Con Eco Exam 2

Why has there been an explosion of genomics in recent years?

1. Development of advanced tech = better research regarding genomics like NGS sequencing machines 2. 6th mass extinction is underway and if we want to save species we are losing, the new need to better understand the genetics f the spice stop save the form situations such as bottlenecking and inbreeding -- 3. Human Genome Project

What is the difference b/w genetic rescue and de-extinction?

Genetic rescue: bringing back a few individuals which different genetic information of a species that is currently alive and introducing new genetic info to boost the genetic variability w/in the species De-extinction: bringing back a species that has lost all of its individuals and is no longer alive at all except for what remains of their genetic information

What is driving the rapid development of camera trap technology and the decline in cost?

Hunters are driving it to come down in cost, since they are interested in finding out local game.

Why are biased density estimates a problem for conservation?

Most densities are overestimated and so this is a problem for jaguar conservation. Jag pop that are thought to be stable are actually smaller than what is needed, having been overestimated by at least a factor of two

What are the advantages of camera trap surveys compared with traditional survey techniques (e.g., visual counts, tracks, scat)? What drawbacks do some camera traps have (e.g., white flash versus infrared flash).

​White flash animal may not become habituated to having huge flash of light, so may decide to leave the area.

What did Jake find in the microbiome of water, catfish, and tilapia? What feed resulted in the greatest growth rates? What was the relationship b/w tilapia relative abundance and survival rate? Using these data, what would be the optimal fish, feed, and stocking density for fish farming in Malawi?

Microbiome diversity in tilapia/water > catfish Broiler feed had greatest growth rates for tilapia/catfish Directly proportional relationship b/w tilapia abundance and survival rate as their survival rate decreased with the decrease of cyanobacteria in the water

What is the microbiome? Compare the number of human vs microbiome (a) cells and (b) genes in the human body. What doe this tell you about the microbiome?

Microbiome: totality of microorganisms in a specified environment and their collective DNA; Humans = 30 trillion, Bacteria = 40 trillion --> 100 x more microbe genes than humans

What is molecular endocrinology?

Molecular approach to studying hormones -- uses in vitro assays on sample obtained through non-invassive techniques. The samples are urine and feces instead of blood. ME looks at the hormones found in the samples

How can camera traps be used in research?

Faunal Inventories Activity patterns Density (capture/recapture), Occupancy Analysis Resource use

What will be the impact on kelp (Macrocystis pyrifera) and the kelp microbiome under 'future conditions' (both increased temperature and carbon dioxide)?

Future conditions --> kelp would increase in growth and species richness Increased temp = decrease in kelp growth, increase species richness Increased CO2 levels = increased kelp growth, decreased species richness Rhode increase, alter decrease

Understand the methods used by Ben-Nun and colleagues to try to rescue the drill and NWR.

1. Generated a cell line of fibroblasts for the endangered species. 2. Took those cells and cultured them using a specific iPSC method of expansion. 3. Transduced a retrovirus into the cells that generated them into iPSCs. These iPSCs and fibroblasts were karyotyped for specific genes, and "immunocytochemistry" was performed. 4. Flow cytometry analysis was done for the quantification of pluripotent stem-cell associated marker expression 5. Reverse-transcriptase-PCR and genomic PCR were performed. 6. Copy number assay was done on the genomic DNA sequence, and the glycomic profiling of proteins were isolated from the cultured cells. 7. The iPSCs differentiated, allowing for teratoma formation and histological evaluation.

What are the issues that need to be considered to make decisions about whether we should use iPSCs to rescue species from the brink of extinction, or extinct species?

1. Should we focus on extinct species or endangered species that are not yet extinct? 2. Can long-extinct species (such as mammoths) be considered for genetic rescue? 3. What would determine whether genetic rescue is feasible for a species that has gone extinct? 4. Are frozen zoos important to the future of genetic rescue ("de-extinction") approaches?

What is the difference between activational and organizational effects of hormone exposure?

Activational effects: reversible Organizational effects: typically permanent; occur when fetus is exposed to hormones during development -Study shows after quantity of phytoestrogens in the diet of SWRs was reduced, more SWRs were still unable to become pregnant -- suggests organizational

What is a minimum viable population (MVP)? Address both the concept and the definition.

Concept: The MVP is not just a population that can maintain itself in regular conditions, but it is the minimum viable population, a population which is just big enough that it can survive the calamities that occur within its biogeographic context Definition: A MVP for any given species in any given habitat is the smallest isolated population having a 99% chance of remaining extant for 1000 years despite the foreseeable effects of demographic, environmental, and genetic stochasticity, and natural catastrophes.

What are the four forces of stochasticity that may result in the extinction of small populations? Be prepared to ID different examples of types of stochasticity (e.g. with heath hen example)

Demographic stochasticity: arises from chance events in a population of finite individuals Environmental stoch: comes from temporal variation of habitats in pop, competitors, etc Natural catastrophes: events such as fires, droughts, etc Genetic stoch: comes from changes in gene frequencies from effects such as the founder effects and inbreeding -- the importance of these factors for conservation increase with a decreasing population HEN example: The heath hen first suffered demographic stochasticity when settlers pushed them out and dangerously reduced the population from lack of land. When the population was once again recovered a natural catastrophe took place which destroyed many of the nests and habitats. This was followed by an environmental stochasticity when a heavy winter that year killed more individuals. This was followed by more environmental stochasticity when disease came and reduced the population back to 100 individuals when it had begun to grow again. Last, due to the lack of genetic diversity from the population which had now been bottlenecked several times as factors decreased its recovered populations, genetic factors came into play as the birds became sterile and the male populations increased disproportionately to the females. They eventually died by 1932. The heath hen, which had thought to be recovered in 1916 when it reached over 800 individuals, succumbed to stochastic forces which whipped out its population.

How can density estimates be biased, and why is this a concern for conservation?

Density estimates often overestimate the population so we think there are more in the population than true so they over hunt/over fish.

What are scat detection dogs and why are they important for conservation?

Dogs who have been specially trained to scent out a specific type of scat. This is important due to the wealth of information: Molecular endocrinology plays a big part of scat analysis. It allows scientists to identify the specific individual through DNA extraction as well as information on its nutritional state, hormone levels, reproductive state, any toxins it has picked up, etc.

What is the difference b/w AIR and PIR?

Early PIP (passive infrared cameras) used film, but digital PIR were introduced in 2006. AIR→ Used an infrared beam across the trail from a transmitter to a receiver PIR → (passive infrared receiver) "passive" means the PIR device does not emit an infrared beam but merely passively accepts incoming infrared radiation

What would be a "naïve test" of the top-down vs bottom up models?

Excluding all relevant predators from a large experimental group

What are the 5 approaches to determining MVP sizes? ID some of the advantages and disadvantages of each approach according to Shaffer 1981.

Experiments: most straightforward approach, crete isolated populations and monitor to see how and where they roam compared to growth, this is not reliable due to lack of consistency Biogeographic patterns: an approach in which individuals and populations are monitored to see how and where they roam compared to growth, this is also not reliable due to the lack of consistency Theoretical models --> used to predict the probability that a small population will go extinct in a certain amount of time; these models are unreliable as they use unrealistic assumptions Simulation models --> similar, however, provide greater realism and are flexible for assessing change; models must be specifically altered for different species and require specific information which takes a long time to gather Genetic consideration --> look at genetics to decide; this approach takes a simplified view of things and should be a guideline not a direct approach ---The most promising approaches are biogeographic patterns and simulations --including genetic factors and other specifics, these approaches could be extended and refined to be used in analysis

Be familiar with the examples of trophic cascades given in class (e.g., Lake Guri, Yellowstone N.P., Zion N.P., Talamanca Mountains, bushmeat in Congo, Barro Colorado Island, dingoes in Australia, coyotes and pronghorn)

If an apex predator is taken out of an ecosystem, the number of medium-sized predators (mesopredators) may increase, resulting in their prey suffering more from predation than when the apex predators were controlling the mesopredators. Yellowstone: Wolf population depletes, elk increase, berry decrease, bears who eat berries decrease Zion: Humans increase, cougars decrease, deer increase, cottonwood decrease, stream channel erosion increases. Dingoes in Australia: dingos decrease, rabbit increase, vegetation decrease, fox increase, small mammals and amphibians decrease Coyotes and pronghorn: The strong, negative correlations between coyote and wolf densities, and coyote densities and fawn survival, support the hypothesis that mesopredator release of coyotes, resulting from the extirpation of wolves throughout much of North America, contributes to high rates of coyote predation on pronghorn fawns observed in some areas.

Understand the steps for computing density estimates using camera trap data. Include in your discussion: individual identification, capturerecapture model, effective survey area, and MMDM.

Individual identification: Capturerecapture model: Effective survey area: MMDM:

How is jaguar density conventionally estimate from camera trap data? Explain the assumptions made.

Jaguar density (e.g., number of jaguar per 100 km2) is conventionally estimated from camera trap data using the closed population capture-recapture model. Very simply, this model assumes that the ratio of jaguar "captured" (photographed) to jaguar "recaptured" (photographed again) is the same as the ratio of jaguar sampled to jaguar not sampled (not photographed), and the number of jaguar sampled + not sampled equals the true population size.

How did Chris and colleagues study the potential effects of phytoestrogens on SWR reproductive success?

Measured activation of ESR1 and ESR2 in the SWR in different zoos across NA compared w/ levels of alfalfa, hay, pellets in their respective diets -- they did this by measuring the hormones in the feces/urine of SWR in zoos -- created two plots showing fertility of captive born females and wild-born females compared to their hormone levels -- looked at genistein, coumestrol, and estrogenicity

What are the reproductive problems faced by the captive population of SWR?

Only 50% of all captive females have ever reproduced and less than 33% of captive born females have ever reproduced

What are phytoestrogens? How might SWR be exposed to phytoestrogens?

Phytoestrogens: work same as DES; mimic estrogen and can activate the receptors - they cause activation effects, which are reversible and organizational effects, which are typically permanent SWRs may be exposed through their feed (pellets, alfalfa, and other sources of food typically given to SWRs could contain them) -- alfalfa have high content

Why are SWR considered to be a conservation success story? What is it important to breed them successfully in captivity?

SWR only had 100 in 1895, but has grown to be about 20,000. Not breeding in captivity, which is bad b/c if anything happened to the wild population conservationists need a healthy, genetically diverse population to draw from

What is the "Frozen Zoo" and why is it important for genetic reduce of endangered species?

Storing of frozen fibroblasts from endangered animals for future use -- can help in de-extinction and conservation attempts

Trophic cascade definition and how it relates to "fishing down the marine food chain" concept

TC: a higher trophic level will dramatically/indirectly affect succeeding levels --predators suppress population, alter behavior, of prey -Fishers take larger fish from ecosystems, leaving medium sized fish -- medium fish targeted next, leaving smaller fish etc.

What did the authors conclude about estimates of jaguar populations from most camera trap studies?

The knowledge of jaguar habitats is still growing and not perfect -- thus, studies are not reliable and the authors state that "populations that were thought to be sufficiently large for long term survival" might actually be in danger of extinction

What did John Terborgh predict is the long-term fate of islands with hyper abundant folivores (leaf-eaters)? What parallel situations the authors cite in other ecosystems?

They predict that hyperabundant folivores will reduce species-rich forests to herbivore-resistant plants, thus causing a loss in plant and animal diversity. This situation parallels the long-term overgrazing of semiarid range that converts grasslands to thornscrub or shrub steppe as the grazers ate the preferable plant, which led to decrease in carrying capacity for grazers. It also it similar to a wild pigs situation in Malaysia, where the pigs are reducing plant recruitment in a remnant forest due to a lack of predators.

What are the sampling problems of using capture-recapture methods for estimating jaguar population size?

Three potential problems are as follows: the potential "maximum distance" is limited by the cameras and does not reflect the true maximum distance of a territory for jaguars, the few "recaptures" distort the data in that they do not reflect that actual distance the organism has moved, and the maximum distance traveled by an individual is underestimated, since only part of the home may overlap with the camera grid.

Difference b/w "top down" vs "bottom up"

Top down: predators limit herbivores and prevent them from using all vegetation Bottum up: plant chemical defenses are what limits plants exploitation by herbivores

What would top down vs bottom up predict in the absence of predators?

Top-down: consumer populations would expand Bottom-up: little change in consumer numbers

What did Tobler & Powell 2013 discover regarding bias in jaguar density estimations?

What factors seem to result in biased (inaccurate) estimates? The authors state that the "main source of imprecision for (all the above models) is the estimation of the home range parameter." Thus, new data using larger camera polygons could correct the small polygon bias.

What are induced pluripotent stem cells (iPSCs)?

iPSCs: adult cells that have been genetically reprogrammed to an embryonic stem cell-like state by being forced to express genes that give them the properties of embryonic stem cells -- do this by extracting the nucleus out of a cell, leaving just the cytoplasm+contents --> nucleus of another cell is inserted using electricity and chemical prompts so that the nucleus will join with the empty cell --the new cell with the new genetic info can be reprogrammed so that it loses its differentiated state, hence, become iPSCs -- it can later then be re-differentiated depending on the conditions the cells are kept in