Download --Biology 321 Spring 2013 Assignment Set #2 Sex Linkage, Sex

--Biology 321 Spring 2013 Assignment Set #2
Sex Linkage, Sex Determination & Probability
 Required Readings Assignments (on web site)
Parthenogenesis in Komodo dragons: should males and females be kept together
to avoid triggering virgin birth in these endangered reptiles?
Nature 444: 1021-1022 Dec 21, 2006
This interesting paper reflects a number of key concepts & themes that we have
already covered or will explore in upcoming lectures:
• Basic Mendel and independently assorting gene loci: calculating genotype
probabilities (in this case probability of homozygosity at all loci if progeny
were produced by sexual reproduction
• How to restore diploidy in the products of meiosis in the absence of a
fertilization event
• Variations on chromosomal sex determination: Z & W sex chromosomes
• Using molecular techniques (DNA fingerprinting) to determine parentage of
offspring in question – the microsatellite sites on the DNA that are examined
behave in proper Mendelian fashion
• Phenotypic plasticity and the role of genes and the environment in
determining phenotype
Required Reading and Problem Assignments in 10th edition of text
Chapter 2 Read carefully pgs 50-65: Section 2.6 on Human Pedigree analysis
Work Chapter 2 problems 10, 47, 57, 60, 61, 66, 77
(Note: pedigree problems will be assigned in Set 3)
Chapter 3
Work problems 30 & 31
Required Reading and Problem Assignments in 9th edition of text
http://fire.biol.wwu.edu/trent/trent/assignmentset2.9.pdf
1
Set 2 Problems sorted by analytical and/or content type
Using and understanding genetic terminology
Text Chapters 2 & 3: most questions
This problem set: most questions
Assigning appropriate allele symbols
Text Chapter 3: 30, 31
This problem set: 2, 5, 7, 8, & 10
Figuring out whether a trait is X-linked (standard XY) or autosomal:
Text Chapter 2: 57 Text Chapter 3: 30, 31
This problem set: 1A, 4, 7 & 8
Figuring out dominance & interpreting crosses when sex determination mechanism is
KNOWN (ie XX & XY vs ZZ & ZW):
Text Chapter 2: 77
Text Chapter 3: 30, 31
This problem set: 1A, 1B, 2, 4, 7 , 8, 9 (Komodo dragon part C),
Figuring out dominance & interpreting crosses when sex determination mechanism is
UNKNOWN (ie XX & XY vs ZZ & ZW):
This problem set: 3, 5
Using Mendel & Morgan (sex linked traits) to deduce parental (and progeny) genotypes from
progeny phenotypic ratios  data set large so ratios more or less match predicted
probabilities for each phenotypic/genotypic class
Text Chapter 3: solved problem 1; 30, 31
This problem set: 1A, 3, 4, 7 & 8
Using Mendel & Morgan (sex linked traits) to predict progeny genotypes/phenotypes and
ratios from parental genotypes/phenotypes
Text Chapter 2: 60, 61, 66, 77
This problem set: 9 (Komodo dragon problem)
Sorting through the complexities of real data or ambiguous data
Text Chapter 2: 57,
This problem set: 9 (Komodo dragon problem)
Basic Probability Product and Sum rules
Text Chapter 2: 47 (uses both rules), 66
This problem set: 6, 9 (Komodo dragon problem)
Conditional probability (limiting the possible outcomes)
This problem set: 6
2
This Table summarizes Chromosomal Sex-determining Mechanisms
DON’T MEMORIZE IT. IF YOU NEED THIS INFORMATION FOR AN
EXAM QUESTION I WILL GIVE IT TO YOU. I will assume though that you
know the sex determination mechanism for mammals and fruitflies!
Shaded cells = diploid animals
Organism
Female
Male
Comments
• Mammals
• Some amphibians and
reptiles
• Many insects such as
the fruitfly Drosophila
• Some plants with male
and female sexes
• Some insects
(including spiders)
• Some roundworms
(such as
Caenorhabditis
elegans)
XX
XY
Males produce two different
types of sperm: 50% carry
an X chromosome and 50%
a Y chromosome
XX
XO
Y chromosome is absent.
Males have a single X
chromosome and produce
two different types of
sperm: 50% bearing an X
chromosome and 50% with
no sex chromosome
Pattern of sex linkage same
as XX, XY species
• Birds
• Some insects (such as
moths and butterflies)
• Some amphibians and
reptiles including the
KOMODO dragon
ZW
ZZ
Bee, wasps and ants
diploid
haploid
By convention, Z and W are
used to indicate the sex
chromosomes in these
species. The Z chromosome
is equivalent to the X
chromosome. Females
produce two different types
of eggs: 50% carry the Z
chromosome and 50% carry
the W chromosome.
Males usually develop from
unfertilized eggs; females
from fertilized eggs
There are no sex
chromosomes per se
3
 Problem 1A Two phenotypically wild-type Drosophila (with long wings and red eyes) are
crossed, and two mutant phenotypes (curved wings and lozenge eyes) are seen to segregate
among the progeny as follows:
Females
600 long-wing, red eyes
200 curved wing, red eyes
Males
300 long wing, red eyes
300 long wing, lozenge eyes
100 curved wing, red eyes
100 curved wing, lozenge eyes
(i). The curved wing mutation is: a. autosomal recessive b. autosomal dominant c. sex-linked
recessive d. sex-linked dominant
(ii). The lozenge eye mutation is: a. autosomal recessive b. autosomal dominant c. sex-linked
recessive d. sex-linked dominant
(iii). The female parent is:
a. heterozygous for both genes
b. heterozygous for the wing gene and homozygous for the eye gene
c. homozygous for the wing gene and heterozygous for the eye gene
d. none of the above
(iv). The male parent is:
a. hemizygous for both genes
b. hemizygous for the wing gene and heterozygous for the eye gene
c. heterozygous for both genes
d. heterozygous for the wing gene and hemizygous for the dominant allele of the eye gene
e. heterozygous for the wing gene and hemizygous for the recessive allele of the eye gene.
Consult the notes on sex determination while you are working on these problems.
 Problem 1B a. A female wasp of genotype aabb mates with a male wasp of genotype AB
(where genes A and B are on different chromosomes). Predict the phenotype & genotypes of the
male and female offspring. Useful info:
• males produce sperm by cell division process that resembles mitosis (why?)
• a mated female usually lays fertilized and unfertilized eggs in an unpredictable ratio
b. Predict the outcome of the reciprocal cross (of that shown in part a) assuming the parents
were from true-breeding strains.
c. An AaBb female mates with a male wasp of genotype AB. Predict the phenotype & genotype
ratios of the male and of the female offspring.
4
 Problem 2 The wildtype wing of a particular species of butterfly has a
single eye- spot. You have found a mutant male with double eye-spots on each
wing. You initiate a breeding study:
double male X single female

all of the females have double eye spots
all males have single eye spots
Circle all allele symbol designations that are consistent with convention and the
information given above. There is more than one correct answer here.
a-c do not imply that the trait is autosomal.
a.
b.
c.
d.
e.
f.
e+ = single eye spot e = double eye spot
e = single eye spot e+ = double eye spot
E = single eye spot e = double eye spot
e = single eye spot E = double eye spot
Ze+ = single eye spot Ze = double eye spot
e+
e
X = single eye spot X = double eye spot
 Problem 3
A friend of yours has two true-breeding strains of a newly discovered insect
species, whose mode of sex determination is unknown. One strain has a green
eyes and jagged wings (wings with a jagged margin). The other strain has red eyes
and smooth wings. She does the following sets of crosses:
Experiment #1
Parental green jagged female X red smooth male

F1
all progeny are red, jagged
 intercross F1 brothers and sisters
F2
3/8
3/8
1/8
1/8
females
red, jagged
green, jagged
red, smooth
green, smooth
F2 males: 3/4 red, jagged
1/4 red, smooth
5
Experiment #2
Parental red smooth female X green jagged male

F1
all females are green, jagged
all males are red, jagged
 intercross F1 brothers and sisters
F2
3/8
3/8
1/8
1/8
females
red, jagged
green, jagged
red, smooth
green, smooth
F2 males:
3/8 red, jagged
3/8 green, jagged
1/8 red, smooth
1/8 green, smooth
Your friend doesn’t know how to interpret these data so she comes to you for help.
You work through a systematic analysis with her:
 First you determine which traits are dominant:
 Next you consider the phenotypes of the F1 progeny from the two experiments.
The mechanism of sex determination is unknown for this species. Your friend
examines a table on sex determination (see last page of exam) and suggests that the
F1 data are inconsistent with an XY sex determination mechanism. Considering
the F1 data only, you agree with your friend. Briefly explain what the F1 data
would have looked like if the species had an XY sex-determining system.
Experiment #1
Experiment #2
 Examine the table again. What is the mode of sex determination of this insect?
No explanation necessary.
Briefly indicate the mode of inheritance of each trait. No explanation necessary.
green/red eye color:
jagged/smooth wing margin:
 Assign allele symbols and next to the crosses on the previous page, indicate
genotypes for P, F1 and F2 for both experiments
6
 Problem 4 DATA are on this page. Questions are on the next page.
You find two fruitflies (one wild-type female and a doubly mutant male) crawling
around on some bananas at home and, inspired by your Biol 321 course, you
decide to mate them and deduce the mode of inheritance of each trait.
Trait
wings
eye shape
wild-type allele symbol
w+ = winged
(wings present)
e+ round
mutant allele symbol
w = wingless (wings absent )
can still mate OK
e = oval
You do the following crosses and score lots of F1s:
P winged & round female
X
wingless & oval male
↓
F1 1000 progeny flies are scored
MALES and FEMALES BOTH:
1/2 wingless & round
1/2 winged & round
You then cross a:
winged & round F1 female
X winged & round F1 male
↓
F2 1000 progeny flies are scored:
all females are winged & round
1/2 males are winged & round
1/2 males are winged & oval
7
Carefully examine the data shown on the previous page and work through a
genotypic analysis using the allele symbols indicated in the table.
a. Which traits are dominant? (no explanation necessary)
b. Is the wing gene autosomal or sex-linked? (no explanation necessary)
c. Is the eye shape gene autosomal or sex-linked? (no explanation necessary)
d. Using the designated alleles symbols, on the previous page clearly indicate
the GENOTYPES OF the parental and F1 generations and F2 generations.
e. Predict the outcome of the following cross. OUTCOME = genotypes and
ratios.
F1 wingless & round female X F2 winged & oval male

 Problem 5 Wild-type North American Coolits (a fictitious animal) have
yellow eyes. Mutant green-eyed Coolits have been discovered. Parents in both
crosses (below) are from true-breeding stocks.
Cross I: green females X yellow males

male and female progeny are green-eyed
Cross II: The reciprocal cross is performed

males are yellow and females are green
a. Which is the dominant phenotype? (No explanation necessary).
8
b. Which sex carries the heteromorphic chromosome pair in North American
Coolits? Briefly defend/explain your answer in a sentence or two. Genotypes
useful here.
c. Which allele symbols are appropriate? Appropriate in this contex means that
they respect conventions of either Mendel or of Drosophila geneticists. A
combination of the two is also OK. There is more than one correct answer here.
You must circle all correct answers (and no incorrect answers) to get full credit.
(i)
Y= yellow y = green
(ii)
g = yellow G = green
(iii)
y = yellow G = green
(iv)
g = yellow g+ = green
(v)
y+= yellow y = green
(vi)
Zy+ = yellow Zy = green
 Problem 6 A self-fertilizing plant is heterozygous (AaBb) for dominant and
recessive alleles of two independently assorting autosomal genes. You and your
lab partner want to generate a strain that is true-breeding for the dominant alleles
of both genes. You let the plant self-fertilize and it is the job of your lab partner to
plant the seeds, pick the progeny and continue the experiment.
AaBb 
self
lab partner picks one progeny plant
a. Your lab partner picks only one progeny plant for further analysis. This plant
shows only dominant phenotypes. What is the probability that a plant exhibiting
both dominant phenotypes is AABB? Show your work to get full credit.
b. You are annoyed that your lab partner only picked one plant. What is the
probability that the plant is heterozygous for one gene and homozygous for the
other? Show your work to get full credit.
9
 Problem 7 Insect Chromosomal Sex-determining Mechanisms
Organism
Many insects such as the fruitfly
Drosophila
Some insects (such as moths
and butterflies)
Bee, wasps and ants
Female
XX
Male
XY
ZW
ZZ
diploid
haploid
Comments
The X chromosome carries
thousands of genes.
The Z chromosomes carries
thousands of genes.
Males develop from unfertilized
eggs; females from fertilized eggs
1. You discover a new species of moth in Whatcom County. The local wild-type
population of this moth has exhibits a naturally occuring variation in wing size
which we will designate as large-winged versus small winged.
Being an admirer of Mendel you do capture moths and set up a breeding
program to generate truebreeding strains. Here is your first cross:
Parental large-winged females X small-winged males

F1
small-winged females and large-winged males
a. Which trait is dominant? Note: if you don’t immediately see the answer, use
a trial and error approach.
b. Define allele symbols:
c. On cross above, show genotypes of Parental and F1 generations
10
 Problem 8 You find two fruitflies crawling around on some bananas at home.
The male fruitfly has a mutant wing and the female mutant bristles (see below).
Inspired by your Biol 321 course, you decide to mate them and deduce the mode of
inheritance of each trait.
Trait
wild-type allele symbol
mutant allele symbol
S
wing edge
w = wing edge straight
wJ =wing edge jagged
color of
bristles
cB brown
cY = yellow
You do the following crosses and score lots of progeny:
P straight & yellow female X jagged & brown male
↓
F1
1/2 females are straight & yellow
1/2 males are straight & yellow
1/2 females are straight & brown
1/2 males are straight & brown
You then cross a
straight & yellow F1 female
X straight & yellow F1 male
F2
↓
3/4 females are straight & yellow
F2
3/8 males are straight & yellow
1/4 females are straight & brown
3/8 males are jagged & yellow
1/8 males are straight & brown
1/8 males are jagged & brown
a. Which traits are dominant? (no explanantion necessary)
b. Is the wing gene autosomal or sex-linked? (no explanantion necessary)
c. Is the bristle color gene autosomal or sex-linked? (no explanantion
necessary)
d. Using the designated allele symbols, next to each cross clearly indicate the
GENOTYPES of the parental and F1 and F2 generations.
11
 Problem 9 Parthenogenesis in Komodo Dragons
NOTE: This problem consists of is a series of short questions. For most, you don’t have to
get the correct answer to one question in order to answer the subsequent question.
Parthenogenesis, the production of offspring without fertilization by a male, is rare in
vertebrate species. The Komodo Dragon paper presented data to show that two female Komodo
dragons, Sungai and Flora, produced parthenogenetic offspring. Our analysis will focus on the
clutch produced by Sungai.
See pg 13. DNA fingerprint analysis was performed on Sungai (mom) and Kimann (with
whom she had cohabitated long before the clutch was laid) and her unusual clutch of four
progeny. This analysis involved six different loci or sites on the genome (A through F). A-F are
located on different autosomal chromosomes. The alleles of each site are indicated by different
numbers. These loci behave like “proper” Mendelian genes, so you should analyze the
genotypes as you would any of the more familiar traits that we have examined. The genotyping
data is on the extra sheet.
The authors of the Komodo Dragon paper based their conclusion of pathenogenetic birth
on various lines of evidence including a probability calculation. Among other observations,
sexual reproduction was excluded by the low probability of the clutch genotypes if sexual
reproduction had occurred. Work through this problem assuming that all four progeny in the
clutch were produced from either sexual reproduction or from parthenogenesis.
Part A: Based on the genotyping data (see pg 14 of this handout), could Sungai’s clutch have
been produced by sexual reproduction with Kimann? Circle YES or NO
One sentence defense of your answer (note I’m not asking for any calculations here):
Part B Based on the genotypes of the 4 progeny, the authors of the Komodo Dragon paper
argued that if Sungai’s clutch was from sexual reproduction (with some unidentified male), the
male would have had to have exactly the same genotype as Sungai at all loci shown above.
Calculate the probabilities below assuming sexual reproduction and a male mate with a
genotype identical to Sungai. You must show your work to get full credit for these
calculations. Set up and label your answer so that I can follow your logic. You don’t have to
do the multiplication and/or addition.
i. What is the overall probability of Progeny 2’s genotype?
ii. For any random, hypothetical offspring, what is the overall probability of homozygosity (for
either allele) at all loci tested? HINT: Don’t make this an overly complicated calculation.
Figure out the probability for one gene and then follow through.
iii: What is the overall probability of a clutch of 4 offspring that are homozygous at all loci?
Part C For the Komodo Dragon, the normal ploidy (chromosome content) is 2n=40 and sex
determination is ZZ, ZW. All the offspring in the unusual clutch were 2n=40 and ZZ.
Interestingly, the authors did not speculate as to what type of abnormal event produced the
parthenogenetic offspring. For each of the abnormal events proposed below indicate whether the
scenario is consistent with the observed genotype homozygosity and the ploidy (chromosome
number) of the offspring
1 Consistent with genotype homozygosity but not ploidy
2 Consistent with ploidy but not genotype homozygosity
12
3 Works for both genotype homozygosity and ploidy
4 Doesn’t work for either genotype homozygosity or ploidy
In the blank before each statement, indicate the appropriate number
____ The products of a Meiosis I division fuse with each other
____ One of the products of Meiosis I fails to undergo MII and starts embryonic development
____ One of the products of Meiosis II starts embryonic development
_____One of the products of Meiosis II fuses with its sister cell (produced in the same cell
division) and starts embryonic development.
_____ All of these explanations are barking up the wrong tree. Clearly this is a type of asexual
reproduction where a premeiotic germline cell (that is, one that has not entered meiosis) started
embryogenesis spontaneously.
DATA: DNA fingerprint analysis was performed on Sungai (mom) and Kimann (with whom
she had cohabitated long before the clutch was laid) and her unusual clutch of four progeny.
This analysis involved six different loci or sites on the genome (A through F). A-F are located on
different autosomal chromosomes. The alleles of each site are indicated by different numbers.
These loci behave like “proper” Mendelian genes, so you should analyze the genotypes as you
would any more familiar traits. The genotyping data is shown below.
A134 A136 = A134 /A136
Sungai previously had cohabitated with Kimann but had not produced any offspring with him
during this time period. She had been kept in isolation before producing the clutch shown
below
SUNGAI
A134 A136; B198 B198; C137 C141; D211 D213; E154 E154; F190 F 190
Kimann
A134 A136; B198 B198; C133 C141; D211 D213; E154 E154; F190 F 190
Sungai’s Clutch
Progeny 1
A134 A134; B198 B198; C137 C137; D211 D211; E154 E154; F190 F 190
Progeny 2
A134 A134; B198 B198; C141 C141; D211 D211; E154 E154; F190 F 190
Progeny 3
A136 A136; B198 B198; C137 C137; D213 D213; E154 E154; F190 F 190
Progeny 4
A136 A136; B198 B198; C141 C141; D213 D213; E154 E154; F190 F 190
13
❖ Problem 10 The wild-type laboratory stock of the worm C. elegans is
“long&slender”. A “dumpy (short and stocky)” animal is mated with an animal
from a true-breeding laboratory stock. One/half of the progeny are dumpy and
one-half are long&slender.
Given this information, which of the following set(s) of allele symbols are
appropriate. Correct answers must follow standard conventions. Circle all correct
answers. (There may be more than one ).
a. D= dumpy d = long&slender
b. d= dumpy d+ = long&slender
c. D+ = dumpy d = long&slender
d. d= dumpy D = long&slender
e. d+ = dumpy d= long&slender
❖ Problem 11 See also next problem (options) about Mendel data fudging..
14
OPTIONAL Challenge Problems in Probability
Optional Challenge Problem 1 Did Mendel fudge his data?
• First work Problem 11 which addresses errors in genotype inference based on a small
sample size of 10.
• When assessing the ratio of F2 homozygotes to heterozygotes, Mendel always reported
the expected 2:1 ratio.
• But Mendel’s famous paper suggests that he only scored 10 offspring of each F1
dominant plant.
• If he really only scored 10 progeny of each F2, the ratio of Rr to RR would turn out to
be 1.7 to 1 instead of 2 to 1.
• Do the calculations to show where the 1.7 to 1 comes from.
Optional Challenge problem 2
❖ Part A Consider a diploid plant where n=4, that is, there are 4 chromosomes in each set. (For
the purposes of this problem, ignore the effects of crossing-over)
a. What proportion of the gametes of this organism will be expected to carry only chromosomes
of paternal origin?
b. Would the proportion of gametes carrying only chromosomes from the maternal parent be the
same? Explain.
c. What proportion of the gametes would carry chromosomes of both the
male and the female parent?
d. Derive a formula that indicates the number of different kinds of gametic chromosomal
combinations an individual with (n) number of pairs of chromosomes can produce.
❖ Part B A friend of yours goes around saying that all of his chromosomes came from his
paternal and maternal grandfathers because he resembles both of his grandfathers, but shows no
resemblance to either of his grandmothers. You get tired of hearing this and decide to do a
probability calculation to show him how unlikely it is that his statement is true.
Calculate the probability that all of his chromosomes came from his grandfathers.
• Recall that humans have 22 pairs of autosomes and one pair of sex chromosomes.
• For this calculation, ignore the effects of crossing over between maternal and paternal
homologs -- in other words, assume it doesn’t happen.
Optional Challenge Problem 3 On the average, what fraction of their
chromosomes will two siblings share in common? Assume that the parents are
heterozygous for four different versions of a given autosome A1, A2, A3, A4 (where
the superscript differentiates homologs); that is, the cross would be A1A2 X A3A4.
15