1,059 Matching Annotations
  1. Mar 2018
    1. anthropogenic

      The influence of humans in the modification of nature.

    2. habitat fragmentation

      The division of large habitats into smaller patches, resulting in discontinuities within the organisms preferred habitat.

      This phenomena results in the degradation of an ecosystem.

    3. hermaphroditic flowers

      A flower that contains sex organs of both the male and female. These organs are known as the carpellate (produces ovules) for females and staminate (produces pollen) for males.

    4. Fig 2. Principal coordinate and STRUCTURE (K = 2) analyses of DNA microsatellite data for the two known populations of Coccothrinax jimenezii. The scatter diagram shows PCO values along the first two coordinates with their respective percentages of variance. Inset in upper right corner shows results yielded by STRUCTURE. Color and box sizes indicate the cluster type of each individual and the number of plants sampled per site. The vertical lines indicate the probability that each individual belongs to an inferred cluster. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

      This figure describes the 2 populations of Coccothrinax Jimenezii and it shows the results that are yielded by the processing computer software called STRUCTURE that is used for analysis of microsattelites.

    5. The Dominican Republic population had a very low Fis value of 0.092 showing only a small degree of inbreeding. The Fst value was 0.497 and Nm between the two sites was 0.253. Over 50% of the molecular variation (AMOVA test) was between populations.

      Statistically the DR populations of the palms were more interbred than the ones that were in Haiti

    6. However, the high proportion of homozygotes detected in these two loci could also be the result of stochastic processes associated to genetic drift and inbreeding.

      Higher proportions of homozygotes have been found to be a result of a random occurrence in the process.

    7. The Bayesian clustering program STRUCTURE v.2.3.4

      In this experiment the authors used The Bayesian clustering program STRUCTURE v.2.3.4 as a way to estimate the underlying genetic structure among populations.

    8. A Monte Carlo Markov chain method was applied with 100,000 iterations, a burn-in of 10,000 and the significance level set at P < 0.001. Principal coordinate analysis (PCO) among all the individuals included in our study was computed with GenAlEx based on the algorithm developed by Orloci (1978) after conversion of the individual-by-individual genetic distance matrix, as defined by Smouse and Peakall (1999), to a covariance matrix and data standardization.

      This experiment was conducted with the purpose of producing a scatter diagram that summarized the original multidimensional data set and revealed the presence of groups. They also used GenAIEx to analyze the principal coordinate among all individuals in the study. This experiment also allowed them to detect the genetic structure of populations projected in a continuous space.

    9. Tests for Hardy–Weinberg Equilibrium (HWE) and the U test (Rousset and Raymond, 1995) for heterozygote excess or deficiency were run with GenePop v. 4.2 (Raymond and Rousset, 1995, 2008) using 10,000 Monte Carlo Markov chain iterations (Guo and Thompson, 1992).

      This experiment was done with GenePop v. 4.2 using 10,000 Monte Carlo Markov chain interactions. Throughout this experiment the researcher tested for Hardy–Weinberg Equilibrium, which says that the genotype frequencies in a population tend to remain constant throughout generations if no evolutionary influences are present. They also used GenePop v.4.2. to do a U test and to look for heterozygote excess or deficiency.

    10. The program Micro-Checker v. 2.2.3 (Van Oosterhout et al., 2004) was used to evaluate the presence of null alleles and allelic dropouts, employing 3000 randomizations. Descriptive statistics

      This experiment was carried out with the purpose of identifying null alleles which are those that express the same trait whether they are homozygous or heterozygous, and allelic dropouts which are copies of a locus that are not amplified by the primer. This part of the experiment was completed through the use of Micro-Checker v. 2.2.3.

    11. PERL script program PAL_FINDER_v0.02.03 to identify potential 4 bp microsatellite repeat elements among the reads (Castoe et al., 2012; Slashdot Media, San Jose, California, USA). Among these SSR loci we selected six that cross-amplified with samples of C. jimenezii and that were polymorphic with different samples of this species.

      This experiment was conducted using the PERL script program PAL_FINDER v0.02.03 and the 100bp Illumina sequences from the previous experiment. This experiment resulted in the identification of potential 4bp microsatellite repeat elements. Of these microsatellite repeats, only six were selected which had different phenotypes than C.jimenezii.

    12. fructifications

      In angiosperms (flower-producing plant), when a plant bares fruit.

    13. inflorescences

      In a flowering plant, it is a cluster of flowers either on a main branch or system of branches.

    14. ethnobotanical

      The study of how humans within a cultures use plants as folk remedy.

    15. Extensive field work that included demographic studies and conservation assessments was conducted both in Haiti and the Dominican Republic. Distribution patterns and discussion of conservation concerns were reported by Peguero et al. (2015a).

      The research here was important because it identified the amount of Coccothrinax jimenezii that were present in the research sites. It also described patterns of palm distributions.

    16. As a Critically Endangered palm, C. jimenezii has been central to our conservation biology activities during the last 2 years as it is one of the most threatened species of this genus

      Given the great threat to the C. jimenezii, conservation efforts have been maximized.

    17. translocate

      To move from one place to another.

    18. genetic bottlenecks

      An event/events that limit genetic variation in a population and result in populations that can lead to genetic drift.

    19. Hardy–Weinberg Equilibrium

      A model used to measure whether a population has reached equilibrium, meaning it stopped evolving.

    1. PCR inhibitors

      Factors that do not allow amplification to occur.

    2. difference plots clearly show the distinct profiles obtained for the mixtures

      Fluorescence is used to determine the profiles of the DNA mixtures between the Symbiodinium types.

    3. an alternative technique to rapidly and accurately genotype monotypic Symbiodinium populations.

      In this experiment, a faster and alternative method was used in order to accurately genotype the monotypic (one type) Symbiodinium populations. This method was compared to those with DGGE profiles, where they extracted the gel bands and sequenced them based on region 2 of the ribosomal DNA transcribed spacer.

    4. The touchdown protocol consisted of an initial denaturing step at 92 "C for 3 min, 21 cycles at 92 "C for 30 s, 62 "C for 40 s, and 72 "C for 30 s, decreasing each cycle 0.5 "C, followed by 15 cycles with a 52 "C annealing step and a final extension at 72 "C for 10 min.

      One PCR cycle consists of denaturing, annealing, and extension steps. Denaturing means that the double-stranded DNA is separating into single-stranded DNA. Annealing refers to primers being added to the DNA strand. The extension step is when Taq polymerase adds dNTPs to the annealed primer.

    5. PCR amplification had the following conditions

      The PCR amplifications exhibited a set of conditions in order to compare the cultures of a HRM analysis to that of a DGGE analysis.

    6. reverse primer

      Primers are sequences where genetic material starts to replicates. Reverse primers are those that replicate from the 3' to 5' end of the DNA strand.

    7. forward primer

      Primers are DNA sequences where genetic material starts to replicate. Forward primers are those that replicate from the 5' to 3' end of the DNA strand.

    8. One limitation of HRM analysis is that genotyping is restricted to the collection of available reference genotypes. The more Symbiodinium strains genotyped by the scientific community, the more power HRM will gain. Another limitation of HRM is that it is constrained to the detection of monotypic Symbiodinium populations. In our case, this limitation was proven when performing the pairwise combinations of Symbiodinium strains. Therefore, in cases where genotypes cannot be identified, these could be the result of either a lack of an appropriate reference genotype at the time of the analysis and ⁄ or the presence of a mixture of strains.

      There are two restrictions to HRM analysis; it only refers to the available genotype collections and can only detect monotypic Symbiodinium populations.

    9. Rotor-Gene 6000 (Qiagen)

      A machine that does PCR in real time.

    10. In this study, we showed that high-resolution DNA melting analysis (HRM) allows precise genotyping of Symbiodinium strains. There are several advantages of HRM, making it an attractive technique. HRM is a closedtube technique that reduces cross-contamination and does not require the handling of hazardous materials, such as acrylamide, formamide and ethidium bromide. It is time-effective, requiring <2 h per run, which facilitates rapid turnover. This technique is sensitive, simple, nondestructive and of low cost.

      HRM analysis was shown to be just as effective in detecting the genetic make-up of Symbodium strains as DGGE analysis. Some examples include less time to run the procedure, cross-contamination prevention, and inexpensive runs.

    11. Fluorescence

      The property of absorbing light of short wavelength and emitting light of longer wavelength.

    12. For each genotype, one of the samples was used as the reference genotype, while the other was treated as an ‘unknown.’

      In order to determine if HRM is accurate, onr of the genotypes was used as the sample and the other was used as an unknown to identify if the template concentration affects accuracy of genotyping.

    13. For (b–d), the difference of the fluorescence between a chosen melting curve set as standard and each melting profile was plotted against temperature resulting in a ‘fluorescence difference’ plot.

      The mixed strains had a different melting point than that of the pure strains.

    14. To understand potential limitations of the HRM technique, three tests were conducted.

      Three different tests were conducted for HRM:

      1. Tested out if the template concentration affected the accuracy.
      2. DNA from Symbiodinium types of the same clade were combined to identify if it will change melting profiles.
      3. DNA from Symbiodinium types of the all clades were combined to identify if it will change melting profiles.
    15. The melting profiles of each clade were clearly distinctive. Moreover, different melting profiles were obtained within Symbiodinium clades (Fig. 1b). These differences were attributed to variation in the nucleotide composition. For example, Symbiodinium types A3 and A4 have 50 bp different when comparing their sequences from DGGE bands, while the difference between types D1a and D1 was only 2 bp. This distinction was clearly seen in their melting profiles (Fig. 1a).

      Keep in mind that even a single base change in the DNA sequence can cause differences in the High-Resolution Melting curve. In this experiment, forms of the same Symbiodinium clade, A3 and A4, have 50 different base pair changes whereas the clade, D1a and D1 have a smaller base pair (bp) difference of 2 bp.

    16. The rest of the samples were assigned to a genotype based on the percentage of confidence

      The amplifications were compared based on the best percentage confidence (accuracy) of the specific culture ( HRM vs. DGGE). This was done through a software. In order to calculate the error, the square of the difference was taken between the fluorescence of each reading sample and reference genotype.

    17. HRM consisted of a temperature ramp between 78 and 90 "C, rising by 0.1 "C⁄ 2 s. Samples with the best amplification were used as reference controls for each genotype

      HRM analysis began after the PCR procedure. The amplicon DNA was gradually heated from 78°C to 90°C. As the temperature increased, the melting point temperature of the amplicon was reached. The sample DNA denatured and the double stranded DNA separated. As a result, the fluorescence faded away.

    18. HRM assays were performed using the Rotor-Gene 6000 (Qiagen) with the provided Rotor-Gene Q Series Software v1.7 (Qiagen). PCR was carried out using the Type-It HRM PCR kit (Qiagen), with 1 lL of 1 ng ⁄ lL template, 1· HRM PCR Master Mix (2· HRM PCR Master Mix containing HotStartTaq Plus DNA polymerase, Type-it HRM PCR buffer (with EvaGreen dye), Q-solution, dNTPs; Qiagen), 0.7 lM of each primer (ITSintfor2 and ITS2rev), and adjusted with RNase-free water to a final volume of 10 lL.

      Within the DNA sequence, the region of interest was first amplified (known as an amplicon) using the polymerase chain reaction (PCR) method. During PCR, a special saturation dye called, EVAGreen, was added to the reaction. This allowed the amplicon product to fluoresce in the presence of double stranded DNA. Moreover, as the amplicon concentration increased in the reaction tube, the more light was emitted.

    19. EtOH

      Ethanol, also called ethyl alcohol.

    20. DNA extractions were carried out using DNeasy# Plant Mini kit (Qiagen)

      A standardized kit was used to extract each culture's DNA, where two replications of the DNA were obtained.

      The ITS2 (a specific gene in a ribosome) was then amplified.

    21. pestle

      Tool for grinding.

    22. lysis

      The rupture or disintegration.

    23. photoperiod

      Periods of light and dark cycles.

    24. Symbiodinium cultures of clades A–E were obtained from Dr Scott Santos

      The experiment consisted of cultures of the Symbiodinium clades A-E for growing marine algae; the media was replaced (only half of it) with fresh medium every month. They were set at a constant temperature of 25˚C and were exposed under a constant light intensity for 12 hours light and a 12 hour dark period.

    25. f ⁄ 2 media

      Solution for growing marine algae.

    26. mass spectroscopy

      An instrument that allows for identification of different chemicals by looking at their mass to charge ratio.

    27. Previous studies have shown HRM as a more effective option

      An extension of High-Resolution Melting (HRM) known as a LunaProbe, was used with LCGreen Plus dye to genotype anonymous blood samples. This eradicated the need for costly probes that could fluorescence, or emit light.

      Read more in Genetic Engineering & Biotechnology News: https://www.genengnews.com/gen-articles/assay-high-resolution-melting-unlabeled-probes/1986

    28. Symbiodinium

      Dinoflagellates that interact and live around other organisms such as a coral.

    29. high-resolution melting (HRM)

      A technique that detects mutations, and differences in DNA samples.

    30. re-amplification

      To increase the amount of genetic material (DNA) once again.

    31. denaturant solvent

      Solvent that alters the qualities of what is being worked with. This usually causes a destruction of it's properties.

    32. ITS2 rDNA,

      The ribosomal DNA with the internal transcribed spacer, specifically region 2. This sequence of the gene varies between species.

    33. internal transcribed spacer

      A spacer DNA (region of noncoding DNA in genes) between the small subunit ribosomal RNA and the large subunit ribosomal RNA.

    34. denaturing gradient gel electrophoresis

      A technique that separates DNA fragments.

    35. PCR-amplified

      Polymerase chain reaction, or PCR, is a technique in the laboratory in which short sequences of DNA are amplified.

      PCR has been used to detect DNA fragmentation on processed foods, where 18S rRNAs where the target for the experiment. Since they are small fragments, they work perfectly with the process since the goal is to amplify them to take a better look at them. The results of this experiment determined that the degree of DNA fragmentation are a great index for the chemical evaluation of various different foods.

    36. Restriction fragment length polymorphism (RFLP

      A technique that can detect variations in homologous DNA sequences.

      RFLP has been used to analyze patterns of DNA cleavage after restriction enzyme treatment. It has also been used to detect mRNA modified bases. The goal of this experiment was to present the ability of RFLP to show the different ptRMs at specific sites of several tRNAs.

    37. pandemic species

      A species that is found within a whole country, or continent.

    38. clades

      Group of organisms that is said to have come from a common ancestor.

    39. genus Symbiodinium

      A group that contains endosymbiotic dinoflagellates. They typically use animals such as corals and anemones as hosts.

    40. dinoflagellates

      Marine photosynthetic organisms that have two flagella (long slender membrane that allows organism to swim).

    41. scleractinian

      Stony or hard coral.

    42. Results showed that twenty cultures were correctly genotyped in <2 h using HRM analysis with a percentage of confidence >90%

      By using the HRM technique, the genetic make-up (genotype) of twenty Symbiodinium cultures were identified in less than 2 hours with a confidence percentage of greater than 90%. A >90% confidence interval means that more than 90% of the population distribution is contained in the confidence interval. In other words, there is only a 10% chance that the cultures were incorrectly genotyped.

    43. (HRM) analysis is a closed-tube, rapid and sensitive technique able to detect DNA variations. It relies on the fluorescencemelting curves that are obtained from the transition of double-stranded DNA (dsDNA) to singlestranded DNA (ssDNA) as a result of temperature increase.

      Melting curves are compared through HRM analysis in order to detect the different sequences in various strains of DNA. There are many new methods and sequence based studies with HRM including gene dosage quantification, mutation identification, gene scanning, to name a few.

      Read more in Biocompare: http://www.biocompare.com/Editorial-Articles/41779-High-Resolution-Melt/

    1. Figure 1.

      The stationary partition (a) yielded the results of 96%-100% bootstrap proportions whereas the nonstationary partition (b) gave results of 100% bootstrap proportions throughout.

    1. impedance

      The resistance of an electric circuit towards a current due to a voltage change.

    2. transdermal

      'Derma" refers to skin and in this case, "trans" means through; so transdermal means the electroreceptors are being emitted through the skin of the fish.

    3. electrosensory lateral line lobe (ELL)

      A structure resembling a cerebellum in electric fish that contains secondary sensory neurons to which sensory signals detected by electroreceptors are relayed.

    4. First, many electric fish scan and swim with rigid control of the spine and body posture, which should maintain the relative orientation of field generator to field receptors and so reduce undesirable reafferent modulations. Our video and simulation results strongly support this conclusion.

      Based on the movement of the electric fish around the "ping-pong ball apparatus" created by the authors, electric fish preserve the positions of their electric field generator and receptors and thus reduce changes to their sensory stimulation by maintaining a rigid body posture and control of their spine while swimming. These important physiological characteristics of electric fish are supported by their precise tail-first cartwheels while interacting with the "ping-pong apparatus".

    5. These scanning and tail-probing behaviors have been described previously

      The scanning and tail probing behavior of fish is the process in which they use certain tail movement around an object in order to discover the depth and size of objects in their environment. Think about what happens when you put a goldfish into bowl after it has been in an plastic bag. It will immediately start swimming around and swishing its tail around. That is a process of scanning and tail probing behavior.

    6. electrophysiological studies at higher levels of the nervous system, for example, by predicting specific emergent features in the midbrain and cerebellum.

      This sentence highlights another example where the products of this research can be used in future experiments. In this example, the authors are stating it can be used in future neurological oriented studies of the midbrain and cerebellum; areas of the brain that are primarily oriented with executive functions.

    7. These ascending patterns should help to elucidate both the descending input and the neural computations within the ELL.

      The author describes here that with the data he has discovered and portrayed in the graph above the understanding of how neural computations and descending input for these fish occur will become clearer to understand and even reproduced if there is a need to help validate the findings of his experiment. Also the visual components of his findings allow the readers, both from the science community and from the general population, to more conceptually understand the travel of the high-frequency electrolocation travels.

    8. The models proposed here may therefore stimulate renewed experimental interest in the neural basis of electrolocation.

      In this statement, the authors concluded that the quantitative models and methods they employed throughout their experiment will attract interest to the neural components of electrolocation by providing visual representations of their results, which ultimately make these complex concepts and relationships between different sets of data easier to understand. In other words, simply just sharing data and results without any visuals using with complicated scientific jargon is ineffective in conveying the author's messages.

    9. Therefore, a considerable volume of the electric fish brain is devoted to electrosensory processing. For the computational algorithms proposed above to be involved in electrolocation, they must have a plausible neural implementation in the fish’s nervous system. We propose one such projection onto the neural networks in the electric fish brain.

      Electric fish are able to receive signals and information from emission of electroreceptors in their environment passing through their skin. After the contact of the electroreceptors and the external stimuli, information is relayed in a pattern to the electro-receptory organs of the fish. Since this is an essential part of their way of life, the authors know a large amount of neurons and brain matter are involved in this process. Therefore, scientists hypothesized that in order to ensure this sensory information is relayed efficiently and quickly to the brain of the electric fish, there must be an algorithm used by the neural networks in the fish in order for this process to occur.

    10. The scanning or probing movements have also been hypothesized to help recognize object features.

      The movements that these electric fish use allows for the recognition of an object's features. Evidence from Heiligenberg's stimulation show that when electric fish bend their tails it increases the spatial contrast and makes it easier to distinguish an object's features. While Bacher's 3-D model showed that fish's tail bending help show a clear difference between the object's location and its shape. The BEM stimulation showed that electric fish control their movement in order to regulate their electrosensory system input by demonstrating a stable image of the rostral body which is thought to help the fish to distinguish features.

    11. Video and simulation results from a scanning behavior of Apteronotus albifrons.

      Data from the videos and the scans (which produced dipolar distortions) provided results showing how certain kinetic movement patterns exhibited by the fish are use to maneuver in their environment.

    12. To address these limitations and to simulate exploratory behaviors further, we built a complementary three-dimensional BEM electric fish model.

      The boundary element numerical method (BEM) simulator was built by the authors to remedy an issue presented by their standard three-dimensional simulator (color-coded mapping of a stationary fish): only the proximal (close to the center/point of origin) side of the fish's body could be digitized since secondary effects of the body could not be accounted for on the EOD. The BEM simulator addressed this problem by allowing objects under analysis to be bent or randomly shaped via nodes placed on their surfaces, thus giving the BEM simulator the ability to analyze secondary effects and other regions of the fish's body.

    13. ellipsoids

      A 3D geometric figure whose planes or sections consist of ellipses or circles.

    14. These results are summarized in Fig. 4

      Overall, multiple features of an EOD map contribute to one physical characteristic of an electric fish, rather than each feature affecting one specific characteristic exclusively.

    15. electric field vectors (EOD maps)

      Electric field vectors (EOD maps) can help determine the size, position, shape, distance, and other physical features of a small object, such as an electric fish, by creating electric images with features that visually represent and correspond to each characteristic of the object in question.

    16. Distinguishing sensory exafference from reafference is critical to the success of active electrolocation

      What is critical to the success of active electrolocation is the knowledge of whether the electricity that is felt between the animal and the object is coming from the animal itself (reafference) or by the objects themselves sending the signal to these animals (exafference).

    17. sensory reafference

      Sensory reafference consists of signals received by a sensory region when the corresponding sensory organ is moved or stimulated.

    18. multiphasic

      Made up of multiple stages, phases, or steps.

    19. EO propagation

      The spread of the signals that are emitted by the electric organs within the organism.

    20. dorsoventrally

      Towards the direction of the dorsal and ventral regions of a fish's body (above and below, respectively).

    21. This allows the fish to swim equally well forwards or backwards and to hold the body in an arc around objects (Bastian, 1986; Toerring and Belbenoit, 1979) while maintaining rigid control over the electroreceptive surfaces. Presumably, by keeping the detector array in a fixed orientation with respect to field generation, this controlled body motion reduces the number of variables that must be taken into account to interpret electrosensory information.

      The author is explaining here that the fish have a certain mechanism in their body that allows them to move much more fluently, whether forwards or backwards, and allows them to wrap around objects while not compromising the information they get from their electroreceptors. The mechanism that allows them to do this is done by keeping their bodies rigid and only moving their dorsal or ventral fin.

    22. curarized and respirated

      The fish that were kept in the lab were curarized (given a drug so their muscles could relax and body) and respirated (to make sure the animals were getting enough oxygen to breath).

    23. impedance

      The resistance of an electric circuit to an opposing or alternating current.

    24. the EOD becomes very complicated and rapidly changing, reflecting a complicated and heterogeneous electric organ

      The complexity, speed, and variability of the electric organ discharge can be linked to the innervation patterns of the electric organ itself, which consists of thin nerve trunks and numerous branches of the electromotor axons leading towards the electric tissue.

    25. ampullary

      Resembling an ampulla which is a dilated piece of a canal or duct.

    26. ampullary electroreceptive predators

      A predator that is able to use to receptors in their electric organs to sense the environment around them. The electrorecptors in the organism are located in a dilated part of a canal or duct.

    27. noninnervated anterior face

      This phrase means that the front-facing side of the organism does not have a supply of nerves. "Non" - not , "innervated"- to supply with nerves.

    28. propagating caudally

      This means to spread toward the tail or posterior section of the body.

    29. biphasic

      A cycle, object or process that has two phases.

    30. rostral

      The anatomical term that refers to the area of the body that located near the oral and nasal region.

    31. Synchronized activation along the length of the electric organ implies effective mechanisms for compensation of neuronal propagation delays along the length of the EO (Bennett, 1971).

      Bennett's article analyzes the anatomy and physiology of the electric organs found within these electric fish. The membrane physiology of these electric organs evolved independently into six different groups and resulted in different membrane functions in different electrolytes which affect the electrorecption in the electric organism.

    32. spatiotemporal

      Spatio means having to do with space, temporal means time, so together this word means having to do with space and time. In this context the EOD potentials have both spatial extension and a time-related duration.

    33. ventral

      The anatomical position that relates to the underside or the abdominal part of an organism.

    34. oscillating dipole

      Dipoles are equal magnetic positive and negative charges separated by a distance. In this case, oscillate means to cause the electric current to move in a way that influences the dipoles to change and fluctuate. Picture strings vertically tied to a rope in the middle, movement to the rope cause the strings to ripple outward in the direction they are facing.

    35. To date we have mapped the EODs of three gymnotiform wave species and seven gymnotiform pulse species. These maps, for the first time, clearly illustrate the full spatiotemporal structure of the EOD (Fig. 1). In the majority of species, the EOD waveforms vary greatly with location, revealing considerably more complex patterns than were previously appreciated.
      • "Wave" fish have longer discharges when it comes to EOD's and continuous charges, "pulse" fish however have silent intervals between discharges.
      • This experiment, as the author illustrated above, allows for the statistical analysis of the EOD discharges rather than the collective qualitative data that stood in its place.
      • With this experiment, the waveforms created by the EOD's are affected by their location and proximity to other objects, and although in the charts both fish have many similarities, it seems the further the fish, the easier it becomes to tell the wavelength between both fish apart.
      • Thanks to this study, it is no longer difficult to explain the results of this experiment, previously there were no numbers to support claims, but now the authors have helped to provide some numerical values to this type of research.
    36. We have developed a powerful system for mapping EOD potentials and electric field vectors in three dimensions.

      Electric organ discharge (EOD) potentials, which are generated by electrodes located near the head and tail of an electric fish, are typically difficult to analyze due to variations among different species and the inconsistent geometry of the EOD spatial patterns. Thus, to overcome this obstacle, the authors devised a system for the visual representation of EOD potentials to facilitate analysis. This was achieved by the creation of a robotic arm that recorded the EOD of an immobile electric fish at multiple positions around its body. The motionless state of the fish also enabled the authors to capture the exact times of numerous EODs. Each EOD measurement collected from the arm was then digitally processed and converted into a color-coded map overlaid on a diagram of the fish's body for further research/analysis in the phenomenon known as electrolocation.

    37. dipolar

      When it says that the spatial pattern of the EOD has dipolar geometry, you can imagine a magnet where the animal is the positive side and the object it is heading towards is the negative side and they attract each other making a sort of map.

    38. electrodes

      Objects or parts that are able to conduct electricity in nonmetallic substances (e.g water).

    39. neurocomputational

      "Neuro" refers to the organism's nerves and nervous system and "computational" refers to a calculation. The study is calculating the work that the nervous system is conducting in order to use electrolocation.

    40. autogenous

      Auto means "self" and genous means "producing/originating from", so this word itself can be defined as self-producing or originating from within.

    41. electrogenesis and electroreception

      Certain marine and aquatic vertebrates have electric organs which allow the organism to produce electric fields (electrogenesis).The electric organs of these organisms contain electroreceptors, which provide the organism the ability to sense the electric fields in their environment. The sensory system created by the electroreceptors within these organism results in the electroreception and allows the organism to be better adapted to their underwater and salty environment. http://onlinelibrary.wiley.com/doi/10.1113/expphysiol.1988.sp003144/epdf

    42. neural substrates

      Functional units of the central nervous system that are organized systematically based on function and vary in their anatomical location in the body; they all work together to carry out complex body functions, in this case the process of electrolocation.

    43. teleost fish

      An extremely large and diverse group of fish that are mainly identified by the presence of a homocercal tail, in which the upper and lower parts of the tail are equal in size. An example of a teleost fish would be a tuna or halibut.

    44. electroreception

      The ability to detect weak naturally occurring electrostatic fields in the environment. Electroreception aides in the detection of prey, food sources, and objects. It can also be used by some species as a means of social communication.

      -This excerpt provides a brief synopsis of what electroreception is and explains its relevance to the experiment discussed in this article.

      https://www.britannica.com/science/electroreception (Hopkins,2017)

    45. electromotor

      This term refers to a machine that is able to produce electricity in order to produce motion. For electric fish and similar organisms, it means their organs have the ability to produce electricity, that is used to produce movement.

    46. electric organ discharges (EODs)

      In some species of electric fish, there are sex-based differences between the EODs of males and those of females, all of which are regulated by steroid hormones. The primary hormones responsible for these variations in EOD are androgen (produces male-type EOD rates) and estrogen (produces female-type EOD rates). A notable example of a sex-based EOD difference is the male fish's ability to attract female fish with EODs that emit energy within the appropriate sensitivity ranges.

    47. electroreceptors

      Organs found in fish that can recognize electric stimuli using specialized sensory cells.

    48. quantitatively

      Measuring things through data and numbers. In this context, scientists currently do not have numbers to describe the process of electrolocation.

    49. electrosensory

      The ability of the nervous system of certain organisms to sense electrical impulses in their environment. It is similar to when a person uses their nose to smell a certain scent or odor in the proximity; in this case the electric fish are able to use their organs to sense electrical pulses nearby.

    1. A. D. Simmons, C. D. Thomas, Am. Nat. 164, 378–395 (2004).

      The researchers examined bush crickets with variability in wing shape. Crickets on the edge of the range had a higher frequency of long wings which aid in dispersal, compared to the individuals at the core of the range which had fewer long-winged individuals. While long-wings allow for better dispersal, they reduce reproduction, which may be why the core population evolves to have fewer long-winged individuals.

    2. E. Pachepsky, J. M. Levine, Am. Nat. 177, 18–28 (2011).

      Looks at the effect of density dependence on the spread of annual plants through a patchy habitat. It was seen that landscape patchiness and the number of annual plant invaders worked together to create a strong role for density dependence. Furthermore, infraspecific competition was seen to limit the spread of annuals through patchy landscapes by limiting the production speed of seeds in plants. Density dependence was not seen when continuous density was used.

    3. J. L. Williams, R. E. Snyder, J. M. Levine, Am. Nat. 188, 15–26 (2016).

      This study looks at the role of evolution in spreading populations in patchy landscapes. While natural selection typically favors organisms who produce many offspring, in these patchy landscapes, organisms that tolerated competition but produced less offspring performed better.

    4. First, the focal populations were effectively asexual, meaning that trait variation was not continuous and traits were perfectly linked. Nonetheless, it is not clear how more continuous variation or less linkage between traits would influence the effect of evolutionary change on spread velocity.

      When comparing this study to results that might be found in the wild, a few things must be taken into consideration. First, the plants used in the study were asexual. This means that evolving traits were the same traits in every population, and the variation developed by evolution would be directly passed on to offspring. The second consideration is that the while the changes to genes were intentional, there's a chance that some of the changes could have been due to unintentional maternal or epigenetic effects. And lastly, the conclusions were made assuming that all genes were carried through the dispersal and none were left behind. This point is important because if genes that favored dispersal were the only genes being carried by dispersing populations, the response of the population would be more due to a genetic drift or narrowing of potential traits than to evolution.

    5. Though weaker, this effect also emerges in models of finite populations in continuously favorable landscapes (fig. S4) (26)

      Instead of looking at how different environmental conditions, such as gaps, changed the migration of plants, research looked at how the variability in population growth of invading species affected their velocity of spread. Variability in population growth was seen to decrease the velocity of biological invasions. However, the decrease in velocity was small enough that it is largely negligible.

    6. Height and the average distance of the farthest dispersed seed, traits correlated with one another (Spearman rank correlation coefficient rs = 0.55, P = 0.046), increased with landscape patchiness (backward and rightward shift of the replicates with increasing patchiness in Fig. 3; P = 0.008 and 0.060, respectively, Table 1).

      The correlation between between height and average dispersal distance is significant. It is very likely that the relationship between height and the dispersal is not caused by random chance. The correlation between landscape patchiness and dispersal distance is significant and It is difficult to dispute the influence of patchiness on the distance a seed is dispersed.

    7. We also found that evolving populations showed significantly less among-replicate variation in spread than nonevolving populations (fig. S1).

      Evolving populations showed less variation in velocity in replicate trials than did non-evolving populations. This means that the amount of spreading from evolving populations was fairly consistent in replicate trials, and population numbers increased at approximately the same rate, making expansion more predictable. Likewise, non-evolving populations did not have consistent spreading rates and varied between replicates in population increases. This made them less predictable for estimating expansion.

    8. The effects of evolutionary change were so strong in patchy landscapes that evolving populations showed no significant reduction in velocity as the size of gaps increased from 4 to 8 to 12 times the mean dispersal distance (generation-six location of dark green line in Fig. 2, B to D) (F1,25 = 0.014, P = 0.908), even as velocity slowed in the nonevolving populations (F1,28 = 8.52, P = 0.007).

      Velocity of spreading kept increasing regardless of distance in evolving populations in variable environments, even as the distance doubled and tripled. Non-evolving populations, however, slowed in population growth.

    9. We found that after six generations of spread in continuous landscapes, evolving populations spread a modest 11% farther than nonevolving populations (Fig. 2A), a difference that was only marginally significant (t13.5 = –2.05, P = 0.060). By contrast, in experimental landscapes with gaps 12 times the mean dispersal distance, evolving populations spread three times as far as their nonevolving counterparts (Fig. 2D) (t10.4 = –3.36, P = 0.007), leading to a significant gap size by evolution interaction (F1,72 = 10.77, P = 0.002).

      Populations which evolved spread slightly faster than populations which did not evolve in continuous landscapes. However, the effect of evolution was much stronger when the landscape had large gaps between soil. This indicates that evolution is very important to promoting biological invasions in fragmented landscapes.

    10. events contributing to the ecological and evolutionary trajectories of spreading populations (5, 19–21)

      Due to the unpredictable nature of environmental events, studies of environmental changes, whether population, genetic or abiotic based, are forced to account for the randomness by repeating these experiments many times in order to ensure that the results are not due to chance, but have actual consistency.

    11. individuals at the leading edge and back of the invasions were genotyped, and traits of all 14 genotypes were measured.

      The authors aimed to determine both the genotype and the phenotype of the plants to determine which traits (phenotype) contributed to successful invasion, and how the diversity of the plants at the leading edge changes with gap size (determined by number of genotypes present). Comparing the leading edge and the back allows for determining the effect of invasion on population evolution.

    12. separating individual pots of suitable habitat by gaps that were 0 (continuous landscapes), 4, 8, or 12 times the mean dispersal distance.

      The question of how evolution occurs in patchy landscapes was addressed by testing both evolving and non-evolving populations in environments in which there was space between the habitable spaces in order to grow. Gaps simulated barriers in landscape which may require certain traits to overcome.

    13. germinants

      Seedlings, or young plants with the potential for growth after germination.

    14. In evolving populations, the resulting plants produced seeds, which dispersed across the array (assisted via a simulated rain event), constituting the next generation of the population (Fig.

      One of the questions addressed in the study is how evolution affects the spreading of plants. To test this, plants in the evolving condition were allowed to spread seeds, and then the seeds grew into the next generation. In the non-evolving condition, the new seedlings were replaced with seeds randomly drawn from the source population. This difference allows for determining if the traits the seeds carry with them are important for how fast they spread.

    15. Arabidopsis thaliana

      Arabidopsis thaliana (A. thaliana) is a commonly used plant for research because of ease of manipulation. With a genome of approximately 125 megabase pairs (Mbp) and only 5 chromosomes, it is relatively quick to sequence and much background literature exists on the genome. It also matures in 6 weeks, and is easily cultivated in confined spaces.

    16. spreading through continuous and fragmented landscapes, each consisting of a linear array of rectangular pots

      The experiments were designed to mimic real-life invasion using a one dimensional (linear) model. Pots filled with soil are places where seeds can grow, while empty pots act as barriers to invasion, resembling a fragmented landscape. The setup allows for the researchers to have precise control over as many variables as possible, and the linear array makes tracking of invasion progress simpler.

    17. Due to these constraints, nearly all empirical evidence for evolution affecting spread comes from a few retrospective, observational analyses

      Retrospective observational studies involve observing the result of a particular phenomenon, in this case an invasion, and collecting data to determine how it happened. While these studies can be effective at describing what evolution in invasions looks like, they are limited in the ability to determine cause and effect.

    18. fecundity

      Individuals vary in the number of offspring they produce. Fecundity is often measured as the number of offspring produced by an individual. When populations have higher fecundity, there are more individuals to populate the region just outside the current species range, which result in increased spread velocity.

    19. It has long been appreciated that habitat fragmentation slows the velocity of spread (3, 4), but its influence on the potential for evolution to increase population expansion is unknown (5). Theory shows that natural selection at the low-density front of populations expanding through continuously favorable landscapes, coupled with the spatial sorting of offspring

      Populations that have been divided or separated from each other spread out slower than other populations but it is unknown how evolution contributes to their dispersal. The theory of natural selection dictates that offspring with traits that assist in dispersal and fecundity, or the number of offspring an organism produces, will be favored when populations are not very numerous and are in an environment well suited for their species' growth. Therefore, individuals best suited for the expansion of the population would be favored from an evolutionary perspective.

    20. global environmental change

      Despite the clear evidence of invasive species and altering ecosystems on global ecosystem sustenance, Kevin Esvelt conceived a technology called a gene drive that could suppress the growth of entire wild populations. Despite outside development, Esvelt has since begun opposing gene drives, arguing they could function in a way similar to introducing invasive species.

      Read more in Pacific Standard: https://psmag.com/environment/should-we-fight-invasive-species-with-genetic-engineering

    21. At the core of each dynamic is the spread of populations across landscapes fragmented by natural

      Many species are becoming threatened or endangered as the result of habitat fragmentation combined with climate change. These include both plant and animal species. When plant species go extinct, valuable genetic diversity is lost which could have helped breed disease or drought resistance in the future.

      Read more in the Guardian: https://www.theguardian.com/environment/2017/dec/05/red-list-thousands-of-species-at-risk-of-extinction-due-to-human-activity

    22. biological invasions and the movement of species ranges with climate change present two of the greatest disruptions to natural and managed ecosystems

      Natural and managed ecosystems are vital to the equilibrium of life on earth, as well as to humans needs which are gathered from ecosystems. The focus of the research question is to determine if biological invasions and movement of species are significant threats to ecosystem health.

    23. spread velocity

      Species acquire new range at a given rate, expressed as land acquired per unit time. How fast species spread into new range is important for how quickly invasive species can take over an area or a native species can adapt to a changing climate.

    1. Using archived specimens and field surveys of bumble bees and host plants, we explored four potential mechanisms for this change in tongue length

      Subalpine bee species have begun to move into alpine climate and compete with the native alpine bees, due to the warming of the alpine climate.

    2. evolution is helping wild bees keep pace with climate change.

      Alpine bumble bee populations are generally isolated from the toxins, diseases, and habitat destruction that affect bumble bee populations in other climates. Yet, they are still negatively affected by climate change. However, the bumble bee populations are adapting to the changes to their habitat by evolving new behaviors that increase their chance of survival.

    3. Using a simple model adapted from (26), we tested whether reduced flowering in other ecosystems could drive the evolution of pollinator foraging traits as indicated for alpine bumble bees (15). The model predicts changes in the energetic advantage of generalization with floral density. Long-tongued bumble bees exhibit greater specialization than that of short-tongued bees (16, 30). Across a range of flight speed and plant community composition (15), the advantage of generalizing increases as flower density declines (Fig. 4).

      The data suggest that the decrease in floral density seen in alpine regions leads to the favoring of short-tongued bumble bees over long-tongued bumble bees across a wide range of plant communities.

    4. [Mount Evans and Niwot Ridge combined (16)] indicate increased species diversity

      Next Generation Science Learning Standard 3LS4-2- Biological Evolution: Unity and Diversity https://www.nextgenscience.org/pe/3-ls4-2-biological-evolution-unity-and-diversity

      This learning standard focuses on how characteristics can play into natural selection as well as evolution. This paper highlights how climate change is causing natural selection to favor bumble bees with shorter tongues.

    5. Alternatively, shifts in bumble bee tongue length may reflect competition from subalpine congeners moving upward with climate change. Comparisons of past (1960s and 1970s)

      Bumble bee communities in the Pennsylvania Mountain and in the Front Range have increased in species diversity and short tongued bees. These short tongue bees come from subalpine climates and could be replacing the long tongue bees, explaining their 24.1% decrease in the community.

    6. Fig. 4. Relative advantage of generalizing as a function of flower density and the proportion of deep flowers in the community. Outcomes with flight speed of 0.5 m s−1 are shown (15). The generalist is favored when its relative advantage is >1 (pink shading).

      The influences of floral density and the abundance of flowers featuring deep corollas are used to identify the advantage that a generalist (short-tongued) bumble bee would have over a specialist (long-tongued) bumble bee where bees have the same flight speed. Pink areas denote conditions that favor generalists.

      This model was adapted from a model that explained the effects of floral density on the composition of pollinators. The means by which the model that was adapted from to produce this model can be found at:


      A list of materials and methods used to produce this figure is found at:


    7. Fig. 3. Change in flower abundance at landscape and local scales along a 400-m altitudinal gradient on Pennsylvania Mountain. (A) Map showing areas where PFD decreased (1.95 km2), is stable (1.29 km2), and increased (0.10 km2). Unshaded (excluded) areas contain cliff, talus, mining disturbance, and subalpine forest. (B) PFD (mean >± SE) for plots in krummholz (KRUM); tundra slopes (SLOPE); wet meadow (SWALE), false summit (FSUMMIT); and summit (SUMMIT) habitats (N = 6 species; F4,385 = 5.55, P = 0.0002). Asterisks indicate significant differences at P < 0.05. (C) Total flower production (in millions) is the product of total surface area for (A) each habitat (table S5) (15) and (B) mean PFD.

      These results show that the peak flower density of the habitat of the bumble bees is mostly decreasing, causing more competition for available nectar to ensue among the bees.

    8. J. Stout, D. Goulson , The influence of nectar secretion rates on the responses of bumblebees (Bombusspp.) to previously visited flowers. Behav. Ecol. Sociobiol. 52, 239–246 (2002).

      Stout and Goulson worked to identify how the nectar secretion rate of a given plant influences the response of bumble bees returning to it after it has already been visited.

      From this, Stout and Goulson developed a model that determines how long a bumble bee will avoid a recently visited flower whose nectar has been depleted based off of the nectar secretion rate of that flower.

    9. R. Levins, Evolution in Changing Environments: Some Theoretical Explorations (Princeton Univ. Press, Princeton, NJ, 1968).

      Levins worked to identify how populations physiologically and behaviorally adapt to both short and long term changes in the conditions of their environment.

      From this, Levins identified how populations of different species spatially divide their environment among themselves, allowing one to estimate how many species can coexist within a given area.

    10. D. Goulson, E. Nicholls, C. Botías, E. L. Rotheray, Science 347, 1255957 (2015).

      Goulson and colleagues worked to identify the reasons behind the decline in populations of bees. Reasons include parasites, a decline in flower populations, and an increased use of pesticides.

      It is noted that efforts to reduce the use of pesticides and to increase the population of flowers visited by bees should be developed.

    11. P. R. Elsen, M. W. Tingley, Nat. Clim. Change. 5, 772–776 (2015).

      Elsen and Tingley worked to determine how the topography of a given mountain influences its relative susceptibility to climate change. From that they looked into how populations inhabiting a given mountain will migrate in reaction to climate change.

    12. R. B. Miller, Evolution 35, 763–774 (1981).

      Miller worked to identify how Hawkmoths influence the physical variation seen in Colorado Blue Columbine (Aquilegia caerulea) in different areas.

      Miller found that areas containing moths with longer tongues also feature plants with longer floral spurs.

    13. D. P. Vázquez, N. Blüthgen, L. Cagnolo, N. P. Chacoff, Ann. Bot. (Lond.) 103, 1445–1457 (2009).

      Vazquez and colleagues review the patterns within ecosystem networks that lead to plant - animal mutualisms.

      Vazquez and colleagues identify many mechanisms that produce mutualisms. It is noted that the relative influence of each mechanism on the production of a mutualism is still unknown.

    14. R. Bommarco, O. Lundin, H. G. Smith, M. Rundlöf, Proc. Biol. Sci. 279, 309–315 (2012).

      Bommarco and colleagues worked to determine how the composition of bumble bee populations have shifted in Sweden.

      It is noted that species richness and evenness of population composition should be developed to promote healthy ecosystems.

  2. Feb 2018
    1. Optimal foraging theory predicts that foragers will expand their niche in response to such resource scarcity (25, 26). When bumble bees (B. balteatus) encounter low densities of preferred host plants, they incorporate shallower flowers into their diet (F1,194 = 29.39, P < 0.0001) (table S4) (15).

      According to optimal foraging theory, organisms will attempt to find the most efficient food source with respect to time and energy used to obtain it. As food becomes more scarce, the organism will increase the range of food sources it will forage. Bumble bees will select to feed from the flower who’s corolla length is closest to the length of their tongue. However, in desperate times, they will feed on shallower flowers, competing with the flower’s original bees for resources.

    2. In response to warmer temperatures and drying soils, flowering has declined in alpine and arctic habitats worldwide (21–24)

      Researchers have found that climate change has increased the temperatures of alpine and arctic habitats. This has caused the soil in this area to dry up thereby decreasing the amount of plants that flower in a given area, negatively affecting the bees ability to forage.

    3. In 2012–2014, we resurveyed bumble bee visitation on Mount Evans and Niwot Ridge in accordance with historical observations (18). Despite a 10-fold difference between past (n = 4099 visits observed) and present (n = 519 visits observed) collection effort, surveys indicate that resident bumble bees have broadened their diet. Resampling historical visitation data to match present collection effort reveals that foraging breadth (Levin’s niche breadth) (15) increased from 2.61 to 7.01 for B. balteatus [z score (Z) = 28.48, P < 0.0001] and 2.09 to 5.07 for B. sylvicola (Z = 19.78, P < 0.0001). Bumble bees have added flowers with shorter and more variable tube depth to their diet (B. balteatus: F1,1997 = 7554, P < 0.0001; B. sylvicola: F1,1997 = 64,851, P < 0.0001) (Fig. 2, E and F, and table S3).

      The researchers analyzed differences in bumble bee diets on Mount Evans and Niwot Ridge, between the 1960s and presently around 2011. Fewer bee visits were recorded during the more recent survey, but it appears that the bees have an expanded range of plants in their diet. This diet includes flowers that have shorter and more varied depths.

    4. Selection to track the floral traits of host plants should favor short-tongued pollinators when flowers become shallower or deep flowers less common (9, 10).

      Rodríguez-Gironés and colleagues saw that competition for resources within a population triggered long tongues in pollinators and deep corolla tubes in flowers.

    5. Temporal changes in bumble bee tongue length are not explained by plasticity in body size. When phenotypic variance in tongue length is partitioned among underlying sources, size accounts for less than 20% of variation (table S1) (15). Size has declined in some populations (B. balteatus: F2,96= 8.61, P = 0.0004; B. sylvicola: F1,76 = 29.01, P < 0.0001) (fig. S1 and table S1) and is phenotypically correlated with tongue length [correlation coefficient (r) = 0.50 to 0.60, P < 0.005] (fig. S1) but contributes little to its reduction over time. After removing variance explained by body size, analysis of covariance shows significant temporal changes in tongue length (B. balteatus: F1,23 = 17.02, P = 0.0004; B. sylvicola: F1,67 = 46.14, P < 0.0001) (Fig. 1 and table S1).

      The variation in the size of the bumble bees only accounts for less than 20% of variation in bee tongue length, and is therefore not a valid explanation for changes in tongue length over time. There is some correlation between decrease in bee size in some populations and their tongue length, however this does not contribute to the reduction in tongue length observed over time.

    6. We measured the change in tongue length of B. balteatus and B. sylvicola using specimens collected from 1966–1980 and 2012–2014 in the central Rocky Mountains (15). These two species historically comprised 95 to 99% of bumble bees at our high-altitude field sites (16–18). B. balteatus workers were collected from three geographically isolated locations: Mount Evans (39°35.033′N, 105°38.307′W), Niwot Ridge (40°3.567′N, 105°37.000′W), and Pennsylvania Mountain (39°15.803′N, 106°8.564′W).

      B. balteatus and B. sylvicola are the most common bumble bee species at the three research sites in the central Rocky Mountains. The sites are Mount Evans, Niwot Range, and Pennsylvania Mountain. To analyze the change in tongue length over time of both species at the sites, recent specimens from 2012-2014 were compared to older specimens from 1966-1980.

    7. Although the climate change impacts on phenological and spatial overlap of mutualists are well known, the role of climate change in generating functional discrepancies between them is less understood. Using historical data, we show that reduced flower abundance in bumble bee host-plants at the landscape scale has accompanied recent warming, leading to evolutionary shifts in foraging traits of two alpine bumble bee species

      It is known that climate change is impacting compatibility of mutualistic species. However, it is unknown which specific mechanisms of the mutualistic relationship are being affected. Using historical data the authors measured flower abundance shifts due to climate change and their effects on foraging behaviors by the bees studied.

    8. Spatial and temporal discrepancies with food plants, habitat destruction, and pressure from invasive competitors have been implicated (3–6), but the details of these declines and their causes remain unresolved

      Researchers have identified potential reasons that could be causing the decrease in long-tongued bees including changes in the location and availability of flowers, habitat destruction, and the presence of invasive species.

    9. Long-tongued bumble bees have coevolved to pollinate plants that possess elongated corolla tubes in a mutualistic relationship. Recent declines in such long-tongued bee populations suggest that historical selection regimes in these systems are changing (1–3)

      Historically, bees with longer tongues have had access to plants with longer corolla tube lengths, increasing selection for these bees that have a wider range of accessible nutrients. Researchers believe, due to a decrease in the population of long-tongued bees, that the long-standing selective pressures that caused long-tongued bees to thrive are changing. The reasons for this change remain unknown.

    10. Bumble bee mutualism

      With new research on the effects of climate change on bumble bee pollination and the decline in pollinators, new man-made developments have risen. We can see the start to a new possible era of man-made pollinators. This could help the declining rate of pollinators but can drastically affect the coevolution of flowers and their pollinators.

      Read more in CNN Tech: http://money.cnn.com/2017/02/15/technology/bee-drone-pollination/index.html

    1. References and Notes

      This article by Hungate et. al applies its findings to the Conservation Reserve Program, attempting to estimate species richness of CRP. This article ( D. L. Carter, J. M. Blair, Recovery of native plant community characteristics on a chronosequence of restored prairies seeded into pastures in West-Central Iowa. Restor. Ecol. 20, 170–179 (2012). ) is cited, yet this cited paper specifically does not use CRP grasslands, suggesting an error on the part of Hungate et al.

      Read more at PrarieBotanist: https://prairiebotanist.com/2017/04/11/a-brief-comment-on-the-economic-value-of-grassland-species-for-carbon-storage/

    2. climate protection

      This paper investigates a means to optimize carbon storage by understanding the diversity of the mechanics and use of plant life as carbon sinks in order to lower atmospheric CO2.

    3. B. J. Cardinale, K. L. Matulich, D. U. Hooper, J. E. Byrnes, E. Duffy, L. Gamfeldt, P. Balvanera, M. I. O'Connor, A. Gonzalez, The functional role of producer diversity in ecosystems. Am. J. Bot. 98, 572–592 (2011).

      Cardinale reviews the roles of "primary producer" biodiversity with respect to ecological processes critical to the functionality and health of terrestrial and marine ecosystems.

    4. Thus, for each of the two grassland experiments, we used data collected from each plot to estimate parameters for a model that projects soil C accumulation over a 50-year time frame

      The author used data collected from each plot to produce a fraction to estimate the carbon accumulation in the soil, on the surface (0 to 20 cm) and at a deeper level ranging from 20 to 100 cm, over time. Using that fraction, the author created an equation that would estimate the amount of carbon accumulating in the soil over a 50-year period.

    5. E141, called BioCON, started in 1997 to explore how plant communities respond concurrently to three forms of environmental change: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity (45).

      In an experiment conducted by P. B. Reich and others in 1997, the effect of increased nitrogen deposits, increased atmospheric CO2 levels, and decreased species richness on plant communities was observed. The author used only the data from the CO2 concentrations and Nitrogen treatments for this research study. With this data the author was able to calculate carbon storage in the BioCON plots because plants store carbon through the accumulation of biomass. CO2 and nitrogen are vital components in the chemical pathways plants use to add on biomass.

    6. represented C4 grasses, C3 grasses, legumes, and other forbs. The species composition of plots was chosen by separate random draws of 1, 2, 4, 8, or 16 plant species from a pool of 18 species, with each level replicated in 30 or more plots.

      The author used C4 grasses, C3 grasses, legumes, and other forbs, in this experiment, as a common variable between all experimental plots. The author mixed the native species, to the American grassland, and a variety of 18 other plant species. The author randomly selected varying levels of species richness, for each plot, by introducing 1, 2, 4, 8, or 16 different plant species. Each mixture of species richness was replicated in 30 or more plots to produce multiple trials of the same level of species richness to produce an average.

    7. J. E. K. Byrnes, L. Gamfeldt, F. Isbell, J. S. Lefcheck, J. N. Griffin, A. Hector, B. J. Cardinale, D. U. Hooper, L. E. Dee, J. E. Duffy, Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions. Methods Ecol. Evol. 5, 111–124 (2014).

      Byrne's review focuses on the impacts of assemblage diversity on ecosystem functions.

      This study acknowledges the impact of diversity on resource utilization and thus productivity, however the focus is on the characterization of multi-functionality.

    8. C. Fissore, J. Espeleta, E. A. Nater, S. E. Hobbie, P. B. Reich, Limited potential for terrestrial carbon sequestration to offset fossil-fuel emissions in the upper midwestern US. Front. Ecol. Environ. 8, 409–413 (2010).

      Fissore's review argues that carbon sequestration by forests in the midwest cannot off-set fossil fuel based carbon dioxide emissions. The study compares hypothetical scenarios necessary to offset significant proportions of the carbon dioxide emissions by converting landscapes into carbon sequestering species.

    9. R. F. Follett, Soil management concepts and carbon sequestration in cropland soils. Soil Tillage Res. 61, 77–92 (2001).

      Follett discusses the role organic soils play in the movement of carbon dioxide from the atmosphere to the soil. This review characterizes terrestrial soils as carbon sinks which is important for crop management.

    10. R. Sedjo, B. Sohngen, Carbon sequestration in forests and soils, in Annual Review of Resource Economics, G. C. Rausser, Ed. (Annual Reviews, Palo Alto, 2012), vol. 4, pp. 126–143.

      Sejo discusses the role species richness plays in affecting economic value.

      This review puts emphasis on the role of biodiversity on marginal economic value represented as carbon storage for conservation efforts.

    11. T. L. Daniels, Integrating forest carbon sequestration into a cap-and-trade program to reduce net CO2 emissions. J. Am. Plann. Assoc. 76, 463–475 (2010).

      Daniels reviews the role the forests play in reducing atmospheric carbon dioxide levels. His focus however is primarily advocating for including carbon sequestering by forests into management plans or a cap-and-trade program.

    12. P. B. Reich, D. Tilman, S. Naeem, D. S. Ellsworth, J. Knops, J. Craine, D. Wedin, J. Trost, Species and functional group diversity independently influence biomass accumulation and its response to CO2 and N. Proc. Natl. Acad. Sci. U.S.A. 101, 10101–10106 (2004).

      Reich compares the role of CO2 and N2 on species richness and functional group diversity.

      This study compares the roles of functional group diversity and species richness on biomass accumulation in an elevated CO2 and N2 environment.

    13. D. A. Fornara, D. Tilman, Plant functional composition influences rates of soil carbon and nitrogen accumulation. J. Ecol. 96, 314–322 (2008).

      Fornara reviews the mechanisms that control carbon and nitrogen accumulation in soils.

      The review covers the relationships between biodiversity and carbon and nitrogen accumulation in soils, with an emphasis on the C3 and C4 grasses.

    14. A. D. Barnosky, N. Matzke, S. Tomiya, G. O. U. Wogan, B. Swartz, T. B. Quental, C. Marshall, J. L. McGuire, E. L. Lindsey, K. C. Maguire, B. Mersey, E. A. Ferrer, Has the Earth's sixth mass extinction already arrived? Nature 471, 51–57 (2011).

      Barnosky discusses the events known as mass extinctions and compares the rates of extinction for these events to modern rates of extinction.

    15. If, as a result of increased plant species richness, carbon storage by grasslands rises

      Grasslands with greater biodiversity were found to feature greater biomass than grasslands with fewer species diversity.

      Read more in ScienceDaily: https://www.sciencedaily.com/releases/2017/04/170419091536.htm

    16. Valuation of the estimated annual marginal changes in carbon storage as species richness increases was then estimated using the social costs of carbon

      The economic value of grassland species for carbon storage is one of the first papers to monetarily quantify the gain or loss of a species from an ecosystem. Even slight additions (as little as one additional species) to the current U.S. Department of Agriculture's Conservation Reserve program could save hundreds of millions of dollars.

      Read more in Michigan News: http://ns.umich.edu/new/releases/24732-diversity-dividends-the-economic-value-of-grassland-species-for-carbon-storage

    17. Species ranges were estimated using occurrence records extracted from the Global Biodiversity Information Facility

      The Global Biodiversity Information Facility provides an open online database of biodiversity data. This service was vital for the outcomes of this paper as it was a source for determining species ranges. The occurrence records used show the location of a given species and the date they were located.

    18. he highest estimate of the social cost of carbon was “included to represent higher-than-expected economic impacts from climate change”

      A previous experiment determined how biodiversity, nitrogen deposition, and CO2 affected grassland soil carbon cycling. The results were vital for this research in that they provided guidelines for the what data should be provided. Specifically, this refers to providing higher and lower amounts of economic change than would be expected in order to provide a range of possible values.

    19. Marginal carbon was computed for each of the 15 incremental steps in species richness described in the modeled data, from S = 1 to S = 2, S = 2 to S = 3, …, to S = 15 to S= 16, bounded by the actual data from the experiments where S varied from 1 to 16 in experimental plots.

      The marginal increase of carbon was estimated for each increasing level of species richness. The model data calculated from equation (2) was bounded by the actual data collected from the experiment in each plot.

    20. For each bootstrapped iteration for each year, the parameter values a and b were used to estimate total soil and ecosystem C content for plots ranging from 1 to 16 species

      The equation above was used by the author to calculate the total amount of carbon, in the soil and ecosystem, between the varying species richness in each plot. The a and b values were parameters calculated, by equation 1, to measure the amount of carbon in the plants and the soil for a 50-year simulation. Using the parameters of a and b and the different amount of specie richness (ranging from 1 to 16), in each plot, the total amount of carbon in the ecosystem was determined.

    21. BioCON

      BioCON stands for Biodiversity, CO2, and Nitrogen. It refers to an experiment which began in 1997 at the University of Minnesota. The factors of this experiment can be related to the economic value of ecosystems, it is vital in the outcomes of the research done in this paper. Without the values from the BioCON experiment many of the results in this paper would not exist.

    22. (reasonable, because all aboveground biomass dies back each year in these perennial plants)

      Perennial plants grow and bloom over the spring and summer, but die back every autumn and winter.

      This seasonal process involves the annual gain and loss of the biomass required for blooming.

    23. [the product of measured maximum root C content and 0.55 year−1, which is an average value for root turnover in grasslands (48)]

      In a previous work produced by R. A. Gill and coworkers, the carbon contained in a plants' root system was calculated (.55 per year). This is also the average value for roots to seep carbon into the soil in grasslands.

    24. In the end, the Metropolis-Hastings algorithm generates a distribution of accepted I and kvalues wherein their means coincide with the minimal value of J (that is, the best fit to the observed data). Soil C content for each plot was projected to 50 years using the mean parameter estimates I and k and measured C0 for both depths (that is, soil C at start of the experiment).

      The author used the equation above, the Metropolis-Hastings algorithm, to calculate the difference between the observed and modeled data of carbon accumulation in the soil for each year the carbon soil data was provided. The equation generated a variety of accepted i and k values. The author then calculated the average i and k values with the smallest J value (best fit for observed data). Using the average i and k values that were calculated, the author was able to find the amount of carbon accumulated, at both the surface and deeper level of the soil, over a 50-year period. The author assumes the calculations to be within a 30% accuracy of the actual amount of carbon in the soil.

    25. For E141, soil C data were available for each plot at the beginning of the experiment (year 0) and after 5 and 10 years of experimental treatment (0- to 60-cm depth); we scaled soil C data to 0- to 100-cm depth for E141 using soil C depth distributions for E120 (20-cm increments to 1-m depth) to determine the proportion of C in the top meter of soil contained in the 60- to 100-cm depth, and then we used this proportion with observed soil C data for each plot to estimate total C to 1 m.

      For the BioCON experiment, the author used soil carbon data collected from each plot at the beginning of the experiment and the 5 and 10 years after the introduction of varying species richness (from a 0 to 60 cm depth). The author then estimated the amount of carbon in the soil, from 0 to 100 cm depth, by using carbon soil depth distribution data, for 20 cm increments up to a 1 meter depth. Using the data from the BigBio experiment, the author developed a proportion that helped determine the amount of carbon in the soil up to a meter depth for the BiCON plots.

    26. To fit the model and obtain plot-level parameter estimates of I and k, we used all available soil C data from the Cedar Creek Ecosystem Science Reserve website (available publicly from www.cbs.umn.edu/explore/cedarcreek). For E120, surface soil data (0 to 20 cm) were available from years 0, 1, 5, 7, 9, and 11 for all plots, and from year 10 for some plots, and data for 0 to 100 cm were available for years 0 and 11.

      The author used data collected on carbon accumulation in the soil from the Cedar Creek Ecosystem Science Reserve website to obtain estimated parameters for: i) the constant rate of decomposition of plants, per year (k) and ii) the annual input of carbon into the soil. In the BigBio experiment, the author used data, on carbon content in the surface of the soil, from years 0, 1, 5, 7, 9, 11 for all plots, and year 10 for some plots. The author also collected data, of deeper soil carbon content, from years 0 and 11.

    27. first-order kinetics

      The elimination of a constant fraction, of the carbon quantity present in plants that goes into the soil, over time. Plants decompose and release their carbon into the soil. The author collected data, from each plot, to produce a constant fraction to be used in the equation.

    28. In both experiments, soils were treated before initiation of the manipulations. Before planting, methyl bromide was applied to soils in the BioCON experiment, and the uppermost layer of the soil (0 to 5 cm) was relocated off plot for BigBio, to reduce the influence of the seed bank on species composition of the experimental plots in both cases.

      The soil in all plots was treated before the experiment was conducted. Methyl bromide was applied to the BioCON plots and the first 0 to 5 centimeters of soil was relocated in the BigBio plots. The author either treated the soil or relocated it to make sure any previously existing seeds would not change the species richness of each plot. The addition of plant species not recorded in the experiment would influence the amount of carbon storage occurring in each plot. This could possibly skew the data collected over the duration of the experiment. The difference in pretreatments between BioCON and BigBio could have contributed to the different rates of carbon accumulation between the two experiments.

    29. These experiments—and our analyses of them—excluded large vertebrate grazers, which can influence grassland carbon storage (47) and, thus, its economic value; our assessment focused solely on species richness and did not consider grazing or other influences on grassland carbon accumulation

      A previous research study, wrote by D. P. Xiong, suggested that the presence of grazing animals influences grassland carbon storage. By consuming plants, grazing animals decrease the total amount of biomass in the American grasslands thereby decreasing the amount of carbon storage in an environment. The author decided not to take into account the effect grazing animals had on carbon storage and only looked at the effects of plant diversity on carbon accumulation.

    30. Thus, any influence of functional groups on carbon accumulation (8, 46) are distributed across treatment levels in our analysis.

      The idea of using C4 grasses, C3 grasses, legumes, and other forbs across all plots in this study was inspired by the works of leading scientists D. A. Fornara and D. A. Wedin. By using the native species in all plots, the author was able to concluded that any disturbances, when considering carbon storage, across the plots was due to the varying levels of species richness. The author used the differences in carbon storage as data during the experiment's analysis, to find out the correlation between increased species richness and its effect on carbon storage.

    31. Species richness was manipulated in subplots (2 m × 2 m) located within the three 20-m-diameter ambient CO2 plots, with 32 randomly assigned replicates for the 1-species treatments

      For BioCON, the author used 2 m x 2 m subplots to see the effects of increased species richness on carbon storage. The author randomly chose 32 identical species mixtures from the experimental plots in E120 with varying levels of species richness. 15 plots were given a mixture of 4 different species and 12 plots were given a mixture of 16 different plant species.

    32. ambient CO2

      The CO2 atmospheric concentration surrounding the experimental plots. The local CO2 atmospheric concentration can vary from plot to plot.

    33. grassland perennials

      The natural vegetation found in grasslands such as: C4 grasses, C3 grasses, legumes, and other forbs.

    34. E120 contained 342 plots laid out as 13-m × 13-m squares with the central 9 m × 9 m actively maintained for the specified species and plant diversity (44).

      A previous work, drafted by D. Tilman and coworkers, suggested the experimental outlay of this research study. By using 342 plots, in Cedar Creek Ecosystem Reserve in Minnesota, United States, the author was able to see the relationship between increased species richness and its effect on carbon storage in the American grassland. The author started in 1994 and used the 13 m x 13 m plots as the experimental group in this experiment. These plots were subjected to varying levels of species richness and observed the carbon uptake response. The central 9 m x 9 m plots were used as a control group because the species inhabiting the plots and plant diversity were constantly maintained.

    35. BigBio

      The BigBio experiment was conducted to examine large scale biodiversity in a grassland setting. The experiment determines effects of plant species numbers and functional traits on the functioning of an ecosystem. Without previous data obtained from this experiment, many values found in this research wouldn't have been able to exist. Therefor the BioCon experiment was vital to the outcomes of this paper.

    36. Despite widespread claims about the economic value of biodiversity for ecosystem services (18–20), quantitative assessments of the relationship between biodiversity and specific services are rare

      Multiple research studies, conducted by leading scientists P. Balvanera, S. Catovsky, and I. D. Thompson, suggest that the economical worth of plant diversity is high for all ecosystem services. The author points out that the research conducted on the correlation between species richness and specific ecosystem services is very rare.

    37. Integrating our approach with robust estimates of diversity effects on multiple ecosystem processes (43) and of their value remains an important task for future studies.

      A research study, drafted by J. E. K. Byrnes and others, states the importance of studying the effect of increased plant diversity on a wide variety of ecosystem processes. This research paper only shares the results of increased species richness on one ecosystem service: carbon storage. There are many more ecosystem services that are only possible because of the wide diversity of plant life on earth. If research studies were conducted on the effect of increased plant diversity on a variety of ecosystem services, then we would gain irreparable knowledge on how the complex systems work and the benefits to society.

    38. no single species appears to be “best” at providing a wide variety of benefits to society (42).

      A research paper, written by J. S. Lefcheck and coworkers, proposes that no single species is the best at providing all the valuable ecosystem services needed for the world to function. No single species can occupy all the vital niches around the world. This is why diversity between the function plant species have and services they preform is so important.

    39. Although there is evidence for trade-offs among species in the functions they perform and services they provide (41),

      A previous research experiment, conducted by E. S. Zavaleta and coworkers, concludes that there is evidence of differences between the function plant species preform and the services they provide. The differences between plant species allows for a wide variety of niches or jobs, in an environment, to be filled. Without different plants occupying the many needed jobs in an environment, the earth's delicate nutrient cycles would not be able to occur and life on earth, for primary and secondary consumers, might not be possible.

    40. For example, in the experiments assessed here—among the longest-running biodiversity experiments in grasslands—the effects of species richness are growing stronger through time and have yet to reach a steady state (40).

      A previous research study, written by P. B. Reich and others, voices that the initial introduction of increased species richness drastically increases carbon storage, but as time goes on, the effectiveness of plant diversity on carbon uptake starts to level off. The author relates these findings to their own experiment stating that even though the research conducted on the American grasslands is the longest-running biodiversity experiments in grasslands, not enough time has passed to see carbon storage levels reach a steady state.

    41. monotonically

      When the effectiveness of increased species richness on carbon storage, in an environment, starts to level off and not increase so drastically. This effect on the relationship between plant diversity and carbon sequestering can be seen the longer time goes on.