1.2: Human - Agricultural Coevolution

Question 1

What is coevolution?

Answer 1

Reciprocal evolutionary responses in a pair of species, caused by selection imposed by each other.

Question 2

What are examples of coevolution?

Answer 2

• Wolves and moose
• Humans and agricultural species: cows
• Sexual coevolution between sexes

Question 3

What imprint does human-agricultural coevolution leave in genomes?

Answer 3

Genetic and ecological processes affecting selection and gene transmission.

Question 4

What is lactase?

Answer 4

An enzyme that humans use to digest milk.

Question 5

What is lactase persistence?

Answer 5

The continued production of lactase into adulthood.

Question 6

Which population shows a decline in lactase production normally?

Answer 6

Most humans, except for people of north European origin.

Question 7

What is the correlation between lactase gene changes and lactose digestion in european cattle farming cultures

and what are the hypotheses of the above observation

Answer 7

Changes in the lactase gene are strongly correlated with the ability to digest lactose as an adult.

hypotheses:
- genetic: the substitutions are the causal variants
- evolutionary: they were favored by natural selection

Question 8

True or False: All human populations practicing dairy agriculture have lactase persistent phenotypes.

Answer 8

True

Question 9

What is convergent evolution?

Answer 9

Independent evolution of the same trait in different groups - groups could be populations or species

Question 10

What does the study of Neolithic human remains suggest about lactose digestion?

Answer 10

They were likely unable to digest lactose as adults. lactase persistence in europeans occurs after cattle domestication

Question 11

What is AMY1?

Answer 11

A gene that encodes salivary amylase, which begins starch digestion in the mouth.

Question 12

What is the significance of the lactase gene in African cultures practicing dairy farming?

Answer 12

They have distinctive forms of the lactase gene that correlate with the ability to digest lactose.

Question 13

What alternative to genetic adaptation is mentioned in relation to lactase persistence?

Answer 13

Fermented milk products aiding digestion.

Question 14

What is the relationship between cultural practices and genetic adaptation?

Answer 14

Cultural practices can provide alternatives to genetic adaptation, such as using fermented milk.

Question 15

What is the expected outcome if substitutions in the lactase gene cause lactase persistence?

Answer 15

Other human populations with lactase persistence should have the same substitutions.

Question 16

Fill in the blank: Evolution by NS is a _______ and ecological process.

Answer 16

[genetic]

Question 17

What does the term ‘selection’ refer to in the context of evolution?

Answer 17

The process by which certain traits become more common in a population due to advantages in survival or reproduction.

Question 18

What are the two types of mutations discussed in relation to selection?

Answer 18

• Non-synonymous (replacement)
• Synonymous (do not change amino acids)

Question 19

What is the significance of studying genetic variability in regions affected by selection?

Answer 19

It helps understand the fate of mutations and their impact on evolution.

Question 20

What is the effect of selection on mutations that change amino acids?

Answer 20

Differences in the fate of those mutations

This includes non-synonymous (replacement) vs. synonymous mutations.

Question 21

What is expected in regions of the genome that experience selection?

Answer 21

Lower genetic variability

Selection reduces variability in the genome.

Question 22

How does selection impact differentiation between populations?

Answer 22

More differentiation at selected sites than the rest of the genome

Selected sites exhibit greater variation between populations.

Question 23

What are the three types of mutations based on their effects on fitness?

Answer 23

• Neutral
• Deleterious
• Beneficial

Neutral mutations do not affect fitness, deleterious mutations have negative effects, and beneficial mutations improve fitness.

Question 24

What is the expected population frequency of replacement mutations that are deleterious?

Answer 24

Lower population frequencies

Deleterious mutations are less likely to be found in larger populations.

Question 25

When are more replacement mutations expected than synonymous mutations?

Answer 25

When mutations are beneficial

Beneficial mutations enhance fitness, leading to higher frequencies.

Question 26

What is the approximate proportion of replacement sites in a gene sequence?

Answer 26

Approx ¾ of sites

This is crucial for fair comparisons in substitution rates.

Question 27

What does a dN/dS ratio of 1 indicate?

Answer 27

Equal rates of substitution for replacement and synonymous sites

This is seen under neutral mutation conditions.

Question 28

What does a dN/dS ratio less than 1 indicate?

Answer 28

Substitution rate for synonymous sites exceeds replacement sites

This indicates that most mutations are neutral.

Question 29

What does a dN/dS ratio greater than 1 indicate?

Answer 29

Substitution rate for replacement sites exceeds synonymous sites

This suggests that beneficial mutations are common.

Question 30

What phenomenon occurs when beneficial mutations fix and drag along nearby mutations?

Answer 30

Genetic hitchhiking

This leads to decreased genetic variation in those regions.

Question 31

What is the relationship between recombination rate and the size of the region affected by selective sweeps?

Answer 31

The region size depends on the rate of recombination

Higher recombination rates can lead to smaller affected regions.

Question 32

What evidence is there of adaptation in lactase persistence?

Answer 32

Longer sections of the genome that are totally homozygous

Indicates low variation due to natural selection.

Question 33

How do lactose intolerant Eurasians compare to lactase persistent Africans?

Answer 33

Lactose intolerant Eurasians vs. lactase persistent Africans

This comparison highlights differing adaptations based on diet.

Question 34

What does selection do to variation?

Answer 34

It affects allele frequency differences as evidence of adaptation

Selection leads to changes in how common certain alleles are in a population.

Question 35

what is sexual coevolution

Answer 35

reciprocal evolutionary responses in the two sexes causes by selection imposed by each other - a lot manifested in sperm egg interactions especially in marine animals with external fertilization

Question 36

evolution by natural selection is a _______ and _______ process

Answer 36

genetic and ecological

Question 37

• ecology produces ________
• genetics provides the material that is transmitted across ____________

Answer 37

selection, generations

Question 38

for humans, ecology includes ? and ?

Answer 38

culture and the organisms we interact with

Question 39

what happens to lactose after interaction with lactase

Answer 39

turns into glucose and galactose

Question 40

(genetics) if substituions in or near the lactase gene cause lactase persistence then we would predict:

Answer 40

other human pops with lactase persistence should have the same substitutions or changes with similar consequences on production of enzyme

Question 41

(evolutionary) if dairy agriculture imposed evolution by natural selection on substitutions that cause lactase persistence, then we would predict:

Answer 41

other human pop practicing dairy agriculture culture should have lactase persistent phenotypes and we should see genetic evidence of past selection at the lactase gene in the human genome

Question 42

t/f do african cultures with dairy farming also have the distinctive forms of the lactase gene. how we know

Answer 42

yes, dna sequence differences correlate significantly with the ability to digest lactose as an adult and it suggests natural selection is at work

Question 43

state the relevant conclusions of lactase digestion regarding what affects phenotype and independent evolution

Answer 43

• strengthens inference that these molecular variants actually affect the phenotype
• independent evolution of same phenotype in different populations supports driving force of natural selection

Question 44

how can independent lines of evidence reject chance

Answer 44

by confirming deterministic explanations - the more times we observe smth the less likely it’s due to random chance

Question 45

what is the relevance on AMY1 evolution

Answer 45

it shows copy # variation, more copies = more digestion. amy1 copy number expansion is linked to agriculture in humans

Question 46

in central asian samples, despite the presence of the lactase mutation, why has this not increased in frequency

Answer 46

mutations associated with lactase persistence have been detected in older central asian samples. the lp alleles are present but not increasing in frequency in central asia. the hypothesis is because of fermented milk products (kumis, ajrag) because the bacteria in fermented milk are ingested with it thus aiding digestion. it allows calories, calcium, vit d, lipids, prots, etc to be consumed

Question 47

how does selection affect the genome

Answer 47

favoring beneficial alleles = less genetic variation for alleles affecting fitness

Question 48

what 3 factors should we expect on how selection affects the genome

Answer 48

1. diff in the fate of those mutations that change aa (non syn) vs syn
2. lower genetic variability in regions of the genome that experience selection
3. more differentiation between pop at selected sites than the rest of the genome

Question 49

what are the mutational consequences of the genetic code for the following: neutral, deleterious, beneficial

Answer 49

neutral (no fitness effects): expect similar properties of both replacement and syn mutations
deleterious (negative effects on fitness): lower pop freq for replacement mutations vs syn
beneficial (improve fitness): more replacement mutations than syn

Question 50

what are the predictions for dna diff between species for the following: neutral, deleterious, beneficial

Answer 50

neutral: equal rates of substitution for replacement (dn) and syn (ds) sites – dn/ds = 1
deleterious: substitution rate for syn sites will exceed replacement sites: dn/ds <1
beneficial: substitution rate for replacement sites will exceed syn sites: dn/ds > 1

**calc req accounting for the number of sites that could potentially be syn vs replacement to make it fair – approx 3/4 of sites in gene seq are replacement sites

Question 51

approx how many sites in gene seq are replacement sites

Answer 51

3/4

Question 52

describe genetic hitchhiking? and the result

Answer 52

as benficial mutations fix, they drag along with them nearby mutations

genetic variation in these regions will go down

Question 53

describe selective sweeps

Answer 53

natural selection favoring something

Question 54

what do the region size of selective sweeps depend on

Answer 54

rate of recombination

Question 55

distinguish between high and low/no recombination in selective sweeps

Answer 55

low/no: when the mutation/polymorphism achieves 100% frequency (fixed) in the chromosomes the fitness will increase but the other mutations on the same chromosome gets fixed also
high: as the mutation/polymorphism achieves 100% frequency (fixed) in the chromosomes, the fitness will increase and the recombination is shrink the fixed region (more narrow) on the chromosome

Question 56

what do longer lines infer on the selective sweep graph

Answer 56

the longer sections of the genome that are totally homozygous thus low variation in this region of the genome

Question 57

what do genetically homozygous regions of the selective sweep graph implicate

Answer 57

natural selection as the cause for evolution of lactase persistence

Question 58

what is the cause for evolution of lactase persistence

Answer 58

natural selection