genetics and evolution exam 3

Among the oldest fossils on Earth are the microfossils from the Agnes gold mine of South Africa, which are __________ years old.

3.2 billion

Which of the following statements regarding the benefit of making the switch from an RNA- to a DNA-based genetic system during the evolution of life is correct?

DNA is a more stable molecule because deoxyribose is less reactive than is ribose. In the RNA world, natural selection would have favored any transmission system that was more efficient than that of RNA and ribozymes. DNA is chemically more stable than RNA, primarily because DNA's deoxyribose sugar is less reactive than is RNA's ribose sugar. The double-stranded structure of DNA reduces the potential for outside molecules to interact with and disrupt the nitrogenous bases, while DNA replication systems also have proofreading capabilities that are not present in RNA replication. Read the subsection titled "From RNA to DNA" in Section 11.5 and compare the molecular structure of these molecules in Figure 11.24.

A number of evolutionary studies show a strong phylogenetic link between prokaryotic and eukaryotic cells. Which of the following is the best statement about the evolutionary origins of eukaryotic cells?

Eukaryotic "informational" genes are closely related to Archaea, while their "operational" genes are closely related to Bacteria.

Which of the following statements about LUCA is not correct?

It is meant to be a single organism.

Which of the following is correct regarding the endemic species as a model for the study of background extinction?

It is much easier to study extinction in endemic species because such local extinction becomes synonymous with global extinction.

Which of the following statements regarding the complexity of living organisms is not correct?

Natural selection always requires that organisms increase in complexity over evolutionary time.

Which gas was most likely the least abundant in early Earth's atmosphere?

O2

Which of the following statements about the Lincoln and Joyce experiment on self-replicating ribozymes is most likely correct?

The self-replicating ribozymes that had more efficient catalytic activities would soon began to dominate their populations.

Elevated levels of iridium are found in the geologic layer at the K-Pg boundary. Is this unusual?

Yes. Iridium is a rare metal on Earth.

Jablonski and his coworkers found that, for slugs and snails (gastropods) of the Late Cretaceous period, the key to a broad geographic range at the species level and increased chances of surviving the mass extinction at the K-Pg boundary was the nature of their larval stage. Which of the following best describes a stage that contributes to the increased geographic ranges of the gastropod taxa?

planktotrophic larvae that feed in the open water on very small prey and develop into adults at a relatively slow pace.Elevated levels of iridium are found in the geologic layer at the K-Pg boundary. Is this unusual?

If a researcher wanted to calculate the age of the planet Earth which radioactive element would he most likely use because of its long half life?

potassium

Fossils are the remains of past-living organisms that could form in several different ways. Which of the following describes fossilization by dissolution?

Water seeps into fossils and breaks it down, but the shape of the fossil is preserved in the sediment around, leaving an image of the organism.

Based on the abundant fossil records, only 10,000 years ago, two-thirds of the 150 genera of the Pleistogene megafauna that were present 40,000 years earlier had gone extinct. What seems to be the reason for this relatively recent extinction of so many large mammal species?

Hunting by humans, habitat fragmentation, and the ice age played a large role in this extinction.

Which of the following statements best explains secondary reinforcement?

If the reproductive isolating mechanisms that developed during the geographic isolation are somewhat weak but the hybrids between two populations have lower fitness, then the speciation process may continue.

Which of the following is not true regarding the evolution of multicellularity?

The transition from unicellular to multicellular life occurred only once in evolutionary history, giving rise to all multicellular organisms today.

Which of the following describes the phenetic species concept?

This concept looks at organisms that are clustered together in a phenotype space and is often used by numerical taxonomists. The phenetic species concept looks at organisms that are clustered together in a given phenotypic space, identifying clusters of individuals who share phenotypic similarities. Species boundaries are then defined by individuals or populations in a set phenotype space. This species concept is used by numerical taxonomists who apply quantitative methods to classify organisms. Read the subsection titled "Identifying Species" and examine Figure 14.2.

What type of infectious disease is devastating populations of frogs in North America, Alaska, and Australia today?

chytridiomycosis, which interferes with the ability of amphibians to transport chemicals across the epidermis Population decline and extinction of many of the Australian rain-forest frog species, as well as North American and other studied populations, shows that frogs are dying due to an infectious disease that causes damage to the inner organs, recently diagnosed as chytridiomycosis. A chytridiomycete fungus, Batrachochytrium dendrobatidis, is responsible. The distribution of the B. dendrobatidis worldwide corresponds to the high extinction rates, as seen in Figure 15.18 Laboratory treatments of the infected amphibians show that infected animals can be cured easily by using readily available fungicides.

Different races of the apple maggot fly have different breeding seasons depending on the host species they prefer (downy hawthorn or apple trees). Because of this temporal difference in breeding, which type of reproductive isolating mechanism is occurring?

prezygotic Because the two races are not interacting during their breeding seasons, which appears to be dictated by their host species, the apple maggot flies are not mating; therefore, fertilization does not occur. This indicates a prezygotic reproductive isolating mechanism. Read the subsection titled "Sympatric Speciation in the Apple Maggot Fly" and examine Table 14.2.

Among the oldest fossils yet discovered on Earth are microfossils from 600 meters below the Agnes gold mine of South Africa, which are __________ years old.

3.2 billion In 2010, Emmanuelle Javaux and her team of researchers published their findings regarding what they thought were possibly the oldest fossils on Earth, found below the Agnes gold mine of South Africa (Javaux et al. 2010). Using sediment samples that they obtained from drill holes, they discovered remarkable evidence of life that had existed billions of years ago—tiny fossils, called microfossils, which were approximately 3.2 billion years old. However, microfossils discovered by Wacey et al. (2011) may be even older, dating to 3.4 billion years old.

Radiocarbon dating (14C) is a useful tool for measuring absolute age for about __________ years into the past.

50,000 Radiometric dating is used as a measure of the absolute age of fossils. Since 14C has a short half-life of 5730 years, radiocarbon dating is a useful tool for measuring absolute age of relatively young fossils and archeological sites (such as human evolution) for no more than 50,000-75,000 years into the past; after this point, there is usually not enough 14C remaining to use the technique. Read about radiocarbon dating and other radioactive isotopes used in measuring the absolute age of fossils.

Why is the higher fidelity of DNA proofreading and repair (compared to RNA) evolutionarily important?

A lower mutation rate allows DNA to specialize in only functioning as a genetic storage system. DNA's proofreading and repair system dramatically lowers the mutation rate that occurs during synthesis, transcription, and translation. In turn, this allows DNA genomes to be much larger in size, allowing organisms to store and transmit much more genetic information than an RNA-based system. Scientists also hypothesize that this led to the specialization of DNA in to functioning exclusively as a genetic information storage system. Read Section 11.5.

Itay Budin and Jack Szostak sought to understand how cell membranes composed of single-chain lipid molecules could possibly evolve to the more complex phospholipids seen in modern cell membranes (Budin and Szostak 2009). Which statement best summarizes their results?

Adding a small fraction of phospholipid molecules resulted in vesicles with higher phospholipid content; these cells tended to grow in size conferring a selective advantage. Adding just a few phospholipid molecules slowed down the rate of movement of fatty acid molecules out of the membrane. This resulted in vesicles with the higher phospholipid content tending to grow in size, rather than shrink. Cells with a greater ability to synthesize phospholipids outcompeted other cells, leading to the evolution of membranes dominated by phospholipids. Read the subsection titled "Lipid Membranes and Reproduction in Early Cells" in Section 11.3, and examine Figure 11.16.

After confirming that Amphilophus citrinellus and Amphilophus zaliosus were indeed two species that originated from a single colonization of Lake Apoyo by their common ancestor, what evidence explained this was a sympatric speciation event rather than an allopatric speciation event?

Although Lake Apoyo is a very homogeneous habitat, body morphology in the two species supported speciation based on habitat and ecological specialization, rather than geographic separation. Sympatric speciation occurs when no geographic boundary separates two diverging populations. In this case, a single species colonized Lake Apoyo, which diverged into A. citrinellus and A. zaliosus even though the lake was very homogeneous with no geographic barriers to separate them. Body morphology indicated habitat and ecological specialization, with A. citrinellus displaying the classic benthic form seen in species that occupy lake bottoms while A. zaliosus displayed morphology consistent with species that are limnetic, preferring the open water. Read the subsection titled "Sympatric Speciation in Cichlids" and examine Figure 14.18.

Based on the figure shown, which of the following statements is correct?

Animals are the only group within the Opisthokont clade whose members are all multicellular. The transition from single-celled (unicellular) to multicelled (multicellular) organisms has occurred independently many times, in many taxa, over evolutionary history. This distribution of multicellularity across the tree of life is a dramatic example of convergent evolution. Examine Figure 12.12 and notice that in the Rhizaria and Excavate clades, all members are unicellular. In the Plants, Amoebozoa, and Opisthokonts, there are groups that have all unicellular members, both unicellular and colonial/multicellular forms, and all multicellular members. Animals are the only Opisthokonts whose members are all multicellular.

Why did the role of horizontal gene transfer ultimately become diminished over evolutionary time?

As cells became more complicated, they also became more integrated, less modular and less likely to take up new genes by horizontal gene transfer. The ready exchange of genetic information through horizontal gene transfer was an early driver of genetic diversity when early cells first evolved. As evolution continued, cells became more complicated in terms of their structure and function and less modular, reducing the likelihood of acquiring new genes via horizontal gene transfer. Read the subsection titled "Horizontal Gene Transfer" in Section 11.5.

In the cliff swallows studied by Charles and Mary Brown, it is common to find a blood-sucking parasite, an insect known as the swallow bug. This bug often clings to the feet of birds, can move from swallow to swallow within colonies, and is responsible for most of the nest failures and juvenile mortality in these birds (Brown and Brown 1996). The graph shows a correlation between the colony size and the number of bugs per nest. What conclusion(s) can we make based on this study?

As group size increases, the fitness cost of parasitism increases. The Browns documented the effects of swallow bugs in their experiment, providing strong evidence for the costs of parasitism. These parasites have a negative effect on fitness, but group living might have some benefits. The graph clearly shows that as group size increases, the cost of parasitism increases as well. In other words, as colony size increases, the number of swallow bugs per nest also increases. While the overall fitness effect of living in groups is positive for swallows, group living does not come cost free, and such costs are important to understand when analyzing the major transition from solitary to social living. Read the subsection titled "Parasite Transmission as a Cost of Increased Group Size" in Section 12.5 and examine Figure 12.28.

The human parasite Mycoplasma genitalium, with one of the smallest genomes of any organism that can be grown, as well as Chlamydia trachomatis, an obligate intracellular parasite, are examples of the types of organisms that functional genomics researchers have focused on. What is the main purpose of the study of such genomes?

By studying such genomes, researchers try to discover the basic and essential cellular functions of early life.

The human parasite Mycoplasma genitalium, with one of the smallest genomes of any organism that can be grown in a laboratory, as well as Chlamydia trachomatis, an obligate intracellular parasite, are examples of the types of organisms that functional genomics researchers have focused on. What is the main purpose of the study of such genomes?

By studying such genomes, researchers try to discover the basic and essential cellular functions of early life. Because of their associations with eukaryotic hosts, species like M. genitalium and C. trachomatis might have reduced metabolic requirements and hence reduced genome sizes. These species have small genomes as a consequence of reductive processes (the loss of genes that were no longer needed). They may share many features in common with simple early organisms and therefore help researchers to discover the essential cellular functions of early life. Read Section 11.6 and consider the types of bacteria with the smallest genomes mentioned in your book. What makes such genomes similar to early life and what makes them different?

Which of the following is FALSE regarding the evolution of chloroplasts?

Chloroplasts are derived from ancient free-living photosynthetic archaebacteria. In the evolution of chloroplasts, we can recognize their close relationship with modern photosynthetic cyanobacteria of the domain Bacteria. Chloroplast RNA shows close relatedness with a specific cyanobacteria lineage. Chloroplasts most likely originated from the free-living, photosynthetic cyanobacteria, before forming a symbiotic relationship with an ancestral eukaryotic species. Read the subsection titled "Endosymbiosis and the Evolution of Eukaryotic Organelles" in Section 12.2 and examine Figure 12.7.

Which of the following is true regarding the evolution of chloroplasts?

Chloroplasts are derived from once free-living photosynthetic cyanobacteria. Cyanobacteria are related to algal plastids. RNA shows that the chloroplasts of plants are closely related to cyanobacteria.

In light of recent achievements in the field of genomics, would it be reasonable to expect that the use of comparative genomics might shed light on the extinct genomes of early life?

Comparative genomics and studies of bacteria with very small genomes shed light on a common ancestor, and researchers can estimate the minimal characteristics that a cell would need to operate as a living organism. Although we cannot make direct phylogenetic inferences about what organisms were like prior to the last universal common ancestor (LUCA), better understanding of what kinds of genes are present in the genomes of extant organisms can help us to make guesses about pre-LUCA genomes. This is why learning about the minimal genomes and their function in living species provides an idea about what kinds of genes may have been present in early forms of life. Read Section 11.6.

Evolutionary biologists are very interested in understanding the patterns and processes that guide the tempo and mode of evolution. In specific clades, they sometimes point to trends (patterns of directional change over time). One such trend is also known as Cope's rule. Which of the following statements is TRUE?

Cope's rule states that species in mammalian clades tend to increase in body size over evolutionary time Paleontologist Edward Cope originally stated his rule as the observation that mammalian lineages tended to increase in body size during the Cenozoic era. Studies of Cope's rule have since been extended to other groups and other time periods. For example, bird taxa appeared to follow Cope's rule throughout the Jurassic and Cretaceous periods (Hone and Benton 2005; Butler and Goswami 2008). But Cope's rule—like most other evolutionary trends—is not universal. During the Cretaceous, groups such as bivalves and gastropod mollusks did not change according to its predictions. Read the subsection titled "Evolutionary Trends" and think of some other possible examples of Cope's rule, as well as its exceptions.

What is the most relevant hypothesis for the benefit of making the switch from the RNA- to a DNA-based genetic system during the evolution of life?

DNA is a more stable molecule because deoxyribose is less reactive than is ribose.

The Hawaiian Islands have gone through at least two waves of human colonization (in prehistoric times and again starting in the seventeenth and eighteenth centuries). Of the approximately 125 to 145 bird species that once inhabited the Hawaiian Islands before human colonization, 90 to 110 are now extinct. Which of the following is most likely true when it comes to these extinctions?

Early human colonization devastated the larger species of birds through hunting. Late human colonization devastated the natural habitats and food sources, such as flower nectar and fruit of the native species.

The Dobzhansky-Muller model explains hybrid infertility in crosses between two close species (such as the fruit flies D. simulans and D. melanogaster). Which of the following is the best explanation of this model?

Epistatic interactions between the alleles of two or more loci, undergoing different evolutionary paths in the two speciating groups, lead to the fitness costs of hybridization.

The Dobzhansky-Muller model explains hybrid infertility in crosses between two close species (such as the fruit flies D. simulans and D. melanogaster). Which of the following is the best explanation of this model?

Epistatic interactions between the alleles of two or more loci, undergoing different evolutionary paths in the two speciating groups, lead to the fitness costs of hybridization. In the Dobzhansky-Muller model, hybrids between two sister species suffer lower fitness and, because of that, less chance of survival and reproduction. This model is based on epistatic interactions between loci A and B. For example, if an ancestral species had two alleles, A1 and B1, with positive epistatic interaction, but an allele A2 emerges and sweeps to fixation in population 1 while allele B2 emerges and sweeps to fixation in population 2, epistatic interactions between the A and B loci result in a fitness cost to individuals with both the A2 and B2 alleles. As a result, hybrids are selected against, driving reproductive isolation between individuals in population 1 and population 2. Read the subsection titled "Reproductive Isolation via Dobzhansky-Muller Incompatibility" and examine Figure 14.30.

A number of evolutionary studies show a strong phylogenetic link between prokaryotic and eukaryotic cells. Which of the following is the best statement about the evolutionary origins of eukaryotic cells?

Eukaryotic "informational" genes are most closely related to archaeal genes, while their "operational" genes are most closely related to bacterial genes. Despite the earlier studies on complex cellular structures, which made controversial predictions regarding the origin of eukaryotic cells, today we know that they have genes from both prokaryotic domains of life, Archaea and Bacteria. The eukaryotic "informational" genes (associated with transcription and translation) are most closely related to archaeal genes, whereas "operational" genes (associated with metabolic processes, cell membrane formation, and so on) are most closely related to bacterial genes. Read about the different hypotheses regarding the origin of eukaryotic cells in Section 12.2 titled "Major Transition; The Evolution of the Eukaryotic Cell."

An analysis by Maria Rivera and James Lake suggests that ancient eukaryotic cells emerged from the fusion of an archaeal cell (most likely from the phylum Eocyta) and a bacterium (Rivera and Lake 2004). Which of the following is correct regarding this working hypothesis?

Eukaryotic cells probably evolved through endosymbiosis, in which either the archaeal or bacterial cell was engulfed within the other. Eukaryotic cells might have evolved because of symbiosis within a cell (endosymbiosis), in which either the archaeal or bacterial cell type began residing within the other, most likely when one cell engulfed the other but did not metabolize it. Through time, this relationship became a mutualistic one in which each provided benefits to the other and such symbionts became dependent on one another for survival and/or reproduction. There is some recent evidence, however, that this relationship began when a bacterial cell became integrated into an archaeal cell. Read the subsection titled "Endosymbiosis and the Evolution of Eukaryotic Organelles" in Section 12.2.

This figure illustrates the concept of a ring species formation in Ensatina eschscholtzii salamanders in California. The species originated in northern California and southern Oregon and then expanded south along the Sierra Nevada range. Which statement accurately describes gene flow and gene patterns in these populations?

Gene flow decreases as you move south, resulting in the southern populations being more genetically distinct from one another than other populations. A ring species exists when individuals living in one of a series of populations establish in a ring, usually as a result of some geographic barrier reducing or eliminating gene flow from the populations as they colonize. In this example, the salamanders migrated south in parallel groups and were separated by the hot, dry Sacramento and San Joaquin valleys, with one group of populations on the Pacific side and the other group of populations on the continental interior side. Gene flow was not consistent and the southernmost populations were more genetically distinct from each other than other populations in the ring. Read the subsection titled "Ring Species" and examine Figures 14.15 and 14.16.

The following graphs show three different types of evolutionary change in a hypothetical clade. The y axis represents time, while the x axis represents a character (body size, in this example). Which of the following graphs represents an active evolutionary trend?

Graph C Active trends may arise when the distribution of trait values in a clade shifts because the body size within each subgroup shifts too. As a result, each lineage tends to increase in body size (as shown in graph C). If there is no evolutionary trend, body size is as likely to increase as to decrease (graph A). If we find a clade with a visible trend, such as an increase in body size over time, but with no directional tendency to change, we would call this a passive trend (as illustrated in graph B). Read about the distinction between passive and active trends in the subsection titled "Evolutionary Trends" in Section 15.5, and examine the graphs in Figure 15.41. Look at a study that links an active trend to the underlying selective conditions (Figure 15.42) and examine the active trend in the selective mechanism behind Cope's rule.

Which of the following is FALSE regarding the evolution of group living?

Group living provides many benefits, but it does not improve foraging success (finding food). Group living provides a suite of benefits, including benefits associated with foraging and safety from predators. Living in groups requires a degree of sociality that is not required for solitary living, and often entails new levels of coordination and communication between individuals to obtain such benefits. According to E. O. Wilson, we can define a group as "a set of conspecific individuals that affect each other's fitness" (Wilson 1980). There is tremendous variation in the types of groups found throughout nature. Read about the evolution of group living and Wilson's definition of a group in the introductory paragraphs of Section 12.5 titled "Major Transition; Solitary to Group Living."

What do we know about horizontal gene transfer (HGT) in the evolution of early life?

HGT was probably a powerful force during early cell evolution, leading to complex cellular organisms. The abundance of genomic evidence indicates that horizontal gene transfer (HGT) has played an important role in the evolution of contemporary prokaryotes and their genomes. Most likely, HGT was also very important in their early history. Carl Woese hypothesized that during early cell evolution, HGT was a powerful force that led to the development of more complex cellular organisms (1998). In those early cells, many functions would have been modular and the HGT would have been a primary means for propagating copies of a gene. See Section 11.5.

In 1977, Sidney Fox tried a different approach to testing the prebiotic synthesis of biological molecules. He mixed a number of different amino acids together at a high temperature (120°C) in an environment lacking water. When he subsequently placed the mixture into water to investigate what the amino acids would form, what happened next?

He found some peptide-like structures, but the bonds between the amino acids were weak and unstable. After the experiments of the 1950s and 1960s, many controversies remained regarding the prebiotic soup model. For instance, the sugar ribose was found in very low supply, and a mechanism for joining the amino acids together to make proteins was completely absent. Sidney Fox mixed a number of different amino acids together at a high temperature (120°C) in an environment lacking water (Fox and Dose 1977). When he mixed large amounts of aspartic acid and glutamic acid, and subsequently placed the mixture into water, the amino acids present were strung together in a peptide-like structure. The bonds between the amino acids, however, were weak and unstable. Subsequent work by Claudia Huber and her colleagues found that amino acids do link together via stable peptide bonds in the presence of a compound such as carbon monoxide (CO), which is thought to have been present in early Earth's atmosphere. Read Section 11.2 titled "The Origin and Evolution of the Building Blocks of Life".

The Hawaiian Islands have gone through at least two waves of human colonization (in prehistoric times and again starting in the seventeenth and eighteenth centuries). Of the approximately 125 to 145 bird species that once inhabited the Hawaiian Islands before human colonization, 90 to 110 are now extinct. Which of the following is most likely TRUE when it comes to the first wave of extinctions?

Human colonization devastated the larger species of birds through hunting. Stuart Pimm and Alison Boyer found evidence that 30 species of land-dwelling birds went extinct during the first wave of human colonization, but just since 1800, at least 19 additional Hawaiian bird species have gone extinct (Pimm et al. 1994, 1995; Boyer 2008). The causes of these large background extinctions are multifactorial (for example, disease introduced by humans, predation by humans and human-introduced species, competition with human-introduced species, and destruction of the native habitat by humans have acted together). Since large species disappeared during the early colonization, they may have been hunted as easy, less mobile prey. Meanwhile, evidence suggests that the recent colonization led to destruction of the natural habitat and species-specific food resources. Read the subsection titled "Multiple Causes of Background Extinction."

By 10,000 years ago, two-thirds of 150 genera of the Pleistocene megafauna that were present just 40,000 years earlier had gone extinct. What seems to be the reason for this relatively recent extinction of so many large mammal species?

Hunting by humans, habitat fragmentation, and the ice age played a large role in this extinction. During an ice age about 18,000 years ago, temperatures were significantly colder than modern temperatures, both at low and high altitudes. These changes would have had direct and indirect effects on survival by changing the food chain, and hence the diet of megafauna. Human hunting seems to have played a role in these extinctions, as archeological remains suggest that human hunters in this period had superior weapons compared to their predecessors. Pleistocene megafauna were probably already on the decline as a result of environmental change, so the intense degree of human hunting may have caused the extinction of almost 100 genera. Read the chapter Introduction and examine Figures 15.2 and 15.3.

Two parapatric subspecies of sagebrush (mountain big sagebrush and basin big sagebrush) produce hybrid sagebrush, which often is found in the intermediate elevation. In the following graph, you can see a relative composite fitness for each of them, raised in three different environments (below 1800 meters in the basin zone, above 1900 meters in the mountain zone, and in the hybrid zone between 1800 and 1900 meters). Which of the following best explains the findings in this experiment?

Hybrids had significantly better fitness than the other subspecies in the hybrid zone, supporting the bounded hybrid superiority model. The basin big sagebrush grows up to elevations of about 1800 meters, while mountain big sagebrush can be found at elevations above 1900 meters. Between 1800 and 1900 meters, the two subspecies form a narrow hybrid zone. To distinguish between the dynamic equilibrium and the bounded hybrid superiority models, Han Wang and his colleagues (Wang et al. 1997) ran a series of reciprocal transplant experiments and found that hybrids have the highest fitness in their zone, but not at higher or lower elevations. Since the ecologically neutral dynamic equilibrium model suggests that hybridization produces hybrids that are always inferior to nonhybrids, these results do not fit such a prediction. Instead, hybrids have superior fitness in their zone to nonhybrids, and the results support an ecologically dependent bounded hybrid superiority model.

How does the dominance theory explain why the heterogametic sex is at a disadvantage in Haldane's rule?

If a recessive allele linked to a sex chromosome has a negative effect on the fitness of hybrids, that allele will always be expressed in the heterogametic hybrids that possess that allele because they only have one copy of the sex chromosome that carries the allele. The example from the textbook explains this best. If the male is the heterogametic sex, and a recessive allele on the X chromosome has a negative fitness effect on the hybrid, those effects will not be expressed in the XX female hybrids. Because males only have a single X chromosome, the effects of the recessive X-linked allele are always expressed and will therefore have a negative fitness effect on male hybrids. Read the subsection titled "Haldane's Rule, Sex Chromosomes, and Reproductive Isolation."

Which of the following defines Haldane's rule and its predictions?

If among hybrid offspring one sex is absent, rare, or sterile, that sex is heterogametic (has two different sex chromosomes). In mammals and fruit flies, males (XY) are heterogametic and females are homogametic, and so Haldane's rule predicts that if one sex formed from the hybridization of incipient species is inviable or sterile, it will be males. In birds and butterflies, on the other hand, females are heterogametic and males are homogametic, and so female hybrids should be the ones that are inviable or sterile. Read the subsection titled "Haldane's Rule, Sex Chromosomes, and Reproductive Isolation."

Which of the following statements best explains secondary reinforcement?

If the reproductive isolating mechanisms that developed during the geographic isolation are somewhat weak but the hybrids between two populations have lower fitness, then the speciation process may continue. In the process of allopatric speciation, geographic barriers may be temporary and if the reproductive isolating mechanisms are sufficiently weak to allow the interbreeding across the reunited populations, then typically the speciation process will halt and a single species will remain. If the hybrids between the two populations have some fitness disadvantage when compared to offspring derived from mating between individuals from within either population, then we use the term secondary reinforcement. Such populations will continue to diverge, even if they appear to be sympatric. Read Box 14.2 titled "Secondary Contact" and examine Figure 14.22.

Why did the human introduction of feral pigs on Santa Cruz Island accelerate the extinction of the native island fox and increase the population of skunks?

Increased pig numbers attracted the golden eagle, which is a fierce predator of foxes, and skunks (the main prey of island foxes) therefore increased in population size. As in many cases observed in conservation biology studies, there are multiple indirect effects of the introduction of nonnative species by humans. In the case of Santa Cruz Island, these are the indirect effects of predation and extinction, which involve several species. The increased feral pig numbers led to more golden eagles visiting the island. The eagles also began attacking foxes, and that almost led to their extinction, although there were small numbers of individuals remaining. The fact that there were almost no foxes on the island led to an increase in the number of skunks, because they previously were hunted by the native island foxes. Read the subsection titled "Predation, Extinction, and Indirect Effects" and Examine Figure 15.15.

Why did the human introduction of feral pigs on Santa Cruz Island accelerate the extinction of the native fox and increase the population of skunks?

Increased pig numbers attracted the golden eagle, which is a fierce predator of foxes. Skunks were the main prey of the island foxes.

Which of the following is correct regarding the endemic species as they relate to the study of background extinction?

It is much easier to study extinction in endemic species because such local extinction becomes synonymous with global extinction for that species. Endemic species are those that are only found in one specific location or area. Because of their limited range, extinctions are common in such species. It is much easier to study extinction in endemic species because local extinction becomes synonymous with global extinction. Read the beginning of Section 15.2 and examine Figure 15.11 titled "Endemic hot spots."

Which of the following statements about LUCA is NOT correct?

It refers to a single, ancestral organism. The last universal common ancestor (LUCA) itself was not the first life-form, nor was it the only life-form present at the time. Although LUCA is the base of the phylogeny of life by definition, it was not conceptualized as a single individual, but rather as a population. Finally, LUCA is also a point in the history of life beyond which phylogenetic analysis cannot see, referred to as the "phylogenetic event horizon." Examine the hypothetical tree of life in Figure 11.5.

Which of the following statements regarding the Midas and Arrow cichlids in Lake Apoyo does NOT suggest that the speciation event responsible for forming these two species occurred in sympatry rather than allopatry?

Lake Apoyo is large, creating geographic isolation between the two species. There are several lines of evidence that suggest the speciation event responsible for forming these two cichlid species occurred in sympatry rather than allopatry. Although Lake Apoyo is small, there must be a mechanism to promote reproductive isolation and speciation of the Arrow cichlids. There appears to be an ecological "divide" in Lake Apoyo (bottom-of-the-lake and open-water areas), offering different environmental resources for these two species. Read the subsection titled "Sympatric Speciation in Cichlids" and examine Figure 14.18.

Biologists have documented asexual reproduction in some animal lineages. Even in some vertebrates, such as reptiles, some species reproduce only with parthenogenesis (development from unfertilized eggs). However, parthenogenesis has never been documented in mammals. What is the current genetic explanation for this difference between mammals and other vertebrates?

Mammals evolved a process of genetic imprinting and therefore some genes from father's genomes need to be expressed.

Biologists have documented asexual reproduction in some animal lineages. Even in certain vertebrates, such as reptiles, a few species reproduce only with parthenogenesis (development from unfertilized eggs). However, parthenogenesis has never been documented in mammals. What is the current genetic explanation for this difference between mammals and other vertebrates?

Mammals evolved a process of genetic imprinting and therefore some genes from the father's genomes need to be expressed. Once species move to a higher level, they often cannot revert to their previous states. For example, parthenogenesis would be favored over sexual reproduction because the mothers would pass down their entire genome. Although recombination and meiosis play an important role in the evolution of sexes, some species do fine with asexual reproduction alone. Recombination is present in mammals and other animals alike, but only mammals evolved extensive genetic imprinting, where alleles are differentially expressed according to whether they are inherited from the mother or the father. In any potentially asexual mammal species, parthenogenically produced offspring would have a mother but not a father, and they would thus fail to express a number of important genes that are expressed only from the paternally derived copy. Read the subsection titled "Explaining Major Transitions" in Section 12.1. Think beyond this example of sexual reproduction and consider how after a transition, the higher-level individuals get "locked in" by some detail of their biology.

What is the meaning of the phrase "dead clade walking," which was coined by David Jablonski in 2002?

Many of the clades that survive a period of mass extinction go extinct during the following geological time period. Jablonski found that the geological time periods immediately following four of the five mass extinctions he examined were marked by the subsequent loss of 10% to 20% of the orders of marine invertebrates that had survived the mass extinction (Jablonski 2002). This rate of extinction was significantly greater than that seen in the geological time period immediately preceding the mass extinction, providing evidence that the post-mass extinction losses were higher than normal background extinction in the marine invertebrate orders in question. Examine Figure 15.24.

This figure illustrates the results of selection for yeast strains that are well adapted to either high-salt or low-glucose environments. Over the course of selection, many mutations have occurred in populations in both environments. If the Dobzhansky-Muller model applies to this experiment, what do you predict will happen if the two strains produce a hybrid?

Matings between individuals from the two strains will have reduced reproductive success compared to the controls. Using the Dobzhansky-Muller model, we would predict that the hybrids would have reduced reproductive success due to epistatic interactions between alleles. New alleles arise as the result of mutations; those mutations are then selected for or against depending on the environment in which they occur. Read the subsection titled "Reproductive Isolation via Dobzhansky-Muller Incompatibility" and examine Figure 14.31.

Which of the following statements regarding the complexity of living organisms is FALSE?

Natural selection always results in an increase of complexity over evolutionary time. The structure of an animal body, for example, is much more complex and larger than that of any early life-form. The same is true along any number of branches of the tree of life; yet there is nothing in the process of evolution by natural selection that should necessarily entail a buildup over time of complexity. Indeed, along some branches of the tree of life, such as bacteria and archaea, there has been very little increase in complexity for billions of years. Examine Figure 12.2 and think about the branches of the tree of life that did not change for millions or even billions of years, as well as groups that have lost complexity (due to parasitic lifestyle, for example).

The origin of cell structures might be hypothesized to have involved a hypercycle, based on mutualism at the molecular level. Which of the following is correct regarding the hypercycle model?

Natural selection will favor a hypercycle that is enclosed in a membrane. Molecular mutualisms may have been important among replicators in the RNA world. The hypercycle model proposed that if the replicators are enclosed in a membrane and the replication rate of the membrane-bound ensemble depends on the replication rate of the RNA species within, then natural selection will favor the hypercycles in which one RNA species increases the rate of replication of the others. On the contrary, in a hypercycle without a membrane, natural selection favors variants that increase their own rate of replication, but not those that increase the rates of others. Read the subsection titled "Hypercycles" in Section 11.3 and examine Figure 11.16.

Which gas was most likely the LEAST abundant in early Earth's atmosphere?

O2 Based on evidence from chemistry and physics, methane (CH4), hydrogen (H2), ammonia (NH3), and water (H2O) might best represent the components of early Earth's atmosphere (about 4 billion years ago). Oxygen (O2) would not be expected to have been in this atmosphere. See Section 11.2.

Which two scientists elaborated on Darwin's idea of the "warm little pond" and formulated the "prebiotic soup hypothesis" as the first hypothesis for the abiotic origin of life on Earth?

Oparin and Haldane In the 1920s, both Aleksandr Oparin and J. B. S. Haldane elaborated on Darwin's "warm little pond" idea and proposed the first scientific hypothesis for the origin of life on Earth. They hypothesized that in a reductive atmosphere (in the absence of oxygen), some available sources of energy, such as ultraviolet light and lightning, might have helped to convert atmospheric gases into a range of molecules that served as the basis for early life on Earth.

It is very difficult to find the fossil remains of an entire organism. Which of the following is NOT a factor that paleontologists use when choosing sites to search for the best fossils?

Paleontologists typically select novel, unexplored areas to search for fossils as this is the best method to fill gaps in information that we see in the fossil record. There are many examples of how paleontologists find clues to some amazing fossil discoveries. They first look for fossils in the areas that might be conducive to fossilization. For example, in Figure 15.8, we can see how important for fossilization the anoxic conditions were. It is also common for paleontologists to search for fossils in their area of expertise at sites that are discovered to have many fossils in general. Finally, it is important to follow the clues from biogeography and phylogeny in choosing the site of interest. These three factors are not mutually exclusive, and in fact, it is a combination of all three that lead paleontologists to choose their sites for excavating the fossil record.

As opposed to background extinction, a mass extinction typically refers to the loss of many groups of organisms over a broad geographic range. Which of the following mass extinction in Earth's geological history was the most devastating for the marine families?

Permian

As opposed to background extinction, a mass extinction typically refers to the loss of many groups of organisms over a broad geographic range. Which of the following mass extinctions in Earth's geological history was the most devastating for the marine families?

Permian Several mass extinctions have been well documented in Earth's geological history—the Ordovician, late Devonian, late Permian, Triassic, and at the Cretaceous-Paleogene boundary. One of the most striking extinctions happened at the end of the late Permian when about 80% to 96% of all marine species went extinct. Examine Figure 15.23 and read the subsection titled "The Permian Mass Extinction."

The first genetic material on Earth was most likely __________.

RNA In 1986, Walter Gilbert coined the phrase "RNA world" to describe the first forms of life on Earth (Gilbert 1986). In support of this, there is some evidence that ribose, phosphate, purines, and pyrimidines likely existed in the prebiotic environment. Scientists also hypothesized that if these compounds had bonded together, RNA-based life-forms might have resulted. Read Section 11.4 titled "RNA World.".

Based on the phylogeny of Lepidosauria, if two sister species from the _____ clade were lost to extinction, this would prune the tree only slightly and would cause only a minimal loss of phylogenetic history. But if the two species of _____ were to go extinct, this loss would prune away a piece of phylogenetic history dating back to well before the divergence of snakes and lizards.

Serpentes, Tuataras If an extinction results in the loss of the longest branch on a phylogeny, this also represents the greatest loss of phylogenetic history. In this example, the loss of the tuataras would be a loss of the longest branch in this phylogeny, and therefore a loss of the greatest phylogenetic history. Losing the two sister species of Serpentes snake, however, would be a loss of the shortest branch and therefore the least phylogenetic history. Read the subsection titled "Extinction and Phylogenetic History."

Slime molds are unusual eukaryotes. They spend most of their life cycle as single-celled organisms, and yet under certain conditions, they form a slug-like multicellular stage and then a fruiting body composed of both somatic cells and reproductive spores. The best known species of slime mold is a soil dweller, Dictyostelium discoideum. Why is it important to study this and related species of slime molds?

Slime molds provide clues as to how multicellularity may have evolved. Slime molds can tell us how one of the most important transitions in evolutionary history may have occurred. They provide hints about the evolution of multicellular organisms. In the life cycle of a free-living soil slime mold, D. discoideum, if food supplies become scarce, between 8000 and 500,000 single-celled individuals come together and form a multicellular slug. The slug then migrates to an area closer to the surface of the soil, where reproduction occurs, and breaks up into a collection of what are called fruiting bodies. There are both somatic and reproductive cells inside the fruiting body, and the reproductive cells continue the life cycle as single-celled organisms again. Read the chapter opener example and examine Figure 12.1.

Slime molds are unusual eukaryotes. They spend most of their life cycle as single-celled organisms and yet, under certain conditions, they form a slug-like multicellular stage and then a fruiting body composed of both somatic cells and reproductive spores. The best known species of slime mold is a soil dweller, Dictyostelium discoideum. Why is it important to study this and related species of slime molds?

Slime molds provide hints as to how multicellularity may have evolved.

Identify which of the given examples is the best match for the following statement. "Individuals give up the ability to reproduce independently, and they join together to form a larger grouping that shares reproduction."

Solitary individuals start living together in colonial groups, sometimes even giving up the possibility of independent replication, as we see in many species of social insects. This process can be found throughout evolutionary history, from primordial life-forms to unicellular organisms joined together to form multicellular creatures. Similarly, repeatedly, and along numerous branches of the tree of life, solitary individuals started living together in colonial groups, even giving up the possibility of reproduction or independent replication. Social insects are a good example of this phenomenon. Read Section 12.1 titled "Overview of Major Transitions" and compare the major transitions with some of the processes they encompass.

Which of the following findings regarding the Midas and arrow cichlids in Lake Apoyo suggests that the speciation event responsible for forming these two species occurred in sympatry rather than allopatry?

The Midas and arrow cichlids are a monophyletic clade. Lake Apoyo is small, shallow, and homogeneous. Not even one mitochondrial haplotype was found in any other Nicaraguan lake that was the same as those found in the two Lake Apoyo species.

In the common bluegill sunfish, foraging in small groups increases success in finding food. They feed on small, aquatic insects that live in underwater vegetation, and when bluegills forage together, they are able to flush out many more insects. Which of the following is correct in this case of group foraging?

The bluegill example illustrates a "passive" benefit of group foraging. The common bluegill sunfish (Lepomis macrochirus) is used as an example of passive benefits of group living (in this case, foraging). Bluegills feed as solitary individuals, but foraging success per fish often increases as a function of group size. They feed primarily on small, aquatic insects that live in underwater vegetation. Aquatic insect prey are quite difficult to catch in such vegetation, but when fish are present in the same place and foraging together, they have more success in finding their prey. However, this is not a result of active communications or complex social structures, characteristic for some other groups of animals. Read the subsection titled "Foraging in Groups" in Section 12.5.

Over the last few decades, there has been a major decline in amphibian populations worldwide, including the extinction of many amphibian species. Which of the following is FALSE regarding the amphibian decline?

The extinctions seem to be due to the increased predation of amphibians around the world. The amphibian decline in the last 30-40 years has been devastating. The rate of this decline is much higher than typical background extinction (41% to 100% in parts of North America, Australia, New Zealand, and other regions). Perhaps many factors contribute to this steep increase in extinction rates in amphibians, yet one of the major culprits seems to be infectious disease. The studies have shown deadly infections with parasitic fungi and perhaps some other pathogenic agents in the freshwater environments. Read the section "Extinction and Disease" and examine Figure 15.17 on "Amphibians throughout the world."

Two parapatric subspecies of sagebrush (mountain big sagebrush and basin big sagebrush) produce hybrid sagebrush, which is often found in the intermediate elevation. In the following graph below, you can see germination early survival rates for each of them raised in three different environments (1,800 meters, above 1,900 meters, and in the hybrid zone between). Which of the following best explains the findings in this experiment?

The hybrid individuals had lower fitness in environments below 1,800 m and above 1,900 m, but a higher fitness than either subspecies when all types were raised in the hybrid zone. These results provide support for the bounded hybrid superiority model.

Eugene Koonin and his colleagues used the distributions of genes in the minimal gene sets of Haemophilus influenza and Mycoplasma genitalium to predict the distribution of a minimal gene set for Bacillus subtilis (Koonin 2003). What did they conclude from their comparison?

The predicted distribution of genes in B. subtilis was a close fit to the minimal gene sets observed. Minimal gene sets comprise the bare minimum of genes necessary for an organism to function (think metabolism, replication, repair, translation, etc.). Using the known minimal gene sets of H. influenza and M. genitalium, Koonin was able to predict a minimal gene set for B. subtilis before determining the minimal gene set experimentally. Minimal gene sets are a way of predicting and studying what actually constitutes the most basic cellular functions, perhaps giving us a glimpse of what early life-forms were like. Read Section 11.6.

Which of the following statements about the Lincoln and Joyce experiment on self-replicating ribozymes is most likely correct?

The self-replicating ribozymes that had more efficient catalytic activities would soon began to dominate their populations. After establishing that the template RNAs in this system could self-replicate, Lincoln and Joyce conducted an experiment in which several variant template molecules were supplied with variant substrate molecules (Lincoln and Joyce 2009). This variation was heritable, and different templates replicated at different rates. They also found evidence for selection, because the self-replicating ribozymes that had more efficient catalytic activities soon began to dominate their populations of self-replicating ribozymes. Read Section 11.4 and examine Figure 11.23.

Which of the following suggests that sympatric speciation is occurring in Rhagoletis pomonella (the apple maggot fly)?

The sympatric races of the apple maggot fly are diverging, and potentially on the path to becoming separate species as evidenced by fruit preference documented in the maggots. The apple maggot fly has formed two sympatric races that are diverging, and potentially on the path to becoming separate species. Studies show that these races (or incipient species) of R. pomonella have evolved specific adaptations that correspond to the different fruiting times of their host (for instance, apple trees produce fruit three to four weeks earlier than hawthorn trees). They also have evolved adaptations to fruit size and nutrient content. The choice of one over another fruit may lead to the further reproductive isolation and accumulation of genetic differences. Read the subsection titled "Sympatric Speciation in the Apple Maggot Fly" and examine Figure 14.19.

Which of the following is true regarding speciation in Rhagoletis pomonella (the apple maggot fly)?

The sympatric races of the apple maggot fly are indeed diverging, and potentially on the path to becoming separate species.

Which of the following is FALSE regarding the evolution of multicellularity?

The transition from unicellular to multicellular life occurred only once in evolutionary history, giving rise to all multicellular organisms today. The transition from single-celled to multicelled organisms has occurred independently many times, in many taxa, over evolutionary history. We most often think of multicellularity as an obligate condition (something that cannot be changed). Yet, in the early evolution of multicellularity, cells may very well have often joined together and then disbanded, which helps us to understand the early multicellularity as a temporary, rather than a fixed, condition. Read Section 12.3 titled "Major Transition; The Evolution of Multicellularity" and examine Figure 12.12.

Many species of mammals and birds are known to live in close communities, while other species live solitary lives. What do we know about the benefits of sociality, such as that observed in cliff swallows?

There is often a significant positive correlation between group size (such as colony size in cliff swallows) and survival rate of the population. Group living provides fitness benefits and increased protection from predators, which promotes evolutionary transition to social groups, not once, but multiple times in the phylogenetic history of birds, mammals, and many other animal lineages. For example, in cliff swallows, survival probability is a function of group size. Their nests are often clustered together on the side of cliffs, and it is evident that the relationship between colony size and survival is positive and statistically significant. It is also important in this species, as well as in many other bird species, to note that as colony size increases, the number of eggs that fail to hatch decreases. Examine Figure 12.27.

Many species of mammals and birds alike are known to live in close communities, while other species live solitary lives. What do we know about the benefits of sociality?

There is often a significant positive correlation between group size, such as, for instance, colony size in birds and survival rate of the population.

The apicoplast is an organelle found only in species in a phylum called Apicoplasta. This phylum includes a deadly human parasite, Plasmodium falciparum, which is responsible for malaria. Which of the following is FALSE regarding the apicoplast organelle?

There was only one endosymbiosis event, which probably involved a large cyanobacterium engulfed by a protozoan cell, and they both developed second membranes for protection. Researchers have reconstructed the history of the apicoplast and today this knowledge is very important in developing methods to combat malaria. The apicoplast arose through a secondary endosymbiotic event. The initial eukaryote (probably red algae) arose by primary endosymbiosis in which one prokaryotic host engulfed a cyanobacterium. Once the ancestral algal species became involved in an endosymbiotic relationship with its original eukaryotic host, it lost its photosynthetic abilities. This eukaryote was then engulfed by another single-celled eukaryote, producing a second endosymbiotic event. Today, we know that apicoplasts produce at least 500 gene products in Plasmodium. Read Box 12.1 and examine Figures 12.10 and 12.11.

The famous Cretaceous-Paleogene (K-Pg) extinction occurred about 65 million years ago, close to the boundary between the Cretaceous and Paleogene periods, with profound effects on many different taxa, including the dinosaurs. Which of the following is widely accepted as the cause of this extinction?

This mass extinction occurred as a result of an impact with an extraterrestrial body, such as an asteroid, as evidenced by the layer of clay demarcating the K-Pg boundary that contains iridium. Walter Alvarez, a paleontologist, began exploring the idea of an extraterrestrial cause for the K-Pg mass extinction. He found that the extinction could not have been gradual, as proposed earlier, and that it most likely had something to do with an asteroid, approximately 10 kilometers in diameter, which struck Earth 65 million years ago. The discovery of 30-fold increased levels of iridium near the K-Pg boundary in some 50 different sites around the world confirms this possibility. Read the subsection titled "Cretaceous-Paleogene (K-Pg) Mass Extinction."

The painted turtle (Chrysemys picta) has an amazing physiology that tolerates wide swings in temperature and oxygen levels and has a wide geographic distribution in North America. In the winter, it goes into hibernation under the ice of the ponds in which it lives and has been observed to tolerate anoxic conditions for up to 170 days at 3oC. What would you predict about this species' ability to survive environmental perturbations that can lead to an extinction event?

This species has a high probability of surviving. This species likely would have a high probability of surviving because it has multiple characteristics that are conducive to surviving environmental perturbation. It has a wide geographic range, and can survive anoxic conditions and substantial temperature changes.

Which of the following is FALSE regarding studies on volvocine algae to explore the evolution of individuality?

Volvox carteri individuals are made up of thousands of flagella-bearing germ cells and only a handful of somatic cells. Volvocine algae are ideal for studying the evolution of individuality because of the exceptional variation found within this group. Some volvocine species are unicellular; some species are made of cells that live in groups but do not have specialized germ and soma lines; and some species, such as Volvox aureus, show well-differentiated germ cell and somatic cell lines. Indeed, the division of labor between germ and soma lines has evolved on at least three separate occasions in this group. Rick Michod and his colleagues focused on Volvox carteri, a species of volvocine algae in which there are both germ and somatic cells (Michod 2007). Individual V. carteri are typically made up of about 2000 small somatic cells and as many as 16 large reproductive cells. Each small somatic cell has two flagella, which are long, hairlike projections that produce motion. Examine Figure 12.19.

Fossils are the remains of past-living organisms that can form in several different ways. Which of the following describes fossilization by dissolution?

Water seeps into a fossil and breaks it down, but the shape of the fossil is preserved in the sediment around it, providing a rough outline of the organism. Organic remains that have been fossilized into rock are not the only way to tap into the fossil record, by which we mean the history of life on Earth as recorded by fossil evidence. Sometimes, water seeps into fossils and breaks down a fossil that has formed (this is referred to as dissolution), but the shape of the fossil is preserved in the sediment around it, providing a rough outline of the organism. Read the subsection titled "Extinctions and the Fossil Record."

The famous radiation of Galápagos finches from the common ancestor species on the western coast of South America is probably a result of __________.

allopatric speciation Allopatric speciation is the process of speciation that takes place in populations that are completely isolated from one another. In the case of Galápagos finches, that is likely what happened once the ancestral species inhabited some of the Galápagos Islands. Parapatric speciation does not require clear geographic boundaries, such as islands away from the main coast, yet the diverging populations on the path to speciation have distributions that are unique and somewhat species specific, within a selective gradient. In sympatric speciation, the populations are diverging into new species while in the same location.

During the 1990s Knowlton and colleagues studied pairs of sister species of the genus Alpheus (snapping shrimp). In each of these sister species pairs, members of one pair lived on the Caribbean side of the Isthmus of Panama, while members of the other pair lived on the Pacific side. What type of speciation might be responsible for this speciation?

allopatric speciation with the dumbbell model

In a study of red spruce trees and black spruce trees, scientists found that the red spruce was living in a smaller geographic area and had much less genetic variation than the black spruce. They proposed that the red spruce might have arisen from a southern population of black spruce, which became geographically isolated from other black spruce populations at some point during the Pleistocene glaciations. What is this an example of?

allopatric speciation with the peripheral isolate model The peripheral isolate model of allopatric speciation includes a stronger role of genetic drift in driving divergence between the populations. The derivative species (such as red spruce) forms when a small subgroup of the progenitor species (black spruce) becomes geographically isolated and begins to diverge from the original population through the process of peripheral isolate speciation. Read the subsection titled "The Peripheral Isolate Model in Black Spruce and Red Spruce Trees" and examine Figures 14.11 and 14.12.

In a study of two spruce species, red and black, scientists found that the red spruce was living in a smaller geographic area and had much less genetic variation than the black spruce. They proposed that the red spruce might have arisen from a southern population of black spruce, which became geographically isolated from other black spruce populations at some point during the Pleistocene glaciations. This is an example of:

allopatric speciation with the peripheral isolate model.

During the 1990s, Nancy Knowlton and her colleagues studied pairs of sister species of the genus Alpheus (snapping shrimp) (Knowlton 1993). In each of these sister species, one species in the pair lived on the Caribbean side of the Isthmus of Panama, while the other species lived on the Pacific side. What type of speciation might be responsible for this speciation?

allopatric speciation with the vicariance model In a shrimp from the genus Alpheus, geographic isolation of the original ancestral species started with the formation of the land barrier at the Isthmus of Panama, about 5 million years ago. The Isthmus of Panama separated sister species of shrimp on the Caribbean and Pacific sides, leading to allopatric speciation. Due to the water currents, an initial large population was subdivided into several large populations (vicariance model). About 3 million years ago (when the Isthmus of Panama was complete), some sister species began inhabiting mangrove areas. Read the subsection titled "Allopatry via the Isthmus of Panama" and examine Figures 14.9 and 14.10.

Miller and Urey developed and conducted some experimental tests for a "prebiotic soup" model of the origin of life, which had been proposed a few decades earlier by Oparin and Haldane. What did Miller and Urey show could be synthesized abiotically?

amino acids

Stanley Miller and Harold Urey developed and conducted experimental tests for a "prebiotic soup" model of the origin of life, which had been proposed a few decades earlier by Aleksandr Oparin and J.B.S. Haldane. What did Miller and Urey show could be synthesized abiotically?

amino acids Miller and Urey tested the plausibility of the prebiotic soup hypothesis in the 1950s (Miller 1953). They were able to produce some very important evidence that organic molecules may form in abiotic conditions. They used simulated lightning (an electric current between two electrodes) in a mixture of gases to replicate the ancient atmosphere. Depending on which combination of gases was used, numerous common amino acids, such as glycine, alanine, and valine, were produced in the experimental apparatus. Using a simple experimental protocol, Miller and Urey produced some of the building blocks of life. Examine Figure 11.8.

In all of the extinctions that have ever occurred on Earth, the majority of species loss was due to __________.

background extinctions Depending on how exactly mass extinction is defined, we have evidence for at least five and perhaps as many as eight mass extinctions over the course of the past 600 million years. Some of these extinctions wiped out 90% of all species alive at the time. But mass extinctions are few and far between, and of all the extinctions that have ever occurred, about 95% have not been associated with a mass extinction; rather, they represent background extinction. Read the subsection titled "Magnitude of Extinction: Background Extinction versus Mass Extinction."

In a hypothetical scenario, imagine that you have discovered a rare species of birds on a remote Pacific island. You spend some time studying their ecology and habitation and discover that although these birds look alike, there are indeed two distinct populations with very different mating calls. You propose that these two populations must be two species, since they no longer mate with one another. Which of the following species concepts would you use to defend your statement?

biological species concept

In a hypothetical scenario, imagine that you have discovered a rare species of bird on a remote Pacific island. You spend some time studying their ecology and habitation and discover that although these birds look alike, they are indeed two distinct populations with very different mating calls. You propose that these two populations must be two species since they are no longer able to mate with one another. Which of the following species concepts would you use to defend your statement?

biological species concept The biological species concept focuses on gene flow and defines species based on their reproductive isolation. If individuals in one population are capable of mating with individuals in another population, then individuals in both populations are part of the same species and are said to share the same gene pool. If populations are reproductively isolated from one another, in this case by different mating calls, then the individuals in such populations are not considered to be part of the same species. Read the subsection titled "Identifying Species" and examine Figure 14.4.

One of the main features of a eukaryotic cell is the nucleus. Recent evidence suggests that the cell nucleus may have evolved from archaeal ancestors and that the organelles may have evolved from bacterial ancestors, but there is another important factor that shaped the evolution of nuclear genomes. Which of the following is a source of the eukaryotic nuclear genes?

both mitochondria and chloroplasts

One of the main features of a eukaryotic cell is the nucleus. Recent evidence suggests that the cell nucleus may have evolved from archaeal ancestors and that the organelles may have evolved from bacterial ancestors, but there is another important factor that has shaped the evolution of nuclear genomes. Which of the following is a source of some eukaryotic nuclear genes?

both mitochondrial and chloroplast genes Many studies have demonstrated the migration of genes between eukaryotic organelles (such as chloroplasts and mitochondria) and the nucleus. Such genes are sometimes described as "promiscuous DNA." The human genome, for example, has somewhere between 296 and 612 insertions of mitochondrial DNA (mtDNA) into the nucleus. Read the subsection titled "Endosymbiosis and the Evolution of the Eukaryotic Nucleus" in Section 12.2. Then examine Figure 12.9 and use this experimental example to understand the significance of gene transfer from these organelles to nuclear genomes.

In order to understand the origin of life on Earth, evolutionary biologists collaborate with__________.

chemists geologists atmospheric scientists Even with recent advances in evolutionary biology, the question of the origin of life on Earth remains a truly interdisciplinary endeavor. While the theory of evolution explains how life diversified subsequent to its origin, understanding the origin of life itself requires that evolutionary biologists collaborate with chemists, geologists, atmospheric scientists, and researchers from other disciplines. For instance, chemists can help us understand what the initial chemical building blocks of life might have been, while geologists and atmospheric scientists can shed light on the possible physical characteristics of the environment in which life originated. See Section 11.1 titled "What is Life?" and examine the timeline in Figure 11.2, "Early Events in the History of Life on Earth."

What type of infectious disease is devastating populations of frogs in North America, Alaska, and Australia today?

chytridiomycosis, which interferes with the ability of amphibians to transport chemicals across the epidermis

In the slime mold species Dictyostelium discoideum, single-celled individuals gather in the migratory slug stage of development, in response to environmental cues. Which molecule is associated with this signaling?

cyclic adenosine monophosphate (cAMP) In D. discoideum, the key to slug responses to the environment is communication via a chemical called cyclic adenosine monophosphate (cAMP). Once the individual cells arrive where cAMP is being emitted, they adhere to each other, surrounding the cells that emitted the cAMP and forming the multicellular slug. The slug is then able to orient itself and move toward stimuli such as light and nutrients. Read the subsection titled "Coming Together; Slime Molds and Multicellularity" in Section 12.3 and look at Figure 12.15. As you can see from this figure, cAMP is released in the densest section of cells in the soil, and this signals cells "downstream" of this point to orient in the direction from which the cAMP was emitted.

Look at this definition of species: "A species is a lineage of . . . populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate." This definition best represents the:

evolutionary species concept

"A species is a lineage of populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate." This definition best represents the __________.

evolutionary species concept The fundamental underlying notion of the evolutionary species concept, first proposed by George Gaylord Simpson and then modified by E. O. Wiley (Simpson 1961; Wiley 1978), is that this group forms a lineage that has a distinct evolutionary fate from other lineages. With this definition, a group of populations can be considered a species when they share a past evolutionary history and a common future evolutionary fate until speciation once again divides the group. See the subsection titled "What is a Species?"

Which of the following molecules involved in membrane structure was likely favored by selection in the evolution of early cells?

fatty acids

Which of the following molecules involved in membrane structure was likely favored by natural selection in the evolution of early cells?

fatty acids Early membranes would have been assembled from simple organic molecules in the environment, and thus would have had a simpler structure than that of more modern membranes. For example, they may have been composed of single-chain fatty acid molecules such as oleic acid (Figure 11.13A). Under appropriate conditions, these molecules can spontaneously self-assemble into lipid bilayers and form enclosed vesicles. In the presence of micelles—small spherical assemblages of fatty acid molecules with hydrophobic tails inside and hydrophilic heads outside—these vesicles can grow as they incorporate the micelles into their walls (Figure 11.13B). Read the subsection titled "Lipid Membranes and Reproduction in Early Cells" in Section 11.3.

Which one of the following is NOT a major transition in the evolution of life, according to biologists John Maynard Smith and Eörs Szathmary?

formation of the solar system including Earth Maynard Smith and Szathmary looked at some of the most critical events in the evolution of life on Earth, which have changed the way that life is organized (Maynard Smith and Szathmary 1997). These include the origin of self-replicating molecules capable of heredity; the transition from RNA as both catalyst and genetic material to a division of labor with protein as the catalyst and DNA as the genetic material; the origin of the first cells; the emergence of eukaryotic cells; the evolution of sexual reproduction; the evolution of multicellular organisms from single-celled ancestors; and others. The origin of the solar system including Earth is important for many reasons, but it precedes the evolution of life. Read Section 12.1 titled "Overview of Major Transitions" and review the transitions already covered in the previous chapter.

In 1977 Sidney Fox tried a different approach to testing the prebiotic synthesis of biological molecules. He mixed a number of different amino acids together at a high temperature (120°C) in an environment lacking water. When he subsequently placed the mixture into water to investigate what the amino acids would form, he:

found some peptide-like structures, but the bonds between the amino acids were weak and unstable.

Which of the following best represents the definition of an individual, as proposed by Michod?

integrated and indivisible wholes that can reproduce and pass heritable variations on to their offspring

Which of the following best represents the definition of an individual, as proposed by evolutionary biologist Rick Michod?

integrated and indivisible wholes that can reproduce and pass heritable variations on to their offspring In defining an individual, one of the important differences between single-celled organisms and multicellular individuals is the transfer of fitness from lower to higher levels of organization. For instance, in multicellular organisms, we always find differentiation of cell lines into those specialized in reproduction (germ cells) and those specialized in maintenance and growth of the organism (somatic cells, or soma). In the definition suggested by Michod, "individuals" are defined as "'integrated and indivisible wholes' that can reproduce and pass on to their offspring heritable variations" (Michod 2007). Read Section 12.4 titled "Major Transition; The Evolution of Individuality."

Two common species of frogs from the genus Bombina (B. bombina and B. variegata) live in similar latitudes and ecological conditions, but in two different regions, Central and Eastern Europe. In a narrow strip between these regions, scientists observed a third species, which might have been a hybrid between the former diverging populations of the ancestral species. What evolutionary process might be responsible for the speciation in Bombina?

parapatric speciation

Two common species of frogs from the genus Bombina (B. bombina and B. variegata) live in similar latitudes and ecological conditions, but in two different regions, Central and Eastern Europe. In a narrow strip between these regions, scientists have observed a third species, which might be a hybrid between the former diverging populations of the ancestral species. What evolutionary process might be responsible for the speciation in Bombina?

parapatric speciation Parapatric speciation occurs when two adjacent populations diverge into separate species without a geographic barrier to dispersal. As a result of this initial divergence, due to a cline or some other differentiation in their habitats, an area might remain in which these diverging populations encounter each other, mate, and produce hybrid offspring. In some cases, the hybrid offspring may become reproductively isolated from both species and produce a third species in that zone. Read the subsection titled "The Hybrid Zone in Parapatric Speciation."

A researcher is trying to determine if populations of a butterfly seen on the eastern slope of the Rocky Mountains in Colorado are actually separate species. The researcher and her graduate students spent a summer capturing the butterflies at several locations, carefully documenting traits such as color, wing span, antennae length, proboscis length, etc. Which species concept could be applied using these data?

phenetic species concept The researchers in this case collected data on the physical characteristics of the species, or their phenotypic traits. The phenetic species concept uses phenotypic traits to identify clusters of phenotypically similar individuals or populations. Read the subsection titled "Identifying Species" and examine Figure 14.2.

David Jablonski and his coworkers found that for gastropods (slugs and snails) of the late Cretaceous period, the key to a broad geographic range at the species level—and thus increased chances of surviving the mass extinction near the K-Pg boundary—was the nature of their larval stage. Which of the following best describes a stage that contributes to the increased geographic ranges of the gastropod taxa?

planktotrophic larvae that feed in the open water on very small prey and develop into adults at a relatively slow rate Planktotrophic larvae feed in the open water on zooplankton and phytoplankton. They also develop into adults at a relatively slow rate. Because they are small for a long period of time and live in the open water, these larvae often are dispersed long distances, leading to a broad geographic range for species with such larvae compared to species with nonplanktotrophic larvae. Jablonski concluded that extinction rates were half as high in planktotrophic species as in the nonplanktotrophic species. Read the subsection titled "Species' Geographic Range and Extinction Probability" and examine Figure 15.36.

In a hypothetical flowering plant species, one population evolves a different response to environmental stimuli and begins to bloom significantly later in the season than nearby populations. What type of reproductive isolating mechanism would this be?

prezygotic Prezygotic isolating mechanisms prevent or deter individuals from different populations from mating with one another or prevent fertilization from occurring if such a mating does take place, while postzygotic isolating mechanisms operate after fertilization and conception. In this case, since flowering plants are pollinated by animal vectors or by wind, the plants of the evolving population are isolated from other populations because of the timing differences in floral maturation. See Table 14.2.

In 1970, Lynn Margulis proposed that the origin of two eukaryotic organelles, mitochondria and chloroplasts, occurred through endosymbiosis. According to more recent phylogenetic analyses based on molecular genetic data, which of these prokaryotic lineages is a candidate for the ancestral source of mitochondria?

proteobacteria Phylogenetic studies indicate that mitochondrial genes in eukaryotes more closely resemble the genes in proteobacteria than other genes in their eukaryotic hosts. Another bacterial lineage, cyanobacteria, is closely related to chloroplasts. Both proteobacteria and cyanobacteria belong to the domain Bacteria. Read the subsection titled "Endosymbiosis and the Evolution of Eukaryotic Organelles" in Section 12.2 and examine Figure 12.7.

Paleontological studies on a lineage of bryozoans (whose fossils preserve many of their morphological characteristics) show a pattern of evolution with little or no change for long stretches of time. Occasionally, however, speciation occurred in a burst of change and diversification. This is an example of __________.

punctuated equilibrium An example of the patterns of change expected under the punctuated equilibrium model was documented by Alan Cheetham in his work on speciation and evolutionary change in aquatic invertebrates called bryozoans (Cheetham 1986). Using the fossil record from the past 20 million years, Cheetham tracked speciation patterns in one genus of bryozoans (Metrarabdotos) by measuring change in 46 morphological characters. Figure 15.40 summarizes these results; periods of stasis are shown in long vertical lines, while punctuated speciation is depicted in horizontal lines. Read the subsection titled "Rates and Patterns of Evolutionary Change."

Which one of the following is not a major transition in the evolution of life, based on Maynard Smith and Szathmary (1997)?

the formation of the solar system including Earth

In paleobiology, one of the main concepts is that fossils found lower down in the sediment at a particular locality are older than those found closer to the surface. This often is called __________.

the law of superposition Paleontologists have many techniques for determining the age of a fossil. Some of these techniques provide a measure of relative age, and others provide a measure of absolute age. An example of the way relative age is gauged is the law of superposition, which states that fossils found lower down in the sediment at a particular locality are older than those found closer to the surface. Read the subsection titled "Extinctions and the Fossil Record."

All of the following are true regarding Sol Spiegelman's experiment on the origins of life, except that __________.

there was no selection for any of the variations in length At the end of Spiegelman's serial transfer experiment (Figure 11.22), he did not find strands of 4000 nucleotides, as in generation 1. This is because the shorter RNA sequences were favored by selection because of their fast reproduction. Since it was also evident that the variation in size was heritable, it was interesting to see that a typical final strand was a little over 200 nucleotides long. Apparently, mutations were damaging to the smaller sequences (those consisting of 50-100 nucleotides). Read the subsection titled "Experimental Evidence on the Origins of Natural Selection" in Section 11.4 and examine Figure 11.22

All of the following is true regarding Spiegelman's experiment on the origins of life except that:

there was no selection for any of the variations in length.