evolutionary biology prolblem set, each question requires a paragraph (unless very simple)
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. b. 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 burrowing behavior in Peromyscus mice. a. Weber et al. (2013) determined the genetic basis for the evolution of burrow length and shape in oldfield mice. How did the authors conclude that burrow length was an additive trait controlled by three loci, while escape tunnel presence was controlled by a single locus? b. How did Metz et al. (2017) conclude that precocious burrowing 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. b. If genotype distributions for the offspring were the same as those of the parents, would you say that this population in Hardy-Weinberg equilibrium? 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 breeding parents for each of the two populations. Neck length of individuals in population 1 Neck length of breeders in population 1 Neck length of individuals in population 2 Neck length of breeders 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 corresponding 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 b. Describe how you would use these data to calculate narrow 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. b. 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 01020304050 Generation 1.0 0.8Frequency of allele A1 0.6 0.4 0.2 0 Final frequencies A1: 0.04966 A2: 0.95034 A1A1: 0.00247 A1A2: 0.09438 A2A2: 0.90315 1020304050 Generation Literature cited Campbell-Staton, S. C., B. J. Arnold, D. Gonçalves, P. Granli, J. Poole, R. A. Long, and R. M. Pringle. 2021. Ivory 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. 2017. Evolution and Genetics of Precocious Burrowing Behavior in Peromyscus Mice. Curr. Biol. 27:3837-3845.e3. Weber, J. N., B. K. Peterson, and H. E. Hoekstra. 2013. Discrete genetic modules are responsible for complex burrow 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 bear anatomical features such as tusks and horns is the basis of a multibillion-dollar illicit wildlife trade (1) that poses an im- mediate threat to the survival of ecolog- ically important megafauna worldwide (2, 3). Megaherbivores are especially vulnerable to overharvesting because of their large habitat requirements, 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 behaviors 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 remains 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) reduced large-herbivore 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 correction, P < 0.001)="" (fig.="" 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="242)" (15)="" under="" a="" scenario="" of="" equal="" survival="" probabilities="" for="" tusked="" and="" tuskless="" females="" (see="" methods).="" on="" the="" basis="" of="" these="" simulations,="" the="" ob-="" served="" increase="" in="" tusklessness="" is="" extremely="" unlikely="" to="" have="" occurred="" 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="" 6.60)="" (fig.="" 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="" between="" 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="" fewer="" rare="" variants="" than="" tuskless="" samples="" (welch’s="" two-sample="" t="" test:="" p="">< 0.0001) (fig. 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) remained significantly elevated over the pre- conflict proportion (18.5%, two-sample equality of proportions test with continuity correc- tion, p = 0.046) (fig. 1a) and was greater than expected in the absence of selection (hyper- geometric distribution, p = 4.3 0.0001)="" (fig.="" 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)" remained="" significantly="" elevated="" over="" the="" pre-="" conflict="" proportion="" (18.5%,="" two-sample="" equality="" of="" proportions="" test="" with="" continuity="" correc-="" tion,="" p="0.046)" (fig.="" 1a)="" and="" was="" greater="" than="" expected="" in="" the="" absence="" of="" selection="" (hyper-="" geometric="" distribution,="" p="">