Allendorf and Luikart review the genetic challenges responsible for the conservation of a population threatened with extinction.

Although the authors concentrate on the genetic factors concerning plant conservation, they note that a true understanding of both plant and animal genetics is necessary to gather the tools needed to preserve a given species.

Abbott along his team of researchers, reviews the role taxonomy plays in understanding the origin of the species and such species’ proper conservation.

The authors recognize that differences in taxa, due to genetic variability, may affect the species’ overall survival and ultimate conservation methods which may currently be contributing to their endangerment.

The authors review how new functions can evolve when existing genes gain new functions.

Visick and Mc-Fall-Ngai review the contributions of Vibrio fischeri to the development of the light organ as Euprymna scolopes matures.

Review of bioluminescence in bacteria. Examines the possible role bioluminescence plays for the bacteria as well as some of the organisms that have symbiotic relationships with these bacteria.

Study showing that E. scolopes is only able to undergo normal development if V. fischeri possesses the ability to produce luminescence.

Study that looked at the reflective tissues of the light organ and established their similarity to the reflective tissues found in the eye.

Early study providing evidence that, in addition to signals coming from the eyes, extraocular photoreceptors also provide signals that contribute to the ability of some species of squid to be able to adjust the amount of light they produce to match the downwelling light in the environment.

Early study detailing physical evidence that some species of squid are able to adjust the amount of light they produce to match the ambient light in the environment, a process called counterillumination.

Review paper outlining the seven subfamilies of opsins, their functions, and possible phylogenetic relationships.

This is a review article, which explains the current understanding of a topic based on a review and summary of the published literature. The authors summarized what was known at the time (2000) about the occurrence of extreme weather and climate events and their effects on human societies and natural systems.

This study combined analyses at both large and small scales to examine the role of climate warming in the extinction of amphibians in tropical regions of the Americas. The extinctions were previously attributed to an epidemic of a fungal disease.

The authors show that climate warming was a key factor in the extinctions. They propose that a warmer climate encourages growth of the fungus and thereby increases disease outbreaks.

This article examines evidence that effects of climate change may be underestimated. The authors show that population declines and range retractions may not be detected if a study does not evaluate the populations at a sufficiently small scale. More detailed studies can also help determine how much climate and other factors have contributed to the effects.

Most studies of the effects of climate on living organisms examine areas of a kilometer-scale size. However, organisms actually experience climate extremes on a much smaller scale.

This study demonstrates the extent of microclimate effects on temperature extremes. Variations in topography and vegetation type generated large local temperature differences in an area.

The authors state that these microclimate effects must be quantified and included in analyses to understand and predict the impacts of climate change on biodiversity.

The authors predicted the velocity of temperature change, a measurement of how annual average temperatures move over time, throughout the world. They found that predicted velocity varies widely depending on the type of topography; values ranged from 0.08 km per year to 1.26 km per year.

Plants and animals may need to shift their ranges along with the average temperature to keep living in a suitable climate. The authors determined that, in some cases, species will not be able to move their ranges fast enough to keep up with climate change.

This article addresses the difficulties the Intergovernmental Panel on Climate Change had reaching an agreement (in 2001) on the extent to which climate change is causing changes in biological systems. The authors suggest that differences in approach, particularly between biologists and economists, were a source of disagreement.

To bridge the gap between the disciplines, they used several analyses, combinations of biological and economic approaches, to analyze a large set of global biological data. They concluded that there is sufficient evidence to say with very high confidence that climate change is already affecting living systems.

The authors examined how changes in climate have influenced the timing of periodic life cycle events, such as leaves unfolding and fruit ripening. They analyzed a large set of data for European plants and a few animals, over the years 1971 to 2000.

They found that spring and summer life cycle events were happening earlier in the year and that these changes matched the patterns of climate warming.

The researchers examined bush crickets with variability in wing shape. Crickets on the edge of the range had a higher frequency of long wings which aid in dispersal, compared to the individuals at the core of the range which had fewer long-winged individuals. While long-wings allow for better dispersal, they reduce reproduction, which may be why the core population evolves to have fewer long-winged individuals.

Looks at the effect of density dependence on the spread of annual plants through a patchy habitat. It was seen that landscape patchiness and the number of annual plant invaders worked together to create a strong role for density dependence. Furthermore, infraspecific competition was seen to limit the spread of annuals through patchy landscapes by limiting the production speed of seeds in plants. Density dependence was not seen when continuous density was used.

This study looks at the role of evolution in spreading populations in patchy landscapes. While natural selection typically favors organisms who produce many offspring, in these patchy landscapes, organisms that tolerated competition but produced less offspring performed better.

Doctors performing brain surgery were able to cause the patient to laugh by electrically stimulating the anterior supplementary motor area. This area of the brain is also involved in human speech.

This paper describes the use of fMRI brain scans of humans experiencing externally produced tickling or self-produced tickling.

The authors conclude that the somatosensory cortex is active in response to tickling and that the cerebellum plays a role in muting this response during self-produced tickling.

Harris and Christenfeld showed that comedy-induced laughter does not increase subsequent tickle-induced laughter and vice versa.

Stout and Goulson worked to identify how the nectar secretion rate of a given plant influences the response of bumble bees returning to it after it has already been visited.

From this, Stout and Goulson developed a model that determines how long a bumble bee will avoid a recently visited flower whose nectar has been depleted based off of the nectar secretion rate of that flower.

Levins worked to identify how populations physiologically and behaviorally adapt to both short and long term changes in the conditions of their environment.

From this, Levins identified how populations of different species spatially divide their environment among themselves, allowing one to estimate how many species can coexist within a given area.

Goulson and colleagues worked to identify the reasons behind the decline in populations of bees. Reasons include parasites, a decline in flower populations, and an increased use of pesticides.

It is noted that efforts to reduce the use of pesticides and to increase the population of flowers visited by bees should be developed.

Elsen and Tingley worked to determine how the topography of a given mountain influences its relative susceptibility to climate change. From that they looked into how populations inhabiting a given mountain will migrate in reaction to climate change.

Miller worked to identify how Hawkmoths influence the physical variation seen in Colorado Blue Columbine (Aquilegia caerulea) in different areas.

Miller found that areas containing moths with longer tongues also feature plants with longer floral spurs.

Vazquez and colleagues review the patterns within ecosystem networks that lead to plant - animal mutualisms.

Vazquez and colleagues identify many mechanisms that produce mutualisms. It is noted that the relative influence of each mechanism on the production of a mutualism is still unknown.

Bommarco and colleagues worked to determine how the composition of bumble bee populations have shifted in Sweden.

It is noted that species richness and evenness of population composition should be developed to promote healthy ecosystems.

The authors identify subgroups of sensory neurons in hairy skin that detect either pleasant sensations (stroking or massage) or unpleasant sensations.

Cardinale reviews the roles of "primary producer" biodiversity with respect to ecological processes critical to the functionality and health of terrestrial and marine ecosystems.

Byrne's review focuses on the impacts of assemblage diversity on ecosystem functions.

This study acknowledges the impact of diversity on resource utilization and thus productivity, however the focus is on the characterization of multi-functionality.

Fissore's review argues that carbon sequestration by forests in the midwest cannot off-set fossil fuel based carbon dioxide emissions. The study compares hypothetical scenarios necessary to offset significant proportions of the carbon dioxide emissions by converting landscapes into carbon sequestering species.

Follett discusses the role organic soils play in the movement of carbon dioxide from the atmosphere to the soil. This review characterizes terrestrial soils as carbon sinks which is important for crop management.

Sejo discusses the role species richness plays in affecting economic value.

This review puts emphasis on the role of biodiversity on marginal economic value represented as carbon storage for conservation efforts.

Daniels reviews the role the forests play in reducing atmospheric carbon dioxide levels. His focus however is primarily advocating for including carbon sequestering by forests into management plans or a cap-and-trade program.

Reich compares the role of CO2 and N2 on species richness and functional group diversity.

This study compares the roles of functional group diversity and species richness on biomass accumulation in an elevated CO2 and N2 environment.

Fornara reviews the mechanisms that control carbon and nitrogen accumulation in soils.

The review covers the relationships between biodiversity and carbon and nitrogen accumulation in soils, with an emphasis on the C3 and C4 grasses.

Barnosky discusses the events known as mass extinctions and compares the rates of extinction for these events to modern rates of extinction.

This study looked at the sources and fate of local marine debris near the Hawaiian islands. Debris from a large community was captured using surface traps, and wooden drifters were released to examine the effect of nearshore currents and tides on debris distribution. This study demonstrated that local pollutants can be retained nearby, contribute to the island's debris-accumulation area, and quickly spread to other islands.

This article discusses the idea of designing buildings and objects to be made using the minimum of materials and a maximum of efficiency. 3D printing and biodegradable materials are explored as examples of ways to improve product design and reduce waste.

This document released by the American Chemistry Council is a reference book on plastic resins. It contains information about North American resin production, sales, industry capacities, and utilization rates from 2002-2012. Sales data are presented for various end-use markets, and tables show historical trends from 1973 to 2012. The publication explains the basic chemistry of plastics and manufacturing processes. It also details the history of plastics development and modern-day applications and provides a glossary of basic plastics terms. Jambeck et al. used this reference to estimate the amounts of plastic production in North America and plastic in the U.S. waste stream.

The juvenile hormone is the most important hormone to all insects, especially in adult female Aedes aegypti. This mosquito uses nutrients to boost JH levels which increases reproduction.

This paper considers the various characteristics that limit the swimming speed of fish. For one, it analyzes how smaller fish are capable of higher tail beat frequencies than larger fish. Also, that the stride length of a fish is not longer than the fish's size. Furthermore, swimming speed is limited by the contraction time of swimming muscle so maximum swimming speeds are determined by muscle contraction time and stride length.

The paper analyzes the limitations that stop fish from swimming faster. Small fish are held back by the power available, and larger fish are limited by cavitation.

In this review the author talks about the characteristics that give tuna fish high performance. These characteristics include 3 things: high rates of somatic and gonadal growth, rates of digestion, and rates of recovery from exhaustive exercise. This study uses these findings to defy the myth that sailfish and other pelagic fish just have high maximum swimming speeds that allows them to avoid cavitation.

Dr. DeGennaro established techniques to edit the genome of mosquitoes. He created the first mosquito mutant using zinc-finger nucleases to initiate the molecular genetic analysis of olfactory receptor function in Aedes aegypti mosquitoes. His work revealed new knowledge about the integration of host cues, mosquito host-preferences, mosquito nectar-seeking, and the mechanism of DEET repellency.

Dr. DeGennaro demonstrated that the mosquitoes use the OR/ORCO olfactory receptor pathway to respond to human odors and DEET as well as nectar volatile. His work implicated the Ionotropic Receptor family of olfactory receptors in host-seeking mosquitoes. Additionally, he showed that DEET repels mosquitoes through ORCO-dependent olfaction and an unidentified taste receptor.

Schleussner and co-authors assessed the impacts of reaching the 1.5°C and 2.0°C thresholds for a number of variables, at a regional level. They found large differences in the impacts of the two scenarios, covering a range of issues from the fraction of global coral reefs at risk of annual bleaching to heat wave duration.

Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.

Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.

Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.

Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophila ovaries are modified by Wolbachia.

While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.

Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.

The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.

Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.

Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.

Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.

Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.

Throughout their research, Steel and Penny explicate the connection between maximum parsimony (MP) and maximum likelihood (ML). According to the paper, they state that there can be a link between both methods when there is no common mechanism between sites. Moreover, throughout this process, Steel and Penny clarify disputed points between the two methods. It was concluded that neither models outperform the other when it comes to recovering the tree.

This paper utilizes this source to support which method would more accurately perform the recovery of the tree. Furthermore, the authors wanted to assure those interested in their work that a variety of techniques including several models of ML and MP if special claims are made can be used.

During their study, Saccone, Pesole, and Preparata concluded that only homologous gene pairs, which whom are also stationary, are truly reliable to consistently provide with trustworthy determinations of phylogeny. Nonstationary genes, in comparison, resulted in outstandingly high rate values eventually resulting in possible systematic failure.

This paper uses such sources as reinforcement of their results as stationary genes were proved to be better supporters in the construction of phylogenetic trees, or in phylogeny overall, providing superior results with an increased level of confidence.

In this paper, Gee concluded that there were no guidelines or factors that could measure the performance of a certain gene.The reason why the author of this paper uses it is to highlight the importance of stationary genes and how helpful they are for generating phylogenetic genes.

In his study, Rokas came to the conclusion that there are no genes that provide more phylogenetic information than others. This led him to believe that in order to create an accurate phylogenetic tree, one would have to study the whole genome of an organism. He believed that an infinite amount of genes will result in an infinite amount of accuracy, which is why he claimed that most phylogenetic trees at the moment were probably inaccurate.

In this paper, the conclusions Rokas came to were disproven by the experiments carried out. Stationary genes were discovered to be better contributors to a phylogenetic tree and are needed only in a relatively small amount to create an accurate tree.

References 1-4 work together in unison to help support the authors statement when saying that DEET is an effective and widely used insect repellent. Sources one, two and four aim to show how DEET sizes up against other repellants, while source number three take a more in depth look into why DEET functions the way it does.

Mosquitoes have an inheritable "immunity" to DEET that seems to express itself as a dominant gene that affects the way they respond to olfactory stimuli, in this case people.

Just as a expressed in source fifty-eight, mosquitoes seem to express distaste towards DEET. Gustatory receptors in Aedis aegypti sense a bitter taste from the repellent, and that gives the mosquito negative feedback, discouraging feeding.

DEET can be considered a "multi-modal" repellent as contributed by the many studies that show its ability to deflect mosquitoes on an olfactory level and, as a demonstrated in this study, a gustatory one. It was found that mosquitoes would not feed on blood treated with DEET, even if they penetrated a feeding membrane with their proboscis.

In their paper, Syed & Leal, 2008, test the effects DEET has on the olfactory receptor neuron (ORN) in mosquitoes. They aim to debunk the former hypothesis that DEET masks the lactic acid odor, attractive to mosquitoes, and naturally produced by humans. Syed & Leal rather suggest, through evidence, that mosquitoes smell DEET and avoid it through their response sense activated by the olfactory receptor neurons (ORNs)

Grant & Dickens, 2011 attempt to investigate the effects of multiple repellents on the vertebrate-secreted, mosquito-attractant odor known as octenol. The study compared repellants 2-undecanone, DEET, and IR3535, and picardin. Overall, they mentioned how repellents affect the mosquito's octenol receptor on its neuron which senses these odors. Specifically, their neurons are attracted to the R enantiomer of octenol rather than the S.

Davis & Sokolove, 1976 investigate the role of DEET on Lactic Acid neurons. They propose that Lactic acid (LA) chemoreceptors located on the mosquito antennae were affected by DEET. DEET inhibited the LA-sensitive neurons, hence concluding that the DEET repellant inhibits the mosquitoes ability to detect and track its host.

Source seven discusses how chemists tested many different compounds as possible key ingredients in repellents, with diethylamides being the focus of their attention. Source eight expands upon this somewhat to show how the repellency of a diethylamide was capable of warding off many species of mosquitoes in Panama during testing.

Testing of different compounds was necessary to determine an effective repellent against the prime target, Aedis aegypti.

Fradin & Day, 2002 suggest that in comparison with repellant IR3535, three types of repellant impregnated wristbands, and a topical moisturizer repellant, DEET repellant was the most effective while conducting their study which was controlled for mosquito age, species, hunger level, and other environmental factors. DEET has been shown the most effective with respect to duration of repellency which was also positively correlated with the amount of DEET applied.

Cooper et al., 2004 suggest that DEET is effective in repellency against cercariae more effectively than regular topical formulations. When DEET was incorporated in silicone-based formulations or Cetomacrogol-based (CMO) formulations it was more effective. DEET is so effective because of its toxicity against the cercariae. The dimeticone formulation however- without incorporation of DEET- also helped to protect as the topical formula was better absorbed in the stratum corneum (skin) and blocked cercariae recognition of the skin.

A 1970's review discussing the formation of integuments (hard, protective layers covering the body), scales, and hair.

The paper explores the different hypotheses of the time, including scaled animals as precursors to nonscaled animals, ossified (bony) scales as a precursor to the scales found on today's reptiles, and the evolution of hair from sensory appendages.

In this landmark paper, Turing proposes the reaction diffusion theory to explain morphogenesis.

This theory states that when two chemicals react with each other they diffuse to form chemical gradients. These gradients form patterns that direct morphogenesis.

Explores the role of β-catenin, which is expressed in the placode.

When this protein was mutated in chickens, their feet were scaleless and they had abnormal feather growth.

Reviews the development of skin cells that give rise to hairs.

A hair placode forms, allowing the expression of genes that direct skin cell and hair follicle development.

Explores the relationship between feathers and scales.

Visualization of the location and amount of β-catenin during the development of feathers and scales revealed similar patterns between the two. The authors concluded that feathers and scales share an evolutionary ancestor.

Proposed the theory that mammalian hair evolved from glandular structures, whereas reptile and bird skin evolved from a thick protective coating.

A revision to a 1972 model of how mammalian hair evolved.

This new model proposes that the development of hair was caused by mutations in patterning genes, which resulted in hair becoming more useful insulation.

This paper discusses the way that crocodile head scales form. Unlike feathers, hair, and other scales, crocodile facial scales are formed when growing cells physically crack to form unique patterns.

This review article summarizes the uses humans have for plastics, the effects of plastics on the living and nonliving parts of the environment, and future concerns about the manufacture and disposal of plastic products.

This population growth data from the United Nations was used to predict future amounts of plastic waste entering the ocean from individual countries.

Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.

P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.

This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.

Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.

The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)

The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)

The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)

Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)

This study investigated offset nicking as a means of reducing off-target modifications. The authors found that by using Cas9 mutants with sgRNAs, a targeted double-stranded break can be performed. Off-target activity was reduced 50- to 1000-fold with this technique.

This study investigates the BRAF mutation in melanoma and the BRAF protein kinase inhibitor vemurafenib (PLX). The researchers found that PLX reduced tumor growth in cells that had a mutated BRAF gene.

This study demonstrated that Cas9 is effective at introducing specific loss-of-function mutations in the genome and creating specific double-stranded breaks in DNA sequences.

In this study Ittner and others described the parts of the APP23 mouse model through artificial stimulation.

Li and others studied how amyloid beta affects synaptic plasticity, or the ability of synapse to weaken or strengthen. The amyloid beta increases activation of extrasynaptic NMDARs.

Mucke and Selkoe show that amyloid beta binds to different parts of plasma membranes and induces neuronal dysfunction and disruption of networks.

In this article, Ittner and others show that the absence of tau in amyloid beta-forming mice lessens the severity of amyloid beta toxicity. These results suggest that tau and amyloid beta together increase the symptoms and progression of Alzheimer’s disease.

Roberson and others conducted an experiment on mice to test targeting tau in Alzheimer’s as an effective treatment. The experiment showed that tau reduction can block amyloid beta neuronal dysfunction, showing that tau reduction could be a future effective treatment of Alzheimer’s.

Ittner and Gӧtz review new findings showing the interactions of tau and amyloid beta. Tau can shift from the axon to the dendrite helping to mediate amyloid beta toxicity.

C. Haass, D. J. Selkoe,Nat. Rev. Mol. Cell Biol.8, 101–112(2007).: Haass and Selkoe show that in AD, small intermediates of amyloid beta, called oligomers, negatively affects synaptic structure and plasticity.

Warming induced early leaf bud bursts, growth, and reproduction but did not effect senescence. Study was performed in multiple sites in the arctic region over a course of four years.

RW

Warming induced early leaf bud bursts, growth, and reproduction but did not effect senescence. Study was performed in multiple sites in the arctic region over a course of four years.

RW

Sea ice decline due to global warming is effecting plant productivity in arctic regions.

RW

Sea ice decline due to global warming is effecting plant productivity in arctic regions.

RW

Heat sum increases for flowering and senescence

RW

Heat sums have increased over time for flowering and senescence.

RW

This paper discusses how inefficient no-take zones are in protecting reef sharks. - Emily

This study was cited to illustrate the effect of marine reserves on the Caribbean sharks. The study found sharks to be less concentrated in areas of high human activity.

The effects of marine reserves on fisheries is discussed in this paper. Marine reserves were sometimes controversial; however, they proved to be a supportive force in the quality and amount of fish caught by adjacent fisheries. - Emily

This article aided in emphasizing the concepts of site fidelity and the effect that migrations have on the density of shark populations in marine reserves. It built upon the idea that reserves increase the overall population of species inhabiting the area due to to the lack of fishing that occurs in these areas in contrast to non preserved locations. -Sindy

This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.

-Otniel Gonzalez

This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.

-Angela Mujica

Hardingham and Bading show that NMDAR responses depend on receptor location. Synaptic NMDARs promotes cell survival, while stimulate of extrasynaptic NMDARs promotes cell death. The unequal stimulation of these receptors neuronal dysfunction, while stimulation of synaptic receptors could be used a protective therapy.

Ballatore, Lee, and Trojanowski review and summarize the recent discoveries of tau-mediated neurodegeneration mechanisms and how they can understand AD progression and discover new drug treatments.

For this experiment to occur, there had to be some kind of data to support what is being presented. Datamonkey is a popular-based web suite of phylogenetic analysis tools for use in evolutionary biology. Analysis options fall into many different categories such as algorithmic methods for recombination detection, evolutionary fingerprinting of genes, codon model selection, co-evolution between sites, identification of sites, etc. For this paper, the data is based on evolution throughout the events and moments shown from these insects. https://academic.oup.com/bioinformatics/article/26/19/2455/228720

The article summarizes all recent findings of the time regarding sexual determination in drosophilids and other non-model insects. The primary concept remains that sexual determination depends on a shared gene switch present in both males and females of the same species. -Eri-Ray

This article explains that holometabolous insects, despite diversity, all generally have the same sex-determining pathway. It also explains how the (tra) goes to the (dsx) gene to go from the on to off position to determine sex of the zygote. - Jake Barbee

This article explains that organisms show a much greater divergence during the later stages of development in comparison to the earlier stages of development. Their conclusions proved that an increasing evolutionary rate (divergence) occurred in later developmental stages. -Elder

The article written by Carl D. Hopkins provides the author with background informational on B.pinnicaudatus and on the electric organs found within the organism . B.pinnicaudatus is a gymmotiform discovered in French Guinea and can be found throughout South America. This species similar to other electric fish is able to generate a pulse-type electric-organ discharge. The two type of electric discharges generated by electric fish tend to a pulse or a wave. This species is part of the largest family that produce electric pulses . Within this species , the males are able to produce a longer discharge than female within the species. http://pages.nbb.cornell.edu/neurobio/hopkins/Reprints/Hypopomus%20Pinnicaudatus,%20a%20New%20Species.pdf -Michelle Oriana Gomez-Guevara

Bennett's article analyzes the anatomy and physiology of the electric organs found within these electric fish. The membrane physiology of these electric organs evolved independently into six different groups and resulted in different membrane functions in different electrolyte which affect the electrorecption in the electric organism . Michelle Oriana Gomez-Guevara Note to Nick: I was only able to find a summary of the article and not the entire article. I checked google scholar, tried fiu library data and tried find it @FIU and I still was unable to find access to the article.

This source provides information about how the various regions of neuronal activity in electric fish response differently in response to variance in body movement.

Specifically, electrosensory pyramidal cells (neurons found in the areas of the brain that are involved in executive functions: memory, emotional responses etc,) activate or discharge electric signals in multiple ways dependent on the re-afferent (sensory information that is received) signals from their external environment.

https://www.ncbi.nlm.nih.gov/pubmed/7823309

-Kierra Hobdy

Bullock's and Heiligenberg's article , Electroreception ,gives an in-depth knowledge on electroreception as well as as review on the electric organs that are found within marine vertebrates . This background provide the author with the basic foundation for understanding how electrolocation works and the purposes it serves these marine vertebrates in their natural environment and daily lives. This citation also helps the author introduce the topic of electrogenesis and electroreception in relation to the location of the organs necessary for the process of electrolocation to occur. Michelle Oriana Gomez-Guevara

This article discusses the effect the addition of nutrients has on an aquatic ecosystem. Originally the author hypothesized an increase of energy transfer from prey to predators because of the increase of nutrients. However, this did not occur because the increase in nutrient led to an increase of predator resistant prey.

This article discusses how an increase in nutrients affects the levels of coarse and fine organic litter. It was observed that there were higher levels of fine organic material which led to an increase in bacteria. However, in the stream with no nutrients added to it, there was an increase in both fungal and bacterial communities.

This article demonstrates how the addition of nitrogen and phosphorus led to an increase in the production of fine organic compound by more than 300%. The article also mentions that this increase in fine organic compound will have an effect on the entire ecosystem in that area in the long term.

This article discusses the importance of terrestrial litter on an aquatic ecosystem. It was observed that organisms that lived in the stream that was being tested were affected the most by the absence of litter and the same effects could be observed throughout the entire ecosystem. However, terrestrial fauna was not affected meaning that it got its carbon from another source.

This article mentions the that the rate at which inland water sources release carbon dioxide is equivalent to the rate at which carbon is absorbed by the ocean. Methane is also being release in higher levels from lakes which are beginning to thaw because of increasing temperatures from global warming.

This experiment was a pan-European research of more than 100 streams in multiple European countries. It helped determine the importance of litter breakdown and states that countries should begin to consider the importance of regulating nutrient levels in aquatic ecosystems.

This article discusses the respiration rate of an aquatic ecosystem and uses it to determine patterns of activity found within a river during different seasons. It was observed that there were higher levels of respiration when there were was more organic carbon in the river.

This article focuses on how nutrients affect the growth of primary producers. The factors that were observed to have the highest effects on the ecosystems were nitrogen and phosphorus levels.

This article discusses how the addition of nutrients in an aquatic ecosystem affects secondary production. It was noted that there was an increase in secondary consumers most likely caused because of an increase in prey. There was also an increase of secondary consumer predators. It is mentioned that the increase of nutrients in the two years the survey was done resulted in positive effects for the secondary consumers, however, this might eventually change as the carbon levels in the ecosystem begin to decline because of the higher nutrient levels.

This article discusses how human practices have led to a increase of nitrogen levels in lakes. The article also mentions that an increase of phosphorus in lakes resulted in the extraction of higher levels of nitrogen. However, the author also states that laws pertaining to the concentration of phosphorus in aquatic habitats should not be removed or relaxed because phosphorus can also have a negative effect on an ecosystem if found in high concentrations.

Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.

GG

The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.

GG

Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.

GG

Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.

GG

Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.

GG

Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.

GG

While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.

GG

Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophilaovaries are modified by Wolbachia.

GG

Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.

Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.

GG

Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.

GG

Supports that a physical barrier will increase the chances of divergence between species creating two or more sub-species decedents . ~S.Z.

This paper contains discussion of species concepts and their application, morphological species characters and sibling species, biological properties of species, isolating mechanisms, hybridization, the variation and genetics of populations, storage and protection of genetic variation, the unity of the genotype, geographic variation, the polytypic species of the taxonomist, the population structure of species, kinds of species, multiplication of species, geographic speciation, the genetics of speciation, the ecology of speciation, and species and transpecific evolution. All of which can contribute a great deal to the topic of this paper. ~S.Z.

P5-P6 pair were isolated from each other just before the final closing of the Panama seaway. This was due to shoaling of water and the environmental change that came with it. ~S.Z.

Because of the long separation from one another, when some connection was established between either sides of the Isthmus, the shrimp pairs no longer had preferences to each other. Their extended sexual isolation probably had them adapted into altering their breeding behavior. ~J.D.A.

The authors performed a similarly designed experiment to the one cited here which was done on drosophila (flies). This is to show that there are other species that have undergone staggered isolation through similar or even different events. (DV)

The authors used this source as a bases to analyze the snapping shrimps mitochondrial DNA data and arrange the organisms in a phylogenetic tree as seen in figure 1. (DV)

The authors site this book as they are referring to the importance of having and maintaining genetic variation within a population. Also they might have utilized the mathematical theory of selection in a fluctuating environments, since the paper focuses on environmental and geographical changes affects on isolation. (DV)

Genetic divergence was observed to have occured at different moments when oceanic changes like the haulting of certain currents across the Panama seaway and the shallowing of certain areas. (DV)

In this review the author talks about the characteristics that give tuna fish high performance. These characteristics include 3 things: high rates of somatic and gonadal growth, rates of digestion, and rates of recovery from exhaustive exercise. This study uses these findings to defy the myth that sailfish and other pelagic fish just have high maximum swimming speeds that allows them to avoid cavitation.

Mikaela

This study investigated how different Cas9 mutants are more effective for different situations.

This study investigated PLX drug resistance in A375 cells. The authors found that NF1 is the most common mutation leading to PLX resistance, a finding that is supported by the current study. The Raf inhibitor vemurafenib was used in both studies. The authors in this paper used a pooled RNAi screen that targeted 16500 genes to look at loss-of-function mutations leading to PLX resistance.

This paper investigates some of the unintended consequences of RNAi, such as the lack of specificity. While one sequence may be the target, other sequences could also be silenced in this process. If a sequence shows some complementarity to the target sequence, it may be targeted, as well. The paper predicts that perfect specificity will be difficult to achieve with RNAi.

This study is another example of a loss-of-function screen. The initial experiment found host factors that were necessary for influenza infection, such as genes important for the synthesis pathway of diphthamide and genes that are necessary for cytolethal distending toxin. The authors knocked these genes out to investigate their effects.

This study uses RNAi to screen for loss-of-function alleles. The initial experiment tested the function of 91% of the genome of Drosophila. Testing was done by using an RNAi of the known 19,470 genes involved in cell growth and viability.

Nei found the average heterozygosity and genetic distance from a small number of individuals.This paper explains how biases arise in calculations when small samples are used. However, this paper establishes an average that reduces bias. (JP)

This paper, through studying 3 different species of Bathygobius, found that morphological divergence is not correlated with reproductive isolation. Their experiment was testing the extent in which these 3 species had evolved reproductive isolation in the Isthmus of Panama. (JP)

This source demonstrates that mitochondrial DNA is able to provide fairly accurate estimates of times since separation of a species in a 3 million year range. Here they also used organisms from the Isthmus of Panama and gel electrophoresis to deduce the time of speciation. (JP)

The authors of this paper found that, through parsimony analysis of the sequence divergence estimates and of sequence polymorphisms of the Holarctic fish's mtDNA, different Holarctic fish species arose from a geographical event that occurred during the beginning of the mid-Pliocene period.

The authors of this paper cited this source because this source conducts a similar study in deducing a time frame in which speciation of the Holarctic fish occurred. (JP)

This source published in 1979 to Nature tests the reliability of the molecular clock hypothesis by using Panamanian sea urchins. The author argues that the molecular clock hypothesis is not tenable or supportable. (JP)

Coral reefs on both the Pacific and Caribbean sides of Panama do not experience extreme weather events such as hurricanes. Coral diversity in Panama is maintained by mechanisms other than extreme weather disturbances, such as predation by the crown-of-thorns seastar, Acanthaster planci.

Note: many invertebrate zoologists insist on the term "sea star" to communicate that invertebrates are not fish. This is similar to the push to move from "jellyfish" to "sea jelly."

Sutherland presents evidence and argues for the existence of "alternative stable states" in several ecosystems—the idea that the history of organisms and physical events in a place can ultimately determine the "final" community. This is opposed to the idea that the community will eventually look the same regardless of which organisms are initially present.

Colonial animals (animals that grow by budding or that live in close association with each other, e.g. the polyps of corals that live together to form a single coral colony) have unique advantages and well as disadvantages compared to solitary organisms.

Jackson's paper describes some of the characteristics of colonial marine organisms, their distributions, and the factors that shape their distributions.

Goreau describes the species of corals found in Jamaica's reefs and the patterns of their distributions. He notes that the northern and southern coasts look different from each other and hypothesizes that these differences are driven by differences in storm frequencies.

This study develops an approach to detect selective sweeps that is also used in this paper,

This interesting paper similarly aims to understand the genetic basis of adaptation but look at the crop pearl millet. The authors were able to detect genetic changes associated with changes in the climate.

This review discusses how the advance in genomic technologies has helped stimulate research on the genetic basis of adaptation.

While strong waves and intense pulses of freshwater can cause immediate damage to coral reefs, coral reefs hit by severe tropical storms also experience significant sustained secondary mortality months after the initial impact of tropical storms as a result of less immediate consequences of tropical storms.

This detailed study of survivorship of Acropora cervicornis after Hurricane Allen showed that later mortality was over ten times more severe than the mortality caused by the storm itself and was caused by disease and coral predators feeding on survivors. This complex pattern may explain why rates of recovery from disturbances may vary widely.

“In press” means that the paper had not actually been published at the time.

Connell describes a mechanism by which the high biodiversity of tropical rain forests and coral reefs is maintained by disturbances, contrary to earlier hypotheses that suggested that tropical environments were very stable.

Researchers in Guam describe minimal damage to hard coral reefs after a typhoon and no long-term impact, even in exposed areas. This is likely due in part to the low, rugged profile of reefs in Guam and the fact that they are hit by hurricanes very often.

These papers investigate axonal injury in the context of TBI. Strich et al. focused on the clinical neuropathology of axonal injury, and Gennarelli et al. focused on the biomechanics.

These works support the idea that head acceleration during injury leads to stress that causes damage to nerve fibers and impairs the brain postinjury.

Omalu et al. presented a single case of CTE in a military veteran. The authors of the present study investigated a controlled case series comparing blast-exposed military veterans and athletes

Dr. Omalu is perhaps best known as the subject of the movie Concussion, starring Will Smith.

A report of the long-term effects of repetitive head injury linked to American football.

This paper provides a thorough case study of CTE in athletes and characterizes some of the key features of the disease. The motivation behind the present study came from identifying similar CTE pathology in the brains of military veterans.

McKee et al. also published a follow-up that includes the largest case series of CTE to date.

This study provided evidence for structural brain injury in blast-exposed military veterans. This brought attention to the reality of blast TBI, which was the signature injury of the Operation Enduring Freedom and Operation Iraqi Freedom conflicts.

A book by RAND corporation that brought the concept of the "invisible injury[should this be "wounds"?] of war" to a broader audience both in the United States and abroad.

This review was written by members of the same lab in which Dr. Roberson did the work described in this paper.

It outlines how the symptoms experienced by Alzheimer's patients seem to fluctuate constantly, suggesting that these symptoms cannot just be caused by dying neurons (which would result in symptoms that would get progressively worse).

The authors discuss known changes in other proteins in the brains of Alzheimer’s patients and how these protein networks might work together to mediate symptoms of Alzheimer’s disease in the brain.

Santa Cruz and colleagues studied genetically modified mice that had a mutation in the human version of the tau gene, which caused those mice to get tau tangles like those seen in Alzheimer’s disease.

Knocking out this tau gene allowed the mice to avoid memory and cognitive problems, although the tangles still formed.

Myers and colleagues examined patients that had died of progressive supranuclear palsy, a disease caused by a mutation in the tau gene.

They found that these patients also had an increased risk for Alzheimer’s disease, pointing to an important connection between tau and Alzheimer’s.

Tanzi and Bertram review the "amyloid hypothesis," which is the idea that a build-up of amyloid-β into plaques causes problems in tau, which then form tangles, causing the symptoms of Alzheimer’s disease.

For example, this study (Rahmstorf et al, 2015):

http://www.nature.com/nclimate/journal/v5/n5/full/nclimate2554.html#corrections

The authors show that microstimulation of regions of the brain associated with reward pathways can trigger 50 kHz USVs in rats.

They also use drug treatments to demonstrate the involvement of dopamine signaling pathways in the prodution of 50 kHz USVs.

Activity in the barrel cortex (a region of the somatosensory cortex) of rats is higher during social touch than it is when the rat is touched by an object. This suggests that the somatosensory cortex plays a role in both detecting touch and integrating information about the social context of the touch.

fMRI imaging shows that the somatosensory cortex plays a role in both the sensory detection of touch and the integration of emotional responses to that touch.

This article describes the use of Pavlovian conditioning in humans to create an "expectation" of tickling. This is offered as an explanation for the tendency of people to respond to tickling gestures in the same way they would respond to actual tickling.

Panksepp and Burgdorf describe the initial discovery and characterization of 50 kHz calls in the rat and present the case for interpreting these calls as laughter.

Harris reviews our current understanding of ticklishness in humans.

This paper includes descriptions of the two types of tickle, different types of laughter, the physiology of human ticklishness, and the possible evolutionary basis of ticklishness.

Millepora spp. fire corals can live detect gorgonians and will actively grow special "attack" branches towards gorgonians and overgrow them.

In a separate study of corals, small corals were less likely to be injured or damaged, but, when they were, they were much more likely to die.

Very interesting, I did not know Brust's novels are connected to Dumas.

Hartshorne and Schachner suggest that replication success should be traced in a database connecting replication attempts with original studies. Based on this information, a replication success score could be computed, which could be used as a criterion for a journal's quality alongside other indicators such as citation counts.

Similarly to the reproducibility project in psychology, Errington and colleagues planned to conduct replication attempts on 50 important papers from the field of cancer biology. While the registered reports are already available online, the replication studies themselves are currently still being conducted.

Read more on eLife:

https://elifesciences.org/collections/reproducibility-project-cancer-biology

Simmons and colleagues conduct computer simulations and two experiments that show how significant results can easily be achieved for a research hypothesis that is false. They show that flexibility --or as they call it: researcher degrees of freedom --in four areas make it more likely to find significant effects for a false hypothesis:

1. Flexibility in choosing the dependent variables reported: When researchers flexibly analyze two related dependent variables, this already almost doubles the probability of finding a positive result for a false hypothesis.

2. Flexibility in choosing the sample size: When researchers stop data collection, find no significant result, and collect additional data before checking for the same effect, this increases the probability of finding a positive result for a false hypothesis by 50%.

3. Flexibility in the use of additional variables included in the analyses: When researchers include additional variables in the analyses, false positive rates more than double.

1. Flexibility in the number of experimental conditions reported: When researchers collect data in three experimental conditions and flexibly decide whether to report the result of comparisons between any two conditions or all three, this more than doubles the false positive rate.

If researchers used research practices where they used all four flexibilities, they would, overall, be more likely to find positive results although the underlying hypothesis was indeed false.

Rosenthal addresses the 'file drawer problem', a questionable research practice where only studies that showed the desired result would be published and all other studies would land in the 'file drawer' and thus unknown to the scientific community.

In the extreme case, this could mean that, if a specific effect did not exist in reality, the 5% of studies that (due to statistical error allowed) find this effect get published and discussed as if the effect were true, whereas 95% of studies do not (and rightly so) find the effect, but are tucked away in a file drawer. This problem hinders scientific progress, as new studies would build on old, but false, effects.

Rosenthal introduces a way to assess the size of the file drawer problem, the tolerance to future null results: calculating the number of studies with null results that would have to be in a file drawer before the published studies on this effect would be called into question.

Nosek and colleagues argue that scientists are often torn between "getting it right" and "getting it published." While finding out the truth is the ultimate goal of research, more immediately, researchers need to publish their work to be successful in their profession.

A number of practices, such as the establishment of journals emphasizing reports of non-significant results, are argued to be ill suited for improving research practices. To reconcile the two seemingly-at-odds motives, Nosek and colleagues suggest measures such as lowering the bar for publications and emphasizing scientific rigor over novelty, as well as openness and transparency with regard to data and materials.

John, Loewenstein and Prelec conducted a survey with over 2,000 psychologists to identify to what extent they used questionable research practices (QPRs). The respondents were encouraged to report their behavior truthfully, as they could increase donations to a charity of their choice by giving more truthful answers.

Results showed that a high number of psychologists admitted to engaging in QRPs. Almost 70% of all respondents admitting to not reporting results for all dependent measures and around 50% of respondents admitting to reporting only studies that showed the desired results.

Moreover, results showed that researchers suspected their peers also occasionally engaged in such QRPs, but that psychologists thought that there was generally no good justification for engaging in QRPs.

Howard and colleagues examine how the file drawer problem---that is, the tendency of researchers to publish positive results but not negative or inconclusive results--affects a body of research literature. They compare "old," existing bodies of literature that could be suffering from the file drawer problem with a newly constructed body of literature guaranteed to be free of the file drawer problem, which they achieved by conducting new studies.

This investigation suggests that some bodies of literature are supported as relatively file-drawer-free, while other bodies of literature raise concern and kindle further studies on the effects they include.

Greenwald examines how research practices discriminate against accepting the null hypothesis (that an effect does not exist). Using a simulation, he suggests that too few publications accept the null hypothesis, and that a high proportion of publications falsely reject the null hypothesis when it would have held.

Greenwald further debunks traditional arguments about why a null hypothesis should not be accepted, and suggests ways to improve research practices to improve the acceptance of accepting the null hypothesis.