midterm

Question 1

what is population genetics

Answer 1

“the study of allele frequencies and the processes that change these frequencies over space and time”

book definition:
“the mathematical theory and empirical analysis of changes to gene frequencies over time”

Question 2

why should we study pop. genetics?

Question 3

what are the five waus evolution in a population can occur?

Answer 3

1. mutation-source of genetic variation
2. gene flow-movement of genes
3. genetic drift-highly correlated with demographic changes
4. natural selection-where individual w stronger fitness, this allele will rise compared to other alleles
5. non-random mating

Question 4

within population genetics, what is the definition of evolution?

Answer 4

changes in allele frequency over time (and space)

changes in allele frequency <-> processes

Question 5

what is the source of all new genetic variation?

Answer 5

mutation

Question 6

an ancestral vs derived trait

Answer 6

depends on the context

ex. the ancestral mammals were mostly herbivores (plant-eating), therefore, the ability to consume animal protein (carnivores) is a derived trait within the mammals)

however, in terms of panda bears, eating plants is a derived trait since their ancestral are meat-eaters

bears to other carnivores-> derived

bears to panda bears-> ancestral

Question 7

in a genetic sequence, what do the letters SKYWRM represent?

Answer 7

represent heterozygous

S: C or G
K: G or T
Y: C or T
W: A or T
R: A or G
M: A or C

Question 8

in addition to mutation, what other ways can new genetic alleles enter a population?

Answer 8

gene flow?

-via genetic exchange (immigration, hybridization, transformation, transduction , conjugation)

Question 9

what is the acronym “SNP” stand for?

Answer 9

Single Nucleotide Polymorphisms

Question 10

what does the term INDEL represent w regards to a genetic sequence?

Answer 10

insertion and deletion
-refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION.

*the larger an INDEL is, the greater the chance it disrupts the gene

Question 11

what is population structure?

Answer 11

differences in allele frequency between groups of individuals within a species
-ex. diff. pop in diff islands

Question 12

what is the most common mechanism by which population structure emerges

Answer 12

when genetic divergence (differences in allele frequencies) emerge between diff subgroups

-can find them between geographically isolated groups

Question 13

why is it important to acct for population structure in genetic studies?

Answer 13

1. human health
   -understanding genetic diseases
   -identifying important genetic variation in pathogen s/parasites
   -selecting optimal treatment strategies
2. food security
3. biodiversity conservation

Question 14

what is principal component analysis? how is it used in population genetics?

Answer 14

non-parametric-used to look at population structure

divided into multiple, independent, principals components, which are ranked in order of how much variation they capture

Question 15

what is the “K” value in a structure analysis?

Answer 15

the number of genetically distinct groups

Question 16

difference between a census population size vs effective size

Answer 16

census size: the total nunber of indiviudals in a pop

effective size: “idealized” pop size that would have the same genetic dynamic as that of the actual population, specifically the way in which alleles are probabilistically lost/ fixed in the absence of other evolutionary factors

*larger census size, larger effective size

Question 17

what is genetic drift? how is it affected by a population size?

Answer 17

stochastic changes in allele frequency between generations due to statistical sampling error in a finite population

-fixed # of indivviduals (some alleles will arise & decrease)
-a large pop. will not be much affected due to genetic drift

*the strength of genetic drift is influenced by the SIZE of THE POP. and the STRENGTH OF SELECTION

Question 18

how does an allele’s frequency in a population affect its probability of being fixed or lost

Answer 18

low-frequency allele: more likely to be lost

high-frequency allele: more likely to be fixed

Question 19

what ecological factors can reduce a population’s effective size?

Answer 19

bottle necks and founder effects

-migration (gene flow)
-natural selection
-non-random mating

Question 20

how does the strength of positive selection acting on an allele affect the speed with which it fixes

Answer 20

it fixes faster

Question 21

what is an individual’s “fitness “

Answer 21

the (proportionate contribution) made by an individual to (future generations) relative to other individuals in the (same population)

1: proportionate contribution (how much genetic material is being on)
L1: 10 children
L2: 10 children
*their relative fitness is the same

but if
L1: 10 children
L2: 100 children
*L2 is much more fit, and L1 fitness has gone down when compared to L1

2: future generations (how much is passed to the future)
L1: lived to be 20 yrs old + 0 children
L2: lived to be 2 yrs old + 1 child
*L2 has higher fitness as its genetic is being passed on in the form of its child

3: same population
Lamp pop:
L1: 0
L2: 1
L3: 0

Buffalo pop:
B1: 100
*L2 has the highest fitness w/in the pop and the fitness of the B1 does not matter bc B1 is not in the same pop.

Question 22

what does the fixation index (F) tell us about a population? what does F greater than 0 mean? What does F less than 0 mean?

Question 23

in a typical population, what is the relative difference between the amt of synonymous site polymorphism and replacement (non-synonymous) site polymorphism observed?

Question 24

what is the relationship between Fst value and migration between population?

Answer 24

low Fst: lots of gene flow between populations (high connectivity)-high migration

high Fst: the more distinct and divergent the populations are becoming (being more different)-little migration