The authors acknowledge that these early-life events may affect microbiota development during infancy, but did not observe an effect of these events on the microbiota composition at adult age in their cohort.

When clustering the data based on taxonomic characteristics, one subset was predominantly female, having lower weight and low Bristol stool scale score and a longer time since last defecation. These individuals showed more equal and higher quantities of different microbial taxa.

The authors could not find any correlation between the presence of Fusobacterium and the set of 18 nonredundant covariates, suggesting that its presence is specifically associated with colorectal cancer.

The researchers wanted to ensure that the phenotypes of interest were not falsely correlated with microbiota genera. To avoid overfitting, they reduced the phenotypic data in different stages. By approaching the problem in a series of distinct stages, the researchers could determine the most important variables that affect the abundance and diversity of gut microbiota.

Researchers found that as both males and females age, the number of genera increases. However, age was negatively correlated with abundance of core genera.

In October 2010, Google announced that its self-driving vehicles had collectively driven more than 200,000 kilometers (about 124,000 miles) on actual roads in California.

The authors note that there is a large gap in their confidence interval, which indicates that there is not public consensus. They point out that this is because autonomous vehicles are a relatively new issue, so different people have thought about it more or less.

As people get used to the idea and think about it more, the gap is expected to narrow.

Outcome on the whole community, not just individuals.

Again, the researchers found that participants thought self-sacrificing AVs are good for other people but would not want to buy one for themselves.

Even though the situations where AVs would sacrifice their passengers are rare, these are emotional events that would have a large influence on the public despite their infrequency.

In 2007, the Defense Advanced Research Projects Agency (DARPA) hosted the DARPA Urban Challenge, which called for self-driving vehicles that could navigate a realistic city environment, and obey traffic rules while doing so.

The requirements for the challenge included passing slowly moving cars, merging into fast traffic, and parking in a parking lot.

Researchers have developed a new set of software that decodes ultrasonic rat vocalizations, including those that come from tickling!

Check it out with this video from Verge Science.

test

AAAS Annual meeting

Beth, Shelby, and I will be in the AAAS Lounge starting at 10am on Friday.

If you are interested in science communication, annotation, or just passionate about connecting students to #ActualLivingScientists, come see us!

SitC

Throughout this paper, the researchers have been making the claim that activity of the NPF system signals the fly's "reward state." According to this theory, when the fly experiences something rewarding (such as mating), the amount of NPF in the brain and the activity of associated neurons increases, which in turn leads to a reduced urge to seek additional rewards (such as alcohol). To this end, they have shown that there is an increased amount of NPF in the flies' brains following mating. However, if their theory were true, then the opposite should also be observed. That is, the consumption of alcohol should also increase NPF levels in the brain, since alcohol is also a source of reward (just like mating).

To test this hypothesis, the researchers decided to measure NPF levels after exposure to both air and an alcohol vapor (the former being neutral/not rewarding, and the latter being rewarding). If their theory about NPF generally signalling reward were true, one would expect to see increased levels of NPF in the brain following exposure to alcohol (just like was observed following mating in Figure 2A).

Since past work in Drosophila, mice, and C. elegans has shown that altering NPF/NPY can affect how organisms react to alcohol, the researchers in this study hypothesized that sexual deprivation might lead to changes in levels of NPF in the flies' brains, which in turn caused them to consume more alcohol. To test this, they extracted the brains from male flies with three distinct sexual histories (mated, virgin, and sexually rejected), and measured their NPF levels.

All neuropeptides in the brain work by attaching to specific receptors found on the surface of cells. Think of the cell surface as a wall, the receptor as an electrical outlet, and the neuropeptide as a plug. In order for the neuropeptide (plug) to have any effect, it has to successfully attach to the correct receptor (socket). Furthermore, a particular neuropeptide (say, a three-pronged plug) cannot attach to just any receptor (for example, a two-pronged socket). The receptor and the neuropeptide have to match in order for the system to have any effect.

Since cis-vaccenyl acetate (cVA) is used by females to turn away unwanted mating attempts by males, it is only released by females who have already mated. Virgin females, who may still be looking to mate, do not release this chemical cue. This difference raises the possibility that the increased preference for alcohol amongst the rejected males could be because they smelled this chemical cue (which the mated male flies would not have smelled).

To test this possibility, they exposed the virgin male flies to dead female flies. These virgin males were still exposed to the visual cue of a female fly (especially the rear half of the body where mating occurs). However, they were neither able to mate, nor were they exposed to active rejection by a female.

For the first follow-up experiment, the researchers ensured that both the mated male flies and the virgin male flies were housed in large groups (consisting exclusively of other male flies). This was done to see if social isolation (as the virgin male flies in the initial experiment might have experienced) might have been the cause for the alcohol preference.

The researchers found that when given a choice between normal food and alcohol-mixed food, male flies who had mated with female flies did not prefer the alcohol, whereas male flies who had been rejected by the female flies did prefer the alcohol.

To test the effect of sexual experience on alcohol consumption, the researchers first had to create two groups of male flies, each with a different sexual history. They did this by allowing one group to mate freely with multiple different females for four days. This became the "mated-grouped cohort." The second group was only exposed to female flies who had already mated. Female flies who have already mated once will not mate a second time until they have laid their eggs. For this reason, the second group of males experienced repeated sexual rejection by the mated females for four days. This became the "rejected-isolated cohort." These two cohorts, (one mated and the other sexually rejected) could then be tested for the differences between them.

The authors used "depletion scores" to compare nucleases. A depletion score quantifies how much expression was reduced by a specific nuclease. The higher the score, the more expression was "depleted."

A type of vector that can use the cell's protein synthesis machinery to express the genes that it carries.

Creating genetic mutations.

Testing a material to figure out its composition and quality.

Remains aren't the only type of archaeologically significant findings. Recently, cliff drawings were found in northwest Saudi Arabia depicting hunting dogs wearing leashes. These carvings date back to more than 8000 years ago, making them the earliest depictions of dogs ever found.

Read more in Science Magazine: https://www.sciencemag.org/news/2017/11/these-may-be-world-s-first-images-dogs-and-they-re-wearing-leashes

Scientists studied the mitochondrial DNA of 654 domestic dogs and 38 wolves, and were able to separate the dogs into four main clades (A, B, C, D), groups that contain an ancestor and all of its descendants. A fifth clade, E, was a very small, isolated group.

Three tools for mining the data for ancestry information.

Principal components analysis (PCA) simplifies the data. The number of variables is reduced but the trends and patterns are retained.

D-statistics detects admixture events; it is used to detect gene flow between closely-related species.

TreeMix is a genetics computer program used to estimate ancestral relationships. It can detect population splits and migration events.

Refers to the earliest stage of the time period known as the Stone Age. The Paleolithic period ran from approximately 2.6 million years ago all the way up to about 10,000 B.C.E.

Wang et al. studied the genomes of 12 gray wolves, 27 ancient dog breeds, and 19 diverse dog breeds from all over the world. They discovered that dogs from Southeast Asia have higher genetic diversity and their DNA is less mixed, meaning that they are the most related to wolves; they estimate that domestication occurred there 33,000 years ago. Dogs were isolated to this region for several thousand years, and about 15,000 years ago they migrated to other parts of the world.

In 2000, Ellstrand and Schierenbeck proposed hybridization as a catalyst for the evolution of invasion.

This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.

This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.

The ultimate summary of the whole paper. It explains why there needed to be side experiment analyzing different variables that would then clarify the conclusion that supports the given hypothesis.

In this study from 2009, the results of diversification, when subpopulations with independent genetic modifications emerge, were concluded not to be homogenous in their relation to performance. This concept is further analyzed through this experiment in the speciation and the variation of defense strategies.

The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.

This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.

The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.

Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.

The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.

This is explaining how the variation of herbivore species is closely related to the variation of plants in the location. The study explains how certain insects prefer to ingest other substances that can be identified, allowing the experimenter to see how the insects lived in accordance to where the plants where, instead of plants appearing around certain species of insects.

The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.

When doing comparison, it helps to create a table to have a better understanding on the differences in leaf defense.

This was done to determine the different variables that affect insect populations and which ones were more important than others. With this information they set the parameters to create an observable experiment with a limited amount of discrepancies.

Main goal for the paper.

The main point the author is trying to make here is that there is a direct correlation between increase in plant defense and increase in land covered by plants as well as speciation of plants. He also explains that due to the expansion, rapid evolution of defenses begin to take place. The herbivores eating these plants do differ in tactics from region to region, increasing the amount of different defense strategies in the plants. He explains an alternative viewpoint stating that predators do not influence speciation much, therefore defenses are similar amongst most plants.

This statement addresses the variables that must be acknowledged when trying to analyze different plants and their different defense strategies. The "resource limitation across habitats" that the author is referring to is what in the environment can the plant use to defend itself in its habitat from threats such as herbivorous insects.

Herbivorous insects are constantly eating plants, creating competition between the plants and insects. What is stated here is that optimal defense may be impacted by the plants environment, giving it access to certain nutrients and materials needed to produce the desired defense mechanism, such as poisonous leaves or indigestible tissues.

http://onlinelibrary.wiley.com.ezproxy.fiu.edu/doi/10.1890/12-1920.1/full#i0012-9658-94-8-1764-Coley2

The idea in place here is the observation of evolution in herbivorous in correlation to the environment and all its factors.

The study provides proof of evolution in herbivorous in respect to the environment by analyzing adaptive radiation. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous.

To further understand adaptive radiation watch [(https://www.brightstorm.com/science/biology/evolution/adaptive-raditaion/)

The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.

The sources mention, that in a habitat with a low amount of productivity there is a good amount of strong plants/ plants that are "rich in chemical defenses". In a habitat with lower productivity, the plants are thought to do this in order to increase its life span. Therefore, as the productivity and the amount of herbivores changes the strength and and amount of the resources changes.

For more information check out: Tropical Blackwater Rivers, Animals, and Mast Fruiting by the Dipterocarpaceae

In Africa, there is a food crisis leaving millions of people without corn, a very important crop for Africa. The reason for these crops not being edible is that a certain species of worm invaded a field of corn and rapidly spread to neighboring farms, killing millions of corn crops leaving thousands hungry. This proves the point how insects differ from each-other depending on what type of plants are around, since this worm is always flocking to this one crop.

The reciprocal transplant experiment is an experiment where organisms from two or more environments are introduced to each other.

The experiment is commonly used to test how well the organisms adapt, and sources of growth variation (genetic or environmental).

Relating to the form or structure of things, having to do with somethings physical appearance/structure.

Referring to something's qualities, not numerical but categorical. Can be described with words, not numbers.

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

Pubescence in this context means small hairs or short down on the leaves and stems of various plants.

A genotypes ability to change as an adaptation to the environment. This refers to the plant's distribution of resources.

Regression analysis is a statistical model made up up of a series of processes used to understand how the dependent variable changes when any of the independent variables are modified.

http://www.discoverlife.org/nh/tx/Plantae/Dicotyledoneae/Burseraceae/Protium/subserratum/images/Protium_subserratum,_baby_leaf_bottom.JP80262_88.320.jpg

The Protium subserratum Engl. is the name of a species that has distinct defense mechanisms and is in the genus Protium, which are flowering plants in the family Burseraceae.

Parapatric distribution refers to a distributional pattern where pairs of taxa are partially overlapping or have separate but adjacent distributions, typically along common boundaries.

incipient meaning the beginning of a process and speciation is the diverging of similar species into two or more differing species due to evolution

Having to do something to both side, the bearing or binding of 2 parties equally.

Describes different sides in comparison to each-other, a gradient can be in reference to water pressure as well as many other things.

An example of this defense is how a monarch butterfly caterpillar holds on to a milkweed's toxins to then use it for their own protection and survival.

The over all number of differing variations in the region.

A progressive change over time of the nonliving factors that make up an environment examples of nonliving factors in an environment would be altitude, temperature, depth, humidity etc.

Habitat-mediated speciation is the emergence of different species throughout evolution, brought about by the natural environment and its effects.

Chlorophyll is a green pigment that is found in the chloroplasts of algae and plant cells. It works well to absorb sunlight which is then used to make carbohydrates, through a process called photosynthesis.

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

Chrysomelid beetles are commonly known as leaf bugs. Their food course are leaves .

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

Allocation refers to the distribution of something for a specific purpose.

Plant defense allocation is one of the ways a plant can protect itself, its resources and reduce the impact of herbivores.

Posits are statements or arguments that are assumed to be true.

Herbivores are animals who get their energy by eating plants.

Flora refers to the diverse plant life that is within a specific region, or time period.

In this case, it's the plant life in the tropics; tropical flora.

Has evolved in some way.

any kind of living organism that is not native to an ecosystem and causes harm. They can harm the environment, the economy, or even human health.

An organism that benefits from living from a host which is another organism.

having a common ancestor.

early stage of development

Reproduction without a male and female.

proteins that have carbohydrate groups.

An organism that can make food.

All the genes expressed by mRNA

means preserved.

In this case, RNA and DNA are aligned to facilitate gene expression.

a complete set of genes that carry information in an organism.

an animal that does not have a backbone

means a living organism that is multicellular.

Looking at phenology through generations can aid us in understanding how the globe is changing. The video linked below shows how recording events can help humans connect and interact with biotic communities. URL: http://climatewisconsin.org/story/phenology

The authors cited performed studies that ants are a very important predators in tropical forest ecosystems.

These are the parameters made to make sure that the experiment itself is not biased and there are different variables being tested.

Authors found out in the field that the sheer caterpillar size was a mechanism of defense to against predators.

A defensive organ found in all papilionid (from the family of Swallowtail butterflies) larvae, in all stages.

To become a pupa.

Based on species abundance, the Pseudomyremx gracilis received the highest score.

The presence of greater variability (statistical dispersion) in a data set than would be expected based on a given statistical model.

The planning, implementation, and coordination of the details of a business or other operation.

Overall, 0.5 hectare gentry plots were the best method.

Figure 1 shows how the coefficient of variability changed for the different types of plots used. The use of smaller plots had a smaller CV meaning that the results had low variance and did not stray much from the standard deviation compared to the larger plots.

It was found that the plots that were smaller than 1 hectare had better results than the plots that were larger (1 hectare).

MCMC methods are a class of algorithms for sampling from a probability distribution. By constructing a Markov chain, a sample of the desired distribution by observing the chain after a number of steps.

TDDs are negative when over zero degrees celcius (thawing) and positive when under zero degrees celcius (freezing). Best for comparing arctic temperatures across specific time periods.

http://psc.apl.washington.edu/nonwp_projects/landfast_ice/freezing.php

Herbaceous (having no stem above ground) plant with grass-like features.

It may take a lot of work to study plants at extreme environments like the tundra. Remote sensing facilitates the studying of plants without having to come in contact with them.

Watch this video by MonkeySee https://www.youtube.com/watch?v=sBI3MIbzIBA

National Science Foundation – Ecosystems. Causes and implications of dry season control of tropical wet forest tree growth at very high water levels: direct vs. indirect limitations (CARBONO - VERANO project).

National Science Foundation – Polar Programs. Arctic Observing Networks: Collaborative Research: Sustaining and amplifying the ITEX AON through automation and increased interdisciplinarity of observations (AON)

NSF-Arctic Natural Sciences. Collaborative Research; cold-season gas exchange of arctic plants - resolving winter carbon and water balances of Alaskan arctic tundra (Coldseason project).

NSF -IPY Arctic Observing Networks Study of Arctic ecosystem changes in the IPY using the International Tundra Experiment. (ITEX-IPY)

DOE-NICCR. Response of carbon dioxide, water, and energy exchange of peat and marl wetlands in the Florida Everglades to changes in hydroperiod (Evergladesflux).

NSF-Biocomplexity. Biocomplexity Associated with the Response of Tundra Carbon Balance to Warming and Drying Across Multiple Scales. Barrowbiocomplexity (this project has sunsetted). Effects of increased season length on plant phenology, community composition, productivity, and ecosystem carbon fluxes in Alaskan tundra Season project (this project has sunsetted)

Carbon stockes and fluxes in a tropical rain forest in Costa Rica Carbono project

NSF- Integrated carbon program. Understanding interannual NEE variability in a tropical rain forest using constrained estimates of carbon exchange. S.F. Oberbauer, D.A. Clark, M. Ryan, D.B. Clark. Carbono-Towers

National Science Foundation - Biocomplexity of the Environment Coupled Biogeochemical Cycles. Complex interactions among water, nutrients and carbon stocks and fluxes across a natural fertility gradient in tropical rain forest. (CICLOS PROJECT).

Spatial and temporal abundance patterns relate to the study. Temporal abundance pattern has to do with quantity over a period of time and spatial abundance patterns have to do with quantity over a particular area of space.

Temporal monitoring is monitoring that is conducted over time.

Focal species are species that are extremely sensitive to the changes in an environment.

This question sheds light on a topic regarding the suitability of marine reserves not only as a permanent safety harbor for recovery and expansion of the species but also the temporary inhibition of the space by species that are mobile, whether they would use the space to breed for protection or for a stable source of food and shelter.

A study in 2 June 2009 conducted by Philip P. Molloy explored the relations with the age of the marine reserves and of the recovery of different species of fish. The studies showed that older marine reserves (15 years and older) were more effective than younger ones. They harbored more fish.

Side-fidelity, also known as philanthropy, is the likelihood of a particular organism to stay in a set habitat, or to return to it. There are many reasons to this, such as breeding and food abundance.

Discolored red patches of coastal waters caused by harmful algal bloom.

the study of cyclic and seasonal natural phenomena, especially in relation to climate and plant and animal life.

Thermal inertia is the ability of a body or object to maintain its temperature when ambient temperature changes. Larger objects have higher thermal inertia, so larger fish lose heat more slowly than smaller fish. Larger fish also have larger hearts, which can pump more blood.

is a suitable gauge for assessing the environmental influence on fish biological performance (Fry 1971)

The increased temperature range allowed the tuna to forage and obtain energy more efficiently.

Isothermal Layer Depth

Sea Surface Temperature

Information relative to the space and time of the tagged fish.

Lower energy intake during migrations.

The quality or state of being diverse in character or content.

insert (something of a different nature) into something else

A big tuna (large body size) requires more energy which means it needs to feed from a higher amounts of prey or big preys. Consequently, the heat production is higher provoking a thermal excess.

California Current Large Marine Ecosystem (CCLME), along the Mexico and California coasts

Stands for Heat Increment of Feeding.

Located in the abdominal cavity.

By analyzing the temperatures of digestion in bluefin tuna, the author can draw conclusions as to what the tuna is eating, how much energy is gained from the meal, and how often the tuna eats. HIF means heat increment of feeding.

Until now or until the point in time under discussion

Internal organs within the main cavities of the body.

means having many curves or turns.

authorization of feeding.

The Pacific bluefin tuna are smaller than the Atlantic bluefin tuna. It reaches the maximum length of 3m and a maximum weight of 540kg.

express or measure of quantity.

means gathering or collecting.

conditions under which an animal lives

Read More: In vitro seed germination and seedling growth of an endangered epiphytic orchid, Dendrobium officinale, endemic to China using mycorrhizal fungi (Tulasnella sp.)

Tan et al. 2014

http://www.sciencedirect.com/science/article/pii/S0304423813005578

Graph illustrating the loss of terrestrial carbon.

Image illustrating the various sources of carbon observed in the experiment.

Effects of Nutrients on Stream Ecosystems

Within an ecosystem, there are external factors which may threaten the balance. Effects on stream ecosystems are heavily influenced by nutrients. Phosphorus, nitrogen, and carbon balance is essential to keep the ecosystem consistent. When carbon is released from the streams, it does not easily re-enter and goes into different forms. An excess of nutrients and the lack of standards for these ecosystems may be detrimental. Why is it important to conduct such research? Why is it important to care for and monitor other ecosystems?

An important paper that shows the role of glue-like polysaccharides in filling the spaces between fungal cells and holding the lichen together. The yeasts described in this paper live in this filler zone.

This paper highlights the possible role bacterial symbionts might play in lichen formation and maintenance.

This review discusses how lichens develop, their structure and function, their growth patterns, and how thalli are differentiated.

Researchers had previously noted the presence of secondary metabolites in the lichen cortex. The researchers initially looked for a correlation between the main fungal species (lecanoromycetes) and the production of these secondary metabolites, but could not determine a correlation.

Perhaps this is easiest to understand with a picture. If you look closely, you can see two layers within the cortex. Photo from University of California Berkeley's Museum of Paleontology.

AP Biology Standards EK1.A.4: Molecular, morphological, and genetic information of existing and extinct organisms add to our understanding evolution. Biochemical and genetic similarities, such as DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.

The sexual life stage of the fungi where cells become polarized, or have two obvious ends, and through cell division form long structures called hyphae. In some fungi, the individual cells are multinucleate. Only some fungi are capable of this form of reproduction; for example, baker’s yeasts used in beer fermentation are not able to grow this way.

A molecular probe is created against a specific DNA sequence, in this case rRNA from either ascomycetes or basidiomycetes. The probe is designed with a recognizable tag on the end. Then a second probe is used to match the first probe, and finally a third probe to match the second one with a fluorescent tag on it. By using multiple probes we can amplify even the smallest signals to our first probe. These probes are then mixed with a biological sample that is fixed in place. If fluorescence is observed the probe has found a target.

In some experiments, as in this example, researchers use multiple probes in a single experiment. This provides information about how close two organisms of interest are in a given sample.

Often researchers only publish a single gene for a newly described taxon, as it is sometimes too expensive to generate sequence information for the entire genome. When research first began working with DNA sequence data to determine evolutionary relationships it was decided that the ribosomal DNA (rDNA), shared by every living thing, was the best single gene to determine evolutionary relationships between taxa. Currently this is hotly debated, however, the use of rDNA is still very common in eukaryotic taxonomy.

Phylogenies are often used to determine the taxonomy of a lineage, that is the evolutionary context of an organism within the greater tree of life. The researchers could recognize that the new symbiont was a basidiomycete from the sequence information, but only by comparing the sequence information of the new organism to the previously known organisms can we determine when and from which ancestor the new species evolved. To account for the millions of years that have passed after all the basidiomycetes diverged from one another, the researchers incorporate as much sequence data as possible. Here, they use 349 loci to determine the placement of the new lineage.

Genetic or molecular diversification. As genetic changes occur over time (evolution), diversity will increase within a group, illustrated by branching on a phylogenetic tree.

A variation in a single base pair (A, T, C, G) in a DNA sequence. Some sites in a gene are more likely to mutate than others. Phylogenetic information is based on genetic differences between organisms, and single nucleotide polymorphisms (SNPs) provide the most information.

A way to study what genes are being expressed and at what level. All messenger RNA (mRNA) is collected from a sample and each mRNA is counted to measure gene expression. The more copies of mRNA associated with a specific gene, the more highly expressed that gene is.

To learn more about gene expression through transcription, see https://www.hhmi.org/biointeractive/dna-transcription-basic-detail

Refers to sequencing of target genes obtained by a procedure called polymerase chain reaction (PCR) using gene-specific primers. Amplicon sequencing provides a snapshot of the microbial populations in an environment.

Generally, lichen thallus (singular form of thalli) types fall into four basic growth forms: crustose, squamulose, foliose, and fruticose.

Lichen thalli can develop into a diverse range of structures: multiple-branched tufts; flat, leaf-like structures; filamentous structures; and aggregates of tiny plates.

Next Generation standard LS2.A: Interdependent Relationships in Ecosystems

AP Biology Standards EK2.D.1: All biological systems from cells and organisms to populations, communities, and ecosystems are affected by complex biotic and abiotic interactions involving exchange of matter and free energy.

Organisms that live on or inside another organism and get their food from or at the expense of their host.

The naming of all living species is governed by rule books called codes of nomenclature. According to these rules, if it is discovered that the same organism has been named twice, for instance by different people who didn’t know each other at different times, then the older name is given priority and the second name becomes a “synonym."

In this case, studies of the main fungal partner in Bryoria fremontii and B. tortuosa showed that they are genetically identical, and thus the two names technically should become nomenclatural synonyms. If this rule would be followed through here, the older name (Bryoria fremontii) must be used because it is older. However, the authors chose not to follow the rule so that they would still have names to use to discuss the two different lichen phenotypes

Several natural scientists in the mid-1800s began to suspect that the lichen was in fact a mixture of two organisms, but it was the Swiss botanist Simon Schwendener who demonstrated that lichens were composed of fungi and algae for the first time in 1869. Initially, he thought the relationship must be antagonistic—that the fungi were “imprisoning” the algae. Ten years later, the German botanist Anton de Bary proposed the idea of mutually beneficial symbiosis for the lichen system.

Read more about Schwendener's discovery and the controversy it caused here. Find the full PDF in the "Related content" tab.

AP Biology Standards EK4.B.2: Cooperative behavior within or between populations contributes to the survival of the populations, i.e. mutualistic relationships.

AP Biology Standards EK1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.

AP Biology Standards EK 1.B.2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested.

AP Biology Standards EK 1.B.1: DNA and RNA are carriers of genetic information through transcription, translation, and replication.

AP Biology Standards EK1.A.4: Biochemical and genetic similarities, such as DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.

Check out this video from SciShow where Hank Green interviews lead author, Toby Spribille, about his research and conclusions. The interview describes the findings, clarifies the different groups of fungi discussed, and describes how they are related to one another. Spribille describes the differences between Ascomycetes and Basidiomycetes and the radiations in the fungal lineage.

This paper describes the cortex deficiencies of lichens grown from only the two previously known symbiotic partners.

The data presented in this paper mean that it can’t be ruled out that the newly identified basidiomycete is involved in vulpinic acid formation. Questions to be tested in the future include whether basidiomycetes produce the acid directly, or whether their presence causes the other fungal players to produce the acid themselves.

These Cyphobasidium cells were found throughout the lichen, and show evidence of living their whole life cycle within the lichen. Therefore, at this point, it cannot be ruled out that these basidiomycetes might be integral to the structure, phenotype, and formation of some lichen species.

The results of imaging showed that more basidiomycete cells were present in the lichen that produce vulpinic acid (B. tortuosa). This result supported the gene expression analysis results.

The researchers demonstrated, using rRNA analyses, that the new basidiomycete probably evolved with the lichen species. They showed that different lichens carried different basidiomycete strains. They concluded that basidiomycete symbionts are present in many lichens, and many lichen carry a specific strain.

The scientists found that genes in Ascomycota (the mycobiont in both lichens) and Viridiplantae (both lichen's photobiont) were expressed similarly in both lichens. Therefore, they concluded it was unlikely that a common gene was causing the production of vulpinic acid in one lichen but not the other. Therefore, the phenotypic differences between two lichen species could not be explained simply by looking at gene expression in the symbionts.

Researchers attempted to grow and isolate basidiomycete cells independent from their lichen partners, the algae and the ascomycete fungus. Often times it is very difficult to culture new organisms because we do not know enough about the growth requirements. This is frequently the case with organisms that form symbiotic relationships, as they often lose the ability to grow independent of their symbiotic partners.

Primers are small oligonucleotide sequences that are used as probes to determine if something is present in an unknown mixed sample. In this case, the primer is designed to match a piece of ribosomal DNA specifically in basidiomycete genomes found in the previous experiments. If the primer finds a target in a biological sample it is highly likely that a basidiomycete is present in the sample. In these experiments, the biological samples are other wild lichens found next to Bryoria lichens in Montana forests. Primers operate on the molecular level, and so very little biological material is needed to determine if basidiomycetes are present.

The author initially looked only at the expressed gene copies (contiguous sections of messenger RNA, or contigs) that corresponded either to known ascomycete or known algal DNA. They limited their search to these two because until then, a lichen was thought to only consist of those two partners. When they could not find any difference that would explain the phenotype differences between the two lichens, they expanded their search to see what other kinds of DNA was found in every single lichen, and perhaps had not been accounted for yet. They found 506 contiguous snippets of DNA that were found in every lichen that appeared to come from a second fungus, a basidiomycete, that wasn’t supposed to occur in lichens.

A transcriptome is a way for researchers to count the number of messenger RNA copies that has been produced from each gene in an organism, which is a measure of how much this gene is expressed. By comparing the level of gene expression between two different species, researchers can get an idea of which genes might be involved in producing different phenotypes in those species.

While these two lichens look very similar, there is an important distinction. There is evidence that Bryoria fremontii has been used and consumed by Indigenous populations for centuries, while Bryoria tortuosa contains a yellowish substance, vulpinic acid, that is toxic to mammals. Indigenous peoples soaked Bryoria collected for food, and it is thought this may have helped rinse background levels of vulpinic acid from mixed samples. Despite this difference between the two lichen species, scientists had been unable to determine a phylogenetic distinction.

Read more in Scientific American: https://blogs.scientificamerican.com/artful-amoeba/2-lichen-mysteries-solved-reveal-a-greater-hidden-truth/

The molecular clock theory posits that changes (mutations) occur at a constant rate, and that we can use the number of changes between any two sequences to find out approximately when the sequences diverged from one another. To apply a molecular clock to a phylogeny one must use a rooted tree (see Figure 2A).

Data used to reconstruct evolutionary relationships, such as in a phylogenetic tree, except extracted at the scale of the whole genome.

From the word contiguous, meaning a continuous set of DNA sequences.

The photosynthesizing partner in the symbiotic relationship; in this case, a type of alga.

Watch a video from the Havard Museum of Natural History about what defines a lichen. This video describes lichens, symbiosis, and the lichen life cycle. Notice that the video makes no reference to basidiomycete yeasts.

Well-known children's book author Beatrix Potter was one of the earliest proponents of the symbiotic nature of lichens in the English-speaking world.

Read more in the BBC: http://www.bbc.com/earth/story/20160215-beatrix-potter-pioneering-scientist-or-passionate-amateur

Group.

Since flies do not have verbal language, they communicate with one another by releasing and responding to chemicals known as chemosensory cues. Different cues can have different meanings. For instance, some cues released by the female can signal to the male that she is ready to mate. Other cues, like the one described here (cVA), can signal that the female is no longer looking to mate, thus driving away any unwanted males.

Past research has shown that interactions between neuropeptide F and its corresponding receptor can alter how much flies are affected by alcohol consumption.

Past research has shown that individual differences in alcohol tolerance amongst C. elegans are related to natural variations in the amount of neuropeptide Y receptor found in their brains.

The researchers found that the flies who had learned to associate an odor with activation of the NPF circuit preferred that odor in the Y maze, relative to the unpaired/neutral odor.

Other control flies who underwent partial genetic manipulations but did not experience NPF activity-odor pairings had no odor preference in the maze.

Excess.

Shortage.

The researchers found that flies that had experienced sexual rejection had significantly reduced levels of NPF in their brain, and flies that had undergone mating had significantly increased levels of NPF. This supports the hypothesis that sexual history can affect the amount of NPF that gets made in the brain, which can in turn change how much alcohol an organism might consume.

Past research has also shown that the amount of neuropeptide Y found in a rodent's brain is related to the amount of stress they might experience during their life.

A mammalian version of neuropeptide F. This molecule is found in the human brain.

For a recent study on the history of dogs in the Americas (published by some of the same authors of this paper), check out the 2018 research article in the "Related content" tab.

The ability to digest starch was important to look at, because it gives an idea of when dogs were domesticated, and who domesticated them—hunter-gatherers (meat-based diet) or farmers (starch-based diet).