Questions and Answers of The Analysis Of Biological Data

Treatment of HIV is challenging in areas where medical clinics are often far away from home and not easily reached by patients, which makes refilling a prescription challenging. Filmão et al. (2019)
Computer optional: Refer to the previous problem. Download the Siberian jay data set from the book website. Use your computer to estimate the hazard ratio of breeders relative to nonbreeders and
Breeding is often a dangerous activity for many animals, requiring a great deal of energy and sometimes an increased exposure to predation. In contrast, animals that have reached breeding age have
Computer optional: Refer to the previous question. Download the Game of Thrones data set from the book website and conduct the following analyses.a. Calculate the hazard ratio of females relative to
Game of Thrones was a television series known for the high frequency of violent acts committed by, and upon, its many characters. Lystad and Brown (2019) tallied the fates of all 359 characters over
The bacteria Pseudomonas aeruginosa is the primary cause of lung infections in people with cystic fibrosis (CF). Babies with CF are born without Pseudomonas in their lungs, but they may quickly
Assume that the probability of an individual dying between day 0 and day 1 is 0.3, and the probability of dying between day 1 and day 2 is 0.25, given that the individual survives past day 1. What is
Which of the following are true about the Kaplan–Meier method? Answer true or false.a. It estimates the probability of survival to a particular time.b. It can be used to calculate the probability
A researcher studies the rate of death for patients in an in-hospital study of a new treatment for colon cancer. Which of the following cases represents an individual with censored data in the
Which of the following cases would be suitable response variables for a survival analysis?a. Number of days a patient survives between admission to hospital and death.b. Age of first mating for a
Phylogenetic trees like those in Figure 20.2-1, if dated, permit us to estimate the rate at which new species have formed over time. For example, the following tree indicates the timing of events in
A regulatory gene controls the expression of other genes—it turns them on and off. Many of these targets are themselves regulatory genes, instructing genes to turn on or off. Guelzim et al. (2002)
Refer to Practice Problem 5.a. Using a spreadsheet or other program, calculate the log-likelihood of values of s between 0.0 and 0.5 in increments of 0.01. Using this information, determine the
“Have you ever stolen something worth more than $10?” Anyone asked this question in a survey might be reluctant to answer truthfully, especially if he or she did not wish to make known a past
Yashin et al. (2000) compared a sample of 197 centenarians (people 100 years old or older) with a group of 465 younger people (aged between 5 and 80) to examine whether the two groups differed in the
Noonan et al. (2006) used DNA sequence data and the method of maximum likelihood to add the extinct Neanderthal species to the tree of humans and other apes (see Figure 20.2- 1). The accompanying
Refer to Practice Problem 1. The accompanying table lists log-likelihoods of values of p between 0.1 and 0.4, in increments of 0.02.a. Using only the table calculations, identify the maximum
Albino animals are well known, but what about plants? Apiron and Zohary (1961) found a recessive mutation in orchard grass (Dactylis glomerata) that causes a chlorophyll deficiency. Individuals with
The variance-to-mean ratio is a useful measurement of how clumped or dispersed events are in space or time relative to the random expectation (see Section 8.6). A high ratio indicates that events are
Outliers can occur in a sample of data for several reasons, including instrument failure, measurement error, and real variation in the population. The “trimmed mean” is a method developed for
In a hypothetical study of a predatory fish, the bootstrap was used to help generate confidence intervals for the mean waiting time between meals. A waiting-time measurement was obtained for 79 fish
Suppose we want to calculate the bootstrap standard errors for the difference between two groups in their medians. We would also like to do the same for the difference between the two groups in their
Prairie voles are monogamous and social, whereas their close relative the meadow voles are polygamous and solitary. The species differ in their expression of a vasopressin receptor gene (V1aR) in
The following table lists 100 bootstrap replicate estimates for an estimate of the mean length (in cm) of timber wolf jaws. (The values have been sorted into ascending order for your convenience.)
Using the data from Practice Problem 1, state whether each of the following data sets (a through f) is a possible bootstrap replicate sample for use in determining a bootstrap confidence interval
The following are very small data sets of birth weights (in kg) of either singleton births or individuals born with a twin.We are interested in the difference in mean weight between singleton babies
Give three reasons that studies in biology sometimes have more than one explanatory variable.
Rest in fruit flies, Drosophila melanogaster, has many features in common with mammalian sleep. Its study might lead to a better understanding of sleep in mammals, including humans. Hendricks et al.
We often assume that the mapping between words and their meanings is completely arbitrary. Maurer et al. (2006) tested whether this was completely true. College students were shown the following two
Cellulose from the butts of smoked cigarettes is commonly used by urban birds in nest construction. In an observational study of the housefinches in Mexico City, Suárez-Rodríguez et al. (2013)
Studying the influence of metabolic differences among individuals on survival or reproductive success in nature requires that an individual’s metabolism doesn’t vary too much from time point to
The slopes of the regression lines on the following graph show that the winning Olympic 100-m sprint times for men and women have been getting shorter and shorter over the years, with a steeper trend
Some species seem to thrive in captivity, whereas others are prone to health and behavior difficulties when caged. Maternal care problems in some captive species, for example, lead to high infant
Calculation problem: Testing the null hypothesis that the slope equals zero. Can the relationship be explained by sampling error? Using the face ratio and hockey penalty data from Practice Problem 1,
Calculation problem: Regression lines. Men’s faces have higher width-to-height ratios than women’s, on average. This turns out to reflect a difference in testosterone expression during puberty.
Most traits of animals, including eye size, are larger in species whose overall body size is larger. On the other hand, some traits may be functionally constrained and not vary much with body size.
Logging in western North America impacts populations of western trillium, a long-lived perennial that inhabits conifer forests (Trillium ovatum; see the photo at the beginning of the chapter). Jules
Use the data in Assignment Problem 16 to calculate a 95% confidence interval for the correlation between attachment and green-space area.Data from problem 16 In an increasingly urban world, are
Does learning a second language change brain structure? Mechelli et al. (2004) tested 22 native Italian speakers who had learned English as a second language. Proficiencies in reading, writing, and
Earwig density on an island and the proportion of males with forceps are estimates, so the measurements of both variables include sampling error. In light of this fact, would the true correlation
Large males of the European earwig, Forficula auricularia, develop abdominal forceps, which are used in fighting and courtship. Smaller males do not develop the forceps. Tomkins and Brown (2004)
In large wolf populations, most inbreeding coefficients of litters are close to zero, and very few are as high or higher than 0.25. What effect is this narrower range of inbreeding coefficients
Use the godwit data in Practice Problem 5 to test whether the mean arrival dates of male and female partners differ significantly. What assumptions are required?Data from problem 5 Birds of many
Imagine that you are a statistical consultant and a researcher comes to you with a problem. The researcher has a random sample of data from each of six groups, and she wants to test whether the means
The graphs at the right are from a study investigating hippocampal volume loss in 107 patients with drug-resistant epilepsy (Cook et al. 1993). The graphs depict the association between hippocampal
Finding the causes of the major mental illnesses, schizophrenia and bipolar disorder, is a major activity in medical research. Tkachev et al. (2003) compared expression levels of several genes
The Tukey–Kramer procedure was carried out on the results of Practice Problem 4, yielding the results at the bottom of this page.a. What are the null and alternative hypotheses being
Example 12.4 described a study in which salmon were introduced to 12 streams with and without brook trout to investigate the effect of brook trout on salmon survival. Is this an experimental study or
Using the data in Practice Problem 11, state whether each of the following sets of numbers (items a through f) is a possible permuted sample for use in testing the difference between the means of
Only about 6% of plant species have separate male and female individuals (a syndrome called dioecy). The rest of the species have individuals with both male and female parts (called monoecy). Why are
In Example 13.1, we described the results of a study that measured the change in biomass in marine areas after an increase in protection. The distribution of biomass ratios (i.e., the biomass with
Using the data in Practice Problem 11 on shell volume and the number of sperm stored, we carried out a bootstrap analysis of the correlation coefficient r between the two variables. The cumulative
The surface of plant leaves is a thriving ecosystem, home to many microorganisms such as bacteria. These bacteria can affect the health of the plant, because some cause disease and some serve as
The snail Helix aspersa has an unusual mating system. Each individual is a hermaphrodite, producing both sperm and eggs, but the truly bizarre part is that these snails have evolved a “love dart”
Assume that you have two moderately small samples, both drawn from separate populations that are normally distributed but with unequal variances. You want to compare the means of these two
Use a six-sided die to generate 10 bootstrap replicates of the following data set, which has three numbers from each of two groups:a. Write out the bootstrap replicate data sets.b. Use these 10
The most common use of the bootstrap in biology is to estimate the uncertainty in trees of evolutionary relationships (phylogenies) estimated from DNA sequence data. For example, the tree provided
The “broken stick” model is often used in ecology to represent how species should divide up space or resources if these are divided randomly. For example, Waldron (2007) compared the geographic
The following table lists the ANOVA results for the linear model fit to the data in Practice Problem 8.a. Explain in words what the F-ratio for WORKERTYPE measures.b. Explain in words what the
For gene has been found to underlie variation in foraging behavior in several insect species. Ben- Shahar et al. (2002) examined whether the gene might influence behavioral differences in the
The ejaculate of male Drosophila contains a protein, called SP, that reduces the life span of mated females. How the protein does this remains mysterious. One possibility is that the protein
Evidence is mounting that a part of the brain known as the hippocampus is crucial for tasks that depend on relating information from multiple sources, such as tasks requiring spatial memory.
Refer to Practice Problem 3.a. Write a complete model statement for a linear model to fit to the penguin data. Indicate what each term in the model represents.b. What are the null hypotheses tested
A study of the Magellanic penguin (Spheniscus magellanicus) measured stress-induced levels of the hormone corticosterone in chicks living in either tourist-visited areas or undisturbed areas of a
Examine the accompanying interaction plots. Each is based on hypothetical data from a factorial experiment with two factors A and B. In each case, indicate which of the main effects and interaction
Can the songs of extinct species be predicted? Gua et al. (2012) used measurements of living species of katydid to predict the call frequency, or “pitch,” of the extinct Archaboilus musicus based
Sex, with its many benefits, also brings risk. For example, individuals that are more promiscuous are exposed to more sexually transmitted diseases. This is true for other primates as well as for our
Is the scaling of respiratory metabolism to body size in plants similar to that found in animals, where an approximate 3/4-power relation seems to hold? The data below are measurements of aboveground
The forests of the northern United States and Canada have no native terrestrial earthworms, but many exotic species (including those used as bait when fishing) have been introduced. These immigrant
We are accustomed to thinking that the proportion of males at birth is fixed by genetics in birds and mammals to be close to 50%. Some have suggested, however, that the sex of offspring can be
Identify the assumption(s) of linear regression that is (are) violated in each of the following residual plots.(a)(b)(c)(d) Residuals X
Spot the flaw. Refer to Problem 14. Grover, a student who skipped reading Chapter 2 of this book, made the following graph when presenting the results of the needle-length study to his epidemiology
Social spiders live together in kin groups that build communal webs and cooperate in gathering prey. The following web measurements were gathered on 17 colonies of the social spider Cyrtophora
Previous studies have shown that the antibody titers in obese people are lower after vaccination than in people of normal weight. One suggested reason is that the vaccines may not effectively
James et al. (1997) demonstrated that the chemical hypoxanthine in the vitreous humor (the colorless jelly filling the eye) shows a postmortem linear increase in concentration with time since death.
Rattlesnakes often eat large meals that require significant increases in metabolism for efficient digestion. Snakes are known to adjust their thermoregulatory behavior after feeding, seeking out
The naked mole rat is a very unusual creature. For one thing, it is the only known mammal that is eusocial, with most individuals forgoing reproduction and instead helping to raise the offspring of
The ANOVA approach was used to test the null hypothesis of zero slope for the regression of lizard territory area on bite force (see Practice Problem 12), and it yielded the following
For each of the following scenarios or questions, say which method for hypothesis testing would be most appropriate to best answer the scientific question. Unless otherwise stated, make any necessary
Male lizards in the species Crotaphytus collaris use their jaws as weapons during territorial interactions. Lappin and Husak (2005) tested whether weapon performance (bite force in newtons) predicted
For each of the following scenarios, state what statistic would be used to estimate the effect of interest.a. How different are the two hospitals X and Y in the frequency of doctors who wash and do
To investigate whether subcutaneous fat provides insulation in humans, Sloan and Keatinge (1973) measured the rate of heat loss by boys swimming for up to 40 min in water at 20.3°C and expending
Hybrid offspring of parents of different species are often sterile. How different must the parent species be, genetically, to produce this effect? The accompanying table (Moyle et al. 2004) lists the
Collins and Bell (2004) investigated the impacts of elevated carbon dioxide (CO2) concentrations on plant evolution. They raised separate lines of the unicellular algae Chlamydomonas under normal and
In an analysis of the performance of Major League Baseball players, Schaal and Smith (2000) found that the batting scores of the top 10 players in the 1997 baseball season dropped on average in 1998.
Van Hylckama Vlieg et al. (2009) investigated the relationship between oral contraceptive use and thrombosis in women. In a sample of 1524 adult female patients who had thrombosis, 103 had taken oral
The following two graphs display data gathered to test whether the exercise performance of women at high elevations depends on the stage of their menstrual cycle (Brutsaert et al. 2002). In the upper
Mendel famously discovered the basics of genetics with garden peas. He proposed a law of independent assortment, that the inheritance of different genes should be independent. We now know that this
Most of us would like science to find ways to extend our lives. Genetic research has found some promising variants of genes in other organisms that greatly increase life span. Some mutations in the
What is the formula for each of the four regression lines shown on the following page?(a)(b)(c)(d) 3 2 1 0 0 NH 2 3
Spot the flaw. In their more recent study of “high-rise syndrome” (see Chapter 1), Vnuk et al. (2004) reported injury scores (0–4) of 119 fallen cats brought to a veterinary clinic in Zagreb,
Golomb et al. (2012) looked at whether higher chocolate consumption predicts higher body mass in humans. They fitted the data using a linear regression having chocolate consumption (number of times
Many species have “assortative mating,” meaning that a female is more likely to mate with a male that is similar to her in some particular feature, such as body size, than with a dissimilar male.
Calculation problem: Standard error and confidence intervals of the slope. How uncertain is our estimate of slope? Using the face ratio and hockey aggressive penalty data from Practice Problem 1,
Assume that the few remaining hairs on a balding man’s head occur independently of each other and with equal probability for each square centimeter (cm) of scalp. Imagine that this man has 2.3
The early movies by Eadweard Muybridge in the late 19th century showed for the first time the exact positions and movements of the legs during walking by horses and other large mammals. How much has
In some parts of the world, collisions with motor vehicles are a major source of mortality for some wildlife species. For example, a major cause of the decline of the koala population in Queensland,
Agricultural and industrial activity have substantially increased the reactive nitrogen content of the atmosphere. To investigate the potential consequences on ecosystems, Stevens et al. (2015)
African armyworm moths often migrate long distances in large numbers, devastating crops along the way. The direction of their movement is often downwind, raising the question of whether the moths
Biopsy is often used to distinguish cancerous from harmless tumors before resorting to surgery. Ridgway et al. (2004) investigated the ability of MIB- 1 monoclonal antibodies, which detect rapidly

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