3,078 Matching Annotations
  1. Jan 2019
    1. quantify depletion

      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."

    2. expression vector

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

    3. mutagenesis

      Creating genetic mutations.

    4. assayed

      Testing a material to figure out its composition and quality.

    1. we compiled evidence for the earliest dog remains across Eurasia

      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

    2. assigned to one of four major well-supported haplogroups (groups A to D)

      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.

    3. We used principal components analysis (PCA), D statistics, and the program TreeMix (12) to further test this pattern.

      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.

    4. Paleolithic

      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.

    5. occurred in Europe (7), Central Asia (8), or East Asia (9)

      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.

  2. Dec 2018
    1. Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.

      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.

    2. Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.

      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.

    3. Populations of white-sand and terra firme ecotypes of Protium subserratum were attacked by herbivore assemblages differing in both abundance and species composition, exhibited significant differences in growth and defense allocation, and expressed qualitatively different secondary compounds. That these phenotypic differences occur in populations involved in incipient (or recent) speciation is consistent with the hypothesis that herbivores interact with environmental gradients to promote the evolution of habitat specialization in plants

      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.

    4. we believe that the differences in defense strategy we find agree with a growing consensus that plant defense traits are involved in diversification

      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.

    5. The existence of this trade-off has been well supported by many different temperate and tropical studies looking at allocation to growth and defense in plants adapted to different light and nutrient availabilities, both within species

      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.

    6. Finally, it is important to recognize that our sampling was limited to juvenile plants and lasted only 12 months. Insect herbivore populations can strongly vary in different years, and thus, it is possible that our sampling missed important herbivores that are associated with P. subserratum.

      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.

    7. We found that insect herbivores collected from Protium subserratum showed strong patterns of dissimilarity across different habitat types (Fig. 3). Moreover, we found significantly more insects feeding on terra firme plants than on white-sand plants, correlating with the large differences in resource availability between the habitat types. Taken together, these results suggest that there exists substantial variation in diversity and abundance of insect herbivores associated with P. subserratumacross white-sand and terra firme habitats.

      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.

    8. unlike most members of the family Burseraceae, P. subserratum does not yield measureable amounts of monoterpenes and only trace amounts of sesquiterpenes

      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.

    9. Terra firme populations exhibited significantly greater height and leaf growth and allocated more to chlorophyll production than white-sand populations in both soil types, demonstrating that different growth strategies have a genetic basis

      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.

    10. Differences between sites, habitat types, and their interaction explained 14%, 15%, and 11%, respectively, of the variation in herbivore species composition among the four sampling locations

      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.

    11. differences among the dominant herbivores, the species composition of the entire P. subserratum herbivore fauna exhibited high turnover among sites and habitats

      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.

    12. We compared absolute and qualitative differences in leaf defense. First, we compared the dry mass of leaf defense chemicals in a linear model with soil type and study region as independent variables. Second, we tested whether habitat type, sampling site, or the interaction of the two, was a significant determinant of the relative allocation among flavan, flavone, quinic acid derivatives, and oxidized terpenes in each plant using a factorial analysis of variance.

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

    13. Second, we used a factorial analysis of variance (McArdle and Anderson 2001) to assess whether habitat type, sampling site, or the interaction of the two was a significant determinant of herbivore species composition.

      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.

    14. In order to study the evolutionary processes involved in habitat specialization and the role of insect herbivores, an ideal study system would include recently derived sister species, or diverging lineages undergoing incipient speciation in different habitats.

      Main goal for the paper.

    15. A long-standing hypothesis has linked escalation in plant defense that allows escape from insect herbivores to range expansion and speciation (Ehrlich and Raven 1964). Such escalation can include increases in the diversity of defense strategy (novel defense types), increases in the total amount of defense investment, or both (Agrawal et al. 2009). Range expansion, or merely an imperfect match between the distribution of plants and their natural enemies, may confront plants with different herbivore assemblages and/or variation in habitat resources across their range (Thompson 2005, Züst et al. 2012). This variation, in turn, may accelerate the evolution of differing defense strategies across habitats. Alternatively, natural enemies may not be major selective agents driving habitat specialization. In this case, we would predict that there would be few qualitative and quantitative defense differences between habitats, especially when diverging lineages of host plants occur in close proximity and also experience some gene flow across the habitat boundary.

      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.

    16. promote very different defense allocation strategies for different plant species depending on the type of defense employed (i.e., their elemental constituents and biosynthetic pathways), as well as the nature of resource limitation across habitats (i.e., light, nutrients, or water) (Bryant et al. 1983, Herms and Mattson 1992).

      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.

    17. the optimal defense allocation may be affected by differential costs of tissue replacement across habitats

      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.


    18. the species composition and relative abundance of herbivore communities may turn over among habitats because herbivores are affected by habitat quality, structure, and interactions with predators

      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/)

    19. But little is known about the mechanisms underlying the evolution of habitat specialization and the extent to which herbivores contribute to phenotypic divergence during the speciation process,

      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.

    20. Herbivores play an important role in habitat specialization because they can magnify the differences in resource availability across habitats

      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

    21. Assemblages of insect herbivores were dissimilar between populations of ecotypes from different habitats, as well as from the same habitat 100 km distant.

      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.

    22. reciprocal transplant experiment

      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).

    23. morphological

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

    24. qualitative

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

    25. chromatography

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

    26. pubescence

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

    27. phenotypic plasticity

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

    28. regression

      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.

    29. Protium subserratum Engl.


      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.

    30. parapatric distribution

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

    31. incipient speciation

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

    32. reciprocal

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

    33. gradients

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

    34. herbivore to circumvent or detoxify defenses

      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.

    35. beta-diversity

      The over all number of differing variations in the region.

    36. Environmental gradients

      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.

    37. habitat-mediated speciation

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

    38. chlorophyll

      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.

    39. hemipterans

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

    40. chrysomelid beetles

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

    41. ecotypes

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

    42. plant defense allocation

      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.

    43. posits

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

    44. Herbivores

      Herbivores are animals who get their energy by eating plants.

    45. flora

      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.

    1. phyletic

      Has evolved in some way.

    2. invasive species

      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.

    3. parasites

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

    4. paraphyletic

      having a common ancestor.

    5. blastula

      early stage of development

    6. asexually

      Reproduction without a male and female.

    7. glycoproteins

      proteins that have carbohydrate groups.

    8. heterotrophic

      An organism that can make food.

    9. transcriptomes

      All the genes expressed by mRNA

    10. conservation

      means preserved.

    11. sequencing

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

    12. genomes

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

    13. invertebrates

      an animal that does not have a backbone

    14. metazoan

      means a living organism that is multicellular.

    1. a prominent position in current scenarios

      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

    1. Ants are important predators in tropical forest ecosystems

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

    2. Treatments applied to caterpillars were: (1) no barriers (no tanglefoot/no cage), (2) tanglefoot present/no cage, (3) no tanglefoot/cage with holes present, (4) tanglefoot present/cage with holes present, (5) no tanglefoot/cage present, and (6) tanglefoot present/cage present.

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

    3. Field observations revealed that sheer caterpillar size was a fair defense against these ants;

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

    4. osmeteria

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

    5. pupate

      To become a pupa.

    6.  Pseudomyrmex gracilis received the highest final score at 52, and C. floridanus had the next highest score at 40; both C. ashmeadiand C. planatus received lower scores of 24

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

    7. overdispersion

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

    8. logistical constraints

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

    1. Gentry plots consistently emerge as the best compromise

      Overall, 0.5 hectare gentry plots were the best method.

    2. Fig. 1.

      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.

    3. The 1 ha plots, despite their relatively high cost to implement (Table 1), were more efficient to inventory than the smallest plots, although 1 ha plots were still inferior to the 0.5 ha modified Gentry plots.

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

    1. Markov Chain Monte Carlo methods

      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.

    2. thaw degree days (TDDs)

      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.


    3. graminoid

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

    4. Remote sensing

      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

    5. Oberbauer

      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).

    1. spatial abundance pattern.

      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.

    2. temporal monitoring studies

      Temporal monitoring is monitoring that is conducted over time.

    3. focal species

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

    4. However, can marine reserves also benefit large, roving reef predators that are potentially mobile throughout their life?

      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.

    5. Marine reserves can clearly enhance exploited coral reef species that have relatively sedentary adult life-stages, in which some individuals live almost exclusively within reserve boundaries

      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.

    6. site-fidelity

      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.

    1. phenology

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

    2. larger fish have greater thermal inertia and increased cardiac capacity

      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.

    3. metabolic scope

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

    4. The largest size-based differences in energy intake were also observed in October (Fig. 6 and table S3), indicating that thermal niche expansion in this endothermic species results in high energetic reward.

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

    5. ILD

      Isothermal Layer Depth

    6. SST

      Sea Surface Temperature

    7. spatiotemporal information

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

    8. Lower energy intake was observed during late summer (August and September), when bluefin tuna are moving up through the Southern California Bight (28° to 32°N).

      Lower energy intake during migrations.

    9. heterogeneity

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

    10. interpolated

      insert (something of a different nature) into something else

    11. Energy intake and thermal excess were positively correlated with body size as measured by the curved fork length (CFL) of tagged tunas

      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.

    12. CCLME

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

    13. HIF

      Stands for Heat Increment of Feeding.

    14. peritoneally

      Located in the abdominal cavity.

    15. Here, we quantify energy intake in 144 wild Pacific bluefin tuna in the CCLME on over 39,000 days (fig. S1), using HIF measurements from implanted archival tags. We estimate energy intake using a model developed with laboratory data collected from similar-sized bluefin tuna (22) at a range of ambient temperatures.

      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.

    16. hitherto

      Until now or until the point in time under discussion

    17. viscerally

      Internal organs within the main cavities of the body.

    18. sinuous

      means having many curves or turns.

    19. a proxy for feeding

      authorization of feeding.

    20. Pacific bluefin tuna (Thunnus orientalis)

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

    21. quantified

      express or measure of quantity.

    22. garnered

      means gathering or collecting.

    23. niche

      conditions under which an animal lives

    1. commercial cultivation in artificial settings

      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


    1. Fig. 2 Terrestrial C loss rates from stream reaches increased with N and P concentrations.

      Graph illustrating the loss of terrestrial carbon.

    2. Fig. 1 Terrestrial C residence time was approximately halved with experimental nutrient enrichment. Increased nutrient inputs (+) reduced terrestrial particulate C residence time (–) and increased export of fine detrital particles (+) and respiration rates [which increased on C substrates (11) but decreased at reach scales; +/−]. Inset graph: Reach-scale leaf litter loss rates were faster in enriched (dashed lines) than in reference (solid lines) streams; the inverse of these rates is residence time. Colors correspond to the same years in (A) (reference versus enriched streams; N+P experiment; n = 12 annual rates) and to the same streams in (B) (pretreatment versus enriched years; N×P experiment; n = 15 annual rates). Data shown for litter loss are untransformed but were natural log–transformed for analyses and the calculation of loss rates (k, per day). The larger image depicts terrestrial organic C inputs, which enter as leaf litter, wood, and dissolved organic carbon (DOC), and outputs as hydrologic export (fine and coarse particles, DOC) and respired CO2 in deciduous forest streams, using an image of one of the N×P experimental stream sites.

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

    3. Experimental nutrient additions accelerate terrestrial carbon loss from stream ecosystems

      Effects of Nutrients on Stream Ecosystems

    4. Editor's Introduction

      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?

    1. D. Anglesea, C. Veltkamp, G. H. Greenhalgh, The upper cortex of Parmelia saxatilis and other lichen thalli. Lichenologist 14, 29–38 (1982).

      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.

    2. I. A. Aschenbrenner, T. Cernava, G. Berg, M. Grube, Understanding microbial multi-species symbioses. Front. Microbiol. 7, 180 (2016).

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

    3. R. Honegger, Developmental biology of lichens. New Phytol. 125, 659–677 (1993).

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

    4. the production of which often does not correlate with the lecanoromycete phylogeny

      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.

    5. Most macrolichens possess a basic two-layer cortex scheme consisting of conglutinated internal hyphae and a thin, polysaccharide-rich peripheral layer

      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.

    6. popular fungal barcode

      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.

    7. teleomorphic

      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.

    8. We therefore developed protocols for fluorescent in situ hybridization (FISH) targeting specific ascomycete and cystobasidiomycete rRNA sequences.

      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.

    9. incorporated into a broader sample of published cystobasidiomycete rDNA sequence data

      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.

    10. using gene sequences inferred from our transcriptome data set and other available genomes (table S1).

      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.

    11. radiations

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

    12. single nucleotide polymorphisms (SNPs)

      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.

    13. transcriptomics

      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

    14. amplicon sequencing

      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.

    15. lichen thalli

      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.

    16. a symbiosis

      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.

    17. parasites

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

    18. nomenclatural synonyms

      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

    19. between a single fungus, usually an ascomycete, and a photosynthesizing partner

      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.

    20. These data suggest that the gall-inducing form of Cyphobasidium completes its life cycle entirely within lichens.

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

    21. phylogenomic tree

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

    22. analysis placed the basidiomycete as sister to Cystobasidium minutum (class Cystobasidiomycetes, subphylum Pucciniomycotina) with high support

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

    23. mRNA transcriptome sequencing

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

    24. genetically distinct strain of the basidiomycete

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

    25. The assumption that stratified lichens are constructed by a single fungus with differentiated cell types is so central to the definition of the lichen symbiosis that it has been codified into lichen nomenclature

      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.

    26. V. Ahmadjian, The Lichen Symbiosis (John Wiley & Sons, 1993).

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

    27. In B. fremontii, differential transcript and cell abundance data, along with physical adjacency to crystalline residues, implicate Cyphobasidium in the production of vulpinic acid, either directly or by inducing its synthesis by the lecanoromycete.

      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.

    28. The discovery of ubiquitous yeasts embedded in the cortex raises the prospect that more than one fungus may be involved in its construction, and it could explain why lichens synthesized in vitro from axenically grown ascomycete and algal cultures develop only rudimentary cortex layers

      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.

    29. Consistent with the transcript abundance data, these cells were more abundant in thalli of B. tortuosa (Fig. 3), where they were embedded in secondary metabolite residues (movie S1).

      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.

    30. As a whole, these data indicate that basidiomycete fungi are ubiquitous and global associates of the world’s most speciose radiation (14) of macrolichens.

      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.

    31. Restricting our analyses to Ascomycota and Viridiplantae revealed little differential transcript abundance associated with phenotype

      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.

    32. attempts to culture the basidiomycete from fresh thalli were unsuccessful

      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.

    33. we designed specific primers for ribosomal DNA [rDNA; 18S, internal transcribed spacer (ITS), and D1D2 domains of 28S) to screen lichens growing physically adjacent to Bryoria in Montana forests.

      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.

    34. expanding the taxonomic range to consider all Fungi, we found 506 contigs with significantly higher abundances in vulpinic acid–rich B. tortuosa thalli

      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.

    35. transcriptome-wide analysis

      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.

    36. These two species have been distinguished for 90 years by the thallus-wide production of the toxic substance vulpinic acid in B. tortuosa, causing it to appear yellowish, in contrast to B. fremontii, which is dark brown (11). Recent phylogenetic analyses have failed to detect any fixed sequence differences between the two 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/

    37. molecular clock

      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).

    38. phylogenomic

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

    39. contigs

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

    40. photobiont

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

    41. lichen symbiosis

      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.

    42. over 140 years

      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

    1. cohort


    2. cis-vaccenyl acetate (cVA)

      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.

    3. system regulates acute ethanol sensitivity in Drosophila

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

    4. NPY receptor homolog NPR-1 regulates ethanol behaviors

      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.

    5. When tested 24 hours later, males in the experimental group demonstrated strong preference for the odor associated with NPF neuron activation. The genetic controls, which did not undergo NPF neuron activation, but were exposed to the same training protocol, developed no odor preference (Fig. 4C). Other controls, which underwent NPF neuron activation but were not exposed to the training protocol, similarly developed no odor preference (fig. S6C).

      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.

    6. surfeit


    7. deficit


    8. Rejected-isolated males showed the lowest transcript levels, virgin-grouped males showed higher levels, and mated-grouped males showed the highest (Fig. 2A and fig. S4). Rejected-isolated males also showed markedly lower NPF protein levels than mated-grouped males

      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.

    9. Intriguingly, stressful experiences regulate mammalian NPY levels.

      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.

    10. neuropeptide Y [NPY

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

    11. Several experiments were designed to determine which of these was the predominant contributor to the enhanced ethanol preference seen in rejected-isolated males

      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.

    12. mated-grouped

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

    1. the complexity of the evolutionary history of dogs

      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.

    2. although this dog was likely able to digest starch less efficiently than modern dogs, it was able to do so more efficiently than wolves

      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).

    3. dogs, like pigs (22), may have been independently domesticated twice

      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

    4. Neolithic

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

  3. Nov 2018
    1. clades

      An ancestor and all of its descendants.

    2. The results of this analysis again revealed a clear East-West geographic pattern across Eurasia associated with the deep phylogenetic split

      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.

    3. D statistics

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

    1. multiprobe

      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.

    2. deep learning

      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.

    3. To perform a fair comparison, we fixed the computational complexity of both algorithms to be the same

      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.

    4. Moreover, the sparse, binary random projection achieved a computational savings of a factor of 20 relative to the dense, Gaussian random projection

      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!

    5. If the web contained many images, but each image was represented by a low-dimensional vector (e.g., 10 or 20 features), then space-partitioning methods (12) would similarly suffice. However, for large databases with high-dimensional data, neither approach scales

      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.

    6. brute force linear search

      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!

    7. provides a conceptually new algorithm for solving a fundamental computational 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.

    1. We have isolated and characterized a gene, Yob, for the M factor in the malaria mosquito Anopheles gambiae

      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.

    2. This female-killing property may be an invaluable tool for creation of conditional male-only transgenic Anopheles strains for malaria control programs

      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

    3. ectopic embryonic delivery of Yob transcripts

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

    4. broods

      In this case, a grouping of young male mosquitos.

    5. In many insects, maleness is conferred by a Y chromosome–linked M factor of unknown nature.

      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.

    6. anopheline

      A general term for the mosquito genus, Anopheles.

    7. However, with the exception of Nix (a homolog of tra2) from a mosquito Aedes aegypti (16), genes encoding M factor have remained enigmatic

      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.

    8. zygotic

      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.

    1. addiction to cocaine (but not to other drugs) accounted for only 9% of the variance

      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.

    2. Our findings are also in line with evidence

      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.

    3. Treatment of cocaine addiction should thus focus on training desirable habits that replace habitual drug-taking while protecting CUD patients from aversive consequences that they may fail to avoid.

      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.