The neural crest is an embryonic structure in vertebrates that gives rise to many types of cells, primarily cells of the peripheral nervous system. So during embryonic development, the neural crest differentiates and migrates to give rise to specialized cell types. They also give rise to melanocytes which will be further discussed in the paper.

Melanocytes are skin cells that produce the pigment melanin. Melanin is the skin darkening pigment that is known for protecting the skin from harmful rays.

Endothelin is a vasoconstrictive peptide produced in endothelial cells. Vasoconstriction means that these peptides constrict blood vessels, increasing blood pressure as a result. These peptides are composed of 21 amino acids and there are three types: endothelin 1, endothelin 2, and endothelin 3.

The continued use of the drug (cocaine) regardless of health and social consequences.

Evidence gathered using model systems like rats and mice. Model organisms are useful for understanding how a treatment or therapy might affect humans, and are often used extensively before human trials begin.

Something that comes before. Here, "antecedent stimuli" means a stimuli that comes before drug use.

Affected.

Characterized by a desire to seek pleasure.

Intended as punishment.

Relating to the use and effects of medicines.

A proposition states a claim that can be either true or false.

The science that studies the relationship between heat (thermo) and work or movement (dynamic).

A locus in DNA where the Melanogenesis Associated Transcription Factor (MITF) binds to exert its effects on gene expression.

MITF earned its name because it is a transcription factor associated with pigmentation. So, MITF binding sites are likely to be near genes involved in pigmentation.

The F_ST is the fixation index, which describes genetic differences between populations by measuring genetic differences among and between populations.

An F_ST value close to 1.0 indicates that the populations being compared are highly divergent (very different) from one another.

A lysosome is an organelle in animal cells where unwanted material gets digested. A lysosomal protein is a molecule that performs its function inside (or on the surface of) the lysosome.

The uneven distribution of species in an area.

This is an organization that works with partners in the Amazonia and they research on things like soil nutrition.

This is a graphical technique for representing a data set, it shows one or more variables and their relationships.

A pressed plant sample deposited and used for future research, this is used when a specific plant cannot be determined during the field work, so it is later researched to determine its species.

Shannon was who introduced the concept of entropy. Entropy is the disorder in the universe.

The amount of species there are in a given plot.

One third of the acre.

Touching or sharing a border.

Describes plots of different vegetation involved.

Set boundaries or limits.

Used to measure the distribution of organisms. The land and the species found there are separated into continuous quadrants.

How species are arranged in an area.

Study of rate of growth.

1 hectare plot = 100 acres.

The Amazon basin covers 40% of South America. It is the part that is drained by the Amazon river. Most is covered by rain forests.

The picogram is equal to one trillionth of a gram.

Plot method where, the lines are laid out one after the other without attempting to maintain a set direction.

The ratio of the standard deviation to the mean. Used to measure variability.

Describes how the flowers are arranged.

The number of different species in a given ecological community.

A large gradual change in nonliving factors through space such as change in tree structure.

Stems and leaves of the tree.

Carbon stored in the forest.

This field inventory method is a way to carefully screen the species that are present

Neotropic forests are found in South and the North American regions of Central America. The Neotropic includes more tropical rainforest than any other realm. These rainforest are one of the most important reserves of biodiversity on Earth.

The variability of different tree species in the ecosystem.

The total mass of the plants' structures that are above the ground (excludes roots) in a given area or volume.

Per capita is a Latin phrase which means for each person. Here, the authors are looking at the mass of waste generated per person per year.

Fragmentation is the process of being broken into smaller pieces or parts.

A standard ton is 2000 pounds, while a metric ton is 1000 kilograms (2205 pounds).

Long term carbon storage.

The global concentration of carbon dioxide. This fluctuates annually.

Average total amount of rain recorded during a certain amount of time.

Coastal wetlands that are flooded and drained by salt water brought in by tides

Freshwater marsh ecosystems are those areas in which fresh water, obtained from groundwater or precipitation surplus, covers the surface for a portion of the year, and where flora and fauna able to survive those conditions, reside.

The capacity of the environment to absorb by-products of production and consumption.

Biogeochemical model that simulates carbon and nitrogen fluctuations in the atmosphere, plants, and soil. Data on the soil, hydrology and temperatures have to be inputted prior to the model working.

Results from temperature differences, instability in the atmosphere.

A slow process that allows the system to be very close to equilibrium.

This is the measure of mass of water per mass of dry soil. This is done by weighing the soil sample, drying it, then weighing the soil dry.

This is the sum of all the respiration that is occurring by the living organisms that inhabit the ecosystem.

This is a measure of the quantity of carbon entering and leaving an ecosystem.

A species that plays a significant role in a biotic community, however with much less importance than the dominant species.

Two or more species that are equally dominant in a biotic community.

Bowen Ratio is the mathematical method that is typically used to calculate heat loss or heat gained in a substance.

Environments and ecosystems perturbed due to human interference.

The biological system includes bacteria, fungi and invertebrates. Fungi colonizes the leaves once they fall in the stream and break down the carbon.

SRP is a measure of the filterable portion of phosphate known as orthophosphate.

Dissolved inorganic nitrogen is the combination of nitrogen forms nitrate, nitrite and ammonium. This is the most available form of nitrogen used by algae.

These forests shed annually and litter the streams, giving them an organic carbon source.

This is organic carbon that can be dissolved in water and run through a filter; it is smaller compared to particulate organic carbon.

Co-limitation is the limiting of growth caused by two factors, both must be present in a set ratio to have an effect.

There is further visualization in figure 2, where the co-limitation of nitrogen and phosphorus are presented.

Terrestrially derived carbon is a source of carbon obtained from land materials such as twigs and leaves.

Particulate organic carbon is a source of carbon for the ocean obtained from living organisms and detritus; it is larger compared to dissolved organic carbon.

An increase in nutrients in nearby river has led to an increase in the levels of algae in these rivers, some of these which are toxic to people.

Read more in nwi.com: http://www.nwitimes.com/business/toxic-algae-once-a-nuisance-now-a-severe-nationwide-threat/article_2b1decfa-43c9-5d80-bf64-173e51a95248.html

These are permanent bodies of waters found interior to the coastal waters. These bodies include rivers, lakes and reservoirs.

This is a carbon source found on land commonly in biotic organisms.

Sequestration is the collection and storage of carbon dioxide.

In this case, the carbon is being removed from the water and depletes the riverine food webs.

Produced by the organism.

Technique that allows high-definition viewing of microscopic samples in 3D.

Open Reading Frames (ORFs) are sequences of DNA that are not transcribed. They can be used to search for transcripts that code for specific proteins of interest.

An organism that lives in close association with a "host" organism.

The relationship may be positive for both the host and the symbiont (mutualistic), positive for the symbiont and neutral for the host (commensal), or positive for the symbiont and negative for the host (parasitic).

Symbiosis: It's Complicated

Membrane-bound "bubbles" that shuttle proteins to different locations in a cell.

Nonhuman animals are used to study, or model, diseases and understand the role of genes or proteins in processes, such as skin pigmentation. Thanks to shared ancestry, there are many similarities between human and nonhuman animals at the cellular and genetic levels. Thus, animals can be used to do experiments than can't be done in people.

Structure, shape, appearance (as opposed to function).

Cells in the basal layer of the epidermis that form a barrier against environmental damage.

Indigenous populations found in Malaysia, Philippines, Indonesia, and Australia.

A cell that produces melanin.

The building or breaking down of pyrimidines in cells—pyrimidines include the DNA/RNA bases uracil, thymine, and cytosine.

A database of results from published studies related to mouse phenotypes.

When one gene (or variant of a gene) has multiple effects on seemingly unrelated traits.

A consensus motif is a pattern of the most frequent nucleotides that are bound by a particular protein, in this case SOX2.

A numeric scale that specifies the acidity (low pH) or basicity (high pH) of a solution (or in this case, cell). The number is based on the molar concentration of hydrogen ions in the sample.

The pH of cells affects the activity of many enzymes and other proteins.

A protein that spans the cell membrane, allowing chloride ions (and sometimes other ions) to enter or exit the cell under specific conditions.

Loss of variation in the DNA near a mutation that has increased in the population due to positive selection.

The KWRS test is a statistical test used to determine whether samples have the same distribution, and unlike the MWW test it can be used on more than two samples. If samples do not have the same distribution, that means something is significantly different between them.

When genetic variants are referred to as "tightly linked," it means that they are close together and usually inherited together.

An ovarian follicle is a group of cells inside of the ovary that releases an egg cell during ovulation. These follicles must be maintained for a female mammal to retain fertility.

An E3 ubiquitin ligase assists in transferring a ubiquitin onto a protein substrate. Ubiquitin is a protein that occurs ubiquitously in mammalian tissues, and is a regulatory molecule that can affect proteins in many ways, including marking them for destruction, causing them to move to a different part of the cell, or altering their ability to interact with other proteins.

Parts of a protein that span the cell membrane.

A pseudogene is a stretch of DNA that looks similar to a gene, but has lost some or all of its function.

An individual with two identical alleles for a given locus.

Bonferroni correction (or adjustment) compensates for the increased likelihood of rejecting the null hypothesis incorrectly due to testing multiple hypotheses (testing multiple hypotheses increases the chance that a rare event occurs).

This correction is performed by dividing the significance level desired (generally 0.05) by the number of hypotheses to be tested (for example, if testing two hypotheses), and testing each individual hypothesis against this new number (for example, 0.05/2 = 0.025).

Primary refers to cells (in this case, human melanocytes) that have been taken from a tissue (human skin) and are growing in a dish without further alterations.

Integrated haplotype score: A statistical test to measure how far from the SNP of interest haplotype homozygosity extends on the ancestral compared to the derived allele. Haplotype homozygosity measures the likelihood of selecting two identical haplotypes at random from a population.

If a SNP is under selection, it will often occur with longer haplotype homozygosity than expected (on either the ancestral or derived allele), and extreme iHS values will result.

A synonymous variant is a change in the DNA that does not lead to a change in the amino acid sequence of the protein encoded by the gene.

This can happen because each amino acid is encoded by a stretch of three nucleotides in the DNA, called a codon, and there are multiple codons for the same amino acid.

A skin condition characterized by patches of skin losing pigment and appearing white.

The most recent common ancestor (MRCA) of a group of organisms is the most recent individual (in this case, a hominid) from which all the organisms in the group are directly descended.

The MRCA of a population is hard or even impossible to determine for a large population, but the time when this individual lived (the time to most recent common ancestor, TMRCA) can be estimated based on mathematical modeling and knowledge of the genetic variation in the population.

A nonsynonymous mutation is a change in the DNA sequence that leads to a different amino acid being used in the encoded protein.

A lentivirus is a type of virus that is often used in research to deliver DNA into cells because it is efficient at doing so across many types of cells. In this case, lentivirus delivered DNA that encodes shRNAs.

A derived allele is an allele that is different from that carried by the common ancestor of the populations being examined.

Proteins in the cell membrane that facilitate the movement of small molecules or ions across the cell membrane.

The MWW test is a statistical test used to determine whether a value selected from one sample at random will be equally likely to be greater than or less than a value selected at random from another sample.

In this case, the test is used to check for allelic imbalance. In heterozygotes, the level of expression of each allele may not be equal; if one is expressed more than the other, this is called allelic imbalance. In homozygotes, expression from the two alleles is more even because they are the same variant.

A difference in expression between the two alleles at a particular locus.

For most genes, expression is usually equal from each of the two alleles a person has. If there is allelic imbalance, one allele will be expressed more than the other.

H3K27ac refers to a specific alteration to a DNA packaging protein that is associated with transcriptional activity, and often occurs on enhancer regions which are considered active when this mark is present.

H3 stands for Histone H3, a protein that DNA is wrapped around in chromatin. K27 refers to the 27th amino acid Lysine in the Histone H3 protein. ac stands for acetylation, a modification in which an acetyl group is added to a protein.

Folate is a B vitamin, and is important for many aspects of health including the prevention of anemia and certain birth defects.

Folate can be broken down by UV radiation (sun exposure), leading to lower levels in people with high UV exposure.

The production of a pigment called melanin. Melanin gives skin and hair its color.

Many factors can contribute to differences between individuals of the same species. Some differences are due to differences in DNA; these are referred to as the "genetic basis" for variation.

A process by which organisms that are not closely related evolve similar traits independently.

A plant with a grass-like physical structure and long blade-like leaves.

Small, sometimes microscopic, animal-like organisms that exist in bodies of water. Can sometimes be made up of the larvae or immature forms of larger animals.

An invertebrate animal in the class Arachnida that includes spiders and scorpions, in this experiment the species observed was Cybaeus reticulates.

A process by which a single gene can encode multiple proteins.

RNA splicing is the removal of introns from the transcript made from a gene, leaving only the exons to be expressed. In alternative splicing, exons are excluded, introns are included, or different junctions are used between the introns and exons, leading to proteins with a different amino acid sequence.

The frequency of the second most common allele in a population for a given locus.

Addition or subtraction of one or more nucleotides in a DNA sequence.

An ecological effect caused by the addition or removal of predators with changes to both the populations of predators and prey. The trophic cascade effect can either be top-down (predator to prey) or down-up (prey to predator). In a simplified food chain, if there is an increase (or decrease) in top predators then there would be a decrease (or increase) in herbivore prey and an increase (or decrease) in plant prey communities.

Compound heterozygotes have two different mutated alleles at the same genetic locus.

A measure of the correlation of two continuous variables.

Regions of chromatin that are highly sensitive to cutting by DNase I, an enzyme that cleaves DNA at many locations in the genome.

Genomic regions are more sensitive to DNase I cleavage if their chromatin has lost its condensed structure, indicating that these regions would also be available for binding by transcription factors and subsequent transcription. Therefore, DNase I hypersensitive sites are associated with regions of the genome that control transcription.

The ancestral allele is the allele that was carried by the common ancestor of the populations.

mRNA stands for messenger ribonucleic acid. mRNA is made based on the sequence of DNA that encodes it, and specifies the amino acid sequence that will be used by the ribosome to make a protein product.

Diversity measure of classified data.

Percent composition of a species compared to the total number of species in the same area.

Measure of the statistical dependence among species' trait values due to their ancestral genetic relationship.

Pressed plant specimen deposited for reference.

Relating to the arrangement of the physical features of an area.

Different in kind.

Abbreviation for hectare which is a unit of area.

A region near the Earth's equator where trade winds of the Southern and Northern hemispheres join to make hot air rise and falls as thunderstorms.

Refers to the relative abundance of species in a community.

Removal of trees in a specific site or area.

Changes in a forest that negatively affect the structure and function of a particular site leading to a diminished capacity to provide services.

The process of removing, and destroying forests, to be replaced by something else.

Also called biodiversity hotpot; a biogeographic area with high levels of organismal and community diversity likely under threat.

The mathematical space within an ecological unit.

A component of biodiversity concerning range in communities and ecosystems performed by organisms (the impact).

All the populations, species, and communities in a defined area.

Refers to the number of species.

Unimodal distribution is a statistical distribution with one clear peak.

Phenology is the study of periodic plant and animal life cycle events and the how the processes are influenced by seasonal and interannual differences in climate and habitat factors.

When an insect of animal undergoes a period of suspended development.

+/- 5% of actual value.

A test which is used in statistical analysis in which there are many comparison test being practiced. Even if the statistical data has no significance, the Bonferroni tests will allow significance to emerge in the data due to multiple testing.

Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed at the same time on a single data set. A Bonferroni correction is performed by dividing the critical P value (α) by the number of comparisons being made.

Post hoc tests are run to confirm where differences in means are when using multiple groups. They are only run after an ANOVA test confirms that there are statistically significant differences between the groups.

ANOVA is a collection of statistical models used to analyze the differences between group means.

Group of genes in the organism that was inherited from a single parent.

The Monte Carlo method is a tool used in statistics which can be applied to scientific research in which a distribution of the possible outcomes in a data set can be produced.

Since the same experiment can be repeated many times we must have outcomes that show the probabilities of different outcome happening.

A program developed by the Pritchord lab at Stanford uses genotype data to investigate population structure. Its uses include discovering distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and mixed individuals, and estimating population allele frequencies.

Biomass: Total mass of an organism or the mass of the organism in a a specific area.

The weight was taken when the plant was dry for the simple reason that different species can hold different amounts of water. In order to obtain a precise measurement and compare the different species, the plant had to be dried.

To soften or the use of liquids to soften.

The field laboratory is a branch of the University of Florida's Everglade Experiment Station. The objective of which is to conduct research on vegetables and forage crops on the sandy soils of lower east Florida.

Read more about the laboratory at https://www.ars.usda.gov/southeast-area/fort-lauderdale-fl/iprl/docs/history-of-the-iprl/

Exocarp: The thin outer layer that covers the fruit.

An example of an exocarp would be the thin layer located on the outside of a grape or apple.

Mettler balance is a laboratory balance used to measure small masses to the sub milligram range. It can measure from .1 mg to .0001 mg depending on the model.

Fleshy middle layer of the fruit.

The outer layer of the pericarp of the fruit. The skin of the fruit.

Phenolic compounds are a class of plant secondary metabolites. These include a range of compounds such as phenolic acids, flavonoids, and other substances. They are responsible for fruit color.

A perennial is a plant that lives for two or more years. Most perennials flower multiple times during their life cycle.

Dioecious refers to a plant or animal that has male and female reproductive organs in separate individuals.

Intraspecific hybridization occurs when the hybrid is born from parents of the same species that belong to different populations or breeds.

Genetic variation is variation in the alleles of genes both within and among populations.

This variation is brought about through mutations.

Founding populations of invasive species are often small, so they experience the founders effect. The founders effect is a loss of a genetic variation due to a smaller population size.

An ancestor or parent.

A study is referred to as high-powered, if the size of the sample from which data is collected is large enough that it becomes highly probable (at least 80% probability) that an effect of interest that exists in the population would actually be found in this data.

For example, let’s say we were interested in finding out whether cupcake consumption increases well-being. Because we cannot ask every person on the planet to please report their well-being, eat a cupcake, and then report their well-being again, we have to restrict our investigation to a certain sample of people.

To be in balance, the solar heat reaching the Earth must be balanced by the amount of heat the Earth emits into space; what comes in is balanced by what goes out.

For more information, check out this NASA video: https://www.youtube.com/watch?v=DOAqECd70Ww&t=22s

Scientists measure distances in meters and not miles, where 1 meter is roughly 3 feet and 1000 meters is about 0.6 miles.

The average depth of the ocean is about 3,688 meters (12,100 ft), and reaches the deepest depth of 10,994 meters (6.831 mi) in the Mariana Trench in the West Pacific Ocean.

Check out this Tech Insider video about how deep the ocean really is: https://www.youtube.com/watch?v=UwVNkfCov1k

A joule is a derived unit of energy that is equal to the energy transferred to (or work done on) an object. One joule can be thought of as the work required to produce one watt of power for one second.

There are 5 ocean basins: the Atlantic Ocean, Arctic Ocean, Indian Ocean, Pacific Ocean, and Southern Ocean. These oceans are all connected and can be defined as a global or world ocean.

The average deviation from an expected value.

Density measures the degree of compactness of a substance. The density of seawater depends on the dissolved salt content as well as the temperature. A high salt content and cold temperatures make seawater more dense.

Measured or evaluated on a yearly basis or from one year to the next.

To function properly, cells are constantly creating, recycling, and transporting proteins. Interruptions in this process can be a cause of disease.

Neurons express special proteins that allow them to adhere to each other and to other cell types. The ability to bind to each other is important for neurons' ability to communicate properly.

The release of glutamate, a common neurotransmitter.

A mutation that changes a codon that would normally correspond to an amino acid to a stop codon.

"Gene dosage" refers to the number of copies of a gene in a particular genotype. A gene is dosage-dependent if a certain number of copies is necessary for proper function.

Although there are many factors that influence gene expression, in general more copies of a gene will result in more protein product (either directly from the gene or as a result of regulatory mechanisms).

A stop codon (or termination codon) is a series of three nucleotides that stops the translation process.

It works by binding special proteins called "release factors." When these release factors reach the ribosome (the site of protein translation), they cause the new amino acid chain to separate from the ribosome, stopping translation.

The term "pro-band" is used to refer to the patient being studied in biomedical research, especially research on genetics.

PCDH10 is a potential tumor suppressor protein. Abnormalities in PCDH10 have been found in many human tumor cells.

A "forward" screen is used to identify the mutation(s) that leads to a given phenotype.

A "reverse" screen is used to identify the resulting phenotype from a given mutation.

The authors propose renaming c3orf58 to deleted in autism-1 (DIA1) because they found evidence that it was causative of autism in patient AU-3101.

Genes are commonly renamed from "generic" names such as c3orf58 to more specific names that provide information about their function. Because there is no formal regulation of gene names, many genes have misleading names or multiple names.

The myocyte enhancer factor 2 (MEF2) transcription factor is important to cell differentiation and embryonic development.

A biological pathway, found in many eukaryotes, in which RNA molecules inhibit gene expression. This is usually caused by the destruction of certain mRNA molecules.

This pathway is used by researchers to increase or decrease the activity of genes of interest.

Genes that are "activated" by neural activity will typically be transcribed more following a depolarization event (i.e., an action potential).

The portion of a cell's DNA that is transcribed. The transcriptome can be identified by looking at all of the mRNA in a cell.

To increase the reliability of the results, the researchers may have removed information identifying samples as "experimental" or "control." This can decrease bias in the analysis of results.

The process of "reading" DNA to create mRNA, which then exits the cell nucleus to eventually be translated into a protein. This is the first step in protein synthesis.

The deletion is homozygous (present on both chromosomes) in the boy, but present on only one chromosome from each parent.

Thus, the boy inherited the deletion from both parents.

A variation of a single nucleotide in a DNA sequence. When less than 1% of a population carries the nucleotide at this position, this variation is classified as a SNP. Some SNPs are associated with certain diseases.

Because first cousins share a larger portion of their genome than two unrelated individuals, there is a higher chance that a child will inherit disease-causing mutations.

A technique used to determine how a trait is inherited, and if it is inherited in a standard (Mendelian) way.

Refers to the autosomes, or the 22 numbered chromosomes (which do not include the sex chromosomes).

Non-parametric (not assuming a normal distribution) statistical test that is used to compare two sample means that come from the same population, and used to test whether two sample means are equal or not. The authors conducted the Mann-Whitney test post hoc (after the Kruskal-Wallis test) in order to compare the groups (to investigate which groups significantly differ) but with corrections to control for inflation of type I error (false positive – determining differences in the dataset when there actually is none).

A plant that is not formally a part of the family Asclepiadaceae.

Diversity describes the number of species, while abundance describes how many individuals of each species.

A type of flower that has a long, thin, tube-like structure. The tube-like structure is formed by the pedals and often separate the mouth into a flared shape.