A tree diagram that demonstrates relationships between different species in their evolutionary track.

the branch of biology that studies structure, function, evolution, and mapping of 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.

In this study, scientists were able to conclude that under certain circumstances (when processes are stationary over lineages and time) short genetic sequences can be used to construct a large phylogenetic tree with very high accuracy, therefore reducing the cost and time spent in creating a tree.

Random sampling extracted from stationary partitions yielded above nonstationary samples, in addition to also resulting superiorly in comparison to the complete data set. Graph six clearly illustrates such observations through its "triangles" and "squares" symbolizing stationary and nonstationary, respectively.

Using the data acquired from Figure 5, the conclusion was made that stationary genes are again much more efficient at producing phylogenetic trees in comparison to nonstationary genes.

In figure 4a, the graph depicts how the third codon position stationary partition outperforms the non stationary partition as the number of genes increase and the bootstrap value rises. In figure 4b, the performance of the all-codon stationary partition was notably better. The amount of genes required to obtain higher than 95 percent of bootstrap value was 8 stationary genes to 21 nonstationary genes.

Partitioned Bremer support is a method for assessing the similarity in joined data collections, although, there are some point of views that require some insight. When more than one similar parsimonious tree is found in the middle of varied ones, averaging Partitioned Bremen support for each set of data over these trees can avoid trouble, and it should ideally be analyzed for each unnatural tree. When numerous most parsimonious trees are examined due to joint data collection, Partitioned Bremen support is generally computed on the common tree. Be that as it may, extra information can be acquired on the off chance that Partitioned Bremen support is computed on each of the most parsimonious trees or less quality trees.

Using the results from Figure 1, the conclusion was made that nonstationary genes provided a less accurate phylogenetic tree compared to the stationary genes because it incorrectly provided a 100% bootstrap value to S. castelli (SCAS).

"Bootstrapping" is a technology based practice for determining the accuracy or precision of many statistical results. For phylogenetic  trees, the bootstrap helps by exampling "confidence" in related organisms (common ancestor) in proportion with organisms from the same "family".

During this procedure, the authors essentially performed an analysis to determine how divergent, or dissimilar, the genes had come to be.

Scientist were able to conclude how stationary genes evolve through the same velocity at the third codon position. In comparison, non-stationary genes were seen to be involved in severely higher conditions. Such differences could therefore lead to drastic results, including systematic error.

"Stinginess". The best hypothesis in making phylogenetic trees is the one that calls for the fewest evolutionary changes throughout time.

Genetic detail from the same chromosome.

Unit of measure for a nucleic-acid chain. Equals 1,000 bases.

Mainly examined for prediction of gene function. Related through vertical descent from ancestors.

A DNA or RNA molecule that is brought up by three nucleotides forming together.

Taxonomic group of any level: species, class, etc.

A compound that forms the basic structural unit of a nucleic acid.

Similar, sharing something in common.

Data at present used to predict that of entire population. Usually completed by the extraction of data, probably randomly, and re-tested. Essentially, bootstrap resembles the confidence level in the values resulted. The results don't necessarily have to be correct, its a measure of certainty.

A constant that defines the function of a certain study.

Rokas et. al came to the conclusion that one needs a minimum of 20 genes in order to compose an accurate phylogenetic tree, and that those phylogenies created from examination of a few genes are unreliable due to the low amount of sequencing data used.

A series of items or information linked together.

Branch of biology that deals with the evolutionary uniqueness of organisms.

Way in which big ideas or parts are connected or arranged to make sense.

Protein or DNA that have the same or similar sequencing due to their ancestry.

A model-based measurement utilized in data sets of phylogenetic comparative analysis made up of qualitative traits observed of species related to the same phylogenetic tree.

Hereditary information that offsprings receive from their parents which makes them unique.

The evolutionary track an organism has taken that sets it apart from the rest.

Unable to be stopped; unpreventable.

The new development of something of high value and/or importance.

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.

Utilizing DEET perfumed traps, the behavior of flies was observed. Flies with the Orco gene responded differently to food-baited traps than flies with the gene knocked out. Low concentrations of DEET cannot repel flies in the absence of food. Electrophysiological studies showed that DEET can influence signaling molecules (or ligands) and their respective olfactory receptors.

Orco mutants are unaffected by the presence of DEET, leading to the conclusion that olfactory receptors are not the sole reason for repellency against DEET.

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.

When speaking with the author of this paper, he explained the importance of understanding the molecular pathways of DEET.

By having a greater understanding of this repellant, it will be possible to create a new insect repellent with better functionality and protection against disease carrying mosquitoes.

DEET, like other pesticides and insecticides, comes with its own cost to the human health and environement.

Read more about it here: http://www.environmentalhealth.ca/spring03hazards.html

The results of this experiment testing the effect of DEET on bitter tasting gustatory receptors conclude that insects are repelled by the taste of DEET which is perceived to be bitter.

Three taste receptor neurons were characterized in female Aedes aegypti mosquitoes. The neuron with the smallest amplitude spike responded to the feeding deterrent, quinine, and other insect repellents. Two other neurons with differing spikes responded to salt and sucrose. This was the first report of a taste receptor neuron specific for insect repellents in mosquitoes.

Female Aedes aegypti mosquitoes fed through a membrane on citrated blood containing DEET. When 0.5% concentration of DEET was present in the blood, the mosquitoes barely touched the membrane and did not insert the proboscis into the blood. When the concentration was lowered to 0.065%, mosquitoes touched the membrane for a longer time period, and/or inserted the proboscis. It was concluded that vapor action was the main cause of repellency, but contact chemoreceptors on the lobes of the proboscis may have been involved during the 0.065% concentration experiment.

The author of this paper is currently doing research on the olfactory receptors that mediate the mosquito’s human and plant host-seeking behavior and the genes that regulate their appetitive drives. This includes research on Ir40a.

This article has been retracted as of 2016 by the request of all authors except Pinky Kain. The authors identified background effects that were originally missed and, as a result, do not have confidence in the data supporting that Ir40a is a DEET receptor. The authors remain confident of the analyses used to identify new repellents which have been replicated in the laboratory.

Remove or dissipate such as by melting, vaporization, erosion, etc.

The CquiIR40a receptor in the Culex quinquefasciatus mosquito was cloned and then expressed in the Xenopus ovary cell along with another co-receptor. The Culex quinquefasciatus mosquito uses an odorant receptor, CquiOR136, to detect insect repellents, such as DEET, picaridin, IR3535, and PMD. The dose-dependent responses elicited by these repellents were analyzed.

When applied to human skin, DEET altered the chemical product by a fixative effect, which may have contributed to repellency. The electrophysiological responses of olfactory receptor neurons (ORNs) were observed in Culex quinquefasciatus mosquitoes. The same ORN responded with higher sensitivity to terpenoid compounds, which are found in essential oils. The studies support the smell and avoid hypothesis.

As the stimulus intensity increases, the firing rate of neurons increases. The firing rate is the rate of action potentials that carry an electrical impulse down a nerve. DEET increased the firing rate of olfactory receptor neurons in A2 sensilla, but inhibited the firing rate in A3 and A4 sensilla. It was concluded that DEET plays multiple roles in olfaction control because it affected OR-expressing and IR-expressing neurons in differing ways. This supports the confusant hypothesis.

Mosquitoes use redundant mechanisms to sense their hosts. This mechanism requires that mosquitoes receive multiple cues for a host to seem attractive. The disruption of one pathway is unlikely to eliminate mosquito host-seeking, however. Stimulating multiple sensory pathways may increase the chance of a mosquito successfully targeting a host.

Zinc-finger nucleases (ZFNs) were used to generate mutations in the Orco gene of Aedes aegypti. ZFNs are a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA. These breaks stimulate the cell’s DNA repair processes, which in turn generates precisely targeted genomic edits.

Interestingly, scientists have found another repellant that could be much more effective than DEET. This repellant, known as VUAA1 triggers Orco directly rather than specific OR regions.

Read more about it here: https://www.popsci.com/science/article/2011-05/new-insect-repellent-thousands-times-more-effective-deet

DEET was concluded to be a compound that reduced the attraction of mosquitoes to lactic acid (a behavioral inhibitor) rather than a compound that caused mosquitoes to display complete avoidance. It is important to note that both DEET and lactic acid were attractive to mosquitoes in the studies.

Studies that observed heart rhythms were used to observe the sensitivity of olfactory sensory neurons (ORs). DEET reduces the sensitivity of ORs by enhancing the expression of lactic acid-inhibited neurons and decreasing the expression of lactic acid-excited neurons. This supports the inhibition hypothesis of host odor detection.

The tendency for the substance to evaporate.

An un-selective approach to the cell membrane function. DEET has a selective effect on the cell membrane function.

Lasting only for a short time.

With the evolutionary mechanism of natural selection, some mosquitoes have become resistant to insecticides such as DEET. This resistance could be inherited by a dominant gene. The development of such a resistance could become a problem in the future since as DEET is one of the strongest insect repellents to date.

Read more about it here: http://www.nature.com/news/2010/100503/full/news.2010.216.html

The Aedes aegypti mosquitoes aided in the discovery of DEET, which is the most common active ingredient in insect repellents. The behavior of the mosquitoes was observed in response to several compounds, but N,N - diethylbenzamide was found to be the most effective. Because this compound is irritating to the skin, the DEET found in repellents today is comprised of derivatives of N,N - diethylbenzamide.

Olfactory receptors are neurons that are responsible for the detection of odorants which allow the sense of smell. Olfactory receptors are one of three types of receptors used by mosquitos, the others include ionotropic receptors and gustatory receptors.

The response to an antennal stimulation in which an insect stick out their proboscis, or tongue.

A substance in certain that adversely affects insects or other animals that eat them.

Properties dependent on the chemical composition or structure of the material.

A measurable/numerical method to gather data.

RNA interference is a gene silencing mechanism that is triggered by the injection by introducing double stranded RNA into the cells.

Cues related to eating and the sense of taste.

An organic compound with a distinct earthy flavor and aroma produced by a type of Actinobacteria.

A type of genetic engineering in which DNA is inserted, deleted or replaced in the genome.

Macromolecular pores in the cell membrane that form an aqueous pathway. Allows rapid flow of cations based on their electrochemical driving force.

A molecule that binds to a central metal atom to form a complex.

Derived from a different organism.

Tiny openings in the membrane that allow specific ions to pass through.

An arthropod sensory organ that consists of a modified cell or small group of cells of the cuticle, typically hair- or rod-shaped cuticle.

A chemical substance emitted by an organism and detected by another of a different species that gains advantage from this.

A field of study that uses genetic methods to investigate nature and origins of behavior.

Early in the discovery/ knowledge of the DEET modulation of multiple olfactory receptors

The process of how a single stranded DNA form hydrogen bonds with other complementary DNA strands to make double stranded DNA.Often used in the PCR steps of creating or mass producing certain DNA sequences. (EM)

Heterospecific is used to classify organisms. "Hetero" means differ, and "specific" pertains to a particular subject/concept. Heterospecific means organisms that aren't the same species. ~J.D.A.

Conspecific is also like heterospecific as it pertains to classifying species. In the sentence it seems to be an opposing word to heterospecific. If heterospecific means organisms of differ species, then conspecfics must mean the opposite--must mean organisms of same species. ~J.D.A.

Parsimony analysis deals with simplicity. In regards to science, there will be various explanations to certain phenomenon. According to parsimony analysis, the simplest explanation is the best one. ~J.D.A.

Tenable is defined as something that can be "holdable". It could mean that something must have enough support for it to be upheld. In other words, if someone has an argument against an idea, the explanation should be enough to defend the concept. ~J.D.A.

Concordant means to agree. A variation of this word would be "concor", which has the same meaning. For this paper, the word may be used to describe how data collected seem to show the same variation or consistency. ~J.D.A.

The word shoal describes a shallow body of water. This is synonymous to sandbars or elevated sand in beaches. Therefore, something that "shoals" means that it doesn't have much depth. ~J.D.A.

Strombinid refers to the taxa Strombidae. It's a family of medium-sized conch sea snails. Gastropods is also another term used to describe the Mollusca phylum. ~J.D.A.

"Intra" means within. Divergence is when something separates. Thus, this word could mean how species diverge from each other from within the same oceanic community. ~J.D.A.

The classic allopatric model is also known as geographic speciation or the dumbbell model. Classic allopatric model is a kind of speciation that occurs when biological populations of the same species become isolated from each other. This isolation is what will prevent genetic exchange between the separated populations. ~S.Z.

mtDNA CO1 is a gene found within the mitochondria, it is used to measure the genetic difference between organisms. A higher mean indicates a larger difference between two organisms, which is indicative of being a different species. (JP)

In general, this graph illustrates that as genetic distance between species increases (this is measured by Nei's D) then mtDNA divergence increases as well. Overall, compatibility between two different organisms will be less if they have high mtDNA divergence and a high Nei's D value. (JP)

Main subjects studied. Planktonic larva is significant in this study because larva shrimp would migrate to different regions of the Isthmus of Panama which may be a significant contributor to speciation events ~J.D.A. (+ JP)

Foraminifera are single-celled planktonic animals. They have an external shell and a granular ectoplasm for catching their food. When they die their shell becomes part of seafloor matter. ~J.D.A.

mtDNA traced pairs back to million years ago. ~J.D.A.

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.

Allozyme is an enzyme. They are coded by differ alleles found at the same locus of the gene. They were studied in this experiment via taxonomic branching to map out closely related pairs. ~J.D.A.

Their collection may have been affected. It was mentioned by the author that she and her colleagues collected from muddy environments since the sites were sewage dump locations. Most of the shrimps were covered in mud, therefore hard to distinguish. Also, the author mentioned transit ships traveling between the Atlantic and Pacific sides of Isthmus. These ships would migrate the shrimps away from their homes; may affect how the team paired shrimps based on their mtDNA. ~J.D.A.

Species so closely related showed two differ clutches. Isolation could've been geographical, though nothing that could completely cut them off from each other since they are similar. If anything, this could infer that they could've been selective in mating, or aggressive in behavior to even mate, thus preventing creation of offspring between them. ~J.D.A

A gene coding for the cytochrome oxidase enzyme. This enzyme is found in the mitochondrial membrane. It is responsible for catalyzing transfer of electrons to the oxygen atom. This is for the electron transport chain to make ATP as a product. ~J.D.A.

The divergence occurred at different points in time rather than at one specific time. (S.Z)

straightforward, clear. (SZ)

Gel Electrophoresis is a method of separating macromolecules such as DNA, RNA, or proteins. The separation is based on the molecules size and charge. The shorter molecules will travel further in the gel agarose than longer molecules. ~ S.Z.

Basically, the null is rejected because it contradicts the observed data. The null states that isolation occurred around at the same time, but the observed data shows divergence indicators such as metabolic enzymes, mtDNA, and mate recognition, all of which are not associated at a single mechanistic basis required for concurrent divergence. ~S.Z.

Rate of divergence for the first four pairs of shrimp was calculated by dividing the allozyme and mtDNA divergence values by the time elapsed since final closure. ~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.

The physical location of the shrimp could effect the divergence associated with the gradual rise of isthmus. ~S.Z

The shrimp located closer to the sea floor had a slimmer chance of being pushed over the isthmus; therefore had a higher chance of isolation and divergence. ~S.Z.

The less compatible they are the more they have diverged. ~S.Z.

Sporadic production is referring to production that occurs in an irregular manner. the fertile clutches will occur in at an inconsistent interval. ~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.

Transisthmian refers to the opposite sides of an isthmus. The authors utilize this term to portray that the shrimps that were measured were from opposite sides (Pacific side and Caribbean side) of the Isthmus of Panama. ~J.D.A. (DV)

The generation types (ex. F1, F2, etc.) and population size were taken into account for each shrimp pair. These factors were found to not support the phenomenon of divergence among shrimp pairs because no differences were found. ~J.D.A.

Speciation is an evolutionary process where populations become distinct from each other over a long period of time and develop into a new species. (JP)

Biological evidence supports an early and complex emergence of the Isthmus of Panama, Christine D. Bacon, PNAS, DOI: 10.1073/pnas.1423853112

https://phys.org/news/2015-04-evidence-isthmus-panama-earlier-thought.html

According to phys.org, a newly published paper suggests that the Isthmus of Panama was formed earlier than conventionally believed. The article states that the isthmus was formed in a stop and go manner over 20 million years ago; meaning that migration of organisms could have also followed the same trend. If migration of animals between North and South America started earlier, then the minimum time required for strong reproductive isolation may actually be longer than 3.5 million years. (JP)

Phylogeny refers to the study of evolutionary history among groups of organisms or individuals. The phylogenetic tree is a diagram that illustrates the relationships among species; this diagram is based on similarities and differences in the physical or genetic characteristics of different organisms. This diagram shows that all organisms originate from a single ancestor but have diverged due to speciation over a long period of time. (JP)

Schein, H. (1975). Aspects of the aggressive and sexual behaviour of alpheus heterochaelis say. Marine Behaviour and Physiology, 3(2), 83–96. https://doi.org/10.1080/10236247509378498

This previous work studies aggressive and sexual behavior in snapping shrimp. Although the snapping shrimps studied were found in North Carolina, their behavior reflects the behavior of the genus. Here they established that males seek females using chemical cues, and in general a male with a larger claw/larger body size favors larger females that can produce more offspring. Also, males with larger claws are stronger and can out compete smaller males. In relation to this publication, this previous work establishes a background of the behavior of the snapping shrimp. Understanding their natural behavior helps in understanding how the authors of this publication reached their conclusion. (JP)

Knowlton, N. (1986). Cryptic and Sibling Species among the Decapod Crustacea. Journal of Crustacean Biology, 6(3), 356-363. doi:10.2307/1548175

This previous work defines the term sibling species. According to Knowlton, sibling species are species that have been shown to be very closely related using biochemical techniques such as electrophoretic analysis. Sibling species are not the same species. This publication also uses electrophoretic analyses, known as starch gel electrophoresis, to differentiate between species of snapping shrimp. (JP)

Taxonomy deals with naming and classifying organisms. A taxonomic group of any rank, such as a species, family, or class is a taxa. ~S.Z.

The mutation rate of biomolecules is calculated and used narrow down the time in prehistory when two or more organisms diverged. (SZ)

Knowlton, Nancy & Mills, DeEtta. (1992). The Systematic Importance of Color and Color Pattern: Evidence for Complexes of Sibling Species of Snapping Shrimp (Caridea: Alpheidae: AZ'heus) from the Caribbean and Pacific Coasts of Panama. Proceedings of the San Diego Society of Natural History. 18.

This past publication explains how loosely related, or distantly related, species in the genus Afpheus Fabricius (snapping shrimp) can be distinguished based on color morphology such as differences in color patterns. This relates with this publication because both are related to the speciation of snapping shrimp in the Isthmus of Panama. Both publications find methods to differentiate between species; while this paper uses mtDNA and allozymes to compare genetic distance, the other paper uses careful analyses of color patterns to separate species. (JP)

How the formation of the Isthmus of Panama has been an impacting event in the divergence of species like that of snapping shrimp, that of which can be seen through comparison of protein, mitochondrial DNA, and reproductive compatibility. (DV)

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)

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)

The intolerant behavior that has been observed in snapping shrimp known as snapping is the production of a water jet created by the larger claw that creates a loud "pop" sound. Although, it has been discovered that the actual threat in this behavior is the subsequent shock wave that comes after the water jet. (DV)

Read more in Shrimp shootouts end with a shock wave bang: http://www.sciencemag.org/news/2017/10/shrimp-shootouts-end-shock-wave-bang?utm_campaign=news_daily_2017-10-30&et_rid=17774509&et_cid=1632982

Staggered suggests that the occurrence or arrangement of events did not happen at the same time. Staggered isolation is the thought of organisms become genetically isolated at different events or moments in time, therefore leading to speciation of these organisms. (DV)

Kimura is a Japanese biologist whose evolutionary theory was based at the molecular level and believed that most genetic differences between species were neutral and not driven by natural selection.

Kimura's corrected percent sequence divergence is an analysis that compares the genomes of species and allows to determine the divergence between their genetic code which can help conclude moment of speciation. (DV)

Sexual selection and dimorphism in two demes of a symbiotic, pair-bonding snapping shrimp Knowlton, N. (1980), SEXUAL SELECTION AND DIMORPHISM IN TWO DEMES OF A SYMBIOTIC, PAIR-BONDING SNAPPING SHRIMP. Evolution, 34: 161–173. doi:10.1111/j.1558-5646.1980.tb04802.x

This previous work provides evidence on how differences between mates affects mate choice and, with environmental constraints, can lead to sexual dimorphism which is a distinct difference in size or appearance between the sexes of the same species. This study found that snapping shrimp are very aggressive and territorial to other shrimps of the same sex. By having these type of aggressive traits, compatibility would decrease as species are more separated. This supports one of the results found in this publication. (JP)

Isthmus is a stretch of narrow land that connects two large landmasses and separates two bodies of water.

The Isthmus of Panama formed 3 million years ago connecting North America and South America, while separating the Pacific Ocean and the Caribbean. (DV)

Taxa refers to taxonomical groups like species, family, or class. Taxa are used in classifying organisms based on relatedness of characteristics.

Sister taxa refers to two groups in which the organisms derived from a common ancestral organism, therefore these two groups are very closely related. (DV)

The physical barrier created by the Isthmus of Panama prevented the exchange of genes; therefore, allowing the organism to develop differently on wither side of the barrier or diverge. (SZ)

Divergence is the differentiation of something (like an organism's genetic information) from its common state.

Molecular divergence is the differentiation between the nucleotide sequence in DNA or amino acid sequences in proteins of organisms. (DV)

The snapping shrimp (Alpheus) is a species of shrimp well known for their asymmetrical claws which when closed produce a loud snapping noise. They borrow in the sand and attack their prey by quickly reaching out with their larger claw to capture it. (DV)

A process by which a species evolves into two or more descendant or different forms (SZ)

This explains the process of gene transfer. Usually this is observed from shifts in genes between different populations. So lets say a blue bird from one population migrates out of its territory and mates with a brown bird from the new population, the allele frequency shifts. ~J.D.A.

How the formation of the Isthmus of Panama has been an impacting event in the divergence of species like that of snapping shrimp, that of which can be seen through comparison of protein, mitochondrial DNA, and reproductive compatibility. (DV)

INTRODUCTION The divergence in allozymes, mitochondrial DNA (mtDNA), and reproductive compatibility for seven shallow water transisthmian snapping shrimp (Alpheus) was studied to test the accuracy of molecular clocks. In order to interpret inconsistencies and estimate differences the relationship among species in divergence rates there must be an increase in the number of taxa and characters studied. This research will provide information on transisthmian pairs of sister taxa in snapping shrimp genus Alpheus. These shrimp are close enough to be studied at the same time, but are completely separated by a physical barrier. How will genetic and geological factors play a role in the divergence of these organisms? What is the minimum time required for speciations or divergence to occur?

(S.Z)

Svitil, K.A. (1993). "Oceans Divided". Discover, pp.1-2.

A magazine article by Kathy Svitil talks about the closure of the Isthmus of Panama. She talked about how the rise of Panama 3.5 million years ago separated Atlantic and Pacific species before the land-bridge could even form. This was caused by the shift in tetonic plates, where the Pacific Ocean floor shifted underneath the Carribean plate before melting/solidifying by lava. She states how animals felt the influence of the rifts coming together, even quoting Nancy Knowlton on the speciation of snapping shrimps on either sides of Isthmus since these shrimps used to live in deeper depths of the ocean.

~(J.D.A.)

Knowlton, N. & Keller, B.D. (1982). "Symmetric Fights as a Measure of Escalation Potential in a Symbiotic, Territorial Snapping Shrimp." Behavioral Ecology And Sociobiology, 10(4): 289-292.

This journal goes into detail the behavioral aspect of the Alpheus shrimp. This species readily defends its territory using its large snapping claw. Results gathered focused on symmetric fights of shrimps in regards to sex, size, and resources. According to this study, larger females are more likely to defend their anemone territories and showed more aggressiveness than the male shrimps. The losers of these contests experienced severe injuries by these large females than any other type of shrimps.

~(J.D.A.)

Glynn, P.W. (1985). “El Nino-Associated disturbance to coral reefs and post disturbance mortality by Acanthaster planci.” Marine Ecology Progress Series, 26(17): pp. 295–300.

Another study shows how in 1985 the coral reefs in eastern Pacific (Panama included) got ruined by El Nino due to very high water temperatures (average of 31 Celsius) and depth penetration (over 100 m). Since most habitats in coral reefs were destroyed, many species were easily exposed to predators. This may affect the results obtained by Mills and co. because barely a decade has passed for the marine habitats in Panama to recuperate.

~(J.D.A.)

Read, A., McTeague, J., & Govind, C. (1991). "Morphology and behavior of an unusually flexible thoracic limb in the snapping shrimp, Alpheus heterochelis". The Biological Bulletin, 181(1): pp. 158-168.

This journal explains the morphology of the snapping shrimp Alpheus. Their second thoracic limb is thinner, flexible, bilaterally symmetrical, and possess larger ganglion. This type of limb is almost always active in regards to grooming and foraging for food. The major cheliped, or the larger claw, is used to produce loud popping noises as a defense mechanism against predators.

~(J.D.A.)

Bermingham, E. & Lessios, H.A. (1993). “Rate Variation of Protein and Mitochondrial DNA Evolution as Revealed by Sea Urchins Separated by the Isthmus of Panama.” Proceedings of the National Academy of Sciences, 90(7): pp. 2734–2738.

Another research was made in regards to the closure of Isthmus of Panama 3 MA based on changes in oxygen/carbon ratios in sea water. The main subject studied was sea urchins. Bermingham and Lessios compared mtDNA and protein divergence among three differ species of sea urchins--Diadema, Echinometra, & Eucidaris. Results concluded that protein divergence between Atlantic and Pacific sea urchin species only differed by 1 order of magnitude, so no significant difference. The Diadema species had an overlap of allele frequencies whereas the other two species displayed fixed loci for differ alleles of both shores, which may hint towards gradual genetic drift or mutations.This proves that other marine life besides the Alpheus shrimp community were also affected by a change in the environment via closure of Panama Isthmus.

~(J.D.A.)

Offspring that have different alleles than their parents as a result of genetic recombination (such as crossing over and random assortment of chromosomes which causes each sex cell to be different from the parents' sex cells). These offspring are then crossed with each other so that resulting generations have nearly identical genes.

The genetic makeup of an individual inherited from one's parents. Genotypes are particularly important in determining which variant of an allele or trait that individual has. When the author says that 14 genotypes were sowed, they mean that 14 different combinations of the same genes were planted in the populations. The plants each had their own variety of these genes. This is an important distinction because a genotype does not mean that the plants had different genes. They simply had different varieties of them.

Random processes, events occurring with no apparent relationship or meaning. Stochastic models are necessary for ecological studies because environmental systems are often impacted by random events such as natural catastrophes or human interference. In order to account for this randomness, multiple trials are done in studies to ensure that the results were not simply a result of randomness. The more trials that affirm a result, the less likely it is that result is due to chance.

The random selection of organisms to survive and reproduce. Unlike other selection devices, genetic drift is completely due to random chance. An example of genetic drift could be something like a volcano erupting and randomly taking out half of the population just due to chance. Genetic drift is typically more pronounced in smaller populations because changes in allele frequencies are more observable when even just a few members of a population are removed. If those members had a unique trait, their removal can be very influential on the traits of that population.

Factors outside the strand of DNA that impact how the genes are expressed. The most common examples of this are DNA methylation and histone modifications. Both essentially make the DNA harder to access by the enzymes that convert it into proteins. These epigenetic regulators are mostly caused by environmental factors such as nutrition or exposure to certain chemicals. These epigenetic changes are heritable, meaning the modifications can be passed on to offspring.

Fig. 1. (C)

Climate change has created longer, more intense dry seasons; which ultimately contributes to later plant reproduction, lower fruit yield, and lower germination rates. Delays in flowering might limit the the amount of time pollinators have to disperse pollen, which will reduce plants' abilities to produce viable offspring.

BD, HW

Fig. 1. (B)

The effects of climate change on leaf production and insect activity. Climate change has resulted in later leaf production, which creates an increased overlap between leafing and insect activity. This increases the likelihood of herbivory damage to plants and ultimately decreases plans' abilities to survive and reproduce viable offspring.

BD, HW

It has been noted that protein divergence increases as divergence time increases, thus being said as time increases more protein divergence occurs. To learn more click here. http://www.pnas.org/content/94/24/13028.full.pdf

• Jake Barbee

Nonsynonymous substitutions are a nucleotide mutations that alters the amino acid sequence of a protein. These differ from silent mutations, because they alter the amino acid sequences. - Jake Barbee

Splicing refers to RNA gene splicing which is, the editing of new messenger RNA transcript into a mature messenger RNA. Splicing removes introns, joining together only the exons to create a mature mRNA. - Jake Barbee

A set of numbers arranged based on frequency.

Describe the features of a set of numbers, for example the average, median, mode.

An increase of one value is associated with a decrease in another value.

A one-ring sugar, cannot be metabolized to a simpler sugar form, unlike disaccharides (two-ring sugars), which can be metabolized to monosaccharides.

Production of egg cells.

Passage of a disease-causing agent from parent to offspring.

A subdivision of the animal kingdom that includes all multicellular animal organisms having cells that are differentiated and form tissues and organs.

Any organism that lives within the body or cells of another, offering some benefit and receiving some benefit in return.

These are two symmetrical extremities underneath the middle of a male ray or shark - Alejandro

It is a software that is engineered to accurately create maps that match with physical geographical sites on the planet - Alejandro

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

The statement reinforces the hypothesis due to the fact that there has been peer reviewed data that can be compared to the research that has been conducted.- Alejandro

The authors results supports their hypothesis, showing that there is a positive correlation between marine reserves and the abundance of reef sharks. - Emily

There are 50 species of carcharhinid sharks that can be grouped into 12 different genera. If the shark follows a migration path, stays in generally warm waters, and contains the stereotypical shark look, it can be considered a carcharhinid shark. - Alejandro

This article is used to explain how creating a marine reserve, even though there has not been enough research conducted to prove beneficial, could possibly have the population of carcharhinid shark begin to increase again. - Alejandro

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

Radiation in the form of sound waves. -Mohammad

In Asia, shark fins are a delicacy and showcase ones wealth. The Asian shark fin trade accounts for the biggest percentage of shark deaths. -Emily

Stands for "boundary element model", which is used to model electric field structure based on the electric organ and to deduce electric field source poles from an electric field.

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

From Table 1, the following sex-determining proteins display InL, InL(clock), and the p-value. These factors display the final calculations. From what the author first concluded, the InL(clock) values show that there is in fact a constant rate with which the proteins evolve. It is tested by the likelihood ratio tests based off the models of evolution defined. -Melanie

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

Episodic selection can be defined as a form of selection that sporadically selects organisms with varying differences per generation, otherwise known as short-term fitness. In this sense, it can be concluded that SXL works alongside episodic selection rather than the molecular clock hypothesis in order to develop sex-specific functions within drosophilids. Learn about episodic selection here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666517/ -Eri-Ray

BIOEDIT is a computer program that is capable of editing and aligning sequences rapidly and effectively. It is meant to be easy to use and is intended to allow researchers to easily create and analyze basic sequences. It is incredibly useful in this case as it allows the researcher to analyze sequences of multiple insect species rapidly and quickly. Learn more at http://www.mbio.ncsu.edu/BioEdit/page2.html -Eri-Ray

First proposed in the 1960s, the molecular clock hypothesis has become universally used in evolutionary biology, especially genetics. The hypothesis states that DNA evolves at a rate that is directly proportional with time, which allows scientists to determine direct relationships and differences between organisms (Ho, S. 2008). Learn More at https://www.nature.com/scitable/topicpage/the-molecular-clock-and-estimating-species-divergence-41971 -Eri-Ray

In the Drosophila group, members of the Drosophila group have either one or two X chromosomes and two sets of autosomes. Sex determination is determined for females by having balanced female determinants on the X chromosome. For males of the Drosophila group sex determination is based on the determinants on the autosomes. If there is only one X chromosome present in a diploid cell the member of the Drosophila group is male, this is shown by the ratio of (1X:2A). To learn more click here https://www.ncbi.nlm.nih.gov/pubmed/18956315 -Jake Barbee

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

Funding for the sequencing research will require collaboration among researchers as well as creative approaches beyond traditional funding. GIGA is open to funding ideas and opportunities.

GIGA plans to continuously expand and improve and welcomes all members of the scientific community to contribute to their cause by helping understand the under-explored phyla. M.G.

GIGA will go beyond just invertebrate genome studies by opening pathways t new research in many other related fields.

Different positions of the fish led to more or less efficient muscle contraction times. So, the authors used the positions that would best decrease contraction time to find the maximum speed of a fish.

Parafilm was used to make sure the needles didn't slip while measuring muscle contraction time, because that would lead to a source of error.

A fish that swims with moderate drag and maximized thrust. These fishes are evasive and have prey locally available near them, unlike cruising specialists. Some acceleration specialists are barracudas, flounders, and pike.

Fishermen most likely overestimated the speeds of the fish they caught out of excitement and pride that they caught "such a fast fish" so they over-exaggerated how fast these fish really swam, contributing to the entrancing myth of the swimming speed of billfishes, what this paper addresses.

Broken curves in the graph represent limits on speed by the environment of the fish such as the strength of water current.

The length a fish swims with one tail beat (one stride). In humans, this would be the amount of distance a person walks with one step they make. Larger fish have larger stride lengths.

The shaded graph shows the contraction times at each location of a fish defined in actual length in meters rather than just as percentage of the fish's body length.

The only places they found significant differences in swimming speeds between fishes were between sailfish and little tunny and between sailfish and barracuda.

In little tunny, the muscles near the head contracted faster than those by the tail, which was different from the other fish that relied more on their tails to propel through water, and hence had lower contraction times near their tails than their heads.

Though sailfish swam the fastest, some of that speed is attributed to the fact that sailfish were the longest fish and larger size increases a fish speed. After considering this and correcting the swimming speeds by the fishes' sizes, it was found that sailfish had the lowest size-corrected speed and little tunny were actually the fastest considering their size.

This paragraph discusses how Ednrb is needed in order to further a melanocyte into melanoma, even if Kitl (another signaling pathway) is present. Therefore, this is the direct link to melanoma.

(NB)