OEB 10 Final

Experimental evidence recently published utilized asexual and sexual lineages of yeast and documented an additional benefit of sexual reproduction that was likened to "picking rubies from the rubbish." Explain how sexual reproduction benefited the yeast cells in this experiment. In your answer be sure to clearly explain the concept of "Mueller's ratchet."

-"Picking rubies" describes the concept of decoupling beneficial and deleterious alleles through recombination. -In exclusively asexual organisms, deleterious mutations should continually accrue in the genome because there is no way of removing them once they arise (Mueller's ratchet). -any beneficial mutations that arise will forever be linked to these deleterious mutations. -Through recombination, however, beneficial mutations can be unlinked from deleterious mutations and can be passed on to subsequent generations without the deleterious mutations.

What is a fixed action pattern? Provide an example. Is a fixed action pattern a result of nature or nurture?

-A fixed action pattern (FAP) is a sequence of behaviors that, once triggered by a stimulus, is followed through to completion. The sequence is not broken down into smaller actions that the organism can complete individually. Rather, the sequence is done as a whole. -One example discussed in lecture was the goose retrieving an egg. If a researcher fixes the egg to the ground so that it doesn't move, the goose will start the FAP for egg retrieval, but continue the motion of rolling the egg even though the egg is absent during most of the sequence.

What is a keystone species? Name a keystone species and describe its influence in a particular ecosystem

-A species that has a disproportionate effect on an ecosystem relative to its abundance or amount of biomass, that usually results in preserving species diversity within the community or preserving the community itself. -otters are a prime example of keystone species. -Otters consume urchins, thereby preserving kelp forests. Kelp forests are incredibly productive ecosystems and harbor numerous species.

It has been suggested that without fungi, the carbon cycle would fail (carbon locked up in lignin in wood). Describe three characteristics of fungi that help to make them such effective decomposers, especially when compared to bacterial decomposers.

-Ability to penetrate wood and then spread throughout the body of the dead tree -dispersal by spores allows fungi to rapidly find new food sources -they can better explore their environment through spreading hyphae -can transport nutrients to other hyphae (even if not long distances) which allows some hyphae to focus on finding new food sources instead of decomposing, etc.

The majority of the temperature change associated with increased global CO2 levels has been absorbed by the world's oceans. One consequence of this increase in ocean temperature is a reduction in arctic sea ice, which has influenced the albedo of the Arctic Ocean. What is albedo, and how can a change in the albedo influence the amount of sea ice in the Arctic Ocean?

-Albedo is the measure of reflectance of a surface. Low albedo implies low reflectance (high absorbance), while high albedo implies high reflectance (low absorbance). -The presence of sea ice (high albedo) can influence the temperature of the Arctic Ocean -There is a feedback loop

-What is an operon? -What impact might operons have on reproduction in prokaryotic cells, specifically genome replication? -Why would gene regulation be more efficient? -How might the utilization of operons facilitate the movement of an entire gene in lateral gene transfer?

-An operon is a cluster of genes in sequence in a genome under control of a single regulatory signal or promoter (i.e., they are controlled together). -The proteins in a single operon are usually involved in a concerted process. -Operons are compact and therefore result in smaller genome sizes. -Operons are efficient because the production of related proteins can be controlled in concert. -Because operons are tightly clustered on the genome, a horizontal gene transfer event would most likely transfer the entire operon to the recipient cell, which would include all of the relevant genes for a given process.

What organisms (domains please!) are capable of nitrogen fixation? Why is nitrogen fixation so important?

-Bacteria and Archaea. -Nitrogen is an essential element for life on earth (component of nucleic acids, proteins, etc), and is often a limiting nutrient in metabolic pathways. -Although nitrogen is the most abundant gas in the Earth's atmosphere, N2 is not useable form by the vast majority of organisms on Earth. -Nitrogen fixers, however, can convert N2 into a useable form (ammonia), which can then be incorporated into organic molecules.

Why might Earth's oxygenation be referred to as the "Oxygen Catastrophe"?

-Because many cellular structures, metabolic processes and enzymes that evolved prior to the release of O2 by oxygenic photosynthesis were damaged by O2, -So, many organisms either went extinct or were restricted to living in anaerobic habitats (does iron oxidation occur in oxic environments?). -However, the rise of O2 allowed other organisms to thrive and the fact that O2 is, from an energetic point of view, such a great electron acceptor, it allowed organisms to obtain more energy during respiration.

Why is left-handedness more prominent in violent and warlike societies, and less prominent in pacifistic societies?

-Being a lefty (southpaw) would provide an advantage in that people would not be familiar with this stance, strategy, etc. This would give the southpaw an advantage, which might most manifest itself in the more violent societies.

List and describe three defining differences between angiosperms and gymnosperms.

-Both are heterosporous, with the microspore developing into pollen (male gametophyte) and the megaspore (female gametophyte) developing within the sporophyte. -In gymnosperms, the male and female gametophytes are produced in physically separate structures (cones), while in the angiosperms they are often in the same structure (flower). -In gymnosperms, the ovules are not fully enclosed in other tissues (hence naked seeds). -In angiosperms, the ovule is entirely enclosed in a secondary structure (carpel). -In gymnosperms, pollination and seed dispersal is mostly abiotic (wind), although there is beetle pollination and animal seed dispersal in some gymnosperms (cycads). -In angiosperms, animals play a large role in pollination and seed dispersal. -In gymnosperms, the female gametophyte develops extensive nutritional reserves prior to fertilization but the female gametophyte in angiosperms essentially dies at fertilization. Instead, the nutritional reserves develop from the triploid endosperm, a product of the second fertilization event. The gymnosperm strategy is costlier than that in angiosperms.

The life cycle of ascomycetes and basidiomycetes are fairly similar, yet fundamental differences occur at various stages within each cycle. Describe two ways that the life cycles in these two groups are different.

-Both ascomycetes and basidiomycetes possess dikaryotic hyphae that develop into a fruiting body. -The haploid nuclei in these hyphae will eventually fuse (karyogamy), the diploid nuclei will undergo meiotic divisions, and eventually spores will be produced. -the fruiting body in ascomycetes is composed of both dikaryotic cells (cells resulting from the fusion of the hyphae from the "parental fungi") as well as haploid cells from each of the "parental fungi." -In basidiomycetes, the fruiting body is made up entirely of dikaryotic hyphae. -Additionally, in ascomycetes the fusion of haploid nuclei occurs in a specialized cell termed an ascus, which produces the zygote. The zygote undergoes meiosis, resulting in 4 haploid products. Each product undergoes a mitotic division, resulting in 8 haploid spores. -In basidiomycetes, the fusion of haploid nuclei occurs in a specialized cell termed a basidium. The zygote then undergoes meiosis, resulting in 4 haploid spores.

Compare and contrast ectomycorrhizal fungi and endomycorrhizal fungi. How are these fungi similar, and how do they differ?

-Both ectomycorrhizal and endomycorrhizal fungi form mutualisms with plants. -In both mutualisms, the fungi form extensive hyphal networks in the soil outside of the plant and also extensive networks within the plant. -In these mutualisms, the fungi get access to fixed carbon from the plant, and in return the plant receives increased access to nutrients and water due to the fungi's increased absorptive capability. -In endomycorrhizae, the fungal hyphae penetrate between the cells of the root and then push their way into the space between the cell wall and the plasma membrane, forming a highly reticulated branching structure that allows efficient nutrient transfer. -In ectomycorrhizae form hyphal networks inside the outer layers of the plant roots, but these hyphae just grow between the cells. The fungi form a dense hyphal sheath around the infected root and within the outer layers of the root itself, but only penetrate the intercellular spaces to form highly branched networks (Hartig nets).

In what ways is the use of inorganic forms of chemical energy similar to the use of organic forms of chemical energy?

-Both uses chemical forms of energy involve oxidation, which supplies energy and electrons to an electron transport chain, which then pumps protons out of the cell, which then drives the synthesis of ATP using the ATP synthase. -- -Both require a terminal electron acceptor (e.g., oxygen in the case of aerobic respiration).

In a previous lecture, we discussed the potential for increasing CO2 levels to actually result in increased rates of photosynthesis. Why, then, are increasing CO2 levels potentially problematic?

-CO2 is a potent green house gas with a positive radiating effect. In other words, increasing atmospheric CO2 will, on average, increase temperatures.

Why is diffusion considered a limit to the size and complexity of organisms?

-Cells require oxygen for respiration. -Diffusion is very slow over long distances, especially in liquids. -Active transport (both cell-to-cell transfer and specialized transfer tissues) is required for transporting oxygen in complex multicellular organisms.

The cellular slime molds are essentially haplontic, however there are unique features to this life cycle when compared to other haplontic orpganisms (e.g., Chlamydomonas reinhardtii). Describe the life cycle of cellular slime molds, emphasizing the unique features to these organisms. Also, what is the benefit of multicellularity in cellular slime molds? What is a potential benefit of sexual reproduction?

-Cellular slime molds persist as haploid amoebae that undergo asexual mitotic divisions. -during periods of nutritive stress, these cells will release an aggregation signal and form aggregations of numerous cells. -will either form a multicellular slug (migrating colony), or compatible mating types can fuse to form the zygote (sexual reproduction). -If a zygote is formed, it releases the aggregations signal but then consumes the haploid amoebae (phagocytosis). -The zygote will eventually form a mature macrocyst, which will undergo meiosis to eventually create the haploid amoebae. -If the aggregating cells form the slug, there is coordinated movement among the cells allowing greater dispersal than could be achieved by individual amoebae. -The slug will then form into the fruiting body, consisting of the stalk (dead cells) and the spores (living cells). -The fruiting body allows for dispersal of the spores, which haploid amoebae will eventually hatch out of.

Describe the life cycle of Paramecium (Ciliates) (i.e., asexual vs. sexual reproduction, gametes, syngamy, zygotes, meiosis, micro- and macronucleus). When is ciliate conjugation utilized by ciliates?

-Ciliates are large, single-celled organisms. - -Asexual reproduction in ciliates consists of a mitotic division of the micronucleus and an amitotic division of the macronucleus. -Each daughter cell receives a copy of the micro- and macro-nucleus. -Ciliate conjugation can be induced by introducing some environmental stress (temp., starvation, crowding, etc.), but it has also been shown that conjugation will occur in some species after numerous rounds of asexual reproduction (cells begin to experience some deterioration).

Mutualisms in nature can often switch from an interaction that benefits both parties to an interaction that's more akin to parasitism, particularly if one species "cheats" in the mutualistic interaction. One such example is the interaction between cleaner wrasses and fish they are servicing. Describe the mutualistic interaction between these species, then explain how the interaction can switch from mutualistic to predatory or parasitic. Provide a scenario that might ensure this relationship remains a mutualism.

-Cleaner wrasses provide a service to other fish by removing decaying skin and parasites from the individuals they are servicing. -It is considered a mutualism because the fish receiving the cleaning are healthier because of the wrasses' efforts, and the wrasses receive sustenance for their services (eating the dead flesh and parasites). -The interaction could rapidly switch, however, depending on the actions of the wrasses and the fish being cleaned. -If the wrasses begin consuming living flesh, the interaction would become akin to parasitism. -If the fish being cleaned consume the wrasse, the interaction would become that of a predator and prey. -The wrasses are encouraged not to cheat in this interaction by the presence of other fish that need cleaning (if the wrasses cheat they might lose their readily available food source). -The fish are encouraged not to cheat (by eating the wrasse) because they are receiving the cleaning service and their health is dependent on the interaction.

What anthropogenic pressures are cone snails experiencing?

-Cone snails are dependent on coral reef habitats. -Degradation of coral reefs will result in a loss of habitat for these snails, most likely resulting in loss of cone snail biodiversity. -Further, cone snail shells are highly sought after by collectors, putting additional pressure on these animals.

Cone snails possess extremely diverse toxic peptides that target multiple channels of its prey's nervous system. Interestingly, these toxins are also species specific, so that for the 700 species of cone snails there may be as many as 140,000 toxins produced. Why might these species have evolved such elaborate toxins, when using one or just a few toxins would likely be much more energetically efficient?

-Cone snails are relatively slow-moving organisms that use ambush techniques to target highly motile prey. -the toxins the snails use must immediately and completely immobilize their prey. -there is strong evolutionary selection for the use of multiple toxins that target several different pathways of the nervous system at once, inducing paralysis. -because there might be reciprocal selection on their prey to develop resistance / defense to these toxins, there would also be strong selection on snails to have highly varied toxins.

Even though humans reap the benefits from agriculture and the crops produced, why might agriculture be considered a mutualism?

-Crop species (corn, potatoes, grains, etc) are maintained in extremely high abundance, probably in higher abundance than the species would have achieved on their own. -Some crops (potatoes, chili peppers, etc.) have experienced strong artificial selection for various traits, and now number in the 1000s of species. Again, above and beyond what might have been achieved naturally.

Describe the life cycle of Diatoms (i.e., asexual vs. sexual reproduction, gametes, syngamy, zygotes, meiosis, 'nested boxes').

-Diatoms are unicellular diploid organisms encased in a pair of silica valves. -Asexual reproduction (mitosis) produces daughter diatoms that each inherits one valve from their parent and then produce the second valve themselves. -successive rounds of mitosis lead to diatoms with smaller and smaller valves. -gametes are produced by meiosis (gametogenic meiosis). -After syngamy, the zygote grows and forms its own pair of silica valves.

Describe double fertilization. Who does it? What structures are involved? Why is it beneficial to the developing embryo?

-Double fertilization is limited to angiosperms. -the male gametophyte, which has been transferred near to the female gametophyte, produces a pollen tube that travels down to the female gametophyte and delivers two sperm nuclei. -One sperm fertilizes the egg and the other sperm fuses with a cell in the female gametophyte that contains two haploid nulcei, and is therefore effectively diploid. -This produces a triploid cell that develops into the endosperm. -The endosperm serves as a nutritional source for the developing embryo.

When thinking about the interaction between the bobtail squid and the bacterium Vibrio fischeri, how would you characterize the mutualism both on behalf of the squid and on behalf of the bacterium, (i.e., what do each species receive out of the association)?

-Facultative mutualism for both. -bacterial cells receive a suitable place to live and nutrients from their host, although the majority of cells are expelled each morning. -bobtail squid receives an anti-predation strategy in the form of counter-illumination.

In some angiosperms, the relationship between pollinator and plant is incredibly specific. One such system is the interaction between fig trees and the wasps that pollinate them. Using the life cycle of the wasp, describe how the pollination of figs occurs.

-Female fig wasps leaving the fig where there were born fly off in search of another fig tree to continue the reproductive cycle. -The female wasp enters the fig through a tiny opening, and must then make her into the fig cavity. -female wasp then proceeds to pollinate the stigmas with pollen she has carried from the fig where she was born and to lay eggs in the ovules of some of the florets. -wasp larvae feed on the endosperm tissue, and can take anywhere from three to twenty weeks to mature depending on the species. -the male wasps emerge first. -wingless males mate with the females before chewing a hole through the fig wall to the exterior to allow the females to escape - the male's only two functions in life, as he dies soon afterwards. -impregnated females emerge next and either actively load up pollen from ripe anthers using special pollen pockets, or in some species passively become covered with pollen, before exiting the fig in search of young receptive figs to complete the cycle.

What is fermentation? How are fermentation and glycolysis linked? What is the difference between fermentation and aerobic respiration?

-Fermentation refers to the oxidation of carbohydrates in the absence of oxygen (anaerobic conditions) as an electron receptor. -The electron transport chain is NOT employed, and there is NO oxidative phosphorylation. But, glycolysis, which also occurs in the absence of oxygen, produces the pyruvate which is the substrate for fermentation pathways. -For example, lactic acid fermentation occurs in human muscles during intense exertion when oxygen becomes limited. -Pyruvate is produced via glycolysis, which then is further oxidized to lactic acid. Note, this is not a complete oxidation process as was discussed in aerobic respiration as lactic acid is still an energy rich molecule (highly reduced relative to oxygen)

Describe the life cycle of ferns. How is this lifecycle similar to that of bryophytes? How is it different?

-Ferns are similar in that they still use water for sperm dispersal and air for spore dispersal. -One of the big differences is that in ferns, the diploid sporophyte stage is photosynthetically active, and capable of living on its own. -Each of the stages of the alternation of generation life cycle is nutritionally independent. -Also, the sporophyte stage is much, much larger than the gametophyte stage.

How can the number of membranes around an organelle indicate the history of endosymbiotic events?

-Free-living bacteria would possess their own cell wall and cell membrane. -An engulfed cell would then have two membranes; its own, and then the membrane of the cell that engulfed it. This would be a primary endosymbiosis, as seen in the double membranes of mitochondria and chloroplasts. -A secondary endosymbiosis involves a eukaryotic host and a eukaryotic symbiont that is already the product of primary symbiosis. A secondary endosymbiosis would result in the addition of two more membranes, the outer membrane of the original host cell and the new phagocytosis vacuole membrane from the new host cell.

In respiration, what is oxidized? What do we call the compound that is reduced?

-Fuel molecules (e.g., carbohydrates) are oxidized. -The electron acceptor is reduced.

Where do fungi get their carbon and energy, and how do they find this food source?

-Fungi are absorptive heterotrophs and get their carbon from the environment from a variety of sources. -energy from aerobic respiration of carbohydrates from the environment. -hyphal cells penetrate a substance then excrete digestive enzymes. -as the organic matter breaks down, the nutrients are transported into the hyphal cells (digest then ingest model). -Some fungi form close associations with plants (mycorrhizae), and obtain nutrients from these plants. -To find their food, fungal hyphae grow out into their environment and can locate potential food sources simply through this exploration. -Additionally, fungi can asexually create spores, which after dispersal could allow the fungi to find additional food sources (asexual propagation).

If Neanderthals are truly a separate species from humans, why is Neanderthal DNA found in some human populations? Would you expect more Neanderthal DNA to be found in African or European populations? Why?

-Hybridization between the two species could have resulted in reproductively viable offspring. -One would expect more Neanderthal DNA in European populations. As the ancestors of modern humans left Africa, they would have eventually encountered Neanderthals that were already inhabiting parts of Eurasia.

What are hyphae? How does the structure of hyphae increase the efficiency of nutrient uptake by fungi?

-Hyphae are the long, branching filaments that make up the bulk of the fungal structure. -Hyphal filaments are extremely thin, but are also very elongated. -increases the surface area-to-volume ratio of the cell increasing transport efficiency.

Both phloem and fungal hyphae use bulk flow to move nutrients. Why is this likely a simpler process in phloem than in hyphae?

-In both plants and fungi, difference in osmotic gradient drives the movement of compounds through cells. -For fungal hyphae, the active absorption of compounds from the environment creates an area of high osmotic pressure (water flows in to hyphae). Areas where compounds are being consumed create areas of low osmotic pressure (water flows out of hyphae). This can create a circulation of nutrients within the hyphal network. -But, unlike plants, this circulation is through living cells with nuclei, organelles, and vacuoles, and these cells are extremely narrow. -Plant phloem cells are elongated and wider than normal cells to increase flow, and they lack nuclei, organelles, and vacuoles, most likely making bulk flow simpler in plants.

Although a moratorium on cod fishing in parts of the northeast U.S. has been in place for several years, the fishery has not rebounded. Why hasn't the decreased fishing pressure resulted in increased abundance of cod?

-Increased sea surface temperatures have been implicated in increased mortality and decreased reproduction (as measured by Age-1 recruitment) in cod. -These reductions in population growth not only contributed to overfishing and the collapse of the fishery, but appear to also have prevented the cod from rebounding even with a moratorium on fishing.

It is generally thought that nutrient availability, particularly N, P, or other trace elements, drives the rates of primary productivity. How does species diversity influence primary productivity, as compared to nutrient dumping? What explains this result?

-Increasing the number of species in an area increases the amount of primary production, even beyond adding nutrients. -The increased species diversity results in an overall more efficient / greater use of nutrients in the soil, sunlight, moisture etc., resulting in increased rates of primary productivity in that region.

The human microbiome has been implicated in numerous aspects of human health. Interestingly, there is quite a bit of variability in microbiomes from individual to individual. Provide 3 examples, scenarios, experiences, etc. that could lead to a difference in microbiome composition between individuals.

-Infections in the mother prior to birth -C-section vs. vaginal birth -breast feeding vs. formula -use of antibiotics -regionally distinct diets -etc.

The foraging gene previously described for fruit flies has also been found in honeybees. In honeybees, there is also a foraging behavior, but interestingly the behavior correlates with age. Young honeybees (nurses) tend to stay at home and take care of the hive / larvae while older honeybees actively forage for food. How does the foraging gene influence honeybee foraging strategy? With respect to the gene, what is the difference between nurses, young foragers, and foragers? What is the selective pressure for this foraging strategy?

-Initially, researchers found that expression of the foraging gene (levels of mRNA) was low in nurses (young bees) and high in foragers (old bees). -But, since there was differential expression between these two groups, it was unclear if this expression was associated with differences in age or behavior. -The researchers then looked at levels of gene expression in nurses and young foragers. -Again, it was found that the foraging gene was more highly expressed in the foragers, providing conclusive evidence that the foraging behavior in honeybees was under genetic control. -The selective pressure for this behavioral strategy could be that since foraging is inherently dangerous, it's a better for the colony as a whole to have older bees partake in this dangerous activity since they're going to die soon anyway.

What is the metabolic difference between iron oxidizing bacteria and iron reducing bacteria?

-Iron oxidizing bacteria are ones that use inorganic forms of chemical energy. Specifically, they oxidize Fe2+, and use O2 as an electron acceptor. The byproducts of this are Fe3+ and water... Iron acts like Glucose -Iron reducing bacteria run a form of anaerobic respiration in which they oxidize organic molecules (e.g., carbohydrates) and use Fe3+ as their terminal electron acceptor. The byproducts of this reaction are Fe2+ and CO2... Iron acts like O2

Why are two photosystems required in order for organisms to utilize H2O as an electron donor in photosynthesis?

-It is extremely difficult to remove electrons from water. -The addition of light energy from the first step (PSII) removes electrons from water. -The addition of light energy from the second step (PSI) raises the energy level of these electrons so that they can be used to reduce CO2.

Following the arrival of humans to the Americas, numerous species of large mammals went extinct. Why did so many species of large mammals originating in the Americas go extinct, while very few species of large mammals originating from Europe and Africa have gone extinct? How does this scenario parallel the types of impacts invasive species are currently having following their introduction to a new area?

-It is thought that the large mammals originating from Europe and Africa co-evolved with humans, a bi-pedal coordinated social hunter (predator). -This co-evolution would have resulted in these large mammals being better adapted to avoid these bi- pedal predators, as well as potentially being resistant to human diseases. -Large mammals originating in the Americas, in the absence of humans, would likely be extremely susceptible to human-related diseases, as well as to predation by this new type of predator. -This latter scenario is obviously extremely similar to the types of impacts invasive species can have. -Introduced species might possess feeding habits (e.g., brown tree snake in Guam), chemical defenses (e.g., many introduced plants), lack of a natural predators (e.g., red lion Mish in Caribbean Ocean), etc. that enables these species to thrive in their new area and become invasive. -The previously established community, having not co-evolved with the introduced species, can be susceptible to these novel characteristics resulting in community degradation and local extinctions.

Professor Farrell argued that biological conservation is closely linked to poverty. How are these linked, and do you agree with this assertion?

-It is very important to realize that poverty can lead to the exploitation of a particular resource. -If it is a choice between feeding one's family or conserving a resource, the latter will lose every time.

Why does the accumulation of protons on one side of the mitochondrial plasma membrane result in energy storage? How is this like a battery? Describe an important feature of the plasma membrane that allows oxidative phosphorylation to function efficiently.

-It takes work (energy) to accumulate so many protons on one side of the membrane, as the increasing positive charge outside of the cell membrane relative to the cytoplasm (charge separation) makes the protons want to come back into the cell. -In a battery we have charge separation between the two terminals; when these are connected, electrons (current) flows until there is no more charge separation (voltage difference). -In respiration, the protons flow back across the membrane, doing work in the form of driving the synthesis of ATP. -The plasma membrane doesn't allow protons to "leak" across -- they are forced to go through the ATP synthase (like forcing water flowing over a dam to go through a turbine).

When thinking about the genetic relatedness of kin (parents to offspring, among siblings, etc.), why is it that kin selection might favor altruism?

-Kin selection is an evolutionary strategy that considers the role organisms take in the reproductive success of their relatives. -kin selection occurs when an organism engages in behavior that benefits the genetic fitness of its relatives, often to the detriment of itself (altruism). -It might be thought that natural selection would select for selfish behavior and eliminate altruistic behavior. However, group selection might strongly favor cooperation, thereby selecting for altruism (particularly among kin). J.B.S. Haldane famously quipped, "I'd lay down my life for two brothers or 8 cousins" as it would be a "fair deal" evolutionarily.

It is well known that resource availability can strongly influence species diversity. One such resource is space, or the amount of area that might be useable to particular species. Describe an experiment that demonstrates the effect that reduced area (patch size) has on species diversity. Why might corridors influence species diversity in this type of scenario?

-Large, untouched patches had the highest diversity. -Small, isolated patches had the highest rates of "extinction." -Small patches connected by corridors prevented the high rates of "extinction" found in unconnected patches. -Corridors can alleviate effects of interspecific competition, predation, etc., and can promote resource partitioning.

Describe 2 consequences that can result from "fishing out the big ones."

-Larger fish, particularly females, are often more reproductively fit compared to smaller individuals. -This was experimentally demonstrated in rockfish, where it was shown that larger females not only produced more females, but devoted more energy reserves to their offspring (oil globule) which increased their offsprings' survival and growth.

We all know that the development of agriculture had profound effects on human society. Interestingly, humans are not the only animals that use agriculture to produce food. What other animals discussed in lecture utilized agriculture to maintain a constant food source?

-Leaf-cutter ants cultivate fungus for food. These ants transport high amounts of leaf matter to their nests, providing food for their fungus. -Ambrosia beetles also cultivate fungi. They carry their fungus deep inside trees, providing the fungus with a food source. -Some termites also cultivate fungi. Some species of termites cannot fully digest cellulose. Instead, using roughly chewed and only slightly digested plant material, they make a small ventilated structure, the fungus comb or garden, on which the mycelium of a will grow.

What is a lichen? Draw the phylogeny of lichens, pine trees, and humans? Why is this an ambiguous question? (How many different phylogenies can you draw?)

-Lichen is a symbiosis between a fungus and phycobiont (algae or cyanobacteria). -The phycobiont is photosynthetic and lives in close contact with the fungus. -Since the lichen is a composite of two organisms, it can't be placed on a phylogeny itself. -Instead, each organism in the symbiosis can be individually placed on a phylogeny.

What is lichen? How does lichen facilitate the growth of late-successional plant species?

-Lichens are made up of 2 (or possibly 3) different organisms that are in a tight symbiotic relationship with one another (often obligatory). -The first organism is a fungus, the second is a phycobiont (alga or bacteria). -Lichens are able to colonize bare rock, and can break down the substrate to begin to form soil. -Late successional species, such as many gymnosperms, would be unable to colonize bare rock, but are able to grow when soil is abundant.

Describe the Debt for Nature idea proposed by Thomas Lovejoy. Why could this be considered a win-win? Why might it be very difficult to implement?

-Lovejoy proposed that countries in debt to another country, where the debt will probably not be paid for quite some time, could serve as sites of biological conservation for the creditor country. -This could be considered a win-win - the creditor country would get some return on its investment, in the form of some biological conservation of its own choosing. -The debtor country would be absolved of some of its debt, but would also potentially become the stewards of endangered organisms, ecosystems, etc. -This might be somewhat difficult to implement because, of course, the creditor country is potentially losing a tremendous amount of money.

While marine aquaculture provides a substantial amount of the world capture of marine organisms (~1/3), there are potentially significant adverse environmental effects associated with aquaculture. How can aquaculture lead to eutrophication in surrounding waters? How might individuals that escape aquaculture pens influence the fitness of natural populations of the same species? Why are mussels thought to be so conducive (and less harmful) to aquaculture?

-Marine organisms that are cultured are fed surplus food to ensure that all individuals have enough food to eat. -Much of this food can go uneaten and sink to the bottom, or is carried away by currents. -Similarly, waste products from cultured individuals that are typically high in nutrients are continually distributed. -This spike in nutrients can lead to eutrophication in surrounding waters, which under the right circumstances could lead to dead zones. -Another problem with aquaculture is that in providing all the food and antibiotics necessary for survival, there is artificial selection taking place. -No longer is there a premium on high fitness, but now there is selection for quick growth, rapid reproductive maturity, or increased reproductive output. -If these less-fit individuals escape their pens and are introduced to native populations, there can be deleterious effects on the fitness levels of native stocks. -Mussels are considered an ideal choice for aquaculture. They are filter feeders, and consume phytoplankton. No need for addition of food. Also, they normally grow in very dense aggregations - no need for antibiotics.

What is the evidence used to demonstrate that bipedalism predated the evolution of large brains? Why was this discovery so important?

-Mary Leakey discovered bipedal, hominin footprints preserved in volcanic ash in the Laetoli site in Tanzania that dated to 3.6 mya. -The footprints demonstrate that the hominids walked upright habitually, as there are no knuckle-impressions. -The feet do not have the mobile big toe of apes; instead, they have an arch (the bending of the sole of the foot) typical of modern humans.

Methane emission from ruminant livestock (enteric fermentation) is currently estimated to be around 100 million metric tons, and is the second largest anthropogenic source of methane emission. What is responsible for the methane production and how is it produced in ruminant livestock?

-Methane is produced in the guts of ruminant livestock as a result of symbiotic methanogens. -Prokaryotic cells, belonging to the Archaea, use CO2 as a terminal electron acceptor in respiration, producing methane (CH4) as a waste product.

Briefly describe the structure and functions of the dynamic cytoskeleton of eukaryotes. How has the cytoskeleton influenced the size that eukaryotic cells can achieve? Do prokaryotes have a cytoskeleton?

-Microtubules and filaments form the backbone of the cytoskeleton of eukaryotes, which allows diverse cell shapes, phagocytosis, new forms of motility, and importantly active transport over large cytoplasmic distances. -It is this last character that has allowed these cells to overcome the size limitations imposed by the surface area-to-volume ratio experienced by prokaryotic cells. -these cells are no longer reliant on simple diffusion for the movement of material within the cell, and as a consequence can increase in size. -Prokaryotes have a less developed cytoskeleton, but they do have one.

Briefly describe the process of meiosis. How does meiosis differ from mitosis? When does crossing over occur in meiosis?

-Mitosis is a process of cell division that results in two genetically identical daughter cells. -Meiosis is a reductive process, whereby a diploid cell will divide into four genetically distinct haploid cells. -Crossing over occurs in Prophase 1

Neanderthals were once thought of as migratory hunter/gatherers without complex societies. What evidence exists that might refute these early ideas?

-Neanderthals not only made Oine tools, they also made necklaces and other jewelry. There was evidence of group care of injured individuals, as well as ritualistic burials. -There is evidence that Neanderthals could produce music (rhythm, chanting) to promote cohesion and community-closeness. -Neanderthals possessed the derived FOXP2 gene that is associated with speech in modern humans.

Explain the difference between nitrification and denitrification? What role does the nitrogen compound play in each metabolism? Why is denitrification called denitrification?

-Nitrification is when organisms used reduced forms of nitrogen (e.g., NH3) as an energy source, oxidizing it to nitrate (NO3-). - -Denitrification is when anaerobic respiration uses NO3- as a terminal electron acceptor, producing N2. Some of these more reduced forms of nitrogen, e.g., N2O, N2 are gaseous, so this results in a net loss of nitrogen from ecosystems/biosphere (i.e., the nitrogen returns to the atmosphere).

What is a nucleomorph and how is the presence of a nucleomorph an indication of a secondary endosymbiosis?

-Nucleomorphs are small, vestigial nuclei that occur in some plastids. -Secondary endosymbioses are thought to have occurred when a free-living photosynthetic eukaryote (red or green alga), which acquired its photosynthetic ability via a primary endosymbiotic event, is in turn engulfed by another eukaryote. -Because the red or green alga was a free-living eukaryote prior to being engulfed, it possessed a nucleus, mitochondria, and other organelles. The nucleus of the once free-living eukaryote became reduced, with most DNA being transferred to the genome of its now-host, until it became the nucleomorph. -The nucleomorph does not occur from a primary endosymbiosis (uptake of cyanobacteria that lack a nucleus), so its presence supports a secondary endosymbiotic event.

In contrast to the movement of water through xylem, the movement of nutrients through phloem is an active process. How are nutrients moved through phloem?

-Nutrients moving through phloem are often described as moving from the source of nutrients to the sink. -phloem loading results in a high solute concentration at the source end of the plant. -This creates an osmotic gradient in the phloem such that water flows into the phloem. -This creates positive pressure in the phloem, which is greatest at the source. -At the sink, osmosis occurs with the unloading of sugar - water flows out of the phloem. -The buildup of pressure at the source and the reduction of that pressure at the sink causes water to flow from source to sink, carrying the sugar along with it.

Why is O2, from an energy point of view, such a good choice for an electron acceptor during respiration? Why, in the context of early earth, might it have been a bad choice?

-O2 is very low on the Redox scale, meaning that it takes very, very little energy to reduce it to H2O. Because of this, the energy gained from the oxidation of any reduced molecule is maximized relative to using some other electron acceptor. -With regards to early Earth, it's not just that O2 was a bad choice, it simple wasn't a choice. Oxygen did not appear in the atmosphere until cyanobacteria evolved the ability to use H2O as an electron donor during photosynthesis (O2 is a by-product as we'll soon see).

-What is the difference between obligate and facultative symbioses? -What about horizontal and vertical transmission of endosymbionts? -Why are obligate endosymbionts often transferred vertically?

-Obligate symbioses refer to interactions where one or more of the partners are unable to live without the other species. -Facultative symbioses refer to interactions where the species engage in the interaction when both (or all) species are present, but the species' survival is not dependent on the interaction. -Horizontal transmission of endosymbionts describes the process whereby one species (host) will acquire the endosymbiont from the environment -Vertical transmission describes the process of transmission of the endosymbiont from parent to offspring. -Obligate endosymbionts are often transferred vertically to ensure the survival of the hosts' offspring. The endosymbiont might not be free-living, or might not be abundant in the environment, so the host ensures its offspring possess the endosymbiont by passing it on directly.

There are pros and cons to living in an aquatic environment vs. on land. What problems did plants have to overcome

-Once plants grew above the boundary layer, desiccation became a problem, and water can become limiting. -One solution used by plants is to be desiccation tolerant. -These plants lack true root structures, and simply become active and photosynthesize when water is available. -When water is not available, they essentially dry out and become dormant, waiting for the next burst of water availability. -Alternatively, terrestrial plants have developed vascular tissue for transporting water from the soil throughout the plant. Keep in mind - a great deal of the structure of vascular plants is non-photosynthetic (roots, trunk, stem, etc.) to accommodate the need for this balance between accessing water (roots) and accessing sunlight (grow taller than neighbor). -Water is taken up from the soil and transported through xylem to the leaves. -The acquisition of CO2 also became problematic because as the plant takes up CO2 into the leaf, water is lost. -Indeed, the majority of water taken up from the soil is lost as evaporation due to the take up of CO2. This lost water is continually replaced by water from the soil. -Additional adaptations to control water loss in the presence of gas exchange necessary for photosynthesis: waxy cuticle and stomata.

How many photosystems are required in anoxygenic photosynthesis? Why? Provide an example of an organism that utilizes anoxygenic photosynthesis.

-Only a single photosystem is needed in anoxygenic photosynthesis. -the electron donors in anoxygenic photosynthesis readily donate electrons (in contrast to H2O) to the bacteriochlorophylls, so the light energy acquired from a single photosystem is sufficient for the reduction of CO2 to glucose. -Green Sulfur Bacteria, Purple Sulfur Bacteria, etc.

An interesting plant-fungal mutualism exists between orchids and their fungal symbionts. Describe this mutualism, being sure to include why orchid reproduction is dependent on fungi.

-Orchids have seeds that lack endosperm. -plants release very small, dust like seeds into the air for wind-dispersal. -When the seeds land on the ground, germination is delayed until a fungus finds the seed. -Once the fungus finds the seed, the fungus surrounds it and the seed germinates. -The fungus actually provides the developing seedling with all the nourishment and water it needs. -When the orchid is photosynthetic and capable of surviving on its own, the fungus will receive nutrients from the plant.

In lecture, Prof. Girguis stressed the importance of thinking about biological entities as being in disequilibrium with the environment. What does it mean to be in disequilibrium with the environment, and how is this disequilibrium set up and maintained? What is an example of disequilibrium at the cellular level?

-Organisms possess physical and chemical properties that are distinct from the external environment. -This disequilibrium is achieved and maintained through harnessing energy through some metabolic pathway and using this energy to do work. -at the cellular level, cells set up concentration gradients of various ions (e.g., Na/K pump)

In the Arctic ecosystem, how is owl reproduction and lemming abundance related? Why?

-Owls prey only on lemmings. -When lemmings are abundant, they owls reproduce. -When lemmings are scarce, owls don't reproduce.

The evolution of complex multicellular animals corresponded with elevated atmospheric oxygen levels (~600mya). Why was elevated O2 so vital for the evolution of large heterotrophs?

-Oxygen was necessary for macroscopic life. -Only the oxidation of organic molecules by O2 provides sufficient energy to allow for large, active heterotrophs.

Some species of phytoplankton have evolved defenses to reduce herbivory and/or disease. Explain how the photoautotroph Phaeocystis can reduce herbivory depending on the size class of the herbivore.

-Phaeocystis can persist in the colonial state or as single cells (both haploid and diploid, although it is unclear if diploid cells in the single-celled state can divide by mitosis. -chemical cues from a micro-heterotroph (ciliate) induces the Phaeocystis cells to enter the colonial state. -in the colonial state there will be reduced grazing efficiency because the ciliate is too small to effectively graze the very large colonies. -chemical cues from a macro-heterotroph (copepod) induces the Phaecystis cells to persist in the single-celled state. -in the single-celled state will reduce grazing efficiency because the copepod is too large to effectively graze the very small cells.

Photosystems are protein:pigment complexes that use light energy to do what?

-Photosystems are where light energy is absorbed and then used to raise the energy level of electrons that are moving through the photosynthetic electron transport chain. -It is this input of energy that allows these electrons to move "uphill" (i.e., towards a more negative value on the redox energy gradient).

Compare plasmogamy with karyogamy? What is the difference between a diploid fungal cell and a dikaryotic fungal cell?

-Plasmogamy refers to the fusion of two cells (the cytoplasms mix). -Karyogamy refers to the fusion of two nuclei (think 'karyotype'). In some fungi (Basidiomycetes and ascomycetes), the mating structures of two fungi of different mating types will fuse (plasmogamy), but the nuclei will remain distinct. In this case, the cells are referred to as: "n + n" (dikaryotic). Since the nuclei have not fused, they are not diploid. Most cells in the fruiting structure are dikaryotic.

What is pollen, and how does pollen allow plants to escape the requirement for swimming sperm? Why is it that seed plants need only produce a few sperm for fertilization, whereas plants that rely on water for sperm transfer need male gametophytes that produce numerous sperm?

-Pollen is the male gametophyte that develops entirely within the walls of the microspore. - -Pollen is carried by the wind all the way to the megagametophyte, where it will eventually open and release sperm directly to the egg. -Because the pollen granule is carried all the way to the megagametophyte, only a couple of sperm are need for fertilization. -In plant species that rely on water for sperm dispersal, there is no guarantee that any one sperm released will encounter an egg, so numerous sperm are produced to increase the likelihood of sperm/egg interaction and fusion. -Keep in mind, even though the male gametophyte is highly reduced in pollen, numerous pollen granules are produced to increase the chances of fertilization.

What is the difference between pre- and post-zygotic barriers to reproduction? Provide a real-world example of each.

-Pre-zygotic = before the zygote forms. -barriers that either prevent mating or that prevent the sperm from fusing with the egg. Examples: -Temporal - differences in reproductive timing (wood frog and leopard frog) -Ecological - species occupy different habitats (Northern & Mexican Spotted Owls) -Behavioral - elaborate dances or displays for mate selection, including songs (meadowlarks, blue-footed booby) -Mechanical - interbreeding structurally impossible (elephant & elephant shrew; wookie & ewok), Post-zygotic = after the zygote forms. -- -reduced fitness of the hybrid Examples -Hybrid inviability - abnormal development of the zygote, which will be aborted (sheep & goat) -Hybrid sterility - the hybrid is healthy but sterile (mule, liger) -Reduced fitness - hybrid is less fit, which will often affect its reproductive fitness, as

Compare the functional differences between the membranes of prokaryotes and eukaryotes.

-Prokaryotes are smaller cells with less developed internal membranes than eukaryotes. -The small surface to volume ratio limits their size compared to eukaryotes since diffusion and ATP production are restricted to the outer membrane. -Eukaryotes have a complex internal membrane structure (nuclear envelope, golgi apparatus, lysosomes, organelles, etc.). -These structures spatially separate transcription and translation (nuclear envelope/golgi apparatus), digest waste materials (lysosomes), export substances to the environment, generate ATP (mitochondria), etc.

Prokaryotic cells can often modify their behavior based on population density. What is the mechanism by which these cells are able to detect their density, and how can their behavior change in response to this information?

-Prokaryotic cells can use quorum sensing to modify their behavior in response to population density. -Cells continually release chemical cues to the environment. As the number of cells increase, the concentration of these cues in the environment increases. This allows the cells to essentially monitor population density. When the density is sufficiently high, gene expression changes from asocial (individual) to social (coordinated) behaviors.

Some plasmids utilize a "toxin/anti-toxin" system that ensures their maintenance within prokaryotic cells, one example being the Hok/Sok system. Describe the Hok/Sok system, and explain how this system ensures that the plasmid coding both genes remains with daughter cells as these cells proliferate.

-Prokaryotic cells replicate via binary fission. -If a daughter cell lacks the plasmid, the remaining short-lived Sok (good guy) mRNA (half-life = 30sec) in that cell will degrade much sooner than the remaining Hok mRNA (half-life = 20min), resulting in the death of that daughter cell.

What is the difference between being radially symmetric and bilaterally symmetric? Before bilaterians, animals couldn't go backwards. How come?

-Radially symmetric organisms lack a left and right side. -many planes of symmetry around this axis. -bilaterians are characterized by their left/right (bilateral) symmetry, which also means there is ventral/dorsal (front/back) and anterior/posterior (top/bottom) asymmetry.

What types of adaptations occurred in early humans that facilitated walking upright?

-Re-positioning of the big toe to provide stability -re-positioning of the foramen magnum to allow the human skull to balance directly on top of the spine (upright posture) -S-shape of the spine to provide support, pelvis is reduced in length and is considerably wider to provide support -the human foot is narrower and possesses a much more pronounced heel.

-system that can ensure plasmid maintenance within prokaryotic cells is the restriction-modification system. -the plasmid encodes for a restriction enzyme that cleaves double stranded DNA at a particular sequence, but also encodes for a methyltransferase that methylates this sequence inhibiting the restriction enzyme. -From the plasmid's point of view, why must the restriction enzyme persist for a longer period of time than the methyltransferase? -How can this system act as an "immune system" for the prokaryotic cell?

-Restriction enzyme persists longer -If the methyltransferase persisted longer than the restriction enzyme, the cell could lose the plasmid without penalty. -This system can be considered an immune system because any foreign DNA that enters the cell will be digested by the restriction enzyme.

Describe how some fungal pathogens are able to manipulate their plant hosts' development to facilitate reproduction and dispersal by the fungus.

-Some fungi can infect a plant and use the plant to facilitate dispersal of the fungus. -Here, fungi induce formation of "pseudoflowers", modified leaves that look like flowers, which even contain a sweet substance secreted by the fungal sporangia. -When potential pollinators visit the brightly colored leaves, fungal spores attach to the pollinator and are transferred to new, uninfected plants.

H2S is exceedingly toxic to most eukaryotes. What physiological effect does H2S poisoning have on eukaryotic metabolism? How are the giant tube worms able to tolerate relatively high concentrations of H2S in their bodies?

-Sulfide can bind and inhibit the cytochrome C oxidase enzyme in Complex IV of the ETC, the last complex prior to ATP synthesis. Similar to the effects of cyanide, sulfide poisoning results in inhibition of the ATP synthase and, if untreated, can lead to death. -Giant tube worms possess hemoglobins with two binding sites; one binding site binds oxygen and the other binding site binds H2S. Because of this H2S binding site, H2S accumulation is limited and the worm is protected from sulfide toxicity.

What is the "Tragedy of the Commons" and how does it factor in to modern conservation policies?

-The "Tragedy of the Commons" is the depletion of a shared resource by individuals, acting independently and rationally according to each one's self-interest, despite their understanding that depleting the common resource is contrary to their long- term best interests. -If a resource belongs to everyone, or to no one, it will be over- exploited and eventually disappear. -In order to conserve these resources, policies must be enacted to ensure the resource is not over-exploited.

In the Arctic ecosystem, how is fox reproduction and lemming abundance related? Why?

-The Arctic Fox preferentially preys on lemmings, but will prey on goose eggs. -If lemmings are abundant, fox reproduction is high. -If lemmings are scarce, fox reproduction drops, but doesn't cease. -Foxes can supplement their diet with goose eggs.

What is the Keeling Curve? What explains the seasonal variation of atmospheric CO2 levels?

-The Keeling Curve is an ongoing plot of atmospheric CO2 levels, started in 1958 and continuing today. -first evidence that atmospheric CO2 levels were rising drastically, with increases observed every year since the study commenced. -intra-annual cycle that shows atmospheric CO2 levels peak in Apr/May and reach their lowest levels in Sept/Oct. This intra-annual cycle is driven by the imbalance of land mass, and as a consequence abundance of terrestrial vegetation, between the Northern and Southern Hemispheres.

Earlier in the semester, the Red Queen Hypothesis was used to help explain why sexual reproduction was so widespread in eukaryotic lineages. Using the Red Queen Hypothesis, explain how after 20 years of biological control the Argentine stem weevil, an invasive species in New Zealand, escaped its biological control agent, a parthenogenetic parasitoid wasp.

-The Red queen hypothesis is an evolutionary hypothesis that proposes that organisms must constantly adapt, evolve, and proliferate simply to survive while pitted against ever-evolving opposing organisms (pathogens) in an ever-changing environment. -Sexual reproduction facilitates a more rapid evolutionary response compared to exclusive asexual reproduction -In the case of the Argentine weevil invasion in New Zealand, the weevil (invasive pest) was able to sexually reproduce while the wasp (control agent) exclusively asexually reproduced via parthenogenesis. -The weevil evolved to resist the wasp, while the was unable to co-evolve with the weevil. The weevil was then able to escape the control of the wasp.

For lichen, sometimes the propagules can be considered lichen, while other times the propagules aren't actually lichen at all. How come?

-The asexual propagules contain the photosynthetic symbiont, so these propagules would be considered lichen. -The sexual propagules of lichen don't include the phycobiont and therefore they are just fungal cells.

What is the function of the carpel in angiosperms? Why is self-fertilization more likely in angiosperms than gymnosperms, and what is the role of the carpel in controlling selfing?

-The carpel is a structure found only in angiosperms that encloses the ovule (or ovules). It possesses a specialized surface (sticky or feathery) that captures pollen and induces pollen germination. -When pollen contacts the carpel, it germinates and a pollen tube forms. The pollen tube elongates down through the carpel towards the ovule, to eventually deliver sperm directly to the egg. -The carpel actually allows for male gametophytic competition and selection, and can also select for pollen from plants of the same species. -Finally, after fertilization the carpel will mature into a fruit, enticing animals to eat or disperse this fruit, resulting in a good method of seed dispersal. -Importantly, the carpel is also a selective surface when thinking about self-fertilization, and it can have self/non-self recognition capabilities and thereby prevent selfing.

Chara corallina is a green alga that is closely related to the land plants, and is considered to be very close to the ancestral state of land plants. Describe the life cycle of this alga. How does reproduction occur?

-The life cycle is haplontic, or haploid with zygotic meiosis -Gametes are produced by the gametophyte, and are formed by mitosis. -For reproduction, the egg is retained on the haploid plant. -Sperm are released to the water, which aids in gamete dispersal. -After fertilization, diploid zygotes are released and dispersed by water currents, but will soon undergo meiosis to return to the haploid state.

As discussed in lecture, water is taken up from the soil and transported throughout the plant through xylem. How does this process occur, and why is the movement of water through the xylem not an energy-dependent process by the plant?

-The movement of water from the roots of the plant to the leaves occurs simply by the evaporative powers of the sun and by the physical properties of water (capillary action). - -As plants open their stomata to take up CO2, H2O is lost due to evaporation (transpiration). -This lost water exerts a force on the water in the xylem, and draws more water into the leaf. -The water can be drawn great vertical distances (root to leaf) because of the cohesion of water molecules; that is, the property of water molecules to adhere to one another through hydrogen bonds. .

Amitochondriate eukaryotic cells, cells which lack mitochondria, were thought to be ancestral eukaryotes representing a phase of eukaryotes prior to the uptake of the α-proteobacterium. Further investigation, however, showed that this was not accurate. What evidence was used to show that these amitochondriate eukaryotes once possessed mitochondria?

-The nuclear genomes of these cells possessed genes that could only have come from the mitochondria, showing that mitochondria were once present in the ancestors of these cells. -Additionally, some of these amitochondriate cells possess hydrogenosomes, which have been found to be organelles that evolved from mitochondria.

A pine seed is actually composed of tissues from three generations occurring in the alternation of generations lifecycle in these species. Describe the tissue layers and the generation that provided each.

-The outer layer is the seed coat. This layer is formed from tissues that surrounded the female sporangium, so it is a product of the initial diploid sporophyte (Gen. #1). -The middle layer is the haploid female gametophyte (Gen. #2), which developed from a female spore produced by the Gen. #1 sporophyte. -The innermost layer is the developing diploid embryo (Gen. #3). The Gen. #2 gametophyte produces an egg that, when fertilized, remains encapsulated by the gametophyte. The developing embryo (diploid) receives nourishment from the gametophyte (haploid), both of which are protected by the outer seed coat (diploid).

Fungi can be major pathogens of plants and animals, and can even influence behavior in their animal hosts. One example of a pathogenic fungus is the fungus that infects ants in tropical forest ecosystems. Describe how the fungus is able to infect its host, and describe how changes in the host's behavior benefit the pathogen.

-The spores of this pathogenic fungus attach to an ant, and can penetrate the hard, chitinous exoskeleton. -The fungus spreads through the ant, and induces behavioral changes. -The ant will experience convulsions that will knock it to the forest floor. It is also thought that the ant will seek out areas with temperature and humidity levels suitable for the fungus. -As the infection proceeds, eventually the ant will head back in to the canopy attach to the underside of a leaf with its mandibles. -The ant dies shortly after, but the mandibles remain clamped onto the leaf, so the ant carcass and fungus remain in place. -Eventually, the fruiting body of the fungus protrudes from the back of the ant's head, and spores are wind dispersed to repeat the process. -Spore dispersal is facilitated both by the ant / fungus being elevated off the ground, as well as by being on the underside of the leaf - both benefits stemming from the ant's modified behavior prior to death.

How does the bobtail squid ensure that it takes up only A. fischeri cells from the environment?

-The squid uses a number of filters to screen out the wrong bacteria. -The squid secretes a mucous that inhibits the movement of bacterial cells. It is thought that V. fischeri cells aggregate together to coordinate their swimming movement, allowing them to outcompete other bacterial cells. -There are also numerous cilia on the squid that create a current that bacterial cells have to swim against. As V. fischeri cells are strong swimmers, these cells are again selected for over other bacterial cells. -Finally, the squid also uses antibacterial compounds to ensure that only V. fischeri inhabit the chamber that supports bacterial growth.

Understanding the role of genetics on a particular behavior has in the past been difficult to assess. With the advent of various genetic techniques, however, the role of genes in an organisms' behavior is becoming elucidated. One example discussed in lecture was the feeding behavior observed in Drosophila melanogaster larvae. What are the two feeding behaviors observed in these larvae, what is the distribution of the feeding types in natural populations, and how are genetics responsible for the difference? What selective pressure exists that could result in the maintenance of these two behaviors in various populations?

-The two feeding behaviors are termed "sitter" and "rover." -Upon encountering a food source, sitter larvae will remain at the food source, and generally will not actively search for new food sources. -In contrast, rover larvae, despite finding a food source, will continue to actively search for new food sources. -Within a normal population, ~70% of fruit fly larvae are sitters, and ~30% are rovers. -difference between the two strategies is due to differences of a single gene. -The gene responsible for this behavior, termed the foraging gene, has two alleles, forS (sitter) and forR (rover) -In crowded environments, the rover strategy would be selected for because it would enable these larvae to find sustenance when food could become limiting (reduce intra-specific competition). -In less-crowded environments, sitter larvae would be selected for because food would not be limiting and sitters take maximum advantage of their current food source.

Accurately assessing global biodiversity is an incredibly difficult process, so much so that it's been estimated that our current global species list could be orders of magnitude lower than the actual diversity that currently exists. Describe three factors that make the process of assessing global biodiversity so difficult.

-There are many difficult to access ecosystems on Earth -some species persist at low abundance requiring labor intensive sampling efforts -host specificity by some species means sampling huge amounts of areas to account for overall diversity, phenotypic similarity can lead to mistakes in properly identifying different species -there are a limited number of experts that can readily identify the different species sampled, etc.

What is the difference between being diploblastic and triploblastic? What are examples of diploblasts? Triploblasts?

-Triploblasts are animals that develop from a blastula that gives rise to three germ layers -they have a mesoderm -Diploblasts are animals that develop from a blastula (hollow ball of cells) that gives rise to only two true germ layers - ectoderm and endoderm. -Cnidarians

Describe the life cycle of Ulva lactuca (i.e., syngamy, zygote, diploid individual, haploid individual, gametes). How does this life cycle differ from Macrocystis pyrifera?

-Ulva possesses an alternation of generation life cycle. -multi-cellular haploid and multi-cellular diploid phase, and the gametes are produced via mitosis. -syngamy results in the formation of the zygote, which undergoes repeated mitotic division to form the diploid sporophyte. -sporophyte will then undergo meiosis to form haploid spores. -spores are released away from the sporophyte, settle, and through repeated mitotic divisions develop into the gametophyte. -multi-cellular, haploid gametophyte will eventually produce gametes, which will fuse to form a zygote. isomorphic= haploid stage (gametophyte) is morphologically similar to the diploid stage (sporophyte). Macrocystis possess a heteromorphic alternation of generations. The diploid sporophyte is enormous (~50m) relative to the haploid gametophyte (microscopic).

Describe three reasons why assessing global biodiversity could be considered of utmost importance.

-Understanding existing diversity can inform various aspects of invasive species (as Brian put it... "to know what's invasive we need to know what's native",) -assessing the current diversity can lead to the discovery of natural products for medicinal applications -understanding diversity in various ecosystems leads to a better understanding of overall ecosystem function -knowing the diversity in particular ecosystems and the role of individual species can lead to more effective conservation methods, etc.

Describe the life cycle of Chlamydomonas reinhardtii (i.e.,asexual vs. sexual reproduction, gametes, syngamy, zygotes, meiosis).

-Unicellular with asexual reproduction (mitosis). -Haploid with zygotic meiosis. -Two mating types (+,-). -At the start of sexual reproduction, the isogamous gametes are produced by mitosis. After syngamy, the zygote undergoes meiosis to produce haploid daughter cells. Uniparental inheritance of organelles: cpDNA (chloroplast) from one 'parent' and mtDNA (mitochondrial) DNA from the other parent

Discuss the vascular tissues of gymnosperms and angiosperms. How are they different? Why might this difference influence species abundance?

-Vascular plants, which include angiosperms and gymnosperms as well as ferns and lycophytes, have xylem. -angiosperms have wider xylem cells, termed vessels, which are much more efficient in transporting water. -Most gymnosperms, such as conifers, rely entirely on the more narrow xylem cells for water transport, which results in increased friction on water molecules and reduces flow. -The increased flow of water in angiosperms actually allows these plants to utilize a modified stoma, which has a larger opening than stomata found in other vascular plants. -The larger opening allows for increased CO2 uptake resulting in increased rates of photosynthesis, providing a distinct selective advantage to angiosperms.

Describe the differences between horizontal and vertical gene transfer. How does horizontal gene transfer obscure the "true" phylogeny? (Hint - Why is "true" inquotes? What does this imply about definition of species?)

-Vertical gene transfer refers to transmission of genetic material from parent to offspring, which means that the gene trees will match the species trees. -Horizontal gene transfer refers to the process by which genetic material is shared between prokaryotes, often of different species. The sharing of genetic material between different species clouds the pattern of similarity by descent.

Describe the life cycle of Volvox carteri (i.e.,asexual vs. sexual reproduction, gametes, syngamy, zygotes, meiosis).

-Volvox carteri is a colonial green algae that superficially resembles a huge spherical colony (~several thousand) of Chlamydomonas cells (i.e., a photosynthetic haploid cell with flagella). -Colonies can reproduce asexually by 'internal budding' to produce daughter colonies inside of the parent colony (see photo in lecture slides). -The parent colony then breaks open to release the spherical daughter colonies. -Gametes are oogamous. -Some of the colonies produce male gametes (small, motile), others produce female gametes (large, non-motile). This is genetically determined. Hermaphroditic (i.e., monoecious) colonies have also been described. -The male gametes are released and will encounter a female cell. -The resulting zygote is resistant to deleterious environmental conditions. -When conditions improve, the zygote undergoes meiosis, and the resulting haploid cells then can form colonies.

In the Arctic ecosystem, how is goose reproduction and lemming abundance related? Why?

-When lemmings are abundant, goose reproduction increases. -The Arctic Fox prefers lemmings, and therefore predation on goose eggs decreases.

Hormones have been shown to influence courtship behavior and reproduction in some animals. Describe how the presence of testosterone can influence reproduction in Anolis lizards.

-a male displaying courtship behavior added to a group of females will induce all females to become reproductively active. In these lizards, however, castrated males do not display courtship behavior. -if testosterone is added to a castrated male, this individual will begin to display courtship behavior and can influence a group of females in the same way a non-castrated male would. -These results suggest that hormones, specifically testosterone in this case, triggers the courtship behavior that then influences reproduction in Anolis lizards.

Possessing a skeleton outside one's body presents distinct challenges when considering growth (simply getting bigger), since growth is restricted to the size of the exoskeleton. How have arthropods adapted to grow despite possessing an exoskeleton?

-ability to shed their chitinous exoskeleton through a process called ecdysis. -secrete a type of hormone, generally called ecdysone, which can trigger molting. -the animals secrete a new cuticle that has not yet hardened. -induce a split in the back of the old exoskeleton, and back out of it. -the new cuticle will eventually harden into the new exoskeleton (a process similar to tanning).

Describe the life cycle common to the bryophytes.

-alternation of generations. -haploid gametophyte is the dominant, photosynthetic state. -diploid sporophyte is often a short-lived structure, but in some (hornworts) can be long-lived. -haploid gametophyte produces gametes; eggs are retained on the plant while sperm are released in wet conditions. -water is still needed for sperm to move from one plant to another. -fertilization results in the zygote, which develops into the sporophyte. -sporophyte remains attached to the gametophyte, and is nutritionally dependent on the photosynthetic gametophyte. -sporophyte grows up out of the boundary layer to release the spores into the air for dispersal. -spore will eventually land and develop into a gametophyte.

Why is the increase in cranial capacity such an important character in the evolution of the hominids?

-bigger brains are not necessarily tightly correlated with higher IQ -There are numerous problems in childbirth, infancy, and locomotion associated with brain expansion. -There are also theories that increased cranial capacity could have led to the extinction of the Neanderthals

Describe the process of cell division in prokaryotic cells.

-binary fission. -the circular DNA is anchored to the inner membrane. -There is a single origin of replication, and replication proceeds bi-directionally. -The newly synthesized chromosome is also anchored to the inner membrane. -These anchors ensure that each daughter cell will get a copy of the circular chromosome. -As replication proceeds, the cell begins to elongate, separating the chromosome attachment points. -Cell division eventually concludes with the formation of the cell wall, and separation of the two daughter cells.

Describe the difference between a haploid with zygotic meiosis and a diploid with gametogenic meiosis. How much DNA (1C, 2C, or 4C) does the cell have after syngamy, meiosis, and after mitosis?

-both life cycles, the zygote has 2C after syngamy and 1C after meiosis. -haploid with zygotic meiosis, DNA replication during S phase increases the amount of DNA from 1C to 2C, which is then reduced to 1C after mitosis. -diploid with gametogenic meiosis, DNA replication during S phase increases the amount of DNA from 2C to 4C, which is then reduced to 2C after mitosis.

What specific influences do these microbiomes have on human health? How does the function of the microbiomes of under-nourished individuals differ from individuals of normal weight?

-can influence brain development and behavior -vitamin synthesis -immune system education -energy metabolism Microbiomes in people's guts that are malnourished harvest fewer calories from ingested food than the microbiome of individuals of normal weight. Conversely, obesity has been linked to microbiomes in that these microbiomes harvest more calories from ingested food compared to individuals of normal weight.

Name and describe the three mechanisms of horizontal gene transfer in prokaryotes?

-conjugation (Pilus) -transduction (virus) -transformation (DNA release)

Describe the life cycle of gymnosperms.

-diploid sporophyte is the dominant stage, as with all seed plants. -sporophyte produces male and female sporangia, which are clustered together in cones. -male spores develop into the male gametophyte within pollen cones, while the female spores develop into the female gametophyte within ovule cones. -female gametophyte (haploid) is surrounded by diploid tissue (from sporophyte), together forming the ovule. -Pollen is released from the pollen cones and is dispersed through the air. - -Some pollen granules will be transported to another tree and land on an ovule cone. -When a pollen grain lands on the ovule cone, the pollen grain germinates and produces a pollen tube that elongates and digests its way towards the female gametophyte. -When the tube contacts the gametophyte, sperm are released and fertilization occurs. -The fertilized ovule then develops into a seed, which is then wind-dispersed and then develops into the sporophyte. -The mother gametophyte persists during seed development, becoming the nutritive tissue for the next sporophyte generation.

Where does the energy come from that drives protons across the plasma membrane?

-electron transport chain is supplied by NADH and FADH2, which are oxidized when they pass energy and electrons to the beginning of the chain. So you can say that it comes from the oxidation of these electron carriers.

How do prokaryotic cells obtain materials from the environment?

-facilitated diffusion (down concentration gradient-energy free) -active transport (against concentration gradient-requires energy) -group translocation (against concentration gradient - requires energy). They can use their flagella to move towards specific chemicals (resources), but no active predation.

While top-down effects are biotic interactions (e.g., grazing, predation, parasitism, etc.), bottom-up effects often stem from abiotic factors. Describe an abiotic factor, and how it might influence an ecosystem from the bottom-up?

-increased water temperatures in the ocean can result in a stable thermocline in an area. -stable thermocline prevents vertical mixing of water, so cold nutrient-rich water never makes it to the surface (where there is light), and the water at the surface is warm nutrient-poor. -result in decreased rates of photosynthesis. -causes crash bottom up

What is convergent evolution? What are examples of convergent evolution in fungi?

-independent evolution of similar features in species of different lineages. -creates analogous structures that have similar form or function, but were not present in the last common ancestor of those groups. Examples of convergent evolution in fungi are unicellular fungi, ectomycorrhizal fungi, lichenization, etc.. Endomycorrhizae is not a result of convergent evolution - it is specific to the Glomeromycetes.

Compare and contrast gene expression in prokaryotic and eukaryotic cells. Why is alternative splicing such a useful mechanism in eukaryotic cells?

-is no membrane bound nucleus in prokaryotic cells, there is no separation between transcription and translation. -this results in extremely efficient gene expression, which allows bacterial cells to rapidly respond to changing environmental conditions. -genes that code for proteins with related functions are often in sequence (operons), a single regulatory signal can result in the expression of all of the genes allowing for efficient production of these related proteins. -In eukaryotic cells, there is a spatial separation between transcription (within the nucleus) and translation (outside of the nucleus), resulting in a delay between the two processes (although a single mRNA can be translated by multiple ribosomes simultaneously). -While this delay could lead to inefficiency in gene expression, this separation allows for strict regulation of each step of the process -alternative splicing

Given a particular predator-prey system, do you believe predators will usually drive prey to extinction? How do Huffaker's experiments with mites support or refute your answer?

-it is thought that predators will usually drive prey to extinction. -If the predators are strongly dependent on that prey species, the predator population will also crash. -Huffaker demonstrated this empirically with his orange mites. -Without refuge, both prey and predator crash. -With proper refuge (toothpicks allowing for escape), the populations oscillate.

Why is CO2, from an energy point of view, a poor choice for an electron acceptor during respiration? Why, in the context of early earth, might it have been a good choice?

-its literally the opposite of O2 -there is less energy that can be used to drive protons out across the membrane and thus to form ATP. -On early earth, most compounds that can exist in a redox couple (i.e, capable of giving up or accepting an electron) were in their reduced form, and thus unable to act as an electron acceptor. CO2, however, was, to some degree, present, providing a potential electron acceptor.

How has human activity on land, specifically land use changes such as deforestation, influenced the emergence of infectious diseases?

-land-use change such as deforestation or habitat fragmentation can alter the niche, movement, or behavior of a particular reservoir, increasing the chance of interaction of this reservoir with humans, increasing the likelihood of transmission of a particular infectious disease -In the case of Ebola, deforestation has restricted the habitable area of the fruit bats, which has increased the likelihood of interaction between humans and bats. This then increases the chance of transmission from the reservoir of the infectious virus to humans, which can then result in the spread of the disease throughout various populations..

Did music pre-date language, or is language needed for music?

-music is so tightly tied to emotions, in that it can cause the release of "feel good neurotransmitters?"

Fishing is a form of unintentional artificial selection. Explain how fishing practices, such as gill-net fishing, are a form of artificial selection, and explain how this selection might influence size at or time to sexual maturation in certain species.

-often the largest individuals of any particular species are targeted. This is particularly true for gill-net fishing, which traps larger individuals and allows smaller individuals to escape. -This form of size-based selection removes large fish from the population leaving many more small fish to reproduce and pass their genes on to the next generation. -The small fish that are sexually mature are either older individuals that were not destined to grow large and eventually become sexually mature, or are individuals that are reaching reproductive maturity at earlier ages (and thus smaller sizes). -Both scenarios will result in smaller and smaller reproducing fish if the size-based fishing pressure remains.

When thinking about trophic levels and energy transfer, what is the 10% law? Why is so much energy lost between trophic levels?

-only about 10% of the energy generated at one trophic level is passed on to the next highest trophic level. -Much of the energy is lost to metabolism and respiration at a trophic level, handling time by consumers, inefficient digestion (can't digest everything), etc.

What is the role of animal pollination in thinking about species diversity in angiosperms?

-particular pollinators only visit specific attractants (flowers), gene flow can become disrupted. -This barrier to genetic exchange can promote genetic isolation, which drives speciation. - -species with very low numbers of individuals can persist because pollinators, responding to some cue, attractant, or reward, specifically seek out these species of angiosperms and transfer pollen from one individual to another.

If gut microbiomes influence whether patients suffer from kwashiorkor (acute malnutrition), it seems possible that antibiotic use and introducing healthy microbiomes into these individuals could "cure" the malnutrition. Why might the introduction of a healthy microbiome not lead to long-term fix for the problem?

-patients that suffer from kwashiorkor likely possess immune symptoms that have developed in the presence of the unhealthy microbiome, thereby "thinking" that this is the normal state. -The immune system could potentially attack the prokaryotic cells in the introduced "healthy" microbiome, preventing it from persisting long-term. -The microbiome could simply revert to what was present prior to the use of antibiotics, as that is what the patient's immune system is accustomed to.

Direct top-down effects (e.g., reduction in prey species limits herbivory) have been shown to influence various ecosystem dynamics, however indirect effects (e.g., behavioral changes in prey species) have also been shown to influence ecosystems. Using the spider/grasshopper experiment as an example, describe how simply the presence of a predator, and not predation itself, can influence an ecosystem.

-presence of the spider influenced behavioral changes in the grasshopper. -spider was unable to prey on the grasshopper, its mere presence resulted in the grasshopper consuming different plants, as well as consuming more carbohydrate-rich food (stress led to high energy consumption - compensated by extra carbohydrates). -grasshoppers also spent less energy on growing and reproducing, so they consumed less protein-rich food. -when the grasshoppers defecated and eventually died, the decreased levels of nitrogen in their fecal material and their bodies decreased rates of decomposition in the soil, which could influence the C:N ration in plants.

In lecture, Professor Kramer likened prokaryotic cells to a motorcycle, and eukaryotic cells to a large R/V (that might eat the motorcycle?). How do prokaryotic cells compete with other cells / microorganisms? Eukaryotic cells?

-prokaryotic cells = speed is the name of the game. -In eukaryotic cells, the selection has not been on speed and small genome sizes, but rather on cell size, structural diversity, and complex cell differentiation. -The evolution of phagocytosis, or the engulfment of large particles, in some cells would have drastically altered the selective pressure experienced by these cells ( i.e., they don't have to compete with speedy prokaryotic cells, they can eat them). Phagocytosis is also thought to be integral to how eukaryotic cells became eukaryotic cells in the first place (more to come on this).

Recently there has been a shift from thinking about the human body as an individual entity, to thinking about the human body as an "ecosystem." Why is it that the human body is now being considered an "ecosystem"? Is this a stable or unstable "ecosystem", and how much variability is there among individuals?

-prokaryotic cells can outnumber eukaryotic cells 10 to 1. -aid in digestion and synthesizing vitamins. -Microbiomes are highly variable between individuals, and are dynamic within individuals. Such things as diet, exercise, antibiotic use, etc. can influence the composition / make-up of these ecosystems.

When thinking about cell division, the process by which eukaryotic cells ensure that each daughter cell receives an equal and complete set of chromosomes is fundamentally different than in prokaryotic cells. Contrast the two strategies.

-prokaryotic cells utilize an anchor to ensure that each daughter cell receives a copy of the replicated genome -eukaryotic cells utilize their dynamic cytoskeleton. -microtubules (stemming from regions on either side of the cell) attach to the centromere that is holding sister chromatids together. -The microtubules then lengthen or shorten to move the chromosomes to the middle of the cell. -Once the chromosomes align, the centromere divides, the microtubules gradually shorten, and the sister chromatids are separated. -The sister chromatids, all of which are now called chromosomes, are gradually pulled to the opposite poles of the cell, where the nuclear envelope of each daughter cell reforms around each complete set of chromosomes.

How do certain management practices facilitate artificial selection in some fisheries?

-restrictions on which individuals can be captured in a fishery are based on minimums (minimum length, weight, etc.). -This practice ensures that the largest individuals from a population will be targeted.

What are the benefits of incorporating sexual reproduction to the eukaryotic life cycle? Specifically, how is genetic diversity generated, and why is this diversity so beneficial?

-sex is defined as a combination of synapsis (crossing over), segregation (independent assortment), and syngamy (fusion of gametes). -When combined, these processes can potentially lead to increased genetic diversity and new, never before seen genetic combinations. -These processes generate the diversity that is the raw material for natural selection and evolution, which can allow individuals to respond to changes in the environment (abiotic or biotic).

How is it that sexual reproduction can lead to the rapid combination of beneficial alleles in populations, compared to exclusive asexual reproduction?

-sex not only combines genes from two individuals, but also can result in the recombination of alleles onto a single chromosome, sexually reproducing populations can more easily combine advantageous genes than can asexual populations. -If, in a sexual population, two different advantageous alleles on different loci of the same chromosome arise, sex between individuals caring these alleles can lead to offspring possessing both alleles not only in one genome but on the same chromosome. -However, should the same two alleles arise in different members of an asexual population, the only way that one individual can acquire both alleles is to independently gain the same mutation, which would take much longer.

How is simple multicellularity different than complex multicellularity?

-simple multicellularity = cells are in close association with one another, but all cells are in direct contact with their external environment. - -all cells can acquire their own nutrients, so there is little need for nutrient transfer among cells. Additionally, all cells retain the ability to reproduce. -complex multicellularity = there is often a complex 3-D component to cell aggregations, resulting in come cells that are not in direct contact with their environment. -These latter cells are dependent on intercellular communication for nutrient exchange, as well as the exchange of environmental signals. -Also, in complex multicellularity many cells have lost the ability to pass genes on to the next generation (reproduce).

What was the social (coordinated) behavior exhibited by A. fischeri, and what does this imply about their normal asocial (individual) behavior?

-social behavior exhibited by A. fischeri is bioluminescence, which the squid uses for counter-illumination. -only bioluminesce when population densities are sufficiently high, a behavior not exhibited when they are free-living.

What is a spore? What produces them? What do they develop into, and how?

-spores are haploid products of meiosis that are produced by sporophytes and eventually develop in gametophytes. -spores usually disperse in the air, and then develop into multicellular gametophytes via mitosis. They are often resistant to poor environmental conditions (resting state) as well.

Both land plants and fungi utilize spores in reproduction. Spore production in fungi, however, can be fundamentally different than the process found in land plants. How come?

-spores produced by land plants and fungi are both haploid -plant spores are produced by the sporophyte (a diploid structure) via meiosis. -fungal spores, however, can be created by both sexual and asexual processes. -spores can develop sexually via zygotic meiosis, or asexually, whereby a haploid parental cell forms spores via mitosis.

Riftia sp. (giant tube worm) has no mouth and no digestive tract: how does it get the energy and materials to build its body?

-symbiotic bacteria that acquire energy by oxidizing H2S, and then use that energy to fix carbon (CO2 ⇒ C6H12O6) via the Calvin cycle (chemolithoautotrophy). This fixed carbon is then available to the worm as an energy source.

Describe the plasmodial slime mold life cycle, and distinguish it from the cellular slime molds.

-the plasmodial slime mold can persist as a diploid cell undergoing repeated mitotic divsions, forming a large, coenocytic cell, or as a haploid cell (amoebae or flagellated) undergoing mitotic divisions (asexual reproduction). -The mature plasmodium, with its numerous diploid nuclei, will eventually produce a sporangium (organ where spores are produced). -The numerous diploid nuclei will develop a wall, then undergo meiosis to create numerous haploid spores. -The spores will be released, eventually giving rise to the haploid amoebae or flagellated cells. -These cells can either asexually reproduce, or fuse (syngamy) to form the zygote, which will eventually develop into the large, coenocytic cell.

When thinking about the origins of photosynthesis in various eukaryotic lineages, what is the difference between primary and secondary endosymbiosis?

-the primary endosymbiosis was the process when a eukaryote engulfed a cyanobacterium. -the secondary endosymbiosis was when a eukaryotic cell engulfed another eukaryotic cell that had undergone a primary endosymbiosis. -it is thought that the diatoms and brown algae derived from a secondary endosymbiosis when a eukaryote engulfed a red alga. -the number of membranes and presence of vestigial nuclei are telltale signs of a secondary endosymbiosis.

When thinking about the response of an organism to some environmental cue, it is common for biologists to attempt to interpret this response in terms of the proximate and ultimate causes. -proximate cause can be thought of as the environmental signal that elicits a particular response from an organism (e.g., lunar cycle and coral spawning), - -ultimate response is evolutionary rationale for an organism to respond to that signal (e.g., reproductive assurance for corals, as well as predator satiation). In lecture, Professor Kramer discussed the ejection of sporangia by the dung fungus, Pilobolus. What was the proximate cause and ultimate cause that explains this method of dispersal?

-the proximate cause of sporangia ejection is light. The sporangia are positively phototactic (orient towards light). The sporangium will orient itself towards the incoming light. -the ultimate cause, or the evolutionary rationale for this response, would be that this orientation prior to sporangia dispersal maximizes the likelihood that the ejected sporangia will encounter grazing herbivores.

How does the genetic diversity of human populations outside of Africa compare to populations within Africa? What does this suggest? Is this supported or refuted by the analysis of the numbers of sounds found in languages around the world? Why?

-there is much higher genetic diversity in African populations compared to populations outside of Africa. -This provides support for the "Out of Africa" hypothesis (think genetic bottleneck in non-African populations).

Why is it thought that without fungi, the carbon cycle would fail?

-without fungi breaking down wood, huge quantities of carbon would remain locked up on forest floors and elsewhere. -Fungi can utilize this carbon as an energy source, releasing CO2 back to the atmosphere and ensuring that the carbon cycle persists.

List two reasons that water might be a good e- donor in photosynthesis.

1) Abundant 2) non-toxic 3) byproduct can diffuse away easily (doesn't build up).

For vertically-transmitted endosymbionts, it is common for the genome of the endosymbiont to deteriorate over time such that the endosymbiont loses gene functions. This could be potentially disastrous for the host species. Describe two processes that could occur that facilitate the survival of the host-endosymbiont lineages despite the loss of gene function in the endosymbiont.

1) Compensation - endosymbiont genes can be transferred to the host genome prior to being lost. Alternatively, genes from multiple endosymbiont lineages could be transferred to the host genome throughout the evolutionary history of the host. 2) Replacement - the host could acquire a secondary endosymbiont that performs the function that was lost in the initial endosymbiont due to genome deterioration.

All chordates, at some point in their life cycle, possess four trademark structures that serve to distinguish this phylum. Name the four structures.

1) notochord 2) dorsal hollow nerve cord 3) pharyngeal slits 4) a postanal tail

Describe two strategies that nitrogen fixing organisms use to protect nitrogenase from O2?

1) the heterocyst cells of some cyanobacteria provide a spatial separation between photosynthesis and nitrogen fixation. 2) some single-celled cyanobacteria use a temporal separation between photosynthesis and nitrogen fixation. The cell ceases photosynthesis, cellular respiration uses up any remaining O2, and then the cell commences nitrogen fixation. And a third... 3) root nodules of legume plants, in which the plant builds a "house" for the bacteria that has low concentrations of O2 within it (the O2 is bound by leghemoglobin).

How long ago was the speciation event that resulted in the split between Homo sapiens and Homo neanderthalensis?

300,000-800,000 years ago.

How many times did complex multicellularity evolve on the eukaryotic tree?

6 (twice in fungi)

What does it mean when a cell is coenocytic?

A coenocytic cell is a multinucleate cell, which can result from multiple nuclear divisions without the accompanying cytokinesis.

How might the surface area to volume ratio of prokaryotic cells limit the maximum size cells can achieve?

A large surface area ensures efficient exchange of nutrients, wastes, gases, etc. across the cell membrane.

Conventional wisdom suggested that introduced plant species usually thrived in their new areas because these species had been released from grazing pressure (escaped their natural "enemies"). To the contrary, recent evidence suggests that this might not be the case. Rather, exotic plants thrive because they were introduced after their "enemies" were introduced. Explain the reasoning behind this latter argument. Why don't exotic herbivores eat exotic plants?

A meta-analysis of numerous studies found that native herbivores eat exotic plants, whereas exotic herbivores facilitated both the abundance and species richness of exotic plants. -When Europeans colonized new lands, native herbivores were mostly removed. -native herbivores able to consume exotic plants were replaced by exotic herbivores that ate native plants, thereby reducing competition for exotic plants. -Exotic herbivores might eat exotic plants. If that happened, the introduced plant would not become established. -only when an exotic is not consumed that it becomes established and can then spread (becomes invasive).

Why is it incorrect to assume that a population with large birth rates will have a large growth rate?

A population's growth rate is the difference between the birth rate and the death rate.

Emerging infectious diseases are infectious diseases whose occurrences have increased, or are likely to increase in the near future. In managing these diseases, it is important to account for the various reservoirs of any particular disease. What is a disease reservoir?

A reservoir of an infectious disease is any entity (animal, plant, etc.) that harbors an infectious agent, allowing the agent to persist and multiply, but that most likely does not experience deleterious effects from that agent. In lecture, Prof. Bernstein described fruit bats as the reservoir of the Ebola virus, where the virus could persist without deleterious effects to the bats.

Which of these structures are also found in Eukaryotes? How do the sizes of prokaryotic and eukaryotic cells compare?

All of these are found in Eukaryotes, although the DNA is organized differently. Eukaryotic cells are generally much, much larger.

Compare and contrast allopatric and sympatric speciation. Why is sympatric speciation such a controversial process?

Allopatric - speciation that occurs when a population of individuals becomes geographically separated into 2 approximately equal sized sub-populations. The separate populations evolve distinctly different characteristics, such that if the barrier were removed the populations would be reproductively incompatible with one another. Sympatric - the process through which new species evolve from a single ancestral species while inhabiting the same geographic region (no reproductive isolation). Sympatry is controversial because if, within a given population, there is no barrier to reproduction regardless of the size of the population (panmictic), how does 1 species split into 2 species that are then reproductively incompatible?

Not all tetrapods possess an amniote egg. Name a group of tetrapods that lack this type of egg, and describe how these animals reproduce.

Amphibians (frogs, toads, salamanders) lack an amniotic egg. Consequently, these animals must return to water to reproduce. -swimming larva

Cell-to-cell adhesion is vital in complex multicellularity. By what mechanism do animal cells achieve this adhesion? Why does this system not work for plant cells? How do plant cells maintain this adhesion?

Animal cells - transmembrane proteins - proteins that extend from the interior of the cell, through the plasma membrane, out into the extracellular space. Transmembrane proteins that bind to other proteins are termed cadherins, while transmembrane proteins that bind to the extracellular matrix are termed integrins. Plant cells - plants possess a cell wall, which prevents the use of transmembrane proteins. Instead, plants use secreted materials (glue-like substances) to achieve cell-to-cell adhesion.

Compare a population growing exponentially vs. logistically (with a carrying capacity of 100). Show that when the population is small (e.g., 5), the logistic growth equation predicts a similar growth rate to the exponential growth rate. Show that when the population is large (e.g., 90), the logistic growth equation predicts a much smaller growth rate than the exponential growth rate.

At N=5, the logistic growth equation would predict: dN/dt = r(5)(1-(5/100)) ≈ 5r. At N=5, the exponential growth equation would predict: dN/dt = r(5) = 5r, a very similar growth rate. At N = 90, logistic growth equation would predict: dN/dt = r(90)(1-(90/100)) = 9r. At N=90, the exponential growth equation would predict: dN/dt = r(5) = 90r, a much larger growth rate.

Sea squirts (see figure) are a sister group to the vertebrates within Chordata. What structures do these animals possess that would signify them as true chordates?

At the larval stage these structures are present. During metamorphosis, the notochord, nerve cord, and tail are resorbed.

Traditionally we used to describe all of the organisms in Archaea and Bacteria as"prokaryotes." Why is it better to describe them as all having a prokaryotic cell structure?

Because "prokaryotes" is not a natural (monophyletic) group.

Today, photosynthesis takes up approximately 27% of the CO2 in the atmosphere each year? Why does this not deplete the atmosphere of CO2?

Because respiration is releasing CO2 to the atmosphere at approximately the same annual rate.

Attempts have been made to quantify the "services" provided by various ecosystems globally. These attempts, however, are considered controversial and have been criticized. Describe the benefit of valuing the world's ecosystem services. Why might this be a detrimental idea?

Benefit - provides a measurable assessment of the benefit of these ecosystems,justify management decisions and can be useful in determining which ecosystems should receive top priority with regards to conservation. Detrimental - Quantifying nature has been criticized because the idea suggests that nature is for sale. To some, commodifying nature causes people to neglect the inherent beauty of nature by simply focusing on the economics.

What is the Cheshire Cat Escape Hypothesis, and how does it help to explain the persistence of sex in coccolithophorids?

Coccolithophorids possess an alternation of generation lifecycle, which experimental evidence has shown can be mediated by viral infection. In the diploid state, these extremely prolific, single-celled algae will form huge blooms in marine waters, which can often be seen from space. -the diploid state is susceptible to viral infection. Conversely, the haploid state is not. -if experiencing viral infection, the diploid cells will undergo meiosis, forming haploid cells. -viral infection will eventually diminish as the number of susceptible cells (diploid) decreases. -After a while, haploid coccolithophorid cells will fuse (syngamy) and return to the diploid state.

What is convergent evolution? How can the wings of these animals be considered both analogous and homologous?

Convergent evolution is the independent evolution of a similar character (functional or structural) in two or more different lineages. Birds and bats independently evolved the ability to fly. Bird wings and bat wings are independently evolved characters. Because of this, the wings in these two groups of animals are considered analogous. However, the bones making up bird and bat wings descend from a common ancestor. Therefore, the wings are analogous and the forelimbs are homologous.

What organisms were responsible of the oxygenation of Earth's atmosphere?

Cyanobacteria

Although cycads and ginkgo use pollen for dispersal of their microgametophyte, they both still rely on swimming sperm. How are sperm transferred to the megagametophyte for fertilization?

Cycads and ginkgo utilize a pollination droplet created by the ovule, which is used to catch the pollen from the air or from a pollinator. The pollen granule becomes entrained in the droplet. Then, as the droplet evaporates, whatever is entrained is drawn in to the ovule, which is fluid filled. Once inside the ovule, the pollen grain cracks open to release the sperm, which swim to the egg for fertilization.

When conditions for growth are good (i.e., resources are abundant), what limits the growth rate of prokaryotic-celled organisms?

DNA replication, including plasmids

Why are decomposers so important to the biological carbon cycle?

Decomposers (both prokaryotes and eukaryotes, but particularly fungi) are an essential component of the biological carbon cycle. Without decomposers, fixed carbon would remain locked up in the dead carcasses of autotrophs and heterotrophs. Over time, inorganic sources of carbon would dwindle, eventually resulting in a collapse of the carbon cycle.

What are examples of density dependent factors? What are examples of density independent factors?

Density dependent - availability of food or shelter, prevalence of disease, ability to find a mate, etc. Density independent - climate, temperature, precipitation, natural disasters, etc.

Is the shape of the logistic growth curve influenced mostly by density independent or density dependent factors?

Density dependent factors - the growth rate decreases as the density increases.

What is 'permissive' ecology? How might permissive ecology have factored in to the diversification of multicellular organisms?

Ecological landscapes in which competition for resources is rare or weak, allowing poorly functioning novelties to persist. Possible causes: (1) environmental change makes new physiologies possible; (2) an evolutionary novelty allows organisms to exploit resources in a new way; (3) environmental catastrophe causing mass extinction

Organisms that make use of inorganic sources of energy are found in which domain(s)?

Eubacteria and Archaea

In what domain are the organisms responsible for fermentation used to make wine, beer, and bread?

Eukaryotes (yeast are unicellular fungi)

Besides plant-pollinator interactions, provide three explanations as to why angiosperms are the most diverse (i.e., most speciose) group of land plants.

Evolution of the carpel, endosperm, wider xylem increasing water use, ability to germinate in the shade, decreased mortality from pathogens due to species surviving at low abundance, etc.

A reduced molecule has less energy than its oxidized form: T/F

F

The ability to use sunlight to produce ATP means these organisms are autotrophic: T/F?

F

Do fermenters use organic or inorganic forms of chemical energy? What are examples of inorganic forms of energy?

Fermentation follows glycolysis, which oxidizes organic molecules. So, fermenters use organic forms of chemical energy. Examples of inorganic forms of energy are H2S, H2 gas, Fe2+, NH3, etc.

Occasionally, populations within a species are reproductively isolated from each other, yet gene flow can occur via a "ring species" situation. Describe the ring species concept and explain how it complicates the Biological Species Concept.

For ring species, some populations of a particular species are reproductively compatible, however some populations are reproductively incompatible. According to the BSC, these reproductively incompatible populations should be considered separate, distinct species. Yet, gene flow can occur indirectly between the incompatible populations via a series of reproductively compatible populations. According to the BSC, can the reproductively incompatible populations truly be considered separate species in light of this gene flow?

If you had a choice: would you choose to be an iron reducing or a sulfur reducing bacteria? Justify your choice.

From an energetic point of view - iron is better; but from a perspective of availability - there are many more habitats with oxidized sulfur compounds than oxidized iron. It all depends on what's available in the environment.

When considering predator-prey interactions, how does the functional response differ from the numerical response? How does handling time factor in to the functional response?

Functional - rate of intake of prey as a function of prey abundance Numerical - rate of reproduction of predator as a function of prey abundance Handling time - amount of prey that can be consumed per unit time.

Describe the difference between an organism's fundamental niche and its realized niche. Name a factor that serves to limit the size of an organism's realized niche.

Fundamental - all of the habitat potentially available to a population. Realized - a subset of that habitat that is actually occupied by the population. Factor - inter-specific competition, predation, abiotic limiting factors

What are the roles of genetic variation and natural selection in the speciation process? Why is reproductive isolation important?

Genetic variation (stemming from genetic drift, mutations, sex, etc.) occurs naturally in populations... common for 2 populations not interbreedig to diverge via random process Natural selection, on the other hand, is non-random and acts to select for particular environmental traits. The carriers of these traits would thus have a distinct advantage, increasing the likelihood that these individuals survive and reproduce, passing all of their genes on to subsequent generations. Natural selection and random chance can drive genetic changes, but reproductive isolation is required to make the changes permanent.

List and briefly describe the four main stages of the cellular respiration of glucose. Where does each occur in eukaryotic cells? What is the relative contribution of electron carriers and ATP from each stage? Where is CO2 produced? What is the role of O2 during aerobic cellular respiration?

Glycolysis - Partial oxidation of glucose, creating 2 3-carbon molecules of pyruvate. In eukaryotes, occurs in the cytosol. Re-generates some, but not much, ATP, and re-generates two electron carriers (reduction of NAD+ to NADH). Acetyl-coenzyme A synthesis - Partial oxidation of pyruvate, creates Acetyl-CoA. Occurs in the mitochondrial matrix. Critical step linking glycolysis and the citric acid cycle. No ATP are re-generated, but 2 electron carriers are produced (reduction of NAD+ to NADH). Citric Acid Cycle - Complete oxidation of acetyl group from previous step. Occurs in the mitochondrial matrix. Produces some, but not much, ATP, but re-generates the majority of electron carriers (3 NADH and 1 FADH2 - reduction of NAD+ to NADH and FAD to FADH2). ETC and oxidative phosphorylation - Electrons are harvested from the electron carriers (NADH and FADH2), which is coupled with the transport of protons across the inner membrane of the mitochondria. This sets up a proton gradient - potential energy used to synthesize ATP. Generates the vast majority of the ATP resulting from cellular respiration of glucose. The CO2 we exhale is generated from the partial oxidation of pyruvate (Stage 2) and from the complete oxidation of the acetyl group (Stage 3). O2 is the terminal electron acceptor in aerobic cellular respiration (forming H2O).

List three inorganic molecules that can be used by organisms as source of energy.

H2, H2S, Fe2+

Name one compound used as a source of electrons in anoxygenic photosynthesis. What is produced as a byproduct?

H2S. Sulfur.

How is heterospory different than homospory?

Heterosporous plants produce two distinct types of sporangia (microsporangia and megasporangia), which create two distinct types of spores (microspores and megaspores). Homosporous plants produce one type of spore, which develops into one type of gametophyte. This gametophyte can then produce both sperm and eggs.

Hox genes are a group of related genes in the Eumetazoa that control the body plan of an embryo along the anterior-posterior axis (head-tail). After the embryonic segments have formed, the Hox proteins determine the type of segment structures (e.g. legs, antennae, and wings in fruit flies or the different vertebrate ribs in humans) that will form on a given segment. Hox proteins thus confer segmental identity, but do not form the actual segments themselves. The expression of Hox genes has been useful in elucidating the relationship of the four main lineages of arthropods. What is the difference between homologous and analogous characters, and what are examples of homologous and analogous structures in these arthropod lineages?

Homologous characters - characters that have the same evolutionary origin as determined by anatomical or genetic studies (four limbs in tetrapods) Analogous characters - characters that have the same function but different evolutionary origin (bat wings vs. bird wings). Chelicerae vs. mandibles

The fact that the two photosystems used in oxygenic photosynthesis are similar to the photosystems from distinct lineages of anoxygenic photosynthesizers suggests that __________ was involved in the evolution of oxygenic photosynthesis? (fill in the blank)

Horizontal gene transfer (most likely explanation)

How might heterospory minimize the likelihood of self-fertilization compared to homospory? Why is self-fertilization potentially problematic?

In homospory, a single gametophyte releases both eggs and sperm. This means that eggs and sperm from the same individual will be in close proximity upon release, increasing the chances of self-fertilization. In heterospory, different individual gametophytes are releasing sperm and eggs. Even though the male and female sporangia originated from the same sporophyte, having the male and female gametes produced on separate individual gametophytes makes self-fertilization much less likely. Routine self-fertilization can result in increased homozygosity in populations, not only potentially resulting in the loss of alleles from the population, but also potentially allowing for the expression of recessive, deleterious alleles.

Peripatric speciation is a variation of allopatric speciation. How does peripatric differ? (Hint: refer to the slide of the New Guinea Kingfishers)

In peripatric speciation, a small subset of a population becomes geographically isolated from the larger population. It is important to distinguish this form of speciation because, due to the much smaller size, genetic variation and natural selection can occur more quickly within the subset, leading to much quicker speciation rates compared to allopatry.

In animals, germ line cells (i.e., cells destined to become gametes) are sequestered early in development. As cells are unable to migrate, this sequestration would obviously be a bad idea in plants. Where do gametes stem from in plants? As a consequence, where can fertilization occur in plants, and what is a benefit to this?

In plants, gametes arise from somatic cells. This then allows for mature plants to possess numerous reproductive structures in numerous areas around the plant, which could increase the number and efficiency of reproductive events.

In lecture Professor Kramer discussed the potential disadvantage of zygotic meiosis in the haplontic lifecycle - each fertilization event only results in 4 spores. Early land plants transitioned from the haplontic lifecycle to an alternation of generation lifecycle. When thinking about spore formation, why is the alternation of generation lifecycle advantageous compared to the haplontic lifecycle?

In the alternation of generation lifecycle found in plants, the zygote resulting from syngamy undergoes mitotic divisions resulting in the formation of the sporophyte (diploid). The sporophyte can then form numerous haploid spores via meiosis. Instead of a single fertilization event resulting in only 4 spores, each fertilization event could result in millions of spores.

GO OVER Describe why the movement of electrons from the reaction center is actually an oxidation-reduction reaction.

In the photosystems, light energy is captured by antenna chlorophylls and the energy is transferred to the reaction center. This transferred energy is used to excite an electron in the reaction center. This electron is then transferred (oxidation) to an electron acceptor (reduction). This process of the reaction center losing its electron is often termed "bleaching" because, as the reaction center (now oxidized) has been stripped of an electron, it can no longer absorb light. The electron is replaced through the oxidation of H2O (e- donor) and the reduction of the reaction center

Describe/diagram a prokaryotic cell, indicating all of its major structures.

Include cell wall, plasma membrane, ribosomes, one circular chromosome (plasmids can also be listed), can have flagella.

What are the two kinds of metamorphic life cycles found in insects?

Incomplete metamorphosis - absence of a pupal stage between the immature and adult stages. The egg develops into what is essential a mini-adult (nymph), but lacking wings. -crickets, grasshoppers Complete metamorphosis - The complete form of metamorphosis in which an insect passes through four separate stages of growth, as embryo, larva, pupa, and adult.

Briefly describe the difference between isogamy, anisogamy, and oogamy.

Isogamy: gametes morphologically similar and motile. Anisogamy: Some gametes are larger than others, all are motile. Smaller gametes specialize to become better at finding large gametes, which contain more cytoplasm. Oogamy: Specialized 'male' (sperm) and 'female' (egg) gametes. Male gametes motile and specialized for finding eggs. Female gametes are large and non-motile, contain most of the cytoplasm and organelles.

What is the difference between an innate and learned behavior? Define and provide an example of each.

Learned - learned behaviors are behaviors that come about based on an individual's experiences, generally through interactions with the environment, interactions with con-specific adults, or both (nurture). Examples - sweet potato washing in Macaques, acquisition of particular songs in some songbirds; cheating by cleaning wrasses in the absence of other fish; imprinting by newborns on adults (and vice versa); avoidance of distasteful prey item (e.g., monarch butterfly); hunting (individually and in packs); humans acquiring specific language / dialect; etc. Innate - innate behaviors are essentially the "hard-wired" behaviors for a particular organism. These behaviors are strongly influenced by genes, and are carried out regardless of an organisms' earlier experience (nature). Examples - male moth flies upward in response to pheromone response by females; fear response (jumping) when seeing a snake; courtship displays in some birds; goose returning egg to nest; migration in some species; courtship displays in some birds; humans acquiring language in general; etc.

How is it that lungfish are able to survive in extremely oxygen-depleted water?

Lungfish possess lungs, or in the case of the Australian lungfish only a single lung, which allows the fish to breath air. Interestingly, the lungs of lungfish are homologous with the lungs of tetrapods.

How does the mode of reproduction found in echidnas differ from that of marsupisals?

Marsupials - have live birth. Marsupials are also born highly undeveloped, with the exception of their front limbs. Once born, the young climb into the mother's pouch and attach to a nipple. They cannot suck, but the mother can eject milk into her offspring. Lactation can last up to 350 days. Echidnas - lay an egg into a specialized pouch. After 10-11 days, a young echidna hatches. The hatchling is quite undeveloped, except for strong front limbs and digits. The hatchling climbs up the mother's fur and attaches to specialized patches on the skin that secrete milk. Monotremes (echidnas and platypus) lack nipples.

GO OVER Syntrophy is when an organism relies on the metabolism of a neighboring organism to run its own metabolic reactions. Explain how syntrophy in ocean sediments prevents methane from entering Earth's atmosphere.

Methanogens are methane-producing prokaryotic cells. In some anoxic ocean sediments, these organisms oxidize organic molecules as an energy source and use CO2 as an electron acceptor, producing methane (CH4). If this methane dissolved into ocean waters, it would eventually enter the atmosphere (ocean-atmospheric gas equilibration) and could have significant impacts on Earth's climate - methane is an even more potent greenhouse gas than CO2. However, the methane produced in ocean sediments doesn't dissolve into ocean water. Instead, chemolithotrophic archaea living in the ocean sediments in close proximity to the methanogens utilize methane as an energy source. These anaerobic microbes oxidize methane as an energy source and use sulfur ( e.g., sulfate) as an electron acceptor.

What is the endosymbiotic hypothesis for the evolution of eukaryotic cells? Describe the supporting evidence.

Mitochondria are descended from endosymbiotic bacteria (alpha- proteobacteria). The evidence: mitochondria contain circular prokaryotic-like genomes, molecular phylogeny of genes on mitochondrial genomes indicates that their closest relatives are prokaryotes, mitochondrial genes have been relocated to the nuclear genome of eukaryotes, etc. Much of the same reasoning applies to the origin of chloroplasts, but remember the endosymbiotic event giving rise to photosynthesis in eukaryotes occurred AFTER the endosymbiotic event resulting in the mitochondria.

One of the results of the evolution of complex multicellularity is that not all cells retained the ability to reproduce (pass genes on to the next generation). For instance, in animals the germ cells, cells that are destined to become gametes, are sequestered early in development and stop dividing. These cells will then migrate to the gonads where they can complete their development. Why are these germ cells sequestered early in development?

Mitosis is not a perfect process, and errors in DNA replication or non-disjunction events can result in genetic abnormalities. By sequestering the germ line cells early, this minimizes the chances that these cells will have experienced an error in mitosis.

The spruce forest community is so named because spruce trees often dominate the area as "climax-species." Their dominance, however, does not occur until after a series of transitions that must occur for the species to even be able to begin growing in an area of land that has recently been disturbed (glaciation, fire) or is considered elemental (hard rocky substrate). Describe the changes that occur that eventually leads to the Spruce Forest Community. How do nutrients play a role in each stage?

Moraine - recently exposed bare rock following glacial retreat. Youngest moraine - populated by bacteria, fungi, photosynthetic microorganisms. Can support themselves on bare rock, with very little nitrogen available. These species have little biomass. Start to break down substrate to form soil. Decomposition of these species also adds soil, and nutrients (N) to soil. Slightly older moraine - populated by lichens, mosses, some shallow-rooted herbs. These species tend to have slightly more biomass, and often have nitrogen-fixing bacteria. These plants improve the soil for later succession species. Older moraine - shrubby willows, alders, and young spruces. This is a transition stage. Nitrogen is accumulating in the soil, supporting larger species with more biomass. Oldest moraine - Dominated by spruce forest (climax species). Spruces are no longer limited by nitrogen or nutrient poor soil, and can grow taller and outcompete / displace the early colonists.

Why might mushrooms (or fruiting bodies, in general) be referred to as "just the tip of the iceberg?"

Most of the fungus is hidden (i.e., below ground, in rotting wood, etc.). The mycelium is usually embedded in the material that it is absorbing nutrients from.

List and describe the five types of interactions that species can experience in nature. Also, provide a real-world example for each interaction.

Mutualism -(+/+) angiosperm-pollinator Antagonistic - (+/-) predator-prey Competition - (-/-) spruce-fir Commensalism -(+/0)buffalo-cattle egret Amensalism - (0/-) Buffalo unwittingly destroying insects Egret could eat

Population size equation

N=MC/R

What does the enzyme nitrogenase do? That is, what reaction does it catalyze?

Nitrogenase catalyzes the formation of a useable form of nitrogen (e.g., ammonia, NH3) from N2.

What are the assumptions of the mark/recapture protocol?

No immigration, emigration, births, or deaths in between sampling events, and marked individuals are not more/less likely to be captured again compared to individuals that have not previously been sampled.

Why are sponges not included in the Eumetazoa?

No true germ layer or tissue layer, and no organ development.

What is the difference between obligatory and facultative symbioses? Provide an example of each.

Obligatory - organisms require the symbiosis for each to survive. Examples - some lichens, cacao plant and midge pollinator (for cacao plant), stony corals / zooxanthellae (stony corals can't survive without symbiont), etc. Facultative - organisms benefit from a symbiosis, but it is not required for each organism to survive. Examples - Anemone fish and sea anemones, goby fish and pistol shrimp, etc.

Compare and contrast open access and catch-share fisheries. In your answer, be sure to fully explain potential management strategies for each fishery.

Open access - In an open access fishery, the fishery is open to anyone wishing to make use of it - access is granted to all. The fishery is managed through seasonal closures, area closures, gear restrictions, size limits, etc. to try to preserve the fishery, but the fishery is open. Catch-share - In a catch-share fishery, access to the fishery is restricted. The fishery is managed through the establishment of a total allowable catch. A dedicated share of this TAC is then allocated to individuals (individual transferable quotas). Because access is restricted, fishers possessing these ITQs are guaranteed their share, which removes the "race to fish" motivation and the "tragedy of the commons" issue. Explain one potential problem with catch-share fisheries. The creation of catch-share fisheries has led to a decrease in fishing fleets. Because the quotas are transferable, consolidation of the fishery by large entities or conglomerates is possible, which can lead to job loss by small-scale, local fishers.

What species make up the great apes (hominids)?

Orangutans, gorillas, chimpanzees and humans.

For electron source, distinguish between organotrophs and lithotrophs.

Organotroph - relies on the oxidation of organic compounds for their electrons. Lithotroph - uses reduced inorganic compounds for electrons

In aerobic respiration, if glucose is being oxidized, what is being reduced? What are the products of respiration?

Oxygen is reduced, forming water, CO2 and energy

What is anoxygenic photosynthesis?

Photosynthesis that does not use water as an electron donor, and thus does not produce O2. Note: anoxygenic photosynthesis does NOT mean photosynthesis in environments without oxygen. Photosynthesis doesn't 'need' oxygen.

What is oxygenic photosynthesis?

Photosynthesis using water as an electron donor and producing O2.

For energy source, distinguish between phototrophs and chemotrophs

Phototroph - able to use energy from the sun to regenerate ATP (harness solar energy to excite electrons to a higher energy state for use in the E.T.C. Chemotroph - relies exclusively on energy from the oxidation of electron donors available in their environment.

In general, for plant species there is often a trade off in growth rate and production of chemical defenses, such that species of plants that produce defenses do so by sacrificing growth rate. Using Phyllis Coley's experiment as an example, explain why this strategy is selected for in certain habitats.

Plants adapted to nutrient rich clay (clay plants) grow fast, plants adapted to nutrient poor sand (sand plants) grow slowly but invest in defense. -In absence of herbivores - clay plants grow much faster in both soil types and have greater leaf area than sand plants. Defenses are energetically costly -In presence of herbivores - clay plants do well in clay habitat, but bad in sand. The high nutrients means repair or new growth following herbivory is not a problem. Sand plants also do well in their habitat. -In nutrient poor soil, clay plants do poorly due to herbivory and lack of nutrients for repair. Sand plants do well due to anti-herbivory defenses. Clay is like r-selected.. Sand is k-selected

Unlike cells in animals, plant cells are unable to migrate. Why?

Plants possess a cell wall, which aids in structural support. As mentioned in a previous lecture, the cell wall precludes the use of transmembrane proteins for cell- to-cell adhesion. Instead, adhesion is accomplished through the secretion of glue- like substances. These substances maintain tight adhesion between cells, and also prevent cell migration.

What is a plasmid? How can plasmids influence the function of prokaryotic cells?

Plasmids are small, circular, self-replicating DNA within prokaryotic (and some eukaryotic) cells that often only carry a few genes. The effects the expression of these genes has on the cell, however, can be immense. For instance, plasmids can confer antibiotic resistance to cell lineages that previously lacked it, control conjugation, and as discussed in lecture possession of different types of plasmids has been shown to influence the symbiotic relationship between legumes and the N-fixing Rhizobia.

Would the bacterial endosymbiont found within aphids be considered a "primary" or "secondary" symbiont? Why?

Primary - Aphids provide specialized cells to house the bacteria (Buchnera), and the bacteria are passed from mother to daughter. Buchnera has lost most genes needed for independent life, and is dependent on the aphids to live.

Compare and contrast prokaryotic and eukaryotic chromosomes. Provide four fundamental differences found between the two cell types.

Prokaryotic - single, circular chromosome, haploid genome, genomes are small, genes are organized in operons, majority of DNA is protein coding, etc. Eukaryotic - multiple, linear chromosomes, genomes are large, cells are diploid at some point, genes not organized in operons, majority of DNA non-coding, dynamic internal membrane system, etc.

Can prokaryotic cells perform the last stage of cellular respiration? If so, where are the electron transport chains situated since they dont have mitochondria?

Prokaryotic cells can perform Stage 4 from cellular respiration. In prokaryotic cells, the electron transport chain used in respiration is located on the plasma membrane.

The Biological Species Concept (BSC), the most widely accepted concept for delineating eukaryotic species, is not considered applicable to bacterial or archaeal lineages. Instead, these prokaryotic cells are grouped into Operational Taxonomic Units (OTUs). Why is it difficult to apply the BSC to prokaryotic lineages and how does the use of OTUs attempt to overcome these limitations?

Prokaryotic cells reproduce asexually through a process called binary fission (more detail in a few lectures). The BSC defines species as a group of interbreeding individuals that are unable to interbreed with another such group. This definition does not necessarily apply to asexually reproducing organisms. Further, Horizontal Gene Transfer (HGT) is the process by which genes can be shared among different bacterial and archaeal lineages. OTUs based on genetic similarity, usually using 16s ribosomal RNA. If two 16s ribosomal RNA sequences from different prokaryotic cells are >97% similar, the two prokaryotes would be grouped as the same OTU. If <97% similar, they would be different OTUs.

What are the three most common distribution patterns that species are found in nature? Provide a biological example that would result in each distribution.

Random - Position of each individual is independent of any other individual... homogenous environments. Example - wind dispersal of seeds (wind is uncontrollable factor). Clumped - actual distance between neighboring individuals is minimized... commonly found when resources are patchy (heterogeneous environment), for safety in numbers (zebras), or to ensure reproductive success. Example - dry season in Africa animals clump around water. Over-dispersed - distance between neighboring individuals is maximized, leading to regular spacing... territoriality (plants and animals) or competition for resources. Example - trees that secrete chemicals in the soil prevent saplings from growing in close proximity to adults

Why do "redox" reactions always come in pairs?

Redox reactions involve the transfer of electrons and energy. When one compound is oxidized, another one has to be reduced because the electron has to go somewhere.

The gain of an electron results in that compound being oxidized or reduced?

Reduced

When thinking about the cell cycle, it's common to think that cells are constantly going through each phase successively (G1, S, G2, M) but, sometimes cells will undergo repeated rounds of DNA synthesis. Why might cells repeatedly go through the S phase without undergoing mitotic divisions?

Repeated rounds of DNA synthesis without mitotic divisions can allow these cells to increase their size substantially. Additionally, the increase in DNA could allow for upregulation of transcription and translation, resulting in the increased expression of a given gene product.

Plants, by and large, are non-motile organisms. Why is motility so important when thinking about dispersal and reproduction in these organisms?

Reproduction - Generally, gametes are not well suited for moving long distances, and being non-motile could present a significant barrier to reproduction for plants. Dispersal - The ability for offspring to disperse can lead to reductions in intra- specific competition, help minimize inbreeding, and aid in colonizing new substrate. Additionally, possessing the ability to move away from conspecific aggregations can also help juvenile plants avoid disease. It's likely that pathogens would be more prevalent in dense, mono-specific aggregations, such as those that occur in many plant species. While these diseases might not be fatal to adults, they could be fatal to the more susceptible juveniles.

When thinking about the net reproductive rate (r) for a particular species, what requirements need to be met to result in exponential growth? Why does exponential growth usually only occur for a short period of time?

Requirements - a constant birth and death rate, and the birth rate (b) must be greater than the death rate (d). As long as r is positive and constant, exponential growth will occur. Exponential growth usually only occurs for a short period of time for a particular population because resources become limited when the population becomes too large (intra-specific competition), disease becomes more prevalent at high population densities, increased grazing/predation on populations experiencing exponential growth would increase the death rate (r no longer constant), etc.

Describe four factors that influence population densities of various species.

Resource use - abundant resources = high densities (and vice versa). Body size - species with small individuals can often reach higher densities Invasives - organisms transported to a new area often escape predation or grazing pressure that would normally keep their numbers in check (biological control). These species can reach densities far beyond those found in their native range for a short time. Sociality - social organisms (ants, bees, termites, humans) can cooperate in terms of resource use, leading to increased densities of individuals.

The Morphological Species Concept groups individuals as a species (or separate species) based on morphological / anatomical similarities (or differences), however the MSC can often be incongruent with the Biological Species Concept. Describe two different scenarios whereby assigning a species designation according to the MSC might be incongruent with a species designation according to the BSC.

Scenario 1 - individuals of the same species appearing vastly different, yet these morphologically distinct individuals could reproduce and create viable, fertile offspring. Scenario 2 - different species that result in all of these individuals appearing very similar due to environmental pressures, yet genetic incompatibility exists among these species reinforcing reproductive isolation.

Explain what Darwin meant when he wrote "...that the characters do not make the genus, but that the genus gives the characters"?

Similar characteristics do not imply relatedness (Convergent Evolution) Relatedness might lead to similar characteristics, but perhaps not

How have animals such as sponges and jellyfish adapted to overcome potential problems of diffusion?

Sponges - extremely porous, so essentially all cells are in contact with exterior. Jelly fish - contain a layer below the surface that is not composed of true cells. Rather, this inner layer, termed mesoglea, separates the true cell layers (endoderm and ectoderm).

Define Spore, Gamete, Sporangia, Gametangia, Sporophyte, Gametophyte

Spores: a spore is a unit of asexual reproduction. In land plants, spores are ALWAYS haploid and are produced by meiosis in the sporophyte. They undergo mitosis to regenerate the gametophyte stage. Gametes: Haploid cells that never divide but rather fuse with another haploid cell to regenerate a diploid zygote. Sporangia: Organs that make spores. Gametangia: Organs that make gametes. Sporophyte: The diploid stage in the plant lifecycle that makes spores by meiosis. Gametophyte: The haploid stage in the plant lifecycle that makes gametes by mitosis.

Moving on to land presented major obstacles for aquatic vertebrates. Describe one structural obstacle and one reproductive obstacle that had to be overcome for vertebrates to live on land, as well as the solution to both.

Structural - need limbs that can support body weight in order to move around on land (walking legs), transition from gills to lungs, interlocking vertebrae (prevent sag), etc. Reproductive - need to overcome the potential limitation of eggs / embryos drying out (amniote egg).

Symbiosis

Symbiosis technically means living together and is commonly used to describe two or more species that live in a close, long-term association.

An organism that used sunlight to make only ATP would necessarily be a heterotroph: T/ F?

T

There are multiple lineages of photosynthetic bacteria: T/F?

T

When a molecule is oxidized, energy is released: T/F?

T

What was the cause of the Irish potato famine, and why was this disease / infection able to spread so wildly?

The Irish potato blight is an oomycete. It is thought that the reduced genetic diversity of the population of wild potatoes in Ireland contributed to the spread of this infection

What is the Red Queen Hypothesis, and how does help to explain the persistence of sex in most eukaryotic lifecycles?

The Red queen hypothesis is an evolutionary hypothesis that proposes that organisms must constantly adapt, evolve, and proliferate simply to survive while pitted against ever-evolving opposing organisms (pathogens) in an ever-changing environment. Based on this hypothesis, sexual reproduction would confer species variability and a faster generational response to selection by making offspring genetically unique. Sexual species are potentially able to improve their genotype in changing conditions, while exclusive asexual species would not.

In general terms, describe the biological carbon cycle.

The carbon cycle describes the movement of carbon from an inorganic form (atmospheric CO2) to an organic form (e.g., C6H12O6) via autotrophic pathways, back to an inorganic form (respired CO2) via respiration.

What does the term carrying capacity mean, in reference to population density?

The carrying capacity is the number of individuals of a particular species that the environment (environmental resources) will support.

In the most general sense, what is oxidized and what is reduced in a photoautotrophic reaction?

The electron donor is oxidized and CO2 is reduced

FoxP2 is thought to be a very important gene in the evolution of hominids. What is the function of FoxP2? What is the evidence that this gene is tightly coupled with speciation in hominids?

The forkhead-box protein P2 (Fox P2) is highly conserved among the vertebrates and has been implicated in neural development, as well as the development of other tissues such as the lung and gut. The 2 amino acid change found between humans and chimps is thought to have led to the evolution of language in humans

A prominent feature found in both ascomycetes and basidiomycetes is the fruiting body. What is a fruiting body, and when in the life cycle of these fungi is it formed?

The fruiting body, or what most people think of as mushrooms, are multicellular structures that facilitate the dispersal of sexually produced spores, usually via wind dispersal. The fruiting bodies are formed during the sexual portion of the fungal life cycle, after haploid mycelia of different mating types fuse (plasmogamy).

What is a mycelium?

The hyphal network of fungi is referred to as the mycelium.

Why might you consider H2O a poor choice as an e- donor in photosynthesis?

The oxidation of H2O, and subsequent reduction of CO2 to carbohydrates, is extremely energetically demanding. It was not until the coupling of PSII and PSI into the same organism (cyanobacteria) via HGT that oxygenic photosynthesis even became possible.

Why do the bacteria found in Riftia sp. accumulate sulfur?

The oxidation of H2S, produces elemental sulfur (S0) as a byproduct. These organisms use H2S as their energy source. They use O2 as their electron acceptor, which produces water.

Thinking about the requirements for complex multicellularity, how are social behaviors in prokaryotic cells linked to the evolution of multicellularity?

The requirements for complex multicellularity include: -cell-cell adhesion (cohesion) -inter-cellular communication (signaling) -cell differentiation, which can be boiled down to cooperation among cells. The social behaviors in prokaryotic cells include these types of cooperative behaviors, such as cell-cell signaling and cell differentiation.

The term "transcription factory" can be used to describe the process of gene expression in prokaryotic cells, as these cells are capable of transcribing DNA and translating mRNA at high rates. How might these gene regulation mechanisms confer a competitive advantage and increase the ecological efficiency of prokaryotic cells?

These mechanisms allow for the coordination of protein synthesis and enzymatic activity, which could allow for a rapid response to changing environmental conditions thereby increasing the ecological efficiency of these cells

Why aren't H2, H2S, Fe2+ a common a source of energy today? (Hint: how has Earth's atmosphere changed?)

These reduced, inorganic molecules would have been more common in early Earth and could be readily used as an energy source (fuel molecule). But, the oxygenation of Earth's atmosphere introduced one of the strongest oxidizing agents (O2), which would have reacted with these highly reduced molecules and oxidized them to a lower energy state.

How might cone snail toxins be used in biomedical research?

These toxins are of great interest as they can be used to target pain channels. The many different peptides can target many different receptors (specific types of Ca2+channels, Na+ and K+ channels, etc.). Further, by using a suite of potential painkillers that target different channels, tolerance to these painkillers could be minimized.

The grasses in the Arctic ecosystem can be under both top-down and bottom-up control. Provide an example of each that could govern grass abundance.

Top-down - herbivory / grazing by geese and lemmings. Bottom up - water availability, dictated by the weather.

Is it true to state that there are no "truly" photosynthetic opisthokonts? Why?

True. Some opisthokonts, such as cnidarians (corals, sea anemones) and acoel flatworms, possess photosynthetic symbionts, but there are no truly photosynthetic organisms in this group (fungi, choanoflagellates, and animals).

List and describe the three types of survivorship curves discussed in lecture. Provide an example of an organism that experiences these types of curves.

Type I - very low mortality early in life, high mortality late in life. Humans. Type II - constant death rate regardless of age. Small mammals and birds. Type III - very high mortality early in life, decreased mortality as one ages. Many herbaceous plants.

Why has our estimation of the diversity of prokaryotic-celled organisms increased dramatically in the last decade?

We can probe genetic diversity of organisms in the environment without having to culture them.

There exist in the fossil record numerous examples of enormous insects that were alive when the atmosphere contained increased concentrations of O2. Based on your understanding of trachea in insects, why might you expect insect size to correlate positively with concentration of O2 in the atmosphere?

When air enters the tracheole, oxygen dissolves into the liquid and will enter the cell through passive diffusion. The size of insects will thus be limited by the rate of diffusion of oxygen into the cells (think SA:Volume). If oxygen concentrations in the atmosphere were considerably higher, it might be expected that insects could attain larger sizes.

Using sea otters as an example, describe a trophic cascade that occurs in kelp forest ecosystems. What occurs in the absence of otters, which is what occurred after otter populations were decimated due to the fur trade, and what occurs in the presence of otters, which is what has happened following restoration efforts?

When otters are abundant... Otters up, sea urchins down, kelp up When otters absent... Otters down, sea urchins up, kelp down

Without fossils, how would we interpret the evolution of the limb bones in tetrapods?

Without the fossil record, we wouldn't know the sequence of events and would have a gap of understanding between the change from the likely ancestral state (single large bone in fins attached to shoulder and pelvic girdle) and the derived character state in extant (living) tetrapods.

What is yeast? Is this type of life cycle considered the ancestral condition in fungi?

Yeasts are single celled fungi, but unlike other multicellular eukaryotes this is not the ancestral condition. In fact, there are lineages of yeast that if you change the environment they are growing in, they will make hyphae.

GO OVER Starting with sulfate (SO42-) ions, describe the Sulfur Cycle.

assimilation- plants can take up sulfate ions and reduce them to a form that can then be incorporated into organic molecules (e.g., the amino acid cysteine). These organic molecules will eventually be decomposed, resulting in the release of inorganic hydrogen sulfide (H2S). Alternatively, sulfate ions can be used as an electron acceptor during anaerobic respiration, forming H2S. These reduced sulfur compounds released by decomposing cells or anaerobic prokaryotes are then oxidized by chemosynthetic or anoxygenic photosynthetic prokaryotes, eventually resulting in the release of sulfate ions and completing the cycle.

What is competitive exclusion? Using predatory newts as an example, explain how top down effects can mitigate competitive exclusion and alter species diversity or distributions.

competitive exclusion - one species prevents another species from using a resource that they both otherwise use. predatory newt - when the newt is absent, the larger tadpoles (Southern Toad / Eastern Spadefoot) outcompete the smaller tadpole (Spring Peeper). In the presence of the newt - the newt preferentially preys on the larger tadpoles. This increases the survival of the Spring Peeper, removing the competitive exclusion.

What is the relative abundance of the gamete types in isogamy, anisogamy, and oogamy (i.e., eggs and sperm in oogamy).

isogamy- the gametes will be equally abundant, in general. oogamy- the male gametes will be much more abundant than the female gametes. anisogamy- there may be slightly more of the smaller gamete, depending on the size difference between the gametes.

Compare and contrast r-selected species vs K-selected species.

r-selected: increased quantity of offspring with reduced parental investment K-selected: reduced quantity of offspring with increased parental investment.

Which evolved first: oxygenic photosynthesis or anoxygenic photosynthesis?

Anoxygenic PS

How does the bobtail squid deal with the high proliferation rates commonly found in prokaryotic cells, including A. fischeri?

As previously stated, the bobtail squid expels the majority (~95%) of cells daily. This ensures that the squid is not maintaining a culture of bacteria with densities so great that it becomes nutritionally expensive to maintain.

For carbon source, distinguish between autotroph and heterotroph.

Autotroph - capable of synthesizing its own organic compounds (e.g., glucose) from inorganic sources (e.g., CO2) - essentially making its own carbon source. Heterotroph - relies on preformed organic molecules for their carbon source