3,050 Matching Annotations
  1. May 2018
    1. 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.

    2. species distributions

      How species are arranged in an area.

    3. allometries

      Study of rate of growth.

    4. 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.

    5. 1 ha plot

      1 hectare plot = 100 acres.

    6. 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.

    7. 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.

    8. 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.

    9. Pg

      The picogram is equal to one trillionth of a gram.

    10. 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.

    11. Gentry plots

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

    12. coefficient of variation

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

    13. floristic composition

      Describes how the flowers are arranged.

    14. species richness

      The number of different species in a given ecological community.

    15. broad gradient

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

    16. aboveground tree biomass (AGB)

      Stems and leaves of the tree.

    17. carbon stocks

      Carbon stored in the forest.

    18. Field Inventory Methods

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

    19. 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.

    20. Tree Diversity

      The variability of different tree species in the ecosystem.

    21. 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.

    14. ANOVA

      ANOVA is a collection of statistical models used to analyze the differences between group means.

    15. haplotype

      Group of genes in the organism that was inherited from a single parent.

    16. Monte Carlo Markov Chain

      The Monte Carlo method is a tool used in statistics which can be applied to scientific research in which a distribution of the possible outcomes in a data set can be produced.

      Since the same experiment can be repeated many times we must have outcomes that show the probabilities of different outcome happening.

    17. STRUCTURE, version 2.3

      A program developed by the Pritchord lab at Stanford uses genotype data to investigate population structure. Its uses include discovering distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and mixed individuals, and estimating population allele frequencies.

    18. We performed a x2 test on the proportions of individuals with the A or B chloroplast haplotype per site (table 1) to verify that our type designations, which were classified according to the results of the Williams studies (Williams et al. 2005, 2007) and following their site locality sampling, were correct.

      Geiger et al. utilized the Pearson's chi-squared test (χ2), a statistical test applied to sets of categorical data to evaluate how likely it is that any observed difference between the sets arose by chance, to conclude the accuracy of the type designations given.

    19. biomass

      Biomass: Total mass of an organism or the mass of the organism in a a specific area.

      The weight was taken when the plant was dry for the simple reason that different species can hold different amounts of water. In order to obtain a precise measurement and compare the different species, the plant had to be dried.

    20. macerated

      To soften or the use of liquids to soften.

    21. USDA-ARS Invasive Plant Research Laboratory in Davie

      The field laboratory is a branch of the University of Florida's Everglade Experiment Station. The objective of which is to conduct research on vegetables and forage crops on the sandy soils of lower east Florida.

      Read more about the laboratory at https://www.ars.usda.gov/southeast-area/fort-lauderdale-fl/iprl/docs/history-of-the-iprl/

    22. exocarps

      Exocarp: The thin outer layer that covers the fruit.

      An example of an exocarp would be the thin layer located on the outside of a grape or apple.

    23. Mettler balance

      Mettler balance is a laboratory balance used to measure small masses to the sub milligram range. It can measure from .1 mg to .0001 mg depending on the model.

    24. as delineated by recent genetic analyses

      Williams found that 51% (301) of Brazilian pepper trees analyzed had a eastern haplotype and 49% (291) had a western haplotype.

      Haplotypes are a set of DNA variations that tend to be inherited together.

    25. mesocarp

      Fleshy middle layer of the fruit.

    26. exocarp

      The outer layer of the pericarp of the fruit. The skin of the fruit.

    27. phenolic

      Phenolic compounds are a class of plant secondary metabolites. These include a range of compounds such as phenolic acids, flavonoids, and other substances. They are responsible for fruit color.

    28. perennial

      A perennial is a plant that lives for two or more years. Most perennials flower multiple times during their life cycle.

    29. that can destroy a significant proportion of the fruit

      Wheeler's paper looked at the impact that Megastigmus transvaalensis had on the Brazillian Peppertree's Drupes. The wasp was found at all 18 sites surveyed containing the Brazilian Peppertree. The wasp damaged 23.5 ± 2.8% of the drupes during 1997–1998 and 38.5 ± 4.2% of the drupes during 1998–1999 in the winter. During the spring fruit production period, 76.3 ± 3.6% of the drupes were damaged by the wasp in 1998 and 74.8 ± 3.4% during the same period of 1999.

    30. (Williams et. al 2007).

      A survey of the Brazilian peppertree variance, was attained through spatial genetic and geostatistical research. Concluding with a history of dispersal, beginning with a short diffusive dispersal from South Florida, in where significant dispersal among intra-specific species is evidenced, instating long-distance jumps to North Florida.

    31. dioecious

      Dioecious refers to a plant or animal that has male and female reproductive organs in separate individuals.

    32. with results showing there is often no proof of an inherent fitness advantage to these hybrids

      Hardiman and Culley examined hybrid populations of the Callery Pear (Pyrus calleryana) in two different generations. They compared transpiration, stomatal conductance, and water use efficiency. In transpiration and stomatal conductance the advanced generation hybrids did better than the new hybrids but the advanced generation did worst in water use efficiency compared to the newer hybrids.

    33. Current research has focused on hybridization, both inter- and intraspecific, as a means of promoting the evolution of invasiveness

      Kolbe's paper looked at the evolutionary history regarding hybridization in lizards of the Galapagos islands.

      Facon's study looked at the evolutionary history of snails.

      Rieseberg's study looked at hybridization patterns in annual sunflowers.

    34. intraspecific hybridization

      Intraspecific hybridization occurs when the hybrid is born from parents of the same species that belong to different populations or breeds.

    35. Dlugosch and Parker 2008

      Dlugosch and Parker 2008- Surveyed the importance of or lack of genetic diversity among founding populations.

    36. genetic variation

      Genetic variation is variation in the alleles of genes both within and among populations.

      This variation is brought about through mutations.

    37. low-density

      Founding populations of invasive species are often small, so they experience the founders effect. The founders effect is a loss of a genetic variation due to a smaller population size.

    38. founding individuals

      http://www.journaloffloridastudies.org/0102peppertree.html

      Brazilian peppertree: a poster child for invasive plants in Florida

      V. Manrique, University of Florida

      J. P. Cuda, University of Florida

      W. A. Overholt, University of Florida

      This article provides an ample description of the impact that the Brazilian pepper tree is having on Floridian land. The article also provides information on measures being taken in order to control the species.

    39. Stockwell et al. 2003

      Stockwell et al. 2003- Discusses issues: (1) alternative perceptions of “evolutionary” and “ecological” time, (2) the role of contemporary evolution as an ecological process, (3) fitness as a bridge between evolution and conservation, and (4) challenges faced by conservation strategies based on gene flow estimation or manipulation.

    40. progenitors

      An ancestor or parent.

    1. G. D. Gilfillan et al., Am. J. Hum. Genet. 82, 1003 (2008).

      This study examines mutations in the SLC9A6 gene. Mutations in this gene have been linked to several neurological diseases, including X-linked intellectual impairment, microcephaly, epilepsy, and ataxia.

      Through sequencing and linkage analysis, the authors determined that a deletion in the region of the gene that codes for the cation exchanger NHE6 is largely responsible for neurological symptoms.

    2. G. A. Cox et al., Cell 91, 139 (1997).

      This study describes the swe (slow-wave epilepsy) mouse mutant as a model for generalized epilepsy in humans.

      The authors identified and mapped the mutation that caused epileptic symptoms, and discussed other effects the mutation might have.

    3. A. E. West, E. C. Griffith, M. E. Greenberg, Nat. Rev. Neurosci. 3, 921 (2002).

      This study examines the regulation of certain transcription factors by neural activity. It also investigated some of the mechanisms that regulate MEF2 activity.

    4. M. L. Jacquemont et al., J. Med. Genet. 43, 843 (2006).

      This study explored the heterogeneous nature of causes of autism, specifically using microarrays.

      One of the major findings from this study was that patients with locus duplications have less severe symptoms than those with deletions.

    5. J. Sebat et al., Science 316, 445 (2007).

      This study looks at de novo copy number variations (CNVs) in autism.

      They found that specific CNVs were present mostly in a single family out of their entire sample. They also showed differences in gene expression between simplex families (in which autism results from a de novo mutation) and multiplex families (in which autism is most likely inherited).

    6. J. A. Vorstman et al., Mol. Psychiatry 11, 1 (2006).

      This is a review of recent cytogenetic (the study of chromosomes) work on autism. The research discussed in this review looks as how large scale deletions, repetitions, and inversions in chromosomes may cause autism.

      A small percentage (around 3%) of patients with autism have cytogenetic abnormalities. Vorstman et al. identify regions of different chromosomes that future researchers should focus on.

    7. P. Szatmari et al., Nat. Genet. 39, 319 (2007).

      This study showed that copy number variants (CNVs) are a risk factor for autism. The authors also suggest that autism could be caused by some oligogenic factors.

      Oligogenically inherited traits are those that are determined mostly by a single gene, with other genes playing a smaller role in regulation and expression.

    8. N. Risch et al., Am. J. Hum. Genet. 65, 493 (1999).

      Risch et al. were among the first to propose that there may be multiple genetic abnormalities that can cause autism, and that these can affect different people in different ways.

    9. E. Fombonne, J. Autism Dev. Disord. 33, 365 (2003).

      A review of epidemiological surveys on autism.

      The author concluded that autism is associated with intellectual impairment in about 70% of cases, and that it occurs more often in males. They also showed that there is no correlation between autism and social class, and that there is not enough evidence to conclude that race or ethnicity have an influence on incidence.

    10. R. Canitano, Eur. Child Adolesc. Psychiatry 16, 61 (2006).

      Canitano discusses the link between autism and epilepsy, showing that epileptic seizures are more frequent in patients who have autism with intellectual impairment.

      The rate of comorbidity (simultaneous occurrence of both diseases) is 20-25%, meaning that around a quarter of people with autism also have seizures. This has to be taken into consideration for treatment plans.

    11. a subset of seemingly heterogeneous autism-associated mutations

      There are many different mutations that can cause autism. The mutations described in this paper are just one type.

    12. Our finding that deletions of genes regulated by neuronal activity or regions potentially involved in regulation of gene expression in autism suggests that defects in activity-dependent gene expression may be a cause of cognitive deficits in patients with autism.

      In some patients with autism, the authors found deletions of genes involved in postnatal brain development, which are normally regulated by neural activity. They also saw deletions in regions that are important to gene expression.

      Taken together, these findings suggest that abnormalities in the expression of neural activity-dependent genes can lead to some of the symptoms associated with autism.

    13. The connection between experience-dependent neural activity and gene expression in the postnatal period forms the basis of learning and memory, and autism symptoms typically emerge during these later stages of development.

      The stages of brain development that occur after a child is born require input from the environment and regulation by neural activity. Some of this neural activity depends on a child's experiences. This is especially true during the later stages of development.

    14. The regulation of expression of some autism candidate genes by neuronal membrane depolarization suggests the appealing hypothesis that neural activity–dependent regulation of synapse development may be a mechanism common to several autism mutations.

      Several of the "candidate" genes (i.e., genes that may cause autism) the authors studied here are regulated by neural activity. Because of this, the authors suggest that disruptions in this regulation by neuron could be a potential cause of autism.

    15. Endosomal trafficking and protein turnover

      To function properly, cells are constantly creating, recycling, and transporting proteins. Interruptions in this process can be a cause of disease.

    16. neuronal cell adhesion

      Neurons express special proteins that allow them to adhere to each other and to other cell types. The ability to bind to each other is important for neurons' ability to communicate properly.

    17. glutamatergic transmission

      The release of glutamate, a common neurotransmitter.

    18. Our data implicating noncoding elements in patients with shared ancestry, as well as the heterozygous nonsense changes in patients without shared ancestry, suggest that loss of proper regulation of gene dosage may be an important genetic mechanism in autism

      In addition to disease-causing autosomal and recessive mutations, the authors showed that in some cases regulatory elements and gene dosage can contribute to autism.

    19. homozygosity mapping provides an important approach to dissect this heterogeneity

      Families that share a larger part of their genome are more likely to be homozygous for certain genes. Studying these families can make it easier to identify and isolate the effects of certain genes.

    20. The heterozygous changes, in particular the nonsense mutation, likely affect gene dosage and suggest that the study of consanguineous pedigrees may identify genes of importance in nonconsanguineous populations as well.

      Heterozygous mutations can be deleterious if two copies of the functional gene are required for a pathway. Even having one copy of the functional gene may not be enough.

      The authors suggest that looking at consanguineous families may help identify genes of interest in nonconsanguineous pedigrees, where there is more diversity.

    21. nonsense

      A mutation that changes a codon that would normally correspond to an amino acid to a stop codon.

    22. carried by two male siblings with autistic disorder as well as their mother

      The authors found the NHE9 nonsense mutation in two male siblings with autism, as well as their mother, who showed childhood signs of intellectual disability.

      In addition, one of the siblings had epilepsy and the other had symptoms of epilepsy (though no diagnosis).

      The authors did not find the mutation in any of the controls, even on resequencing.

    23. gene dosage-dependent

      "Gene dosage" refers to the number of copies of a gene in a particular genotype. A gene is dosage-dependent if a certain number of copies is necessary for proper function.

      Although there are many factors that influence gene expression, in general more copies of a gene will result in more protein product (either directly from the gene or as a result of regulatory mechanisms).

    24. A similar nonsense mutation in the final extracellular loop has recently been found in the related NHE6 gene in a patient with an Angelman-like syndrome, which involves both autism symptoms and epilepsy

      The mutation to NHE9 is also similar to a mutation in NHE6, which has been linked to a patient who exhibited symptoms of autism and epilepsy.

    25. This nonsense change occurs within two amino acids of a similar nonsense mutation in Nhe1 that causes slow-wave epilepsy in mice

      In the patients with epilepsy and autism, the authors found a NHE9 mutation that is similar to a mutation in Nhe1 that causes epilepsy in mice.

      Mice with this mutation, called swe mice (which stands for slow-wave epilepsy mice), were the first mouse models of human generalized epilepsy.

    26. we sequenced NHE9 in other patients with autism and epilepsy

      The authors compared the genotypes of patients who have both autism and epilepsy to determine if these patients had similar mutations to NHE9 and surrounding genes.