The data do not support the competing hypothesis that reef shark relative abundance was primarily driven by environmental variation between sites.
The data did not support this particular hypothesis because there was very little variation between the sites to begin with. The BRUV's were positioned in locations that did not vary in high arrays therefore a correlation between the abundance and environmental variation as not conclusive. -Sindy
The second prediction of our main hypothesis is that the relative abundance of Caribbean reef sharks is higher in reserves than similar fished reefs. The factor “marine reserve” was the most important predictor of shark presence or absence on BRUVs in the GLM, which is consistent with this prediction.
This indicates that their second prediction was also correct and they again failed to reject the null hypothesis meaning that there was a correlation between population density of sharks and a marine reserve. -Sindy
Sharks often exhibit an ontogenetic expansion of home range size [45] and we would expect a positive correlation between MLD and shark size if this is true for Caribbean reef sharks.
MLD is mixed layer depth, they expect a correlation between MLD and shark size because shark size normally correlates to its age and thus its experience. So the older and more experience a shark is, the more likely to go into ocean parameters with a mix of density or temperature etc than a smaller or younger shark. -Sindy
Transmitters are also more likely to be detected in the fore-reef because seafloor relief is low relative to water depth, whereas receivers in the lagoon are partially blocked by emergent patch reefs.
The complication arises in the fact that the transmitters may have a hard time ensuring accuracy due to the enviroment in which they are in. For example, in the fore-reef, the see level is too shallow so it may be spotted and cause the shark to drift away from it. And in the lagoons, not many sharks may approach either simply for the reason that the transmitters are being blocked by the reef. It is a complication related to placement of the transmitters and its unforeseen consequences. -Sindy
We tested the hypothesis that Caribbean reef sharks are to benefit from the local respite from fishing occurring within marine reserves by examining two of its key predictions. The first prediction is that Caribbean reef sharks exhibit high site-fidelity to reserve areas. Acoustic monitoring showed that most individuals exhibit a high degree of site-fidelity at GRMR.
This shows that the authors predictions were correct and thus fail to reject his null hypothesis. -Sindy
Additional BRUV survey sites
BRUV's were placed in sites different to the determined video sites in order to serve as a control for the experiment. The author expected to see distinct measures of site fidelity and examine these results in order to prevent false positives and ensure that the results gathered from the no take marine reserves were higher or more accurate than results measuring site fidelity in open waters. -Sindy
Baited remote underwater video (BRUV)
BRUV is a system used in marine biology research. By attracting shark into the field of view of a remotely controlled camera, the technique records sharks diversity, abundance and behavior of species. -Sindy
coelom
The coelom is the body cavity in which the intestines and digestive organs lay in. -Sindy
If sharks exhibit fine-scale site-fidelity to certain parts of GRMR, then the number of detections on a monitor should decrease with distance from the shark's tagging location.
As the shark gets further away from the initial location of tagging, its prevalence of location indicating site fidelity decreases because it is getting further and further away from its initial site. -Sindy
A recent survey of recreational SCUBA divers in the Caribbean found that shark sightings are quite rare, except for some places that have shark conservation regulations or large marine reserves in place
According to the NOAA, the removal of shark fins is prohibited by federal law. This practice, coined "shark finning" has been abolished in the United States since 2000. For further information on government involvement in shark regulations and management, visit this NOAA page
Furthermore, the Caribbean Reef and Caribbean Sharpnose sharks are both prohibited from being harvested, as this Florida Fish and Wildlife Conservation Commission site shows shows. -Sindy
They are considered “Near Threatened” by the International Union for the Conservation of Nature, with a range-wide population trend listed as “Decreasing”
The Caribbean reef shark is considered near threatened due to the increased consumption of shark fin delicacies and the selling of shark fins on the black market. This is precisely the reason that no-take marine reserves are crucial to the preservation of Caribbean Reef sharks. -Sindy
Caribbean reef shark (Carcharhinus perezi) i
Starvation Increases Insulin Sensitivity and Reduces Juvenile Hormone Synthesis in Mosquitoes
"If Mosquitoes Eat More, It Will Produce Hormones That Will Allow Them to Reproduce More." -Nicole Jones
titers
A titer is a laboratory test that measures the presence and amount of antibodies in blood.
The reproductive cycle of female mosquitoes proceeds through a previtellogenic stage (PVGS), an ovarian resting stage (ORS) and a vitellogenic stage (VGS)
One of the most significant stages of the reproductive cycle is vitellogenesis which involves massive production of yolk protein and their accumulation in developing oocytes. Vitellogenesis is dependent on the availability of a blood meal and, as a consequence, is linked to transmission of pathogens. Therefore, vitellogenesis and other aspects of mosquito reproductive physiology is critical for their management of disease. The ovarian resting stage in the reproductive cycle of female mosquitoes is a time when the eggs are not being produced. In addition, the ovaries will not develop beyond a resting stage until a blood meal of adequate size has been taken.
Our results reveal that starvation decreased JH synthesis via a decrease in insulin signaling in the CA. Starvation-induced up regulation of the insulin receptor increased CA insulin sensitivity and might “prime” the gland to respond rapidly to increases in insulin levels after feeding resumption. During this response to starvation the synthetic potential of the CA remained unaffected, and the gland rapidly and efficiently responded to insulin stimulation by increasing JH synthesis to rates similar to those of CA from non-starved females.
When insulin signaling and JH synthesis are low this causes starvation in mosquitoes. When these mosquitoes were fed again the gland was "primed"; which means it responds faster to insulin levels. Now that the gland has been primed it responds faster that way insulin signaling and JH synthesis return to their normal rates. -Emma
Electric organ discharges and electric images during electrolocation
Title : Zapped Up Fish: Electrolocation in Electric Fish
Electric images Quantitatively accurate electric images of small elliptical objects can be directly computed from electric field vectors (EOD maps) measured without the object (Rasnow, 1996). The electric images resulting from this semi-analytical simulator have 1–3 phase potential ‘bumps’ across the body, bumps that are weak and broad (no high spatial frequencies) (Fig. 3; Rasnow, 1996; Bacher, 1983; Heiligenberg, 1975). A systematic analysis suggested the following mapping between sensory image features and corresponding physical features of the objects. The location of the phase-averaged (e.g. RMS) image peak coincides with the object’s position over the body surface and thus unambiguously reveals two of the object’s three spatial position coordinates. Because the peak amplitude of the image is affected by multiple object parameters (its size, shape, distance and impedance), the object’s distance depends on more than one image parameter. A simple solution to distinguish a spherical object’s distance from its size is that the relative spatial width of the image (i.e. a parameter like the standard deviation of a Gaussian function) depends solely, and linearly, on the distance to the sphere’s center, and is independent of the sphere’s size (Fig. 3). Object impedance can be extracted from the image polarity and relative phase of the EOD and the electric image. Finally, object size can be determined unambiguously from the distance, the impedance and the peak amplitude of the image, the latter being proportional to the sphere’s volume. These results are summarized in Fig. 4 (for details, see Rasnow, 1996).
there are no annotations here, but there is a good amount of information. explain what this approach is about.
This allows the fish to swim equally well forwards or backwards and to hold the body in an arc around objects (Bastian, 1986; Toerring and Belbenoit, 1979) while maintaining rigid control over the electroreceptive surfaces. Presumably, by keeping the detector array in a fixed orientation with respect to field generation, this controlled body motion reduces the number of variables that must be taken into account to interpret electrosensory information.
There should be an annotation here.
curarized and respirated
what do these terms mean?
electrophysiological studies at higher levels of the nervous system, for example, by predicting specific emergent features in the midbrain and cerebellum.
This sentence highlights another example where the products of this research can be used in future experiments. In this example, the authors are stating it can be used in future neurological oriented studies of the midbrain and cerebellum; areas of the brain that are primarily oriented with executive functions.
-Kierra Hobdy
electroreception
" the ability to detect weak naturally occurring electrostatic fields in the environment. Electroreception is found in a number of vertebrate species, including the members of... of teleosts (a group of ray-finned fishes) and...Electroreception facilitates the detection of prey or other food sources and objects and is used by some species as a means of social communication." (Hopkins,2017)
-This excerpt provides a brief synopsis of what electroreception is and explains its relevance to the experiment discussed in this article.
teleost fish
An extremely large and diverse group of fish that are mainly identified by the presence of a homocercal tail;in which the upper and lower parts of the tail are equal in size. An example of a teleost fish would be a tuna or hailbut.
-Kierra Hobdy
ampullary electroreceptive predator
A predator that is able to use to receptors in their electric organs to sense the environment around them . The electrorecptors in the organism are located in a dilated part of a canal or duct . -Michelle Oriana Gomez-Guevara
EO propagation
The spread of the signals that are emitted by the electric organs within the organism -Michelle Oriana Gomez-Guevara
ventral
The anatomical position that relates to the underside or the abdominal part of an organism -Michelle Oriana Gomez-Guevara
However, this hypothesis has not been fully tested because the electrosensory input has not yet been well described during exploratory behaviors in freely moving fish.
The author states that it's difficult to examine the exploratory behavior of a free moving fish because the data typically used does not accurately describe the fish's behavior. The EOD geometry and the electric images are complex because they can change based on the fish's movement. The movement changes the source of the electric organs and in laboratory setting the behavior that use electrorepection are hard to maintain preparations for . The difficulty experienced in a control laboratory setting to examine the certain behaviors, makes collecting and analyzing data of a free moving fish ,a challenge .
biphasic
A cycle, object or process that has two phases -Michelle Oriana Gomez-Guevara
Hopkins, 1991
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
rostral
The anatomical term that refers to the area of the body that located near the oral and nasal region . -Michelle Oriana Gomez-Guevara
phylogenetic relationships.
Relationships between the evolutionary history of a group of organisms . "poly" - many "genetic"- origin -Michelle Oriana Gomez-Guevara
ampullary
Resembling an ampulla , An ampulla is a dilated piece of a canal or duct. -Michelle Oriana Gomez-Guevara
noninnervated anterior face
This phrase means that the front-facing side of the organism does not have a supply of nerve. "non" - not , "innervated"- to supply with nerves
Michelle Oriana Gomez-Guevara
Synchronized activation along the length of the electric organ implies effective mechanisms for compensation of neuronal propagation delays along the length of the EO (Bennett, 1971)
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.
(Bastian, 1986),
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
Video and simulation results from a scanning behavior of Apteronotus albifrons.
Data from the videos and the scans (which produced dipolar distortions,) provided results showing how certain kinetic movement patterns exhibited by the fish are use to maneuver in their environment.
-Kierra Hobdy
Bullock and Heiligenberg, 1986
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
Finally, it is important to recognize that our sampling was limited to juvenile plants and lasted only 12 months. Insect herbivore populations can strongly vary in different years, and thus, it is possible that our sampling missed important herbivores that are associated with P. subserratum.
This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.
We asked whether similarities among plants in relative allocation to the four chemical classes were correlated to similarities in the herbivore fauna and soil resources experienced by the plant while controlling for the genetic and geographic distance among populations.
You need to include this as well.
We compared absolute and qualitative differences in leaf defense. First, we compared the dry mass of leaf defense chemicals in a linear model with soil type and study region as independent variables. Second, we tested whether habitat type, sampling site, or the interaction of the two, was a significant determinant of the relative allocation among flavan, flavone, quinic acid derivatives, and oxidized terpenes in each plant using a factorial analysis of variance.
this is important to summarize
-Nick 2pts
Reciprocal transplant experiment
briefly describe this process. What is a reciprocal transplant?
Second, we used a factorial analysis of variance (McArdle and Anderson 2001) to assess whether habitat type, sampling site, or the interaction of the two was a significant determinant of herbivore species composition.
this should be part of your annotation. What were they testing by sampling all these insect herbivores?
ecotypes
The word ecotypes refers to different species of a plant or animal living in a specific habitat.
we believe that the differences in defense strategy we find agree with a growing consensus that plant defense traits are involved in diversification
In this study from 2009, the results of diversification, when subpopulations with independent genetic modifications emerge, were concluded not to be homogenous in their relation to performance. This concept is further analyzed through this experiment in the speciation and the variation of defense strategies.
The existence of this trade-off has been well supported by many different temperate and tropical studies looking at allocation to growth and defense in plants adapted to different light and nutrient availabilities, both within species
The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.
Parapatric
This term is used to describe speciation that happens when populations are separated by an acute difference in habitat opposed to a separation by a physical barrier.
promote very different defense allocation strategies for different plant species depending on the type of defense employed (i.e., their elemental constituents and biosynthetic pathways), as well as the nature of resource limitation across habitats (i.e., light, nutrients, or water) (Bryant et al. 1983, Herms and Mattson 1992).
This statement addresses the variables that must be acknowledged when trying to analyze different plants and their different defense strategies. The "resource limitation across habitats" that the author is referring to is what in the environment can the plant use to defend itself in its habitat from threats such as herbivorous insects.
hemipterans
Hemipterans are an order of insects that share the common characteristic of a sucking mouthpart. Beatles are different because they have chewing mouthparts.
Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.
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
Assemblages of insect herbivores were dissimilar between populations of ecotypes from different habitats, as well as from the same habitat 100 km distant.
In Africa, there is a food crisis leaving millions of people without corn, a very important crop for Africa. The reason for these crops not being edible is that a certain species of worm invaded a field of corn and rapidly spread to neighboring farms, killing millions of corn crops leaving thousands hungry. This proves the point how insects differ from each-other depending on what type of plants are around, since this worm is always flocking to this one crop.
Link:A table showing variation in herbivore communities and relative abundance of leaf secondary metabolites
-Otniel Gonzalez
Differences between sites, habitat types, and their interaction explained 14%, 15%, and 11%, respectively, of the variation in herbivore species composition among the four sampling locations (Appendix F)
This is explaining how the variation of herbivore species is closely related to the variation of plants in the location. The study explains how certain insects prefer to ingest other substances that can be identified, allowing the experimenter to see how the insects lived in accordance to where the plants where, instead of plants appearing around certain species of insects.
-Otniel Gonzalez
A long-standing hypothesis has linked escalation in plant defense that allows escape from insect herbivores to range expansion and speciation (Ehrlich and Raven 1964). Such escalation can include increases in the diversity of defense strategy (novel defense types), increases in the total amount of defense investment, or both (Agrawal et al. 2009). Range expansion, or merely an imperfect match between the distribution of plants and their natural enemies, may confront plants with different herbivore assemblages and/or variation in habitat resources across their range (Thompson 2005, Züst et al. 2012). This variation, in turn, may accelerate the evolution of differing defense strategies across habitats. Alternatively, natural enemies may not be major selective agents driving habitat specialization. In this case, we would predict that there would be few qualitative and quantitative defense differences between habitats, especially when diverging lineages of host plants occur in close proximity and also experience some gene flow across the habitat boundary.
The main point the author is trying to make here is that there is a direct correlation between increase in plant defense and increase in land covered by plants as well as speciation of plants. He also explains that due to the expansion, rapid evolution of defenses begin to take place. The herbivores eating these plants do differ in tactics from region to region, increasing the amount of different defense strategies in the plants. He explains an alternative viewpoint stating that predators do not influence speciation much, therefore defenses are similar amongst most plants.
-Otniel Gonzalez
unlike most members of the family Burseraceae, P. subserratum does not yield measureable amounts of monoterpenes and only trace amounts of sesquiterpenes
Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.
chromatography
a process of separation where components are distributed; in this case the chemical components of the gas
Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.
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
We found that insect herbivores collected from Protium subserratum showed strong patterns of dissimilarity across different habitat types (Fig. 3). Moreover, we found significantly more insects feeding on terra firme plants than on white-sand plants, correlating with the large differences in resource availability between the habitat types. Taken together, these results suggest that there exists substantial variation in diversity and abundance of insect herbivores associated with P. subserratumacross white-sand and terra firme habitats.
The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.
-Angela Mujica
Terra firme populations exhibited significantly greater height and leaf growth and allocated more to chlorophyll production than white-sand populations in both soil types, demonstrating that different growth strategies have a genetic basis
The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.
Figure four illustrates these results.
-Angela Mujica
differences among the dominant herbivores, the species composition of the entire P. subserratum herbivore fauna exhibited high turnover among sites and habitats
The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.
-Angela Mujica
parapatric distribution
Parapatric distribution refers to a distributional pattern where pairs of taxa are partially overlapping or have separate but adjacent distributions, typically along common boundaries.
-Angela Mujica
Protium subserratum Engl.
The Protium subserratum Engl. is the name of a species that has distinct defense mechanisms and is in the genus Protium, which are flowering plants in the family Burseraceae.
-Angela Mujica
Herbivores play an important role in habitat specialization because they can magnify the differences in resource availability across habitats
The sources mention, that in a habitat with a low amount of productivity there is a good amount of strong plants/ plants that are "rich in chemical defenses". In a habitat with lower productivity, the plants are thought to do this in order to increase its life span. Therefore, as the productivity and the amount of herbivores changes the strength and and amount of the resources changes.
For more information check out: Tropical Blackwater Rivers, Animals, and Mast Fruiting by the Dipterocarpaceae
Angela Mujica
To dissect the transcriptional regulatory circuitry of the insulin signaling cascade in the CA in response to starvation, transcript levels for 4 key genes were analyzed in the CA of 4 days old adult females fed sugar or water (Fig. 3).Transcript levels for the insulin receptor (INSr), the Forkhead-box-binding protein (FOXO) and the translation initiation inhibitor eIF4E-binding protein (4EBP) were significantly increased in the CA of starved females. Transcripts for the target of rapamycin (TOR) protein were significantly decreased in the CA of starved females.
why are they interested in "transcript levels"?
You havent done any annotation here and this is one of the important findings of the paper
-Nick 1 pt
To determine the effect of starvation on lipid reserves, the total lipid contents of mosquitoes were quantified in either sugar-fed or starved females.
what does starvation have anything to do with lipid reserves
Lipid assays
For each of these subheadings in the procedure, you can annotate them and just give us a really rough description of what they were trying to do. I know this is technical stuff but even if you can just give us the goal of the step, it would help.
Corpora allata-corpora cardiaca complexes (CA-CC)
we need to know what this is
Our results reveal that starvation decreased JH synthesis via a decrease in insulin signaling in the CA. Starvation-induced up regulation of the insulin receptor increased CA insulin sensitivity and might “prime” the gland to respond rapidly to increases in insulin levels after feeding resumption. During this response to starvation the synthetic potential of the CA remained unaffected, and the gland rapidly and efficiently responded to insulin stimulation by increasing JH synthesis to rates similar to those of CA from non-starved females.
these results have to be annotated. summarize them in your best words
-Nick, 2pts
Here diet restriction, in vivo depletion of INSr and FOXO using RNA interference (RNAi) and insulin treatments were used to modify insulin signaling and study the cross-talk between insulin and JH in response to starvation.
You should tell us more about INSr and FOXO. Also what is RNA interference?
Nick
You still havent done this
Nick -5 pts
PI3K
define this
-Nick 1pt
Changes in JH synthesis in female adult A. aegypti mosquito are very dynamic and nutrition-dependent
this would be under "previos work". you need to look at the citation and explain this further.
Nick 2pts
RNAi and rapamycin administration had inhibitory effects on JH synthesis
you need to go to this source and determine what these are
diapause
The pause that occurs in an insect during development. - Nicole Jones
metamorphosis
Transformation from juvenile to adult where the adult will have similar hormone levels before and after metamorphosis. - Nicole Jones
versatile
able to adapt or be adapted to different functions. In this case, the juvenile hormone is a molecule that adjust to different environments. - Nicole Jones
fluorescent
means to show radiation from somewhere else by allowing the wavelength to become shorter with a x-rays or ultraviolet ways. - Nicole Jones
derivatization
this a technique used in chemistry. It is important because it allows for a chemical compound to become a similar product of a desired chemical structure. - NAJ
1.Boggs CL (2009) Understanding insect life histories and senescence through a resource allocation lens. Functional Ecology 23: 27–37.
Mosquitoes carrying Zika can contaminate and spread the disease in the human population in a second. Zika is a yellow fever. This 2017 news relates to the article because if mosquito populations are controlled by hormone regulation, then genetically modifying a suppressor can develop a method to prevent the disease from spreading. - NAJ
Our reanalysis of Rokas et al.'s data indicates that their estimate of the number of genes required to infer a phylogeny confidently was inflated by signal heterogeneity caused by their inclusion of nonstationary genes. In addition, the conclusion that there are no useful predictors of phylogenetic performance does not hold.
needs annotation- 3pts
A final question concerns methods of sampling nucleotide sequences for phylogenetic analysis. Rokas et al. (2003)suggested that randomly sampled orthologous nucleotides were superior to contiguous gene sequences. This superiority of randomly sampled nucleotides was thought to be due to avoidance of within-gene nonindependence of nucleotides linked in a functional gene. An examination of figure 5 from Rokas et al. suggests that randomly sampled nucleotides had considerably higher bootstrap values for similar levels of sampling, and remarkably low variance in bootstrap values. In fact, the confidence intervals are not visible in this figure, overlapping almost completely with the plotted average data points. This result is, however, largely an artifact of differing bootstrap resampling techniques applied to the randomly sampled and contiguous gene sequences. A typical nonparametric bootstrap was applied to the contiguous gene sequences: a sample (an individual gene) was taken and pseudosamples of the same size were generated from this sample by sampling with replacement. This gives the variance about the estimate of the phylogeny for that sample. Randomly sampled orthologous nucleotides were sampled with a different strategy, using the variable-length-bootstrap option in PAUP*. In this case, a sample of a given size was taken from the complete data set and the phylogeny was estimated. Then a new sample of a given size was taken, and the phylogeny estimated. So, for even the smallest sample size of 1000 nucleotides, 1000 replicates would have sampled the vast majority of nucleotides from the complete data set. This sampling scheme did not, therefore, measure the variance on the estimate of the phylogeny from a particular random sample, as in the contiguous gene sequences, but is instead akin to the variance on the phylogeny for repeated sampling of a given size from the complete data set. This difference in treatment explains the extremely small confidence intervals for the randomly sampled nucleotides in the Rokas et al. analysis. When the randomly sampled orthologous nucleotides are bootstrapped in the same manner as the contiguous gene sequences, much greater variances are apparent (Fig. 6, open circles), although these variances are not directly comparable to the contiguous gene bootstrap variances because they do not include a variance component related to variation in gene size. We also find that orthologous nucleotides randomly sampled from the stationary partition are superior to those sampled from the nonstationary partition (Fig. 6, triangles and squares). It is certainly a reasonable expectation that nucleotides sampled from within a gene would have greater nonindependence than randomly sampled nucleotides, but the phylogenetic performance difference, if present, appears to be much more subtle than would be inferred from examination of figure 5 of Rokas et al.
This paragraph is saying a lot but hasnt been annotated. -4 pts
nonsynonymous substitutions
define this
nick pts -2
Regression analyses describing the relationships between protein divergence estimates and divergence time estimates were implemented for each sex-determining protein as well as for SSX using the program
what is the relationship between protein divergence and divergence time?
nick -2 pts
Under this model, trans-regulatory elements more recently recruited into sex determining pathways are expected to cause divergence toward the top because of recent regulatory change (e.g., the Sxlgene in Drosophila) while ancient elements at the bottom would remain conserved (e.g., the dsxgene in Drosophila) ensuring the correct functionality of the cascade (Verhulst et al. 2010) (Fig. 1b). However, an alternative interpretation of the evolution of the cascade (Artieri et al. 2009) suggests that genes involved in early aspects of development (which, as in the case of Sxl, are likely to regulate a large number of downstream effectors through hierarchical regulatory cascades) would be more constrained due to the large deleterious pleiotropic effects of mutations, resulting in increased levels of purifying selection at top positions of the cascade
this needs explanation- Nick -5 pts
Because the vast majority of BRUV deployments in the non-reserve sites resulted in zero reef sharks being observed it was not possible to evaluate the impact of environmental variables and reserve versus non-reserve effects in the same model
In the study, the majority of the BRUV deployed sharks developed no observable reef sharks . Because of this, environmental factors were not able to be considered.
Large-Scale Absence of Sharks on Reefs in the Greater-Caribbean: A Footprint of Human Pressures
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.
For example, sharks may move between proximate reefs; they may migrate at higher latitude reefs in response to seasonal temperature changes and they may be more likely to emigrate from a reef as competitor density increases or prey availability decreases. Caribbean reef sharks could be acoustically monitored at reefs of different levels of isolation, latitude and prey abundance to further test these hypotheses.
This passage indicated that while the results obtained were conclusive in terms of the hypothesis promoted by the author, it was inconclusive in terms of the greater picture because there were many sources of error or outcomes that could not have been taken into account due to the settings of the reserves. The author mentioned that the results could have been bettered if accounted for prey-predator relationships in the reserves. This is because it could have provided more data as to why sharks were only being pinged the certain amount of times that they were as opposed to more or less times.<br> -Sindy
Heupel MR, Simpfendorfer CA, Fitzpatrick R (2010) Largescale movement and reef fidelity of grey reef sharks. PLoS ONE 5: e9650.
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
log distance
Log distance predicts the path loss a signal encounters inside a building or densely populated areas over distance. -Sindy
spurious detections
Detection's that appeared valid but in fact were not. -Sindy
We purposefully put the larger tags in larger sharks because of concerns that small sharks might be adversely affected by the V16 transmitters. As a result, the 14 V9 tagged sharks were smaller than the 20 V16 tagged sharks
Tag size was an important consideration when it came to the assigning of a tag size and type to a specific shark. Smaller sharks were placed with smaller tags because the size and density of the tag could have affected the health of the overall infantile or smaller shark that it was paced in. This measure ensured that results and data for the experiment were viable and the the loves of the sharks were also accounted for and their safety ensured in that area of the study. -Sindy
V16 transmitters
The previously mentioned transmitters all starting with the letter V are versions of acoustic telemetry monitors. -Sindy
A recent survey of recreational SCUBA divers in the Caribbean found that shark sightings are quite rare, except for some places that have shark conservation regulations or large marine reserves in place
Shark conservation regulations entail the prohibition of shark fin trade actions such as the removal cutting of shark fins or the pursuit of hunting sharks for any other purpose. -Sindy
More information on shark movements and relative abundance in different management zones is needed to understand the extent to which marine reserves benefit Caribbean reef sharks and reef sharks in general.
This research is centered around this idea of uncovering information on the abundance of sharks in zones that are monitored but reserved for marine animals It tests the efficiency of no-take marine reserves and its correlation to the site fidelity of reef sharks. -Sindy
endemic
An endemic species is a species that tends to stick in one area or habitat for its whole life. Examples of an endemic species include the vasayan spotted deer, and the lemurs in madagascar.
site-fidelity is high enough to drive the observations of increased shark abundance in these areas, even though large juveniles and adults are vulnerable to fishing as they move between management zones
Site fidelity is the idea that an organism is primed for a certain place or spatial area and that this place is a reoccurring habitat to which that organism returns to or permanently lives in. This section of the passage states that increased levels of site fidelity correlate to increased levels of shark abundance in these areas despite the fact that risks pursue the movement of the sharks between the site to which fidelity is displayed. -Sindy
spatial abundance pattern
Spatial and temporal abundance patterns relate to the study. Temporal abundance pattern has to do with quantity over a period of time and spatial abundance patterns have to do with quantity over a particular area of space. -Sindy
focal species
Focal species are species that are extremely sensitive to the changes in an environment. -Sindy
temporal monitoring studies
Temporal monitoring is monitoring that is conducted over time. -Sindy
Sharks are currently experiencing intense fishing pressure worldwide, largely due to the Asian shark fin trade
The Asian shark fin trade has been detrimental to the shark population and according to the The National, a Marine Conservation group called Sea Sheppard Global is campaigning for shark conservation and cleaner oceans in the Middle East. Finning is one of if not the greatest threat to sharks. It entails the process of cutting of the sharks fin and leaving its body in the sea to bleed to death or be eaten by other fish. The point of finning is to make shark fin soup which is an Asian delicacy or to sell for price ranged between $10,000-$20,00. In 2016, congress passed the Shark Fin Trade Elimination act which banned the shark fin trade. Despite this, Shark fins are still being trafficked to the country. https://www.thenational.ae/uae/environment/marine-conservation-group-launches-in-middle-east-1.673006 -Sindy
However, can marine reserves also benefit large, roving reef predators that are potentially mobile throughout their life?
This question sheds light on a topic regarding the suitability of marine reserves not only as a permanent safety harbor for recovery and expansion of the species but also the temporary inhibition of the space by species that are mobile, whether they would use the space to breed for protection or for a stable source of food and shelter. -Sindy
Marine reserves
A marine reserve is an area of the ocean that is protected and allows for the recovery of marine life and the expansion of it as well. -Sindy
site-fidelity
Side-fidelity, also known as philanthropy, is the likelihood of a particular organism to stay in a set habitat, or to return to it. There are many reasons to this, such as breeding and food abundance. -Sindy
invasive
can spread something harmful (NAJ)
blastula
early stage of development (NAJ)
The answers to fundamental questions about the origins of animal life and the evolution of their diverse phenotypes may be held in the genomes of distinct invertebrate phyla.
The conclusion explains why they investigated what standards an invertebrate must reach to be tested for a successful genome sequencing. The researchers also add that geneticists could choose another option than searching an organism that meets their criteria. This option is sequencing organisms and modeling them for another organism. This would allow the geneticist to understand the other organism by having an idea of how the genome functions.
The researchers also state a challenge faced by the science community is understanding the data they collect from the genome sequence, apart from also gathering the sequences. They state the research they do will help advance knowledge about invertebrate genomes by providing the necessary tools to investigate the sequences. (NAJ)
GIGA Community Resources
A group that investigates invertebrate genomics. (NJ)
Invertebrates have long served as model organisms, providing insights into fundamental mechanisms of development, neurobiology, genetics, species diversification, and genome evolution. Two invertebrates—the fruit fly Drosophila melanogaster (Adams et al. 2000) and the nematode Caenorhabditis elegans (C. elegans Sequencing Consortium 1998)—were the first animal species targeted for complete genome sequencing, setting the stage for other invertebrate-based studies such as i5K for insects (Robinson et al. 2011) and the 959 Nematode Genome program (Kumar et al. 2012), which target up to several thousand whole-genome sequencing projects.
The researchers organized requirements of what an organism should have to use in a genome sequence experiment. The organisms that have already been investigated are a fruit fly and a nematode. The fruit fly and nematode were used to sequence genomes. The reason for the report was to learn more about invertebrate genomes since researchers have concluded there are a lot of invertebrate genomes among different organisms. The aim was to collect enough data to create appropriate tools to use in the future for these different genomes. The strategy was to create a guideline on what an organism should have. The purpose of this was to help advance the understanding of the diverse genomes of invertebrates. (NJ)
terrestrial
anything having to involve only earth's resources. (NJ)
nematodes
relating to a round-worm or thread-like worm. (NJ)
inaugural
Initiation of a group. (NJ)
biomimetic
A copy of a natural system. (NJ)
vectors
An organism that spreads diseases. (NJ)
synthetic
A design of a biological system. (NJ)
parasites
An organism that benefits from living from a host which is another organism. (NJ)
paraphyletic
Having a common ancestor. (NJ)
glycoproteins
proteins that have carbohydrate groups. (NJ)
asexually
Reproduction without a male and female. (NJ)
heterotrophic
An organism that can make food. (NJ)
sequencing
An order. In this case, RNA and DNA are aligned to facilitate gene expression. (NJ)
conservation
Preserved. (NJ)
transcriptomes
All the genes expressed by mRNA. (NJ)
phyletic
Has evolved in some way. (NJ)
genomes
a complete set of genes that carry information in an organism. (NJ)
invertebrates
an animal that does not have a backbone. (NJ)
metazoan
means a living organism that is multicellular. (NJ)
Brill, R. W. (1996). Selective advantages conferred by the high performance physiology of tunas, billfishes, and dolphin Fish. Comp. Biochem. Physiol. A Comp. Physiol. 13A, 3-15.doi:10.1016/0300-9629(95)02064-0
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
Our data suggest that sailfish are not able to achieve the extremely high speeds claimed by earlier studies (Barsukov, 1960; Lane, 1941). These speed assessments (approximately 35 m s−1) are based on fishermen’s records of hooked specimens and are most likely overestimations.
Here the author ties the goal of this study with the data collected. The goal of this study was to test whether earlier studies were correct in their estimations of maximum swimming speeds in sailfish. The author describes that the data collected disproves earlier studies and provides explanation as to why the data of the prior studies may have been skewed. -Kyrsten
Based on the estimated absolute speeds, sailfish appear to be the fastest of the four species investigated here, however, they were also 50-80 cm longer than the other three species and maximum speed is known to increase with fish length (Wardle, 1975). Using a length-speed relationship based on burst swimming performance of various species (Videler, 1993), we found that the size-corrected speed performance is highest in little tunny and barracuda, followed by dorado and sailfish (Fig. 2D).
The goal of this study was to determine whether earlier studies were correct in their determination of maximum swimming speeds in sailfish as well as comparing sailfish speeds to other large marine predators. Here the author explains that compared to the other predators, the speed performance in sailfish based on size was the lowest. This is supported with Figure 2D. -Kyrsten
The calculated maximum attainable swimming speeds for the four species expressed in m s−1 (A) and in Lf s−1
From graph A it can be seen that the sailfish had the highest maximum swimming speed. Next was the Barracuda, then the Little tunny. The Dorado had the lowest max swimming speed.
Mikaela
Experimental measurements were conducted on dead animals within 5 min from being killed.
You should mention why the authors are trying to measure this within 5 minutes of being killed
Nick
The goal of this study was to estimate the maximum swimming speeds potentially attainable (i.e. based on measurements of muscle contraction times) by sailfish and other large marine predators
Somewhere in your annotation you should talk about the relationship between maximum swimming speed attainable and muscle contraction times. Look at the authors' sources
Nick
for swimming animals longer than ∼1 m, the speed at which cavitation occurs,
What is cavitation here? And what are the destructive consequences? You should look at the source that the author cites here.
Nick
Animal maximum speeds play a significant ecological role, particularly in the context of predator-prey interactions
Definitely look at the authors sources that they cited here and talk a bit about what animal maximum speed does to their predator-prey interactions. This would be considered "PreviousWork"
Nick
Although it is likely that early work overestimated swimming speeds, speeds higher than those predicted based on the twitch contraction methods might theoretically be possible if fish were able to change their mode of swimming to accommodate for the otherwise lack of increase in tail beat frequency
The maximum frequency at which a fish can oscillate its tail is limited by the twitch contraction time of the white lateral muscle. The maximum swimming speed is then predictable if the distance moved forwards on completion of each oscillation (the stride) is known. -Mikaela
Parafilm
primarily used in laboratories. It is commonly used for sealing or protecting vessels (such as flasks or cuvettes). It is a ductile, malleable, waterproof, odorless, translucent and cohesive thermoplastic.
-Mikaela
maneuverability
the quality of being able to sail close to the wind with little drift to the leeward.
-Mikaela
deviation
the amount by which a single measurement differs from a fixed value such as the mean.
-Mikaela
anaerobic
Relating to, involving, or requiring an absence of free oxygen. -Mikaela
pelagic
Of or relating to the open sea. -Mikaela
accelerometry
use of a accelerometer to quantify movement -Kyrsten
propulsive
creating force to result in movement -Kyrsten
post hoc
occurs after the event -Kyrsten
elongated
stretched out or extended -Kyrsten
thermocouple
sensor used to record temperature -Kyrsten
Marine reserves can clearly enhance exploited coral reef species that have relatively sedentary adult life-stages, in which some individuals live almost exclusively within reserve boundaries
A study in 2 June 2009 conducted by Philip P. Molloy explored the relations with the age of the marine reserves and of the recovery of different species of fish. The studies showed that older marine reserves (15 years and older) were more effective than younger ones. They harbored more fish.
tonic immobility
Tonic immobility is a state of paralysis that occurs in animals. They become immobile and appear dead. In sharks, tonic immobility may be achievable by flipping the sharks onto their back.
Fig. 7 On this figure of electrosensory pathways in the gymnotiform fish (modified from Carr and Maler, 1986), we have labeled regions where the proposed computations for high-frequency electrolocation might be implemented.
The author using results from video , electric images and BEM simulations was able to depict the electrosensory pathways in the fish and where the fish has organs with receptors that are able to sense electric fields. By knowing where these electroreceptors are , the author is able to determine where the organism is able to conduct electrolocation. -Michelle Oriana Gomez-Guevara
impedance
The resistance of an electric circuit towards a current that is different from which it usually interacts with.
-Kierra Hobdy
Finally, knowing object distance is a prerequisite (or corequisite) in the model for deconfounding size, impedance and shape, so these features would first appear in the torus and higher areas. Although this proposal is not yet based on quantitative simulation or modeling, we believe it may be a useful working hypothesis for interpreting and further exploring parts of the electrosensory nervous system.
In this sentence, the authors are hypothesizing that the EOD pattern incorporated into electrosensory nervous system of the electric fish uses the information of size, shape, and distance of the objects in an algorithm used to process and relay information to the electric fish brain.
-Kierra Hobdy
Ultimately, weakly electric fish must extract and interpret any useful signals contained in small-field perturbations superimposed upon the intrinsic EOD pattern. Therefore, a considerable volume of the electric fish brain is devoted to electrosensory processing. For the computational algorithms proposed above to be involved in electrolocation, they must have a plausible neural implementation in the fish’s nervous system. We propose one such projection onto the neural networks in the electric fish brain.
Electric fish are able to receive signals and information from their environment though the emission of electroreceptors thorough their skin. After the contact of the electroreceptors and the external stimuli, information is relayed in a pattern to the electro-receptory organs of the fish. Since this is an essential part of their way of life , the authors know a large amount of neurons and brain matter are involved in this process. Therefore, they hypothesized, that in order to insure this sensory information is relayed efficiently and quickly to the brain of the electric fish, there must be an algorithm used by the neural networks in the fish in order for this process to occur.
-Kierra Hobdy
small-field perturbations
Perturbations in this instance are disturbances in the surroundings of the fish, such as a duck swimming or a fly landing in the water. Small-field refers to the small range in which the fish can detect movements or perturbations in its environment.
-Kierra Hobdy
transderma
'Derma" refers to skin and in this case, "Trans" means through; so transdermal means the electroreceptors are being emitted through the skin of the fish.
-Kierra Hobdy
These scanning and tail-probing behaviors have been described previously
The scanning and tail probing behavior of fish is the process in which they use certain tail movement around an object in order to discover the depth and size of objects in their environment. Think about what happens when you put a goldfish into bowl after it has been in an plastic bag. It will immediately start swimming around and swishing its tail around. That is a process of scanning and tail probing behavior. - Kierra Hobdy
quantifying
To quantify means to organize into a numerical format . -Kierra Hobdy
ellipsoids
A 3D geometric figure whose planes or sections consist of ellipses or circles. -Kierra Hobdy
impedance
The resistance of an electric circuit to an opposing or alternating current. -Kierra Hobdy
propagating caudally
This means to spread toward the tail or posterior section of the body-Kierra Hobdy
oscillating dipole
Dipoles are equal magnetic positive and negative charges separated by a distance. In this case oscillate means to cause the electric current to move in a way that influences the dipoles to change and fluctuate. Picture strings vertically tied to a rope in the middle, movement to the rope cause the strings to ripple in the direction they are facing outward. -Kierra Hobdy
neural substrates
Functional units of the Central Nervous System that are organized systematically based on function and vary in their anatomical location in the body; they all work together to carry out complex body functions, in this case the process of electrolocation. -Kierra Hobdy
But little is known about the mechanisms underlying the evolution of habitat specialization and the extent to which herbivores contribute to phenotypic divergence during the speciation process
The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.
-Luisa Bermeo
Protium (Burseraceae)
Observe this Protium, a species of flowering plants [(https://www.kew.org/science/tropamerica/imagedatabase/large1/cat_single1-3438.htm)
-Luisa Bermeo
the species composition and relative abundance of herbivore communities may turn over among habitats because herbivores are affected by habitat quality, structure, and interactions with predators
The idea in place here is the observation of evolution in herbivorous in correlation to the environment and all its factors.
The study provides proof of evolution in herbivorous in respect to the environment by analyzing adaptive radiation. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous.
To further understand adaptive radiation watch [(https://www.brightstorm.com/science/biology/evolution/adaptive-raditaion/)
-Luisa Bermeo
tropical tree genus, Protium (Burseraceae)
link to pictures of the plant
Nick
In order to study the evolutionary processes involved in habitat specialization and the role of insect herbivores, an ideal study system would include recently derived sister species, or diverging lineages undergoing incipient speciation in different habitats.
You need to mention that this is the goal of the paper.
Nick
herbivore to circumvent or detoxify defenses
give an example here. Look at the monarch butterfly caterpillar on its milkweed host for instance. how do they protect themselves from being killed by the plants toxins?
Nick
physical and chemical defenses
define some of these. What are some physical and chemical defenses of plants?
Nick
the optimal defense allocation may be affected by differential costs of tissue replacement across habitats
Herbivorous insects are constantly eating plants, creating competition between the plants and insects. What is stated here is that optimal defense may be impacted by the plants environment, giving it access to certain nutrients and materials needed to produce the desired defense mechanism, such as poisonous leaves or indigestible tissues.
-Otniel Gonzalez
reciprocal
Having to do something to both side, the bearing or binding of 2 parties equally.
-Otniel Gonzalez
gradients
Describes different sides in comparison to each-other, a gradient can be in reference to water pressure as well as many other things.
-Otniel Gonzalez
morphological
Relating to the form or structure of things, having to do with somethings physical appearance/structure.
-Otniel Gonzalez
pubescence
Pubescence in this context means small hairs or short down on the leaves and stems of various plants.
-Otniel Gonzalez
qualitative
Referring to something's qualities, not numerical but categorical. Can be described with words, not numbers.
-Otniel Gonzalez
phenotypic plasticity
A genotypes ability to change as an adaptation to the environment. This refers to the plant's distribution of resources.
regression
Regression analysis is a statistical model made up up of a series of processes used to understand how the dependent variable changes when any of the independent variables are modified.
habitat-mediated speciation
Habitat-mediated speciation is the emergence of different species throughout evolution, brought about by the natural environment and its effects.
incipient speciation
incipient meaning the beginning of a process and speciation is the diverging of similar species into two or more differing species due to evolution
-Luisa Bermeo
heterogeneity
describes a state of being different in character in this case in reference to the environment
-Luisa Bermeo
bovine insulin
define this
Nick
diapause
define this, too
Nick
with the clear implication that the majority of current molecular phylogenies must be considered unreliable.
try to describe why Rokas et al. feel this way.
Nick
dipterans
what are dipterans?
Nick
sex-specific splicing of the primary transcript of the gene immediately downstream
This needs annotating. What do they mean by "splicing"? and what does it mean a gene that is immediately downstream?
NICK
In insects, the sex determination pathway constitutes a regulatory cascade that evolved in reverse order, from the final step in the hierarchy that creates the required product to the first step in the pathway that allows synthesis of the initial precursor
This needs to be explained a little. what is a regulatory cascade? Take a look at the sources to understand this reverse order process.
-Nick