transition: purine to a purine (A for G)

transversion: purine for pyrimidine and visa versa (A for T)

synonymous is when there is no ultimate change in amino acid sequence due to genetic redundancies

nonsynonymous is when there is a change in aa sequence

frame-shift mutation

two types

when either a removed or added base effects the reading from of the gene. 

two types are insertion and deletion

You could be observing a polytypic triat.

Geographically, in two separate locations you see what looks like discrete phenotypes. However if you look in the intergrade zones (between the discrete areas) you may see intermediate phenotypes. 

Vp = √[(ΣYi-Ȳi)²/(n-1)]

Yi equals each measurement

Ybar = mean

n= number of measurements

Calculate Vp for tibia length for each population given these numbers:

Popn 1: .5, 1.8, 1.5, 2, 3.5, 3, 3.5, 2.5, 1.6, 1.8, 1.9, 2.1, 2.2, 2.7, 2.9

Popn 2: 1, 1.5, 2, 2.9, 3.7, 3.5, 4, 1.7, 2.3, 2.6, 3.4, 2.8, 3.7, 3.4, 3.9

Avg-Popn 1: 2.23

Avg-Popn: 2.83

Genetic

Va Additive variance, Vgxe genetic by environment, Vi epistatic

Non-genetic

Ve Environmental/Proximate/Unexplained, 

Tibia length is positively correlated with leg length which is positively correlated with speed and negatively correlated with digging power. Sooo our hypothesis is:

There is a selective benefit to having long tibias in open areas and to having short tibias in grassy areas, and therefore a population in either given location will not be in HWE.

Environemtal (Ve): the portion on Vp that isi due to random, environmentally induced variation among induviduals. ex. energy acquisition or sampling bias

Epistatic (Vi): interaction between two or more loci in which the experssion of one of more is modified (ex. albino mice)

Gene by Environment (Vgxe): variable eniveronment cues that affect the expression of genes as well as neural and hormonal mechanisms

Additive (Va): variability in a trait due to the effects of several alleles at a diff loci that add to a background value

Consider a diallelic locus.

After a single gen of mating, determine the mathematical relationship between allele and genotype frequencies. 

p²+ 2pq+q² =1

where p is the frequency of A

q is the frequency of a

p² is the frequency of AA

2pq is the frequence of Aa

q² is the frequncy of aa

We know the frequencies of all the genotypes:

AA = p²

Aa = pq for each of Aa and aA=2pq

aa= q²

We know how to mathematically find an allele frequency for A. It is the frequency of the homogenous  + 1/2 the heterogenous. So: freq of A= p² + pq. This can be simplified as p(p+q). We know p+q = 1 by addition rule. So therefore freq of A= p.

Then we do the same for q.

Guppies live in enviros with predators that like large spot size. But, femails select males that have large spots too. Some ppl count spot size in guppies (its incompletely dominant) where SS is lrge, Ss is intermediate and ss is small.  SS=53, Ss=24, ss=23

1. Determine p and q

2. Determine expected HW frequencies

3. Plot that on a HWE graph. Should fit in. Seem good?

4. Determine the expected HW counts

5. State the null hypothesis

6. determine if it can be rejected.

1. p is going to equal  the p² value + .5(2pq)

p=.53 + .5(.24)

p=.65

same process works for q. 

q=.35

2.  SS= .65²= .422

 Ss= 2pq=2(.65)(.35)=.455

 ss=.352 =.122

3. Looks good!

4. SS: .422*100=42.2

Ss: .455*100=45.5

ss: .122*100=12.2

5. Observed frequencies are the same as expected frequencies in HWE. There is no difference between these values.

6. we solve for x²⁼sum of [(observed-expected)²/expected]=22.48 REJECT

For two unlinked diallelic loci, give the expected HW genotypes

(C1C2   D1D2)

Each loci have their own p2+2pq+q2 equation that describes them.

C1C1D1D1

C1C1D1D2

C1C1D2D2

C1C2D1D1

C1C2D1D2

C1C2D2D2

C2C2D1D1

C2C2D1D2

C2C2D2D2

discrete populations are distinctly different and genes dont move between them.

a metapopulation is a popn with little sub popns in it that can interbreed/have genes move across them.

continent island (dispersal is peripheral unidirection)

island (dispersal is random among popn)

stepping stone (dispersal is linear

isolation by distance (limited gene flow in a continuous distribution that result in a genetically differentiated individuals that are distantly separated)

freq of B1= p

freq of B2=q

freq of B3=r

p²+2pq+q²+2qr+r²+2pr=1

Coefficient of Disequilibrium

= (p₁q_{1 x} p₂q_{2) - (}p₁q₂ x p₂q₁)

In the case of papilio memnon, linkage-disequilibrium results from NS on allelic combos.

Papilio memnon is a SE Asian butterfly that has geogrphic phenotypic variation. It is a non-toxic (Batesian) mimic of other toxic butterflies.

Wing shape, color and pattern are determined by several linked loci, most of which have multiple alleles. The different discrete morphs have different genotypes. In a given area these big sets of linked loci are selected on and act like a "supergene" allowing the mimic to adapt to match the local model.

Intermediates are not seen b/c they are recognized by predators.

What is Ne?

Determine Increase, Decrease, No Change (I, D, NC) in rate of random genetic drift for the following:

a. change in mutation rate from .001 to .000001 per gamete per generation

b. an increase in the rate of migration into a popn

c. a change in Ne from 600 to 150

d. An increase in the rate of selfing in a popn of plants

e. The establishment of "local neighborhoods" within a popn

a. I (mutation slows RGD)

b. I

c. I

d. I

e. I

look in book

Heterozygosity (H)

= 1-Σp_i² 

where pi is the frequency of each allele.

and avg H (Hbar)

avg freq of heterozygotes (H) across all loci

RGD: Alleles that establish the next generation are assumed to be a random sample from parental gene but are really not due to sampling bias as well as random drift of the frequency of a given allele

Founder Effect: a genetic drift like process. Founders are individuals that form a new popn and the genetic composition of the new popn is thus a subset of the parent popn

Genetic Bottleneck: another genetic drift like process. a rapid decrease in popn size and thus a big decrease in genetic variation

1. this could lead to inbreeding and a decrease in the overall genetic exchange. Not only will the effective population decrease, but also mortality may increase while vitality may decrease in the offspring.

2. a. try to decrease inbreeding among populations

b. introduce individuals from one small population to another population to promote genetic variation.

What is population fragmentation?

What's one type of it?

reduction of a single popn into several smaller popn

Range retraction: when a geographically widespread popn becamoes smaller populations