Evolution_ProblemSet3_S22
Evolutionary Biology Spring 2022 Problem Set 3
1. You are studying patterns of color differentiation in a small population of Chilean monkeyflowers (Mimulus cupreus). Individual plants can have flowers that range from yellow to red, with many different shades of orange in between. You think that flower color is a quantitative trait that is variable in populations.
a. Describe the steps you would need to take in order to find quantitative trait loci linked to differences in flower color.
. Describe one mechanism by which you could imagine allele frequencies for color changing over time without selection.
2. In group conference, we read several papers that explored the evolution of bu
owing behavior in Peromyscus mice.
a. Weber et al XXXXXXXXXXdetermined the genetic basis for the evolution of bu
ow length and shape in oldfield mice. How did the authors conclude that bu
ow length was an additive trait controlled by three loci, while escape tunnel presence was controlled by a single locus?
. How did Metz et al XXXXXXXXXXconclude that precocious bu
owing behavior was not due to learning from the behavior of parents?
a. Discuss one other example of evidence of how selection affects the extended phenotype of an animal species (not from your textbook). Provide a citation for your answer. Don’t forget to have a bibliography at the end of your problem set!
3. You are studying a population of 100 flowers that has two alleles at a locus for flower color, blue (B) and green (G). There are 15 individuals with the BB genotype, 70 individuals with the BG genotype, and 15 individuals with the GG genotype.
a. What are the allele frequencies of B and G in the starting population? Show your calculations.
. If genotype distributions for the offspring were the same as those of the parents, would you say that this population in Hardy-Weinberg equili
ium? Show your calculations.
c. Given the results of part b and the distribution of genotypes, offer a hypothesis that could explain the results, and explain your reasoning.
4. Revisiting the tusklessness paper (Campbell-Staton et al. 2021), is there any ONE metric that was used to identify candidate genes for tusklessness that you understand a bit better following our discussions in lecture and readings in the textbook? Describe the concept and how it was used in the elephant paper here. You can do two metrics for extra credit! (Hint: see Figure 2c)
5. You are studying selection on neck length in two giraffe populations. Below you can see data on neck length (in inches) of the whole population and
eeding parents for each of the two populations.
Neck length of individuals in population 1
Neck length of
eeders in population 1
Neck length of individuals in population 2
Neck length of
eeders in population 2
50
90
55
90
80
80
75
60
90
75
45
70
45
95
60
75
60
60
40
80
35
90
95
45
40
70
75
80
a. Calculate the selection differential (S) for each population. Show your work. Hint: This should only involve calculating averages and subtracting.
You also have some data you on the length of necks for parents and their offspring (offspring co
esponding to each midparent listed in adjacent cell). Midparent neck length is the average neck length of the two parents; midoffspring neck length is the average neck length of all offspring from that pair of parents.
Midparent neck length, population 1
Midoffspring neck length, population 1
Midparent neck length, population 2
Midoffspring neck length, population 2
85
84
80
65
90
88
75
90
75
75
85
55
65
62
65
75
70
69
70
85
80
82
95
75
95
94
60
80
. Describe how you would use these data to calculate na
ow sense heritability for each population. You don’t need to calculate it directly (but you can try for extra credit) – just describe how you could do this.
c. Based on parts ‘a’ and ‘b,’ in which population would you expect to see the largest evolutionary change in neck length in the next generation? Explain your answer.
d. Is this an example of directional, stabilizing, disruptive, or balancing selection? Why?
6. The graphs below show the results of simulations of the effect of selection on deleterious alleles. Population size is infinite in both simulations and the starting frequency and the strength of selection are the same.
a. Based on the shape of the curves, why do the results of the simulations differ? Explain your answer.
. The allele in the bottom simulation is not eliminated entirely from the population. Would this change if the population was finite in size? Why or why not?
1.0Final frequencies A1: 0
A2: 1
A1A1: 0
A1A2: 0
A2A2: 1
0.8Frequency of allele A1
0.6
0.4
0.2
0 10 20 30 40 50
Generation
1.0
0.8Frequency of allele A1
0.6
0.4
0.2
0
Final frequencies A1: XXXXXXXXXX
A2: XXXXXXXXXX
A1A1: XXXXXXXXXX
A1A2: XXXXXXXXXX
A2A2: XXXXXXXXXX
10 20 30 40 50
Generation
Literature cited
Campbell-Staton, S. C., B. J. Arnold, D. Gonçalves, P. Granli, J. Poole, R. A. Long, and R.
M. Pringle XXXXXXXXXXIvory poaching and the rapid evolution of tusklessness in African elephants. Science 374:483–487.
Metz, H. C., N. L. Bedford, Y. L. Pan, and H. E. Hoekstra XXXXXXXXXXEvolution and Genetics of Precocious Bu
owing Behavior in Peromyscus Mice. Cu
. Biol. 27: XXXXXXXXXXe3.
Weber, J. N., B. K. Peterson, and H. E. Hoekstra XXXXXXXXXXDiscrete genetic modules are responsible for complex bu
ow evolution in Peromyscus mice. Nature 493:402–405.
Ivory poaching and the rapid evolution of tusklessness in African elephants
POACHING IMPACTS
Ivory poaching and the rapid evolution
of tusklessness in African elephants
Shane C. Campbell-Staton1,2,3*†, Brian J. Arnold4,5†, Dominique Gonçalves6,7, Petter Granli8,
Joyce Poole8, Ryan A. Long9, Robert M. Pringle1
Understanding the evolutionary consequences of wildlife exploitation is increasingly important as
harvesting becomes more efficient. We examined the impacts of ivory poaching during the Mozambican
Civil War (1977 to 1992) on the evolution of African savanna elephants (Loxodonta africana) in
Gorongosa National Park. Poaching resulted in strong selection that favored tusklessness
amid a rapid population decline. Survey data revealed tusk-inheritance patterns consistent with
an X chromosome–linked dominant, male-lethal trait. Whole-genome scans implicated two
candidate genes with known roles in mammalian tooth development (AMELX and MEP1a),
including the formation of enamel, dentin, cementum, and the periodontium. One of these loci
(AMELX) is associated with an X-linked dominant, male-lethal syndrome in humans that
diminishes the growth of maxillary lateral incisors (homologous to elephant tusks). This study
provides evidence for rapid, poaching-mediated selection for the loss of a prominent anatomical
trait in a keystone species.
T
he selective killing of species that bea
anatomical features such as tusks and
horns is the basis of a multibillion-dolla
illicit wildlife trade (1) that poses an im-
mediate threat to the survival of ecolog-
ically important megafauna worldwide (2, 3).
Megahe
ivores are especially vulnerable to
overharvesting because of their large habitat
equirements, small population sizes, and long
generation times (4, 5). As ecosystem engi-
neers, these species also behaviorally regulate
ecological processes (5–8); anthropogenic se-
lection on phenotypes that influence these
ehaviors may, therefore, have cascading ef-
fects on ecosystem functioning. However, most
work that details human-driven selection has
focused on smaller species in which evolution-
ary change is more readily studied (9, 10). It
emains unclear to what extent, at what rates,
and throughwhatmechanisms harvest-induced
phenotypic change occurs in the world’s largest
land animals.
Warfare is associated with intensified ex-
ploitation and population declines of wild-
life throughout Africa (11), and organized
violence has long been intertwined with the
ivory trade (12–14). In Gorongosa National
Park, theMozambican Civil War (1977 to 1992)
educed large-he
ivore populations by >90%
(15), and armies on both sides of the conflict
targeted elephants for ivory (15, 16). Intensive
poaching in Africa has been associated with
an increase in the frequency of tuskless ele-
phants, exclusively (or nearly so) among females
(table S3). No record of tuskless male elephants
within Gorongosa National Park exists (table
S2). Analyses of historical video footage and
contemporary sighting data (supplementary
materials) show that the precipitous decline
of the Gorongosa elephant population was
accompanied by a nearly threefold increase
in the frequency of tuskless females, from 18.5%
(n = 52) to 50.9% (n = 108) (two-sample equality
of proportions test with continuity co
ection,
P < XXXXXXXXXXFig. 1A).
To test whether the increased frequency of
female tusklessness was a chance event asso-
ciated with the severe population bottleneck
(17), we simulated the observed population
decline in Gorongosa from 1972 (n = 2542
individuals) to 2000 (n = XXXXXXXXXXunder a
scenario of equal survival probabilities fo
tusked and tuskless females (see methods).
On the basis of these simulations, the ob-
served increase in tusklessness is extremely
unlikely to have occu
ed in the absence of
selection (hypergeometric distribution, P =
1.8 × 10−15) (Fig. 1B). The relative survival of
tuskless females across this 28-year period
was estimated to bemore than five times that
of tusked individuals (maximum-likelihood
estimate = 5.13, 95% confidence interval 3.98
to XXXXXXXXXXFig. 1C). Thus, we conclude that the
population bottleneck in Gorongosa was ac-
companied by strong selection favoring the
tuskless phenotype.
If there were strong selection against tusked
elephants, we might also observe divergent
genomic signatures of population-size change
etween the two tusk morphs. We sequenced
whole genomes from blood samples of 18 fe-
male elephants (n = 7 tusked, 11 tuskless). We
mapped sequence reads to the annotatedAfrican
savanna elephant genome (Loxafr3.0) and gen-
erated alignments with ~30× coverage for 13
samples and 14× coverage for 5 samples (sup-
plementary materials). Using the 30× coverage
samples (n= 6 tusked, 7 tuskless), we calculated
Tajima’s D (18) genome-wide in nonoverlap-
ping 10-kb windows. Both groups displayed
a slight excess of rare variants, indicated with
negative D values (tuskless: −0.27, tusked: −0.2).
However, tusked sampleshad significantly fewe
are variants than tuskless samples (Welch’s
two-sample t test: P < XXXXXXXXXXFig. 1D and
supplementary materials), which is consistent
with a more severe population contraction of
tusked individuals.
To evaluate the evolutionary response to
selection, we quantified the frequency of
tusk phenotypes among adult females born
after the war (estimated birth years 1995 to
2004). We found that tusklessness among
female offspring of survivors (33%, n = 91)
emained significantly elevated over the pre-
conflict proportion (18.5%, two-sample equality
of proportions test with continuity co
ec-
tion, P = XXXXXXXXXXFig. 1A) and was greater than
expected in the absence of selection (hyper-
geometric distribution, P = 4.3