BIO 345 ASU MidTerm Detailed Exam with Correct Solution Study Guide 2026

BIO 345 ASU MidTerm Detailed Exam with Correct Solution Study Guide 2026 Anatomical Homology structural similarities between different species like the bones in bird's wing being similar to the bones in a human's arm Example: most fish bodies are the same. Sharks and dolphins are NOT related at all but very similar looking Vestigial Traits Structures or attributes who have lost some or all of their ancestral function Example: Wings on penguins that they can't fly with Developmental Homologies Similarities in forming embryos that you cannot see in adult animals. Example: Mice, alligators and humans all are very similar at an embryotic level. Molecular Homology similar DNA (amino acid sequences) among different species from a common ancestor Example: Humans, chimps, bonobos Biogeography Geographic distribution of species. Example: Prickly Pair cactus on different continents Fossil Record information about past life, including the structure of organisms, what they ate, what ate them, in what environment they lived, and the order in which they lived Parthenogenesis Asexual reproduction in which females produce offspring from unfertilized eggs. Reproduction by making a clone of yourself. Key differences between eggs and sperm 1. Sperm is small and mobile & eggs are large and immobile. 2. Females make far fewer eggs and males make a large amount of sperm. Different methods of sex determination 1. In mammals; females have two X-chromosomes & Males have one X & one Y-chromosome. 2. In birds females have two different chromosomes (Z&W) while the males have two Z-chromosomes. 3. Temperature controlled sex determination: in some species, cold temperatures cause the eggs to develop into males while warm temperatures cause the eggs to turn into females. 4. Angler fish: females lure in infant males who then latch onto her body and all of the organs degenerate while they basically turn into giant testicles attached to the female. The female then releases her eggs into the water and the male does the same with the sperm and they fertilize within the environment. 5. Sexual Dimorphism: when the sexual traits of males and females are different and distinguishable. The twofold cost of males If all else is equal, the production of males in a sexual population reduces its reproductive potential by a factor of two. Half the individuals produced will NOT reproduce, reducing the male population by a twofold. Parthenogenesis advantage 1. Sexual reproduction requires finding a partner, which is sometimes difficult. 2. Sexually transmitted diseases, which are suffered by plants as well as animals, are avoided by organisms without sex. Example: Dandelions do not require any other individuals of its own species to spread its seeds. Sexual Reproduction advantage genetic diversity Recombination happens between loci on the same chromosome by crossing over, which joins together a piece of a chromosome inherited from the mother with a piece inherited from the father Benefits of recombination Helps create new gene combinations that may help organisms have higher fitness Recombination Rate is the probability that recombination occurs between a given pair of loci When the loci are close together the probability is at it's highest (r= ½). When the DNA bases are adjacent on the chromosome, the probability can be as low as r=0. linkage equilibrium The association of two alleles at two or more loci at the frequency predicted by their individual frequencies. For the equation, D=PAB-pApB, the population is in linkage equilibrium when D=0. linkage disequilibrium When a pair of alleles from two loci are inherited together in the same gamete more/less often than random chance would expect Equation for Linkage Disequilibrium (D) D=PAB-pApB PAB is "frequency of gametes carrying both the A2 and the B2 alleles." pA is "frequency of gametes with the A2 allele (no matter which B allele they have." pB is "the frequency of gametes with the B2 allele (no matter which A allele they have)." How are recombination rate and linkage disequilibrium connected? Recombination discourages linkage disequilibrium from continuing. A higher recombination rate will degrade linkage disequilibrium between two loci because recombination is more likely to occur. How does asexual reproduction maintain linkage disequilibrium? Recombination moves the population toward a state where there is no statistical association between the alleles at the two loci. So an asexual reproducing organism occurs more disequilibrium and less mixing. Epistasis interaction between alleles in which one allele hides the effects of another allele What conditions favor sexual reproduction? Changing environments tend to favor sexual reproduction. Also, situations in which other species are in an "arms race", where it is beneficial to shuffle genes into new combinations that may protect against the invasion of parasites and other competing species. Red Queen Hypothesis each species has to run (evolve) as fast as possible just to stay in place -- because predators, competitors, and parasites also continue to evolve. Recombination of genes is necessary so as predators and parasites adapt, so is the prey and host and there is a balance that keeps everyone in the "same" place population wise. Rather than seeing a massive decline or extinction of a species. Selective interference The chance that a particular copy of an allele is passed to the next generation depends in part on the rest of the genome in which it is carried. Adaptation can be hampered as a result, particularly if there is not much genetic mixing. sex reduces selective interference because it separates alleles from their genomic backgrounds Asexual being will not have as much genetic mixing Define clonal interference, and explain what is happening in the first figure - why does sex allow for more rapid accumulation of beneficial alleles? "When two or more beneficial mutations spread through a population at the same time." When a mutant allele that has provides a fitness advantage appears in an asexual individual, that allele will likely cause the extinction of other organisms who do not have that new mutation. Even if other beneficial mutations show up in other individuals at different loci, they will likely still go to extinction due to their fitness disadvantage. These other beneficial mutations will not gain higher frequency in the population until they appear in individuals who already have the allele with the higher fitness advantage. This limits the ability of asexual organisms to quickly accumulate many beneficial traits. "In a sexual population, recombination can bring together in a single genotype several mutations that originally appeared in different individuals. This reduces clonal interference and accelerates adaptation." Ruby in the rubbish effect The loss of a beneficial mutation (the "ruby") that occurs in a genotype that has low fitness because of deleterious mutations (the "rubbish") that it carries at other loci. Muller's ratchet the irreversible accumulation of deleterious mutations in an asexual population. Each time the most fit genotypes fail to reproduce, the population's mean fitness is ratcheted downward. It can never recover, and in principle this process can lead to the extinction of an asexual species. horizontal gene transfer the movement of DNA between different individuals without help from sexual reproduction genetic hitchhiking The process by which a neutral or even disadvantageous allele is able to "ride along" with a nearby favorable allele to which it is physically linked, and thus increase in frequency. How can scientists deduce if selection acted in standing genetic variation, and how is linkage disequilibrium is involved? Changes in the environment can suddenly give a fitness advantage to a mutation that is already present in a population—a situation called selection on standing genetic variation. (A) Three copies of the mutation (yellow, orange, and red) have already recombined onto chromosomes with different neutral variants at other sites (blue). (B) As the copies of the beneficial mutation spread to higher frequency, the neutral variants linked to each of them hitchhike to higher frequency. (C) When the beneficial mutation becomes fixed, the region of reduced variation nearby on the chromosome is much smaller than if the mutation had a fitness advantage when it first appeared. Patterns of variation along the chromosome can therefore be used to determine whether adaptation resulted from selection on standing genetic variation or from a mutation that was beneficial initially. Why do genome size vary? due to differences in the amplification, deletion, and divergence of various kinds of repetitive sequences, including the transposable elements, which constitute a large fraction of the genome How do TEs contribute to genome size? Each of us has more than a million copies of Alu that together make up more than 10 percent of our genome How do TEs contribute to genome evolution? they are modified viruses that evolved the ability to reproduce without leaving the cell How does genetic drift contribute to coding gene evolution? Evolution occurs most rapidly in the 3rd base of codons because that position is most likely to result in synonymous mutations. Drift can cause these kinds of mutations to spread rapidly through a population because they do not cause much if any change to the fitness of individuals in a population who carry them. Drift is responsible for much of the evolution of coding genes. Motoo Kimura's neutral theory of evolution the vast majority of differences among species and variation within species in DNA sequences are due to mutations that are nearly selectively neutral and have evolved mainly by drift positive selection natural selection that increases the frequency of a favorable allele purifying selection Selection that lowers the frequency of or even eliminates deleterious alleles. dN/dS permits evaluating the role of natural selection in the evolutionary history of a protein-coding gene Explain dN/dS dN , the fraction of sites that differ at nonsynonymous sites (those that do change an amino acid) dS , the fraction of sites that differ at synonymous sites (those that do not change an amino acid) dN /dS to be 1 if both types of mutations will have the same chance of drifting through the population to fixation dN /dS will be much less than 1 if most nonsynonymous mutations are deleterious and are removed by purifying selection How does population size affect the distribution of dN/dS more beneficial mutations enter a big population than a small population, which further tilts the balance of molecular evolution away from drift and toward adaptation Duplication mechanisms retrotransposition unequal crossing over replication slippage unequal crossing over crossing over between homologs that are not perfectly aligned replication slippage When the DNA polymerase loses its place and copies a segment of chromosome twice Retrotransposition a form of transposition in which the element is transcribed into RNA. The RNA is then used as a template via reverse transcriptase to synthesize a DNA molecule that is integrated into a new region of the genome. The result is a duplicate gene that is far from the parental copy, often on a different chromosome. de novo genes Coding DNA sequences that originate from noncoding DNA. Paralogs are homologous genes that have evolved by duplication and code for protein with similar, but not identical functions Fates: -duplicate is redundant and does not provide a fitness benefit, it will be lost by deletion or the accumulation of lossof- function mutations -a duplicate can simply retain its original function concerted evolution the phenomenon where paralogous genes within one species are more closely related to one another than to members of the same gene family in closely related species Neofunctionalization An evolutionary process in which duplicated genes diverge, and one copy takes on a new function Subfunctionalization each duplicate carries out only some of the roles that the ancestral gene performed. Explain how genes "die" There are many ways that a gene can die. When a gene is duplicated, the new copy is often dead on arrival. The duplicate many not include the entire gene. Even if it does, if often lacks the regulatory elements needed to express it at the right time and in the right places. Duplicates produced by retrotransposition face an additional challenge. Since they lack introns, there is no opportunity for post transcriptional regulation that involves splicing. Pseudogenes genes that have become inactivated by mutations gene trafficking Movement of genes to new sites in the genome. gene splicing the process by which the DNA of an organism is cut and a gene from another is inserted. alternative splicing brings together different combinations of exons from the same locus. As a result, a single gene can produce more than one protein overlapping genes two or more genes in which part or all of one gene is embedded in the other Are all changes to karyotype for the benefit of the organism? they are the messy outcomes of competing evolutionary processes that act at different levels of selection Inversions affect A chromosome with an inversion has the same genes as one without it, but they are in a different order. an inversion is produced when a chromosome breaks at two places and the middle segment is then reinserted back-ward some inversions benefit from meiotic drive. Ontogeny the development of an individual organism or anatomical or behavioral feature from the earliest stage to maturity. Why is it that the phrase "ontogeny recapitulates phylogeny" seldom holds? various features develop at different rates, relative to one another, in descendants than in their ancestors, and embryos and juvenile stages have stage-specific adaptations of their own morphogenesis the origin and development of morphological characteristic quantitative traits traits that show continuous variation (most traits, i.e.: height, intelligence, athleticism) genotypic variation is discrete and phenotypic variation is continuous The distinction between phenotypes and genotypes is particularly important for quantitative traits: the phenotype can be directly seen, but the genotype cannot. The variation in quantitative traits like height that is visible is measured by the phenotypic variance. This is simply the variance in the measurements of the trait in the population. The phenotypic variance results from both genetic and environmental (nongenetic) causes. breeder's equation -h2, which represents the trait's heritability I-f h2 is 0, then there is no resemblance between offspring and their parents. -At the other extreme, if h2 is 1, then offspring look exactly like the average of their parents -S, which is the amount of change in the mean of the trait caused by selection within a generation. That is, S equals the difference between the mean of the population after selection, which is written z, and the mean before selection, z environmental variance the phenotypic variance of a trait in a population that is attributed to differences in the environment Methylation Suppresses gene activity and expression trans regulatory elements DNA sequences that modify the expression or activity of genes that are NOT nearby on the chromosome, often by coding for transcription factors cis regulatory elements DNA sequences that modify the expression of other genes that are nearby on the chromosome, often by acting as binding sites for transcription factors heterochrony Evolutionary change in the timing or rate of an organism's development. Paedomorphosis The retention in an adult organism of the juvenile features of its evolutionary ancestors. Neoteny A slowing of the process of maturation, allowing more time for growth; an important factor in the development of large brains Heterotrophy organisms that cannot make their own food and must feed on other organisms for energy and nutrients reaction norm the pattern of phenotypic expression of a single genotype across a range of environments phenotypic plasticity the ability of an organism to change its phenotype in response to changes in the environment. canalized Describing traits that are very insensitive to environmental conditions during development, resulting in similar phenotypes in a wide range of environments. genotype-environment interaction the portion of phenotypic variation that results from the reactions of genetically different individuals to similar environmental conditions Cooperation An interaction in which two individuals each receive a net benefit from their joint actions What are some reasons natural selection should favor cooperation? Kinship, reciprocity, and group selection Kinship Taking care of your kin at a cost. Raising it to maturity. Reciprocity When one individual provides a fitness benefit to another, as long as the second individual is likely to return the favor later. If the group sees a helpful individual they're more likely to reciprocate during their next interaction. When one individual provides a fitness benefit to another, as long as the second individual is likely to return the favor later. When the group recognizes a lazy or freeloading individual and they stop taking care of it or allowing free benefits. Group Selection Benefit to being in large numbers. The fitness of an individual is higher when in groups than when alone. The idea that groups compete just as individuals do, and the behavior of the individuals within a group affects each individual's own fitness. Altruism The behavior of an animal that benefits another at its own expense. Where there is a cost to the behavior and you're benefiting someone else like kin or relatives. What are 2 ways you can pass your alleles on to the next generation? If you reproduce and through your relatives/ kinship Genetic Relatedness The probability that two individuals share an allele due to recent common ancestry. It's the percentage of similar genes shared by two persons. Example: when Dad's sperm fuses with Mom's eggs, the newly created embryo will have half of Dad's genes and half of Mom's genes. Therefore the relatedness of a child to either of his parents is 50%. Coefficient of relatedness A measure of the probability that two individuals share the same allele via a recent, common ancestor, and thus it is "identical by descent". Mathmatically it is denoted by the symbol r and it ranges from 0 (unrelated) to 1 (clones or identical twins). How to calculate the coefficient of relatedness (r) 1. Find the most recent common ancestor of A & B family members. 2. For this MRCA, calculate the probability that a given allele copy was passed on to both A & B Because of Meiosis, this is 50% or 0.5 per generation 3. k= number of meiotic events & r=0.5k Why do groundhogs make dangerous alarm calls? The females will make the call and risk sacrificing themselves in an effort to alarm the other females and kin that danger is coming. The males migrate and are typically absent so the females have a system to protect one another. Can your mom love you too much? Decisions are made by how much energy the parent has available and by how many offspring the parent is likely to have in the future. Mutualistic When the fitness of both individuals is increased. Cooperative Relationship. Altruistic The actor suffers but the recipient benefits. Cooperative Relationship. Selfish Actor's fitness increases but the recipient's is harmed. Conflict Relationship. Spiteful If both individuals are harmed. Conflict Relationship. Conflict Relationship When the fitness interests of two individuals are different. Cooperative Relationship When one individual's behavior benefits another (as in mutualism and altruism) When is it beneficial for unrelated individuals to cooperate? When the fitness costs of cooperation are equaled or greater than they would be if the individual were to perform the task itself and there is an increase in fitness of the individual performing the behavior. Example: This explains why birds fly in flocks, fishes swim in schools, and ungulates roam in herds. Example: Predators such as wolves hunt cooperatively, and share prey that a single individual could not capture by itself Kin Selection Parents are altruistic. They enhance the fitness of other individuals—their offspring—at a cost to themselves. So, when the parent invests in the survival of their offspring to an extend that it costs them some fitness of their own. This may decrease their chance of survival but increases that of their kin (who share a proportion of their genes). Direct fitness An individual carrying the allele can pass copies of it to his or her own children. Indirect fitness When an organism's genetic success is believed to be derived from cooperation and altruistic behavior. Fitness is increased because the alleles will pass on again as a result. Inclusive Fitness The fitness of an individual organism as measured in terms of the survival and reproductive success of its kin, each relative being valued according to the probability of shared genetic information, an offspring or sibling having a value of 50 percent and a cousin 25 percent. Is also the sum of its direct and indirect fitness. Hamilton's rule Specifies the conditions under which reproductive altruism evolves. An allele that causes an altruistic behavior will spread if the following condition is met: rBC. 1. The left-hand side of this inequality represents the effect of the behavior on the indirect fitness of the allele 2. "r" is the relatedness, also known as the coefficient of relationship. r is the probability that if the allele is carried by the actor, then it is also carried by the recipient of the altruistic behavior 3. "B" s the fitness benefit to the recipient, that is, the average increase in the number of offspring that the recipient will have as a result of the altruistic behavior 4. "c" is the fitness cost to the actor, that is, the decrease in the number of offspring that individual will have as the result of acting altruistically. Game theory The study of how and why people make decisions. (Specifically, it is "the study of mathematical models of conflict and cooperation between intelligent rational decision-makers".) Evolutionarily stable strategy (ESS) This is a behavior (or "strategy") with fitness greater than, or at least equal to, that of any other possible behavior if all individuals in the population behave that way. A strategy that maximizes fitness and will not change unless the new strategy offers stability of or increase of the groups fitness. What do game theory models suggest about when selfishness vs. cooperation is favored? Some situations that occur in humans and other animals are described by the "prisoner's dilemma". Here each of two individuals will do best by acting selfishly, but if both individuals act selfishly, they will do worse than if they both cooperate. Explain the purpose of punishment. Cooperation is enhanced if one of the partners in an interaction punishes selfish individuals; the punishing partner may impose "sanctions," terminating the relationship by withholding benefits from the other partner. Explain when cooperation may be favored or selected against, based on the Pseudomonas experiment. Cooperation Selected against: When the bacteria have low relatedness and are in a strongly competitive environment, the cheaters win. Cooperation Selection Favored: When the bacteria are closely related and are in a weakly competitive environment, the cooperators can drive the cheaters to extinction. The Green Beard Effect Occurs when a single gene codes for a phenotypic trait that enables its carrier to recognize and help other individuals with the same trait (for example, a bright green beard.) Explain spite A behavior is spiteful if it harms both the actor and the recipient. Version 1: The conditions needed are that the actor be less closely related to the recipient than to an average member of the population, and that harming the recipient enhance the fitness of other individuals in the population that are more closely related to the actor. Version 2: If there is a negative outcome to the behavior exhibited by the actor, that effects itself & others that are not closely related to it, but the action of this spiteful behavior enables others in the population to benefit or thrive in some way. Such as killing off individuals and harming yourself but freeing up a ton of resources so your relatives can keep surviving. Eusocial These are species in which some individuals do not reproduce much or at all themselves, and instead rear (raises to maturity) the offspring of others, usually their parents. Reproductive females are called queens, and most of their eggs develop into workers, which are the non reproductive females that maintain the colony. Example: Ants & Bee's What condition is necessary for natural selection to favor sterile (non-reproductive) individuals? Some origins of hymenopteran eusociality may well have been facilitated by kin selection. But ecological and behavioral factors were also important. Eusociality probably evolved frequently in Hymenoptera (com- pared with other insects) because single females of solitary wasps and bees construct a nest such as a burrow, which requires hard work but provides shelter for the young, and the offspring are helpless larvae that the mother must feed. These hymenopterans were predisposed to sociality because they already had the habit of caring for offspring and because the nest provided a safe place—a fortress—for grown offspring to stay and to interact with their mother and younger siblings. In the case of other eusocial insects, such as termites that live in dead wood, the fortress is also the food source. Another advantage of having helpers is that some can defend the larvae while others forage for food; a single female cannot do both. Moreover, dispersing from the natal nest and constructing a new nest is very risky, and the great majority of young mated females do not succeed. Thus, even a slight increment in inclusive fitness from rearing siblings may have made it advantageous to stay and help mother instead of leaving home. Policing Behavior Queens of many species therefore destroy their workers' eggs, and in some species (including honeybees, Apis mellifera) workers destroy the eggs of other workers. This is because they gain higher fitness from workers raising their own sons rather than allowing their own kin to reproduce and raise their "grandchildren". symbiosis interaction between two different organisms living in close physical association, typically to the advantage of both. OR Intimate associations between species that may be either mutualists or parasite and host. endosymbiont Cell that lives within another cell (host); one supplies energy, the other supplies raw materials and protection. Lives within the other organism's body Coevolution the process of two species evolving in response to long-term interactions with each other Escape-and-radiate coevolution: a species evolves a defense against enemies, and is then able to diversify a species evolves a defense against enemies and is thereby enabled to radiate into diverse descendant species, to which different enemies may later adapt Ecological character displacement: Evolution driven by competition between species for a shared resource. Traits evolve in opposing directions, minimizing overlap between the species. Ecological release: in an ecosystem, the freedom of a species to expand its use of available resources due to an elimination of competition Interference competition: individuals suppress competitors by behavioral dominance or by other means, such as poisoning them (as do some plants, fungi, and bacteria). How is altruism different from mutualism? Mutualism's are interactions between species that benefit individuals of both species, immediately. Altruism is indirect fitness where the actor only benefits once its kin reproduces and spreads its genes to another generation. How do mutualisms form and how are they maintained? 1. They have arisen from parasitic or other exploitative relationships. 2. Another possibility is that one or both partner species may be able to choose to reward the most cooperative or beneficial individuals of the other species, or exclude cheaters. 3. Possible factors can reduce the fitness of cheater genotypes, and thus maintain a mutualistic relationships. What are some examples of interactions between enemies/victims? 1. predators and their prey 2. parasites and their hosts, 3. herbivores and their host plants How does the Red Queen Hypothesis relate to this enemy/victim dynamics? In the long term, the dynamics may lead to indefinite coexistence of enemy and victim species, a switch by the enemy to a different victim species, or extinction of one or both species. Explain an evolutionary arms race and its possible outcomes: Also called escalation, may occur if the capture rate of the prey by the predator increases with the difference between the defensive trait of a prey species and a corresponding character in a predator. Example: If a cheetah becomes faster and the gazelle does not also become faster as a tactic to avoid its predator, then the cheetah may prey on the gazelle to extinction and also the cheetah will go extinct too due to lack of food source. Escalations: When a trait in either the predator or the prey, escalates faster than the opposing species. This can lead to extinction or to a stable point when the costs of increasing the trait (e.g., speed, or a plant's defensive chemicals) become too great. In some cases, prey species have evolved defenses that can make them as dangerous to predators as predators are to prey. Oscillations If the capture rate of the prey by the predator depends on a close match between the predator and prey traits. If the prey's trait will evolve in one direction, the predator's trait will evolve to track it. The result may be continuing cycles of change in the characteristics of both species. Aposematic An evolved warning such as bright coloring to warn the predator that they are poisonous. Batesian mimicry A type of mimicry in which a harmless species looks like a species that is poisonous or otherwise harmful to predators. Müllerian mimicry two or more unpalatable species resemble each other Plant secondary compounds: Chemicals produced by plants that are not immediately important to survival but are generally important to long term prosperity through benefits in competition. These compounds are known to be toxic or repellent to animals, and there is plentiful evidence that insects and other herbivores impose selection for chemical and other defenses. How does escape-and-radiate apply to herbivores and plants? When a plant species that evolves a new and highly effective chemical defense may escape many of its associated herbivores and give rise to a clade of species that share the novel defense Vertical transmission: from parent to child Horizontal transmission: From one member of a species to another, transmission via the environment. Example: Virus or diseases spreading Virulent: Parasites that reduce the survival or reproduction of their hosts (adj.) extremely poisonous; full of malice; spiteful Briefly and very generally compare and contrast gene-for-gene and matching allele models.: Gene-for-gene models (see the figure (A) below) are based on interactions between some plants and fungal pathogens. Matching allele models (see the figure (B) below) may assume that a pathogen can infect a host only if it has a protein that matches a cell surface receptor protein of the host, like a key and a lock. Explain the daphnia "resurrection study" The Daphnia changed so that they were no longer as easily infected by past bacteria, and the bacteria changed and were able to infect contemporary Daphnia. Even though both host and parasite underwent continual cyclic coevolution, the average virulence of the parasite (measured by how much it reduces the host's fecundity) increased over time Explain the Daphnia magna study: found that microsporidian parasites (Pleistophora intestinalis) that reproduce in the gut produced more spores, and caused greater mortality, when they infected Daphnia from their own or nearby populations than when they infected hosts from distant populations How does genetic diversity relate to pathogen resistance? Genetic diversity in host populations is important for maintaining resistance to pathogens. Conversely, populations that are inbred or have low genetic diversity may be at risk of infection. Life history traits: Characteristics and developmental stages that influence reproductive rates. Examples include longevity, age at sexual maturity, and length of time between births. Ecological niche: A specific role of a species within an ecosystem, including its use of resources, and relationships with other species. the range of conditions they live in and resources they use Trade off's: a fitness benefit of one function that is correlated with a fitness cost of another function. This is another way of saying "there is no such thing as a free lunch." Gaining a benefit that in turn decreases another benefit. Reproductive Effort: allocation of energy, time, and other resources to the production and care of offspring Cost of reproduction: the total physical and energetic costs of reproduction- including; nest or territory defense, mating, and producing and raising young. Why would there be trade-offs between survival and reproduction? There may be more energy and requirements to the individual to abide by in order to reproduce that may affect their longevity of life. Semelparous: Species that breed only once in their lives. Iteroparous: species can reproduce multiple times Be able to interpret a life table: x= age lx = survivorship (probability of surviving to that age) mx = average fecundity for a female at that age (avg. number of offspring produced at that age) lxmx= survival probability and the fecundity for the given age (get this number by multiplying lx and mx together) R = lifetime reproductive success (sum of numbers in last column) r= intrinsic rate of increase (ln(R)) What information can a life table provide you with? shows the probability that a newborn will live to age x, symbolized as lx, and the average fecundity for a female at that age How does R help you evaluate fitness? 1. If R is greater than 1, each female leaves more than one offspring, and the population size increases. 2. In a sexually reproducing population, we can also use a life table to find the fitness of an allele. 3. Alleles with larger values of R have higher fitness and will spread. 4. Natural selection does not act to prolong survival beyond the last age of reproduction. Why do we become decrepit as we age? The answer is that, all else being equal, the selective advantage of reproducing declines with age. Why does increasing survival and fertility at earlier ages have a larger effect on fitness than at later ages? simply because predators, disease, and all sorts of accidents make individuals less likely to survive to the later ages. What 2 major factors are responsible for the evolution of senescence and lifespan? antagonistic pleiotropy and mutation accumulation Mutation accumulation: accumulation of random detrimental mutations causing aging mutations that compromise biological functions reduce fitness less, the later in life they exert these effects antagonistic pleiotropy: occurs when a mutation with beneficial effects for one trait also causes detrimental effects on other traits What life history traits does resource depletion select for? growth to be density-dependent and constrain population size What life history traits does predation select for? fecundity Traits of an R-selected population: They require short gestation periods, mature quickly (and thus require little or no parental care), and possess short life spans. Traits of a K-selected population: Species that are well adapted to crowded conditions near carrying capacity. Slow development, Low reproductive rate, Late reproductive age, Large body size, Multiple reproductive cycles, Long lifespan, Strong competitive ability, Low offspring mortality. What factors make deferred (delayed) reproduction advantageous? Allocating resources to growth, self maintenance, and self-defense rather than to immediate reproduction is an investment in the much greater fecundity that may be attained later in life. Explain the findings of the study on guppies in Trinidad: Low population guppies mature earlier and have more offspring. High population guppies mature later and have less offspring. What factors select for semelparity? If the probability of survival increases with body mass and if there is an exponential relationship between body mass and reproductive output. What are benefits of iteroparity? 1. It increases the chance of successful reproduction in fluctuating environments, when reproduction or offspring survival vary from one reproductive season to another. 2. It is also advantageous if adult mortality is low and greater fecundity can be achieved by deferring reproduction to older age classes Why do humans have such few offspring? 1. A modest number of eggs per clutch may therefore result in higher fitness than a greater number. 2. Trade-off's 3. The survival rate of fewer offspring is much higher than that of species who lay a large amount of eggs or birth a large litter of offspring. When are larger vs. smaller offspring advantageous? Larger are advantageous in species in which, because of their habitat or mode of life, starting life at a large size greatly enhances the chance of survival. There are far fewer offspring in a larger born species. Smaller species will have larger clutches and many more offspring but will have a survival disadvantage with predation. When might sequential hermaphroditism be advantageous? Is when organisms can change their sex orientation over the course of the life span. Advantageous if reproductive success increases with size to a greater extent in one sex than in the other. Cis-regulatory and trans-regulatory elements are important for evolutionary changes to morphology because A) Cis- and trans- regulatory elements evolve rapidly B) Changes to the loci acted on by cis- and trans- regulatory elements affects which genes are expressed, how much, and when C) Mutations in cis- and trans- regulatory elements can create novel proteins D) Mutations to cis- and trans- regulatory elements can alter the genotype without affecting the phenotype B) Changes to the loci acted on by cis- and trans- regulatory elements affects which genes are expressed, how much, and when Daphnia water fleas have evolved to have both sexual and asexual reproduction. Asexual reproduction is favored when the biology and chemistry of the lake is most likely to change across generations, while sexual reproduction is favored when conditions are most stable across generations. True or False? False Which of the following is an example of heterotopy (an evolutionary change in the spatial position of a feature within an organism)? A) Entire young plants develop on the leaf margins of the Mother of Thousands B) Axolotls grow to full size but do not undergo metamorphosis, so that they retain many juvenile characteristics C) Teeth in a lizard's head resemble each other in morphology D) During human postnatal growth, the head grows at a slower rate than the body while the legs grow at a faster rate A) Entire young plants develop on the leaf margins of the Mother of Thousands "Ontogeny recapitulates phylogeny" is a statement describing: A) proximate causes (ones that affect the individual) of the developmental changes in organism B) ultimate causes (ones that affect the entire population) of the developmental changes in organism B) ultimate causes (ones that affect the entire population) of the developmental changes in organism What is a major difference in the genomes of virus/bacteria vs. plants/animals? A) The genomes of viruses/bacteria have great genetic diversity; those of plants/animals are simpler and less diverse B) The genomes of viruses/bacteria are typically large; those of plants/animals are smaller C) The genomes of viruses/bacteria consist almost or entirely of coding sequences; in those of plants/animals most DNA is non-protein coding C) The genomes of viruses/bacteria consist almost or entirely of coding sequences; in those of plants/animals most DNA is non-protein coding Which statement about phenotype is false? A) Phenotypes are unlikely to be influenced by genes with pleiotropic effects B) Differences in environment can lead the same genotype to produce different phenotypes C) Phenotypes with continuous variation can be produced by the discrete variation in DNA A) Phenotypes are unlikely to be influenced by genes with pleiotropic effects Bat wings likely arose from: A) Mutation that affects regulation of a single gene (Bmp) B) Multiple simultaneous mutations in bone genes C) Gradual increases in digit size over time, eventually leading to long wing bones A) Mutation that affects regulation of a single gene (Bmp) Which of these is not an advantage of asexual reproduction? A) No need to find a mating partner B) Lack of sexually transmitted diseases C) Alleles inherited from different organisms can create novel phenotypes D) All individuals have the potential to reproduce C) Alleles inherited from different organisms can create novel phenotypes The definition of phenotypic plasticity is when a single genotype may produce different phenotypes in response to environmental stimuli. True or False? True The breeder's equation shows that the rate of evolution depends on the strength of heritability, and the strength of directional selection. Evolution can be expected when: A) S is 0 and h^2 0 B) S is negative, and h^2 is 1 C) S is equal to 0, and h^2 is 0 D) S is not equal to 0, and h^2 is 0 B) S is negative, and h^2 is 1 What has new evidence suggested is the driving force of evolution in coding regions (especially in species with a large effective population size)? A) Purifying selection on synonymous mutations and positive selection on non-synonymous mutations B) Purifying selection on non-synonymous mutations and positive selection on synonymous mutations C) Positive selection on nonsynonymous mutations and drift D) Purifying selection on synonymous mutations and drift C) Positive selection on nonsynonymous mutations and drift Which of the graphs below depicts a genotype x environment interaction? A) (A) B) All graphs depict a genotype x environment interaction C) (B) D) (C) C) (B) For two loci that are very close to each other on a chromosome, how might they show signatures of selection? A) A selective sweep would cause linkage disequilibrium between the gene selected for and nearby loci, reducing variation in the area around the gene B) A selective sweep would cause linkage disequilibrium between the gene selected for and nearby loci, increasing variation in the area around the gene C) Recombination increases linkage equilibrium between loci that are next to each other, decreasing variation in the area around the gene D) Recombination erodes the linkage disequilibrium between loci that are next to each other, increasing variation in the area around the gene A) A selective sweep would cause linkage disequilibrium between the gene selected for and nearby loci, reducing variation in the area around the gene You sequence a genome and find two duplicated genes next to each other that have the same sequence. This sequence differs by one base pair from a gene which existed as a single copy in an ancestral species. Which process explains this observation? A) Subfunctionalization B) Horizontal gene transfer C) Neofunctionalization D) Concerted evolution D) Concerted evolution Which factors affect linkage disequilibrium between loci? A) Selection on a particular combination of traits that are controlled by different loci B) All answers are correct C) Being located close to each other on the same chromosome D) Being located close to each other on the same chromosome, or selection on a particular combination of traits that are controlled by different loci E) Being in the same asexually reproducing organism B) All answers are correct Which mode of chromosomal evolution can create new proteins and also changes genome size? A) Inversions B) Single-nucleotide substitutions C) Allopolyploidy D) Alternative splicing E) None of these options change genome size D) Alternative splicing A gene can appear to move from one spot in the genome to another, a phenomenon called gene trafficking. How is this related to the death of a gene? A) When a gene moves to another part of the genome, it can’t survive there so it “dies” (becomes a pseudogene) B) When a gene is copied to another part of the genome, the copy at the old location might “die” (disappear) C) A deleterious gene might move to a different part of the genome so it does not “die” (undergo purifying selection) B) When a gene is copied to another part of the genome, the copy at the old location might "die" (disappear) A region of chromosome surrounding a selected-for gene has much lower heterozygosity in domesticated maize than in its ancestor, teosinte. This is most likely due to: A) A selective sweep on standing genetic variation B) loss of genetic diversity due to background selection C) purifying selection on a region of chromosome in linkage disequilibrium D) a selective sweep on a gene with a novel mutation D) a selective sweep on a gene with a novel mutation Which of the following statements about asexual organisms is true? A) Asexual organisms can unlink deleterious mutations from beneficial ones B) Populations of asexual organisms suffer when the most fit individuals fail to reproduce, causing the population’s mean fitness to fall C) Asexual organisms can bring together two beneficial mutations that arise in different individuals B) Populations of asexual organisms suffer when the most fit individuals fail to reproduce, causing the population's mean fitness to fall Which of the following is an example of evidence for evolution based on developmental homologies? A) Whale flippers have the same number of bones as human hands B) Birds and crocodiles have more genes in common that birds and mice, because birds and crocodiles have a more recent common ancestor C) Marsupials are common in Australia but not in North America D) Bird-like dinosaur fossils have been discovered in China E) All vertebrate animals have pharyngeal slits early in development E) All vertebrate animals have pharyngeal slits early in development Drake wants to know how related he is to his cousin's new baby. Calculate r for him please. A) 0.0625 B) 0.125 C) 0.5 D) 2.5 E) 0.03125 A) 0.0625 When a population evolves predator defenses, this reduces selective pressure and can lead to population growth and diversification into new species. This is called: A) Interference competition B) Escape-and-radiate coevolution C) Ecological character displacement D) Ecological release B) Escape-and-radiate coevolution Which term defines a relationship with a positive effect on the actor but a negative effect on the recipient? A) Spiteful B) Mutualistic C) Altruistic D) Selfish D) Selfish The Red Queen hypothesis is closely tied to the concept of an evolutionary arms race. Which examples below depict an evolutionary arms race? A) A butterfly species that is non-toxic mimics the aposematic coloration of a toxic species of butterfly B) An ant colony feeds its fungus garden, and the fungus garden feeds the ants C) An allele that causes female frogs to prefer males with loud calls spreads through a population, so the population evolves to have males with louder and louder calls D) A plant evolves toxins that causes a herbivorous beetle population to dwindle, until an allele for a detoxifying chemical spreads through the beetle population D) A plant evolves toxins that causes a herbivorous beetle population to dwindle, until an allele for a detoxifying chemical spreads through the beetle population In which case is it better for an organism to reach sexual maturity when it is older? A) When predation is high B) When population density is low C) When others in the population reproduce at younger ages D) When small individuals have higher mortality than larger ones D) When small individuals have higher mortality than larger ones An animal lives in an environment where there are few predators, but the population is very dense. They likely have a life-history that is: A) K-selected, meaning that the species will likely be well-adapted to crowded conditions B) r-selected, meaning that the ability of individuals to compete with others is favored C) r-selected, meaning there is rapid exponential increase in population growth D) K-selected, meaning high fecundity is favored A) K-selected, meaning that the species will likely be well-adapted to crowded conditions Two semelparous species of fish lay about 100 eggs when reproducing. One reaches reproductive age a year before the other. Assuming there is no competition for resources in the lake they inhabit (population density is low), which species has higher absolute fitness? A) The species that reproduces earlier has higher fitness, as their genes will spread faster B) Both have the same fitness as they lay the same number of eggs C) The species that reproduces later has higher fitness as they also live longer A) The species that reproduces earlier has higher fitness, as their genes will spread faster In which of the following scenarios is kin selection least important? A) Belding’s ground squirrel females stay and reproduce in the same population from birth while males tend to disperse to other groups, females tend to make alarm calls more often than males B) Vampire bats will quickly die without feeding, but they aren’t always successful in finding a meal. However, unsuccessful bats ask for and usually receive regurgitated blood from a successful member of their roosting group C) Eusocial animals evolve sterile worker castes D) Many female animals have evolved to produce nutrient-rich secretions that they use to feed their young B) Vampire bats will quickly die without feeding, but they aren't always successful in finding a meal. However, unsuccessful bats ask for and usually receive regurgitated blood from a successful member of their roosting group The height at which green anoles and brown anoles perch in trees overlaps a bit. When brown anoles were introduced to islands inhabited by green anoles, the green anoles evolved a higher number of specialized toe scales in order to perch higher than they previously did when they were the sole species on the island. This is an example of: A) Interference competition B) Ecological character displacement C) Escape-and-radiate coevolution D) Ecological release B) Ecological character displacement What causes differences in life history traits? A) Genes that cause a variety of effects on phenotype B) Limits on available resources C) Declining likelihood of survival over time D) All things listed E) Limits on available resources and declining likelihood of survival over time D) All things listed Calculate the number of half-brother's grandsons Anne would have to raise to gain more indirect fitness than raising her own child. A) 9 B) 8 C) 5 D) 4 A) 9 Anne's r to her own child = 0.5 Anne's r to the grandchildren = 0.0625, so at least 9 (1 more than 8*0.0625 which = 0.5 The tradeoffs that underlie antagonistic pleiotropy** are due to negative effects of _______ on survival. A) maximum lifespan B) predation C) early reproduction D) competition E) population density C) early reproduction The idea behind inclusive fitness is that alleles that cause socially helpful behaviors promote their own fitness by increasing the fitness of those with the same genes for helping behavior. True or False? True The two most accepted hypotheses for the evolution of senescence, mutation accumulation and antagonistic pleiotropy, are based on the principle that: A) the fitness benefit provided by successful reproduction declines with age. B) the probability of survival declines with age. C) senescence provides an individual-level selective advantage. D) senescence provides a group-level selective advantage. E) senescence is an evolutionarily stable strategy. B) the probability of survival declines with age. Amy is wondering how related she is to her half-brother's grandson. Calculate r for her so she can figure it out. A) 0.125 B) 0.5 C) 0.0625 D) 2 E) 0.03125 C) 0.0625 In which situation would you expect individuals to act selfishly? A) A small community that most individuals spend their whole life in. B) A populations where 99% of individuals act altruistically C) A family group D) A population where 99% of individuals act selfishly D) A population where 99% of individuals act selfishly In which situation would you find parent-offspring conflict? A) Meerkats teaching their young to hunt B) Fish mass spawning offspring upstream in a river C) A goat weaning her two kids off milk D) A male lion becomes head of the pride and kills cubs sired by his predecessor C) A goat weaning her two kids off milk An escalation of attack and defense traits is the only possible outcome of an evolutionary arms race. True or False False The Red Queen hypothesis is named by paleontologist Leigh Van Valen for the Red Queen whom Alice meets in Lewis Carroll's Through the Looking-Glass. What is the analogy? A) Species who are at the top of a hierarchy (queens) have more resources than those at the bottom (peasants) B) You have to outrun your competitors in order to "win" and become "queen" C) For two species that are in conflict, each species has to run (i.e., evolve) as fast as possible just to stay in the same place (survive) C) For two species that are in conflict, each species has to run (i.e., evolve) as fast as possible just to stay in the same place (survive) Use the life history table above to answer the following question. An individual of this species produces an average of __________ offspring in their 2nd year, has __________ probability of surviving to age 3 and has a lifetime reproductive success of _________. A) 0.5; 2%; 1 B) 0.5; 2%; 3 C) 1; 25%; 3 D) 1; 25%; 1 D) 1; 25%; 1 Many organisms in the deep sea live in conditions where resources are rare and populations are small and sparse. Many of those species are also hermaphroditic. Which of these is a plausible explanation for high rates of hermaphroditic species there? A) Reproductive assurance: any individual of the same species is a potential mate B) Excess energy: excess resources can be allocated to the other sex function C) Size advantage: males are more successful when large, but female fitness does not change with size D) Small body size: one sex or the other needs only a miniscule body size for full function A) Reproductive assurance: any individual of the same species is a potential mate Which other locus is most likely to be in linkage disequilibrium with the mutation (all else being equal; assume a sexually reproducing organism)? A) A B) B C) C D) D E) Based on the supplied information, there is equal probability of linkage disequilibrium at all loci. C) C Which of these provides the selection pressure maintaining sexual reproduction, according to the Red Queen hypothesis? A) Females are able to choose males with superior genes. B) Sexual populations have only half the fitness of asexual populations. C) Pathogens of the sexual organism evolve to overcome the organism’s defenses. D) Stabilizing selection maintains a 50:50 sex ratio. E) Strains with different beneficial mutations are able to come together during recombination. C) Pathogens of the sexual organism evolve to overcome the organism’s defenses. What is the best explanation for the observation that eukaryotes that seem superficially simple can have much larger genomes (in terms of mass or number of base pairs) than organisms that have complex anatomy, structure, or behavior? A) Alternative splicing and overlapping genes are rampant among eukaryotes. B) Some organisms have a tremendous amount of noncoding DNA, like repetitive sequences. C) Simpler organisms require more chemical defenses against enemies. D) Animals with simple body plans are adapted for rapid DNA replication. B) Some organisms have a tremendous amount of noncoding DNA, like repetitive sequences. Which mechanism for the appearance of a new gene in a species’ genome could also explain different phylogenetic tree topologies when using different genes? A) Retrotransposition B) Neofunctionalization after gene duplication C) Horizontal gene transfer D) Exon shuffling C) Horizontal gene transfer Which event will not alter an organism's karyotype? A) Allopolyploidy B) Chromosome fission C) Chromosome fusion D) Sequence inversion D) Sequence inversion Human eyes have a very different morphology from that of fly eyes. If Pax6 sequence and function is highly conserved, how can one explain morphological divergence in eyes and their ectopic expression in these flies? A) Pax6 and eyeless genes arose independently, but have similar function. B) Both genes turn on eye development, but different genes are regulated by them in different species. C) Pax6 does not suppress eye development as well as eyeless. D) Pax6 and eyeless must not be part of the developmental pathway. B) Both genes turn on eye development, but different genes are regulated by them in different species. Imagine a scenario in which several lakes have been colonized by marine-origin sticklebacks. In each lake, body armor disappears over time. Which change most likely caused this? A) Independent, unique mutations occurred in each population that rendered enhancers in the armor pathway useless, which were then favored by natural selection. B) Each population had the exact same mutation in a protein coding gene that produces the armor, which increased in frequency by natural selection. C) Novel trans-regulatory elements functioned to build new, armorless morphologies that increased in frequency because of gene flow from oceanic populations. D) Lack of armor reduces fitness, so only genetic drift could cause the armorless condition to increase in frequency. A) Independent, unique mutations occurred in each population that rendered enhancers in the armor pathway useless, which were then favored by natural selection. Which observation is inconsistent with Haeckel's idea that "ontogeny recapitulates phylogeny"? A) The backbone—the common structure among all vertebrates such as fish, reptiles, and mammals—appears as one of the earliest structures in all vertebrate embryos. B) Snakes and legless lizards develop "leg buds" as embryos, only to have them reabsorbed prior to hatching. C) All tetrapod embryos display pharyngeal clefts, a notochord, segmentation, and paddlelike limb buds. D) The pharyngeal clefts and branchial arches of embryonic mammals and reptiles never acquire the form seen in adult fish. D) The pharyngeal clefts and branchial arches of embryonic mammals and reptiles never acquire the form seen in adult fish. Suppose five boats are adrift at sea, each one containing a number of your relatives, and you have the power to save one boat from a dire fate. According to kin selection theory, it would be in the best interest of your genome to save a boat that contains ______. A) two of your brothers B) both of your parents C) one sister, one half-brother, and three cousins D) four half-siblings C) one sister, one half-brother, and three cousins In which situation would you expect the interacting parties not to cooperate? A) The individuals are closely related. B) The individuals have a history of repeated social interactions. C) The individuals are unlikely to encounter each other again in the future. D) The individuals are part of a social group in which noncooperating individuals are punished. C) The individuals are unlikely to encounter each other again in the future. Individual amoebae of the slime mold Dictyostelium discoideum aggregate to form a spore-producing fruiting body. Cheaters make spores, but do not contribute to the stalk. Since many more spores with cheating genotypes are dispersed, they have higher fitness. Why does directional selection not lead to fixation of the cheater genotype? A) This is actually a case of frequency-dependent selection. With too many cheaters in a population, the fruiting body's stalk is not built well, and all individuals have lower fitness. B) Noncheating genotypes are maintained for the harmony and balance of nature. C) Individual amoebae compete against groups of multicellular predators; the noncheating genotype is favored during this competition. D) Individual amoebae form "slugs" only with other amoebae that have the same genotypes. E) Reproductive success is independent of whether an organism exists as a single cell or as part of a multicellular "slug." A) This is actually a case of frequency-dependent selection. With too many cheaters in a population, the fruiting body's stalk is not built well, and all individuals have lower fitness. Plants that evolved resistance to herbivores were able to diversify rapidly. Some butterflies overcame these defenses and also diversified rapidly. This is an example of _________. A) specific coevolution B) diffuse coevolution C) escape-and-radiate coevolution D) guild evolution E) simple coevolution C) escape-and-radiate coevolution You are in an area famous for the presence for cuckoo birds, and you notice a mother bird kicking eggs out of its nest. What is the most likely explanation? A) The bird is sacrificing the eggs to distract the cuckoo birds from its other eggs. B) The mother does not want its offspring to be stolen by the cuckoo birds. C) The bird wants to have fewer offspring to reduce the effort involved with rearing them. D) The bird has recognized an attempt at brood parasitism and is removing the threat. E) Too many eggs attract cuckoo birds and the mother is reducing the threat. D) The bird has recognized an attempt at brood parasitism and is removing the threat. Which is an example of aposematism? A) The snowshoe hare's coat color helps it effectively hide from predators. B) Brightly colored wings on a butterfly warns predators that it is toxic. C) Eyespots on a moth's wings deceive a predator into believing it is being watched. D) Cleaner wrasse sit still in a conspicuous location to advertise that they will eat parasites off of the gills of larger fish. E) The dominance of a male gorilla is indicated by silver-gray hair on its back. B) Brightly colored wings on a butterfly warns predators that it is toxic. Because increased fecundity means increased fitness, we might expect to observe the evolution of ever-increasing fecundity, but this is not the case. Which reason for lower-than-expected fecundity is plausible? A) While beneficial to the population or species, selection for increased fecundity is harmful to the individual. B) There are allocation trade-offs between fecundity and other traits. C) All of the above are plausible reasons. D) Increased fecundity leads to overpopulation and mass starvation, due to increases in individual fitness. B) There are allocation trade-offs between fecundity and other traits. Which of these describes antagonistic pleiotropy? A) Mating only once in life, then dying B) Steep