Midterm 2

Question 1

How do we know if two loci are in linkage equilibrium (3)

Answer 1

1. when D=0
2. frequency of B x A = frequency of AB
3. frequency of B on A = frequency of B on a

Question 2

What are the 3 ways (aside from loci being close on a chromosome) that can cause LD

Answer 2

1. genetic drift
2. selection on multilocus genotype
3. population admixture

Question 3

How can genetic drift cause linkage disequilibrium

Answer 3

a mutation can create a new haplotype in a small population and drift acts on it and changes the haplotypes frequencies causes it to be in disequilibrium

Question 4

Why is max r = 0.5

Answer 4

recombinant frequency is equal to the number of recombinant progeny divided by the total number of progeny
only a total of half the chromosome can recombine

Question 5

a population in linkage disequilibrium only has individuals with AB and ab chromosomes. linkage decay occurs faster than expected. what might cause this

Answer 5

there may be a heterozygous advantage meaning that selection helps to break down linkage disequilibrium

Question 6

what causes linkage decay

Answer 6

recombination! (sexual reproduction)

Question 7

how can linkage disequilibrium help us identify alleles under positive selection

Answer 7

alleles with a high frequency and high linkage disequilibrium indicates recent positive selection.
(neutral alleles would be expected to have either high LD and low frequency or low LD with high or low allele frequency

Question 8

What is the maynard-smith model for why sex persists (2)

Answer 8

1. offspring of sexually reproducing individuals either have higher fitness and/or 2. produced in greater numbers than offspring of sexual reproducing individuals
   we saw that asexual reproduced in greater numbers, but sex persists as offspring have higher fitness/survival

Question 9

Explain the process of identifying candidate loci as quantitative trait loci (5)

Answer 9

1. identify markers throughout the gene, throughout QTL mapping and physically locating the genes
2. look for candidate loci linked to the markers
3. use the known location of the marker to sequence the candidate locus
4. do a transmission equilibrium test
5. observe if there is a correlation or not with the mutation/allele at the candidate locus and the trait
   (if not, then candidate locus is not QTL)

Question 10

can an apomorphy be a synapomorphy

Answer 10

Yes, because an apomorphy is a derived trait and a synapomorphy is a shared derived trait so if the apomorphy is shared by two or more lineages then it is also a synapomorphy

Question 11

how is phenotype determined through multiple loci and environment

Answer 11

phenotype is determined by a combination of genotype (alleles) and environmental factors
ex. height is influenced by many genes with additive effects and produce a reaction norm (possible range of heights). the environment also contributes to the final phenotype such as nutrition

Question 12

What are some best practices when building phylogenies (3)

Answer 12

1. use multiple approaches
2. include bootstrapping (for confidence in branching)
3. include outgroup to root tree (provides a starting point to know what the ancestor looks like)

Question 13

What are some common causes of complications in inferring phylogenies (4)

Answer 13

1. homoplasy = similarity not due to descendant but due to convergence or reversal
2. paralogs = gene duplication results in the same gene being present in two different forms and in different lineages
3. analogous traits = species may have similar traits due to convergent evolution even though they do not share a recent common ancestor
4. divergence = some species may have very different phenotypes even though they are closely related

Question 14

Explain the dangers of paralogs

Answer 14

paralogs are identical due to duplication rather than due to descent, so they may give the wrong phylogeny if different paralogs are used. orthologs should be used
(may make species look closer in relation than the real tree)

Question 15

Differentiate between methods used to build trees (4)

Answer 15

1. UPGMA = quick and easy, makes many assumptions (such as assuming equal rate of branches) and averages branch lengths
2. parsimony = makes assumption that simplest solution is correct, time consuming, more robust than UPGMA, no information on branch lengths
3. maximum likelihood = gives information on branch length, very robust, uses computer and relies on mathematical models
4. Bayesian inference = robust measure of probability, can suffer assuming local maximum is global maximum, uses computer and relies on mathematical models