Posted: April 30th, 2020

Molecular Ecology Midterm #2

Molecular Ecology Midterm #2
Spring 2022

Identify: ___________________________

My typed title signifies that I’ve abided by the ideas of Tutorial Integrity at Rutgers College (

Typed title in lieu of a signature: _____________________________

That is an open guide examination to be accomplished individually. You aren’t allowed to get assist from anybody else. It’s due by 11:59pm on April 10, 2022 by way of Canvas.

You have to present the equations you might be utilizing, your work, and clarify your pondering course of clearly and legibly to get full credit score (I strongly encourage typing your solutions). Exhibiting your work and explaining your reasoning may also enable for the potential for partial credit score. Please use as a lot area as you want.

1. You resolve to conduct an Evaluation of Molecular Variance (AMOVA) on two populations of irises in New Jersey. The genotypes at two mitochondrial SNPs (alleles A or G and C or T) are listed under. Do not forget that distance amongst genotypes is measured because the variety of alleles that don’t match (e.g., dij2 between A/C and C/T is 12 + 12 = 2).

Inhabitants Particular person Locus 1 Locus 2
1 1 G T
1 2 G C
1 Three A C
1 four G C
1 5 G C
1 6 G T
2 1 A T
2 2 A T
2 Three G T
2 four A T
2 5 A T
2 6 G T

a. What number of levels of freedom do you may have amongst populations?

b. What number of levels of freedom do you may have inside populations?

c. What number of levels of freedom do you may have in whole?

d. You calculate the gap matrix:

Inhabitants 1 Inhabitants 2
Particular person 1 2 Three four 5 6 1 2 Three four 5 6
1 zero
2 1 zero
Three 2 1 zero
four 1 zero 1 zero
5 1 zero 1 zero zero
6 zero 1 2 1 1 zero
1 1 2 1 2 2 1 zero
2 1 2 1 2 2 1 zero zero
Three zero 1 2 1 1 zero 1 1 zero
four 1 2 1 2 2 1 zero zero 1 zero
5 1 2 1 2 2 1 zero zero 1 zero zero
6 zero 1 2 1 1 zero 1 1 zero 1 1 zero

What’s your sum of squares inside populations?

e. What’s your whole sum of squares?

f. What’s your estimated variance inside populations?

g. What’s your estimated variance amongst populations?

h. What’s your worth of PT?

2. I’ve put three recordsdata on Annotate:
• /native/house/MolEcol/4Class/midterm2.vcf has the genotypes
• /native/house/MolEcol/4Class/midterm2_A.pop has the checklist of people in inhabitants A
• /native/house/MolEcol/4Class/midterm2_B.pop has the checklist of people in inhabitants B

Please use vcftools to calculate the weighted FST between populations A and B.

Three. Think about that almost each tree in Hopkins Memorial Forest has its personal ant inhabitants. There are such a lot of timber, the quantity is successfully infinite. Every ant inhabitants has an efficient inhabitants dimension of 100. The populations are related by gene move of fee m = zero.2. What worth of FST do you anticipate finding? Word that m is excessive and doesn’t meet an assumption of small m.

four. A inhabitants of 40 asters segregating at two loci with two alleles every (A/T and G/C) has eight people with the AAGG genotype. The allele frequencies of A and G are zero.5 and zero.5 within the inhabitants.

a. What’s the coefficient of gametic disequilibrium, D?

b. What’s the worth of Lewontin’s D’? (that’s “D prime”)

5. We be taught locus in eucalyptus timber codes for drought tolerance. On common throughout a drought, genotype AA produces two offspring per era, whereas genotypes AB and BB produce one offspring. In 2019, the allele frequency p of the A allele is simply 2%, however the inhabitants may be very, very giant. A really lengthy drought hits the inhabitants. What’s the anticipated equilibrium allele frequency p* after numerous generations go by?

6. A special locus codes for drought tolerance in desert tortoises. On common throughout a drought, genotype AA produces 7 offspring, genotype AB produces eight offspring, and genotype BB produces Three offspring. The genotype frequencies in 2019 are 10% AA, 10% AB, and 80% BB. What’s the anticipated equilibrium allele frequency p* after numerous generations go by in the course of the drought? Assume the tortoise inhabitants can be very giant.

7. You pattern DNA from seven bighorn sheep from a inhabitants of two,000 within the Rocky Mountains of Colorado. You sequence 10,000 basepairs from an intron in a diploid coat coloration locus. You assume the SNP mutation fee is someplace round 10-Three per era for the entire locus. What number of SNPs do you anticipate finding?

EXTRA CREDIT You’re learning a inhabitants of oysters in Delaware Bay and you discover allele frequencies of zero.four and zero.6 at a locus with alleles A and T, respectively. You realize from different analysis that the migration fee from the continental shelf populations is zero.2, and that the allele frequency of T on the shelf is zero.2. What’s the choice coefficient for T in Delaware Bay?

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