1,273 Matching Annotations
  1. Aug 2018
    1. R. Rowan, D.A. Powers, Marine Ecology Progress Series 71, 65–73 (1991).

      Gives background information on different types of amplification techniques used to determine molecular identification.

    2. D.L. Taylor, In: Symbiosis in the Sea (ed. Vernberg WB), pp. 245–262. (University of South Carolina Press, South Carolina, 1974).

      Prior to the introduction of molecular techniques, early work such as this reference discusses dinoflagellates and how they were thought to belong to one pandemic species.

    3. X. Pochon, R.D. Gates, Molecular Phylogenetics and Evolution 56, 492–497 (2010).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    4. M.A. Coffroth, S.R. Santos, Protist 156, 19–34 (2005).

      Gives background information on the Symbiodinium genus for the reader to understand the main interest of the research in this paper.

    5. H.D. Freudenthal, Journal of Protozoology 9, 45–52 (1962).

      This reference explains why there are so many types of Symbiodinium.

    6. J.H. Connell, Science 199, 1302–1310 (1978).

      This information is used in order to introduce what species this research is going to focus on. Although the focus is on Symbiodinium, this information highlights the importance of this genus.

    1. C.D. Hopkins, Copeia 1991, 151–161 (1991).

      The article written by Carl D. Hopkins provides the author with background informational on B.pinnicaudatus and on the electric organs found within the organism. B.pinnicaudatus is a gymmotiform discovered in French Guinea and can be found throughout South America. This species similar to other electric fish is able to generate a pulse-type electric-organ discharge. The two types of electric discharges generated by electric fish tend to a pulse or a wave. This species is part of the largest family that produce electric pulses. Within this species, the males are able to produce a longer discharge than females.

    2. M.V.L. Bennett, Fish Physiology 5, 347–491 (1971).

      In his paper Electric Organs, Fishes, Bennett explains the various mechanisms behind electric fish organs and how they generate electricity, such as electrocytes and discharge patterns. He also describes several vital functions of electric organs and how they vary depending on the strength of the species' electricity, or the power of its voltage emission. For example, the electric organs of more strongly electric fish, or those who emit higher voltages, emit electricity to defend against predators. Conversely, in more weakly electric fish, their electric organs emit electricity that serves as a method of communication.

      This reference is significant to this paper, Electric organ discharges and electric images during electrolocation, because it gives a broad overview on electric fish, their anatomy, and their functions. It serves as a source of background information and context for this paper, which can be especially helpful for readers who possess limited knowledge on electric fish.

    3. J. Bastian, Electrolocation: behavior, anatomy and physiology.  (New York: Wiley, 1986).

      This source provides information about how the various regions of neuronal activity in electric fish respond differently to variance in body movement.

      Specifically, electrosensory pyramidal cells (neurons found in the areas of the brain that are involved in executive functions: memory, emotional responses, etc.) activate or discharge electric signals in multiple ways dependent on the re-afferent (sensory information that is received) signals from their external environment.

    4. E. Knudsen, J. Comp. Physiol. 99, 103–118 (1975).

      This source provides information about how the electrical patterns of small fish work compared to dipolar geometry and how that changes as the fish become larger in size.

      Specifically, the smaller electrical fish, which the author of this article is studying, have electrical currents that work like magnets. These smaller fish are much easier to measure and experiment on since their electrical currents and fields can be predicted. The bigger electrical fish are the more likely the electrical fields are to deviate from a dipole field.

    5. T.H. Bullock, W. Heiligenberg, Electroreception. (New York: Wiley, 1986).

      Bullock's and Heiligenberg's article, Electroreception, gives an in-depth knowledge on electroreception as well as a review on the electric organs that are found within marine vertebrates. This background provides the author with the basic foundation for understanding how electrolocation works and the purposes it serves these marine vertebrates in their natural environment and daily lives. This citation also helps the author introduce the topic of electrogenesis and electroreception in relation to the location of the organs necessary for the process of electrolocation to occur.

    1. C. Parmesan, G. Yohe, Nature 421, 37–42 (2003).

      Identifying effects of climate change on recent biological trends is difficult because non-climatic changes greatly influence local, short-term biological changes. Parmesan and Yohe study the differences between climatic and non-climatic effects on over 1700 species. A diagnostic indicator of temporary, geographic shifts was found with confidence for 279 species.

    2. M. H. Williamson, Biological Invasions (Chapman & Hall, 1996).

      A collection of invasive species and the damages they can cause, summarized by an invasive species expert. The focus of the text is on approach to biological control and releasing genetically modified organisms.

    1. National Research Council, “Air quality management in the United States” (2004).

      This document sets standards for ensuring good air quality in the United States. Most of the recommendations focus on transportation and industrial sources. This paper suggests that household VCPs are becoming an ever increasing source of VOCs.

    2. X. M. Wu, M. G. Apte, R. Maddalena, D. H. Bennett, Environ. Sci. Technol. 45, 9075–9083 (2011).

      Monitored air pollution at various small industrial buildings in California. This monitoring included measurements for VOCs.

      This experimental data was used to compare with the model calculations in this study.

    3. California Air Resources Board, “The California Consumer Products Regulation” (2015).

      California looks to regulate the emission of VOCs and thus regulates and keeps records of VOCs in various products. The authors of this paper were able to utilize that database to know what chemicals are present in various products.

    4. J. M. Logue, T. E. McKone, M. H. Sherman, B. C. Singer, Indoor Air 21, 92–109 (2011).

      Compiled results from 77 separate studies to look at typical levels of indoor air pollution in household environments. The study includes VOCs.

      This experimental data was used to compare with the model calculations in this study.

    5. A. Borbon et al., J. Geophys. Res. Atmos. 118, 2041–2057 (2013).

      An experimental study that monitored the presence of VOCs in the outdoor air near Los Angeles, California during 2010.

      This study uses the experimental data by Bordon to compare with their model calculations.

    6. J. L. Jimenez et al., Science 326, 1525–1529 (2009).

      Jimenez and colleagues developed a model to show and predict how VOCs react to turn into aerosol particles in the atmosphere.

      Understanding VOC emissions is important to understanding aerosol formation.

    7. GBD 2016 Risk Factors Collaborators, Lancet 390, 1345–1422 (2017).

      This study compiled a large number of studies on human health to examine various risk factors for disease and death.

      Air pollution was found to be the fifth leading risk factor for human health.

    1. R. J. Müller, H. Schrader, J. Profe, K. Dresler, W. D. Deckwer, Macromol. Rapid Commun.

      The authors reported a hydrolase from Thermobifida fusca. The authors noted that the hydrolase successfully degrades PET. They note that it is helpful that PET has a glass transition temperature near the temperature where the enzyme can be incubated with the plastic.

    2. 3. D. Kint, S. Munoz-Guerra, Polym. Int. 48, 346–352 (1999).

      Discusses the synthetic methods of preparing biodegradable copolymers that include PET as well as the mechanisms that break down the resulting products.

      The review details several areas of research needed if PET copolymers are to become a feasible biodegradable material, including finding a polymer with sufficiently high melting point to be bonded to PET and ensuring the resulting copolymer has the correct properties for practical use.

    3. 5. T. Nimchua, H. Punnapayak, W. Zimmermann, Biotechnol. J. 2, 361–364 (2007).

      This paper took samples of fungi from a variety of tropical locations in Thailand and then tested them for cutinase production. It found 22 samples able to use a cutinase enzyme to degrade PET.

    4. T. Nimchua, D. E. Eveleigh, U. Sangwatanaroj, H. Punnapayak, J. Ind. Microbiol. Biotechnol. 35, 843–850 (2008)

      Reports on a fungus that is capable of turning PET yarn into terephthalic acid (TPA). The enzyme responsible was identified as a hydrolase. PET degradation was measured by the production of TPA and the increasing hydrophilicity of the PET fiber.

    1. Musiba CM, Mabula A, Selvaggio M, Magori CC. 2008. Pliocene animal trackways at laetoli: research and conservation potential. Ichnos 15:166–178. doi: 10.1080/10420940802470383

      The authors discuss the animal tracks at a newly discovered Laetoli exposure and other sites. Animal trackways serve as ecological indicators.

    2. Maslin MA, Shultz S, Trauth MH. 2015. A synthesis of the theories and concepts of early human evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 370:20140064. doi: 10.1098/rstb.2014. 0064

      The authors examine the African paleoclimate and tectonics to determine how climate variability provides a framework within which to understand human evolution. The varying East African climate supports the pulsed climate variability hypothesis. Drying trends punctuated by short periods of high humidity may have driven hominin speciation and migration.

    3. Leakey MD. 1981. Tracks and tools. Philosophical Transactions of the Royal Society B: Biological Sciences 292: 95–102. doi: 10.1098/rstb.1981.0017

      Dr. Leakey and associates discovered the footprints left by three hominins in the Laetoli beds. In this article, it is reported that the trackway extends 27 meters and provides evidence of upright, bipedal locomotion. Radiometric dating places the tracks at 3.6 million years ago. There have been no stone artifacts found in the Laetoli area. The earliest evidence of stone tools in the region was found in Olduvai Gorge and dates to about 2 million years ago. Consequently, it can be inferred that bipedalism evolved prior to formalized tool-making.

  2. Jul 2018
    1. 17. M. Hosaka et al., Appl. Environ. Microbiol. 79, 6148–6155 (2013).

      This paper reported two genes that code for two separate proteins that sit in a cell membrane and help TPA get into the cell.

  3. Jun 2018
    1. W. Zimmermann, S. Billig, Adv. Biochem. Eng. Biotechnol.

      This is a chapter in a book about biofunctionalization of polymers. The authors focus on how using biological methods to modify PET might make it more hydrophilic and therefore allow it to be used for a greater variety of applications in, for example, engineering and medicine.

      The authors do not focus on the use of methods of degrading polymers for recycling or disposal, however many of the biofunctionalization processes they describe involve degrading portions of PET polymer to give it better properties.

    1. E. A. Posner, C. R. Sunstein, Univ. Chic. Law Rev. 72, 537–598 (2005).

      This article discusses how governments should assign dollar values to human lives when someone dies. One consideration is whether children and adults should be valued differently.

    2. W. Wallach, C. Allen, Moral Machines: Teaching Robots Right from Wrong (Oxford University Press, 2008).

      This book discusses how robots should be able to factor morality and ethics into their decisions, and discusses some ways engineers can program morality into machines.

    3. R. M. Dawes, Annu. Rev. Psychol. 31, 169–193 (1980).

      This study reviews the nature of social dilemmas, investigates potential solutions to social dilemmas, and lists psychological studies that have shed insights on the topic.

    4. K. Spieser et al., in Road Vehicle Automation, G. Meyer, S. Beiker, Eds. (Lecture Notes in Mobility Series, Springer, 2014), pp. 229–245.

      This paper investigates what would happen if personal transportation in Singapore was replaced by self-driving cars. Results suggest that far fewer vehicles would need to be on the road if such a system were implemented.

    5. M. M. Waldrop, Nature 518, 20–23 (2015).

      This feature article describes the rise of driverless cars and the technologies being implemented to make them drive on roads.

      The article argues that self-driving vehicles could help make roads safer, as about 90% of driving accidents are due to human error.

    6. B. Deng, Nature 523, 24–26 (2015).

      This feature article describes the challenges in programming robots to make ethical decisions.

    7. B. Montemerlo et al., J. Field Robot. 25, 569–597 (2008). C. Urmson et al., J. Field Robot. 25, 425–466 (2008).

      References 1 and 2 describe two entries for the DARPA Urban Challenge, which brought together self-driving cars that could navigate realistic city environments.

    1. Acero F., Ackermann M., Ajello M. et al (Fermi-LAT) 2015 arXiv:1501.02003Preprint

      Starting in 2014-2015, AAS/IOP started linking to preprints in reference lists if they were the version cited by the author and an accepted manuscript did not at that time exist.

      Thus we now have built in "categories" for references, which could be expanded to include data/software sections.

    1. Barbary K. 2014 sncosmo Zenodo, 10.5281/zenodo.11938

      This software citation losts its version information. We will have to work on our typsetting and production rules, as well as develop formal JATS/NLM XML schema to contain versioning information.

    1. K. E. Taylor, R. J. Stouffer, G. A. Meehl, An overview of CMIP5 and the experiment design. Bull. Am. Meteorol. Soc. 93, 485–498 (2012)

      Taylor, Stouffer, and Meehl provided an overview of phase five of the Climate Model Intercomparison Project (CMIP5), written while the project was underway. The project aimed to produce a new set of freely available coordinated climate model experiments and data sets. The paper describes the plan for the experiments and a discussion of issues related to interpreting the results.

    2. A. Indermühle, T. F. Stocker, F. Joos, H. Fischer, H. J. Smith, M. Wahlen, B. Deck, D. Mastroianni, J.Tschumi, T. Blunier, R. Meyer, B. Stauffer, Holocene carbon-cycle dynamics based on CO2 trapped in ice at Taylor Dome, Antarctica. Nature 398, 121–126 (1999).

      Indermühle and colleagues developed an atomospheric CO<sub>2</sub> concentration reconstruction for the entire Holocene from ice core samples from the Taylor Dome in Antarctica.

      The ice cores have trapped air bubbles, which were only exposed to atmosphere when the bubbles were at the top (youngest) layer of the ice. The CO<sub>2</sub> concentration of these bubbles were measured using infared spectroscopy. By testing many layers throughout the entire core sample, the researchers reconstructed the atmospheric CO<sub>2</sub> levels throughout the last 11,000 years, to the start of the Holocene.

    3. C. B. Yackulc, J. D. Nichols, J. Reid, R. Der, To predict the niche, model colonization and extinction. Ecology96, 16–23 (2015).

      In this report, Yackulc and colleagues argue that niche-based models, which predict future species distribution using current plant or animal distributions, assume that the observed species are in equilibrium, which may not be a valid assumption for many ecosystems that are in flux. They proposed a process-based model that uses colonization and extinction rates for a given species in a given environment, and use case studies to show the model's applicability.

    4. J. Geophys. Res. 121, 2060–2074 (2016).

      Cook and coauthors analyzed variations in droughts in the Mediterranean region over the past 900 years (1100–2012), using tree-ring data. They found a number of patterns in drought variation and distribution, and also determined a 98% likelihood that the current drought in the Levant region (Cyprus, Israel, Lebanon, Palestine, Syria, and Turkey) is the worst in the past 500 years, and an 89% likelihood that it is the worst in 900 years.

    5. D. Kaniewski, E. Van Campo, H. Weiss, Drought is a recurring challenge in the Middle East. Proc. Natl. Acad. Sci. U.S.A. 109, 3862–3867 (2012).

      In this integrative study, Kaniewski, Van Campo, and Weiss examined the trends of water availability during the Medieval Climate Anomaly (900–1300 CE) and the Little Ice Age (1550–1850 CE) in Northern Mesopotamia, and how those trends affected human systems.

      The study combined archaeological data, climate proxies, and an agricultural record based on pollen. The researchers found that changes in precipitation had an impact on yield and productivity of crops, and these changes were correlated with changes in agriculture and settlement activities.

    6. E. Xoplaki, J. F. González-Rouco, J. Luterbacher, H. Wanner, Wet season Mediterranean precipitation variability: Influence of large-scale dynamics and trends. Clim. Dyn. 23, 63–78 (2004).

      Xoplaki and co-authors examined how different variables affected the wet season patterns across the Mediterranean region for the years 1950–1999. They found that while large-scale atmospheric features had a high influence on the variability, smaller scale factors also impacted the rainfall across the region.

    7. J. Guiot, D. Kaniewski, The Mediterranean Basin and Southern Europe in a warmer world: What can we learn from the past? Front. Earth Sci. 3, 28 (2015)

      Guito and Kaniewski present the "inverted" BIOME4 method of reconstructing climate variables and biomes from pollen core data that is the basis for the current paper.

      They developed a climate data for a small set of gridpoints in the Mediterranean region for two time frames: 1901–2000 and 10,000 years ago to the present. They found that the climate dynamics of 1901–2000 differed from those of the past 10,000 years in several ways, and that the warming pattern in the past decades does not have an equivalent match in the earlier Holocene period.

    8. W. Cramer et al., in Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, C. B. Field et al., Eds. (Cambridge Univ. Press, 2014), pp. 979–1037.

      The Intergovernmental Panel on Climate Change develops reports on climate change that provide information for the United Nations Framework Convention on Climate Change. The Fifth Assessment Report was published in 2014, in advance of the Paris Agreement meeting.

      This report section focuses identifying impacts of climate change that have already happened. The report found more observations of regional climate change impacts than in the past, and reaching all continents, but also found gaps in knowledge of climate change impacts at regional levels.

  4. May 2018
    1. (Feng, C.-L. Chinese Academy of Forestry, personal communication)

      Personal communication was made between the author and other researchers to confirm that this species of orchid is rare and its populations are unknown due to orchid poaching.

    1. Zabierowski SE, Herlyn M. Melanoma stem cells: the dark seed of melanoma. Cancer Lett. 2008;26:2890–93.

      This study investigated the hierarchy of characteristic genes of melanomas with the goal of developing new therapeutic treatments.

    2. Spinella F, Rosano L, Di Castro V, Decandia S, Nicotra MR, Natali PG, Bagnato A. Endothelin-1 and endothelin-3 promote invasive behavior via hypoxia-inducible factor-1alpha in human melanoma cells. Cancer Res. 2007; 67:1725–34.

      The study investigated the interactions between hypoxia, an oxygen deficiency, and the ET axis, or the ET receptors, in primary melanoma cell lines and metastasized melanoma cell lines. Metastasized means that the tumor beyond the tissue initially affected by the tumor.

      The study found that ET-1, ET-3 and the ET(B)R react with HIF-1alpha-dependent molecules to promote melanoma invasion of tissues. The HIF-1alpha is the hypoxia-inducible factor-1alpha, a transcriptional factor that induces a signaling by growth factor receptors and hypoxia.

    3. Shackleton M, Quintana E, Fearon ER, Morrison SJ. Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell. 2009; 138:822–9.

      This study focused on targeting genes present in malignant cancer cells to develop novel therapeutic treatments for cancers.

    4. Schatton T, Murphy GF, Frank NY, Yamaura K, Waaga-Gasser AM, Gasser M, Zhan Q, Jordan S, Duncan LM, Weishaupt C, et al. Identification of cells initiating human melanomas. Nature. 2008; 451:345–9.

      This study was designed to investigate tumor promoting cells, which could have therapeutic benefits if they are targeted with a specific treatment. The targeted cells accumulate in advanced cancers.

    5. Pla P, Larue L. Involvement of endothelin receptors in normal and pathological development of neural crest cells. Int J Dev Biol. 2003; 47:315–25.

      This study examined how mutations that affect neural crest development pathways affect neural crest cells. It also examines how endothelin receptors act during cell development, movement, and differentiation.

    6. Larue L, Beermann F. Cutaneous melanoma in genetically modified animals. Pigment Cell Res. 2007; 20:485–97.

      This study examined the effects of NRAS gene mutations in mouse models and how these mutations affect cancer development. The conclusion reached was that somatic mutations in the NRAS gene are risk factors of primary melanoma in mouse models and in children.

    7. Garcia RJ, Ittah A, Mirabal S, Figueroa J, Lopez L, Glick AB, Kos L. Endothelin 3 induces skin pigmentation in a keratin-driven inducible mouse model. J Invest Dermatol. 2008; 128:131–42.

      This experiment was conducted at Florida International University as well.

      The results indicate the Endothelin 3 originating outside of the nucleus affects melanocyte precursors and differentiated melanocytes. It causes a phenotype similar to dermal melanocytosis to be developed.

      Dermal melanocytosis is a blue-grey pigmentation of the skin that usually occurs in newborn humans.

    8. Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000; 406:536–40.

      The authors examined melanoma development in a series of samples with the use of mathematical techniques. A subset of melanomas was discovered with the use of these samples and mathematical models. Many of the genes used to identify this subset are regulated differently in aggressive melanomas that have metastasized.

    9. Bellahcene A, Castronovo V, Ogbureke KU, Fisher LW, Fedarko NS. Small integrin-binding ligand N-linked glycoproteins (SIBLINGs): multifunctional proteins in cancer. Nat Rev Cancer. 2008; 8:212–26.

      The researchers investigated the role of a group of glycophosphoproteins known as SIBLINGs, or small integrin-binding ligand N-linked glycoproteins, in cancer development. The results indicated that the SIBLINGs could be used in therapy development, diagnosing cancers, or predicting prognoses.

    10. Bagnato A, Rosano L, Spinella F, Di Castro V, Tecce R, Natali PG. Endothelin B receptor blockade inhibits dynamics of cell interactions and communications in melanoma cell progression. Cancer Res. 2004;64:1436–43. [PubMed]

      Bagnato investigates the agonists of the endothelin B receptor (ET(B)R), endothelin-1 (ET-1) and ET-3 and the role that they play in tumorigenesis.

      Bagnato states that (ET(B)R) is a marker for tumor progression. This study supported the role of ET-1 and ET-3 to impede the usual interactions between hosts and tumors.

      The ligands also promote development of cutaneous melanoma. Melanoma is a cancer in melanin-producing cells. Cutaneous melanoma is melanoma that occurs on skin.

    1. J. D. Salamone, M. Correa, Behav. Brain Res. 137, 3–25 (2002).

      Salamone and Correa review evidence for the fact that motivation is the main process for reinforcement. They also discuss how low/moderate doses of a dopamine receptor-blocking drug can block some actions but leave other behavior intact.

      This study and others suggest that the behavior in drug addiction can’t be explained simply by dopamine activation of reward responses, but is instead a complex subject.

    2. G. Schoenbaum, B. Setlow, Cereb. Cortex 15, 1162–1169 (2005).

      Schoenbaum and Setlow were interested in what drives continued drug use even if when it has negative consequences.

      The authors use reinforced devaluation to test whether drug exposed rats respond persistently after devaluation of a food reward.

    3. E. Dias-Ferreira et al., Science 325, 621–625 (2009).

      Dias-Ferreira et al. used rats as a model to study how chronic stress affects decision-making processes. His group was able to show that stress affects this process by causing changes in the physiology of neurons and brain regions associated with these functions.

    4. L. H. Corbit, B. C. Chieng, B. W. Balleine, Neuropsychopharmacology 39, 1893–1901 (2014).

      Corbit et al. were interested in how control can be reestablished after drug abuse.

      The authors assessed whether chronic drug use shifts behavior from a goal-oriented process to a habit learning process, and studied the physiological implications of those changes. In addition, they tested whether N-acetylcystine, a treatment previously shown to prevent relapse into cocaine use, could prevent the rapid formation of habits after drug exposure.

    5. B. W. Balleine, J. P. O’Doherty, Neuropsychopharmacology 35, 48–69 (2010).

      Balleine and O’Doherty review what is known about the decision-making process, looking at the relationship between action and outcome (goal-directed behavior) and the stimulus-response association (habitual behavior).

      The authors discuss the similarity between humans and rats in the decision-making process, showing that for both organisms the cortex and striatum areas are involved in goal-directed and habitual actions.

      It is this similarity that suggests that cooperation or competition between habitual and goal-directed actions mediates the integration of new information (learning).

    6. A. Dickinson, Philos. Trans. R. Soc. London Ser. B 308, 67–78 (1985).

      This article discusses whether a given behavior is an acquired habit to a stimulus or is a choice made due to an association between action and outcome (i.e., goal-oriented).

      For this study, the author used a food-reward experiment in rats and assessed their actions when the reward was gradually decreased. Extended training affected the relationship between stimulus and outcome, and limited training resulted in the rats being more likely to react to reward devaluation.

    7. B. J. Everitt, T. W. Robbins, Nat. Neurosci. 8, 1481–1489 (2005).

      This review by Everitt and Robbins discusses what is known about the transition from initial drug use to a habit.

      The article takes a physiological perspective by looking at the role of different areas of the brain in this transition, such as the amygdala and hippocampus.

    1. N. G. Jablonski, G. Chaplin, The evolution of human skin coloration. J. Hum. Evol. 39, 57–106 (2000). doi:10.1006/jhev.2000.0403pmid:10896812

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

      They argue that protection against lysis 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.

      They also argue that skin pigmentation is so responsive to environmental conditions that skin pigmentation is not valuable when assess the genetic relatedness of human groups.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    2. Nutrient co-limitation of primary producer communities

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    10. Human influences on nitrogen removal in lakes

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

    1. Visick KL, Ruby EG, (2006) Vibrio fischeri and its host: It takes two to tango. Current Opinion in Microbiology 9:632–638.

      Review of the factors that support horizontal acquisition of symbionts from the environment, using the Euprymna scolopes and Vibrio fischeri model. Horizontal acquisition occurs when symbionts are transferred from one host species to another.

      This paper is from the symbiont perspective.

    2. Nyholm SV, McFall-Ngai MJ, (2004) The winnowing: Establishing the squid-vibrio symbiosis. Nature Reviews Microbiology 2:632–642.

      Review of the factors that support horizontal acquisition of symbionts from the environment, using the Euprymna scolopes and Vibrio fischeri model. Horizontal acquisition occurs when symbionts are transferred from one host species to another.

      This paper is from the host perspective.

    3. Foster RG, Soni BG, (1998) Extraretinal photoreceptors and their regulation of temporal physiology. Reviews of Reproduction 3:145–150.

      Extraocular photoreceptors were generally thought to be primarily involved in the regulation of daily and seasonal cycles. Their other functions were unknown.

      This review paper outlines the variety of extraocular photoreceptors present in nonmammalian organisms and their importance in regulating time-related physiological processes.

    1. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46, 1173–1186 (2014). doi:10.1038/ng.3097pmid:25282103

      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. Like skin pigmentation, height is a complex trait (a trait controlled by more than one gene), so it is interesting to compare the number of variants associated with height to the number of variants associated with skin pigmentation

    2. R. Yu, R. Broady, Y. Huang, Y. Wang, J. Yu, M. Gao, M. Levings, S. Wei, S. Zhang, A. Xu, M. Su, J. Dutz, X.Zhang, Y. Zhou, Transcriptome analysis reveals markers of aberrantly activated innate immunity in vitiligo lesional and non-lesional skin. PLOS ONE 7, e51040 (2012). doi:10.1371/journal.pone.0051040pmid:23251420

      Yu et al. compare gene expression (as well as immune cell presence) in lesional (lack of melanin) and nonlesional (containing melanin) skin of vitiligo patients. They identify 17 genes that have different expression in the different patches of skin, despite being on the same person and having the same genetic background.

      The authors of the current paper look at expression of one of the genes identified in Yu et al., MFSD12, because they identify SNPs near and in this gene that are associated with skin pigmentation in their study.

    3. S. Mallick, H. Li, M. Lipson, I. Mathieson, M. Gymrek, F. Racimo, M. Zhao, N. Chennagiri, S. Nordenfelt, A. Tandon, P.  Skoglund, I. Lazaridis, S. Sankararaman, Q. Fu, N. Rohland, G. Renaud, Y. Erlich, T. Willems, C. Gallo, J. P. Spence, Y. S. Song, G. Poletti, F. Balloux, G. van Driem, P. de Knijff, I. G. Romero, A. R. Jha, D. M. Behar, C. M. Bravi, C. Capelli, T. Hervig, A. Moreno-Estrada, O. L. Posukh, E. Balanovska, O. Balanovsky, S. Karachanak-Yankova, H. Sahakyan, D. Toncheva, L. Yepiskoposyan, C. Tyler-Smith, Y. Xue, M. S.Abdullah, A. Ruiz-Linares, C. M. Beall, A. Di Rienzo,  C. Jeong, E. B. Starikovskaya, E. Metspalu, J. Parik, R.Villems, B. M. Henn, U. Hodoglugil, R. Mahley, A. Sajantila, G. Stamatoyannopoulos, J. T. S. Wee, R.Khusainova, E. Khusnutdinova, S. Litvinov, G. Ayodo, D. Comas, M. F. Hammer, T. Kivisild, W. Klitz, C. A.Winkler, D. Labuda, M. Bamshad, L. B. Jorde, S. A. Tishkoff, W. S. Watkins, M. Metspalu, S. Dryomov, R. Sukernik, L. Singh, K. Thangaraj, S. Pääbo, J. Kelso, N. Patterson, D. Reich, The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016). doi:10.1038/nature18964pmid:27654912

      This report describes the data set obtained by the Simons Genome Diversity Project (SGDP), which contains genome data from 300 individuals from 142 diverse populations, and reveals more features of human genetic variation. The SGDP focused on smaller populations than the 1000 Genomes Project.

    4. 1000 Genomes Project Consortium, A global reference for human genetic variation. Nature 526, 68–74 (2015). doi:10.1038/nature15393pmid:26432245

      The 1000 Genomes Project was a massive effort toward understanding human genetic variation. This report describes the distribution of genetic variation across over 2500 individuals from 26 populations.

      For each individual, there is data available from sequencing of the whole genome, deeper sequencing of the exome (to identify rare variants in coding genes), and for some individuals SNP microarray data is available.

    5. F. Liu, M. Visser, D. L. Duffy, P. G. Hysi, L. C. Jacobs, O. Lao, K. Zhong, S. Walsh, L. Chaitanya, A.Wollstein, G. Zhu, G. W. Montgomery, A. K. Henders, M. Mangino, D. Glass, V. Bataille, R. A. Sturm, F. Rivadeneira, A. Hofman, W. F. J. van IJcken, A. G. Uitterlinden, R.-J. T. S. Palstra, T. D. Spector, N. G.Martin, T. E. C. Nijsten, M. Kayser, Genetics of skin color variation in Europeans: Genome-wide association studies with functional follow-up. Hum. Genet. 134, 823–835 (2015). doi:10.1007/s00439-015-1559-0pmid:25963972

      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 current paper as being associated with skin pigmentation in Africans.

    6. L. Teng, B. He, J. Wang, K. Tan, 4DGenome: A comprehensive database of chromatin interactions. Bioinformatics 31, 2560–2564 (2015). doi:10.1093/bioinformatics/btv158pmid:25788621

      Teng et al. describe a database they have curated called 4DGenome. They have collected published data related to how chromatin interacts with itself and make it available through a database that other researchers can use as a centralized location for chromatin interaction data.

    7. Roadmap Epigenomics Consortium, Integrative analysis of 111 reference human epigenomes. Nature 518, 317–330 (2015). doi:10.1038/nature14248pmid:25693563

      The Roadmap Epigenomics Consortium set out to generate a resource consisting of a large number of epigenomes (the modifications that occur on top of the genome and impact gene expression, such as H3K27ac, used in this paper) of human cells.

      This analysis begins to explore the connection between genetic variants and epigenomic states.

    8. F. Hormozdiari, E. Kostem, E. Y. Kang, B. Pasaniuc, E. Eskin, Identifying causal variants at loci with multiple signals of association. Genetics 198, 497–508 (2014).doi:10.1534/genetics.114.167908pmid:25104515

      This paper describes the development of a new statistical framework to estimate the probability that variants cause phenotypes. This new method, called CAVIAR (Causal Variants Identification in Associated Regions), is an improvement over previous methods because it allows for the possibility that multiple variants in a region are causal.

      The authors of this paper used CAVIAR in their study to identify variants that are associated with skin pigmentation.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

      A review of epidemiological surveys on autism.

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

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

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

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

    1. Intergovernmental Program on Climate Change, Climate Change 1995: The Science of Climate Change, the Contribution of Working Group 1 to the Second Assessment Report of the Intergovernmental Panel on Climate Change (Cambridge Univ. Press, Cambridge, UK, 1996).

      This group of scientists issue comprehensive assessments on climate science using the best available data at the time. The IPCC was awarded the 2007 Nobel Peace Prize for their work on climate change.

      To read the most recent IPCC report visit: https://www.ipcc.ch/report/ar5/

  6. Mar 2018
    1. Materials and methods are available as supporting material on Science Online.

      This note references information provided by the authors that has been excluded from the main body of the paper to streamline it and save space in the journal. These supporting materials are made available online, instead: Supporting Online Material

      The supporting materials include additional data tables, the complete list of references, and the Materials and Methods (MM) section. A MM section is a description of how the study was conducted so that 1) readers can evaluate the quality of the scientific methods, and 2) others can repeat the study to verify that the results are reproducible.

      Here the MM section includes descriptions of how the studies were selected for the meta-analysis, the statistical tests that were used, and how the temperature changes and expected range shifts were calculated.

    2. C. Rosenzweig et al., in Climate Change 2007: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, M. L. Parry, O. F. Canziani, J. P. Palut., P. J. van der Linden, C. E. Hanson, Eds. (Cambridge University Press, Cambridge, 2007), pp. 79–131.

      This reference is Chapter 1 of the Assessment Report Climate Change 2007 of the Intergovernmental Panel on Climate Change of the United Nations. Thousands of experts were involved in developing the report, which compiled and evaluated published research related to climate change and was reviewed by the governments of the member countries.

      The chapter documents how climate change, especially increasing temperatures, is affecting many systems on Earth, including the physical characteristics and living organisms of land, freshwater, and oceans.

    3. R. Hickling, D. B. Roy, J. K. Hill, R. Fox, C. D. Thomas, The distributions of a wide range of taxonomic groups are expanding polewards. Glob. Change Biol. 12, 450 (2006). doi:10.1111/j.1365-2486.2006.01116.x

      The authors examined the ranges of a wide variety of taxonomic groups in the United Kingdom between 1960 and 2000, a period during which the regional climate warmed. They studied many groups, including many invertebrate species, fish, mammals, birds, and herptiles.

      Most of the taxonomic groups expanded their ranges to higher latitudes and/or elevations during the period. These range shifts were comparable to those identified in other studies for more well-documented species.

      This study was an important source of data for the current meta-analysis.

    4. A. Fischlin et al., in Climate Change 2007: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, M. L. Parry, O. F. Canziani, J. P. Palutikof, P. J. van der Linden, C. E. Hanson, Eds. (Cambridge Univ. Press, Cambridge, 2007), pp. 211–272.

      This reference is Chapter 4 of the Assessment Report Climate Change 2007 of the Intergovernmental Panel on Climate Change of the United Nations. Thousands of experts were involved in developing the report, which compiled and evaluated published research related to climate change and was reviewed by the governments of the member countries.

      The chapter summarized what was known at the time about the impact of climate change on the Earth's ecosystems. Among other effects, the authors estimated that 20 to 30% of animals and plants that were assessed face an increasing risk of extinction as global temperatures rise.

    5. D. R. Easterling et al., Climate extremes: Observations, modeling, and impacts. Science 289, 2068 (2000).doi:10.1126/science.289.5487.2068 pmid:11000103

      This is a review article, which explains the current understanding of a topic based on a review and summary of the published literature. The authors summarized what was known at the time (2000) about the occurrence of extreme weather and climate events and their effects on human societies and natural systems.

    6. J. A. Pounds et al., Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 439, 161 (2006). doi:10.1038/nature04246 pmid:16407945

      This study combined analyses at both large and small scales to examine the role of climate warming in the extinction of amphibians in tropical regions of the Americas. The extinctions were previously attributed to an epidemic of a fungal disease.

      The authors show that climate warming was a key factor in the extinctions. They propose that a warmer climate encourages growth of the fungus and thereby increases disease outbreaks.

    7. C. D. Thomas, A. M. A. Franco, J. K. Hill, Range retractions and extinction in the face of climate warming. Trends Ecol. Evol. 21, 415 (2006). doi:10.1016/j.tree.2006.05.012 pmid:16757062

      This article examines evidence that effects of climate change may be underestimated. The authors show that population declines and range retractions may not be detected if a study does not evaluate the populations at a sufficiently small scale. More detailed studies can also help determine how much climate and other factors have contributed to the effects.

    8. A. J. Suggitt et al., Habitat microclimates drive fine-scale variation in extreme temperatures. Oikos 120, 1(2011). doi:10.1111/j.1600-0706.2010.18270.x

      Most studies of the effects of climate on living organisms examine areas of a kilometer-scale size. However, organisms actually experience climate extremes on a much smaller scale.

      This study demonstrates the extent of microclimate effects on temperature extremes. Variations in topography and vegetation type generated large local temperature differences in an area.

      The authors state that these microclimate effects must be quantified and included in analyses to understand and predict the impacts of climate change on biodiversity.

    9. S. R. Loarie et al., The velocity of climate change. Nature 462, 1052 (2009). doi:10.1038/nature08649pmid:20033047

      The authors predicted the velocity of temperature change, a measurement of how annual average temperatures move over time, throughout the world. They found that predicted velocity varies widely depending on the type of topography; values ranged from 0.08 km per year to 1.26 km per year.

      Plants and animals may need to shift their ranges along with the average temperature to keep living in a suitable climate. The authors determined that, in some cases, species will not be able to move their ranges fast enough to keep up with climate change.

    10. C. Parmesan, G. Yohe, A globally coherent fingerprint of climate change impacts across natural systems. Nature 421, 37 (2003). doi:10.1038/nature01286 pmid:12511946

      This article addresses the difficulties the Intergovernmental Panel on Climate Change had reaching an agreement (in 2001) on the extent to which climate change is causing changes in biological systems. The authors suggest that differences in approach, particularly between biologists and economists, were a source of disagreement.

      To bridge the gap between the disciplines, they used several analyses, combinations of biological and economic approaches, to analyze a large set of global biological data. They concluded that there is sufficient evidence to say with very high confidence that climate change is already affecting living systems.

    11. A. Menzel et al., European phenological response to climate change matches the warming pattern. Glob. Change Biol. 12, 1969 (2006). doi:10.1111/j.1365-2486.2006.01193.x

      The authors examined how changes in climate have influenced the timing of periodic life cycle events, such as leaves unfolding and fruit ripening. They analyzed a large set of data for European plants and a few animals, over the years 1971 to 2000.

      They found that spring and summer life cycle events were happening earlier in the year and that these changes matched the patterns of climate warming.

    1. azareno and Dos Reis, 2014 A.G. Nazareno, M.S. Dos ReisAt risk of population decline? an ecological and genetic approach to the threatened palm species Butia eriospatha (Arecaceae) of Southern Brazil J. Hered., 105 (2014), pp. 120-129

      Nazareno and Dos Reis review the ecological and genetics basis of the conservation of a threatened population.

      Although population ecology parameters as well as genetic data are very important in the analysis of a population threatened with extinction, there are other factors such as policy actions and reinforcement that also play a role in this loss of biodiversity and should also be analyzed.

    2. Maunder et al., 2008 M. Maunder, A. Leiva, E. Santiago-Valentín, D.W. Stevenson, P. Acevedo-Rodríguez, A.W.Meerow, M. Mejía, C. Clubbe, J. Francisco-OrtegaPlant conservation in the Caribbean Island biodiversity hotspot Bot. Rev., 74 (2008), pp. 197-207

      Authors review how human efforts made towards plant conservation can have an effect on the biodiversity of an area.

      Although both environmental and genetic factors are needed for the survival of a species, the authors note other factors such as understanding the taxonomy, systematics and ecology of the flora, can be just as important in the survival of plant species.

    3. Höglund, 2009 J. HöglundEvolutionary Conservation Genetics Oxford University Press, Oxford (2009)

      The authors review the role of inheritance in the survival of a population.

      Although gene variability is important in a population, the authors note that the inheritance of the genes responsible for this variability may also play a major role in ensuring either extinction or survival of a population.

    4. Giovino et al., 2014 A. Giovino, S. Scibetta, S. Saia, C. GuarinoGenetic and morphologic diversity of European fan palm (Chamaerops humilis L.) populations from different environments from Sicily Bot. J. Linn. Soc., 176 (2014), pp. 66-81

      The authors review the contribution of genetic diversity in the survival of species of palms.

      The authors note that there is a clear relationship between genetic variability in a population and its chances of survival in degrading or changing environments.

    5. Foxx, 2012 R.M. FoxxTe Terre a fatige ‘the Earth is tired’: reversing deforestation in Haiti Behavio. Interv., 27 (2012), pp. 105-108

      Foxx addresses the prevalent issue in Haiti regarding a major lack of plant biodiversity due to both human and natural forces.

      Although very little can be done to combat natural disasters responsible for the decline in biodiversity in Haiti, the author notes that reforestation can at the very least lessen the effects that the aforementioned has on both the country and the planet.

    6. Duminil et al., 2009 J. Duminil, O.J. Hardy, R.J. PetitPlant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure BMC Evol. Biol., 9 (2009), p. 177

      Duminil and his team, reviewed how a plant’s generation time can affect their genetic structure.

      The authors note that the mating system of plants has a great influence in genetic differentiation between different species and that generation time can affect this mating system in some species, therefore, modifying genetic drift and flow in a population.

    7. erazaín Iturralde et al., 2005 R. Berazaín Iturralde, F. Areces Berazaín, J.C. Lazcano Lara, L.R. González TorresLista roja de la flora vascular cubana Doc. Jard. Bot. Atlántico, 4 (2005), pp. 1-86

      The authors review the implications leading to and from red-listing flora in Cuba.

      The focus surrounds the reinforcement of conservation of species that were part of the red-list, this paper notes that the global loss of biodiversity is a current issue which can affect areas like Cuba where environmentally there is potential for greater biodiversity.

    8. Alscher, 2011 S. AlscherEnvironmental degradation and migration on Hispaniola island Int. Migr., 49 (s1) (2011), pp. e164-e188

      The authors explore the the concept of environmental degradation as an incentive leading to migration as a survival strategy of C. jimenezii.

      Given the observed endangerment of C. jimenezii, the authors sought out answers outside of the C. jimenezii genetic makeup which could have led to the migration of the plants and how this affected their survival.

    9. llendorf and Luikart, 2007 F.W. Allendorf, G. LuikartConservation and the Genetics of Populations Blackwell, Malden (2007)

      Allendorf and Luikart review the genetic challenges responsible for the conservation of a population threatened with extinction.

      Although the authors concentrate on the genetic factors concerning plant conservation, they note that a true understanding of both plant and animal genetics is necessary to gather the tools needed to preserve a given species.

    10. Abbott et al., 1985 L.A. Abbott, F.A. Bisby, D.J. RogersTaxonomic Analysis in Biology Columbia University Press, New York (1985)

      Abbott along his team of researchers, reviews the role taxonomy plays in understanding the origin of the species and such species’ proper conservation.

      The authors recognize that differences in taxa, due to genetic variability, may affect the species’ overall survival and ultimate conservation methods which may currently be contributing to their endangerment.

    1. True JR, Carroll SB, (2002) Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53–80.

      The authors review how new functions can evolve when existing genes gain new functions.

    2. Visick KL, McFall-Ngai MJ, (2000) An exclusive contract: Specificity in the Vibrio fischeri-Euprymna scolopes partnership. J Bacteriol 182:1779–1787

      Visick and Mc-Fall-Ngai review the contributions of Vibrio fischeri to the development of the light organ as Euprymna scolopes matures.

    3. Nealson KH, Hastings JW, (1979) Bacterial bioluminescence: Its control and ecological significance. Microbiol Rev 43:496–518.

      Review of bioluminescence in bacteria. Examines the possible role bioluminescence plays for the bacteria as well as some of the organisms that have symbiotic relationships with these bacteria.

    4. Visick KL, Foster JF, Doino J, McFall-Ngai M, Ruby EG, (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J Bacteriol 182:4578–4586.

      Study showing that E. scolopes is only able to undergo normal development if V. fischeri possesses the ability to produce luminescence.

    5. Crookes WJ, et al., (2004) Reflectins: The unusual proteins of squid reflective tissues. Science 303:235–238.

      Study that looked at the reflective tissues of the light organ and established their similarity to the reflective tissues found in the eye.

    6. Young RE, Roper CFE, Walters JF, (1979) Eyes and extraocular photoreceptors in midwater cephalopods and fishes: Their roles in detecting downwelling light for counterillumination. Mar Biol (Berlin) 51:371–380.

      Early study providing evidence that, in addition to signals coming from the eyes, extraocular photoreceptors also provide signals that contribute to the ability of some species of squid to be able to adjust the amount of light they produce to match the downwelling light in the environment.

    7. Young RE, Roper CF, (1976) Bioluminescent countershading in midwater animals: Evidence from living squid. Science 191:1046–1048.

      Early study detailing physical evidence that some species of squid are able to adjust the amount of light they produce to match the ambient light in the environment, a process called counterillumination.

    8. Terakita A, (2005) The opsins. Genome Biology 6:213.

      Review paper outlining the seven subfamilies of opsins, their functions, and possible phylogenetic relationships.

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

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

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

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

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

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

    1. I. Fried, C. L. Wilson, K. A. MacDonald, E. J. Behnke, Nature 391, 650 (1998).

      Doctors performing brain surgery were able to cause the patient to laugh by electrically stimulating the anterior supplementary motor area. This area of the brain is also involved in human speech.

    2. S. J. Blakemore, D. M. Wolpert, C. D. Frith, Nat. Neurosci. 1, 635–640 (1998).

      This paper describes the use of fMRI brain scans of humans experiencing externally produced tickling or self-produced tickling.

      The authors conclude that the somatosensory cortex is active in response to tickling and that the cerebellum plays a role in muting this response during self-produced tickling.

    3. C. R. Harris, N. Christenfeld, Cogn. Emotion 11, 103–110 (1997).

      Harris and Christenfeld showed that comedy-induced laughter does not increase subsequent tickle-induced laughter and vice versa.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  7. Feb 2018
    1. S. Vrontou, A. M. Wong, K. K. Rau, H. R. Koerber, D. J. Anderson, Nature 493, 669–673 (2013)

      The authors identify subgroups of sensory neurons in hairy skin that detect either pleasant sensations (stroking or massage) or unpleasant sensations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    1. H. S. Carson et al., Mar. Environ. Res. 84, 76–83 (2013).

      This study looked at the sources and fate of local marine debris near the Hawaiian islands. Debris from a large community was captured using surface traps, and wooden drifters were released to examine the effect of nearshore currents and tides on debris distribution. This study demonstrated that local pollutants can be retained nearby, contribute to the island's debris-accumulation area, and quickly spread to other islands.

    2. M. Braungart, Nature 494, 174–175 (2013).

      This article discusses the idea of designing buildings and objects to be made using the minimum of materials and a maximum of efficiency. 3D printing and biodegradable materials are explored as examples of ways to improve product design and reduce waste.

    3. “2013 resin review” (American Chemistry Council, Washington, DC, 2013).

      This document released by the American Chemistry Council is a reference book on plastic resins. It contains information about North American resin production, sales, industry capacities, and utilization rates from 2002-2012. Sales data are presented for various end-use markets, and tables show historical trends from 1973 to 2012. The publication explains the basic chemistry of plastics and manufacturing processes. It also details the history of plastics development and modern-day applications and provides a glossary of basic plastics terms. Jambeck et al. used this reference to estimate the amounts of plastic production in North America and plastic in the U.S. waste stream.

    1. 12.Noriega FG (2004) Nutritional regulation of JH synthesis: a mechanism to control reproductive maturation in mosquitoes? Insect Biochem Molec Biol 34: 687–693.

      The juvenile hormone is the most important hormone to all insects, especially in adult female Aedes aegypti. This mosquito uses nutrients to boost JH levels which increases reproduction.

    1. Wardle, C. S.​​​​​​​ (1975). Limit of fish swimming speed. Nature 255, 725-727.doi:10.1038/255725a0

      This paper considers the various characteristics that limit the swimming speed of fish. For one, it analyzes how smaller fish are capable of higher tail beat frequencies than larger fish. Also, that the stride length of a fish is not longer than the fish's size. Furthermore, swimming speed is limited by the contraction time of swimming muscle so maximum swimming speeds are determined by muscle contraction time and stride length.

    2. Iosilevskii, G. and Weihs, D. (2008). Speed limits on swimming of fishes and cetaceans. J. R. Soc. Interface 20, 329-338. doi:10.1098/rsif.2007.1073

      The paper analyzes the limitations that stop fish from swimming faster. Small fish are held back by the power available, and larger fish are limited by cavitation.

    3. Brill, R. W. (1996). Selective advantages conferred by the high performance physiology of tunas, billfishes, and dolphin Fish. Comp. Biochem. Physiol. A Comp. Physiol. 13A, 3-15.doi:10.1016/0300-9629(95)02064-0

      In this review the author talks about the characteristics that give tuna fish high performance. These characteristics include 3 things: high rates of somatic and gonadal growth, rates of digestion, and rates of recovery from exhaustive exercise. This study uses these findings to defy the myth that sailfish and other pelagic fish just have high maximum swimming speeds that allows them to avoid cavitation.

    1. DeGennaro M, McBride CS, Seeholzer L, Nakagawa T, Dennis EJ, Goldman C, Jasinskiene N, James AA, Vosshall LB.. orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET. Nature 2013; 498:487-91;

      Dr. DeGennaro established techniques to edit the genome of mosquitoes. He created the first mosquito mutant using zinc-finger nucleases to initiate the molecular genetic analysis of olfactory receptor function in Aedes aegypti mosquitoes. His work revealed new knowledge about the integration of host cues, mosquito host-preferences, mosquito nectar-seeking, and the mechanism of DEET repellency.

      Dr. DeGennaro demonstrated that the mosquitoes use the OR/ORCO olfactory receptor pathway to respond to human odors and DEET as well as nectar volatile. His work implicated the Ionotropic Receptor family of olfactory receptors in host-seeking mosquitoes. Additionally, he showed that DEET repels mosquitoes through ORCO-dependent olfaction and an unidentified taste receptor.

    1. C.-F. Schleussner, T. K. Lissner, E. M. Fischer, J. Wohland, M. Perrette, A. Golly, >J. Rogelj, K. Childers, J.Schewe, K. Frieler, M. Mengel, W. Hare, M. Schaeffer, Differential climate impacts for policy-relevant limits to global warming: The case of 1.5°C and 2°C. Earth Syst. Dyn. Discuss. 6, 2447–2505 (2015)

      Schleussner and co-authors assessed the impacts of reaching the 1.5°C and 2.0°C thresholds for a number of variables, at a regional level. They found large differences in the impacts of the two scenarios, covering a range of issues from the fraction of global coral reefs at risk of annual bleaching to heat wave duration.

    1. Caragata, E. P., Rancès, E., Hedges, L. M., Gofton, A. W., Johnson, K. N., O'Neill, S. L. and McGraw, E. A. (2013).Dietary cholesterol modulates pathogen blocking by Wolbachia. PLoS Pathog. 9, e1003459.

      Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.

    2. Bordenstein, S. R. and Bordenstein, S. R. (2011). Temperature affects the tripartite interactions between bacteriophage WO, Wolbachia, and cytoplasmic incompatibility. PLoS ONE 6, e29106. Boyle, L., O'Neill, S. L., Robertson, H. M. and Karr, T. L. (1993). Interspecific and intraspecific horizontal transfer of Wolbachia in Drosophila. Science 260, 1796-1799.

      Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.

      Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.

    3. Christensen, S., Pérez Dulzaides, R., Hedrick, V. E., Momtaz, A. J. M. Z., Nakayasu, E. S., Paul, L. N. and Serbus, L. R. (2016). Wolbachia endosymbionts modify Drosophila ovary protein levels in a context-dependent manner. Appl. Environ. Microbiol. 82, 5354-5363.

      Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophila ovaries are modified by Wolbachia.

    4. Dale, C. and Moran, N. A. (2006). Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453-465.

      While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.

    5. Mouton, L., Henri, H., Charif, D., Bouletreau, M. and Vavre, F. (2007). Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis. Biol. Lett. 3, 210-213. Musselman, L. P., Fink, J. L., Narzinski, K., Ramachandran, P. V., Hathiramani, S. S., Cagan, R. L. and Baranski, T. J. (2011). A high-sugar diet produces obesity and insulin resistance in wild-type Drosophila. Dis. Model. Mech. 4, 842-849.

      Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.

    6. Teixeira, L., Ferreira, A. and Ashburner, M. (2008). The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol. 6, e2.

      The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.

    7. Wang, M. and Wang, C. (1993). Characterization of glucose transport system in Drosophila Kc cells. FEBS Lett. 317,241-244.

      Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.

    8. Serbus, L. R., White, P. M., Silva, J. P., Rabe, A., Teixeira, L., Albertson, R. and Sullivan, W. (2015). The impact of host diet on Wolbachia titer in Drosophila. PLoS Pathog. 11, e1004777.

      Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.

    9. Ponton, F., Wilson, K., Holmes, A., Raubenheimer, D., Robinson, K. L. and Simpson, S. J. (2015). Macronutrients mediate the functional relationship between Drosophila and Wolbachia. Proc. Biol. Sci. 282, 20142029.

      Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.

    10. Min, K.-T. and Benzer, S. (1997). Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death. Proc. Natl. Acad. Sci. USA 94, 10792-10796.

      Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.

    1. Steel, M., and D. Penny. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839–850.

      Throughout their research, Steel and Penny explicate the connection between maximum parsimony (MP) and maximum likelihood (ML). According to the paper, they state that there can be a link between both methods when there is no common mechanism between sites. Moreover, throughout this process, Steel and Penny clarify disputed points between the two methods. It was concluded that neither models outperform the other when it comes to recovering the tree.

      This paper utilizes this source to support which method would more accurately perform the recovery of the tree. Furthermore, the authors wanted to assure those interested in their work that a variety of techniques including several models of ML and MP if special claims are made can be used.

    2. Saccone, C., G. Pesole, and G. Preparata. 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29:407–411.

      During their study, Saccone, Pesole, and Preparata concluded that only homologous gene pairs, which whom are also stationary, are truly reliable to consistently provide with trustworthy determinations of phylogeny. Nonstationary genes, in comparison, resulted in outstandingly high rate values eventually resulting in possible systematic failure.

      This paper uses such sources as reinforcement of their results as stationary genes were proved to be better supporters in the construction of phylogenetic trees, or in phylogeny overall, providing superior results with an increased level of confidence.

    3. Gee, H. 2003. Ending incongruence. Nature 425:782. Phillips, M. J., F. Delsuc, and D. Penny. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455–1458.

      In this paper, Gee concluded that there were no guidelines or factors that could measure the performance of a certain gene.The reason why the author of this paper uses it is to highlight the importance of stationary genes and how helpful they are for generating phylogenetic genes.

    4. Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798–804.

      In his study, Rokas came to the conclusion that there are no genes that provide more phylogenetic information than others. This led him to believe that in order to create an accurate phylogenetic tree, one would have to study the whole genome of an organism. He believed that an infinite amount of genes will result in an infinite amount of accuracy, which is why he claimed that most phylogenetic trees at the moment were probably inaccurate.

      In this paper, the conclusions Rokas came to were disproven by the experiments carried out. Stationary genes were discovered to be better contributors to a phylogenetic tree and are needed only in a relatively small amount to create an accurate tree.

  8. Jan 2018
    1. 1. Schreck CE. Techniques for the evaluation of insect repellents: a critical review. Annu Rev Entomol1977; 22:101-19; PMID:319738; http://dx.doi.org/10.1146/annurev.en.22.010177.000533 [PubMed][Cross Ref]

      References 1-4 work together in unison to help support the authors statement when saying that DEET is an effective and widely used insect repellent. Sources one, two and four aim to show how DEET sizes up against other repellants, while source number three take a more in depth look into why DEET functions the way it does.

    2. 62. Stanczyk NM, Brookfield JFY, Ignell R, Logan JG, Field LM.. Behavioral insensitivity to DEET in Aedes aegypti is a genetically determined trait residing in changes in sensillum function. Proc Natl Acad Sci USA 2010; 107:8575-80; PMID:20439757; http://dx.doi.org/10.1073/pnas.1001313107 [PMC free article] [PubMed] [Cross Ref]

      Mosquitoes have an inheritable "immunity" to DEET that seems to express itself as a dominant gene that affects the way they respond to olfactory stimuli, in this case people.

    3. 59. Sanford JL, Shields VDC, Dickens JC.. Gustatory receptor neuron responds to DEET and other insect repellents in the yellow fever mosquito, Aedes aegypti. 2013; 100:269-73; PMID:23407786 [PubMed]

      Just as a expressed in source fifty-eight, mosquitoes seem to express distaste towards DEET. Gustatory receptors in Aedis aegypti sense a bitter taste from the repellent, and that gives the mosquito negative feedback, discouraging feeding.

    4. 58. Bar-Zeev M, Smith CN. Action of repellents on mosquitoes feeding through treated membranes or on treated blood. J Econ Entomol 1959; 52:263-7; http://dx.doi.org/10.1093/jee/52.2.263 [Cross Ref]

      DEET can be considered a "multi-modal" repellent as contributed by the many studies that show its ability to deflect mosquitoes on an olfactory level and, as a demonstrated in this study, a gustatory one. It was found that mosquitoes would not feed on blood treated with DEET, even if they penetrated a feeding membrane with their proboscis.

    5. Syed Z, Leal WS.. Mosquitoes smell and avoid the insect repellent DEET. Proc Natl Acad Sci USA2008; 105:13598-603; PMID:18711137; http://dx.doi.org/10.1073/pnas.0805312105 [PMC free article][PubMed] [Cross Ref]

      In their paper, Syed & Leal, 2008, test the effects DEET has on the olfactory receptor neuron (ORN) in mosquitoes. They aim to debunk the former hypothesis that DEET masks the lactic acid odor, attractive to mosquitoes, and naturally produced by humans. Syed & Leal rather suggest, through evidence, that mosquitoes smell DEET and avoid it through their response sense activated by the olfactory receptor neurons (ORNs)

    6. Grant AJ, Dickens JC.. Functional characterization of the octenol receptor neuron on the maxillary palps of the yellow fever mosquito, Aedes aegypti. PLoS ONE 2011; 6:e21785; PMID:21738794; http://dx.doi.org/10.1371/journal.pone.0021785 [PMC free article] [PubMed] [Cross Ref]

      Grant & Dickens, 2011 attempt to investigate the effects of multiple repellents on the vertebrate-secreted, mosquito-attractant odor known as octenol. The study compared repellants 2-undecanone, DEET, and IR3535, and picardin. Overall, they mentioned how repellents affect the mosquito's octenol receptor on its neuron which senses these odors. Specifically, their neurons are attracted to the R enantiomer of octenol rather than the S.

    7. Davis EE. A receptor sensitive to oviposition site attractants on the antennae of the mosquito, Aedes aegypti. J Comp Physiol 1976; 105:43-54;

      Davis & Sokolove, 1976 investigate the role of DEET on Lactic Acid neurons. They propose that Lactic acid (LA) chemoreceptors located on the mosquito antennae were affected by DEET. DEET inhibited the LA-sensitive neurons, hence concluding that the DEET repellant inhibits the mosquitoes ability to detect and track its host.

    8. 7. McCabe Insect repellents. III. N,N- Diethylamides. J Org Chem 1954; 19:493-8; http://dx.doi.org/10.1021/jo01369a003 [Cross Ref] 8. Gilbert IH, Gouck HK. Evaluation of repellents against mosquitoes in Panama. The Florida Entomologist 1955; 38:153-63; http://dx.doi.org/10.2307/3492706 [Cross Ref]

      Source seven discusses how chemists tested many different compounds as possible key ingredients in repellents, with diethylamides being the focus of their attention. Source eight expands upon this somewhat to show how the repellency of a diethylamide was capable of warding off many species of mosquitoes in Panama during testing.

    9. 5. Knippling EF, Mcalister LC, Jones HA. Results of screening tests with materials evaluated as insecticides, miticides, and repellents at the Orlando, Fla., laboratory. April 1942 to April 1947. USDA Publication E-733; 1947. 6. Travis BV, Morton FA, Jones HA, Robinson JH.. The more effective mosquito repellents tested at the Orlando, Fla., Laboratory, 1942-47. J Econ Entomol 1949; 42:686-94; PMID:18138206; http://dx.doi.org/10.1093/jee/42.4.686 [PubMed] [Cross Ref]

      Testing of different compounds was necessary to determine an effective repellent against the prime target, Aedis aegypti.

    10. Fradin MS, Day JF.. Comparative efficacy of insect repellents against mosquito bites. N Engl J Med2002; 347:13-8; PMID:12097535; http://dx.doi.org/10.1056/NEJMoa011699 [PubMed] [Cross Ref]

      Fradin & Day, 2002 suggest that in comparison with repellant IR3535, three types of repellant impregnated wristbands, and a topical moisturizer repellant, DEET repellant was the most effective while conducting their study which was controlled for mosquito age, species, hunger level, and other environmental factors. DEET has been shown the most effective with respect to duration of repellency which was also positively correlated with the amount of DEET applied.

    11. Cooper E, Iqbal A, Bartlett A, Marriott C, Whitfield PJ, Brown MB.. A comparison of topical formulations for the prevention of human schistosomiasis. J Pharm Pharmacol 2004; 56:957-62; PMID:15285838; http://dx.doi.org/10.1211/0022357043996

      Cooper et al., 2004 suggest that DEET is effective in repellency against cercariae more effectively than regular topical formulations. When DEET was incorporated in silicone-based formulations or Cetomacrogol-based (CMO) formulations it was more effective. DEET is so effective because of its toxicity against the cercariae. The dimeticone formulation however- without incorporation of DEET- also helped to protect as the topical formula was better absorbed in the stratum corneum (skin) and blocked cercariae recognition of the skin.

    1. P. F. A. Maderson, When? Why? and How?: Some speculations on evolution of vertebrate integument. Am. Zool. 12, 159–171 (1972).

      A 1970's review discussing the formation of integuments (hard, protective layers covering the body), scales, and hair.

      The paper explores the different hypotheses of the time, including scaled animals as precursors to nonscaled animals, ossified (bony) scales as a precursor to the scales found on today's reptiles, and the evolution of hair from sensory appendages.

    2. A. M. Turing, The chemical basis of morphogenesis. Philos. Trans. R. Soc. London Ser. B 237, 37–72 (1952).

      In this landmark paper, Turing proposes the reaction diffusion theory to explain morphogenesis.

      This theory states that when two chemicals react with each other they diffuse to form chemical gradients. These gradients form patterns that direct morphogenesis.

    3. R. B. Widelitz, T.-X. Jiang, J. Lu, C.-M. Chuong, b-catenin in epithelial morphogenesis: Conversion of part of avian foot scales into feather buds with a mutated b-catenin. Dev. Biol. 219, 98–114 (2000).

      Explores the role of β-catenin, which is expressed in the placode.

      When this protein was mutated in chickens, their feet were scaleless and they had abnormal feather growth.

    4. C. Blanpain, E. Fuchs, Epidermal stem cells of the skin. Annu. Rev. Cell Dev. Biol. 22, 339–373 (2006).

      Reviews the development of skin cells that give rise to hairs.

      A hair placode forms, allowing the expression of genes that direct skin cell and hair follicle development.

    5. J. M. Musser, G. P. Wagner, R. O. Prum, Nuclear b-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol. Dev. 17, 185–194 (2015).

      Explores the relationship between feathers and scales.

      Visualization of the location and amount of β-catenin during the development of feathers and scales revealed similar patterns between the two. The authors concluded that feathers and scales share an evolutionary ancestor.

    6. D. Dhouailly, A new scenario for the evolutionary origin of hair, feather, and avian scales. J. Anat. 214, 587–606 (2009).

      Proposed the theory that mammalian hair evolved from glandular structures, whereas reptile and bird skin evolved from a thick protective coating.

    7. P. F. A.Maderson,Mammalian skin evolution: A reevaluation. Exp. Dermatol. 12, 233–236 (2003).

      A revision to a 1972 model of how mammalian hair evolved.

      This new model proposes that the development of hair was caused by mutations in patterning genes, which resulted in hair becoming more useful insulation.

    1. R. C. Thompson, C. J. Moore, F. S. vom Saal, S. H. Swan, Philos. Trans. R. Soc. London Ser. B 364, 2153–2166 (2009).

      This review article summarizes the uses humans have for plastics, the effects of plastics on the living and nonliving parts of the environment, and future concerns about the manufacture and disposal of plastic products.

    2. “Probabilistic projections of total population: Median and confidence intervals,” (United Nations, Department of Economic and Social Affairs, New York, 2012); http://esa.un.org/unpd/ppp/Data-Output/ UN_PPP2010_output-data.htm.

      This population growth data from the United Nations was used to predict future amounts of plastic waste entering the ocean from individual countries.