EVOLUTION EXAM 2-SCOTT ROGERS BGSU

Explain the factors that may limit adaptations.

1) Lack of GeneticVariation. Limit the response of a trait to natural selection. Organism may not have the genetic variation that will allow for tall adaptations to develop. Example: The ability of leaf beetles to shift host plants. Some species of beetles can not use another plant host, because they do not have the genetic variation to use the new plant as a feeding source. 2) Evolutionary Trade-offs. Compromises among competing demands. Example: Begonia flower size. It is advantageous for the female flower to be bigger, but in the process of getting bigger the plant produces fewer flowers. Example: Development time and aging in Drosophila. One can select for reduced development time, but you also get a reduction in lifespan. 3) Evolutionary Constraints. Restrictions, limitations or biases on the outcome of adaptive evolution. Traits that would appear to be adaptive may be physiologically or mechanically problematic. Their evolution may be constrained by their structural or functional organization or by their phylogenetic history. Example: An evolutionary constraint may help explain why something did not evolve: Why elephants do not have wings?, Why couldn't arthropods evolved to be as large as elephants? Functional Constraints: defines the range of alternative nucleotides that is acceptable at a site without affecting negatively the function or structure of the gene or the gene product. The stronger the functional constraints on a macromolecule are, the slower its rate of substitution will be. Developmental Constraints: defined as biases on the production of variant phenotype tions on phenotypic variability caused by the structure, character, composition, or d the developmental system Phylogenetic Constraints: defined here as any result or component of the phylogenetic history of a lineage that prevents an anticipated course of evolution in that lineage. Example: Phylogenetic congruence and discord for doves and their feather lice (SEE SLIDE)

How old is Earth?

4.55 billion years old

Why was the 1918 influenza pandemic so serious

A susceptible host population and a changing influenza A virus population

What are quantitative traits?

A trait for which phenotypes do not fall into discrete categories, but instead show continuous variation among individuals; a trait determined by the combined influence of the environment and many loci of small effect.

What are qualitative traits?

A trait for which phenotypes fall into discrete categories (such as affected versus unaffected with cystic fibrosis)

Describe adaptation and fitness

Adaptation- A trait that increases the ability of an individual to survive and reproduce compared to individuals without the trait. Examples: giraffes neck, elephant trunk, camel hump, defensive traits, ability to fly, to camouflage, hibernation, evolution of complex social system Fitness- The extent to which an individual contributes genes to future generations, or an individual's score on a measure of performance expected to correlate with genetic contribution to future generations (such as lifetime reproductive success)

What is aging?

Aging is a late-life decline in an individual's fertility and probability of surviving. Aging and death are necessary to assure enough genetic variation in each generation to meet continuous environmental changes and challenges. There are limited resources so immortality would eventually lead to depletion of food and energy supplies.

which one of these is an example of macroevolution

Antibiotic resistance in bacteria

How do the proportions of alleles in the population change based on selection, random drift, and linkage?

As Natural selection is the process by which the most adaptive traits for an environment become more common generation after generation. It is not a random process. However, genetic drift is random. Genetic drift is nonadaptive, it changes allele frequency without regard to fitness.

How have asexual multicellular plants and animals managed to persist as species over millions of years?

Asexual plants and animals have managed to persist through alternating between asexual reproduction. Scott says: I indicated this is a few lectures. Most have become polyploid, includingmany plant species, and some animal species (including some nematodes). Because theyhave multiple copies of each gene, some of the genes can mutate, thus becoming allelesof the genes. Therefore, they can have more genetic diversity to react to environmentalchanges. Also, recombination does occur in somatic cells during mitotic divisions(although at lower rates than in meiosis), so there are recombination events that scramblethe alleles, similar to those events in meiosis.

Explain how the bar-headed goose evolved gradually as the Himalayas grew higher.

Bar-headed goose flies long distances at high altitudes. (29,500 ft) They fly along a path that follows the curvature of the Himalayas in order to conserve energy to stay warm even though it makes their flight path longer They have added cytochrome oxidases in their bodies in order to have a higher affinity for oxygen intake, and to change their metabolic oxygen utilization and cellular ATP supply Their lungs (which are larger than average) allow high ventilation rates and an effective breathing pattern, and have a thin, strong, and large gas exchange surface They also utilize a lung air sac system Their brain blood vessels have an insensitivity to low CO2 levels They have a large heart with highly capillarized muscle Have abundant subsarcolemmal mitochondria Highly capillarized flight muscles

Describe how chromosomes evolve among species.

Chromosomes evolve in species through new genetic combinations through sexual reproduction, meiosis, and recombination. Sexual reproduction involves two "n" ploidies from two different individuals joining during fertilization to create a new, unique genetic combination. Meiosis is characterized by independent assortment, where, when the chromosomes line up along the metaphase plate, the chromosomes can be on either side (mom and dad's chromosomes align in any order). Recombination occurs at cross-over points in prophase I of meiosis. The sister chromatids overlap creating a tetrad, where random crossing over occurs. Three sources of variation also affect different individuals. Genotype by environment cause a phenotype to form due to a suite of traits in an individual from both genetic and environmental influences. Phenotypic plasticity occurs in genotype by environment. This is the ability of a genotype to change its phenotype in response to changes in the environment. Genetic variation (see above) also affects chromosome evolution. Environmental variation also influences chromosomal evolution. Environmental variation causes death to individuals that are not fit to live in the current environment and thus gets rid of unfavorable genotypes.

Explain the concept of evolutionary trade-offs in relation to the development of particular lifestyles and traits.

Concept of Trade-off: losing one quality or aspect of something in return for gaining another quality or aspect. Examples: Sockeye salmon early spawners reserve more energy for nest defense, and live longer, than late spawners Tradeoff between reproduction and flight capacity in female sand crickets. Short-winged females have limited distribution of eggs, better flight while long-winged females have a broad distribution of eggs, not good flight. Giraffes can reach high branches where others cannot reach. Has difficulty drinking, and is vulnerable to predation when in a drinking position. Has a huge heart and high blood pressure to pump blood to heart. When dipping head to drink, blood flow is restricted to head.

Selection occurs within cells because of mutations that cause problems with:

DNA replication RNA transcription RNA processing translation

Who helped to develop the theory of the origin of species by natural selection?

Darwin, Wallace, and Bates

Describe directional, stabilizing, and disruptive selection.

Directional selection- That which occurs when individual fitness tends to increase or decrease with the values of phenotypic trait; can result in steady evolutionary change in the mean value of the trait in the population. Disruptive selection- Occurs when individuals with more extreme values of a trait have higher fitness; can result in increased phenotypic variation in a population. Stabilizing selection- That which occurs when individuals with intermediate values of a trait have higher fitness; can result in reduced phenotypic variation in a population and can prevent evolution in the mean value of the trait.

What are the differences between disruptive selection and stabilizing selection?

Disruptive selection- Occurs when individuals with more extreme values of a trait have higher fitness; can result in increased phenotypic variation in a population. Stabilizing selection- That which occurs when individuals with intermediate values of a trait have higher fitness; can result in reduced phenotypic variation in a population and can prevent evolution in the mean value of the trait.

How does genetic recombination affect linkage disequilibrium?

Genetic recombination breaks down the linkage disequilibrium generated between genes. RECOMBINATION breaks down the linkage disequilibrium generated between genes. In the absence of mutation and in a constant environment, the linkage disequilibrium present in a population will largely be a product of selection favoring specific gene combinations. In this case, one would expect that recombination would be detrimental and that genes that modify recombination rates would evolve to reduce recombination. This intuition is confirmed by the "reduction principle": in models at equilibrium under viability selection, modifier alleles that reduce recombination are favored in the absence of mutation

Which one of these is an example of microevolution?

Genetic variation among African elephants (Loxodonta africana)

Be familiar with the Hardy/Weinberg equilibrium equation and graph.

Hardy Weinberg equilibrium- A situation in which allele and genotype frequencies in an ideal population do not change from one generation to the next, because the population experiences no selection, no mutation, no migration, no genetic drift, and random mating. H/W as a null hypothesis Example: If you were interested in the influence of the drought on beaks of finches. You would want a control when there is no drought, This would be the null hypothesis. Then, you would compare beak sizes when there is no drought (null hypothesis) to those when there is a drought event. Equation: p2+2pq+q2=1 p2= frequency of AA (homozygous dominant) 2pq= frequency of Aa (heterozygous) q2= frequency of aa (homozygous recessive)

What are the main assumptions that Hardy and Weinberg used to develop their ideas on gene equilibria within populations?

Hardy and Weinberg assumed that if Mendel's laws apply then the frequencies of alleles and genotypes in a population remain constant from generation and generation. Mendel's laws that they used were: there are no mutations within a population, the matings are controlled, there is no natural selection, there is no genetic recombination, there is no migration or gene flow, and there is no genetic drift. The dominant allele is called "p". The recessive allele is called "q". p+q=1. Allele frequencies: "AA" is p2, "Aa" is 2pq, "aa" is q2. p2 +2pq +q2=1.

What are the possible causes of linkage disequilibrium?

Linkage disequilibrium- Nonrandom association between alleles at two or more loci (in the same or different chromosome). If in the same chromosome= linkage due to limited recombination between them Causes of linkage disequilibrium -Genes close in the same chromosome (Limited recombination) -Genetic drift -Population admixture (when 2 or more previously isolated populations begin interbreeding) -Selection

What can reduce or eliminate linkage disequilibrium in a population?

Linkage disequilibrium= Nonrandom association b/t alleles at two or more loci (in the same or different chromosome). If in the same chromosome= linkage due to limited recombination b/t them. Sexual Reproduction: Genetic recombination resulting from meiosis and outbreeding breaks up old combinations of alleles and creates new ones.

Be able to explain Mendelian inheritance, as well as crosses that result in results that appear non-Mendelian.

Mendelian inheritance occurs when two discrete traits are crossed and the outcomes can be easily traced. Each gene can only have 2 discrete traits (two different outcomes). Monohybrid cross ratio is 3:1. Dihybrid cross is 9:3:3:1. Codominance is 1:2:1. Incomplete dominance is 1:2:1. Recessive epistasis is 9:3:4. Complementary gene action is 9:7. Recessive lethal alleles is 2:1. Dominant epistasis is 12:3:1. Novel phenotypes are 9:6:1.

How do multigene families evolve and lead to the evolution of species and higher taxonomic groups?

Multigene families include groups of genes from the same organism that encode proteins with similar sequences either over their full lengths or limited to a specific domain. DNA duplications can generate gene pairs. If both copies are maintained in subsequent generations then a multigene family will exist. A multigene family is a member of a family of related proteins encoded by a set of similar genes. Multigene families are believed to have arisen by duplication and variation of a single ancestral gene. Examples of multigene families include those that encode the actins, hemoglobins, immunoglobulins, tubulins, interferons, histones etc. Scott says: I discussed a few examples of this in class. One was the globin gene family. I described the globin genes that were turned on early in development, and those used later in adults. There was a progression from invertebrates, to fish, to amphibians, to marsupial mammals, and then to placental mammals. I also described the evolution of histone genes, although not in as much detail. Go back through those slides in the notes.

Explain why evolution fails to produce perfect organisms (10 points) [HINT: Use mutation, natural selection, and random genetic drift in your answer.]

Mutations cause random (or nearly random) changes in the DNA, and there is no direction to this process, which is not perfect at all. Natural selection acts on the results of those mutations, but it does so for the organism as a whole. Therefore, while some mutations might increase the fitness of the organism for one particular environment at on specific time, the organism carries mutations in other genes that might decrease its fitness in another environment at another time. Additionally, because environments are always changing, there can be no perfect organism for every possible environment or environmental change. Random genetic drift is the process of the accumulation of random mutations that are neutral (i.e., neither positive nor negative selection acts on them). These mutation cause genetic variation in the population for large numbers of genes, which may be under selection in a different environment at a different time. With so much variation among the alleles and genes, no perfection is possible.

Do all eukaryotes engage in sexual reproduction? If not, how do they survive and evolve?

No not all eukaryotes engage in sexual reproduction and some can change from sexual to asexual and back. There are asexual lizards, salamanders and fish species Female desert grasslands whiptails lay unfertilized eggs that hatch into clones of their mother. There are no males. Numerous plant species that are asexual (clonal) Other species alternate between aexual and sexual reproduction Aphids reproduce asexually in the spring and summer (parthenogenesis); and sexually in the fall The water flea, Daphnia may shift from asexual to sexual dependent on environmental conditions

What is parthenogenesis?

Parthenogenisis is an asexual mode of reproduction, in which an embryo develops from the egg without fertilization. Occurs in nematodes, water fleas, some scorpions, aphids, some mites, some bees, some Phasmida and parasitic wasps, and a few vertebrates (such as some fish, amphibians, reptiles and very rarely birds).

How do alterations in cell cycles lead to polyploidy, polyteny, amplification, and other variations in DNA amounts per cell?

Polyploidy is the state of a cell or organism having more than two paired (homologous) sets of chromosomes. Polyteny chromosomes are large chromosomes which have thousands of DNA strands. Gene amplification refers to a number of natural and artificial processes by which the number of copies of a gene is increased "without a proportional increase in other genes".

What are some prezygotic and postzygotic barriers that cause reproductive isolation?

Prezygotic barriers: impede mating between species or hinder the fertilization of ova if members of different species attempt to mate Habitat isolation- populations live in different habitats and do not meet Behavioral isolation- little or no sexual attraction b/t males and females Temporal isolation- mating or flowering occurs at different seasons or times of day Mechanical isolation- structural differences in genitalia or flowers prevent copulation or pollen transfer Gametic isolation- female and male gametes fail to attract each other or are inviable Postzygotic barriers: often prevent the hybrid zygote from developing into a viable or fertile adult. Reduced hybrid viability- hybrid zygotes fail to develop or fail to reach sexual maturity Reduced hybrid fertility- hybrids fail to produce functional gametes Hybrid breakdown- offspring of hybrids have reduced viability or fertility

Describe the differences between qualitative and quantitative genetic loci.

Qualitative traits: phenotypes fall into discrete categories. Quantitative traits: phenotypes do not fall into discrete categories, but instead show continuous variation among individuals. These phenotypes are determined by a combination of many loci of small effect plus influences from the environment. Mendelian model genetics can explain these (the F2 generation will give a normal distribution of phenotypes). Environmental variation also affects quantitative traits.Quantitative trait loci are genes/loci that can explain a significant proportion of the variation in a quantitative trait (can be identified using QTL mapping or candidate loci). SEE CHART

Be able to describe and/or draw various life histories/cycles.

SEE CHART

Draw a phylogenetic tree that includes the following: you, a dog, an alligator, a bacterium, an chimpanzee, and an oak tree (10 points).

SEE CHART

Draw the life cycle of one or two different types of organisms. Be sure to include chromosome and/or DNA levels in cells at the various life stages.

SEE CHART

Place the following events on the timeline below: a. Darwin's voyage on the HMS Beagle; b. Determination of DNA structure; c. Invention of the microscope; d. Mendel reports his experiments on inheritance of characters in peas; e. Field of Genetics founded. [10 points. Please use arrows to indicate the position of each event.]

SEE CHART

Place the following events on the timeline below: a. Formation of the Moon; b. First dinosaurs appear; c. First Bacteria appear; d. First red algae (plants) appear; e. First Eukaryotes appear. [10 points. Please use arrows to indicate the position of each event.]

SEE CHART

What are the advantages and disadvantages to sexual versus asexual reproduction?

SEE CHART

Describe how selection, mutation, migration (gene flow), and genetic drift can affect allele frequencies in a population.

Selection (artificial or natural) is when certain traits (alleles) are removed or promoted in a population. This depends on how fit the allele is in an environment. If an allele is less fit, the organism that exhibits that trait will die and the allele will cease to exist. If an allele is fit in an environment then the individual that has those traits is more likely to live and reproduce thus spreading those alleles into more of the population. Natural selection can cause microevolution, or a change in allele frequencies over time, with fitness-increasing alleles becoming more common in the population over generations. It refers to how many offspring organisms of a particular genotype or phenotype leave in the next generation, relative to others in the group Mutations occur in many different ways. If a mutation is a positive mutation it will be favored when the organism reproduces. This mutation will then be passed down from generation to generation so that those individuals will remain more fit in the population. If a mutation is negative, then that individual will be less fit for the environment and will thus die keeping that individuals mutations and genes out of the population. Mutation is a weak force for changing allele frequencies, but is a strong force for introducing new alleles. Mutation is the ultimate source of new alleles in plant pathogen populations. It also is the source of new alleles that create new genotypes (such as new pathotypes) within clonal lineages. Migration also affects allele frequencies in a population. When a population of species diverges and migrates apart, each population will have mutations occur to make them more fit for the specific environment that they are in. Reproduction also causes these changes. If the two species migrate back together then they may not be able to reproduce due to being too different. Migration is another source of genetic variation that can also change gene frequencies and result in evolution. When organisms join a population and interbreed with residents, the subsequent generation will exhibit gene frequencies that differ from those in the population prior to the arrival of the migrants. Genetic drift is a change in allele frequencies in a population from generation to generation that occurs due to chance events. To be more exact, genetic drift is change due to "sampling error" in selecting the alleles for the next generation from the gene pool of the current generation

Why does sexual reproduction persist, in spite of the fact that it is expensive and hazardous?

Sexual reproduction generates genetic variation by reshuffling the various genes carried by individuals in a population. The genomes of diploid/polyploid sexually reproducing organisms can become even larger due to increased copies of genes which adds more correction of mutations.

Explain some of the causes and effects of aging.

Some aging is caused by DNA replication and telomere shortening. DNA polymerase cannot add nucleotides to the end of linear chromosomes Telomeres are added early in development (in the womb) and are added to the ends of the chromosomes by telomerase (a reverse transcriptase enzyme) to protect the chromosome. Once born, the telomerase is never active again. Chromosomes get shorter with each replication cycle. Once the telomeres are gone parts of the gene begin to disappear leading to aging and death Long lived species have long telomeres and robust DNA repair systems Some aging has been explained by DNA mutation and dysfunction Mitochondrion: site of oxidative phosphorylation and highest concentrations of oxygen This process oxidizes the mitochondrial DNA causing mutations, failure of genes, and eventual death of the mitochondria and then the cell. Rate-of-living theory Aging is caused by the accumulation of irreparable damage to cells & tissues by errors during DNA replication (or by unrepaired to somatic mutation damage), telomerase shortening, transcription or translation, plus any poisonous metabolic by-products Ex: oxygen gas free radicals that are known to cause mutations Age should be correlated to metabolic rate Organisms should not be able to evolve longer life spans because they have been selected to resist and repair damage to the maximum extent possible Genetic constraint: lack of variation to evolve causes more effective mechanisms Experimental data is NOT consistent with this theory because all organisms do not have the same lifetime energy expenditure Evolutionary theory of aging Mutational accumulation theory: we age because the strength of selection decreases with age. Any deleterious mutations that act after reproductive age will not be selected against. This can lead to deleterious mutations that cause organisms to become less fertile and less able to survive as they age Antagonistic pleiotropy theory: there are deleterious mutations late in life that might have been beneficial early in life Ex: Huntington's disease; individuals with HD have more offspring during reproductive years, but they die from neurological problems right afterwords

Explain how speciation events occur.

Speciation occurs when a group within a species separates from other members of its species and develops its own unique characteristics. New species arise in a three-stage process A barrier is established Divergence of traits Reproductive isolation Examples: Males song and female preferences in Hawaiian crickets. Speciation involving mating behavior= assortative mating can contribute to reproductive isolation Temporal isolation among Japanese winter moth populations Speciation by reversal of shell-coiling direction in Japanese land snails (single gene). Reproductive isolation due to anatomical reproductive incompatibility= mechanical isolation Speciation by dispersal and colonization events Allopatric speciation single species distributed over a broad range. leads to Geographic barrier, local adaptation, reproductive isolation Examples: Hawaiian Drosophila, Galapagos finches Speciation by Hybridization two species interbreed (hybridize) and give fertile offspring, producing an immediate speciation event. Leads to hybrids that may have higher fitness (Formation of Stable Hybrid Zones) Examples: Annual sunflowers, oaks hybrids Sympatric Speciation in plants autopolyploidy: multiple chromosome sets derived from same species allopolyploidy: multiple chromosome sets derived from different species

What are the general steps of sexual reproduction, and how has it been successful and important in the evolution of eukaryotes?

Steps in sexual reproduction Meiosis: creates new combinations of alleles through recombination (formation of tetrads/crossing over sites), resolution, and separation of chromosomes. Production of gametes: must have opposite mating types (+/-, a/𝛼, X/Y etc) or egg cells/sperm cells Fertilization: this mixes different allele combinations (half of genes from mom and half of genes from dad). This is also a test to see if the combination will produce viable offspring. Development: only in multicellular species. This is also a test to see if the combination will produce viable offspring

How can bacterial infections affect sex ratios?

The sexual dimorphism in bacterial infections has been mainly attributed to the differential levels of sex hormones between males and females, as well as to genetic factors. This can effectively change sex ratios in some species. Bacterial infections follow the Red Queen Hypothesis (pathogen-host coevolution). This states that the host organism must keep evolving to have some resistance to the parasite because the parasite is also evolving (can include change in sex).

Darwin had problems explaining the elaborate tail of the peacock. The tail is clearly visible to predators. The males of other bird species have brightly colored and elaborate plumage. Explain why these brightly colored patterns continue to persist in these species (10 points)

The tail feathers of the male attract females, such that there are more successful matings by males with showy tail feathers. Although predation also increases in the showy birds, the rate of offspring produced is higher than the loss due to predation. Also, when measured, it was found that the offspring produced by the showiest males lived longer than those produced by males with less showy tail feathers. Therefore, the showy tails also indicated a better set of genes.

Endosymbiotic bacteria (e.g., Wolbachia) can cause a number of different changes in host organisms. Describe some of these.

Wolbachia (a bacterial genus) Parasitic in some insects and nematodes Can change sex ratio's in some species They are mutualistic: they are helpful in some species by increasing reproduction They can cause resistance to viruses in some species They are endosymbionts: the live inside host cells without killing them They can aid in nutrition in some species Endosymbionts are organisms that form a symbiotic relationship with another cell or organism. Some endosymbionts can be found either inside cells (intracellular), while others attach to the surface of cells (extracellular). Other examples of these are chloroplasts (absorbs sunlight and use it in conjunction with water and carbon dioxide gas to produce food for the plant) and mitochondria (They are organelles that act like a digestive system which takes in nutrients, breaks them down, and creates energy rich molecules for the cell. The biochemical processes of the cell are known as cellular respiration. They allow us to be aerobic organisms)

A transposon is:

a DNA element that can move from one chromosomal region to another

A transversion is:

a change from a purine to a pyrimidine, or vice versa

A transition mutation is:

a change from a purine to different purine, or a pyrimidine to a different pyrimidine

A missense mutation in an mRNA is when the mutation causes:

a change in the amino acid sequence

Which of the following pairs represents homologous structures:

a human arm and a bird wing

Natural selection:

acts on the individual but affects the population

Natural selection:

eliminates individuals that are generally less fit than others in the population

Introns:

have been important in evolution

The numbers of black individuals and white individuals of peppered moths changed in England during the 1800's because of:

increasing amounts of soot on tree trunks increased predation on white individuals by predators (i.e., birds) natural selection industrialization

A phylogenetic tree:

is a model of evolutionary relationships among taxa (species, etc.) is usually constructed using DNA, RNA, or protein sequences indicates the distances between the individual taxa based on shared characters provides information regarding ancestral groups

in mammals and birds, if there is competition among males for females:

males are usually larger than females

biological evolution is the result of

mutation, natural selection, and random drift

A synonymous mutation in an mRNA is when the mutation causes:

no change in the amino acid sequence

Influenza A viruses are able to change rapidly to avoid immune systems by

recombination and reassortment of its genes

Spliceosomal introns are found in:

ribosomal RNA genes or messenger RNA genes

In the hollyhock weevil, the female is larger and has a longer snout than the male because:

the female needs a longer snout to bore holes into the hollyhock flower buds in order to lay her eggs

Evidence that strongly supports evolution is

the large fossil record the presence of vestigial structures breeding to accomplish artificial selection homologous traits among species

A nonsense mutation in an mRNA is when the mutation causes:

translation to stop

Just before life began on Earth, what biologically important chemicals were present

water, amino acids, RNAs, fatty acids, simple sugars, and hydrogen