1,000 Matching Annotations
  1. Aug 2018
    1. The overall morphology of the S1 tracks matches those at Site G (Figure 11) and is similar in particular to the prints of the larger individual

      Analysis of the footprints discovered by Dr. Leakey and colleagues determined that the big toes of the hominids leaving the trail aimed forward and that the toes were not distinctly different from each other. This is not true of the feet of hominids such as the chimpanzee.

      Source of image ttps://corewalking.com/chimpanzee-feet-vs-human-feet/

    2. It is reasonable to assume that complex relationships among body size, sexual dimorphism, mating system (and/or reproductive strategy) and social structure/behaviour also applied to extinct hominins, including our bipedal relatives of the Plio-Pleistocene

      Modern humans do not exhibit a high degree of sexual dimorphism. However, other hominid relatives, such as gorillas and orangutans, are highly dimorphic. Based on a limited number of fossils, it has been assumed that early hominins were highly dimorphic. Knowing more about the degree of sexual dimorphism would provide information about mating behavior and social organization.

    1. 1The distortion of the oval orbits of planets round the sun (confirmed in the case of the planet Mercury).

      In A New Determination of the Orbit of Mercury and its Perturbations (1843), Urbain Jean Joseph Le Verrier reported a peculiar precession of Mercury's orbit that was not accounted for by Newtonian mechanics.

      Relativity theory, however, provides a robust account of Mercury's motion.

    2. Euclidian geometry

      Euclid was a mathematician in Ancient Greece. His book Elements is arguably the first mathematics textbook. In the text, Euclid describes the geometry we seem to experience in our everyday lives in which parallel lines do not intersect.

      This is also the same geometry we still learn in high schools across the country (2000 years after Euclid wrote it).

    3. The application of this general theory of relativity was found to be in conflict with a well-known experiment, according to which it appeared that the weight and the inertia of a body depended on the same constants

      The Eötvös experiment measured the correlation between inert and heavy mass (or inertia of a body and its weight) and showed that these two masses have the same value although are conceptually distinct.

    4. special relativity theory and the general theory of relativity

      Einstein came up with the theory of special relativity before general relativity.

      Special relativity assumes the laws of physics are constant in all inertial frames of reference (frames of reference that are assumed to be stationary).

      General relativity expands on this, and describes the fabric of space-time on the scale of the universe (which Einstein suggests is warped by massive bodies).

      Einstein expanded special relativity to general relativity over the course of about 10 years as he realized that special relativity was insufficient to explain some phenomena in the universe.

  2. Jul 2018
    1. Since the time of the ancient Greeks it has been well known that in describing the motion of a body we must refer to another body.

      Aristotle contemplates absolute and relative motion in his book On the Heavens. He describes how heavy bodies move down and lighter bodies (like air or fire) move up relative to the center of the universe.

      Read more: https://plato.stanford.edu/entries/spacetime-theories/#2

    2. The deviation of light-rays in a gravitational field (confirmed by the English Solar Eclipse expedition).

      Again, this was found by Arthur Eddington and Frank Watson Dyson in their paper.

    3. Maxwell-Lorentz theory

      Maxwell's equations describe how electric and magnetic fields manifest from charged particles. Together, Maxwell's equations suggest the speed of electromagnetic waves (i.e. light) is constant.

      The Lorentz Force Law says that the force felt by some charged particle is related to the surrounding electric and magnetic fields.

      Together their work describes special relativity, but only for electromagnetism.

    4. I am none the less very glad to express my personal thanks to my English colleagues in this branch of science; for without their aid I should not have obtained proof

      Einstein's "English colleagues" are Arthur Eddington and Frank Watson Dyson, astronomers who obtained experimental evidence of Einstein's theory of relativity.

      Modern physicists have debated whether the error bars in the Eddington experiment were larger than the effect they measured. Nevertheless, the results have been confirmed.

      Read Eddington and Dyson's work here.

    5. rays of light

      In the image below, the solar gravitational field influences the sun's rays framing the moon. Notice that the light bends around the moon due to the gravitational field, rather than forming a spherical halo.

    1. Exposure to air pollution is the fifth ranking human health risk factor globally, following malnutrition, dietary risks, high blood pressure, and tobacco (1).

      Understanding the causes of disease and death are crucial to better health outcomes. A look at health data from 1990 to 2015 identified factors that lead to negative health outcomes. Exposure to increased air pollution primarily leads to increased respiratory and cardiovascular disease.

    1. We followed the power law computed by Alexander (1976):

      Alexander originally obtained this equation to calculate estimates of dinosaur speeds.

  3. Jun 2018
    1. Recently some of these problems were overcome using an RNA biosensor that is dislodged by translating ribosomes

      Researchers have been able to visualize where and how quickly mRNA translation is occurring during development, but not for single molecules.

    2. Although transcription is now regularly quantified in real-time with single gene resolution in vivo

      Researchers have described how fluorescent markers can be used to visualize and describe transcription in vivo, but the present study is the first to do so for translation.

    1. Climatic Research Unit TS3.1 gridded observations (20)

      This data set was developed and maintained by the Climatic Research Unit in the United Kingdom. It provides several climate values for locations covering the globe, on a monthly basis, from 1901–2009. The data set covers the world's land surface (excluding Antarctica) and is reported in a 0.5° x 0.5° grid. The climate variables, including temperature and precipitation, are based on actual observations from a number of sources, using appropriate methods to integrate the different sources and calculate the values for locations that are missing data.

  4. May 2018
    1. (Ding et al. 2008).

      In this study they use SRAP marker which is sequence-related amplified polymorphism to study the genetic diversity of plant species. It is a technique that helps detect genetic variation within plants.

    2. (Jiang et al. 2008)

      This paper focuses on the environmental issues such as natural occurrences that affect land, water, and soil loss.

    3. (Zhou and Grumbine 2011)

      This article talks about the different areas that have been built in order to increase preservation. There has been some limitations in terms of funding, administrative authority, and proper development. They continue to address these concerns and find possible ways to create more protected areas.

    4. by taking only the older stems that have already flowered and fruited, thereby giving the planted individuals chances to recruit naturally in largely natural forests. Plants can be harvested annually in this manor for up to a decade

      In a recent study it was discovered that Dendrobium orchids can be sustainably harvested once a year if harvesters only take the old stems that have already produced fruit and flowers so that the younger stems will be allowed to reproduce.

    5. Liu et al. 2011, 2013).

      Publication accounts for confusion among scientific and Chinese names for this orchid, and provides clarification on taxonomy and nomenclature.

    6. (Kirkpatrick and Emerton 2009;

      This paper discusses efforts to reduce poaching of wild tigers by breeding tigers to increase their numbers and in theory, reduce their [tigers generally] worth. However, the argument is made that wild tigers cannot be substituted by farmed tigers to alleviate poaching because they are not valued the same by hunters. Because of this difference in worth (perceived or real) flooding the market with farmed tigers will have no effect on the demand for wild tigers.

    7. China adopted its protected areas system in the most strict sense, i.e. nature reserves allow minimal human interferences

      China’s government authority have employed new park policies in Yunnan, where explicit management zoning systems are implemented towards the local people. Tourism has been known to provide a source of income for these environmental programs.

    8. (Godefroid et al. 2011;

      Using 12 years of seizure records covering nearly 1000 seizures from ivory to live reptiles, the authors review and describe current status of illegal trading of wildlife and wildlife products. The authors conclude that regulation and enforcement are not enough to control illegal trade, but that education at the community scale combined with empowerment of locals to value their own wildlife, international regulation and ground-level enforcement will result in more effective control.

    9. Francisco-Ortega et al. 2010).

      This group surveyed all of the plants on Hainan Island and published a checklist.

    10. (Qin et al. 2012)

      This group looked at the conservation status of over 1300 native orchids distributed among 543 reserves in order to assess their status, and make recommendations for improving efforts where needed.

    11. (Xu et al. 2009

      This paper reviews the progress made toward the national objectives for reducing biodiversity loss using time-series data sets against national indicators. Substantial movement forward was achieved, with stable increases in forest resources, improvements in marine ecosystem integrity, stable water quality, etc. as of 2009.

    12. reintroduction (sensu Menges 2008)

      Looking at translocation efforts (including introduction, reintroduction and augmentation of wild populations) for conservation and supplementing declining species to return to self-sustaining numbers.

    13. tonic for traditional vocal artists to protect their voices and its use extended to cancer prevention and cure, as a boost to the immune system, and for other illnesses (The State Pharmacopoeia Commission of P. R. China 2010; Ng et al. 2012).

      Although other studies have mentioned that orchids have certain compounds such as alkaloids that help combat illnesses, there are not enough clinical studies (except for animals) to support its medical use.

    1. Genetic studies have also suggested that Sox10and Ednrb do not interact during murine melanocyte development (Hakami et al., 2006).

      Sox10 is expressed in melanoblasts, which are the precursors of melanocytes, that do not contain Ednrb. Ednrb is expressed in embryos that do not contain Sox10. Therefore, Sox10 expression does not depend on the expression of Ednrb.

    2. High VEGF levels are in turn associated with poor prognosis in human melanoma tumors (Giatromanolaki et al., 2003).

      Studies show that there is a high expression of VEGF in human melanoma tumors, indicating that VEGF can serve as a marker for melanoma prognosis. Moreover, tumors with a high vascular density (VD) were also associated with poor prognosis.

    3. Moreover, in situ melanomas appeared in adult skin grafts, while invasive melanomas developed in newborn skin grafts indicating that the susceptibility of skin to environmental tumor promoters is dependent on age (Berking et al., 2004).

      Exposure to ultraviolet (UV) radiation is a risk factor for the development of melanoma. Researchers have shown that people who sunburned in childhood are at a greater risk of developing melanoma than are people who sunburned in adulthood. This study suggests that age is associated with the susceptibility of skin to environmental carcinogens.

    4. This increase in cell numbers in the treated cultures could not be accounted for solely by a proliferative effect, pointing to a possible role for Edn3 in the survival of melanoblasts from the NC (Opdecamp et al., 1998).

      Mutations in genes that code for Edn3 result in deficiencies in melanocytes. Edn3 serves as a stimulator of melanoblast proliferation and differentiation. When melanoblasts differentiate, they become melanocytes.

    5. Edn3 was most effective in promoting the long-term propagation of glia-melanocyte precursor cells as opposed to the other precursors (Real et al., 2006).

      Researchers have shown that individual melanocytes produce multipotent cells that are able to regenerate during consecutive subcloning. This indicates that the multipotent cells display stem cell qualities. Edn3 encourages the maintenance of the multipotent cells. Moreover, Edn3 stimulates the proliferation of melanoblasts, which are the precursors of melanocytes.

    6. cells treated with Edn3 were found to proliferate for two weeks without producing pigment (Lahav et al., 1996).

      Cells proliferate in the presence of Edn3. The cells that are produced are melanoblasts, which subsequently become melanocytes.

    7. It was first identified as a potent vasopressor derived from vascular endothelial cells (Yanagisawa et al., 1988).

      Researchers isolated Edn1 to determine its function. Edn1 was shown to be responsible for an increase in blood pressure. Expression of the gene was controlled by factors that affect blood vessels, suggesting that there is a cardiovascular control system.

    1. evidence in alcoholism has already shown disruptions in the balance of action control for appetitive behavior

      Alcohol use in humans alters brain regions involved in goal-directed behaviors, which can lead to an increase in habit-learning behaviors in these patients.

      There is a shift from goal-directed actions towards habitual actions in patients with alcohol dependency. It is possible that alcohol-seeking behavior alters the capacity of individuals to shift between these two types of behaviors.

    2. manipulations of dopamine neurotransmission alter instrumental learning

      Participants with Parkinson's disease have deficits in learning from trial and error. They also had difficulty learning from a positive outcome. Dopamine administration allowed participants with Parkinson's to learn from both positive and negative outcomes, suggesting that their impairment resulted from depletion of dopamine in the basal ganglia.

    3. compulsive cocaine-seeking, even in the face of aversive consequences

      Impulsivity in rats’ behavior is what leads to compulsive cocaine-seeking behavior despite negative outcomes.

    4. impairments in the initiation of goal-directed avoidance behavior have previously been reported

      Animals under dopamine depletion or blockade respond to fear conditioning by urinating, but they fail to respond by avoiding electric shock. These animals show a deficit in initiating a response, but they do not show deficits in their ability to learn associations.

    5. Cocaine administration also diminishes information processing about consequences

      Rats who were given cocaine respond normally to tasks that are meant to completely remove an association with a stimulus. However, they did not respond normally to tasks that were meant to devalue an association with a stimulus, suggesting they were unable to use new information about consequences to guide their behavior.

    1. Reports of plastic pollution in the ocean first appeared in the scientific literature in the early 1970s

      Plastic pollution in the ocean has been known to be a problem for a long time.

    2. In 1975

      This early work (reference 1) looked at which types of pollutants might pose a future threat to ocean resources and mechanisms of how each pollutant ended up in the ocean.

    1. Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation

      The work of Jablonski and Chaplin strongly supports the theory that melanin pigmentation in human skin is an adaptation that helps regulate the amount of UV radiation that gets into the epidermis, with different populations having different selective pressures based on their environments.

      They argue that protection against UV breakdown of nutrients (such as folate) was the primary selective agent that led to darker pigmentation of people living near the equator, because folate is closely linked to reproductive success in humans.

      Jablonski and Chaplin also argued that skin pigmentation is so responsive to environmental conditions that it is not valuable when assessing the genetic relatedness of human groups.

    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. 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.

    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. (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.

    3. Ferrati et al. 2005, 

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

    4. (Burkett and Kusler 2000)

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

    5.  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.

    6. (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.

  5. Apr 2018
    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. mutant V. fischeri strains defective in light emission (lux mutants) have demonstrated that symbiont luminescence somehow participates in the transformation of the organ from its juvenile morphology

      The lux genes in Vibrio fischeri code for the proteins that produce bioluminescence.

      Visick et al. (2000) created three mutant lux genes that were unable to produce bioluminescence. The mutant strains of V. fischeri carrying the modified genes were used to test whether bioluminescence was a key factor in development from juvenile to adult.

    3. tissues surrounding the eye and those dorsal to the symbiont-containing crypts share the expression of a family of proteins, the reflectins

      Crookes et al. (2004) determined that the composition of reflective tissue found in the tissues of E. scolopes was different from the composition of reflective tissue commonly found in other animal tissues.

      In most animals, the reflective tissue is composed of thin layers of purine crystals, which are able to bend light (i.e., they have a high refractive index). The reflective tissue in E. scolopes is composed of a group of proteins high in methionine, tyrosine, arginine, and tryptophan.

    4. 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

    5. The complexity of such photoreceptors can vary from diffusely distributed photoreceptive cells, characteristic of dermal light sense, to complex organs in discrete locations on an animal's body

      In many organisms, the ability to sense light is especially important for allowing organisms to sync to the various rhythms of light in the environment, e.g., daily, monthly, or yearly rhythms.

      This has allowed for the diversity of structures other than the eye that can sense light. Researchers are still working to learn more about about these structures.

    6. Opsin proteins typically mediate the associated phototransduction, although often through isoforms distinct from those produced in the retina (1⇓–3).

      Opsins are a group of proteins that are sensitive to light. There are many different forms of opsin, and they are involved in both visual and nonvisual systems throughout the animal kingdom.

      Some opsins bind to retinal (a chemical involved in animal vision) and undergo a change in their structure when subjected to light.

      This change in conformation is the signal that initiates the series (cascade) of proteins in the retina responsible for the ability to see (this process is called phototransduction).

    1. Of these, there is limited knowledge about loci that affect pigmentation in populations with African ancestry (6, 7).

      Two different research groups used the same population to look for genetic determinants of both skin and eye pigmentation in a population of people in Cape Verde. In this population, there has been extensive admixture (interbreeding) between European and African populations.

      OCA2 was identified as being related to both skin and eye pigmentation, and another overlapping variant with this study, SLC24A5, was identified as being associated with skin pigmentation. Further work identified two additional genes associated with skin pigmentation; one (DDB1) was also a candidate gene in this paper.

    2. only a subset of these genes have been linked to normal variation in humans (5)

      Liu et al. perform a GWAS study similar to those performed in this paper, looking for genetic variants that correlate with skin pigmentation in a population of European people.

      They identify 9 genes that may be associated with skin pigmentation in Europeans, one of which (HERC2/OCA2) overlaps with the genes identified in this study as being associated with skin pigmentation in Africans.

    3. MC1R, which is under purifying selection in Africa

      Harding et al. sequence the MC1R gene in individuals from Europe and Africa, and by a variety of statistical tests they determine that the gene is under purifying selection (selective removal of alleles that are deleterious, in this case, alleles that lead to reduced melanin) in Africa, but not Europe.

    4. This observation indicates that the genetic architecture of skin pigmentation is simpler (i.e., fewer genes of stronger effect) than other complex traits, such as height

      Wood et al. analyze multiple independent studies to identify the SNPs that are most strongly associated with adult height (in Europeans).

      They identify thousands of variants that are associated with height, and even with the top ~9500 SNPs they can only explain ~29% of height variance.

      Their work also suggests that increasing the number of individuals in a GWAS analysis will initially suggest new variants, but will eventually reach a point of "saturation" where new variants will highlight the same genes that have already been seen.

    5. affects pigmentation by modulating melanosomal

      Bellono et al. identify OCA2 as being essential for eye and skin pigmentation. The gene encodes a protein that is a transmembrane channel in the membranes of melanosomes which allows passage of chloride out of the melanosome, thereby regulating melanosome pH.

      Bellono et al. find that this passage of chloride ions out of the melanosome is essential for melanin formation, and changing the function of OCA2 by mutations that have been identified in albinism (a condition characterized by lack of melanin) reduces melanin formation.

    6. both SNPs interact with the promoters of DDB1 and neighboring genes in MCF-7 cells (46, 47)

      Li et al. develop and perform ChIA-PET (Chromatin Interaction Analysis by Paried-End-Tag sequencing), a method to identify regions of chromatin that interact with each other at higher resolution than previous methods.

      Using this method in MCF7 cells (a breast cancer cell line), they identify interactions between the location of several variants of interest to Crawford et al. with the promoter of the gene DDB1.

    7. within SLC24A5 (rs1426654) (14)

      Prior research used positional cloning (a genetic tool used to identify regions of the genome before sequencing was widely available), morpholino knockdown (a way to reduce specific protein levels), and DNA and RNA rescue, to identify a mutation in slc24a5 as being responsible for the reduced pigmentation phenotype of "golden" mutant zebrafish.

      They also analyzed human data and identified a SNP in the coding region of SLC24A5 that was present at highly different frequencies in European and African populations, suggesting that it may have been the target of selection, and may be associated with skin pigmentation.

    8. The introduction of predators to islands provides an opportunity to explore the indirect effects of predators on vegetation. Introduced predators commonly have devastating direct effects on their prey

      In the paper by M. Williamson, islands are subjected to introduced predators and the environment was monitored. Clusters of islands are ideal for demonstrating top down trophic cascades because similar ecosystems may be differently impacted by a single variable (with or without the top predator) and the insular ecosystems prevent the spread of the predator. The procedure of the two different predator locations allows for accurate monitoring of the different island ecosystems.

    1. 1993 to 1998 that a relative maximum in global mean sea level and sea surface temperature

      Nerem and coauthors found that during the 1997–1998 El Nino event there was a 20 mm rise and subsequent fall of mean sea level was observed. As these changes occurred alongside a rise and fall of global mean sea surface temperature anomalies, their work suggests the observed mean sea level change is mostly caused by thermal expansion.

      Thermal expansion means that as water warms it expands to take up more space, which causes sea levels to rise.

      For more information about thermal expansion watch this video from AsapScience: https://www.youtube.com/watch?v=fuvY5YG5zA4

    1. 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.

    2. (McGill et al. 2006

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

    1. 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.

    2. 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.

    3. (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.

    4. 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.

    5. 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.

    6. Dlugosch and Parker 2008

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

    7. founding individuals


      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.

    8. 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.

    1. 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.

    2. 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.

    3. previously reported to have been disrupted in a pedigree with a developmental neuropsychiatric disorder and mild mental retardation

      Disrupted NHE9 has been found in a family with a developmental neuropsychiatric disorder and mild intellectual disability.

      The fact that disrupted NHE9 has been found in multiple patients with neuropsychiatric disorders suggests it may be a cause of these.

    4. A large study, using identical BAC arrays run in the same lab as our study, found 5.6% (84 of 1500) of patients referred to Signature Genomics with de novo or pathogenic CNVs (chi-square = 3.052, df = 1, P < 0.05) (25). The HMCA rate of de novo CNVs was similar to previously reported rates in multiplex pedigrees with autism [1.28% in the HMCA versus 2.6%, or 2 of 77, in multiplex autism (6), chi-square = 0.557, df = 1, P = 0.22] and in controls [1.28% HMCA versus 1.0%, or 2 of 196, in control subjects (6), chi-square = 0.001, df = 1, P = 0.49], despite the fact that the 500K platform used here has significantly higher coverage

      Here, the authors compare their findings to other studies of de novo CNVs. They show that their results are similar to previous studies (such as Sebat et al.) that established the detection of de novo CNVs as a way to identify genes linked to autism.

    5. what would be predicted if the prevalence of autism were doubled in these families

      Hoodfar and Teebi studied the link between inbreeding and the prevalence of different genomic abnormalities.

      IThey found that the prevalence of autosomal recessive disorders was more than doubled in consanguineous families.

    6. The accumulating number of distinct, individually rare genetic causes in autism (5, 10, 11) suggests that the genetic architecture of autism resembles that of mental retardation and epilepsy, with many syndromes, each individually rare, as well as other cases potentially reflecting complex interactions between inherited changes (12).

      Studies have shown that there are many unique combinations of mutations that can cause autism, as is the case with intellectual disability and epilepsy.

      Unfortunately, given that there are so many ways for autism to occur, it is difficult to identify all of the mutations and changes that can lead to symptoms.

    7. chromosomal anomalies have been reported in 1 to 2% of cases of autism

      Data supports the fact that autism is linked with several genomic regions. Nnew regions are still being identified today.

    8. Autism includes mental retardation in up to 70%

      Autism is associated with intellectual disability (formerly called mental retardation*) about 70% of the time, and males are more often diagnosed.

      There is no evidence that social class has an impact on the incidence of the disease, but there is not enough data to know if race or ethnicity influence the incidence of autism.

      There is also no available data to support the idea that incidence of autism is changing over time.

      *For more on the movement to change the language of disability, see the Wall Street Journal.

    9. highly heritable, they exhibit wide clinical variability and heterogeneous genetic architecture, which have hindered gene identification

      Several research teams have worked independently to identify loci that could be responsible for autism. However, this has been difficult due to the high number of genes that could be involved and the high variability between affected individuals.

    1. Our results contrast with the findings of Moré et al. (2007) and de Araújo et al. (2014), who reported that flowers of Mandevilla spp. were pollinated exclusively by pollinators with long, thin proboscides. Additionally, de Araújo et al. (2014) reported that Agraulis vanillae and Ascia monuste are the effective pollinators of Mandevilla tenuifolia; coincidently, these two taxa were the same non-skipper butterfly visitors of A. berteroi in southern Florida.

      Results were different from previous research who showed that one species were pollinated by long, thin mouth parts.

    2. The principal pollinators of A. berteroi in the pine rocklands of south Florida are two native bees; bee pollination (mostly by Euglossine bees) has been previously reported for this family (Lopes and Machado 1999; de Moura et al. 2011).

      The author is explaining that the pollination of the species "Euglossine" has been experimented on before. With this being said, the previous work tested these bees and how they interact with plants.

      In the above article, the author is specifically experimenting on this family of bees and how they interact with A. berteroi in the pine rockland environment. The author is more concerned with how these bees interact with this specific plant.

    3. We chose the sites based on the presence of many individuals of the study species

      This study site was a part of a previous experiment. In the previous experiment, the study site was chosen due to the abundance of individuals that were present. Essentially, the area with a higher abundance of individuals is beneficial to the experiment. It is beneficial to use previous work as a reference, especially if there is a common factor.

    4. In hawkmoth-pollinated plants, floral tube length determines which species may transfer pollen; hawkmoths with tongues that are too short or too long will not pick up pollen effectively

      Floral tube length in hawkmoth-pollinated plants will determine which insect will transfer pollen. if it is too short or too long they will not be effective.

    5. Several studies have reported that the body structure of floral visitors, especially the feeding apparatus associated with the dimensions and the morphology of the flowers, is one of the factors determining which visitors can effectively function as pollinators

      The structure of the insect determines the effectiveness of the pollination as well as the shape of the flower like the length of mouth part and floral tube.

    6. the majority of plant species are visited by a variety of pollinator groups, but visitation does not necessarily imply pollination; not all flower visitors are important and effective pollinators (Stebbins 1970; Waser et al. 1996; Fenster et al. 2004; Ne'eman et al. 2010).

      Most plants show visitation from other insects but not all pollinate.

    1. Sedio et al. 2013

      Sedio describes the phylogenetic niche conservatism (PNC) phenomenon that occurs in plants.

      In this phenomenon, a plant's microhabitat patterns are influenced by the biogeographical history of the plant's ancestors. He explains how related taxa are able to coexist since they were able to retain significant niche characteristics of their common ancestors.

    2. Kursar et al. (2009)

      The young leaves make large energy investments in chemical, developmental defenses, and floral nectar.

      There were many variations among species suggesting that herbivory is a strong selective agent.

    3. Cavender-Bares et al. 2004

      The research performed by Cavender-Bares and his colleagues highlights the importance of evolutionary processes combined with community interactions in community dynamics.

      The combination of phylogeny with their functional attributes help in better understanding communities.

    4. MacArthur and Levins 1967

      MacArthur and Levins explain that diversity of species living within the same environment can be explained as a result of limiting similarity.

    5. (Götzenberger et al. 2012)

      Götzenberger's research suggest that species distribution is largely influenced by intraspecific competition (competition within the same species)

      As the number of superior competitors increases, diversity decreases. This holds true only until other species are excluded.

    6. Hartmann 2007

      Hartman's research focused on secondary metabolism in plants. These were associated with genes that have a high ability to change and adapt to the pressures of their environment.

      Each plant population has unique secondary chemicals that have adapted to a plant's specific niche.

    7. Swenson 2013

      Swenson summarizes how to estimate the similarity between species by using both functional traits and phylogenetic trees.

      He uses the data from these approaches to test the mechanistic community hypothesis.

  6. Mar 2018
    1. Micosatellite SSR data have proven useful to reveal patterns

      Microsatellites, have been used by geneticists on plants in order to identify gene loci and how they can affect a certain trait or disease.

    2. however, it appears that they are related to unusual rain fluctuations (Romero Luna, 2011). Because the Dominican Republic population of C. jimenezii is located near the shoreline of this lake, there is concern that the soils where the species occur can be negatively affected by saline intrusion.

      The research here describes the changes in genetics that have been triggered by environmental factors so that the palms can deal with salt and increased water amounts.

    3. Nauman and Sanders (1991a) who suggested that it is composed of three major groups: the argentata group (with ten species, including the Critically Endangered C. crinita, C. cupularis, C. leonis, C. montana, C. victorinii, C. borhidiana), the argentea group (with six species, including the Critically Endangered C. spissa), and the pauciramosa group (with 31 species, including the Critically Endangered C. nipensis, C. pauciramosa and C. yuraguana). Nauman and Sander's (1991a) phylogenetic research was based on morphological traits.

      This taxonomic research was done in 1991 by Nauman and Sanders. Essentially it explained why there is genetic diversity amongst the Coccothrinax populations, and it is essentially because they come from three main groups each comprised of different traits.

    4. In an unpublished study focusing on the genetic structure of con-specific populations of Coccothrinax argentata from the Lower Florida Keys and the Florida mainland, Zona et al. (in preparation) found a much lower Fst value of 0.24.

      This study yielded a Fst value, which essentially describes the degree to which a population interbreeds and how freely they do so. The current Fst value are very low compared to what was found in the experiment done in this paper. This is cause for further testing.

    5. 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.

    6. 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.

    1. crypt regions of the organ

      See Dr. Bethany Radar and Dr. Ned Ruby use confocal images and immunocytochemistry to look at Vibrio fischeri in the crypts of the light organ:

      A look at Vibrio fischeri

    2. In bacterial light organs, the animal host must control not only light emission but also the symbiont populations. This management of the symbionts by the host is essential to maintain symbiont number and to sanction cheaters (i.e., dark mutants that might arise and compromise the function of the organ)

      Bacteria in the light organ continue to grow and multiply. If the numbers get too high, the bacteria could potentially switch from being beneficial to being harmful.

      Additionally, if bacteria develop mutations that cause them to stop producing luminescence, the mutants will use resources without providing benefit to the squid.

      Consequently, the squid must have a way to control the number of bacteria that colonize the light organ. They do this by ejecting 75% or more of the bacteria in the light organ each day.

    3. Components of visual transduction cascades, including opsin, arrestin, and rhodopsin kinase, co-localize in the retina, because they function in concert during phototransduction

      Work by Hargrave and McDowel (1992) and by Ridge et al. (2003) on phototransduction in the retina established that these three proteins are part of the G-protein-coupled pathway required in order for phototransduction to occur.

    4. Recent studies of the transcriptome of the light organ of E. scolopes revealed the expression of several genes that encode proteins with sequence similarity to components of visual transduction cascades

      Chun et al. (2006) generated 11 cDNA libraries from the light organ of the bobtail squid.

      Developmentally important time periods were chosen for analysis in order to provide a tool that would allow researchers to ask questions about how the bobtail squid responds to colonization by Vibrio fischeri.

    5. The morphology of the light organ, as well as behavioral studies, have suggested that the animal uses the light in counterillumination

      Jones and Nishiguchi (2004) were the first to test the hypothesis that Hawaiian bobtail squid use bioluminescence for counterillumination (a strategy for camouflage). They measured changes in bacterial luminescence that matched changes in down-welling light (light coming from above).

    6. previous studies of the anatomy and biochemistry of the light-organ lens and reflector demonstrated dramatic biochemical convergences with those of eyes

      Montgomery & McFall-Ngai (1992) and others discovered that proteins in the lens of the light organ of E. scolopes were similar to the proteins commonly found in the lenses of some mammal and cephalopod eyes.

    7. system for the analysis of tissues that interact with light and as a natural model of symbiosis

      The Euprymna scolopes-Vibrio fischeri symbiosis is a system with a single host and single symbiont, making it a great system to study how bacterial symbionts are acquired.


    8. the PSVs in certain bioluminescent squid species have been implicated in the perception and control of light emission, particularly in counterillumination

      The structures that control the amount of light emitted to produce counter-shading (PSVs) are different from the structures that produce the light.

      Counter-shading refers to the fact that parts of animals that are exposed to light are usually lighter in color than those parts that are not exposed to light.

    1. the required distances to track climate are much shorter than for latitudinal shifts (20)

      Loarie et al. found that spatial temperature gradients (degrees per distance) are larger for mountainous areas compared to flat areas. This means that, for the same change in temperature, a species that lives in a flat area must move much farther than one that lives in a mountainous area.

      Therefore, the authors conclude that it should be easier for a species to keep up with climate change by changing elevation than by changing latitude, if distance is the only factor.

    2. differ across the world, so a given level of warming leads to different expected range shifts of species in different regions (20), assuming that species track climate changes

      As the climate warms, plants and animals may need to shift their ranges to keep living in a suitable climate. Because temperature gradients vary in different types of ecosystems, we expect the size of range shifts to be variable, too.

      For example, two regions experience the same increase in temperature over a period of 20 years. The temperature gradients are 1.3° per 100 km in the first region and 0.9° per 100 km in the second. Species in the first region will have to move farther to maintain their climate than those in the second region.

    3. species have changed the timing of their life cycles during the year and that this is linked to annual and longer-term variations in temperature

      These studies show that increases in temperature are linked to changes in the life cycles of plants and animals. The dates of seasonal events, such as blooming, migrating, and egg laying, have changed for many species as their habitat has warmed.

      The studies have demonstrated a statistical relationship between temperature and the timing of life cycle events: Larger changes in event timing occur in areas with greater temperature changes.

    4. make it important to identify the rates at which species have already responded to recent warming

      References 1-8 link biodiversity declines to climate change by showing that extinctions occur or are predicted to occur in areas where the climate has warmed.

      This risk of biodiversity loss is a reason that the current meta-analysis is important: Quantifying how species ranges respond to climate change will help scientists and policymakers predict and hopefully prevent biodiversity loss in the future.

    5. Species are also affected to different extents by nonclimatic factors and by multispecies interactions, which themselves depend on a diversity of environmental drivers

      Climate is only one of many factors that determine the range of a species. These other factors may alter the way a species responds to climate change.

      In the following sentence, the authors give examples of this.

    6. Species may also show individualistic physiological responses to different aspects of the climate, such as different sensitivities to maximum and minimum temperatures at critical times of their life cycles. These sensitivities will combine with variable wait times for different novel climatic extremes to take place

      Climate change can produce changes in extreme temperatures in addition to, or instead of, changes in average temperatures. A species that is sensitive to extreme high or extreme low temperatures may respond to these extremes rather than to the average.

      Because extremes may change at a different rate from averages, these species may not appear to track climate change when it is measured by average temperatures (as in the current analysis).

    7. that cannot colonize across fragmented landscapes (17, 21–23), or if they possess other traits associated with low extinction or colonization rates

      Different species have different traits that may affect how quickly they can shift their range boundaries in response to changing temperatures. These traits include reproduction rates, ability to move, and ability to thrive in different habitats.

    8. Published studies have shown nonrandom latitudinal and elevational changes (1, 7, 13–17) but have not previously demonstrated a statistical linkage between range shifts and levels of warming

      Researchers have documented that many species' ranges have shifted to higher latitudes and/or higher elevations during the same time period that the climate has warmed. However, they have not shown that the range shifts are statistically linked to the temperature change.

      If species range shifts are directly linked to climate warming, we should find a positive trend between the two: the larger the temperature increase, the larger the range shift.

    9. A previous meta-analysis (14) of distribution changes

      A meta-analysis, published in 2003, found range shifts in a large number of species, in directions consistent with climate change.

    10. Many species have also shifted their geographic distributions toward higher latitudes and elevations

      Large studies have shown that land-based populations of many living organisms have shifted to higher latitudes and/or elevations as the climate has warmed during the 20th century. These studies include plants and animals in many different locations around the world.

    1. 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.

    1. 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.

    2. 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).

    3. 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.

    4. 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.

    5. 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.

    1. Seventy human-like tracks arranged in two parallel trails (39 prints in G1 and 31 in G2/G3) are reported at Laetoli Site G (Leakey, 1981). Unfortunately, the whole set of morphometric data for the unearthed tracks was never published; only average values obtained from a selected number of tracks were provided. In the case of G2/G3, data are incomplete, largely because the prints of G3 are superimposed onto those of G2, so that it is difficult to collect the measurements (Tuttle, 1987).

      Only some data were published for site G. As a result, the data are less complete and less reliable. There are some differences in the measurements published by individuals viewing the original G tracks and those made by others using the fiberglass casts.

    1. The slope of this relationship (β in days °C−1) has been termed the temperature sensitivity by other authors

      Large species sampling size necessary (or interspecific variation in species may be too high)

      Warming experiments underpredict the advance of spring events

      Experimental results alone cannot be used for parameterizing species distribution and ecosystem models

      Best (currently) measure: observational data

    1. with many reports of butterflies and hawkmoths pollinating species of this family (Haber 1984; Darrault and Schlindwein 2005; Sugiura and Yamazaki 2005; Moré et al. 2007).

      Haber found that hawkmoths are frequent pollinators of these families, but require a significant nectar reward to do so.

      Darrault and Schlindwein found these butterflies and moths do pollinate. Furthermore, in contrast to this study, they found that diameter of the mouth parts showed no correlation with pollen collected.

    2. Many studies of other plant–pollinator systems provide evidence that the morphological match between the pollination apparatus and the length of the proboscis is associated with pollination effectiveness (Inouye 1980; Waser et al. 1996; Castellanos et al. 2004; Moré et al. 2012; Miller et al. 2014).

      Inouye found that proboscis length was correlated with a bee's time spent at a flower. Waser found that many pollination systems tend towards specialization.

      This implies that flowers adapt their shape and length to accomodate one group of pollinators. Length is a great determinant in these cases.

    3. In many self-incompatible Apocynaceae, flower revisitation increases the probability that self-pollen is deposited onto the stigma, leading to ovule and fruit abortion (Lipow and Wyatt 1999, 2000; Wyatt et al. 2000; Wyatt and Lipow 2007).

      Lipow and Wyatt found in multiple studies that self pollination in this family of plants prevents fruit bearing. This can be problematic, as it can decrease seed output. As such, it could create pressure for plants to evolve to punish revisitors.

    1. 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.

    2. 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.

    3. 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.

    4. 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.

    5. 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.

    1. Rat 50-kHz vocalizations indicate positive emotional valence

      Scientists characterized rat USVs and demonstrated that some (22 kHz) are associated with negative reactions and others (50 kHZ) are associated with positive reactions to their environment.

      "Valence" is a psychological way of categorizing an emotional state as good (positive) or bad (negative).

    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.

  7. Feb 2018
    1. 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.

    2. 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.

    3. 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.

    4. 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.

    1. Central mechanisms of tickling were investigated by functional magnetic resonance imaging (fMRI) in human brains (9); that study, which used tickling stimuli evoking knismesis and observed somatosensory cortex activation, suggested that self-tickle suppression might be mediated by the cerebellum.

      fMRI was used to detect brain activity in healthy volunteers who were being tickled. The somatosensory cortex was one region that was activated by tickling.

      When patients were asked to tickle themselves, there was also activity in the cerebellum, a region of the brain associated with coordinating movement. The researches suggest that the cerebellum may have a role in detecting self-tickling and suppressing the tickle response.

    2. Anxiogenic conditions suppress tickling-evoked USVs in rats (7)

      This idea may have been originally proposed by Charles Darwin. He wrote that if a child is tickled by a stranger, the child would scream from fear rather than laugh.

    1. Within-species variability in body size often relates to sexual dimorphism and/or to adaptation to different ecologies

      Traditionally, paleobiologists hypothesized that early hominids exhibited a high degree of sexual dimorphism. This thinking is based on limited fossil evidence and consequently is being questioned by a number of researchers.

    1. 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.

    2. 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.

    3. 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.

    4. [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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    11. grasslands, C4 grasses and legumes tend to promote greater soil carbon accumulation (8).

      In a research study, conducted by D. A. Fornara and other scientists, C4 grasses and legumes were found to promote the greatest amount of carbon accumulation in the soil. If these two plant species were to go extinct, the total amount of carbon storage would vastly decrease because they are the main contributors to carbon accumulation in the soil. The results of this previous research study support the conclusion that different plant species affect ecosystem services differently.

    12. Moreover, species identities influence ecosystem services (39), such that the order in which species are lost from ecosystems could influence the quantitative responses of ecosystem services, like carbon storage.

      A research paper, drafted by C. M. Tobner and others, states that specific characteristics of different plant species influences ecosystem service such as: climate regulations, the amount of atmospheric CO2 converted into biomass (carbon storage), and water purification. All plant species do not affect atmospheric CO2 reduction in the same capacity. The loss of certain plant species could have a greater impact on ecosystem services, like carbon storage, than others plant types.

    13. Although the pattern of increasing plant carbon storage (and thus value) with plant species richness may be general, reflecting the well-documented relationship between plant species richness and plant productivity (4), it is possible that biome-specific estimates of the value of species richness will reflect variation in the relationships between species richness and carbon storage.

      A previous research paper, written by B. J. Cardinale and others, showed that there may be a general relationship, in all environments, that increased plant diversity increases the amount of carbon storage. Different environments around the world could respond differently to the same level of species richness, but will have an overall increase in carbon uptake.

      The author suggests that the estimated values of the most effective amount of plant diversity, for different environments, could show variation in the relationship between species richness and carbon uptake. By conducting experiments, on a variety of different environments, we will be able to figure out the best level of plant diversity, in specific environments, for the highest level of carbon storage. These results could greatly help reduce the CO2 pollution in the atmosphere and help deter global warming.

    14. incorporating this information into the C storage valuation of conversion of marginal or abandoned agricultural land into forests (17) (where forests rather than grasslands are the typically native vegetation) would also advance our knowledge about economic consequences of management decisions.

      A research study, by K. Paustain and others, indicates that the increased uses of forest species, in stripped farmlands, rather than using grassland species could help advance the knowledge of what is the best way to benefit the human population. This gain of knowledge, about land management, would help find the most effective way to decrease the amount of CO2 pollution in the earth's atmosphere. At the very least, the increased awareness of different methods of restoration, for different land types, would determine the additional increase in carbon uptake and its economic worth to total carbon reduction.

    15. Similarly, assuming that higher forest species richness also enhances C storage (5, 6)

      In multiple research papers dictated, by leading scientists A. Paquette and L. Gamfeldt, that higher species diversity in forests correlates to increased carbon storage. This research gives insight into the possibility of using forest species, for restoration purposes, instead of grassland species to increase the total amount of carbon storage in a environment.

    16. It is also worth noting that converting marginal or recently abandoned agricultural land (with typically very low soil C and species richness) to diverse prairie (for example, 11 species) would result in even greater increases in C storage than increasing CRP grasslands from 6 to 11 species (38).

      A previous research study, conducted by C. Fissore and coworkers, proposed that increasing species richness in recently abandoned farmlands, with low levels of carbon in the soil, to become diverse prairies would result in a higher increase of carbon uptake when compared to increasing plant diversity from 6 to 7 in CRP grasslands. Meaning that the addition of species richness, in environments with low levels of carbon, has a greater affect on carbon storage than conservation grasslands. By turning recently abandoned farmlands into diverse prairies, through the introduction of plant diversity, the amount of carbon sequestered from the atmosphere increases and helps deter global warming faster than the use of CRP grasslands.

    17. Although this may be more expensive up front than seeding monocultures (37)

      In a previous work written by P. Torok and research team, concluded that the use of a diverse seed mixture is more expensive to farmers than growing only only type of seed. This is a drawback to the the benefit of increased species richness in farmlands, but the advantage of a diverse array of plant species far out weights the initial cost when considering carbon uptake in an environment.

    18. Practices as simple as using more diverse seed mixes can promote higher species richness in prairie restoration (35, 36).

      A previous research paper posted, by leading scientists E. Grman and D. L. Larson, reported that the practice of increasing plant diversity is simple. All farmers have to do is use a seed mixture with a more diverse array of plant species. The use of the diverse seed mixture will help increase the carbon uptake in the farmers fields and help decrease atmospheric CO2 levels.

    19. from the Minnesota grassland experiments, the marginal value of gaining one additional species over this entire CRP area (increasing species richness from S = 6 to S = 7), would amount to ~$722 million. Restoring species richness on CRP grasslands to levels observed for the remnant grasslands (from S = 6 to S = 11) would confer a value for the increased carbon storage of ~$2.350 billion

      In a previous Minnesota grassland experiment, the addition of species richness from 6 to 7, increased the carbon uptake, of the CRP grasslands, by about $722 million. The increase of species richness from 6 to 11 increased the total carbon uptake, of CRP grasslands, by $2.350 billion. The authors used the economic worth or carbon to calculate the numbers seen above. Overall the author is trying to convey that increased species richness, in CRP grasslands, vastly increases the amount of carbon sequestered by the plants and is a huge benefit to carbon reduction in the United States.

    20. We synthesized published estimates of species richness in CRP grasslands and paired reference native grasslands (16, 31–34) and found that species richness in CRP grasslands (S = 6.5 ± 1.1) was lower than in adjacent remnant grassland sites (S = 11.4 ± 1.8), indicating the potential for CRP restoration to achieve higher species richness and associated ecosystem services.

      J. L. O'Connell and coworkers published estimates of plant diversity in CRP grasslands compared to native grasslands. The author of this research paper found similar results that species richness in CRP grasslands was lower than the native grasslands.The lower recorded plant diversity means there is a higher potential, in conservation grasslands, for increased species richness and ecological benefit.The increased plant diversity, in CRP grasslands, will benefit the ecosystem by increased uptake of carbon from the atmosphere and contributions to nutrient cycles.

    21. Across the conterminous United States, approximately 12.34 million ha of land under cultivation have been converted to CRP grasslands, increasing land C uptake by approximately 6.54 teragrams C year−1 [area and C uptake estimates averaged from (17, 27–30)].

      The author of this research paper used the findings of K. Paustain and coworkers to estimate the carbon uptake of CRP grasslands over 12.34 million hectares. The conversion of previous farmlands to grasslands helps increase the amount of carbon taken from the atmosphere by 6.54 teragrams per year. This helps reduce the total pollution of CO2 in the earth's atmosphere and restore nutrients to the deprived farmlands.

    22. These scenarios are hypothetical because species richness is not uniformly distributed, because species loss does not occur independently of other shifts in community and ecosystem processes, and because the selection of the median range is arbitrary, given the large variation among species and the marked reduction in the ranges of grassland species due to extensive historical conversion of grasslands to agriculture

      The previous research (26) states that species richness is not uniform throughout an ecosystem since the amount of species throughout an ecosystem can vary due to different conditions.

      The paper also points out that other conditions besides carbon storage can affect biodiversity of an ecosystem. This paper takes that into consideration by comparing the results of the experiment to the historical levels of biodiversity recorded in the grasslands.

    23. Conservation Reserve Program

      The establishment of the Conservation Reserve Program was important in determining the results of this experiment. The program was created to encourage farmers to use some land to plant vegetative cover rather than crops to provide habitat for pollinators, reduce erosion, and improve water quality.

      The federal government pays farmers to make these land conversions, which places an economic value on species richness.

    24. despite some evidence that species richness also stimulates soil carbon turnover (23).

      A previous research paper, drafted by J. P. Reid and others, suggests that increased plant diversity, in a grassland environment, shows evidence of stimulating carbon turnover in the soil. The greater the number of plant species, the faster carbon cycles through the environment.

      The cycle is as follows: atmosphere -> plant (via photosynthesis) -> soil -> back to plant -> back to atmosphere due to plant respiration.

    25. Valuation also provides a quantitative foundation for assessing decisions about land use involving trade-offs (21),

      A research paper, composed by J.H. Goldstein and others, states that the price of carbon emissions (provided by the carbon market) influences the amount of land companies are allowed to obtain. If companies have a high rate of carbon emissions going into the the earth's atmosphere then the amount of land they can use decreases.

    26. Our approach to this question offers a quantitative monetized view of one of the values of biodiversity that contrasts with the typically qualitative nature of most other assessments of biodiversity value (18–20).

      In multiple research papers biodiversity was calculated using a number, rather then a qualitative assessment. This paper takes the same approach. Diversity is thus assigned a number instead of an observation for further calculations to determine the affects of biodiversity on carbon storage.

    27. Reduced carbon gain as species diversity declines reduces carbon input to soil and, in some longer-term experiments, reduces soil carbon stocks (8).

      In a previous research paper, written by D. A. Fornara and coworkers, it was described that as species diversity declines carbon gain is reduced and in long-term experiments the decline of species richness reduced the total amount of carbon in the soil. Meaning that as plant diversity decreases the amount of carbon taken up by plants decreases and in the long-term the amount of carbon stored in the soil also decreases. If the amount of carbon in the soil decreases that means that there is more carbon being stored in the atmosphere, which proves that plant species diversity is vital for climate regulation.

    28. Observations in forests also indicate that local species richness contributes to carbon gain across broad gradients of climate and soil conditions (5–7).

      In multiple research studies conducted by leading scientists, A. Paquette, L. Gamfeldt, and J. Liang, proposed that local species richness contributes to carbon gain across a variety of different climate and soil conditions. Meaning that plant diversity in an ecosystem, regardless of climate and soil conditions, causes an increase in carbon uptake by plants. Which can be seen through the increased growth of plants in an environment.

    29. Syntheses of experiments across different ecosystems indicate that biomass accumulation tends to decline as local species richness decreases (4)

      A previous research paper, by B. J. Cardinale and others, states that a decrease in species richness causes a decrease in biomass accumulation. This shows that carbon sequestration diminishes as ecosystem biodiversity decreases. This is driven by less competition among species which in turn increases carbon availability and decreases total carbon uptake.

    30. (3)

      Has the Earth's sixth mass extinction already arrived? 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

      This article suggests that the current rate of species extinction is higher than what has been expected in the past (compared against fossil records). The authors propose that this elevated rate of extinction may possibly be the beginning of the 6th known mass extinction event on earth.

      This extinction would drastically lower biodiversity by killing off many species that would otherwise function as carbon sinks. The release of such massive amounts of carbon might have dramatic effects upon the environment.

    31. “the variety of living [photosynthetic] organisms, the genetic differences among them, and the communities and ecosystems in which they occur”

      A previous research paper, written by Keystone Center, states that genetic diversity in the plant life along with the way communities of plants interact in an ecosystem is vital for the carbon storage cycle on earth. Different species of plants are able to store different amount of carbon, if there was no diversity between plant species then the amount of carbon storage in an ecosystem would be altered. Without diversity in plant species, our oxygen-dependent existence and regulation of global climate might not be possible.

    32. The rise of photosynthesis nearly 4 billion years ago initiated the transfer of carbon dioxide in the atmosphere to organic carbon, much of which is now contained in rocks (1)

      Past and present of sediment and carbon biogeochemical cycling models

      By: Mackenzie, FT (Mackenzie, FT); Lerman, A (Lerman, A); Andersson, AJ (Andersson, AJ)

      This is a secondary study of the history of the carbon cycle, with respect to the onset of industrialization as well as the dynamic role the ocean plays in carbon storage. Prior to industrialization, the ocean was a net source of CO2 emissions due to the net carbon differences between photosynthesis and respiration. However, the massive CO2 releases from the burning of fossil fuels have made the ocean into a net carbon sink.

      This citation is referring to the storage of carbon within calcium carbonate (CaCO3), or limescale within the ocean. This limescale comprises most of the 'rocks' in reference.

    1. JH and insulin are involved in a complex regulatory network, in which they influence each other and in which the insect's nutritional status is a crucial determinant of the network's output [5].

      Typically, insulin is obtained from the food we eat, if the mosquito does not have enough nutrition and food the insulin levels will be low. If the mosquito's nutrition improves than the insulin will be obtained from the food she eats.

      When insulin or the juvenile hormone binds to a receptor it carries out a process so it can send a message to the nucleus of the cell, this allows for activation of regulation. When insulin binds to the insulin receptor that stimulates development and growth. In this case, the juvenile hormone regulates metabolism, reproduction, and nutrition within the cells of mosquitoes. This way insulin and the juvenile hormone are working together in keeping the insects healthy.

    1. for swimming animals longer than ∼1 m, the speed at which cavitation occurs, with destructive consequences for the tissues

      Longer fish would be affected by limits in their water environment more than smaller fish because their length and greater ability to swim faster makes them more likely to have cavitation occur in their bodies. The increase of cavitation bubbles in their bodies would injure them and ultimately lead to their death.

    2. high-speed video are usually confined to relatively short time intervals, reducing the chance of detection of high speed events, which are thought to occur only rarely during an animal's lifetime

      The researchers tried to understand more about the maximum speeds of these fishes but unfortunately the technique of videotaping the fish in action were not able to provide enough information because they could never catch the fish swimming at their true maximum speed.

    3. theoretically, fish swimming speeds are physiologically limited by the tail-beat frequency attainable in a given environment

      In reality, even if you could see a fish swimming at its maximum speed, what that speed is would differ based on the environment of the fish. One variable in a fish's environment that affects its speed is the strength of the water current. If the current is great, then a fish swimming against it at its maximum ability would have a lower tail-beat frequency compared to the same fish swimming at its maximum ability in the direction of the current. You can think of how water current affects underwater organisms the same way how strong winds affect land organisms.

    4. More recently, work on billfishes using data storage tags has shown that blue marlin (Makaira nigricans) rarely exceed speeds of 2 m s−1, with a maximum of 2.25 m s−1 (Block et al., 1992) and a study of sailfish hunting schooling sardines reported an upper speed limit of 8.19 m s−1

      Recent studies have shown that billfishes often prefer slower, more accurate swimming rather than fast swimming. This is said to be preferred due to their prey's maneuverability which is achieved by swimming unsteadily. Unsteady swimming refers to the sharp turns and quick changes in acceleration that smaller fish often use to escape larger predators.

    5. Animal maximum speeds play a significant ecological role, particularly in the context of predator-prey interactions

      The speed an animal can achieve when chasing prey is one factor that determines what type of prey they can or cannot eat. In terms of this, the more different types of speeds a fish can achieve, the more varieties of smaller fish it can successfully chase and eat. For the fishes studied, none of them swim at their maximum speed because it is not required to swim that fast to consume their prey.

    1. The molecular mechanisms that regulate Wolbachia titer are not well understood. Body-wide Wolbachiatiter has been reported to vary up to 180,000-fold in lab-reared offspring of mosquitoes collected from nature (Ahantarig et al., 2008), and 20,000-fold between wild-caught Drosophila innubila individuals (Unckless et al., 2009). This titer variation may be due in part to sensitivity to host temperature (Bordenstein and Bordenstein, 2011; Mouton et al., 2006, 2007; Wiwatanaratanabutr and Kittayapong, 2009, 2006), host crowding (Hoffmann et al., 1998; Wiwatanaratanabutr and Kittayapong, 2009), host genetic background (Boyle et al., 1993; Poinsot et al., 1998; Veneti et al., 2004; Serbus et al., 2011) and host age (Tortosa et al., 2010; Unckless et al., 2009).

      Background information on Wolbachia colonization mechanisms in germ line cells is not well known. Concentration variation may be due to multiple factors.

    2. Thus, persistence of Wolbachia in maternal germline cells is of critical importance for transmission to progeny. In the Drosophila melanogaster model system that naturally carries wMel Wolbachia (O'Neill et al., 1992; Riegler et al., 2005), the GSC are infected with these bacteria. This ensures that differentiating daughter cells (cystoblasts) inherit Wolbachia during mitosis (Ferree et al., 2005; King, 1970; Serbus et al., 2008). While the cystoblast undergoes mitosis to generate an interconnected cyst of 16 germline cells, Wolbachia exiting the nearby somatic cell niche also invade the germline cyst (Toomey et al., 2013). After the cyst is coated with a blanket of somatic follicle cells, creating a unit referred to as an egg chamber (King, 1970), additional horizontal invasion events may also occur (Casper-Lindley et al., 2011). Wolbachia also replicate to populate the germline cells of the egg chamber, including the oocyte cell that ultimately takes over to form a completed egg (King, 1970; Serbus et al., 2011). Similar germline loading mechanisms are expected to apply to other Wolbachia-Drosophila combinations, with differential contributions to germline colonization by GSC loading and horizontal invasion in each case (Toomey et al., 2013).

      Wolbachia enter several different types of cells with the ultimate goal of infecting eggs and passing on to the next generation.

    3. Though Wolbachia occupy the germline stem cells (GSC) of male and female hosts, removal of the bacteria during spermatogenesis creates a ‘dead end’ with respect to transmission (Bressac and Rousset, 1993;

      Wolbachia ensures maternal transmission by leading to the death of eggs fertilized by infected male flies. This does not occur, however, when an infected female and her eggs mate with an infected male fly. Wolbachia modify sperm in infected male flies, but do not reside within the sperm.

    4. Conversely, the wMelPop Wolbachia variant lyses brain cells and shortens insect lifespan (Min and Benzer, 1997)

      wMelPop Wolbachia variant is unique in being more pathogenic than symbiotic (as with most other strains of Wolbachia). It is not harmful to developing flies, but divides quite vigorously in adult flies, damaging several tissues, and ultimately prematurely killing the adult fly.

    5. protect the host from lethal RNA viruses (Chrostek et al., 2013; Hedges et al., 2008; Martinez et al., 2014; Teixeira et al., 2008)

      Wolbachia is known to confer resistance to viruses in hosts it infects.

    6. promote host reproduction (Dedeine et al., 2001; Landmann et al., 2011; Starr and Cline, 2002)

      Wolbachia have been found to be essential for proper production of offspring by certain organisms.

    7. Of those, some are reported to provide essential cofactors to the host (Ghedin et al., 2007; Hosokawa et al., 2010; Nikoh et al., 2014)

      Hosokawa et al. found that Wolbachia bacteria are essential for proper development of the bedbug, Cimex lectularius, through provisioning of vitamin B, an essential cofactor. Cofactors ensure that enzymes function correctly.

    8. At least 470 distinct Wolbachia strains have been reported to date (Baldo et al., 2006)

      Genus Wolbachia is quite diverse.

    9. 52% of all insect species

      It was found that about 52% of all insect species are infected with Wolbachia endosymbiotic bacteria.

    10. Wolbachia are Alphaproteobacteria that reside within the cells of mites, crustaceans, filarial nematodes (Werren et al., 2008)

      Wolbachia are found in various nematodes (e.g. roundworm) and arthropods (e.g. insect, spider, crustacean).

    11. Symbiotic interactions within the collective unit of an organism range from mutualistic to parasitic (Dale and Moran, 2006).

      Although a symbiont is typically understood to be helpful for the host organism, the line between endosymbionts and parasites is not well delineated. This is especially the case, for example with Wolbachia. This bacterium is capable of ensuring its transmission by favoring the survival of fly egg cells that are infected, and leads to the death of uninfected fly eggs. On the other hand, Wolbachia is also known for making infected fruit flies resistant to certain viruses that would otherwise afflict the flies.

    1. In fact, the confidence intervals are not visible in this figure, overlapping almost completely with the plotted average data points. This result is, however, largely an artifact of differing bootstrap resampling techniques applied to the randomly sampled and contiguous gene sequences. A typical nonparametric bootstrap was applied to the contiguous gene sequences: a sample (an individual gene) was taken and pseudosamples of the same size were generated from this sample by sampling with replacement. This gives the variance about the estimate of the phylogeny for that sample. Randomly sampled orthologous nucleotides were sampled with a different strategy, using the variable-length-bootstrap option in PAUP*. In this case, a sample of a given size was taken from the complete data set and the phylogeny was estimated. Then a new sample of a given size was taken, and the phylogeny estimated. So, for even the smallest sample size of 1000 nucleotides, 1000 replicates would have sampled the vast majority of nucleotides from the complete data set. This sampling scheme did not, therefore, measure the variance on the estimate of the phylogeny from a particular random sample, as in the contiguous gene sequences, but is instead akin to the variance on the phylogeny for repeated sampling of a given size from the complete data set.

      The author is stating that when Rokas et al. carried out the experiment to record bootstrap values in randomly sampled and contiguous gene sequences, the methods used to test variance were flawed. Rokas used two different techniques to test bootstrap value variance for randomly sampled and for gene sequences. The use of a different method when testing the randomly sampled sequences resulted in bootstrap values with very little variance, Rokas' conclusions were no longer considered reliable.

    2. took this as evidence of the misleading signal in individual genes resulting from the nonindependence of nucleotides within genes.

      In this previous study, the authors had come to the inaccurate conclusion that single genes provide misleading phylogenetic signals because the results they gave varied widely when compared to random genes and also had low confidence levels.