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.

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.

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.

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.

straightforward, clear. (SZ)

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

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)

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)

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)

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)

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)

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.

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.

a molecular technique that purifies proteins and finds binding partners by using antibodies that can bind specifically to the protein. Can help find protein complexes.

a test used to confirm the presence of a protein species or to identify natural binding partners for the RNA

computer run simulations

The coelom is the body cavity in which the intestines and digestive organs lay in. -Sindy

An empirical research is a research that uses observations that are verifiable rather than theories. The level of significance in an empirical research is the probability of rejecting the null hypothesis.

The HIF pathway is one of the molecular pathways used to regulate angiogenesis. The Hypoxia inducible factor (HIF) proteins act as transcription factors by inducing the vascular endothelial growth factor (VEGF) promoter. HIF proteins are activated as a result of low oxygen concentration. In normal conditions, the HIF protein is rapidly degraded by the actions of Von Hippel–Lindau (VHL) tumor suppressor proteins. VHL proteins bind to hydroxylated HIF and targets HIF for proteasomal degradation. However, under hypoxia, HIF is no longer bounded to oxygen and VHL can’t bind to HIF, resulting in the activation of HIF. HIF can then induce angiogenesis by activating VEGF genes.

Gene Ontology is an initiative that aims to address different concepts and vocabularies aimed to describe the functions of a gene and its products. Gene ontology studies genes based in three major categories: biological component, molecular functions and cellular compartments.

In genetics, candidate genes are genes that are likely to cause a disease due to their location or their protein products. Candidate genes are studies based on a priori knowledge. A priori knowledge is gained based on detective and derivative reasoning. Hence, a priori candidates are genes that cause disease and have been studied and analyzed.

Normally, under hypoxic conditions, the blood vessels constrict. In Tibetans this physiologic reaction does not occur.

The levels of oxygen in the blood have fallen below normal

The "typical" phenotype that is seen in nature.

The tumor necrosis factor (TNF) superfamily is a group of proteins involved in programmed cell death.

A type of dominance where two alleles of a gene in a heterozygote are fully expressed.

Placodes are very short-lived during development and do not form in the same place.

Bumps in the layer that joins the epidermis (outer layer of the skin) and the dermis (middle layer of the skin).

Small, spherical groups of cells that contain a cavity from which hair, teeth, feathers, etc. can grow.

Covered by bony or horny plates or scales.

Related to birds.

Similarity of structure, physiology, or development of different species that is a result of a common evolutionary ancestor.

Refers to evolutionary lineage (species linked by a common ancestor).

Specific molecules that, when present, indicate the presence of a structure or a particular stage of development.

Cells shaped like columns.

A protein involved in cell signaling between two layers of skin (ectoderm and mesoderm). It is especially important in embryo formation and promotes the formation of hair follicles, sweat glands, and teeth.

Related to the study of tissues.

The process by which a structure or pathway that evolved for one function gains additional functions.

The idea that two species share an ancestor somewhere in their lineage. Common ancestry is visualized in a phylogenetic tree.

Perennial plants grow and bloom over the spring and summer, but die back every autumn and winter, This seasonal process involves the annual gain and loss of the biomass required for blooming.

These tests involved cars driving on actual roads, instead of test (or "simulated") roads used for experiments.

Autonomous vehicles can navigate an environment without input from humans. One example of an autonomous vehicle is a self-driving car.

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

time elapsed between start and completion of the morris water maze

Amyloid beta precursor protein (APP); The protein is found in many tissues and concentrated at the synapses of neurons.The protein itself is not dangerous, it is found in many tissues and concentrated at the synapses of neurons. Truncated forms of APP can form plaques that cause AB toxicity.

Receptor and ion channel protein found in neurons, which controls the ability of synapses to weaken or strengthen due to brain activity level and memory function.

A kinase that helps transfer a phosphate group to a specific site on the tau protein. Each isoform of the p38 kinase phosphorylates tau at a different site. A kinase is a protein that catalyzes the transfer of a phosphate group to a specific site on a specific protein.

Alzheimer’s disease is a brain disorder that worsens with age and has no known cure. The disease affects different aspects of cognition and memory, and can eventually lead to shutdown of the body. https://www.youtube.com/watch?v=fT7UovfLl8c

Amyloid beta is a short chain amino acid and is a main component of amyloid plaques that are associated with Alzheimer’s. Amyloid beta plaques are located outside of neurons. Amyloid beta plaques are composed of amyloid precursor protein (APP) that is truncated into a shorter form. Amyloid beta toxicity occurs when the build of of amyloid beta plaques becomes toxic to neural cells.

A mutant variant of T205 with the mutation in the phosphorylation site

A mutant variant of T205 that changes the site to act like a constitutively active phosphorylation site

Mice are placed in a circular pool of water. In one of the quadrants, a hidden platform is present. The platform allows the mice to stand instead of swim.The mice are shown where the platform is and how to get to it multiple times. After showing the mice, the researchers put the mice somewhere in the four quadrants and track their movement as the mice attempt to find the platform. Time to escape can also be quantified. (https://www.jove.com/video/2920/morris-water-maze-test-for-learning-memory-deficits-alzheimers)

Tau is a protein that stabilizes microtubular cytoplasmic components in neurons.

A technique to find protein-protein complexes by precipitating an antigen protein from a solution using an antibody that binds to a particular antigen from a sample.

response of a neuron to a stimulus

electrical signals recorded from individual neurons

after the initial step

the time between seizures

change or variation

to add an inorganic phosphate group to a substance, usually to affect the activity of the substance

completely; throughout

death

to move up and down on a scale

A protein that phosphorylates Tau and is involved in neuronal growth.

A wave on an EEG that is a sharp wave or spike that is a marker for patients with epilepsy or a focus of seizure studies.

Electroencephalography (EEG), measures electrical activity of the brain Epileptiform: A wave on an EEG that is a sharp wave or spike that is a marker for patients with epilepsy or a focus of seizure studies.

to aggravate, make a situation worse

to amplify, make greater in size or value

Pentylenetetrazole, a central nervous system (CNS) stimulant used to assess the excitability of the CNS. The drug is administered and 30 minutes after, seizure profiles are examined.

The death or damage of nerve cells by over stimulation by neurotransmitters.

A deviation from the normal type behavior

The Human Genome Project was an effort to map and understand all of the genes that make up the human genome. Although it was announced complete in 2003, we still have much to learn about the genome.

Genome-scale CRISPR knockout.

Unitless measure of how much light bends when passing through a substance.

On the "bottom" surface, or siphon side of the squid.

All of the mRNA transcripts in a cell.

Biologically produced light.

"Bootstrapping" is a process that allows scientists to ensure that their statistical data sets are correct by doing hundreds of random samplings.

RW

Vertical lines in these graphs represent error bars, which represent the level of uncertainty in results. The larger the variation in data, the longer the error bars will be. These graphs have been created with 95% certainty.

RW

This p value is considered "significant", meaning that the results did not happen by chance.

RW

P values greater than .001 are generally considered insignificant in statistics

RW

marriage between close relatives

enzyme that produces fluorescent colors when activated and is often used to study gene expression

bacterial DNA sequences that contain snippets of viral DNA, allowing scientists to modify genes within an organism (by removing or adding DNA)

the change that occurs in a cell due to disease or infection

newborn children, specifically up to 4 weeks old

single stranded RNA viruses that are transmitted by insects, such as mosquitos

a genetic technique that genetically modifies genome sequences to have a specific missing or inactivate gene that is “knocked-out” of the organism

when mitotic cells fuse with interphase cells, causing premature mitosis

a gene or characteristic that prevails among individuals in natural conditions

a virus belonging to the herpesvirus family causing a variety of symptoms in those with a weakened immune system or pregnant

The observable characteristics/traits of organisms

An idea that is credible and reasonable

Is a drug that targets peroxisome proliferator-activated receptor. Peroxisome proliferator-activated receptor are nuclear receptors, which also act as transcription factors.

drugs used by diabetic patients to regulate blood glucose levels.

Normal oxygen levels.

Able to be passed on to the next generation

Data was arranged on a table or chart

Are genes that are not on sex chromosomes

Localization signals are amino acid sequences that aid in nuclear transport by tagging proteins destined into the nucleus.

A measurement unit: 200 kilobytes

Calcium found on the inside of the cell, typically found in the mitochondria.

CAMK2D gene encodes for calcium dependent protein kinase type 2 delta, which is a serine/threonine protein kinase family.

Heme oxygenase 2 (HMOX2) is an enzyme that catalyzes the breakdown of heme.

Family of genes that regulate lipid synthesis and drug metabolism.

Is one of the member of the cytochrome P450 superfamily, and regulates metabolism of xenobiotics in the body. Xenobiotics are chemical compounds found in the body, but are not synthesized within the body.

Cytochrome P450 17A1 is a gene encoding for enzymes of the cytochrome P450 superfamily, which regulate the synthesis of various lipids and drug metabolism.

The breakdown or storage of fats that occurs within cells, primary in the liver.

Peroxisome proliferator activated receptors are receptors found on the nuclear membrane that can act as transcription factors that induce certain genes.

Following a certain phenomenon

Structures that do not extend over one another

A continuous uninterrupted sequence

The evolutionary process in which organisms acquire adaptations to allow survival in an environment.

The phenomenon is which two or more alleles are associated more frequently than expected.

Beneficial mutations that increase an organism's survival and reproductive rate are favored by natural selection. That is, alleles that increase an individual’s fitness are increased in frequency. Eventually most beneficial mutations become fixed : their frequency will reach 1. However, mutations increase in frequency but don’t get fixed. Beneficial mutations that are nearly fixed result in partial selective sweep.

A change in the gene pool where one allele becomes the dominant allele.

The ratio of one allele to other alleles in a particular population.

A set of genes inherited by a single parent.

A DNA sequence variation that occurs in a single nucleotide base.

One or two alternate forms of a gene that have arisen via mutation, that are found at the same location on the same chromosome.

resting breathing rate

The tendency of a body toward balanced physiological conditions in reaction to specific stimulus. For example, maintaining a body temp of 98.6 F regardless of the environmental temperature.

A protein or molecule that regulates the transcription of DNA to RNA.

When a specific trait is made more prevalent overtime in a population (the Tibetan highlands people in this case), because this trait increases the survival and reproduction of the person who expresses it.

The exchange of air between the lungs and atmospheric air.

The widening of blood vessels, which decreased blood pressure.

Nitric oxide

The oxygen transport system consists of the lungs and blood vessels. Oxygen is transported from the lungs through blood vessels.

Cellular process where energy generated by the cell (in the form of ATP) is made through oxidative phosphorylation (the electron transport chain) where oxygen is the final electron acceptor.

low oxygen concentration

To make up for

A molecule found on red blood cells that is responsible for the transport of oxygen in the body of vertebrates.

A characteristic associated with the normal function of the body.

A time period between 2.6 million years ago to 11,700 years ago.

Kinases are proteins that help move phosphate groups from one protein to another. p38 kinase phosphorylates tau and each form phosphorylates at a different site.

An accession number in BLAST is the specific identification number of a sequence. AT

Homology in protein sequences means that the sequences are similar enough that we can assume they developed from the same ancestral gene. AT

This marine biotoxin is incredibly common in aquatic environments because of pollution and other factors. Thus it was important to investigate how it affects the DNA/chromatin of mussels. Researchers mapped out the specific effects of the biotoxin and compiled it in a database.

A model organism is a species with a fast regeneration time and a relatively simple genome. We try to find similarities between model organisms and complex ones in order to make a clinical use of the research. AT

fixed in one place; immobile. EM

A regulated process during gene expression that results in a single gene coding for multiple proteins. EM

Alleles are different possible expressions of a single gene. When one is expressed the other is silenced. For nonallelic genes, both can be expressed at the same time. AT

A core protein as opposed to a variant. AT

Upregulation stimulates transcription and makes it go faster. Downregulation would make transcription go slower. AT

pertaining to the sex or reproductive glands of an organism that produces gametes (sex cells) and sex hormones.

The promoter is a region in DNA that tells the RNA polymerase protein where to begin transcription. AT

The H2A.Z.1 and H2A.Z.2 came from a common ancestor and developed mutations in their amino acid sequences that eventually gave them their own separate functions. AT

A complex of nucleic acids and proteins, which condense to form chromosomes during cell division, is highly consisted of DNA, RNA and proteins.

Similar to H2A.Z.1 in structure. Mediates cell proliferation, which is defined by the balance between cell divisions and cell loss through cell death or differentiation. EM

H2A.Z.1 differs from H2A.Z.2 by three amino acids. Functions range from transcriptional regulation, chromosome transmission and DNA damage repair. EM

H2A.Z is another variant in the H2A family. It replaces the core H2A protein and is involved in gene silencing. It wraps the DNA tighter than a normal H2A protein would. It is also involved in sensing heat which can damage the DNA or proteins. AT

H2A.B histone is present in actively transcribing DNA and helps during the elongation stage of transcription. AT

macroH2A is a variant that represses transcription (the transfer of genetic information from DNA to messenger RNA). It also works to inactivate the expression of alleles on one of the X chromosomes. AT

A variant histone is a substitute protein that acts in place of a real histone protein. They have mutations that result in a functional group. A functional group is an additional group on a protein that carries out a particular job (ie. signal, attachment point, etc). AT

A protein structure that DNA winds around to compact the DNA into tight structures instead of being loose in the nucleus. The protein amino acid sequence has two tail ends, the N-terminal at the beginning and C-terminal at the end. For histones these ends act as receptors to a signal that tells them to either open up to allow transcription or close to inhibit transcription. AT

A threadlike structure of nucleic acids tightly wounded by histone proteins that carry complex genetic information in the form of genes.

KM

There are five main families of histone proteins in eukaryotic cells. The family consists of several closely related histones. AT

A region's plants and their traditional uses- N.S.

Currently the most widely used pesticide in the world. It is used to control pests in agricultural crops and forests. It is also sold for home use, such as for gardening, killing household pests, and treating fleas in pets.

Resources and benefits that humans receive from properly functioning environments (e.g., clean water, pollination, flood protection, waste decomposition, and recreational enjoyment).

The concentration of a chemical at which effects on the body can be observed.

Different terms are used to standardize the question, "How much of chemical X does this sample contain?" The smallest concentration at which a chemical can be feasibly measured is known as the limit of detection, or LOD. The limit of quantification (LOQ) is the LOD plus any adjustment for known measurement bias or imprecision. LOQ can be thought of as the lowest LOD that can be made confidently.

Because of different instruments and protocols, LOQs vary across studies, which may make comparison difficult. (See definition for "quantification thresholds" above.)

A term used in food safety by the European Commission, a legal body of the European Union: "The traces pesticides leave in treated products are called 'residues.' A maximum residue level (MRL) is the highest level of a pesticide residue that is legally tolerated in or on food or feed when pesticides are applied correctly."

Sensitivity in detecting a chemical of interest. Varying quantification thresholds make comparisons across studies difficult, because there is no standardized baseline measurement. For example, if Lab A uses an instrument that is much more sensitive than Lab B's, then Lab A may report measurements that were too low for Lab B to detect. As a result, Lab B will appear to report higher results than Lab A. (See definition for "limit of quantification (LOQ)" below.)

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

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

Radiation in the form of sound waves. -Mohammad

Log distance predicts the path loss a signal encounters inside a building or densely populated areas over distance. -Sindy

Detection's that appeared valid but in fact were not. -Sindy

The previously mentioned transmitters all starting with the letter V are versions of acoustic telemetry monitors. -Sindy

The word ecotypes refers to different species of a plant or animal living in a specific habitat.

• Carolina Jimenez-Pinilla

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.

• Carolina Jimenez-Pinilla

Hemipterans are an order of insects that share the common characteristic of a sucking mouthpart. Beatles are different because they have chewing mouthparts.

• Carolina Jimenez-Pinilla

a process of separation where components are distributed; in this case the chemical components of the gas

• Carolina Jimenez-Pinilla