929 Matching Annotations
  1. Oct 2018
    1. A. Gargas, P. T. DePriest, M. Grube, A. Tehler, Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268, 1492–1495 (1995).

      This is a foundational paper that describes how lichen symbiosis arose multiple times through evolutionary history.

    1. N. E. Klepeis et al., J. Expo. Anal. Environ. Epidemiol. 11, 231–252 (2001).

      Telephone survey that monitored where people in the United States spent the majority of their time. Found that 87% of time was spent in buildings and 6% of time was spent inside of automobiles.

      Since 93% of human activities are indoors, indoor air quality is extremely important.

    2. G. J. Dollard, P. Dumitrean, S. Telling, J. Dixon, R. G. Derwent, Atmos. Environ. 41, 2559–2569 (2007).

      Study analyzed VOC emissions in the United Kingdom from 1993 to 2004. Found that VOC emissions from automobiles were decreasing at a rate of 20% per year due to more stringent automobile emissions regulations.

    3. B. C. McDonald, D. R. Gentner, A. H. Goldstein, R. A. Harley, Environ. Sci. Technol. 47, 10022–10031 (2013).

      Study looked at emissions from automobile traffic in the United States between 1990 and 2010. Found that fuel consumption increased by 10% - 40% during the time period, but emissions such as carbon monoxide and VOCs decreased by 80% - 90% due to increased fuel efficiency and regulations.

    4. Q. Di et al., N. Engl. J. Med. 376, 2513–2522 (2017).

      The United States' air quality standards sets advisable levels for different pollutants. Human health was shown to be negatively impacted even when fine particulate matter and ozone were present at levels below the current air quality standards.

    1. 8. D. Ribitsch et al., Biocatalysis Biotransform. 30, 2–9 (2012).

      Rititsch et al. report cutinases from the bacteria Thermobifida alba. While the reported cutinases don't degrade PET particularly quickly, they do produce a novel degradation product.

      The authors were able to obtain a crystal structure, a type of picture on a molecular scale, of the enzyme degrading PET. This allowed them to identify parts of the enzyme that may be responsible for PET degradation.

    2. 1. V. Sinha, M. R. Patel, J. V. Patel, J. Polym. Environ. 18, 8–25 (2010).

      In this paper, Sinha et al. discuss the current best methods of disposing of and recycling plastic. The authors focus in particular on tertiary recycling techniques. These techniques use chemicals to break down the chemical bonds inside polymers.

    1. K. J. Willis, S. A. Bhagwat, Biodiversity and climate change. Science 326, 806–807 (2009).

      This article is a review about species distribution modeling, or, the ability to predict how species ranges could change under global warming. Authors highlight the fact that models published in the past have overlooked microclimates (small places that provide species with climate different than in the overall area). For example, in a place where heat waves are felt, some species could be able to use the surrounding vegetation to remain cool, and essentially be unaffected by the heat wave. Willis et al. (2009) show how important it is to consider such areas when estimating species’ future ranges under climate change since they could halt or at least slow many species’ extinctions.

    2. J. M. Sunday, A. E. Bates, M. R. Kearney, R. K. Colwell, N. K. Dulvy, J. T. Longino, R. B. Huey, Thermal-safety margins and the necessity of thermoregulatory behavior across latitude and elevation. Proc. Natl. Acad. Sci. U.S.A. 111, 5610–5615 (2014).

      Thermal limits of ectotherms (cold-blooded species) are often much higher than the temperature of the surrounding air. When limits are exceeded however, it was previously thought that organisms internally regulated their body in order to survive. However, this study shows that most ectotherms must use their behavior by retreating to suitable habitat when the air temperature becomes unsuitable (too cold or too hot). These behaviors are costly, obligating ectotherms, like bees, to direct their energy into preserving their heat/cool, instead of directing it into reproduction, feeding, and other essential activities. Extreme temperatures are predicted to happen more often as climate change progresses, and is likely to be problematic to bees.

    3. P. Rasmont, S. Iserbyt, The bumblebee scarcity syndrome: Are heat waves leading to local extinctions of bumblebees (Hymenoptera: Apidae: Bombus)? Ann. Soc. Entomol. Fr. 48, 275–280 (2012).

      Authors discuss the effect of heat waves on bumblebee decline. Heat waves and drought occurrences in France, the United Kingdom, Scandinavia, and Turkey led to bumblebee declines. It highlights that bumblebees are sensitive to extreme temperature events.

      Different aspects of heat waves could be affecting bees, as discussed in this paper. It could be that temperatures are rising above a tolerable threshold killing the bees, the length of the heat wave, the drought that is often associated with heat waves, starvation if bees are overheating and cannot feed themselves properly, or that heat waves are occurring during winter which could interrupt the queens’ hibernation while flowers providing their food are not yet available. Climate change is estimated to increase the probabilities for the occurrence of extreme temperature events in the future, a factor that may further threaten bee decline.

    4. S. J. Leroux, M. Larrivée, V. Boucher-Lalonde, A. Hurford, J. Zuloaga, J. T. Kerr, F. Lutscher, Mechanistic models for the spatial spread of species under climate change. Ecol. Appl. 23, 815–828(2013).

      Authors described an approach to model species’ distributions under climate change which takes into consideration ecological characteristics of species like reproduction, dispersal, and adaptation. We call these “mechanistic” models because they include mechanisms into their predictions.

      Using this approach, they modeled the distribution of 12 butterfly species and found that the ability to colonize unoccupied areas that are newly suitable and maintain populations in these areas is essential for species to track their suitable conditions. Otherwise, species can fall behind the pace of climate change and loose range.

    5. P. R. Whitehorn, S. O’Connor, F. L. Wackers, D. Goulson, Neonicotinoid pesticide reduces bumble bee colony growth and queen production. Science 336, 351–352 (2012).

      Testing for the effect of pesticides was important as field experiments have their negative impacts on bumblebees in the past. Whitehorn et al. (2015) showed that Bombus terrestris colonies exposed to pesticides in a lab had a lower growth rate and produced 85% fewer queens (bees that would eventually leave the colony to start a new colony) than those that were not exposed to the chemical. While this was observed on a small scale, the effect of pesticides was not measurable when Kerr et al. (2015) asked if it affected bumblebees’ wide scale shrinking range.

    6. D. Goulson, E. Nicholls, C. Botías, E. L. Rotheray, Bee declines driven by combined stress from parasites, pesticides, and lack of flowers. Science 347, 1255957 (2015).

      This review explains the multiple threats that bees are currently facing. Pesticides and other agrochemicals, parasites spread by humans, climate change, and land use change, are threats that either act on their own or interact, to cause negative effects on bees.

      For the study design, Kerr et al. (2015) took these threats into consideration to measure what effect was responsible for the results that they obtained, and chose to look at pesticides and land-use change; effects which, surprisingly, were not responsible for bumblebee range loss in the south and the inability for them to expand their range in the north. This is not to say pesticides and land-use change cannot create population declines at a smaller scale.

    7. V. Kellermann, J. Overgaard, A. A. Hoffmann, C. Fløjgaard, J. C. Svenning, V. Loeschcke, Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically. Proc. Natl. Acad. Sci. U.S.A. 109, 16228–16233 (2012).

      This study showed that Drosophila (a type of fruit fly species) adapted to hot and dry regions were more resistant to heat. The upper thermal limits tolerated by Drosophila could influence range limits. Authors conducted trait analyses and found that heat tolerance was an ancestral trait, kept over time. Trait-based analyses for bumblebees conducted by Kerr et al. (2015) also correspond to these results.

    8. M. B. Araújo, F. Ferri-Yáñez, F. Bozinovic, P. A. Marquet, F. Valladares, S. L. Chown, Heat freezes niche evolution. Ecol. Lett. 16, 1206–1219 (2013).

      This paper answers the research question “Can species physiologically adapt to climate warming?” They analyzed data from numerous other studies that described the thermal tolerances of species worldwide. Main findings of this study are that tolerance to heat was mostly conserved within closely related species, whereas tolerance to the cold was a trait that could vary.

      Trait-based analyses conducted by Kerr et al. (2015) correspond to these results. The upper thermal limits of bumblebees were found to be an ancestral trait, since it was conserved across closely related species.

    9. I. C. Chen, J. K. Hill, R. Ohlemüller, D. B. Roy, C. D. Thomas, Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).

      Authors conducted a meta-analysis, a type of analysis that looks at a group of studies on the subject. They demonstrate that many terrestrial species shifted their range higher in altitude as well as further north. Chen et al. (2011) found that the rate at which species can shift varies strongly between species. Thus, it is likely for individual species traits to play an important role in their ability to shift.

      Findings by Chen et al. (2011) were important to frame the research question in Kerr et al. (2015). Since species from many different taxa have shifted, it was reasonable to ask if bumblebees are shifting as well.

    10. M. Pacifici, W. B. Foden, P. Visconti, J. E. M. Watson, S. H. M. Butchart, K. M. Kovacs, B. R. Scheffers, D. G. Hole, T. G. Martin, H. R. Akçakaya, R. T. Corlett, B. Huntley, D. Bickford, J. A. Carr, A. A. Hoffmann, G. F. Midgley, P. Pearce-Kelly, R. G. Pearson, S. E. Williams, S. G. Willis, B. Young, C. Rondinini, Assessing species vulnerability to climate change. Nat. Clim. Change 5, 215–224 (2015).

      This paper is a review of the different ways to measure how much species are threatened by climate change, and how they might respond. For instance, you can do this by estimating how a species range could change in the future. Understanding how climate change is affecting specific species is the first step to develop conservation strategies. Kerr et al. (2015) accomplished a first step toward this goal by demonstrating that climate change is linked to widespread losses and an overall shrink in distribution.

    11. C. D. Thomas, A. Cameron, R. E. Green, M. Bakkenes, L. J. Beaumont, Y. C. Collingham, B. F. Erasmus,M. F. De Siqueira, A. Grainger, L. Hannah, L. Hughes, B. Huntley, A. S. Van Jaarsveld, G. F. Midgley, L.Miles, M. A. Ortega-Huerta, A. T. Peterson, O. L. Phillips, S. E. Williams, Extinction risk from climate change. Nature 427, 145–148 (2004).

      It is now clear that climate change has affected species, as shown by endless amounts of papers in the primary literature. This paper estimates sizeable species extinctions by 2050 linked to climate change. They do this with species distribution modeling. This technique uses known species distributions and climatic conditions, and estimates how the distribution could change in the future according to models of future climate. Authors used optimistic and pessimistic estimates of future climate data (since, we do not know how much humans will cut down on activities that aggravate climate change), and even took into account the capacity for some species to move to and colonize other places. They estimated extinctions of 15% to 37% of the species included in their study. Studies that look at future impacts of climate change yield uncertain results since these cannot be verified.

      The IPCC (Intergovernmental Panel on Climate Change) put together a report summarizing climate literature. Refer to the PDF of the synthesis of this report here if you are interested in finding out more information on climate change: https://www.ipcc.ch/pdf/assessment-report/ar4/wg1/ar4-wg1-spm.pdf

    1. S. H. Schneider, Encyclopedia of Climate and Weather (Oxford Univ. Press, 1996

      A comprehensive description of the phenomena responsible for the world's climate and weather events, as well as the history of atmospheric science.

    2. S. Narayanan, S. Yang, H. Kim, E. N. Wang, Int. J. Heat Mass Transfer 77, 288–300 (2014).

      A computational modeling study of adsorption dynamics evaluating how multiple parameters such as vapor pressure and porosity affect the adsorption performance. The simulation results were confirmed experimentally with an adsorbing zeolite.

    3. J. H. Cavka et al., J. Am. Chem. Soc. 130, 13850–13851 (2008).

      The design and characterization of a zirconium-based MOF displaying very high thermal and chemical stability.

    4. H. Furukawa, K. E. Cordova, M. O’Keeffe, O. M. Yaghi, Science 341, 1230444 (2013).

      A review on the preparation of MOFs and their structural properties as well as their applications.

    5. J. Lee et al., Chem. Soc. Rev. 38, 1450–1459 (2009).

      An overview of the usage of the use of MOFs as selective catalyst to perform chemical reactions between substrates.

    6. H. Furukawa et al., J. Am. Chem. Soc. 136, 4369–4381 (2014).

      The same group previously described how to prepare MOF-801 and characterized its water adsorption properties.

    7. R. V. Wahlgren, Water Res. 35, 1–22 (2001).

      A review on existing systems to extract water from the atmosphere.

    8. M. M. Mekonnen, A. Y. Hoekstra, Sci. Adv. 2, e1500323 (2016).

      A study showing that about 4 billion people do not have access to fresh water for at least a month per year, half of them in China and India.

    1. K. D. Ersche et al., Science 335, 601–604 (2012).

      Ersche et al. studied the brain structure and behavior control capacities of 50 sibling pairs where one of the siblings was considered drug dependent, and compared them with 50 volunteer controls. The authors found that both siblings had deficits in regulating behavior with brain structure. They saw a reduction of white matter in drug dependent individuals and their biological siblings, which may predispose to drug use and indicate a genetic component to drug dependency..

    2. F. J. Miles, B. J. Everitt, A. Dickinson, Behav. Neurosci. 117, 927–938 (2003).

      In this study, Miles et al. were interested in looking at how chronic cocaine use in rats affects response to outcome devaluation. His group noted that chronic cocaine users were not responsive to changes.

    3. R. J. Beninger, S. T. Mason, A. G. Phillips, H. C. Fibiger, J. Pharmacol. Exp. Ther. 213, 623–627 (1980).

      Beninger et al. studied the effect of pimozide treatment, a dopamine receptor blocker, to determine if treated rats would avoid the negative outcomes that were previously associated with a particular stimulus.

      They found that treated animals could not avoid the negative outcomes due to their inability to initiate a response to the stimulus.

  2. Sep 2018
    1. C. S. Velden, T. L. Olander, R. M. Zehr, Weather and Forecasting 13, 172 (1998)

      Velden and co-authors came up with an algorithm based technique for examining satellite imagery and cataloging storm systems. Their "Objective Dvorak Technique" is a modified version of the original Dvorak scheme which uses patterns in winds and moisture content to rate a storm on its intensity and characteristics.

      Instead of humans eye-balling characteristics, now computers do the calculations for us to determine storm behavior.

    2. G. J. Holland, Aust. Meteorol. Mag. 29, 169 (1981)

      Greg Holland studied a subset of global data in order to see how enhanced observational technology has improved the detection of intense tropical storms.

      He found that prior to the use of satellite imagery to recognize storms, records tend to underestimate the true number of events. This may be due to the amount of storms which form and remain far offshore which did not make it into historical records. Thus in the 1960's when satellites really started getting widespread usage for tracking weather, scientists "saw" more hurricanes than previously reported.

    1. White TD. 1980. Evolutionary implications of pliocene hominid footprints. Science 208:175–176. doi: 10.1126/science.208.4440.175, PMID: 17745537

      At the time this article was written, the author stated that the 3.6-million-year-old Laetoli footprints were the earliest evidence of bipedalism in human evolution.

    2. Reno PL, Meindl RS, McCollum MA, Lovejoy CO. 2003. Sexual dimorphism in Australopithecus Afarensis was similar to that of modern humans. PNAS 100:9404–9409. doi: 10.1073/pnas.1133180100, PMID: 12878734

      The authors estimated the degree of sexual dimorphism present in Australopithecus afarensis through a systematic, random sampling of skeletal fossils. Simulations using the same sampling strategy with modern humans, chimpanzees, and gorillas confirmed the accuracy of the technique. It was determined that A. afarensis exhibited moderate sexual dimorphism similar to that of modern humans. This, coupled with the presence of a reduced male canine, is consistent with monogamy.

    3. Johanson DC, White TD, Coppens Y. 1978. A new species of the genus Australopithecus (Primates: Hominidae) from the Pliocene of eastern Africa. Kirtlandia 28:1–14.

      A large assortment bones was unearthed in Laetoli, Tanzania and Hadar, Ethiopa. The authors attribute them to a new species of Australopithecus. The soil types and depth of each bone is described and mapped.

    4. Harcourt-Smith WEH. 2005. Did Australopithecus Afarensis make the Laetoli footprint trail? New insights into an old problem. American Journal of Physical Anthropology S40:116. doi: 10.1002/ajpa.20217

      The authors investigated the hotly debated question: "Did early bipeds walk more like humans or more like apes?" Modern humans walk with extended hind limbs whereas apes walk with flexed hind limbs. By comparing the Laetoli trackway prints with those made by modern humans walking along a sand pathway, the authors conclude that A. afarensis walked in an energetically economical way—more like modern humans.

    5. Haile-Selassie Y, Latimer BM, Alene M, Deino AL, Gibert L, Melillo SM, Saylor BZ, Scott GR, Lovejoy CO. 2010. An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. PNAS 107:12121–12126. doi: 10.1073/pnas.1004527107

      The partial skeleton of A. afarensis specimen KSD-VP-1 was studied to learn more about stature, body mass, and bipedality in the species. KSD-VP-1/1 antedates Lucy (A.L.288-1) by about 0.4 million years. Based on measurements of bones it was determined KSD-VP-1/1 is a larger-bodied specimen than Lucy and likely a male. There is evidence of a high degree of sexual dimorphism and a well-developed thorax different from present-day apes.

    6. Gordon AD, Green DJ, Richmond BG. 2008. Strong postcranial size dimorphism in Australopithecus afarensis: results from two new resampling methods for multivariate data sets with missing data.

      There has been much debate over the degree of sexual dimorphism and implied social behavior in Australopithecus afarensis. Previous studies have suffered from limited sample size. The authors present two new resampling techniques that do not rely on template specimen and its associated assumptions. Postcranial size dimorphism is determined measuring the femur, tibia, humerus, and radius in samples of A. afarensis, modern humans, chimpanzees, gorillas, and orangutans. Based on their findings, the authors concluded that postcranial dimorphism in A. afarensis is similar to that of gorillas and orangutans, and significantly greater than in modern humans and chimpanzees. Though not conclusive, the authors feel that there is a strong evidence of behavioral and mating strategies employed by A. afarensis.

    7. Bennett MR, Reynolds SC, Morse SA, Budka M. 2016. Laetoli’s lost tracks: 3D generated mean shape and missing footprints. Scientific Reports 6:21916. doi: 10.1038/srep21916

      The authors employed a new technique, color-rendered optical laser scanning, to decouple the G2/3 Laetoli hominin footprints. Scientists had speculated that the G2/3 print was made by a smaller individual walking in the footsteps of a larger individual. Some had argued that the G2/3 trackway was made by only one individual and not a composite. Until this study, the G2/3 trackway had not been well studied. This article describes how the use of color-rendered optical laser scanning allowed the authors to decouple the G2 and G3 tracks, end the argument, and render the footprints usable for data analyses.

    8. Anton SC, Potts R, Aiello LC. 2014. Human evolution. Evolution of early Homo: an integrated biological perspective. Science 345:1236828. doi: 10.1126/science.1236828, PMID: 24994657

      Three lineages of early Homo evolved between 2.5 and 1.5 million years ago. Evidence collected over the past few decades has resulted in a revision in the thinking about how and when adaptations such as our large, linear bodies, long legs, large brains, and reduced sexual dimorphism first appeared. Originally, it was thought these adaptations occurred as a package. Fossil analysis and environmental data indicate that many of the traits associated with Homo sapiens appeared at different times. Some arose earlier and others later. Environmental changes gave a selective advantage to different traits.

    1. There are several reasons why the Aleutian archipelago provides an ideal large-scale experimental system to study the effects of introduced predators: (i) Most islands are small; (ii) high-latitude floral diversity is relatively low; (iii) there are no native vertebrate herbivores; (iv) the islands are geologically and climatologically homogeneous with similar overall soil properties; (v) the large number of islands in the archipelago provides the opportunity for meaningful replication; (vi) the islands are isolated from anthropogenic nutrient inputs; and (vii) fox introductions were not targeted for particular island types, and the history of introductions is reasonably well known.

      The Aleutian Islands were chosen to be the place of study for many reasons, the main one being the similarity between the individual islands in the chain. The islands are of fair size, with similar soil makeup and weather. There are also numerous islands making the sample size large enough to be used for replication and to ensure the results were not due to chance. There was also the curious distribution of fox introductions that directly lead to a split in islands by type: fox-free vs. fox-infested.

    2. J. Terborgh et al., Science 294, 1923 (2001).

      In the paper by Terborgh et al., the different views on trophic cascades are investigated: top-down where predators limit herbivores and therefore prevent large destruction to vegetation, whereas bottom-up looks at the effects of plant defense in keeping predators at bay. This study touched upon the idea of top down interactions with the predation of seabirds by foxes having effects on plant communities, but in a more indirect way.

    3. N. G. Hairston Jr., F. E. Smith, L. B. Slobodkin, Am. Nat. 94, 421 (1960).

      The paper by N. G. Hairston, F. .E. Smith, and L. B. Slobodkin, "Community structure, Population Control, and Competition," observed what and how organisms are limited by their respective resources. Producers may be limited by an array of variables: light, water, and nutrients. These limiting resources can cause a change in competition throughout the trophic levels. In this paper, the limiting resources are the nutrients from guano. As the foxes prey and decrease the number of seabirds visiting the island, the dispersal of guano also decreases on the island.

    1. 15. S. Dasgupta, A. Gupta, Random Structures Algorithms 22, 60–65 (2003).

      Dasgupta and Gupta prove one result of the Johnson-Lindenstrauss theorem. This proof shows that a set of points in high-dimensional space can be mapped into a smaller dimensional space such that the distance between any two points changes only by a very small amount (1 ± ε).

      This result forms the foundation of many LSH algorithms.

    2. 10. A. Andoni, P. Indyk, Commun. ACM 51, 117 (2008).

      Andoni and Indyk provide an overview of efficient algorithms for nearest neighbor search problems.

      They focus specifically on locality-sensitive hashing algorithms, highlighting one specific option within the LSH family that provides near-optimal performance on nearest neighbor search problems.

    3. 8. S. R. Olsen, V. Bhandawat, R. I. Wilson, Neuron 66, 287–299 (2010).

      Olsen, Bhandawat, and Wilson describe one specific type of computation that occurs in olfactory processing in flies.

      They show that this computation, known as divisive normalization, helps to equalize responses to different input stimuli. This same computation is also known to serve a similar purpose in many parts of the visual system.

    4. 2. D. Owald, S. Waddell, Curr. Opin. Neurobiol. 35, 178–184 (2015).

      Owald and Waddell explore how memories of odors manifest in the fly's olfactory circuit and drive fly behavior

      Specifically, they discover that dopamine plays a key role in this process. During learning, dopaminergic neurons reactivate Kenyon cells associated with specific odor tags. In this way, the fly recalls previously-learned odors.

    5. 1. C. F. Stevens, Proc. Natl. Acad. Sci. U.S.A. 112, 9460–9465 (2015).

      Stevens outlines the three-layer architecture that makes up the fly's olfactory circuit.

      He also presents the idea of a unique odor label, or "tag" that is comprised of a small set of neurons and helps the fly identify distinct odors.

    1. V. Devictor, C. van Swaay, T. Brereton, L. Brotons, D. Chamberlain, J. Heliölä, S. Herrando, R. Julliard,M. Kuussaari, Å. Lindström, J. Reif, D. B. Roy, O. Schweiger, J. Settele, C. Stefanescu, A. Van Strien, C.Van Turnhout, Z. Vermouzek, M. WallisDeVries, I. Wynhoff, F. Jiguet, Differences in the climatic debts of birds and butterflies at a continental scale. Nat. Clim. Change 2, 121–124 (2012).

      This paper demonstrates how bird and butterfly communities have changed over time, and while they shifted through time, they failed to keep up with climate change. They show that northward shifts for bird communities shifted by 37 km, and butterfly communities shifted by 114 km. The climate shifted much faster than this, leaving lags of 212 km for birds, and 135 km for butterflies. These are the distances that birds and butterflies would need to travel to reach temperatures similar to that of their historical range shifts.

  3. Aug 2018
    1. T.C. LaJeunesse, Marine Biology 141, 387–400 (2002).

      Following LaJeunesse and Trench's 2000 publication on DGGE, this work expands on the applications, effectiveness, and usefulness of DGGE -a technique that separates DNA fragments.

    2. T.C. LaJeunesse, Journal of Phycology 37, 866–880 (2001).

      This work was used in this research since it is based on a characteristic molecular region in the Symbiodinium species.

    3. T.C. LaJeunesse, R.K. Trench, Biological Bulletin 199, 126–134 (2000).

      Reviews the technique denaturing gradient gel electrophoresis (DGGE) and how it is used for molecular identification.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

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

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

    9. 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.

  4. Jul 2018
    1. M. C. Goldstein, D. S. Goodwin, PeerJ 1, e184 (2013).

      An ocean gyre is a circular ocean current formed by the Earth’s wind patterns and rotation. The area in the center of a gyre tends to be very calm, and the circulation patterns of the currents draw debris into the stable center, where it becomes trapped. The debris is composed of objects both manmade and natural (i.e. driftwood). Many kinds of sea life live on and near the debris. Gooseneck barnacles are one of these types of organism. Goldstein and Goodwin examined the digestive tracts of gooseneck barnacles to see if the barnacles consumed any plastics. One third of the 385 barnacles examined had plastic particles present in their digestive tracts, and larger barnacles tended to contain more plastic particles. The effects of the plastic particle ingestion on the ecosystem are still unknown.

    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.

  5. 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.

  6. 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.

  7. 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.

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      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.

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      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/

  8. 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.

  9. 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.