ‘discoveries concerning the genomes of extinct hominins and human evolution’

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9
Q

What did Svante Paabo discover?

A

a new species of hominin, Denisova

genes were transferred from the extinct hominins to Homo sapiens ~70,000 ya = physiological relevance to now including how modern human immune systems respond to infections

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10
Q

T or F: Denisovan DNA has been transferred into all humans

A

False. Only some, for ex. it has contributed to adaptations to high altitude in Tibetan people

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11
Q

Define adaptation

A

a characteristic that enhances the survival or reproduction of organisms that possess it compared to those that do not

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12
Q

How have adaptations evolved?

A

by natural selection

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13
Q

What needs to be present for natural selection to act on?

A

a phenotypic difference amongst individuals of a species

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14
Q

Describe natural selection

A

any consistent difference in fitness among different classes of biological entities

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15
Q

Describe fitness

A

the number of offspring an individual produces for the next generation (aka reproductive success)

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16
Q

What are some examples of how Tibetans have adapted to high altitudes?

A

lower concentrations of hemoglobin
lower accounts of chronic mountain sickness
lower infant mortality rate + higher fertility (compared to acclimated women originating from lower altitudes)
lower cases of preeclamspsia

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17
Q

Describe a study that provides evidence supporting the adaptations of Tibetans to high altitudes

A

A study was done measuring the average birth weights (a good measure of fitness) of Tibetans vs Han people (closely related geographically)

Tibetans on average produced babies with higher birth weight than Han people did = clear effect on fitness and evidence of natural selection

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18
Q

Describe a study that provides GENETIC evidence supporting adaptations of Tibetans to high altitudes

A

A study looked at the genetic variation across the genome of Tibetans in Yunnan Province to look for an association between the phenotype of low hemoglobin and genetic variation

they found that chromosome 2 had a gene with variation EPAS1 which had a statistically significant association with low hemoglobin

there were multiple linked SNPs (haplotype) in the EPAS1 gene

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19
Q

What is biological evolution?

A

the central concept that holds biology together
“descent with modification” –> genetics and inheritance
fundamentally, it’s genetics and populations genetics
it’s an organizing principle

the framework, organizing principle, for understanding how and why Earth has so much biological diversity, including features and processes essential to human health and welfare

a science that makes testable predictions

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20
Q

T or F: all organisms share the same blue print?

A

true

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21
Q

Describe the basics of the Killer X chromosomes in Drosophila flies

A

A pattern emerging that shows that some males produce almost entirely daughter offspring due to a gene (or genes) on the X chromosome that destroy Y chromosome-bearing sperm

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22
Q

What phenotype does the Killer X chromosome in Drosophila flies cause?

A

causes the destruction Y-bearing sperm in males that have the Killer X chromosome so that almost all of the offspring of those males are female

destroys their reproductive tracts, turns an organized reproductive tract into chaos

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23
Q

How is the Killer X chromosome inherited in Drosophila flies?

A

Would be inherited by the female offspring of a male parent that possesses the allele for the Killer X chromosome and passed on to her male offspring when she reproduces

Because the X chromosome of a male will always be passed on to the daughters, and the killer X chromosome of the mother will be passed on to some of the male offspring

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24
Q

What are some hypotheses for why a Killer X chromosome would evolve?

A

Maybe there’s some benefit to having more females in the population - reproductive rate increase and growth rate increase, as long as some males persist

maybe there’s no benefit to the species, the mutation is passed on 100% of the time through the X chromosome, so it will just become more frequent in the population

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25
Q

Why might a gene on an X chromosome evolve to destroy sperm that carry a Y chromosome?

A
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26
Q

Could the Killer X chromosome evolve without benefitting the organism?

A
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27
Q

What is a rooted phylogenetic tree?

A

A phylogenetic tree that consists of an outgroup (ie., is rooted by the outgroup), branch lengths (which show amount of change), and percentage values to support the confidence of the closeness of relatives

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28
Q

What is an outgroup (in a phylogenetic tree)?

A

A group that is closely related to the species we’re interested in that roots a phylogenetic tree and gives it directionality to show patterns of evolution

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29
Q

What do branch lengths mean?

A

Show the amount of change that has occurred

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30
Q

What do the numbers indicate?

A

the percentage value reflecting the confidence of the closeness of the two relatives

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31
Q

Can you interpret the D. testacea phylogenetic tree for what lineages are most closely related to each other?

A
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32
Q

Studying evolution is about trying to answer what two major questions?

A

HOW much genetic variation is there?

WHY do we see the genetic variation we see? (ie., how did it occur?)

33
Q

What are the spandrels of San Marco? What are they a metaphor for?

A

the extra spaces between the arches of a chapel that were painted beautifully

people think that the spandrels are the reason for the arches, but the spandrels are only there because of the architecture of the arches

metaphor for how, in biology, there’s a tendency to explain patterns as beneficial for adaptation/evolution - even though there’s lots of non-adaptive reasons for patterns

a well-known and controversial example of inferring adaptation in evolution

34
Q

What do Gould & Lewontin mean when they call something “Panglossian”? what is this a metaphor for? Who was Pangloss?

A

Pangloss was a character from the Voltaire novel, “Candide,” who believed there was always an explanation for everything that happened, no matter how ridiculous the explanation was.
Ex. he believed we had noses to hold our spectacles, if we didn’t have noses, how could we wear glasses?

a metaphor for how in biology we tend to believe that everything happens for a reason and that reason is natural selection

35
Q

What do Gould & Lewontin mean by ‘adaptionist’ in their paper title?

A

adaptionist could mean the tendency of biologists when explaining an evolutionary pattern to assume there must be an adaptational advantage to this pattern because natural selection will only act in a beneficial way

their argument is that this is not always the case

it’s hard in evolutionary biology to explain WHY things happen, but the answer may not always be that it’s beneficial (ex. look at the Killer X chromosomes in Drosophila testacea).

36
Q

What is another example of a spandrel or Panglossian trait?

A
37
Q

What does one need to do in order to demonstrate that something is adaptive? (and not just using a Panglossian/spandrel explanation)?

A

there has to be evidence that there is a difference in fitness between the phenotypes where it improves survival or reproduction and the number of offspring produced by an individual, and that natural selection acts on it, of an organism when compared to the unaltered phenotype

38
Q

What are microcephalin and ASPM?

A

microphealin and ASPM (abnormal spindle-like microcephaly associated) are genes that are involved in cell division (neural and non-neural cells) and mutations of which may be related to brain size defects (microcephaly) - other function is not well understood

39
Q

What happens if you break these genes? what is the phenotype?

A

mutations of the genes are related to microcephaly (brain size defects)

40
Q

What do the patterns of variation in microcephalin and ASPM look like in humans? How does it compare across the world?

A

according to the study:

there is genetic variation in microcephalin/ASPM genes across humans because one haplotype of microcephalin was found at very high frequency (hap. 49)

the ‘adaptive’ haplotype of microcephalin has very high frequency across the world, but only in some places (ex. NA, SA, Europe, Asia, but very low in Africa)

and the ‘non-adaptive’ haplotype of microcephalin has very high frequency in Africa

41
Q

What is a haplotype?

A

a set of alleles that are inherited together (ie., on a single chromosome) from a single parent

42
Q

How did Bruce Lahn and co-authors interpret the patterns they found in microcephalin/ASPM? why is this controversial?

A

They attributed the high frequency of the one ‘adaptive’ haplotype to natural selection - ie., natural selection must be acting on it because it is beneficial

controversial because a second study was done and there was no evidence supporting any significant phenotypic fitness differences between people with the adaptive and ‘non-adaptive’ alleles - ie., natural selection could not have acted on this phenotype
- very racialized = the haplotype was not abundant in every part of the world

43
Q

What are some alternative explanations for the frequency of microcephalin/ASPM haplotype?

A

could be due to movement of ancient humans - gene flow
migration/immigration - gene flow

44
Q

What kinds of data can you use and what kinds of experiments could you perform to distinguish between the different interpretations? (are these polymorphisms, alleles, what might these variants look like in PopG?)

A
45
Q

If change in the frequency of microcephalin alleles is due to selection, what would this look like in PopG? What kinds of selection coefficients/fitness differences would be involved?

A
46
Q

Is there a phenotype associated with the common haplotypes of ASPM/microcephalin? How is this related to Lahn’s hypothesis and interpretations?

A

it is not clear that there is a phenotype associated with the common haplotypes / there isn’t

a study looked at multiple phenotypes which Lahn’s study associated with the derived common haplotypes and the results showed no significant differences in fitness

this undermines Lahn’s hypothesis/interpretations = the reason for the patterns they saw were not strictly because of natural selection

47
Q

What are 3 contributions Svante Paabo made?

A
  1. sequenced entire genome of Neanderthal
  2. discovered unknown hominin, Denisova
  3. discovered that gene transfer occurred between the extinct Denisovans to Homo sapiens after the migration from Africa (~70,000 ya)
48
Q

What is known about Denisovans? What is not known?

A

known:
- gene transfer occurred between Denisovans to Homo sapiens after migration from Africa
- finger and molar bones discovered in cave in Siberia - a cave that had been repeatedly settled
- closely related to Neanderthals but distant from modern humans
- Denisovan DNA has made its way into some but not all modern humans

unknown:
- most of their anatomical features, only bones found were finger and molar
-

49
Q

Where and how were Denisovans discovered?

A

bones were discovered in a cave in Siberia and Paabo’s lab sequenced the genomes from these bones and discovered they were not of Neanderthal or Homo sapien origin

50
Q

How are Denisovans related to Neanderthals?

A

closely related to Neanderthals

51
Q

How are Denisovans related to modern humans?

A

Distantly related to modern humans, yet some modern humans contain some Denisovan DNA

52
Q

What are adaptations?

A

characteristics that improve the survival or reproduction of organisms that possess it in comparison to those that do not

evolve by natural selection

53
Q

What does it mean for something to be adaptive?

A

for a phenotype to be advantage, there has to be a difference in fitness between it and the alternative version which improves survivability and reproductivity of an organism that bears it - ie., something that natural selection can act on

54
Q

What do we mean by fitness?

A

the number of offspring an individual leaves in the next generation - includes survival and reproduction

55
Q

How does one study measure, infer, demonstrate adaptation, natural selection, and fitness?

A

when an evolutionary trend is observed, these can be measured by selecting a related and measurable phenotype (ex. hemoglobin concentrations in Tibetan highlanders) which can demonstrate an explanation for why this characteristic would persist in the population

ex. low hemoglobin concentrations in Tibetans being evolutionarily advantageous for living in high altitudes

56
Q

What is natural selection?

A

any consistent difference in fitness among different classes of biological entities

57
Q

What are some adaptations to high altitudes found in Tibetans?

A

low prevalence of chronic mountain sickness
low concentration of hemoglobin
low infant mortality and higher fertility
lower incidence of preeclampsia during pregnancy
higher birth weights

58
Q

What is evidence for adaptions to high altitudes in Tibetans?

A

1 study measured birth weights: a good signifier of fitness
- on average, Tibetans produced babies with higher birth weights than Han Chinese people (closely related, geographically close)

1 study measured hemoglobin concentration:
- natural selection on EPAS1 gene related to low hemoglobin concentration
- found statistically significant connection between low hemoglobin levels and EPAS1 = related to turning on and off genes that are associated with being in high altitude areas including hemoglobin

59
Q

What is the phenotype Cynthia Beall looked at in her study of Tibetan adaptations?

A

low hemoglobin concentrations

60
Q

How did Beall find an association between variation in the EPAS1 gene and adaptation to high altitude?

A

they scanned the genome of Tibetans in high altitudes and used a Manhatten Plot to look for associations between SNPs (single-nucleotide polymorphisms) and hemoglobin concentration

= EPAS1 showed significance - multiple linked SNPs (haplotype) in the gene

61
Q

What phenotype is associated with variation in the EPAS1 gene?

A

low hemoglobin concentrations

62
Q

What is the EPAS1 gene? distinguish between gene, alleles, variants, haplotypes

A

EPAS1 is the hypoxia-inducible factor 2A gene located on chromosome 2, endothelial PAS domain protein 1, a transcription factor

the EPAS1 gene contained multiple linked SNPs (haplotype)

if homozygous for the derived EPAS1 variant, there was lower levels of hemoglobin
heterozygote did not show the phenotype, the phenotype is not dominant

63
Q

What did Huerta-Sanchez and colleagues find about the origin of the EPAS1 variant common in Tibetans? What evidence/data did they use?

A

it likely came from introgression with Denisovans

they looked very closely at the EPAS1 sequence between Tibetans and Han Chinese (closely related populations) and added a Denisovan sample when it was available

one section, associated with the derived haplotype, appeared very different between the 2 populations but was common between Tibetans and Denisovans
- there were no similarities between Tibetans and other human EPAS1 sequences

64
Q

What is hybridization?

A

occurs when 2 different species (usually closely related) produce offspring

65
Q

What is introgression?

A

the movement of genes resulting from successful hybridization

66
Q

T or F: hybridization always results in introgression

A

false, it usually doesn’t but introgression has occurred enough that it has contributed new variation (ex. hemoglobin adaptations to high altitude in Tibetans)

67
Q

What evidence/data did Huerta-Sanchez use in their study?

A

they looked specifically at the EPAS1 sequence in Tibetans and compared it to closely related Han Chinese populations and found no similarities

then compared to Denisovan sample and found similarities

68
Q

Are there alternative interpretations of Huerta-Sanchez’s results? how might we rule them out? what data could we use to distinguish between them?

A

mutations emerged separately in two distantly related species that both lived in high altitudes

more comparisons between Denisovan and Tibetan phenotypes and genoptypes would help rule out or provide more information

rule them out by comparing to other human populations

69
Q

What would a phylogeny of the EPAS1 gene look like if it included data from Denisovans, Neanderthals, Tibetans, and Han Chinese, and other people from around the world?

A
70
Q

What could genetic variation at EPAS1 look like in samples looking at different genes (not EPAS1) across Denisovans, Neanderthals, Tibetans, and Han Chinese, and other people from around the world?

A
71
Q

What is ancient introgression?

A

a potential source of genetic variation that has influenced evolution and diversification

72
Q

How could one tell if an introgression was ancient or more recent?

A

by looking at genomes of 2 species and determining the SNPs? ? ??

73
Q

What are alleles?

A

an allele is one of two versions of a gene which have specific associated phenotypes

ex. A and a

74
Q

What are genotypes?

A

the combination of alleles which produce phenotypes

ex. AA, Aa, aa

75
Q

What is polymorphism?

A

genetic variation within a species

76
Q

What is heterozygosity?

A

when both alleles of a gene are present in an organism and the dominant allele is expressed

ex. Aa

77
Q

What is nucleotide diversity?

A

a measurement of genetic variation (ie., the polymorphism) in a population

78
Q

What does it mean when an allele becomes fixed/has reached fixation?

A

the frequency of a fixed allele is at 100% and it is the only allele present for a gene

ex. 100% a and 0% A

79
Q

How do we measure allele and genotype frequencies?

A

by comparing the fitness differences of alleles within a population

knowing the fitness associated with a particular allele can be used to determine the frequency of that allele, and the genotype

Evolution (11 decks)

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