The location or position in a chromosome of a particular gene. Plural of locus.

Microsatellites, also known simple sequence repeats (SSRs) in plant genetics, are identified through sequencing. This research helps to identify the biological functions of the genes and how they affect the plant in terms of its genomic makeup.

Differences in the genetic makeup within populations over time.

Differences within the movement and quality of water.

A branch of phylogeny that uses molecular and statistical techniques to determine hereditary differences within organisms.

Plants or animals that exist in one geographical location.

Genetic differentiation is the variation between allele frequency in populations that have been isolated.

A land-locked lake in Hispaniola that contains a high concentration of salt.

The process of taking a data set of any size and mapping (or organizing it) into a specific structure of a set size, such as a table. This makes it easy to find the data later if you need it.

A good example would be books in a library. By assigning each book a call number associated with its location, you can easily look up the book in a database and see where you should go in the library to find it.

To represent by breaking up into individual, separate quantities.

A distinctive, recurrent pattern of activity.

This is a matrix that is generated from a Gaussian distribution. In a Gaussian distribution, also called a normal distribution, the mean value has the highest probability of occurring, and values further away from the mean in both directions have a smaller chance of occurring. An example is a bell curve of grades, where most students get an average C grade and only a few students get either Fs or As.

This is a common technique the brain uses in many different sensory systems (vision, hearing, smell, etc.). The calculation incorporates information about the neuron's receptive field (the area in which it is sensitive to a stimulus) as well as a measure of the contrast (difference) between local stimuli.

Transferred.

In statistics, this is the process of organizing a set of objects (such as data points) into groups (or clusters) based on similar features.

Related to the meaning of words in a language.

Known in mathematics as a "helping theorem," this is a proposition that forms one part of a larger or more general theorem.

A mathematical expression that defines the distance between any two elements in a set. Finding the distance between each of the elements in two feature vectors (each representing an image) would let you determine how similar those two images are. That is, the smaller the distance between the elements, the more similar the images are.

A row of numbers.

Blocking an action or making it less likely to occur.

A type of hashing that aims to reduce the size of a large data set by mapping it into a table with fewer entries than pieces of data. To do this, similar pieces of data are assigned to the same entry in the table.

A set of instructions that tells a computer how to carry out a task or solve a problem.

To organize into a numerical format.

Associations between the evolutionary history of a group of organisms where"poly" means many and "genetic" refers to origin.

The act of inserting one object or substance into another. For this study, the slices from the EOD records taken through time are put into the slices from EOD records taken through space to create a map that shows the potential and amplitude of the EOD.

An order of freshwater bony fish that can be identified by a long body, anal fins, nocturnal behavior, and the ability to generate electric fields for communication, navigation, and defense. The eel, for example, is a well-known gymnotiform.

This is when animals use electric fields in their surroundings to detect their own location in space. Only certain species with electroreceptors can do this, consider how bats perform echolocation with their vibration detections.

Refers to something that was caused by humans. Anthropogenic barriers could include roads, agricultural areas, or cities. These barriers can reduce the ability for species to migrate.

In the case of this paper, referring to the capacity of individuals within a population to establish themselves in an area. Unlike fitness, this has less to do with surviving to seed, and more to do with being dominant in a space shared with other populations.

As human activities have cleared habitats to extract resources or establish agricultural land or housing, habitats have become concentrated in smaller patches with unfavorable land in between. This is also known as habitat fragmentation, and can impede the migration of species to more favorable habitats.

As species move to new places with different environmental conditions, species evolve. Which traits are favored and how trait and gene frequencies change are aspects of evolutionary dynamics. For example, plant traits including height and dispersal change as plants spread to new areas.

The spreading of, in this case, a plant species due to its dispersal of seeds. The plant itself does not move to new locations like when animals migrate, but instead, it refers to the spreading distribution of the plant species.

Events in which a new organism is introduced to the environment, then grows and reproduces to the point that it becomes common in the new environment. These events are often associated with harming the native species, but are also how species adapt to changing conditions.

Teragram, grams in the trillions.

Research into the amount, source, spread, and control of diseases.

Molecules that lead to the formation of aerosols (suspended particles in air).

Chemical reactions that remove hydroxyl radicals from the atmosphere.

Molecules that contain only carbon and hydrogen atoms (hydrocarbons). Nonane has 9 carbon atoms, decane has 10 carbon atoms, and undecane has 11 carbon atoms.

Calculation that predicts the chemical make-up of air due to emissions and various reactions that occur to transform those emissions.

Movement of chemicals away from their initial emission source.

Molecules that contain carbon atoms that somewhat evaporate into the gas-phase at typical pressures and temperatures.

To hydrolyze a molecule is to break it into two pieces by adding a water molecule to it. Some chemicals undergo this process spontaneously, but in biological systems enzymes often help hydrolyze large biological molecules.

Enzymes are large biological molecules that help speed up the transformation of one molecule into another. Degrading a polymer generally involves breaking it down into smaller pieces. Enzymatic degradation uses natural or lab-made enzymes to break down polymers that could harm the environment into something smaller and more benign.

When an organism picks up new DNA from another organism that is not its parent.

Indicates how much of a chemical per volume (concentration) in a solution with a given amount of enzyme needed to make the reaction go at half of its maximum possible rate.

https://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/biomolecules/modules/enzymes/enzyme4.htm

Sets of DNA in different organisms that encode similar traits in different organisms. Homologs are often used to show how certain traits, like the ability to digest PET, developed over the course of evolution.

A publicly accessible database with information gathered on all the DNA from all the organisms who have had their genome sequenced.

A section of DNA that contains information to build at least two proteins. Those proteins then perform related functions in a cell.

Types of proteins that go through a cell membrane. A transporter will help carry a molecule from the outside to the inside of a cell and vice versa.

A process that occurs outside of the cell.

We often think of metabolism as the process by which humans break down food into energy; however, it can also be used to describe the process by which a cell breaks down a molecule, like PET in this case, for energy.

The total population of mRNA in a cell. mRNA is the compound that helps carry information carried in DNA to the parts of the cell that use it to create proteins.

Reads all of the RNA in a cell and records the order of base pairs.

The liquid above a solid sample. In this case, the solid sample is composed of l. sakaiensis cells.

In this case, a highly specific enzyme would degrade PET but not other esters.

Describes how much an enzyme prefers one chemical to others.

The temperature above which a polymer becomes flexible and pliable. Below the glass transition temperature the polymer will be hard and brittle, like glass.

Indicating a material that is very ordered on a microscopic scale, like a grain of salt or a diamond. An amorphous solid, for example, lacks this order.

The basic monomer of PET. It is made up of TPA with two ethylene glycol groups attached to opposite ends.

Used to show what percent of times a node, or a place where two different branches originate, shows up in a phylogenic tree. The tree is recreated many times using slightly different data samples. Higher bootstrap values suggest the node is more likely to be correct.

A diagram that shows how different organisms or biological species, like enzymes in this case, are related to each other. A node, where there is a branch in the tree, represents when the two species have evolutionarily diverged from each other.

A technique for separating different compounds. The compounds are dissolved in some solvent and run through a thin tube called a column lined with a solid substance. Compounds that are attracted to the solid substance come out of the column after the compounds that are less attracted to the solid in the sample.

Amino acids that are directly involved with speeding up a reaction. In this case, the degradation of PET.

A stretch of DNA that the cell is able to read and translate into mRNA which can be used to make a single protein.

Enzymes that are built inside a cell, but later sent outside the cell. In this case, the secreted enzymes end up on the PET film.

A cell that is sticking to a surface.

Stands for Scanning Electron Microscope. The microscope uses an electron beam that produces signals about the sample's surface and then converts that information into a picture. SEM allows us to see things too small to visualize with a more common light microscope.

A type of single-celled organism. There is a lot of diversity among the different types of protozoa. Although they are single-celled like bacteria, they have different forms and behaviors. They typically lack a cell wall, for example, and many will survive by eating other organisms rather than by photosynthesis.

The morphology of a PET fiber describes its shape and surface texture. For example, we might describe its morphology as being rough, smooth, or flat. If there are morphological changes, that implies something about the bacteria changed the shape of the PET film.

A set of microscopic organisms, typically bacteria, from two or more species.

A solution of water and whatever chemicals an organism, in this case these fungi, need to grow. It will often include vitamins, minerals, and some type of food source.

These are types of fungi. Both fungi cause disease in some plants and F. solani also causes disease in humans. Previous research has shown that they can produce enzymes that can degrade PET to some extent.

The simplest form of the monomer, or repeating unit, of the polymer PET.

Any compound that has six carbons bonded together in a ring and sharing three double bonds. Aromatic compounds tend to be unusually stable.

Any foreign organism that can cause disease. Common pathogens are viruses, bacteria, and fungi.

Bumble bee pathogens are organisms that cause detrimental effects in bumble bees.

Since the mountainous regions occupied by bumble bees lack pathogens, the pathogens do not influence the evolution of mountainous bumble bees.

The physical expression of an organisms genetic makeup. Everything we physically observe in an organism is due to the expression of their genes (their genetic information).

The phenotype of tongue length in bumble bees is highlighted in this study. Bumble bees featuring different genes that express tongue length display a variation in tongue length.

A theoretical model used to indicate how an animal will look for food. Factors that influence how an animal will forage for food depend on the costs of energy or risk gathering the food compared to the energy gain benefit from the food.

A constant used to compare the relative size of an organism's foraging area. Larger numbers indicate a larger foraging range.

The range or obtainable food sources for an organism.

For the alpine bumble bees, this includes sources of nectar and nest building materials.

This paper highlights how the foraging breadth of native bees is decreasing due to increasing competition from immigrant species.

Species of bees from subalpine climates, that are within the same genus.

Climate change has warmed the alpine climate, making it's temperature closer to a subalpine climate, and increasing the range of the subalpine bee species.

Plants that are in a mutualistic relationship with the pollinators.

In this paper, host plants are involved in a mutualistic relationship between themselves and bumble bees.

A species of bumble bee known as the forest bumblebee. It is native to North America and is found in open alpine grasslands near mountains.

Bombus sylvicola feeds on plants such as lupines, fireweeds, and groundsels, which are all plants found in alpine habitats.

A species of bumble bee known as the golden belted bumblebee. It lives in high altitude alpine habitats and has a long tongue that is more than two-thirds of its body size.

Evolution is the change in alleles (genetic information) in a population over time. Coevolution is when two species influence the evolution of each other.

Coevolution is generally observed when a long lasting mutualistic relationship between two species exists.

As plants and bumble bees evolved alongside each other, each acted as a selective pressure for the other, altering their evolutionary paths so that each is better suited to live alongside the other.

The study of an organism's physical characteristics and their function.

In a mutualistic relationship between species, scientists are able to match the morphological traits that directly affect the symbiotic relationship (morphological matching).

This paper highlights the morphological matching between the corolla length of flowers and the tongue length of bumble bees.

Foraging is the act of an organism searching for food. Generalist foraging is when an organism forages for a wide variety of food, or in other words is more adept at foraging for whatever is more convenient. Bees showing generalist foraging will eat from a wider range of flowers.

The common weather patterns of a given area.

As climate change occurs, the prevailing weather patterns of all areas are viable to change as well.

Changing climate of bumble bee habitats are causing changes in pollination requirements of bumble bees to flowers.

The cylindrical opening created by the petals of a flower that leads to the reproductive organs of a given plant. The tube also leads to rewards for pollinates, such as nectar.

The corolla tube is what a bumble bee sticks its tongue down to acquire nectar. The longer the corolla tube, the longer the tongue of a bumble bee must be to access the nectar held within the tube.

A living organism capable of spreading pollen from one flower to another.

Generally pollinators are insects or birds. The pollinator highlighted in this paper is the bumble bee.

A measurement of the number of species in an ecosystem.

The greater the number of different species in a given ecosystem, the greater the biodiversity measurement of said ecosystem.

The practices used in farming to produce goods, such as crops and animals.

Agriculturally based mutualisms consist of symbiotic relationships between organisms and cultivated organisms.

A relationship between two different organisms where both species benefit from that relationship.

The symbiotic relationship highlighted in this paper is the one between long-tongued bumble bees and plants. The bumble bees benefit the plants by pollinating them as they move from plant to plant and the plants benefit the bumble bees by giving them nourishment.

Used in the last step of the juvenile hormone biosynthesis pathway that converts acids into hormones.

High performance liquid chromatography (HPLC) is a technique commonly used in analytical chemistry to help separate, identify and quantify components in an organic mixture.

Lipid assays include utilizing synthetic lipids to construct a lipid bilayer similar to the cell membrane. Lipid assay kits may be used to measure concentrations of lipid mixtures in comparison to membrane proteins in a cell membrane.

One of the most significant stages of the reproductive cycle is vitellogenesis which involves massive production of yolk protein and their accumulation in developing oocytes. Vitellogenesis is dependent on the availability of a blood meal and, as a consequence, is linked to transmission of pathogens. Therefore, vitellogenesis and other aspects of mosquito reproductive physiology is critical for their management of disease. The ovarian resting stage in the reproductive cycle of female mosquitoes is a time when the eggs are not being produced. In addition, the ovaries will not develop beyond a resting stage until a blood meal of adequate size has been taken.

RNA Interference is a response to double-stranded RNA that is responsible for the resistance of pathogenic nucleic acids such as certain mutations in base pairs, and regulates how genes express a particular protein.

Found in the head of insects. It is responsible for the regulation of metamorphosis and reproductive functions in most insects.

A signaling pathway allows an activation process to occur for a cell to have a specific function. In this case, communication takes place between these two different hormones, juvenile and insulin. These hormones work with energy to develop an insect.

A chemical signal that regulates larva development and metamorphosis in insects.

Primarily used in laboratories. It is commonly used for sealing or protecting vessels (such as flasks or cuvettes). It is a ductile, malleable, waterproof, odorless, translucent, and cohesive thermoplastic.

Put to death with minimal pain.

They would injure themselves too much, potentially leading to death.

A type of fish that swim around and look for their prey, which are widely dispersed. They also have a stiff body with minimal drag when they swim. Sharks and salmon are also cruise specialists.

Type of skeletal muscle in a fish; slow-twitch muscle on the outer sides of a fish.

https://esi.stanford.edu/exercise/exercise6.htm

The study of the relationship between the ecological role of an individual and its morphological (i.e. structure/form) adaptations.

Members of a large and extremely diverse group of ray-finned fishes.

Billfish have long bills (elongated upper jaw), which allows them to cut through water, and aerodynamic bodies so they can swim in speeds of up to 120 kilometers per hour. Billfish include sailfish, swordfish, and marlin.

Binomial nomenclature for the arctic fox. They are native to the arctic regions in the northern hemisphere, and are commonly found in the arctic tundra biome. They are carnivorous with a common diet of birds, hares and insects in the Aleutian islands.

The amount of time that has passed since two species have shared their most recent common ancestor.

In Brownian motion model of evolution, traits change randomly in distance and direction.

The model uses two parameters: the population mean trait and the evolutionary rate parameter.

This model is used in biology to compare traits between individual species and create phylogenetic trees.

The likelihood that taxas with a shared common ancestor will have similarities in their appearance, behavior, and in their interactions with others.

A large and diverse group of organic compounds that are present in many plants and insects.

Terpenes are often found in conifers, which release a distinct scent.

Mixtures that can readily become vapors or gases.

Narrow paths through which one collects information on the species that is being studied.

A taxonomic category that can be found throughout the tropics.

The process of choosing that leads to the formation of new species due to the accumulation of differences between species.

A characteristic that can be measured based on an observable standard or quality.

A characteristic that can be measured based off of its amount or quantity.

The job/role that an organism performs in its environment.

Nephrogenic diabetes insipidus (NDI) is a congenital disease characterized by the body's inability to make concentrated urine. It can be caused by mutations in two different genes, including AVPR2.

Able to change or move.

A common form of mica. https://geology.com/minerals/biotite.shtml

The tuff is situated on top of the Footprint Tuff, therefore it was more recently formed.

Palaeontology sites in Ethiopia. Lucy, the well-known early hominin fossil, was found near Hadar.

By grouping the Pliocene and Pleistocene epochs, scientists have informally created a time period that runs from about 2.5 to 1.5 million years ago. This is when Australopithecus expanded into East Africa. https://www.grossmont.edu/people/bonnie-yoshida-levine/online-lectures/plio-pleistocene.aspx

A statistical calculation to determine the accuracy of predictions made using the regression line.

A form of linear regression used to determine the best fit line.

A survey technique used to determine the location of points. Distances along the sides of a triangle are measured and angles computed. By constructing a series of adjacent triangles, distances between points can be accurately determined.

A method of taxonomic analysis involving the external measurement of the form of an object, organism, or landform.

Generally considered or reputed to be.

Means "in the broad sense."

Represents a time unit of one million years. 1.0 Ma means one million years before the present.

A way to statistically summarize the relationship between two quantitative variables.

A family that includes horses, zebras, and other related mammals.

A family that includes the modern-day giraffe. Giraffids share a common ancestor with bovids.

These are antelopes such as Kirk's dik-dik.

The branch of science that studies fossilized footprints, animal burrows, and other traces of the existence of an animal and its behavior.

Here, undulating indicates that the upper edge of the soil layer has a continuous up and down shape. It is not flat.

Particles that are of the same kind.

Desiccation polygons are areas bordered by cracks in the mud found in sedimentary rocks and mud flats. Disarticulation suggests that the polygons separated from the mud and formed individual clods of earth or rock.

Describes the surface of a rock or mineral that is made up of crystals too small to be seen with without magnification.

A mineral involved in the formation of many igneous and metamorphic rocks.

A large-scale photograph made up of many smaller photographs.

A water-worn trench.

Existing or occurring in the same period of time.

A mammal of the cattle family.

That is, a fault line running east to west.

The side of a cliff or a steep slope. It can form as a result of faulting or erosion.

A raised flat land area with sides that slope.

Stratigraphy is the study of rock layers. An analysis of a stratigraphic sequence would be looking at the types of sedimentary deposits, their age, and distribution from one area to another.

A soft, porous rock that is formed from volcanic ash and or cinders. Over time it is compacted into solid rock.

The single specimen that is used by the author of an article to describe and name a new species. It could also refer to two or more specimens described by the author when a single holotype is not identified.

Formed when preexisting rocks are subjected to intense heat and pressure. This results in the original rocks changing both physically and chemically. Common examples are marble, slate, and schist.

In this case, a series of fossil footprints made by hominids or other animals.

Animals that typically have more than one mate.

Refers to differences in appearance and size between males and females of the same species. Modern humans show a low level of difference in size and appearance. Differences between the sexes is much more pronounced in early hominins and in primates such as gorillas and orangutans.

A period during Earth's history that occurred between 23 million and 5.3 million years ago.

A land surface resulting from erosion that occurred during ancient times.

A country located south of the equator in East Africa. (See the map of Africa in Figure 1 for the location of Tanzania and Laetoli.)

Malaria is a flu-like disease caused by a parasite. The parasite infects and kills blood cells while also releasing toxins. If left untreated, this infection can result in organ failure and death. It is transmitted by certain species of mosquitoes.<br>

Mosquito larvae live in the water and feast on microorganisms. They go through four growth spurts before becoming a pupa.

The pupal stage is the time at which the mosquito transforms from a water-inhabiting larvae to a wing-bearing adult. Much like butterfly metamorphosis, the mosquito is encased in a hard but thin shell-like structure.

This is a denotation for a nucleotide change. This is ribonucleotide 1 changed from an A to a C.

A technique to deliver nucleic acids to eukaryotic cells through membranes. There are many ways to do this, but two common ones are through chemicals or electricity.

A collective sample. In this case, mRNA samples from multiple female mosquito embryos of the same age were combined before being sequenced. The same was done across different time points and for male mosquitoes. Because mosquitoes are small organisms, there is not enough cells/RNA to perform a quality sequencing reaction. Thus, several or maybe even hundreds of organisms must be combined in order to have enough material. When looking at sequencing data from "pools", you are actually observing the "average", but since these are laboratory raised mosquitoes, it is assumed that they are genetically identical. So the "average" is likely true for all organisms in the population.

Changes in the mosquito genome have made them no longer susceptible or at least not as sensitive to insecticides. Much the same as bacteria developing genetic resistance to antibiotics.

In an abnormal place. In this case, nucleic acids are injected into mosquito larvae leading to expression of a gene that is not normally there.

The female egg cell is a rather large cell compared to the fertilizing male sperm cell. This large egg cell has more mRNA in the cytoplasm (as well as things like mitochondria) than the sperm cell. When the zygote is formed, there is a large maternal contribution of cytoplasmic goodies.

A process by which the expression of genes on the autosomes (all the other chromosomes that are not sex chromosomes) and sex chromosomes (in both sexes) are balanced through either inactivation of chromosomes or increased gene expression from a chromosome.

A particular version of an expressed gene (mRNA), may or may not have all of the exons encoded by the gene.

An organism that has some amount of genetic material from another unrelated organism.

Exposure to radioactive compounds.

Referring to chromosomes.

Having three sets of chromosomes. Most animals are diploid, having two sets of chromosomes, one from mom, one from dad.

Reduced expression of a gene, not complete removal.

Having two different sex chromosomes. In humans, males are the heterogametic sex.

Having two of the same sex chromosomes. In humans, females are the homogametic sex.

Order of butterflies and moths.

Increased expression of genes.

Any change in DNA that results in a non-functional protein. Many different types of mutations can accomplish this, nonsense mutation and large deletions are the first thing that come to mind. They can render a protein non-functional by it being completely absent. Even missense mutations that change a single amino acid can render a protein non-functional if it hits a functional domain, even if the protein itself is present.

A visualization of the number and kinds of chromosomes present in an organism. This term is used loosely here, as XY males were determined through PCR, not the traditional means of visualizing chromosomes under a microscope.

A mobile DNA sequence that contains a gene. In genetic engineering, these sequences can be moved between plasmids or other useful vectors through restriction or recombination sites.

A protein derived from jellyfish that emits a neon green light when excited by UV or blue light.

A continuous circular molecule of DNA. Originally derived from bacteria, plasmids have proven to be a useful delivery system of DNA in molecular biology.

Injecting two or more things (in this case nucleic acids) at once.

This level of structure in a protein is when the amino acid chain begins to have three-dimensional shape. Side chains of the amino acids fold and interact through chemical forces like hydrogen bonds, van der Waals interactions and hydrophobic interactions. The most common secondary structures are helices, sheets, loops and turns.

This type of secondary structure in an amino acid chain is comprised of two alpha helices connected by a loop. This type of structure is indicative of the protein's ability to bind DNA as a transcription factor.

A stop codon (UAA, UAG or UGA (RNA)) that occurs earlier in the sequence than intended, usually due to a change in the DNA. This results in a truncated (not full length) protein.

Start codon (ATG (DNA) AUG (RNA))

Selection against deleterious traits (negative selection).

A stretch of DNA sequence that has the ability to be translated into protein (exons only). An ORF usually begins with a start codon (ATG) and ends with a stop codon (TAA, TAG or TGA).

Changes in DNA that end up coding for a different amino acid in the protein product.

Changes in DNA that ends up coding for the same amino acid in the protein product.

Similar to PCR, RT-PCR is a method that first converts mRNA in to DNA by use of a RT polymerase (enzymes like this are used in viruses like HIV). Once the RNA is in DNA form, the traditional PCR method can be used to amplify transcripts of interest.

in vivo inside of a living organism. In this case an experiment that was done in a cell line (in vitro) and worked, was then done in a living organism to see if it would also work in the context of the whole animal.

A population of cells derived from a single cell isolated from an organism. Thus, all cells in the culture are genetically identical. Often different cell lines have unique experimental qualities to them. In this case, this line lacks the Y chromosome, which may have been genetically engineered or may have occurred by chance.

mRNA molecules that were made in a tube (in vitro outside of a living organism).

A control that helps to ensure that the same amount of RNA is added from each sample, so that if lower or higher levels of RNA are seen in different samples you can ensure it's due to biological differences and not just human loading error.

There is a maternal to zygotic transition (MZT) in the zygote after blastoderm formation but before gastrulation. During this process maternally deposited RNAs from the egg are degraded and the new genome of the zygote is activated and begins transcription and translation of genes. The zygote is now on its own, without the support of good old mom.