Evolution Exam 2

Explain genetic assimilation.

A character state that initially developed in response to the environment had become genetically determined.

What factors might maintain both reproductive modes?

Access or availiablity of mates, disease, or parasites might maintain both reproductive modes.

what is the red queen hypothesis and why is it closely related to the evolutionary benefits of sex?

All species are in an arms race with each other. sexual reproduction allows for new recombinants in species in order for them to "get ahead" in the "race" through beneficial recombination.

hermaphrodite

An individual that functions as both male and female in sexual reproduction by producing both sperm and eggs.

copy number variation

As a chromosome with a new gene duplicate spreads through a population, there is polymorphism in the number of copies of the gene that individuals carry.

asexual vs sexual reproduction

Asexual reproduction generates offspring that are genetically identical to a single parent. In sexual reproduction, two parents contribute genetic information to produce unique offspring.

How might studies of these species shed light on the factors that maintain sexual reproduction?

Because only fit males are able to mate, sexual selection is thought to be one way by which sexual reproduction is maintained. Asexual reproduction would be favored in an environment free from enemies, but it is unlikely they will persist over time, because it is harder for them to adapt when the environment changes.

Spiteful

Both individuals are harmed

In the figure, the star represents a recent mutation at a gene locus. The letters represent other loci. Which other locus is most likely to be in linkage disequilibrium with the mutation (all else being equal; assume a sexually reproducing organism)?

C

nonsynonymous

Changes to first and second positions are likely to be nonsynonymous, that is, to change the protein

direct fitness.

Consider an allele that causes individuals to act altruistically, for example by saving drowning brothers. An individual carrying the allele can pass copies of it to his or her own children.

How can changes in cis-regulatory elements happen? Where do new cis-regulatory elements come from?

Deletion of an enhancer can prevent a characteristic from developing. Many changes in cis-regulation evolve by mutational changes in the enhancer's sequence.

What is the famous breeder's equation and explain the message from this Equation?

Delta z=z'-z = h^2S The Breeder's equation is used to predict how much evolutionary change will result from selective breeding.

sexual dimorphism

Differences in physical characteristics / traits between males and females of the same species.

gene duplication

Duplication is the most common way that new genes arise in eukaryotes. At the molecular level, duplications are caused by several mechanisms. One is unequal crossing over, in which recombination happens between different positions on chromosomes that are misaligned during meiosis. Another is replication slippage, in which the DNA polymerase loses its place and copies a segment of chromosome twice.

What is the mst common way that new genes arise in eukaryotes? Explain it.

Duplication is the most common way that new genes arise in eukaryotes. At the molecular level, duplications are caused by several mechanisms. One is unequal crossing over, in which recombination happens between different positions on chromosomes that are misaligned during meiosis. Another is replication slippage, in which the DNA polymerase loses its place and copies a segment of chromosome twice. In either event, the resulting chromosomes can carry a gene that is duplicated in tandem with the parental copy. A third way that gene duplicates arise is by retrotransposition, Here the messenger RNA from a gene is reverse-transcribed to DNA, which is then integrated into the genome. The result is a duplicate gene that is far from the parental copy, often on a chromosome. Duplicates that originate this way can be distinguished from their parental genes because they lack introns, which were spliced out of the MRNA before it was reverse-transcribed.

cis-regulatory elements

Enhancers means that the element regulates a gene on the same stretch of DNA.

Explain the difference between cis and trans regulatory elements.

Enhancers are often called cis-regulatory elements. Cis means that the element regulates a gene on the same stretch of DNA. Transcription factors are trans-regulatory elements, meaning that they are encoded by DNA distant from the genes that they regulate.

Explain how tissue differentiation is possible if all of an organism's cells have (nearly) identical DNA

First, all cells in an organism have the same set of genes, based on replication during mitosis. Second, the differences among cells, tissues, and organs must result from differences in the activity of certain genes. Third different cells have properties that affect morphogenesis (the development of form). These include growth of individual cells, change in cell shape, adhesion to certain other cells, mitosis in certain dimensions (e.g, forming sheets or masses), cell movement (in animals but not plants), and programmed cell death (apoptosis). Fourth, many aspects of growth and differentiation are affected by chemical signals, especially hormones. For example, metamorphosis in amphibians is triggered by thyroxine, produced in the thyroid gland. The axolotyl does not synthesize thyroxine, and it differentiates into a typical adult form if it is injected with that hormone.

What is horizontal gene transfer and how does occur? Why is it beneficial?

HGT is the movement of DNA between different individuals without help from sexual reproduction. HGT can move genes between individuals of the same species and sometimes different species. For example, viruses do this by inserting a piece of the hosts genome into its own and then transferring it to another host. HGT is important to the evolution of antibiotic resistance in bacteria that are responsible for important human diseases.

additive genetic variance.

Here G is an important quantity. It is the part of the phenotypic variation that is caused by genetic variation and that contributes to the resemblance between parents and offspring.

Retrotransposition

Here the messenger RNA from a gene is reverse-transcribed to DNA, which is then integrated into the genome.

Define heterochrony and heterotopy.

Heterochrony is broadly defined as an evolutionary change in the timing or rate of developmental events. Heterotopy is an evolutionary change in the spatial position of a feature within an organism.

When does hitchhiking happen and what is its responsibility?

Hitchhiking happens when an allele at one locus spreads by natural selection acting on a second locus that is in linkage disequilibrium with the first. It is responsible for the evolution of genes that themselves do not impact survival or fecundity, but that do have other effects.

Compare how biologists define male and female sexes with common stereotypes of differences between human males or females.

Humans are more compared through what they look like, as well as the differences in the number of sex chromosomes they have. Other organisms are compared based on the physical and social environments around them.

What is the reason for differences in the number of chromosomes between humans and great apes?

Humans have 23 pairs of chromosomes, but all of the other great apes have 24 pairs. At some point since our lineage split from that of chimpanzees, two chromosomes fused. That mutant chromosome spread throughout our species, resulting in the second-largest chromosome in the human karyotype.

Selfish

If the actors fitness increases but the recipients is harmed

transcription factors and enhancers

In eukaryotes, transcription of a protein-coding gene is initiated when RNA polymerase II binds to an upstream region, the promoter. This occurs when certain regulatory proteins(1) that determine transcription of a gene bind to a short upstream region. (2)

male/female

In humans, the male has an X and Y sex chromosome. The human female has two X chromosomes. In Birds, the female has a Z and a W sex chromosome while the male has two Z chromosomes. In other organisms, sex is determined by the physical or social environment.

phenotypic plasticity

In some cases, a single genotype may produce different phenotypes in response to environmental stimuli

Cheating

It can benefit from the actions of others without providing benefits to them in return.

explain a linkage disequilibrium and importance of it.

Linkage disequilibrium is the non-random Association of alleles at different loci. It is important because it affects how genes evolve and because it allows us to find genes that affect traits of interest.

What are the risks and benefits of cooperation?

Natural selection favors the evolution of cooperation among unrelated individuals when the fitness costs of cooperation are equaled or surpassed by the direct fitness benefits, that is, an increase in fitness of the individual performing the behavior. An individual that joins a group can lower its risk of predation simply by finding safety in numbers Predators such as wolves hunt cooperatively, and share prey that a single individual could not capture by itself. These behaviors are beneficial to both the actor and the recipient.

What explains the large scatter in the DNA content of eukaryotes compared with prokaryotes?

Neither of them have huge genome sizes, and they both have little to no non-coding DNA.

Ontogeny does not recapituale phylogeny

One of Darwin's most enthusiastic supporters, the German biologist Ernst Haeckel, reinterpreted such patterns to mean that "ontogeny recapitulates phylogeny"-that is, that the development of the individual organism (ontogeny) repeats the evolutionary history of the adult forms of its ancestors, and could indicate its phylogenetic relationships. By the end of the nineteenth century, however, it was already clear that Haeckel's dictum seldom holds2), For example, the pharyngeal clefts and associated branchial arches of embryonic mammals and reptiles never acquire the form typical of adult fishes. Moreover, 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. Thus ontogeny is not a very useful guide to phylogenetic history.

Provide two reasons or scenarios that explain why scientists have not found bat ancestors with proto-wings.

One reason could be that the evolution of the wing was a fairly fast and this is because we have no evidence of evolution in the wings. Another reason could be that we just haven't found the evidence in the fossil record yet, and it could happen in the future.

neoteny

One way paedomorphosis can happen, seen in the axolotl, a salamander that grows to full size but does not undergo metamorphosis, as most salamanders do. Instead, it reproduces while retaining most of its larval (juvenile) characteristics.

New phenotypes without mutations.

Quantitative traits can evolve to produce entirely new phenotypes, using only alleles that are already in the population, without the introduction of new mutations.

what is a selective interference and explain it's types?

Selective interference is when alleles are not selected independently, and there is not much genetic mixing. The first type, clonal interference, happens when two or more beneficial mutations spread through a population at the same time. Next, the ruby-in -the-rubbish effect, which is the loss of beneficial mutations as the result of their linkage to deleterious mutations. Lastly, Muller's Ratchet, which is the irreversible accumulation of deleterious mutations in an asexual population.

Would you expect such populations to become entirely asexual or sexual?

Sexual because entirely asexual populations are extremely rare. The cost of sexual reproduction is considered to be twice that of asexual reproduction, because sexual females produce about 50% male offspring, and males typically contribute only their genes to reproduction. Asexual reproduction should dominate, according to this logic, but that is not the case.

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.

Some organisms have a tremendous amount of noncoding DNA, like repetitive sequences

There are many traits for which it seems natural selection should favor an increase every generation, such as survival from birth to reproduction. In most cases, when we look for such increases in natural populations we do not see the predicted change. Make a list of all the reasons we might not see a response to directional selection on such a trait. Include reasons suggested by the material in this chapter, as well as any other reasons you can think of.

Some reasons could be a lack of genetic variation, a lack of additive genetic variation, conflicting selection on other traits genetically correlated with the trait of interest, environmental change from one generation to the next, and a continuing deterioration in the environment that causes evolutionary increases to be balanced by environmentally driven decreases.

serially homologous

Some such modules are repeated at various sites on the body

alternative splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins or protein isoforms. Increases the diversity of proteins.

Altruistic

The actor suffers but the recipient benefits

DNA methylation

The addition of methyl groups to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression.

the result indirect fitness.

The allele can also pass extra copies of itself to the next generation as the result of the increased fitness of relatives that benefit from the altruistic individual's actions.

modules-distinct

The bodies of many organisms consist of distinct units that have distinct genetic specifications, developmental patterns, locations, and interactions with other modules.

genotype-environment interaction

The differential response of individuals with different genotypes to the same environments.

genetic assimilation

The disappearance of a species as its genes are diluted through crossbreeding with a closely related species.

At many sites in the genome, an Alu element is present in humans but absent in chimpanzees, while at many other sites a Alu element is present in chimpanzees but absent in humans. What are two hypotheses that could explain this situation? For any particular site, how could the hypotheses be distinguished?

The first hypothesis was that the Alu element was present at the site in the common ancestor of humans and chimps, and then was lost within the two lineages. The next hypothesis is that it was inserted into the site in one of the two lineages since they diverged. They can be distinguished by examining the same site of the gorilla genome.

Mutualistic

The fitness of both indiciduals is increased

gene family, biochemical

The loci that encode hemoglobins are members of a gene family, which is a set of loci that arose by duplication and that code for proteins that typically continue to have similar biochemical function.

Explain the relation between phenotypic distribution and environmental variation if a single locus or ten loci affects the trait.

The phenotypic distributions become smoother with larger numbers of loci. The combination of a moderate number of loci with some environmental variation explains why so many familiar traits such as body height vary in a smooth, continuous way

Which elements affect on the variation of phenotype?

The phenotypic variance results from both genetic and environmental (nongenetic) causes

What is "reaction norm"?

The set of phenotypes that genotype is capable of expressing under different environmental conditions and can be visualized by plotting the genotypic phenotypic value in two or more environments.

quantitative traits.

These are traits that vary continuously and that are affected by several, sometimes thousands, of loci (and for that reason they are also called polygenic traits).

environmental variance

These contribute environmental variance to the trait, causing individuals with the same genotype to have different phenotypes.

hitchhiking

This happens when an allele at one locus spreads by natural selection acting on a second locus that is in linkage disequilibrium with the first

by phenotypic variance factors combine

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.

Recombination

This is the process that combines in a gamete a gene copy at one locus that was inherited from the mother with a gene copy at a second locus that was inherited from the father.

trans-regulatory elements,

Transcription factors they are encoded by DNA distant from the genes that they regulate.

True or False. Guided in part by Charles Lyell's teachings in Principles of Geology, Darwin concluded that Evolution by Natural Selection often occurs through a slow, gradual process. Provide an example in living organisms that supports your answer.

True. An example of this could be how the grand canyon came to be how it is today. The idea of common decent also is an example of this.

pseudogene

When a nonfunctioning duplicate is fixed in the population, or a functioning gene becomes nonfunctional, the result is a genetic skeleton

linkage disequilibrium

When an allele at one locus is found together in a population more than expected by chance with an allele at a second locus, we say the loci are in linkage disequilibrium.

Cooperative

When one individuals behavior benefits another

subfunctionalize

a duplicate gene and its parental copy can subfunctionalize so that each carries out only some of the roles that the ancestral gene performed.

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.

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

Heterotopy

an evolutionary change in the spatial position of a feature within an organism.

Heterochrony

an evolutionary change in the timing or rate of developmental events.

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.

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 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.

synonymous

changes to third positions or codons are likely to be synonymous, that is, to have no effect on the protein

Which event will not alter an organism's karyotype? a. Allopolyploidy b. Chromosome fission C. Chromosome fusion d. Sequence inversion

d. Sequence inversion

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.

Define dN and dS and explain what does it mean the ratio of dy/ds when it is-1,>1 or <1?

dN is the number of non-synonymous mutations while dS is the number of synonymous mutations. The ratio gives us a rough idea of the relative importance of purifying selection, drift, and positive selection using a simple statistic based on a comparison of the DNA sequences of the same gene from two species. When it is 1, synonymous and nonsynonymous mutations both have very little effect on fitness. Then both types of mutations will have the same chance of drifting through the population to fixation, and so we expect dN /dS to will be much less than 1. When dN/dS->1, more nonsynonymous mutations, which are likely to affect fitness be 1. If most nonsynonymous mutations are deleterious and are removed by purif selection, then dN /dS have been fixed than synonymous mutations, which are likely to be selectively neutral. That suggests the nonsynonymous mutations that fixed had a boost from positive selection.

Heritability

h2 measures the strength of inheritance.

Explain what are Transposable Elements and how they can cause problems in their host genome?

home-they make up almost half our genome Transposable Elements are a type of selfish DNA that is closer to The insertion of a TE into the host's genome causes a mutation that can disrupt a coding sequence or its proper expression. A second problem for the host is that two copies of a TE at different places in the genome can recombine, causing a chromosomal mutation.

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

Breeder's equation

is used to predict how much evolutionary change will result from selective breeding.

what are the evolutionary costs of sex?

less offspring, requirements to find a partner, and sexually transmitted diseases

Some salamander species retain gills and other larval characteristics throughout adult life. This is an example of ______?

neoteny

Neofunctionalization

one of the possible outcomes of functional divergence, occurs when one gene copy, or paralog, takes on a totally new function after a gene duplication event.

Allometric growth, or allometry

refers to the differential rate of growth of different parts or dimensions of an organism during its ontogeny.

Promoters

region of DNA that indicates to an enzyme where to bind to make RNA

partgenogenesis

reproduction that involves the organism to make genetic clones of itself.

group selection

selection arising from variation in fitness among groups

Hox genes

series of genes that controls the differentiation of cells and tissues in an embryo

paedomorphosis

some characteristics of the adult of a species may have a more juvenile form than in the species' ancestor.

individualization

the acquisition of distinct identities by such modules

Morphogenesis

the development of form These include growth of individual cells, change in cell shape, adhesion to certain other cells, mitosis in certain dimensions (e.g., forming sheets or masses), cell movement (in animals but not plants). and programmed cell death (apoptosis).

Von Baer's law

the features common to a higher taxon (such as the Vertebrata) often appear earlier in development than the specific characters of lower-level taxa (such as orders or families)

Purifying Selection

the form of natural selection that acts to eliminate selectively deleterious mutations

Muller's Ratchet

the irreversible accumulation of deleterious mutations in an asexual population

reaction norm

the pattern of phenotypic expression of a single genotype across a range of environments

kin selection

the process by which evolution selects for individuals who cooperate with their relatives

Canalization

the tendency of heredity to restrict the development of some characteristics to just one or a few outcomes

Genome size.

the total amount of DNA contained within one copy of a single genome.