Since the initial experiment does not allow us to clearly conclude why the virgin males preferred the alcohol (the list of possible reasons is given in the prior sentence), the researchers designed a series of follow-up experiments, each designed to examine a slightly different possibility.

The group of male flies that experienced repeated, lengthy mating sessions with multiple virgin female flies.

Some of the authors of this paper have also looked at the genetic information for domestication in other species, like pigs.

To learn more about the similarities and differences of pig domestication compared to dog domestication, check out this article in Science Magazine: https://www.sciencemag.org/news/2015/08/taming-pig-took-some-wild-turns

Marks the final stage of the time period known as the Stone Age.

An ancestor and all of its descendants.

When the DNA sequences of 605 dogs were examined, two different groups were identified—the East Asian and Western Eurasian core groups. A dog may fall into either group, or between groups, with elements of both groups in its DNA (admixed).

The 605 dogs were from different parts of the world, and when represented on a map (as in Figure 1A) it was clear that dogs are mostly of the East Asian core group (in red dots) in East Asia, and mostly of the Western Eurasian core group (in yellow) in Western Eurasia.

Can detect admixture events; it is used to detect gene flow between closely related species.

Genetic sequences of the modern and ancient dogs used in this study are publicly available. Check out their data on Dryad!

A technique that looks at the pattern of DNA sequence changes (mutations) in multiple individuals, focusing on the most recent common ancestor of any two sequences. It can provide information about the timing of shared ancestry, population sizes, population splits, and migration rates.

Referring to the point in time when dogs first appeared.

This refers to a specific type of indexing (listing) strategy that is used in LSH to limit the number of hash tables and reduce computational time. Multiprobe also means that instead of only checking a single bin for similar items, it will look at nearby bins, as well, just in case.

This is a type of machine learning. Machine learning is the process of getting computers to run without being directly programmed. To do this, a computer scientist will use a sample data set to "train" a computer how to respond to a particular problem. The goal is that the computer could then learn certain rules so it can also solve the same or similar problems, even with data it's never seen before.

Deep learning extends this process to multiple layers, creating artificial networks of problem solving so that computers can solve more complicated problems without human input.

The fly algorithm is so much more efficient that it can perform more computations for the same cost as the LSH algorithm. This is the because the cost per projection is so different—for each projection in LSH, it requires 2d operations. For each projection in the fly algorithm, it only requires 0.1d operations. To even it out so that the total operational cost is the same means that the fly algorithm is able to generate 20 times the number of projections as the LSH algorithm.

Computational savings refers to the efficiency of an algorithm—that is, how much time and space on the computer it requires to run. Especially when working with very large data sets, computational savings is an extremely important factor to consider since analyzing the data can take a very long time (imagine if you had to wait more than a fraction of a second every time you entered search terms into Google).

Here, the authors note that by modifying their experimental algorithm to include sparse, binary random projections instead of dense, Gaussian random projections, they were able to make the algorithm 20 times more efficient. That's big!

Effective computer search algorithms need to have the ability to scale in order to handle data sets of different sizes and levels of complexity.

For example, while a brute-force method would work well if you only had to compare a few images, it becomes slow to the point of being impossible when you want to compare all the images on the internet.

There are other methods (like the space-partitioning method) that work well for many images, but only if those images are very simple—that is, their feature vectors are very small.

In order to handle complicated problems like searching high-resolution images on the web, it's therefore extremely important for researchers to find algorithms that can scale to handle both large and complex data sets.

This is a general problem-solving technique that involves listing all possible candidates for a problem and checking one by one to see which one(s) provide a solution.

In this example, it would be like taking your picture of an elephant and manually comparing it to every other image on the internet to find the 100 that are most similar. In problems where there are many possible candidates for a solution (like this example), brute force linear search is an extremely slow way of trying to solve the problem!

This "fundamental computing problem" is the problem of being able to quickly and efficiently pick out objects that are similar to one another from very large data sets.

For example, Google needs to be able to pick out search results that are similar to what you typed—and it needs to do this very quickly. Likewise, Netflix needs to compare your watch history to that of all its other users so that it can make recommendations for what else you might like.

These and other similar problems pop up all over the place in your everyday life. The process of solving them is called a "similarity search" and is of intense interest to computer scientists who want to make these searches faster, more efficient, and better quality.

The authors identified a genetic culprit, which they call Yob, which explains the factors that initiate the genetic pathway to maleness in Anopheles gambiae mosquito embryos.

Malaria is a severe illness caused by parasites that are transmitted to humans (and other animals) from the bites of infected female Anopheles mosquitos. With over 200 million cases of life-threatening malaria each year, scientists are looking for ways to eradicate the disease. Learning about the genetic pathways of sex determination in mosquitos can help, along with genetic technologies like CRISPR.

Learn more about about how genetic modification of mosquitos might help in the fight against malaria in Vox. https://www.vox.com/science-and-health/2018/5/31/17344406/crispr-mosquito-malaria-gene-drive-editing-target-africa-regulation-gmo

The scientists artificially inserted the gene-reading Yob into the embryos of Anopheles gambiae.

In this case, a grouping of young male mosquitos.

Insect species employ a variety of different genetic mechanisms to confer either the female or male sex. The default mode, generally, is the development of female embryos; but there is not much understanding of the factors that lead to male-specific development.

A general term for the mosquito genus, Anopheles.

Though details on insect sex determination are scare, a year before this study was published, Hall et al. (2015) discovered a male determining factor (M factor) in another disease-causing mosquito, Aedes aegypti.

A zygote is the cell that is formed by the male sex cell (sperm) and the female sex cell (egg). Zygotic refers to the characteristics of these early cells involved in replication.

In other flies, there is a female "default" mode of sex determination. Only a maleness signal on the Y chromosome can initiate the male pathway.

A compound that is required for the activity of a protein; in this case, TRA2 is needed to help tra cut dsx.

The fact that cocaine use accounts for only 9% of the observed variance in avoidance response learning indicates that there are other variables (not taken into consideration) that could influence why CUD patients respond to stimuli that they should be avoiding.

Cocaine causes physiological changes that lead to impairment of brain regions involved in control functions.

Cocaine blocks dopamine re-uptake, leading to overstimulation. Overstimulation affects the way individuals assimilate and learn new information. A lack of control over actions after cocaine dependence makes individuals respond based on habit rather than a structured plan.

The author's findings might have implications for the future treatment of CUD patients.

Cultivating desirable habits or replacing bad ones could be effective treatments for cocaine use disorder patients. Introducing these types of interventions could be essential to reducing one of the major public health problems that we currently face.

Executive impairments refers to reduced function of processes such as memory, controlled response to stimuli, capacity to shift between different topics and tasks, and focus—which regulate and control cognitive functions.

Training that is done to reinforce a particular response.

Describes waste excreted after the digestion of food from the bowels or intestines.

The authors performed a power analysis study, which allows researchers to determine the sample size required to detect an effect, due to the large number of samples with broad characteristics. They first calculated the number of samples needed to determine a difference in microbiota diversity when the cause is unknown. To do so, they need to determine the effect size (the minimum deviation that is considered significant), the significance level (the probability of determining that a condition is true given that it is false), and the power (the probability of determining that a condition is false given that it is true).

Read more: http://www.biostathandbook.com/power.html

A building block molecule, can combine to create polymers.

Aliphatic means that there is no aromatic group on the ester part of this molecule. A p-nitrophenol group is an aromatic ring with an oxygen linked to one carbon and a nitrogen attached to two oxygens linked to the opposite carbon.

When the authors removed l. sakaiensis from sample no. 46, the plastic was not degraded. The authors therefore concluded that I. sakaiensis is responsible and necessary for the PET degradation activity in the sample.

There have been a variety of recent scientific reports focusing on degrading PET. While they are scientifically exciting, Chemical and Engineering News (C&EN News) wrote an article detailing work that needs to be done before such methods could be viable on a large scale.

Read more at C&EN News: https://cen.acs.org/environment/sustainability/Plastics-recycling-microbes-worms-further/96/i25

In 2015, the Ocean Conservancy and McKinsey Center for Business and Environment showed that there will be 1 pound of plastic for every 3 pounds of fish by 2025.

Here is the report in full: https://oceanconservancy.org/wp-content/uploads/2017/04/full-report-stemming-the.pdf

In vitro: takes place outside the organism (in a test tube, culture dish, etc.)

In vivo: takes place inside the organism

Changing the function of an enzyme.

A domain is a section of a protein that has a specific function.

A common method of RNA editing in which the nucleoside adenosine is converted to inosine by the removal of an amino group.

A process when expression of a particular protein is suppressed at the level of RNA.

This is similar to knockout, where the expression of a protein is blocked at the DNA level. Unlike knockout, knockdown can be reversed.

The most widely used method for knockdown is RNA interference.

Cells that are no longer capable of dividing (undergoing mitosis).

Cutting.

Prokaryotes are a class of single-celled organisms with no membrane-bound nucleus, mitochondria, or other membrane-bound organelles.

Examples include bacteria and archaea.

A nuclease is a special enzyme that catalyzes reactions that break down nucleic acids.

A ribonuclease specifically works on RNA molecules.

A type of organic molecule that is made of chains of compounds called nucleotides.

Common examples are DNA and RNA.

Drugs that inhibit the effects of histamines, compounds released by cells in response to inflammatory reactions. These are commonly used to treat allergies.

A redundant covariate is a factor that either has the same value for every sample or multiple factors that are highly correlated and can be used as substitutes for one another. The researchers removed redundant covariates from their study because they can hamper interpretability of the results.

Describes systems consisting of living organisms. Here, the authors believe that interactions between different microbiota communities may contribute to some variation in genera abundance they could not account for.

26 of the 69 (37.6%) covariates found in the FGFP data had a comparable factor in the LLDeep cohort.

Two variables are collinear if they can be predicted from each other accurately, suggesting that they are highly correlated. It is often redundant to have both variables if they are collinear because they can be used as proxies for each other and may hamper interpretation of results.

These drugs might include birth control.

Refers to organisms that convert hydrogen into an energy source.

Plural form of the taxonomic rank, genus.

This paper describes the use of the phylogenetic marker that is used to barcode fungal species. One of the reasons that the yeast symbiotic partner was missed is because this barcode doesn't work for that species.

This paper describes the discovery of the genus Cyphobasidium.

This paper examines the specificity of fungal and algal partners in the lichen symbosis.

Genomic data is used to show that the two main species of Bryoria fungi examined in this work are conspecific, that is they are genomically identical to one another.

This paper used pyrosequencing to look for additional eukaryotic symbiotic partners in lichens, like the one discovered in this paper.

Lichens evolved independently many times as a symbiosis between fungi and algae.

This is a foundational paper that describes how lichen symbiosis arose multiple times through evolutionary history.

The old definition of one fungus with one photobiont was helpful in guiding science's understanding of lichens. Yet, sometimes strict definitions can prevent us from asking good questions. This paper concludes that researchers should always push their investigations further. There might still be interactions we haven't identified in symbiotic relationships.

Any organic substance that is not directly involved in the growth, development, or reproduction of an organism. Vulpinic acid is an example of a secondary metabolite.

A segment of DNA that does not code for proteins and interrupts the sequence of genes.

Multi-template polymerase chain reaction (PCR) is a technique to amplify multiple targets in a single PCR experiment. However, this technique sometimes produces bias and overamplifications in specific templates.

To learn more, check out this seminal paper by Polz and Cavanaugh (1998).

This is the asexual life stage of fungi, where reproduction is achieved by budding of mononucleated cells.

In bright field microscopy, an image is produced by bouncing light off of an object and the image is magnified by lenses. In scanning electron microscopy, an image is produced by bouncing electrons off of an object and the image is interpreted and produced by a computer. By using electrons instead of light, researchers can observe incredibly fine detail in the image created.

The shape or form of an organism.

NGSS Nature of Science: Scientific Investigations Use a Variety of Methods and Scientific Knowledge is Open to Revision in Light of New Evidence

Researchers look at a sample through a bright field microscope to look for evidence of cell morphology that could be basidiomycetes.

The molecular clock can be adjusted (i.e. calibrated) using fossil data from any taxa represented in a rooted phylogeny, in order to put an approximate date on the nodes of a phylogeny.

Recently, new lichen fossils were found, giving us more insight into the co-evolution of lichen symbionts.

https://blogs.scientificamerican.com/artful-amoeba/new-trove-of-lichen-fossils-expands-total-from-15-to-167/

A group of organisms that clusters together on a phylogenetic tree to the exclusion of all other groups.

In this case, meaning an abnormal outgrowth on the Parmeliaceae thalli.

Plural form of the taxonomic rank, genus.

To take a measurement of a sample, usually meaning a biochemical or chemical measurement of a biological sample; in this case, basidiomycete yeasts.

This is a gene that helps stabilize the ribosome. It is found in all living organisms, so this gene is often used in phylogenetic comparisons of different species.

How do scientists learn to ask the right questions about novel data?

Read about the life and academic path of the first author in The Atlantic at: https://www.theatlantic.com/science/archive/2016/07/how-a-guy-from-a-montana-trailer-park-upturned-150-years-of-biology/491702/

After concluding that gene expression in the two symbionts could not account for lichen differences, the authors continued to investigate what might account for vulpinic acid production. The results of the transcriptome analysis indicated that gene expression from a basidiomycete was correlated with the presence of vulpinic acid.

Researchers have compared the genomes of these two lichen species and found that, for the most part, these two organisms have the same sets of genes.

A taxonomic group of any rank, such as species, family, or class.

In a biological sample that contains more than one organism, before gene expression can be evaluated, the researchers must identify which genes belong to which organism. To do this, gene expression data is mapped onto the genomes of the organisms that are known in the mixture, and genes are sorted, or binned, into groups by the genomes they match. This way the gene expression data for each known organism can be determined.

The traits that an organism displays. Phenotype results from the interaction of a genotype with the environment.

The gene sequence that an organism carries.

Next Generation Standards LS3.B Cross cut: Cause and Effect

The authors knew that the difference between these two lichen species was poorly understood. One species produces vulpinic acid, and the other does not. Phylogenetic analysis could not identify differences in the symbionts of the two species. The authors decided to test if differential gene expression of a gene shared between the species might be the cause of the phenotypic difference.

The fungal partner in the lichen symbiosis.

A transcriptome sample that is taken from a collection of organisms. mRNAs must be mapped onto each of the genomes from the organisms in the sample in order to figure out which gene came from which organism. In some cases, there is not a genome available for mapping and instead mRNA is mapped against a large database in order to find a close relative and guess where the mRNA could have come from.

In a laboratory setting; that is, outside of their normal biological context.

Resistance, in this case.

Denotes a laboratory culture that is free from living organisms other than the species required. In this case, lichens could not be formed in a laboratory using only the two known species.

Researchers have tried to create a lichen in the laboratory by only mixing an algae and a fungus known to produce lichens in the wild. These attempts were not successful as the cortex layer did not develop.

Next Generation Standards LS1.A: Structure and Function LS2.A: Interdependent Relationships in Ecosystems

AP Biology Standards EK2.D.1: All biological systems are affected by complex biotic and abiotic interactions.

A type of symbiosis in that the relationship is beneficial to both organisms involved.

A 60-second podcast on the findings of this paper from Scientific American at: https://www.scientificamerican.com/podcast/episode/for-lichens-3-s-not-a-crowd/

The outermost layer of the lichen's thallus, where the lichen comes into contact with the environment.

Two's Company, Three's a Lichen?

Read more about the results of this study in The New York Times Science column at: https://www.nytimes.com/2016/07/22/science/lichen-symbiotic-relationship.html

Organisms, often fungi or bacteria, that live within a plant.

A specific statistical method that compares the proportions in a group of samples against those of another group of samples.

The authors found that the enzyme (ISF6_4831 protein) they determined was responsible for degrading PET in l. sakaiensis was better at degrading PET than its ability to degrade other molecules, in this case paranitrophenol linked aliphatic esters also called pNP-aliphatic esters, that don't look like PET.

Furthermore, the authors saw that other enzymes that are known to sometimes degrade PET degraded more pNP-aliphatic esters relative to PET than this new enzyme ISF6_4831. This led them to include that ISF6_4831 was specifically specialized at degrading PET.

Thus, the authors begin referring to the ISF6_4831 protein as PETase.

Using genetic engineering, the authors isolated the protein strand the two organisms had in common and exposed it to a PET film without any microbes present.

Commonly accepted. In this case, the hydrolase from Thermobifida fusca is already known to break down PET.

Plastics are wreaking havoc to ecosystems all over the planet. An ecologically harmless solution for plastic recycling is desperately needed.

Learn more from this 2012 case study created by Montana State University: https://serc.carleton.edu/NAGTWorkshops/health/case_studies/plastics.html

The authors added more protein to a sample of PET. The three previously discovered enzymes produced more product as the enzyme concentration increased. The new enzyme, PETase, did not increase the amount of product as more enzyme was added. The authors concluded that this was because PETase was attached to the film. So adding more enzyme once the film was already covered would not increase the rate.

The authors exposed all of the enzymes to the different oligomers and measured the activity of each enzyme. The other enzymes did a better job of degrading substrates without aromatic groups, but ISF6_4831 did the best job degrading PET. From these results the authors concluded that ISF6_4831 had high specificity towards PET.

The authors found a part of I. sakaiensis's DNA that had 51% of the same patterns found in another protein known to degrade PET. They concluded that this stretch of DNA also made the protein that allowed l. sakaiensis to degrade PET.

In 2015, J. R. Jambeck et al. calculated that about 8 million tons of plastic make it into the ocean each year.

A previous study measured the amounts of VOCs present in outdoor air in Pasadena, California from 15 May to 15 June in 2010. The research included both measurements on the ground and measurements via aircraft.

This study is using those measurements to test their model.

R-squared (\(R^2\)) values represent how close the data points are to the predictions from a model. An \(R^2\) value of 1 means that all of the data points lie on the prediction from the model. In this case, the researchers are using the solid line that represents perfect agreement between the box model calculation and the experimental data. An \(R^2\) value of 1 in this case would mean that the box model calculations and the experimental data are in perfect agreement. In general, the closer the \(R^2\) value is to 1, the closer the model and data match.

Without the inclusion of VCPs in the model calculation the \(R^2\) value was 0.59 (Panel A of Figure 3). With the inclusion of VCPs into the model the \(R^2\) value improved to 0.94 (Panel B of Figure 3).

One possible explanation of why some temperate species' ranges would expand with climate change is that these species evolved in the tropics, and have not lost a high tolerance for heat, even as they moved further north. Therefore, even as temperatures heat up in the southern regions of their current ranges, these temperature still do not approach their ancestral tolerances, and species can continue to live there. This could explain why species in the tropics are currently suffering under warming climates; the increase in temperature is surpassing their ancestral heat tolerance.

Whitehorn and colleagues took laboratory colonies of a common European bumblebee species (Bombus terrestris), and exposed them to levels of neonicotinoids similar to what they might be exposed to near a farm field. They found that colonies exposed to these levels had slower growth rates and produced less queens than "control" colonies that were not exposed.

Every living organism has certain traits. For example, reptiles have scaly skin, birds have feathers, mammals produce milk, and so on. These traits are inherited from the organisms' parents, of course, but ultimately, those traits tend to remain similar across very large periods of time.

We can trace how traits change over evolutionary time scales, and show that some traits tend to remain quite similar, even though a huge amount of time might have passed. Traits like a species' tolerance to heat are like this: This trait tends to remain similar across evolutionary time, despite the fact that a species might evolve and change in many other ways, even splitting into two or more different species. In other words, it's hard to evolve tolerance to hotter temperatures—at least for many species.

In one study, Chen and colleagues put together a huge analysis of 1367 species from the United Kingdom and some other places around the world. Those authors looked at whether the places those species were found had changed over time. On average, those species were shifting toward cooler areas at about 17 kilometers every 10 years. They were also shifting upward in elevation by about 11 meters every ten years, reflecting the fact that it is generally cooler at higher elevations than at lower elevations.

The Chen study is called a meta-analysis, where they take results from many other studies and put them all together into one big analysis. That work focused especially on butterflies, which are very sensitive to climate change, but it did not include critical pollinator species, like bumblebees.

Latitudinal range limits are the northernmost and southernmost edges of where a species can be found.

Thermal range limits are the hottest and coldest places of where a species live.

A Framework for K-12 Science Education: Disciplinary Core Ideas, Practice ETS1.A: Defining and Delimiting an Engineering Problem.

In 1997, Andrei Broder invented MinHash, which is a type of LSH that allows a user to quickly estimate how similar two data sets are. In his seminal paper on this topic, Broder discussed the math behind this idea and applied it specifically to the process of comparing two documents on the internet.

This symbol means "much less than."

When a vector is d-dimensional, d refers to a placeholder value that could stand for any integer, depending on how many feature values are associated with each image.

Hashing is used in computer science to reorganize large data sets (regardless of their size) into tables of fixed size. During this process, multiple data points will typically be stored in the same bin (or hash) based on how similar they are. The hash is then represented with a shortened name, or key, that takes up less storage space in the computer.

In other words, this process helps compress the data so that a computer can use it more efficiently. It also makes it easier and faster to look up data in the table.

![] (https://upload.wikimedia.org/wikipedia/commons/5/58/Hash_table_4_1_1_0_0_1_0_LL.svg)

Here, the authors use chemicals (ethanol, methanol, and dimethyl sulfide) to demonstrate similarity tagging/hashing.

Common Core State Standards English Language Arts-Literacy, RST 11-12.6: Students should be able to explain why the authors provided this example in the paper, specifically addressing how it adds to the reader's understanding of the research.

http://www.corestandards.org/ELA-Literacy/RST/11-12/

A simplified and symbolic representation of elements in a system. Here, the authors use a schematic to represent cell types in the fly olfactory circuit.

A grouping of neurons organized to process specific kinds of information.

Two factors that help determine how well a species will track climate change are dispersal (how well the species can move to new areas and start new populations) and persistence (how well the species can maintain and grow these new populations).

From analysis of aerial surveys, Gehrig-Fasel and colleagues found that about 4% of upward shifts in tree line (i.e. trees growing further uphill than previously) from 1985 to 1997 could be attributed directly to climate change. The rest were attributed to changes in land-use.

Cameron, Hines, and Williams used DNA sequence data on 218 of the 250 currently known bumblebee species to create a phylogeny (phylogenetic tree).

Using museum records, Bartomeus and colleagues found that bumblebee species richness in northeastern North America has decreased significantly since 1877.

More recently, a 2017 study found that one third of bumblebee species are in decline.

Goulson and colleagues review the various global change drivers that are causing declines in bees, and by extension their pollination services.

This infographic from their study shows some of the main drivers and how they may interact together. (c) Goulson et al. 2015

By modelling the probability of extinction for lizards in Mexico, Sinervo and colleagues found that unabated climate change would result in the extinction of 58% of species in the Schleporus genus. They determined that increasing temperatures forced Schleporus lizards to spend more time in cool refuges avoiding the heat, therefore limiting time for foraging and reproduction, and reducing population growth rates. They also found that high-elevation species were particularly at risk from increased competition as low-elevation species moved higher.

Most species that have been studied so far are expanding further north as climate warming makes these areas habitable for them, but are still able to tolerate to increasing temperatures in the equator-ward regions of their ranges. In other words, it appears that climate change has helped many species increase their total range sizes! (Although it likely still affects their ability to live within these expanded ranges.)

As we can see in Table S3, the land-use and pesticide variables were not useful in predicting range shifts.

See the Supplementary Materials for more information.

The VOC measurements were part of a large community-wide effort by atmospheric scientists to better understand issues posed by air pollution and climate change in California. A link to the field study (including a white paper and policy-relevant findings) can be found at: https://www.esrl.noaa.gov/csd/projects/calnex/.

Behaviors that can help someone escape uncomfortable feelings and unpleasant situations (such as electric shock).

Behaviors that someone develops as a way to respond to their environment, but that end up causing them harm instead of good.

Not smoothly rounded. The particles would have blunt, not sharp angles.

Soil composed of clay and sand that contains decomposed organic matter (leaves, grasses, etc.).

Photogrammetry is a 3D measuring system that uses photographs. In this study, the Laetoli footprints were measured and photographed from two different locations. Lines of sight were developed from each camera to points on the footprint. The lines of sight were then used to mathematically produce 3D coordinates of the points of interest.

Faults are cracks in Earth's crust due to movement. Fractures are cracks in Earth's crust along which there is no movement. A fracture is called a fault when stresses cause the rock surfaces along the fracture to move in opposite directions.

The discovery of the first Laetoli trail during an expedition led by Dr. Mary Leakey helped to settle one of the great paleoanthropological debates. Some argued that upright posture and bipedalism had to evolve before the hands would be free to make tools. Stone toolmaking was thought to be the critical factor in the evolution of hominins. The analysis of hominid bones could not provide the answer. The discovery of the Laetoli footprints provided evidence that dated bipedalism to 3.6 million years ago. The earliest stone tools are known to be around 2.6 million years old. The feet came first.

An extinct hominin species that lived between 3.9 and 2.9 million years ago. It is one of the longest lived and best known early human species.

Hear one of the authors of this paper, Marco Cherin, discuss the findings of this research in the eLife Podcast.

Referring to the highest point of the thigh bone, called the femur.

An area where fossils of prehistoric organisms can be studied.

An area of land that is saturated with water, either permanently or seasonally.

Carbon Dioxide gas.

A wetland that is dominated by leafy rather than woody plant species and is predominately freshwater.

A daily time series model used in ecosystems to simulate influxes of carbon and nitrogen between the atmosphere, vegetation, and soil.

Parts per million.

Carbon.

Flooding.

Very moist or containing large amounts of water.

Land-based.

Will not lose carbon (which is actually bad).

NEE stands for net ecosystem exchange, referring to the ecosystem's carbon cycle.

GEE stands for gross ecosystem exchange, referring to the ecosystem's carbon cycle.

The dry season in the Everglades is typically November through March.

Here, the authors explains how they ran different scenarios in the simulation system with the data they had collected in the field, making for more realistic results.

The highest temperature which will allow for production.

The temperature which is best for production.

These data collected from 1963-2012 wereinputted into the DAYCENT system to simulate conditions during the next 100 years (from 2000-2100).

This table shows the two different sites, Taylor Slough (TS) and Shark River Slough (SRS) along with their exact location using the coordinate system, characteristics of each site, such as root:shoot ratio, soil composition, depth of roots, Nitrogen deposition along with the amount of Carbon found at each site.

A freshwater organism that is attached to plants above the bottom of sediments.

A C4 plant has light dependent reactions in its mesophyll cells and the Calvin Cycle in the specialized cells around the leaf veins. The 4-carbon organic acid, oxaloacetate is fixed from CO2. This is carried out by PEP carboxylase.

Most types of plants are C3, meaning that it does not have photosynthetic adaptations to reduce photorespiration. It utilizes the Calvin cycle.

The seasonal pattern of water levels in a specific wetland. Typically a wetland's hydroperiod is unique "signature" of that specific wetland.

A process where plants take up oxygen and give out some carbon dioxide.

SPAC for short, is the pathway for water moving from soil through plants to the atmosphere.

Environmental pollution usually caused by human activity.

Meter, measure of distance.

Gram, measure of weight.

Degrees Celsius, measure of temperature.

Seasonal pattern of the water level of a wetland.

Intergovernmental Panel on Climate Change, a scientific and international body of experts under the United Nations.

The scientific study of the movement, distribution, and quality of water.

An area or ridge of land that separates waters flowing to different rivers, basins, or seas.

The process in which living organisms are said to have developed and diversified from earlier forms in the past.

A species distinguished from others by its morphology —that is, its form/structure.

In ecology, refers to when new individuals join the population.

Stands for diameter at breast height, which is the standard method of measuring tree trunks at the height of an adult's breast. It is now standardized to 1.3m above the ground.

Phrase that describes deductive reasoning made without reference to facts or experience, presumptive.

Also known as ecosystem functions, these are the biological, geochemical, and physical factors that take place in every ecosystem (including water, nutrient, and energy cycles).

Services are the benefits that people gain from nature.

The Aleutian Islands were chosen to be the place of study for many reasons, the main one being the similarity between the individual islands in the chain. The islands are of fair size, with similar soil makeup and weather. There are also numerous islands making the sample size large enough to be used for replication and to ensure the results were not due to chance. There was also the curious distribution of fox introductions that directly lead to a split in islands by type: fox-free vs. fox-infested.

In the paper by Terborgh et al., the different views on trophic cascades are investigated: top-down where predators limit herbivores and therefore prevent large destruction to vegetation, whereas bottom-up looks at the effects of plant defense in keeping predators at bay. This study touched upon the idea of top down interactions with the predation of seabirds by foxes having effects on plant communities, but in a more indirect way.

Relating to Earth or an organism residing on land. In this experiment, the foxes and plants are terrestrial organisms.

The birds of a particular geographic region, in this case seabirds such as; the lapland longspur and song sparrows that are being reduced by fox populations.

It would be more accurate to say that the models used to describe physics had to be modified.

As physics progressed, physicists revised their theories in light of new evidence and knowledge (and they continue to do so today). Here, Einstein describes how the special theory of relativity came about, in part, to solve the problem of classical mechanics' compatibility with electromagnetic theory.

Modern physicists consider classical mechanics an approximate theory that is useful for the study of non-quantum mechanical, low-energy particles in weak gravitational fields. It is usually the starting point for students learning physics.

A group of scattered islands within a larger body of water. In this case, the Aleutian archipelago is a grouping of volcanic islands located in the Pacific ocean that are under the possession of both the United States and Russia.

The total mass of an organism or multiple for any given area or plot. Usually refers to dried mass of plant matter from above or below ground.

Categorical feeding positions of groups of organisms in a food chain or web. Some common trophic levels would be primary producers (grasses), primary consumers (birds), and secondary consumers, (birds or foxes).

Following LaJeunesse and Trench's 2000 publication on DGGE, this work expands on the applications, effectiveness, and usefulness of DGGE -a technique that separates DNA fragments.

This work was used in this research since it is based on a characteristic molecular region in the Symbiodinium species.

Dr. Rachel Levin and her team of researchers may have found a solution to minimize coral bleaching, which is caused by ocean warming and is a huge threat to coral reefs. She proposed a way to genetically modify Symbiodinum (a group of microalgae in corals) such that they may increase their stress tolerance to changes in ocean temperature and inherently save coral reefs.

Read more in the Science Daily: https://www.sciencedaily.com/releases/2017/07/170720095111.htm

Reviews the technique denaturing gradient gel electrophoresis (DGGE) and how it is used for molecular identification.

Gives background information on different types of amplification techniques used to determine molecular identification.

Prior to the introduction of molecular techniques, early work such as this reference discusses dinoflagellates and how they were thought to belong to one pandemic species.

Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

This reference explains why there are so many types of Symbiodinium.