3,103 Matching Annotations
  1. May 2018
    1. Ants, particularly P. gracilis, may pose a significant threat to butterfly eggs and larvae, but butterflies have developed ways to cope with such predators

      Authors found that this species of ants are more efficient at being predators.

    2. we assumed they would interact with caterpillars more frequently than other predators

      Since the ants were found more in caterpillar at BNP authors assumed that the ants are the primary predators of caterpillars.

      Some other predators also influence caterpillar mortality, but ants are more abundant.

    3. ubiquitous

      Present, appearing, or found everywhere.

    4. elucidated

      Make (something) clear; to explain.

    5. early instar (small) caterpillars suffered higher mortality than late instar (bigger) caterpillars

      Authors ended up concluding that the smaller the caterpillars, the higher the rate of mortality.

    6. caterpillar absence assumed caterpillar mortality

      The authors conclude that since there is an absence of caterpillar it is assumed that there have been a sort of mortality for this species.

    7. that crawling predators such as ants, beetles, true bugs, spiders, and even lizards play a significant predator role

      This is a result where the authors implied that the crawling insects are the major predators of the species studied.

    8. parasitoid

      An insect whose larvae live as parasites that eventually kill their hosts.

    9. pupal stage

      Life stage of some insects undergoing transformation between immature and mature stages.

    10. instar

      A phase between two periods of molting in the development of an insect larva or other invertebrate animal.

    11. Lepidoptera

      Order of insects that includes butterflies and moths.

    12. Early instar caterpillars suffered the most damage when interacting with P. gracilis (n = 15 trials, 86.7% mortality); late instar caterpillars successfully foiled P. gracilis advances (n = 15 trials, 0% mortality).

      The ant species C. floridanus death rate is at 56.3% during this experiment. They have forced some or all instar caterpillars to leave their habitat.

    13. Contingency table

      A table showing the distribution of one variable in rows and another in columns, used to study the association between the two variables.

    14. Exclusion experiments revealed that early instar caterpillars were vulnerable to both crawling and non-crawling predators.

      The instar caterpillars were vulnerable to be eaten, or killed by other predators.

    15. However, individual parameters (tree groups) were investigated to determine significance using non-host trees as the baseline group to compare the frequency of P. gracilis collected for each tree group.

      Each species was investigated to determine and compare each tree group.

    16. omnibus test

      Omnibus tests are statistical tests that are designed to detect any of a broad range of departures from a specific null hypothesis.

    17. Ants collected in pitfall traps in the canopies of Amyris elemifera and Zanthoxylum fagara: number of individuals of each species, and status

      The details of the ants captured by pitfall traps near the host plants of the Swallowtails. 5 of the 12 ant species captured were exotic and out of the total 243 individual ants caught, 144 were exotic

    18. Percentage of ant species captured in pitfall traps at Elliott and Adams Keys (tree canopy, trunk, and base). Overall, 1418 total ants comprising 25 ant species were captured and identified from pitfall traps

      The experiment was conducted at Biscayne National Park and was split into three parts. The first part was using pitfall traps to collect ants at Biscayne Park near the host plants. Secondly, the host plants with known caterpillars were protected with various combinations of cages and tanglefoots. Concluding the author was keeping track of how long it take for certain species of ants to first find the caterpillars. Authors assumed that the ants would interact with caterpillars more frequently than other predators.

    19. Ants collected in pitfall traps at Elliott and Adams Keys: number of individuals of each species, and status

      All of the ants found in pitfall traps that were placed all around the canopy in the keys. 11 out of 25 species were found to be exotic and 735 out of 1418 of the total amount of ants were exotic.

    20. Taxa

      A taxonomic category, as a species or genus.

    21. instar 

      A phase between two periods of molting in the development of an insect larva or other invertebrate animal.

    22. terrestrial

      Of, on, or relating to the earth.

    23. deleterious

      Causing harm or damage.

    24. subtropical dry forest

      Subtropical dry broadleaf forest biome, also known as tropical dry forest, monsoon forest, vine thicket, vine scrub and dry rain forest is located at tropical and subtropical latitude.

    25. captive-breeding

      The process of breeding animals in controlled environments within well-defined settings, such as wildlife reserves, zoos and other commercial and noncommercial conservation facilities.

    26. In 2012, two projects were implemented to increase H. a. ponceanus population:

      Authors obtained this information from the following News

      Daniels JC (2014) Conservation matters: status and conservation of the federally endangered Schaus swallowtail butterfly. News of the Lepidopterists’. Society 56:138–139

    27. primary larval host plant

      The first host plant supplies food resources to micropredators, which have an evolutionarily stable relationship with their hosts - similar to ectoparasitism.

    28. Pseudomyrmex gracilis and C. floridanus were more aggressive towards caterpillars in comparison to other ant species;

      After the experiment was finished, they have found that the Pseudomyrmex gracilis and C. floridanus interacted more aggressively toward the subject compared to another species.

    29. host plants

      A plant upon which an organism (such as an insect or mildew) lodges and subsists.

    30. exclusion experiment

      Experiments used by ecologists to determine the effectiveness of putative plant pollination vectors.

    31. relative abundance

      The number of organisms of a particular kind as a percentage of the total number of organisms of a given area or community.

    32. species diversity

      Species diversity is defined as the number of species and abundance of each species that live in a particular location.

    1. Preclinical evidence

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

    2. antecedent

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

    3. modulated


    4. appetitive

      Characterized by a desire to seek pleasure.

    5. punitive

      Intended as punishment.

    6. pharmacological

      Relating to the use and effects of medicines.

    1. Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2 and HERC2 that are identical by descent from Africans.

      Crawford et al. find evidence that genetic variants associated with dark skin pigmentation have a single origin within Africa. Not only is this interesting from an evolutionary standpoint, it demonstrates that using only skin pigmentation to infer modern population structure is highly ineffective and erroneous.

      For example, if scientists wanted to explore the relationships between modern human populations, and used only the genetic variants associated with skin pigmentation to do so, they might end up lumping many of the African populations in with South Asian and Australo-Melanesian populations. Focusing solely on the genetic determinants of pigmentation would lead to inaccurate conclusions about relationships among modern human populations.

    1. We propose that appropriate plot methods, together with information from ad hoc sampling (Foster et al. 1998), will assist in the identification and monitoring of forest areas to meet conservation priorities.

      The results found from the experiment and those from ad hoc sampling can be used to enhance conservation of Neotropical forests.

      Ad hoc typically means a solution designed for a specific problem. Therefore, ad hoc sampling means a sampling method that would solve the conservation methods problem.

    2. spatial heterogeneity

      The uneven distribution of species in an area.

    3. RAINFOR consortium

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

    4. Our analysis of the BCI dataset demonstrates how this choice of minimum diameter can influence interpretations. BCI has a relative ratio of overall richness between communities with minimum diameters of 10 cm vs. 2.5 cm that is only slightly higher than that of Yasuní

      This shows that there was higher species richness in species of 10 cm diameter versus 2.5 cm.

    5. quantitative plot data.

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

    6. herbarium vouchers

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

    7. Shannon's entropy

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

    8. plot-level richness

      The amount of species there are in a given plot.

    9. aggregate plots

      One third of the acre.

    10. contiguous

      Touching or sharing a border.

    11. vegetation plots

      Describes plots of different vegetation involved.

    12. demarcate

      Set boundaries or limits.

    13. belt transects

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

    14. First, we test a range of plot sizes and shapes to determine the most accurate (least bias and greatest precision) and most efficient (accuracy per unit effort) method to estimate AGB and tree biodiversity. Second, we evaluate whether there exists a general trade-off among methods in the accuracy of information they provide for tree diversity vs. aboveground biomass estimates. Third, we analyze the extent to which different inventory methods may be appropriate among forests differing in structure and floristic composition.

      How the authors obtained AGB and tree biodiversity, evaluated trade off among tree diversity and aboveground biomass

    15. Herein, we use a simulation approach to estimate AGB and tree biodiversity within large permanent plots from six Neotropical forests representing a broad gradient in tree species richness (88–821 species among trees ≥ 10 cm in diameter at 1.3 m height [dbh] per 50 ha plot) and forest structure (AGB of 283–494 Mg ha−1)

      Table 2 shows the area, dimension, year of census, aboveground tree biomass, species richness, and stem density in plots that are permanently placed in six Neotropical Forests. This is pre-existing information.

    16. species distributions

      How species are arranged in an area.

    17. allometries

      Study of rate of growth.

    18. Several alternatives to 1 ha plots have been suggested, differing primarily in their sizes, shapes, and the minimum size of trees inventoried

      Table 1 shows the different types of plots used and how they differed in size, area covered, areas inventories, shape, and number of days used.

    19. 1 ha plot

      1 hectare plot = 100 acres.

    20. we test a variety of plot methods to establish the most accurate and efficient way to reach this goal.

      Many different plot methods were used in order to see which method would provide better carbon and biodiversity information.

    21. A standardized rapid inventory method that provides information on both biodiversity and carbon stocks will thus represent an important tool to enhance our ability to maximize biodiversity conservation and to help quantify potential carbon emissions that result from deforestation and degradation (REDD).

      The purpose of the experiment is to find a proper method to measure biodiversity and carbon stocks of a community. Doing so will allow for better conservation methods and help quantify the amount of carbon emissions that result from deforestation and degradation of forests.

    22. Amazon basin

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

    23. Pg

      The picogram is equal to one trillionth of a gram.

    24. Tropical forests have long been recognized to harbor a significant proportion of global biodiversity 

      Biodiversity experiments have been performed on tropical forests and it has been concluded that they are a large portion of the Earth's biodiversity.

    25. Gentry plots

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

    26. coefficient of variation

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

    27. floristic composition

      Describes how the flowers are arranged.

    28. species richness

      The number of different species in a given ecological community.

    29. broad gradient

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

    30. aboveground tree biomass (AGB)

      Stems and leaves of the tree.

    31. carbon stocks

      Carbon stored in the forest.

    32. Field Inventory Methods

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

    33. Neotropical Forests

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

    34. Tree Diversity

      The variability of different tree species in the ecosystem.

    35. Aboveground Biomass

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

    1. Hulme 2005

      This is from a journal: Applied Ecology. The author discusses climate change and how it is negatively impacting global ecosystems and how not much is being done to alleviate the problem.

    2. C sequestration

      Long term carbon storage.

    3. (Nowak et al. 2004),

      Fundamental paper which shows how plants will uptake more CO2 when it is present in higher and higher quantities.

      At 600 parts CO2 per million parts air, plant carbon uptake is limited due to low levels of CO2 present in atmosphere.

    4. atmospheric CO2

      The global concentration of carbon dioxide. This fluctuates annually.

    5. (Stanton and Ackerman 2007)

      This is a report commissioned by the EDF. It is an analysis on the consequences of letting climate change continue unchecked on the economy of Florida.

    6. mean annual precipitation

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

    7. Ferrati et al. 2005, 

      The objective of this study was to measure the hydrometerological and hydrological aspects of Esteros del Ibera.

    8. (Burkett and Kusler 2000)

      This author's research is focused on wetlands and global climate change impact on them.

    9.  Erwin 2009)

      The author's research centers around the global impact of climate change on the world. He brings into question how wetland systems (most vulnerable) will be impacted and how, if there is a way to save them.

    10. Fig. 6. Observed (solid) versus modeled (hollow) CO2 exchange rates (NEE, Reco and GEE) at TS (A) and SRS (B). Atmospheric convention is used here and positive numbers indicate a loss of C to the atmosphere.

      The solid bars show the actual data gathered. They measure the different rates of carbon exchange.

    11. Fig. 7. The effect of elevated atmospheric CO2 concentration (550 ppm, 850 ppm and 950 ppm) on cumulative (A) NEE, (B) Reco and (G) GEE, at TS. The influence of rising temperatures (1°C, 2.7°C and 4.2°C) on cumulative (B) NEE, (E) Reco and (H) GEE and shifts in seasonal and annual precipitation patterns (−2%, +7% and +14%) on cumulative (C) NEE, (F) Reco and (I) GEE. Atmospheric convention is used here and positive numbers indicate a loss of C to the atmosphere. All simulations were compared to current weather and atmospheric CO2concentration (red line).

      Figures displays projections for the effect of three climate-induced environmental changes on ecosystem processes (NEE, Reco, GEE).

      As CO2 levels and temperature increase, the ecosystem will uptake more and more CO2, and will retain more carbon.

    12. Fig. 5. Observed versus modeled soil temperature at (A) TS and (B) SRS, and soil volumetric water content (VWC) at (C) TS and (D) SRS.

      The figures show what happened to the actual data vs the data from the model. They are very close and show that the model is reliable, in other words, the data is precise.

    13. marsh ecosystems

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

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

    14. sinks

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

    15. DAYCENT

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

    16. Atmospheric convention

      Results from temperature differences, instability in the atmosphere.

    17. ran the model for 100 years (1) under climate change projections,

      Remember, this is a simulation! It was done on the DAYCENT simulation model.

    18. quasi-equilibrium

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

    19. Fig. 4. Climate change scalars for (A) elevated atmospheric CO2 concentration, (B) air temperature, and (C) precipitation. The distributions for (D) minimum temperature, (E) maximum temperature and (F) precipitation were modified to match projected seasonal change.

      These charts show the different magnitudes, at differing scales of CO2, temperature, and rainfall, respectively, projected out to the year 2076.

    20. soil volumetric water content

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

    21. ecosystem respiration [Reco],

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

    22. net ecosystem exchange (NEE)

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

    23. subdominant

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

    24. co-dominant

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

    25. Bowen Ratio (β)

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

    26. (Davis and Ogden 1994)

      Everglades: The Ecosystem and Its Restoration. This book summarizes recent studies on the vegetation, alligators, wading birds, and endangered species. It also covers the physical driving forces that created and continue to shape the everglades and patterns and processes of its flora and fauna.

    1. K.D. Whitney, C.A. Gabler, Divers Distrib 14, 569–580 (2008).

      Whitney et al. analyzes the obstacle within risk assessment in calculating "invasive potential". Markers studied include predictors of "rapid microevolution such as extent of heterosis, adaptation to novel habitats, and hybridization impacts. They study 38 documented species known for their invasiveness and proceed to mark their generation times, growth rates, and populations in studied areas.

    2. J.M. Rhode, M.B. Cruzan, Am Nat 166, 124–139 (2005).

      Rhode et al. examined the molecular and genetic processes of heterosis and epistasis in reference to hybridization within Piriqueta caroliniana (Turneraceae) plant complex. Using controlled plant crosses, they determined the effects of heterosis and epistasis on hybrid fitness.

    3. J.F. Morton, Econ Bot 32, 353–359 (1978).

      Morton observes and studies the impacts of the Brazilian pepper tree in regards to its ecological role in its native habitat, its invasiveness in new Southern habitats, and the animal and human interactions it garners.

    4. J.G. Lambrinos, Ecology 85, 2061– 2070 (2004).

      Lambrinos analyzes a collection of studies of invasion dynamics through the following observations: 1) the extent of the effect of interbreeding, founder effects, drift, and migration on population dynamics, 2) landscape change and human activity, and 3) selection pressures through dispersal patterns and life histories.

    5. J.J. Kolbe, R.E. Glor, L. Rodriguez Schettino, A. Chamizo Lara, J.B. Losos, Nature 431, 177–181 (2004).

      Kolbe et al. fielded Cuban lizard populations to determine molecular markers for genetic variation in these invader populations. They concluded that multiple introductions have likely occurred before and the respective high levels of genetic diversity which have confirmed its invasive success.

    6. L.G. Campbell, A.A. Snow, C.E. Ridley, Ecol Lett 9, 1198–1209 (2006).

      Campbell et al. studied weed evolution utilizing crop gene introgression to measure the fecundity and survival success of hybrid plants relative to wild plants. Hybrids comparatively had 22% greater survival than wild counterparts, which concludes that they will be able to replace wild parent plants.

    7. M.L. Ainouche, A. Baumel, A. Salmon, G. Yannic, New Phytol 161, 165–172 (2003).

      Ainounche et al. analyzed how the Spartina system has provided a foundational study of genomic characteristics of allopolypoid speciation through the lens of hybridization to form a more genetically varied allopolypoid species.

  2. Apr 2018
    1. Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem

      This article discusses how the addition of nutrients in an aquatic ecosystem affects secondary production. It was noted that there was an increase in secondary consumers most likely caused because of an increase in prey. There was also an increase of secondary consumer predators. It is mentioned that the increase of nutrients in the two years the survey was done resulted in positive effects for the secondary consumers, however, this might eventually change as the carbon levels in the ecosystem begin to decline because of the higher nutrient levels.

    2. Nutrient co-limitation of primary producer communities

      This article focuses on how nutrients affect the growth of primary producers. The factors that were observed to have the highest effects on the ecosystems were nitrogen and phosphorus levels.

    3. Ecosystem metabolism and turnover of organic carbon along a blackwater river continuum

      This article discusses the respiration rate of an aquatic ecosystem and uses it to determine patterns of activity found within a river during different seasons. It was observed that there were higher levels of respiration when there were was more organic carbon in the river.

    4. Long-term nutrient enrichment decouples predator and prey production

      This article discusses the effect the addition of nutrients has on an aquatic ecosystem. Originally the author hypothesized an increase of energy transfer from prey to predators because of the increase of nutrients. However, this did not occur because the increase in nutrient led to an increase of predator resistant prey.

    5. Nutrient enrichment alters storage and fluxes of detritus in a headwater stream ecosystem

      This article demonstrates how the addition of nitrogen and phosphorus led to an increase in the production of fine organic compounds by more than 300%. The article also mentions that this increase in fine organic compounds will have an effect on the entire ecosystem in that area in the long term.

    6. Lakes and reservoirs as regulators of carbon cycling and climate

      This article mentions the that the rate at which inland water sources release carbon dioxide is equivalent to the rate at which carbon is absorbed by the ocean. Methane is also being released in higher levels from lakes which are beginning to thaw because of increasing temperatures from global warming.

    7. Stream nutrient enrichment has a greater effect on coarse than on fine benthic organic matter

      This article discusses how an increase in nutrients affects the levels of coarse and fine organic litter. It was observed that there were higher levels of fine organic material which led to an increase in bacteria. However, in the stream with no nutrients added to it, there was an increase in both fungal and bacterial communities.

    8. Multiple trophic levels of a forest stream linked to terrestrial litter inputs

      This article discusses the importance of terrestrial litter on an aquatic ecosystem. It was observed that organisms that lived in the stream that was being tested were affected the most by the absence of litter and the same effects could be observed throughout the entire ecosystem. However, terrestrial fauna was not affected meaning that it got its carbon from another source.

    9. Continental-scale effects of nutrient pollution on stream ecosystem functioning

      This experiment was a pan-European research of more than 100 streams in multiple European countries. It helped determine the importance of litter breakdown and states that countries should begin to consider the importance of regulating nutrient levels in aquatic ecosystems.

    10. Human influences on nitrogen removal in lakes

      This article discusses how human practices have led to a increase of nitrogen levels in lakes. The article also mentions that an increase of phosphorus in lakes resulted in the extraction of higher levels of nitrogen. However, the author also states that laws pertaining to the concentration of phosphorus in aquatic habitats should not be removed or relaxed because phosphorus can also have a negative effect on an ecosystem if found in high concentrations.

    11. Management of nutrient effects on both of these pathways would positively affect riverine health.

      The purpose of these experiments were to test the effects of nutrients on terrestrial carbon loss that ultimately leads to a change in ecosystems.

      Learning the effects and ideal ratios of nitrogen to phosphorus for ecosystems will lead to better policies to protect them.

    12. human-disturbed landscapes

      Environments and ecosystems perturbed due to human interference.

    13. stimulated at nutrient concentrations that are now common

      A city releases water contaminated by agriculture which will have an adverse effect on local ecosystems.

      Read more in Lawrence-Journal World: http://www2.ljworld.com/news/2017/nov/15/short-notice-citys-release-nitrogen-contaminated-w/

    14. They may limit terrestrial C loss as CO2 and maintain downstream C export, but contribute to depletion of local C resources

      Detrivores have a different method of carbon depletion from streams. finer particulate organic carbon travels faster and further away from an area, deleting the area of carbon sources.

      Invertebrates may leave the system if there are no food sources and alter the food chain.

    15. agricultural streams

      Poultry producer is fined by $1.4 million for polluting a local stream.

      Read more in WJCT: http://news.wjct.org/post/live-oak-poultry-producer-environmental-groups-reach-deal-over-suwannee-river-pollution

    16. biological, rather than physical, processes drove reach-scale rates (table S5)

      Biological factors that drive the decomposition of carbon include the consumption and respiration from microbes, vertebrates, and in-vertebrates.

      Physical factors include temperature, flow of water, and sediment.

      The alignment of the reach-litterbag scale rates show that the bags represent the actual rates, and that the bags were not simply filtered by increased water flow or torn apart because of temperature.

    17. litterbag

      The litterbag technique can be used to measure the density lost due to composition by microbes and fungi.

      A known type and amount of litter is stuffed in the bag and is left for a certain amount of time in the stream. The bag is then later taken out and weighed while wet. The bag is allowed to dry and then the dry weight is taken.

    18. Reach-scale outputs of C increased as fine POC export, as well as respiration

      Fine POC export represents the movement of broken down carbon along the stream. Finer particles move faster and further down a stream as biological factors such as microbes and fungi decomposing the terrestrial organic carbon.

    19. pools of benthic fine and coarse POC declined

      Benthic fine and coarse particulate organic carbon can be used as a measurement when observing loss of carbon caused by detrivores.

    20. consideration of differences among litter species and potential divergence in rates due to the degree of biological processing

      In this experiment, leaf litter from different types of trees were used. The results are in Figure 3.

      The structure and chemistry of leaves are different and this determines how fast they may decompose.

      For example, tulip poplar decomposes the quickest and has a low carbon to nitrogen ratio. Comparatively, oak decomposes slowly and has a higher carbon to nitrogen ratio.

    21. Our results generally support the use of litterbags to measure larger-scale C dynamics

      It is often necessary to use a simpler model version of a larger system because it is easier to observe.

      It is difficult to observe the effects on a whole stream, but the litter bags are observed and represent the carbon loss in streams.

    22. Higher C loss rates at the litterbag scale than the reach scale are expected, because litterbags track distinct parcels of C, whereas reaches receive additional C inputs over time.

      Litter in the litter bags have a higher concentration of carbon than the stream, which has carbon more spread out. The litter will have higher loss of carbon but generally represents reach-scales.

    23. biological processing of C

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

    24. soluble reactive phosphorus (SRP)

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

    25. dissolved inorganic nitrogen (DIN)

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

    26. deciduous forest streams

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

    27. dissolved organic carbon (DOC)

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

    28. Litter quantity in the streambed was predicted to be 2.8 times and 7.7 times higher in reference versus nutrient-enriched streams after 6 and 12 months

      In the experiment, it was found that the addition of nutrients encouraged terrestrial organic carbon loss.

      This was tested by observing the litterbags of the experimental streams and comparing the data to the litterbags of the control stream.

      Since a large amount of mass was lost in the stream with nutrient additions, this gives some evidence that too many nutrients off-balances organic carbon levels.

    29. However, roughly similar-sized effects of N and P on loss rates are strong evidence of co-limitation (Fig. 2 and table S3).

      Both nitrogen and phosphorus are contributing factors to changes in terrestrial carbon loss.

      Within the ecosystem, different organisms require different ratios of nutrients to react and convert terrestrial carbon to carbon dioxide.

    30. co-limitation

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

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

    31. phosphorus (P) additions

      The levels of phosphorus in Lake Coeur d’Alene have doubled since the 1990's. This worries authorities about the potential growth of algae and increase in heavy metals in the lake.

      Read more in The Spokesman-Review: http://www.spokesman.com/stories/2017/nov/15/phosphorus-pollution-flowing-into-lake-coeur-dalen/

    32. We conducted two manipulative experiments at large spatial and temporal scales and focused our measurements on forest-derived leaf litter, because it is the most biologically active pool of terrestrial C in forest streams and is renewed annually (7).

      Two experiments were done separately to test the effects of nitrogen to phosphorus ratios on streams.

      Pre-treatment of streams include recording the levels of nutrients and typical conditions throughout a year.

      The first experiment had two watersheds with one being the control and the other having an addition of nitrogen and phosphorus to match a ratio that was decided by the scientists.

      The second experiment was done on five streams with different combinations of the nitrogen and phosphorus ratio.

    33. not been previously assessed in response to human-influenced stressors

      Although this experiment focuses on microbial and fungal effects on streams, humans sometimes also have an impact.

      These effects may include the leaking of septic tanks into bodies of water that increase human waste and phosphorus levels. Fishing and polluting also affect stream ecosystems.

    34. We measured the response of terrestrial C loss rates in whole 70- to 150-m stream reaches (tables S1 and S2).

      The experiments were conducted on streams in the Appalachian Mountains of North Carolina.

      Because of the elevation, there are little to no fish influencing the data. Mainly microbes and fungi influence the nutrient levels of the streams.

    35. flow-proportional nitrogen (N) and phosphorus (P)

      An irrigation line was used along the 70-150 meter streams to pump in liquid nutrients. The nutrients were pumped proportional to the flow of the water.

    36. terrestrially derived POC

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

    37. Nutrients stimulate microbial processing of POC, which results in increased losses of CO2 to the atmosphere

      William & Mary’s Virginia Institute of Marine Science are studying oysters to see if they could be used to reduce nitrogen levels.

      Read more in the Williamsburg Yorktown Daily: https://wydaily.com/2017/11/05/study-suggests-oysters-offer-hot-spot-for-reducing-nutrient-pollution-tek/

    38. particulate organic C (POC)

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

    39. Algal production increases

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

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

    40. inland waters

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

    41. Nutrient pollution

      Nutient pollution is affecting the production of fisheries in the ocean by creating dead zones in the ocean where there are low levels of oxygen.

      Read more in the Iowa Public Radio: http://iowapublicradio.org/post/farmers-sea-say-livelihood-dying-midwest-ag-pollution#stream/0

    42. terrestrial organic C

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

    43. sequestration

      Sequestration is the collection and storage of carbon dioxide.

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

    1. A squid host lacking luminous symbionts is affected not only in its behavior but also in other features of the symbiosis.

      See Dr. Margaret McFall-Ngai discuss the daily behavior patterns of the bobtail squid and why counterillumination is important for its survival:

      Daily behavior of the Hawaiian bobtail squid.

    2. light organ of E. scolopes has been studied for the past 20 years

      See Dr. McFall-Ngai discuss the structure of the light organ and the symbiosis with Vibrio fischeri. She also discusses how the light organ is able to modulate the amount of light produced by the Vibrio to match down-welling light:

      Structure of the light organ

    1. Selective logging is responsible for the conversion of at least 15 000 km2 of primary tropical forest in the Amazon each year (Asner et al. 2005; Asner, Loarie & Heyder 2010), and the resulting consequences for important ecosystem services including carbon storage and water and nutrient cycles remain unknown

      Global Changes influenced the expansion of selective logging, and brings questions about carbon emissions and the effects on recruitment and therefore diversity in forests.

    2. Our results further imply that communities may be altered by disturbance in ways significant to ecosystem processes, even when some measures of functional diversity do not change

      The authors suggest that losing or damaging communities would have considerably more negative effects on the ecosystem even if the sites are still diverse.

    3. gap edges discriminated slightly from gap centres, with a particular complement of heliophilic species (Table 2)

      Gap edges had more species that consumed higher amounts of sunlight (heliophiles).

    4. Some shade-tolerant species and some canopy taxa (Table 2) simply did not recruit into logged sites, even after 20 years

      Species that can grow in a closed forest canopy did not grow in sites that were logged after 20 years. These understory plants are important habitat and provide the forest with key services.

    5. we observed lower species evenness, as estimated by Pielou’s J, and much lower FEve, as estimated by Villéger’s FEve, in unlogged relative to logged habitats

      The authors did find that the relative number of species was lower in unlogged compared with logged habitats.

    6. We found no difference among logging habitats in taxonomic or FRic, with high richness in each of the three habitats (Fig. 2a, Table 1).

      There was no difference in the diversity of logged and unlogged habitat on either the types of species present or the functions they serve the community.

    7. quadratic entropy

      Diversity measure of classified data.

    8. relative abundances

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

    9. phylogenetic signal

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

    10. The resulting database contained 4140 individuals and over 2500 herbarium vouchers.

      These numbers refer to the total sample size in the experiment.

    11. herbarium voucher

      Pressed plant specimen deposited for reference.

    12. We therefore stratified our study design such that each habitat was sampled once within each of the six combinations of two topographic positions (hilltop and slope) and three taxonomic blocks, for a total of 18 samples.

      In statistics, stratification allows a researcher to divide entire populations in to subgroups.

      The authors divide the data set into hilltop and slope, and 3 differently identified groups.

    13. topographic features

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

    14. In particular, the proportion of edges and centres may differ depending on the gap shape (Broadbent et al. 2008; Lopes et al. 2009)

      Broadbent et al. focused on ecological changes caused by fragmentation. They determined that edges of a range are dominant and affects tree mortality, microclimates, and other aspects of tree communities; surrounding fragments may show differences in vegetation.

      This influenced the decision to look at gap edges and centers for the study.

    15. heterogeneous

      Different in kind.

    16. ha

      Abbreviation for hectare which is a unit of area.

    17. Inter-Tropical Convergence Zone

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

    18. Paracou experimental site (5°18′N, 52°55′W), a lowland tropical rain forest near Sinnamary, French Guiana (Gourlet-Fleury et al. 2004)

      The Paracou experimental site is located near the Paracou Field Station in French Guiana.

      Read more about the field station at: https://paracou.cirad.fr/station/overview

    19. (i) How does logging disturbance affect tropical tree community structure, in terms of diversity, evenness and composition? (ii) How do the taxonomic and functional responses of tree communities to logging differ? (iii) What guidelines can we give to timber harvesters to improve biodiversity conservation in selectively logged forests?

      The objective of the study is to address whether logging affects the forest species; is there a difference between what types of species and what each species contributes to the community when logged; and how this information can be used to improve how the forest is logged.

    20. evenness

      Refers to the relative abundance of species in a community.

    21. selective logging

      Removal of trees in a specific site or area.

    22. forest degradation

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

    23. deforestation

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

    24. reservoir of global biodiversity

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

    25. functional composition

      The mathematical space within an ecological unit.

    26. functional diversity

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

    27. (McGill et al. 2006

      Global change and species interactions are the focus of this study. Discusses how functional trait attributes emphasize global changes.

    28. biodiversity

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

    29. species richness

      Refers to the number of species.

    1. Australo-Melanesians

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

    2. Kruskal-Wallis Rank Sum (KWRS) Test

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

    3. 4.9 times lower expression in luciferase assays

      The authors explored if luciferase expression could be driven by different haplotypes; in other words, if the haplotypes had an effect on the expression of the luciferase reporter gene.

      If the expression from different haplotypes has the same distribution, the medians from the two groups would be equal, indicating that the different haplotypes have no impact on expression.

      In this case, the distribution of expression is not the same, indicating that the median expression is not equal, and the haplotypes do have an effect on on expression.

    4. We do not detect evidence for positive selection at MFSD12 using Tajima’s D

      Directional selection occurs when one trait is favored over others, leading to a shift in allele frequency toward the allele associated with the favored trait. This also leads to an excess of low-frequency alleles, and a negative value of Tajima's D.

      Balancing selection is a process by which multiple alleles are maintained in the population, for example when heterozygotes are at an advantage (which keeps both of their alleles at a relatively high frequency). This leads to a lack of rare alleles, and a positive Tajima's D.

      Tajima's D statistic of approximately zero indicates that the population is evolving with little or no selection.

    5. luciferase expression assays

      The luciferase expression assay is also known as the luciferase reporter assay, and is a method to detect how much expression can be driven by a particular enhancer.

      The assay is described in detail here: https://bitesizebio.com/10774/the-luciferase-reporter-assay-how-it-works/. Briefly, the authors put DNA that corresponds to the predicted, potentially causal regulatory regions into a vector that also has the luciferase gene, and then put this vector into cells. In this experiment, the authors use WM88 melanoma cells, which are a cell line grown from a patient who had melanoma.

      The luciferase gene will only get expressed (and the luciferase protein made) if the regulatory region ahead of it gets expressed in these cells. To detect whether there is luciferase in the cells, the authors break open the cells to release their proteins, add additional reagents that interact with luciferase (if it is present), and use a detector to see how much light gets emitted. More light emitted means more luciferase was present, which means that there was more expression being driven by the regulatory region.

    6. rs1426654 SNP between the West African Yoruba (YRI) and Ethiopian Amhara populations is 0.76

      An F<sub>ST</sub> of 0.76 here indicates that 76% of the variation in the people in these populations occurs between the two populations, whereas the remaining 24% of genetic variation occurs within the individual populations.

    1. Ewel JJ, DS Ojima, DA Karl, WF DeBusk 1982 Schinus in successional ecosystems of Everglades National Park. Report T-676. South Florida Research Center, National Park Service, Everglades National Park, Homestead, FL.

      Ewel et al. gives a recent and brief historical outlook on the introduction of the Brazilian pepper into South Florida and its subsequent ecological invasion and settlement in the Everglades.

    2. unimodal distribution

      Unimodal distribution is a statistical distribution with one clear peak.

    3. phenology

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

    4. diapausing

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

    5. The calculation of total fitness across the four life stages measured revealed that hybrid total fitness was more than 50% greater than either of their progenitors.

      This is a remarkably large increase in fitness due to hybrid. According to Dr. Geiger most plant hybrids that he's studied have shown a significant increase of 5-10% would already be impressive.

    6. The cumulative superiority of hybrids resulted in the establishment of nearly 45% more hybrid individuals than either parental type. In terms of seed germination, hybrids produced 20% more seedlings than eastern plants did. Hybrid seedlings had greater survival rates than western seedlings, with nearly 20% more living to the end of the experiment. The biomass of the resulting hybrid seedlings was also greater than that of the western seedlings; their average weight was 20% heavier.

      Hybrids had significantly better fitness in all categories tested. They germinated faster, produced more seeds, and grew to a larger size than the other types.

    7. Dry weight of harvested seedlings (i.e., biomass) was influenced by type (F ¼ 4:25, df ¼ 2, P ¼ 0:015), with hybrid seedlings obtaining greater dry weights than their western counterparts, 0:121 6 0:006 versus 0:100 6 0:005 g, respectively (fig. 6).

      Hybrid plants grew to the largest size of the three types.

    8. 1 standard error

      +/- 5% of actual value.

    9. Mean proportion of fruit with exit hole

      Hybrids had the lowest rate of exit holes caused by predation due to the wasps, followed by eastern and western.

    10. Hybrid seeds germinated at higher rates (18:4% 6 0:009%) than eastern seeds (14:6% 6 0:008%); however, no differences were found in the germination rate of the western seeds (16:0% 6 0:007%) and the other types

      Hybrids had a significantly higher germination rate than the other two types. The other two types had no significant difference between each other. This may be a cause for hybrids higher fitness.

    11. Bonferroni tests

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

    12. Bonferroni correction

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

    13. Post hoc tests

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