1,059 Matching Annotations
  1. Dec 2018
    1. Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, et al. 2012. Nature. 490:49–54.

      This paper focuses on the member of the Mollusca phyla, Crassostrea gigas. It goes into depth on how the genome of the oyster reveals how it has been able heat chock protein 70 and apoptosis inhibitors contribute to the organisms ability to survive in very stressful environmental conditions. this contributes to the GIGA project because the genome had to have been coded and that can go towards the GIGA coalition.

    2. Vinson JP, Jaffe DB, O’Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, et al. 2005. Genome Res. 15:1127–1135.

      "Whole-genome assembly is now used routinely to obtain high-quality draft sequence." This supports the main idea of which GIGA stands for. A database for easy access to high- quality sequences of a certain organism.

    3. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, et al..; Taenia solium Genome Consortium. 2013. Nature. 496:57–63.

      This paper speaks of how parasitisms has developed in worms. Scientist have been able to figure this information out using the genome of 3 different tapeworms. They also identify treatments to ride humans of these parasites. This aids with the GIGA project because uses the genetic code of invertebrates, which can be a part of the GIGA database.

    4. Struck TH, Paul C, Hill N, Hartmann S, Hösel C, Kube M, Lieb B, Meyer A, Tiedemann R, Purschke G, et al. 2011. Nature. 471:95–9

      This paper is on ring phylum Annelid. With the information in this study Animal body plan evolution can be more defined which can help researchers better understand the evolution of metazoans. It mentions on how other organisms who were classified under different phyla should actually fall under Annelid. Showing how this paper can help researchers narrow down the evolution of these creatures consisting of invertebrates.

    5. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, et al. 2008. Nature. 454:955–960.

      This study focuses on the Placozoan Trichoplax genome in order to understand the organisms that fall under this category. It focuses in where they stand in categories of animals as one of the first emerging animals. It can be used to study how the first animals ever looked on this earth and their DNA can present a lot more information that can still be found out.

    6. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. 2010. Nature. 463:1079–1083.

      This has to do with how arthropods are more closely related to aquatic invertebrates than other terrestrial invertebrates. This shows how evolution of invertebrates were different then originally thought and with the help of data from this study other scientist can know this and use it for themselves.

    7. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ. 2011. Nature. 470:255

      This paper focuses on how to two taxa are actually very similar to one another. This all contributes to the database for flatworms and the taxa they pertain to.

    8. Mardis ER. 2011. Nature. 470:198–203

      This study focuses on how the Human Genome Project has lead humanity to leap into the future and gain a ton of knowledge. This is more of an example of how the GIGA project can be of use. It goes into detail of what we have learned since the HGP was completed. This is more of a reflection of the possibilities the GIGA project can have for marine invertebrate genome.

    9. Lewin HA, Larkin DM, Pontius J, O’Brien SJ. 2009. Genome Res. 19:1925–1928

      This is an article that is justifying the reasons for mapping a genome and how it can be useful in advancing knowledge, research, and technology.

    10. Jeffery NW, Jardine CB, Gregory TR. 2013. Genome. 56:451–456.

      Focuses on the genome size of an early branching phylum. This is all scarce information so this study is important into better understanding the entire phylum which is pretty wide spread. This is perfect example of what GIGA is trying to prevent. They want to create a global database of information of marine invertebrates especially due to the lack of information on these creatures.

    11. Human Microbiome Project. 2012. Nature. 486:207–214.

      This project is essentially a genomic mapping project of the the microbes that live within humans. Another example of how databases are useful, which supports the reasoning for creating the GIGA project.

    12. Hill CA, Wikel SK. 2005. Trends Parasitol. 21:151–153.

      This is a perfect example of how creating a database of a genome can enhance the spread of information and the use of certain standards and information in order go further into research of the tick genome. Shows how the GIGA initiative can be of use.

    13. Funch P, Kristensen RM. 1995. Nature. 378:711–714

      This is an older paper, published establishing a new phylum Cycliophora. This contributes to database on new discoveries on marine invertebrates. it foes into depth on the larva of the organism and what makes it different form other invertebrates.

    14. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. 2012. Nature. 489:52–55

      This article focuses on the ENCODE project and goes to explain its functions and what it can lead to. It focuses on learning and understanding the functional regions of the human DNA, but it makes you think that if this can work for humans why can it not work for any other species? This shows incentive to the GIGA coalition and what it can mean for researchers in the marine invertebrate field.

    15. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Nature. 439:965–968.

      This paper focuses on how Tunicates are the closest living relatives to vertebrates. This study can assist from en evolutionary standpoint to picture a transition from an invertebrate to vertebrate creatures. This pertains to paper at hand because it will contribute to the database for GIGA.

    16. Davidson EH, Erwin DH. 2006. Science. 311:796–800.

      This article focuses on the evolution of body plans of invertebrates. So due to the nature of the paper it refers to a lot of invertebrates and focuses on their development. The GIGA project focuses on invertebrates

    17. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. 1994. Science. 263:802–805.

      The name of this paper is called "Green Fluorescent Protein as a Marker for Gene Expression." The marine invertebrate mentioned is the Aequorea victoria. This will contribute to the papers database. Can help with focusing on proteins of jelly fish.

    18. C. elegans Sequencing Consortium. 1998. Science. 282:2012–2018.

      This article contains the genome of the nematode C. elegans. The main purpose of GIGA is to obtain and database the genomes and infomration of the genome for others to use so this paper is a perfect candidate that reach this criteria.

    19. Birney E. 2012. Nature. 489:49–51

      This article speaks on the ENCODE project. ENCODE is a mass collection of functional parts of DNA. It focuses on the do's and do not's of database creation. This can serve as a source of how the creators of GIGA can go about creating their database, and steps they should take to ensure its success.

    20. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, et al. 2009. Nature. 460:352–358.

      "Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries." It contains the genome for this species and goes into depth the characteristics of the genetic code. for instance it says that it contains a large amount of introns. Also shows how the information gathered has led researchers to begin new ideas of possible treatments and regulations of the disease.


      This paper proposes a project so it isn't necessarily a topic that many people have researched. Due to the nature of the paper, the resources and past works will consist of published works that describe the pros of creating a database and examples of the types of works that will contribute to the GIGA project.

    22. A collective effort to sequence thousands of invertebrate genomes will only be feasible with participation and commitment from the scientific community. The large breadth of invertebrate diversity will require taxon-specific expertise and integration of traditional biology with molecular advances, both in data generation and analysis. The GIGA team has already expanded beyond initial participants in the first GIGA planning workshop, where the cooperative spirit and ability to work in concert to establish a common platform for data sharing and analysis were demonstrated.

      This database will only be able to be completed with the participation and commitment from the scientific community around the world.

    23. Ecdysozoa (molting animals) is a major protostome clade (Figure 1) proposed by Aguinaldo et al. (1997) that includes the large phyla Arthropoda (Figure 3) and Nematoda (both of tremendous ecological, economic, and biomedical importance) and their close relatives (Tardigrada [water bears, 1150 species], Nematomorpha [351 species], Onychophora [velvet worms; 182 species], Kinorhyncha [179 species], Loricifera [30 species], and Priapulida [19 species]). Ecdysozoans are characterized by their ability to molt the cuticle during their life cycle, and for having reduced epithelial ciliation, which requires locomotion via muscular action. They include segmented or unsegmented, acoelomate, pseudocoelomate, or coelomate animals; many have annulated cuticles and a mouth located at the end of a protrusible or telescopic proboscis, and some lack circular musculature (i.e., Nematoda, Nematomorpha, Tardigrada). Here we restrict the proposed sampling to the noninsect and nonnematode ecdysozoans. The clade includes the only animals (loriciferans) thought to complete their life cycles in anoxic environments (Danovaro et al. 2010). This group is also relevant for studies of extreme cell size reduction. Other than the mentioned arthropod and nematode genomes, no genome is available for any member of the Ecdysozoa.

      This is one of the limitations that will be placed on researchers that plan on conducting research to contribute to this database. They restrict a certain proposed sampling to the non-insect and non-nematode ecdysozoans.

    24. Many of the roughly 70 invertebrate species whose genomes have been sequenced belong to the Arthropoda or Nematoda, although the number of other invertebrate genomes continues to grow (e.g., Olson et al. 2012; Takeuchi et al. 2012; Zhang et al. 2012; Simakov et al. 2013; Tsai et al. 2013; Flot et al. 2013). We propose to focus on noninsect/nonnematode phyla, and specifically on an important group of currently neglected arthropods, the crustaceans.

      They propose a certain focus for researchers that wish to dedicate time to contributing to the database by stating that they should focus more on neglected groups of arthropods, specifically crustaceans.

    25. GIGA has adopted a set of standards and best practices to help ensure that genomic resources, data, and associated metadata are acquired, documented, disseminated, and stored in ways that are directly comparable among projects and laboratories. These data should be easily and equitably shared among GIGA members and the broader scientific community, and GIGA will obey appropriate laws and regulations governing the protection of natural biodiversity. Briefly, all genome projects will report on a set of parameters that will allow assessment of genome assembly, annotation, and completeness (e.g., NG50, N50 of contigs and scaffolds, number of genes, assembled vs. estimated genome size) (Jeffery et al. 2013). Detailed descriptions of these standards and compliant protocols will be posted on the GIGA Web site. These will be revised periodically to facilitate the establishment and maintenance of current best practices common to many invertebrate genome and transcriptome sequencing projects and to help guide the researcher in selecting and assessing genomes for further analyses. The following recommendations summarize minimal project-wide standards designed to accommodate the large diversity of invertebrates, including extremely small and rare organisms, as well as those that live in close association with other organisms. Permissions: GIGA participants must comply with treaties, laws, and regulations regarding acquisition of specimens or samples, publication of sequence data, and distribution or commercialization of data or materials derived from biological resources. Participants must acquire all necessary permits required for collection and transport of biological materials prior to the onset of the work. The CBD recognizes the sovereignty of each nation over its biological resources, and under the auspices of the CBD, many nations and jurisdictions rigorously regulate the use and distribution of bioIogical materials and data. GIGA participants must be aware of these regulations and respect the established rights of potential stakeholders, including nations, states, municipalities, commercial concerns, indigenous populations, and individual citizens, with respect to any materials being collected, to all derivatives and progeny of those materials, and to all intellectual property derived from them. GIGA participants must also familiarize themselves with the conservation status of organisms to be sampled and any special permits that may be required (e.g., CITES). Moreover, GIGA participants should collect in ways that minimize impacts to the sampled species and their associated environments. Field collection and shipping: Methods for field collection and preservation of specimens and tissues should be compatible with recovery of high-quality (e.g., high molecular weight, minimally degraded) genomic DNA and RNA (Dawson et al. 1998; Riesgo et al. 2012; Wong et al. 2012). Many reagents commonly used for tissue and nucleic acid preservation (e.g., ethanol, dry ice) are regulated as hazardous and/or flammable materials. These reagents may be restricted from checked and carry-on luggage and may require special precautions for shipping or transport. GIGA participants should contact the appropriate airline carriers or shippers for information regarding safe and legal shipment of preserved biological materials. When possible, multiple samples will be collected so that extractions can be optimized and samples resequenced as technologies improve. Specimens of known origin (i.e., field-collected material) will be favored over specimens of unknown origin (e.g., material purchased from the aquarium trade). Collection data will include location (ideally, with GPS coordinates) and date, and also other data such as site photographs and environmental measurements (e.g., salinity) when relevant. Selection and preparation of tissues: It is often advisable to avoid tissues that may contain high concentration of nucleases, foreign nucleic acids, large amounts of mucus, lipid, fat, wax, or glycogen or that are insoluble, chitinous, or mineralized. To obtain the highest quality material for sequencing or library construction, it may be preferable to extract nucleic acids from living or rapidly preserved tissue from freshly sacrificed animals, from gametes or embryos, or from cell lines cultivated from the target organism (Ryder 2005; Rinkevich 2011; Pomponi et al. 2013). When appropriate, select tissues or life history stages that will avoid contamination by symbionts, parasites, commensal organisms, gut contents, and incidentally associated biological and nonbiological material. Whenever possible, DNA or RNA will be sequenced from a single individual because many taxa display sufficient polymorphism among individuals to complicate assembly. Similarly, heterozygosity can also hinder assembly: inbreeding may be used to reduced heterozygosity (Zhang et al. 2012) or, when crossings are impossible (for instance in asexual species), haplotypes may have to be assembled separately (Flot et al. 2013). Quantity and Quality: The quantity of DNA or RNA required for sequencing varies widely depending on the sequencing platform and library construction methods to be used and should be carefully considered. Recent consensus from the G10KCOS group of scientists suggests that at least 200 – 800 µg of high-quality genomic DNA is required to begin any project because of the requirement for large insert mate-pair libraries (Wong et al. 2012). However, these minimum quantities are expected to decline with improving technology. DNA quality can be assessed by size visualizatons and 260/280nm ratios. Quality of RNA will be checked using RNA integrity number (RIN > 7 is preferred); however, these values have been shown to appear degraded in arthropods due to artifacts during quantification (Schroeder et al. 2006; Winnebeck et al. 2010). Taxonomic identity: The taxonomic identity of source organisms must be verified. Whenever possible, consensus should be sought from expert systematists, supportive literature, and sequence analysis of diagnostic genes (see next section). Voucher specimens: As a prerequisite for inclusion as a GIGA sample, both morphological and nucleic acid voucher specimens must be preserved and deposited in public collections, and the associated accession numbers must be supplied to the GIGA database. Photographs should be taken of each specimen and cataloged along with other metadata. The GIGA Web site lists cooperating institutions willing to house voucher specimens for GIGA projects, such as the Smithsonian Institution or the Ocean Genome Legacy (http://www.oglf.org). Documentation of projects, specimens, and samples: Unique alphanumeric identification numbers (GIGA accession numbers) will be assigned to each GIGA project and to each associated specimen or sample used as a source of genome or transcriptome material for analysis. A single database with a web interface will be established to accommodate metadata for all specimens and samples. Metadata recording will also aim to coordinate and comply with previously established standards in the community, such as those recommended by Genomics Standards Consortium (http://gensc.org/; Field et al. 2011). Sequencing Standards: Standards for sequencing are platform and taxon specific, and sensitive to the requirements of individual sequencing facilities. For these reasons, best practices and standards will be established for individual applications. Coverage with high-quality raw sequence data is a minimal requirement to obtain reliable assemblies. An initial sequencing run and assembly will be used to estimate repeat structure and heterozygosity. These preliminary analyses will make it possible to evaluate the need for supplemental sequencing, with alternative technologies aimed at addressing specific challenges (e.g., mate-pair sequencing to resolve contig linkage). Moreover, all raw sequence reads generated as part of a GIGA project will be submitted to the NCBI Sequence Read Archive. Sequence Assembly, Annotation, and Analyses: Because assemblies vary widely in quality and completeness, each assembly should be described using a minimum set of common metrics that may include: (1) N50 (or NG50) length of scaffolds and contigs (see explanation of N50 in Bradnam et al. 2013), (2) percent gaps, (3) percent detection of conserved eukaryotic genes (e.g., Core Eukaryotic Genes Mapping Approach (Parra et al. 2007), (4) statistical assessment of assembly (Howison et al, 2013), (5) alignment to any available syntenic or physical maps (Lewin et al. 2009), and (6) mapping statistics of any available transcript data (Ryan 2013). The current paucity of whole invertebrate genome sequence projects can pose problems for gene calling, gene annotation, and identification of orthologous genes. In cases where the genome is difficult to assemble, we recommend that genome maps be developed for selected taxa via traditional methods or new methods (e.g., optical mapping of restriction sites) to aid and improve the quality of genome assembly (Lewin et al. 2009) and that GIGA genome projects be accompanied by transcriptome sequencing and analysis when possible. Such transcriptome data will assist open reading frame and gene annotation and are valuable in their own right.

      GIGA aims to set standards for data acquisition and the processing of that data as well as the input of that data into their system. These standards will be progressively revised as better methods are discovered. These standards are to be used for a large variety of invertebrates. This standardization will allow for a more easily accessible and usable bank of information.

    26. We also recognize the existence and formation of other recent genome science initiatives and coordination networks and will synchronize efforts with such groups through future projects. Because GIGA is an international consortium of scientists, agencies, and institutions, we will also abide by the rules of global funding agencies for data release (e.g., those proposed by the Global Research Council; http://www.globalresearchcouncil.org). We are aware that different nations have different constraints and regulations on the use of biological samples. Given the international nature of GIGA, we will work to ensure that national genomic legacies are protected and will consult with the pertinent governmental agencies in the countries from which samples originate. We will deposit sequence data in public databases (e.g., GenBank), as well as deposit DNA vouchers in publically accessible repositories (e.g. Global Genome Biodiversity Network, Smithsonian). GIGA is an inclusive enterprise that invites all interested parties to join the effort of invertebrate genomics. We will attempt to capture the impact of the effort in the wider scientific and public arenas by following relevant publications and other products that result from GIGA initiatives.

      The project coordinators will also join with other networks to work together on future projects of common interest. They also understand that different countries have limits on the use of biological samples and thus their governments will be consulted with so that the international program is protected from any government agencies in the countries where the samples come from.

    27. GIGA embraces a transparent process of project coordination, collaboration, and data sharing that is designed to be fair to all involved parties. The ENCODE project may be emulated in this regard (Birney 2012). We are committed to the rapid release of genomic data, minimizing the period of knowledge latency prior to public release while protecting the rights of data product developers (Contreras 2010). The data accepted as part of GIGA resources will undergo quality control steps that will follow preestablished and evolving standards (see Standards section) prior to data release. Efforts such as those of Albertin et al. (2012) have addressed data sharing issues relevant to GIGA and other large-scale genomics consortia.

      Once the data has been submitted by researchers, it will go through a quality control process to make sure that it reaches the quality and accuracy which the project requires. As well as to avoid duplicate data being published.

    28. but there are currently no published genomes for the other 21 invertebrate phyla. We examined current phylogenetic hypotheses and selected key invertebrate species that span the phylogenetic diversity and morphological disparity on the animal tree of life (see Supplementary Material). New invertebrate genome data can reveal novel sequences with sufficient phylogenetic signal to resolve longstanding questions.

      The currently available genome sequences at the time were reviewed and the missing phyla were taken note of. These missing areas in the so called "tree of life" were added to the list of species to be researched so that the data could be used to further other research.

    29. Therefore, the geographic scope of the project in terms of participation, taxa collected, stored, and sequenced, data analysis and sharing, and derived benefits, requires global partnerships beyond the individuals and institutions represented at the inaugural workshop. Because international and interinstitutional cooperation is essential for long-term success, the new GIGA Web site will be used to foster cooperative research projects. For now, the GIGA Web site can serve as a community nexus to link projects and collaborators, but it could also eventually expand to host multiple shared data sets or interactive genome browsers. The broad scope of GIGA also necessitates growth in the genomics-enabled community overall. Sequencing and analyzing the large amount of resulting data pose significant bioinformatic and computational challenges and will require the identification and creation of shared bioinformatics infrastructure resources.

      The information gathered from experimentation will be unified by being submitted to the GIGA website, thus allowing researchers from all over the world to have access to the information at a moments notice. The website will also be used to host cooperative research projects that scientists from around the world could participate in and contribute data towards.

    30. Selection and prioritization of taxa to be sequenced will occur through future discussion and coordination within GIGA. Thus, the target number is a somewhat arbitrary compromise between the desire to encompass as much phylogenetic, morphological, and ecological diversity as possible and the practical limitations of the initiative. Given the large population sizes of many invertebrate species, collection of a sufficient number of individuals may be relatively easy for the first set of targets. Collection of invertebrates usually involves fewer difficulties with regard to permits than collection of vertebrate tissues. However, some invertebrate taxa pose various logistic and technological challenges for whole-genome sequencing: many species live in relatively inaccessible habitats (e.g., as parasites, in the deep sea, or geographically remote) or are too small to yield sufficient amounts of DNA from single individuals. These challenges will be considered with other criteria as sequencing projects are developed and prioritized.

      Selecting which organisms genetic information is to be gathered and recorded first will be determined at a meeting among researchers in the field. The priority of these organisms will also be determined by their accessibility to researchers as well as their ease of retrieving genetic information.

    31. We propose to sequence, assemble, and annotate whole genomes and/or transcriptomes of 7000 invertebrate species, complementing ongoing efforts to sequence vertebrates, insects, and nematodes (Genome 10K Community of Scientists [G10KCOS], 2009; Robinson et al. 2011; Kumar et al. 2012) (Table 1).

      The purpose of the experiment is to create a genetic database of 7000 invertebrate species.

    32. Human-based studies such as the ENCODE (Encyclopedia of DNA Elements) (Ecker et al. 2012) and “Human Microbiome” projects (Turnbaugh et al. 2007) demonstrate the extraordinary power of genomic technologies to produce data resources that can promote hypothesis generation and more powerful analytical tools.

      Read more on New York Times, which illustrates the founding and main goal in regards to the Human Microbiome projects.

    33. A main goal of GIGA is to build an international multidisciplinary community to pursue comparative invertebrate genomic studies. We seek to develop tools to enable and facilitate genomic research and encourage collaboration. We will develop standards that ensure data quality, comparability, and integration. By coordinating sample collecting and sequencing efforts among invertebrate biologists, we aim to avoid duplication of effort and leverage resources more efficiently. We envision a scientific commons where shared resources, data, data standards, and innovations move the generation and analysis of invertebrate genomic data to a level that likely could not be achieved with the traditional piecemeal single-investigator–driven approach.

      The main goal of the project is to build an international community whose goal is to perform invertebrate research. This community will be used to avoid duplicate research and wasting time on studies that have already been conducted. They will also set in place standards by which the data must be gathered and presented so that is can be universally understood by everyone around the world and so that the data is accurate enough.

    34. These include the sessile mangrove tunicate, Ecteinascidia turbinata, and the development of the anti-cancer drug, ET-743 (Yondelis®).

      Read more in The Pharmaletter's article, where Zeltia's president has begun second-phase testing with the ET-743 anti-cancer drug for breast cancer and sarcomas.

    35. Invertebrates are becoming increasingly important sources of protein for human nutrition worldwide. Particularly with the collapse of a number of vertebrate fisheries

      Read more in New York Times, where China's overfishing led to the inevitable diminishing of multiple species, which led to the collapse of fisheries whose livelihoods depended on the fish.


    1. Datta, A., Rane, A., 2013. Trop. Conserv. Sci. 6, 674–689.

      Referencing Box 1, this study was reviewed by the author classified this study as looking at population/species and as qualitative or quantitative estimate of flower or fruit production. The big conclusion of this study is that a rare species is seed-limited while dispersal limitation may play a secondary role in determining its abundance.

    2. Peres, C.A., 1994a. Biotropica 285-294.

      Referencing Box 1; The author of this paper looks at how plant phenology changes across succession in a community. Peres is studying keystone resources over many different seasons and how phenology changes over time. This aids in answering this papers research question of how phenology can be used in conservation to help keystone species.

    3. Schmidt, I.B., Figueiredo, I.B., Scariot, A., 2007. Econ. Bot. 61, 73–85.

      Referencing Box 1; Schmidt and his colleagues focused on sustainability in harvesting non-timber forest products. They did this by analyzing flowering and fruiting time, as well as, the abundance and size of the fruits produced. This conservation effort was done using a large scale population control effort.

    4. Rossi, S., Morin, H., Deslauriers, A., 2012. J. Exp. Bot. 63, 2117–2126.

      Referencing Box 1; Rossi and his colleagues focused their studies and conservations efforts on estimating carbon stocks and developing growth models in order to track and plan for future phenological changes and their effects on different tree species. Their models were developed by looking at tree growth rings within the trunks of various trees in order to look at the relative amounts of carbon dioxide intake and atmospheric carbon stocks at the time of the ring growth.

    5. Garwood, N.C., 1983. Ecology 53, 159–181

      Garwood focused on seed germination in tropical environments in Panama. He was looking to help determine primary selective factors that controlled the timing of germination, the significance of seed dormancy, and to identify any major seed germination syndromes. These are all related to the success of a plant population and help scientists better understand and map out conservation efforts for species diversity.

    6. Galetti, M., Dirzo, R., 2013. Biol. Conserv. 163, 1–6.

      Galetti and Dirzo reviewed the anthropogenic drivers of defaunation. They determined that direct drivers include hunting, poaching, and the presence of invasive species. Indirect drivers of defaunation include deforestation and fragmentation as a result of human activities. Some of the many consequences of defaunation are reduced ecosystem services and evolutionary changes in populations.

    7. Bond, W.J., Keeley, J.E., 2005. Trends Ecol. Evol. 20, 387–394. Borchert, R., 1998. Clim. Chang. 39, 381–393.

      Bond and his colleagues reviewed previous research in order to draw parallels between the effects of fire and herbivory on ecosystems. They concluded that, like herbivores, fires select for particular plant traits. For example, small herbaceous plants that require a lot of light for growth and seed establishment are more likely to be wiped out by fires. They also suggested that species that thrive under conditions of repeated defoliation would dominate communities where fires are likely to occur.

    8. Alvarado, S.T., Buisson, E., Rabarison, H., Rajeriarison, C., Birkinshaw, C., Lowry Ii, P.P., Morellato, L.P.C., 2014. S. Afr. J. Bot. 94, 79–87.

      Alvarado and colleagues analyzed the reproductive success of Madagascar sclerophyllous tapia woodlands in relation to fire frequency. They determined that more frequent fires resulted in increased latency of reproductive phenological events (flowering and fruit production in particular). Additionally, frequent fires reduced the overall number of individuals producing flower and fruits. It should be noted that the fires mentioned in this study were related to human activities.

    9. Ali, N.S., Trivedi, C., 2011. Biodivers. Conserv. 20, 295–307.

      Referencing Box 1; Ali and his colleagues established a calendar for the collection of seeds and other plant resources in order to properly manage the conservation of genetic resources in natural plant populations. This was done throughout population and species scale conservation. They made direct ground observations of plant phenophases (leafing, flowering, fruiting) and the environmental factors that effected these actions. Advancements in this conservation can be seen in efforts such as seed banks.

    10. Ali, N.S., Trivedi, C., 2011. Biodivers. Conserv. 20, 295–307.

      Ali and his colleagues focused their studies on the species diversity and conservation of various bird communities in Pakistan. This is important in understanding the relationship between the animal organisms within an ecosystem and their neighboring plants in order to obtain an optimal amount of species diversity within the ecosystem. This helps answer the question: what are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

    11. Alberton, B., Almeida, J., Helm, R., da Torres, S.R., Menzel, A., Morellato, L.P.C., 2014. Ecol. Inform. 19, 62–70.

      Alberton and colleagues tested whether or not digital cameras (used as a near-surface monitoring system) can be used effectively for measuring phenological changes in plants (specifically leaf color change). They determined that digital cameras are a reliable tool to monitor change in regional leafing patterns. This means that on-the-ground phenological observations of individual plants may no longer need to be used. However, the authors suggest that both methods, on-ground and near-surface monitoring through photographs, should be used to collect the most accurate picture of phenological change.

    12. The advancements in information science technologies to digitalize herbaria records and retrieve the historical phenological information from herbaria, satellite images and field cameras, will be essential to improve our capability to define proximate triggers and forecast the effects of climate change. The very essence of the importance of recovering historic phenological information, and its wide application for conservation, are illustrated by the work of Primack (2014) on the Thoreau records. As technology evolves and Land Surface Phenology becomes more likely, the ubiquity of ground-based phenology and remote sensing approaches will play an increasingly important role for phenology and conservation. This will help answer questions about the timing and drivers of phenological events under climate and land-cover change scenarios, especially in highly diverse and heterogeneous tropical system.

      The application of Land Surface Phenology may become increasingly important as technology advances. As scientists continue to better understand the drivers of phenological changes in the past, it can help us to plan for future changes within complex ecosystems such as tropical ecosystems.

    13. We therefore propose a series of measures and research topics that can increase the contribution of phenology research to conservation science (Box 1). We have described how phenological studies can support conservation management protocols in actively triggering or accelerating the resilience of degraded ecosystems, potentially making a large contribution to the general research framework on global climate and land-use change.

      The authors analyzed how phenology can aid in conservation science. With understanding the importance of this knowledge, scientists have laid out goals for future phenology studies, which includes creating a global model for monitoring changes in phenology to improve biodiversity. The key finding of this paper is understanding the importance of phenology and how it can help in future management discussions.

    14. The understanding and support of ecosystem services provided by biodiversity should take into account the temporal dimension in resource abundance and dynamics across the landscape (Schellhorn et al., 2015).

      Although there is a lot of focus on what an ecosystem can offer us within society, in terms of a tropical ecosystem, managers of the specific services need to take into account the relative abundance of the various resources within the ecosystem. This is important in order to healthily sustain the diversity within the ecosystem while at the same time maximizing the productivity within the ecosystem for human use.

    15. Recent advances in digital technologies to retrieve historical phenological information from herbaria, satellite images and field cameras will be essential to improve our capability to define proximate triggers, and forecast the effects of climate change.

      The causes for latent reproductive phenology in plants have yet to be determined. However, scientists can now use digital technologies (like digital cameras and remote sensing) to capture phenological events as they occur. This gives them the opportunity to examine changes without having to worry about the amount of time they have to analyze those changes.

    16. hyperspatial

      Using three or more dimensional spaces in imaging techniques.

    17. hyperspectral

      Imaging used to collect and process information across different wavelengths in the electromagnetic spectrum. The goal of hyperspectral imaging is to locate objects, identify materials, or detect processes. For example, this type of imaging has been used to detect early warning signs of disease in agricultural settings. This aids phenology in how individual species are identified and analyzed.

    18. cambial activity

      In plants, the layer of actively dividing cells that is responsible for secondary growth of stems and roots.

    19. keystone

      A keystone species is one that plays a particularly important role in an ecosystem; a species in which other species in a shared ecosystem depend on for survival.

    20. desiccation-tolerant

      The ability of an organism to withstand extreme weather conditions (such as drought).

    21. desiccation-sensitive

      The inability of an organism to withstand extreme weather conditions (such as drought).

    22. For instance, datasets resulting fromphenological studies can be organized as a seed collection calendar, supporting restoration efforts or ex situ genetic conservation (e.g. Packard et al., 2005). Also, those data sets make an invaluable contribution for initiatives such as the Kew's Millennium Seed Bank, aiming to harbour the germplasm of up to 25% of the world's plant diversity (Ali and Trivedi, 2011).

      Understanding the life cycle of plants helps us understand part of the world's plant diversity. This shows how phenology can make contributions to conservation biology.

    23. coexisting conspecifics

      Conspecific: individuals belonging to the same species.

      Coexisting conspecifics: two species living together in the same habitat.

      Extreme changes in climate decreases organisms' (of the same species) abilities to live together in the same habitat. This could be due to competition for resources.

    24. reproductive isolation

      Barriers that prevent different species from interbreeding. These could include isolation between habitats (physical barriers), behavioral isolation (differences in mating rituals), or mechanical isolation (incompatible reproductive structures).

    25. Intraspecific variation

      Variation within a species group or between individuals of the same species.

    26. biomes

      A large naturally occurring community of plants and animals in a specific climate. Some examples of biomes include the tundra, forests, grasslands, and deserts.

    27. clades

      A group of organisms that evolved from a common ancestor.

    28. biomass

      The complete mass of a living organism or the collective mass of entire community of living organisms. Biomass can be measured in total weight (with water) or dry weight.

    29. hybridize

      The interbreeding between two individuals of a different species or variety of species.

    30. This has been the case of Ibity New Protected Area (NPA) in Madagascar. Phenology observations showed that high fire frequency reduce flower and fruit production of tapia woodlands (Alvarado et al., 2014), indicating the limited potential for natural regeneration of the vegetation (Alvarado et al., 2015). Phenological information has been used to improve the management actions for the Ibity NPA, and is considered as an important issue for the successful implementation of an integrated conservation strategy, targeting restoration of plant communities and reintroduction of threatened plant species.

      Phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology. This study looked at a forest that developed under the selective pressure of fire which allowed scientist to study the forests reproductive phenology and how it was effected by the fire. They found that fire effects the timing of plant reproduction at community and landscape levels. This is a great example of how plant phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology.

    31. physiognomy

      The assessment of an organism's functions based on the outer appearance of the organism.

    32. taxonomic

      Relating to the classification of organisms based on their shared characteristics.

    33. animal symbionts

      Two organisms of different species depend on each other for survival.

    34. defaunation

      The loss of organisms from ecological communities.

    35. episodic community-wide fruit shortages following an El Niño event greatly elevated mortality of frugivorous and granivorous vertebrates in Barro Colorado Island, Panama (Wright et al., 1999)

      Scientists are trying to gain an understanding on how relationships between plants and insects are affected by the changing climate. This helps us to understand how phenology can be used to study the effects of climate change.

    36. temperate

      A forested ecosystem that receives heavy rainfall and contains primarily deciduous and some trees.

    37. folivorous

      A folivore is an herbivore that primarily consumes leaves (foliage).

    38. biocontrol measures

      Biocontrol measures or biological control is a method of controlling pests using natural enemy organisms. For example, mites, insects, and pathogens have all been used to eliminate invasive species.

    39. phytophagous insects

      Insects that feed on green plants.

    40. increases in temperature and drought frequency may lead to premature leaf senescence in deciduous forests, affecting the efficiency of nutrient resorption and the length of growing seasons, impacting carbon uptake and ecosystem nutrient cycling (Estiarte & Peñuelas 2015), and therefore management practices (e.g. Eriksson et al., 2015)

      This study looks at how climate change alters the rate of leaf senescence in which drought advances it and warming decreases it. This change affects the flow of nutrients within an ecosystem. This information helps us to understand how shifts in climate activity influences plant phenology, such as losing leaves sooner and disrupting the nutrient cycle.

    41. photosynthesis

      The process by which autotrophic organisms use the suns energy to make its own food. An autotroph is an organism that does not rely on anything but itself for ways of gathering essential nutrients. Phenology can change the rates at which photosynthesis in tropical plants.

    42. carbon sequestration

      The process by which CO2 is removed from the atmosphere and stored in a physical structure (e.g. oceans, terrestrial ecosystems, geologic formations). This process can occur naturally or artificially.

    43. primary productivity

      The rate at which organic matter is produced in an ecosystem through photosynthetic and chemosynthetic organisms. For example the amount of carbon that is stored within a tree as a result of photosynthesis. Phenology can determine this rate.

    44. senescence

      The deterioration or aging of the functional characteristics of an organism. Leaf senescence is the last stage in leaf development. During leaf senescence, nutrients are eventually reused by the plant in other areas. For example, nitrogen from lost leaves is later used for the creation of stem proteins. This is key for understanding how plants grow and how plants cycle energy and matter.

    45. Leaf flushing

      The appearance of a large number of new leaves in a relatively short period of time. New leaves are produced simultaneously on all branches of a bare plant.

    46. conservation science

      As concern for extinction rates rises, the need for conservation efforts to counteract these rates grows as well. Areas are being mapped out throughout Earth that are ranked by their ecological and economic significance for sustaining life on our planet. For more information about applications of conservation science, follow this link to see research and applications done by Groves and his colleagues. (https://academic.oup.com/bioscience/article/52/6/499/240341)

    47. conservation practices

      The process of managing an ecosystem to achieve maximum diversity in plant species in order to have a healthy fitness level within the ecosystem. Understanding changes in plant phenology will be necessary in order to develop the most effective conservation practices.

    48. Schematic diagrams exemplifying multiples hypothetical outcomes of human-induced shifts in plant phenology with implications for conservation. Human induced changes on abiotic and biotic factors affect the timing of plant and animal reproductive cycles and mutualistic interactions (A), ultimately with consequences for the conservation of biological diversity

      Fig. 2. (A)

      The abiotic and biotic effects of human activities on plant life cycles. Abiotic influences as a result of human activities include climate change, modifications of geochemical cycles, and frequency of fires. Biotic influences as a result of human activities include habitat loss and fragmentation, hunting, and species invasion. These factors collectively influence plant phenology, including leafing, flowering and fruiting, and seed germination and establishment.

    49. citizen science

      The collection and analysis of ecological data by the public alongside scientists.

    50. dendrochronology

      A scientific method of dating historical events using the growth pattern of tree rings. These rings can be used to analyze the atmospheric conditions that would've existed during a specific time period.

    51. herbaria

      A collection of dried plants.

    52. edge effects

      Changes in community structures that occur at the outermost boundaries of a habitat. The edges of a habitat are its first defense against extreme weather conditions and other harmful disturbances. Phenology can help determine how edges in an ecosystem change over time.

    53. habitat fragmentation

      Habitat fragmentation is a direct cause for the extinction of many plant and animal species. However, a recent study found that timely actions could easily slow extinction rates and save species as we implement more effective conservation efforts.

      Read more in Science Daily: https://www.sciencedaily.com/releases/2016/07/160725090002.htm

    54. habitat fragmentation

      Habitat loss due to the division of large, continuous habitats, into smaller isolated patches of habitats.

    55. bottom-up trophic organization

      Hierarchal levels within a food chain. Bottom-up trophic organization is ordered as 1.) producer, 2.) primary consumer, 3.) secondary consumer, and 4.) tertiary consumer.

    56. species niche concept

      The role that an individual organism has in its respective ecosystem. An individual's niche includes its methods of survival (acquiring food, shelter, etc), how it reproduces, and all other interactions it has with the abiotic and biotic factors in its environment. Changes in plant phenology can affect the ability of organisms in a community to live and survive amongst each other.

    57. community-level coexistence theory

      The coexistence between two competing species in a community results from stabilizing (different niches) and equalizing forces (similar fitness). Equalizing forces reduce differences in fitness between two or more species, which makes competition relatively equal between them. Stabilizing forces promote greater competition between individuals of the same species as opposed to competition between two or more separate species.

    58. ecosystem services

      Contributions from the natural environment that benefit human populations. In this case, the medicinal value that may be present in the plants within the tropical environment.

    59. herbivores

      An organism that feeds on plant material.

    60. detritivores

      Organisms that break down organic matter, primarily detritus. Detritus includes dead organisms and fecal materials.

    61. decomposers

      Organisms that break down organic material, primarily the remains of other dead organisms. An example is the denitrification done by bacteria in order for plants to obtain natural nitrogen.

    62. synchrony of plant reproduction

      Whether or not plant reproductive processes (e.g. flowering) occur at the same time in a particular population. Synchrony of reproduction can either be advantageous or disadvantageous for a plant. For example, plants that reproduce within the same time period increase the number of potential plants with which an individual can exchange genes. However, if a large proportion of plants in a population are reproducing at the same time, seedling death could increase as a result of density-dependent processes.

    63. photoperiod

      The amount of time within a 24-hour period in which an organism is exposed to light; generally the length of a day.

    64. (van der Sleen et al., 2015)

      Van der Sleen and colleagues determined that higher concentrations of atmospheric CO2 (as a result of human activities) increase plant photosynthetic rates and improve plants' water use efficiency. Increased CO2 increases the rate at which carbon can be used by plants as carbohydrates in light-independent reactions. However, photosynthesis rates eventually plateau as a result of another limiting factor (light intensity, temperature, etc).

    65. biogeochemical processes

      Biological, geological, and chemical processes in which elements and other substances are moved through living systems and the surrounding environment.

    66. (Chuine and Beaubien, 2001

      Chuine and Beaubien used a process-based model (PHENOFIT) to predict species distribution. This model focuses on survival and reproductive success in relation to climatic variations. They determined that the phenology of plant species as it relates to variations in climate is a major determinant for species distribution. This model could potentially be used to predict the future distribution of plant species and make adjustments to our current practices accordingly.

    67. global warming

      The gradual increase in the overall temperature of Earth's atmosphere as a result of the greenhouse effect (trapping of the sun's warmth in the atmosphere), increased atmospheric CO2 and other greenhouse gasses, and pollution.

    68. phenological events

      Living and non-living factors control what physical attributes are expressed in a plant species, due to changing environmental stresses.

    69. (Rosenzweig et al., 2008)

      Rosenzweig and colleagues noted that some major changes in phenology can be attributed to climate change. For example, rising oceanic temperatures are known to impact marine and freshwater biological systems in terms of phenology, migration, and community composition in algae, plankton, and fish.

    70. We advocate the inclusion of phenology into predictive models integrating evolutionary history to identify species groups that are either resilient or sensitive to future climate-change scenarios, and understand how phenological mismatches can affect community dynamics, ecosystem services, and conservation over time.

      "Construct an argument supported by evidence for how plants and animals (including humans) can change the environment to meet their needs"<br> This paper constructs an argument on how plants phenology changes due to the warming climate and how they adapt to these changes. Link: https://www.nextgenscience.org/pe/k-ess2-2-earths-systems

    71. temporal

      Relating to time. Temporal ecology focuses on the timing of ecological processes; for example, the timing of flowering events.

    72. spatial

      Relating to space. Spatial ecology focuses on the distribution of species. By understanding how the distribution of species changes overtime, scientists can better understand the ecological influences of climate change.

    73. exotic and invasive species

      Invasive and exotic species are organisms that are either native or non-native to a particular ecosystem and could potentially cause harm to systems within that ecosystem.

    74. anthropogenic disturbances

      Disturbances (in this case, ecological) as a result of human activities (e.g., agricultural practices, technology, and urbanizations).

    75. mutualistic interactions

      A relationship between two organisms of different species in which each benefit from the other. For examples, yucca moths lays their eggs in the flowers they pollinate; the eventual yucca larvae consume the flowers' seeds.

    76. species diversity

      The number and abundance of the various species living in an ecological community. Species abundance is the number of a specific species relative to surrounding species within that community.

    77. We focus on shifts in plant phenology induced by global change, their impacts on species diversity and plant–animal interactions in the tropics, and how conservation efforts could be enhanced in relation to plant resource organization

      Research question:

      How can phenology be used to further our knowledge and success in conservation biology? What are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

    78. evolutionary biology

      A subfield of biology that focuses on the evolutionary processes (mutation, gene flow, genetic drift, and natural selection) that eventually resulted in the diversity of life on Earth, originating from a common ancestor.

    79. ecology

      The study of the relationships between all of the organisms within an ecosystem and their surrounding environment. Like in this paper looks at how plants interact with their environment and the changing climate.

    80. biometeorology

      The study of the interactions between living organisms and their surrounding atmospheric conditions. Some examples include, the relationship between agricultural yields and weather, plant tolerance to extreme weather conditions, and the impacts of pollution on plant species.

    81. global change

      Changes in system processes within Earth's biosphere. The system includes land, oceans, the atmosphere, biodiversity, and the impact of human activities on key processes. An example is the effect of rising atmospheric carbon dioxide on sea levels and permafrost melting.

    82. Phenology

      The study of life cycle events in living things; more specifically, the timing of these life cycle events. For example, a phenologist might study migratory patterns, hibernation cycles, seed dispersal, and dormancy. In this study, phenology is used to help scientists understand the effects of a changing climate.

    1. Vandegehuchte, M.B., Lemiere, F., Janssen, C.R., 2009. Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 150, 343–348.

      A paper published in 2009, concluding that different exposure histories results in different levels of methylation.

    2. Valdiglesias, V., Fernandez-Tajes, J., Mendez, J., Pasaro, E., Laffon, B., 2013. The marine toxin okadaic acid induces alterations in the expression level of cancer-related genes in human neuronal cells. Ecotoxicol. Environ. Saf. 92,303–311

      A study in which the effect of the marine toxin Okadaic acid (OA) on certain genes that are related to cancer. In the study it was seen that there are alterations to the genes that could explain the relationship of OA to cancer.

    3. Sunda, W.G., Burleson, C., Hardison, D.R., Morey, J.S., Wang, Z., Wolny, J., Corcoran, A.A., Flewelling, L.J., Van Dolah, F.M., 2013. Osmotic stress does not trigger brevetoxin production in the dinoflagellate Karenia brevis. Proc. Natl. Acad. Sci.U. S. A. 110, 10223–10228.

      Sunda has previously concluded that exposure to brevetoxins limit growth

    4. Murrell, R.N., Gibson, J.E., 2009. Brevetoxins 2, 3, 6, and 9 show variability in potency and cause significant induction of DNA damage and apoptosis in Jurkat E6-1 cells. Arch. Toxicol. 83, 1009–1019.

      Murell and Gibsons reviewed the effect of Red Tides on human health, particularly on the effect it has with DNA strands. It further supported their reasoning into investigate on Histone 2 dynamics during the toxic experiment.

    5. Flewelling, L.J., Naar, J.P., Abbott, J.P., Baden, D.G., Barros, N.B., Bossart, G.D., Bottein,M.Y., Hammond, D.G., Haubold, E.M., Heil, C.A., Henry, M.S., Jacocks, H.M.,Leighfield, T.A., Pierce, R.H., Pitchford, T.D., Rommel, S.A., Scott, P.S., Steidinger, K.A., Truby, E.W., Van Dolah, F.M., Landsberg, J.H., 2005. Brevetoxicosis: red tides and marine mammal mortalities. Nature 435, 755–756

      Flewelling published a paper pinpointing areas in which saxitoxin (HABs) were found in food around the world. The Southeastern U.S was one of these areas in which saxitoxins were found. (DZ)

      Also the paper talks about the effect of Karenia brevis's brevetoxins on food webs and the effects.

    6. Dame, R.F., 1972. The ecological energies of growth, respiration, and assimilation in the intertidal American oyster Crassostrea virginica. Mar. Biol. 17, 243–250

      Dame's paper studies the interactions between the grazing of bivalves and their role in their respective environments (specifically, carrying capacity).

    7. Cardozo, K.H., Guaratini, T., Barros, M.P., Falcao, V.R., Tonon, A.P., Lopes, N.P.,Campos, S., Torres, M.A., Souza, A.O., Colepicolo, P., Pinto, E., 2007. Metabolites from algae with economical impact. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 146, 60–78.

      Cardozo focuses on the effects of the biotoxins released by the algae. From these effects the experiment is conducted upon what the toxins do on marine life organism in which the toxic effect is a natural defense mechanism.

    8. Brand, L.E., Campbell, L., Bresnan, E., 2012. Karenia: the biology and ecology of atoxic genus. Harmful Algae 14, 156–178.

      A paper describing the dinoflagellate, karenia brevis. The paper explains the biotoxins released by it, how the biotoxins build up in shellfish, and what damage it does to other marine organisms.

    9. Additionally, the study of DNA methylation patterns revealed significant differences between early (T0, T1) and late (T2, T3) stages of the HAB simulation. More precisely, a decrease in genome-wide DNA methylation levels was observed as the simulation progressed.

      The author further determined that due to the cause of the toxins released by the bacteria from the Red Tide it can influence methylation patterns of DNA. By influencing methylation , there exists a relationship in environmental stress and epigenetics. As the amount of time increases with the concentration of toxins remaining stable within the sample, the less there are accounts of genome wide DNA methylation.

    10. Based on these results, the application of H2A.X as a biomarker of oxidative stress seems plausible

      Ultimately, the authors have observed a positive correlation between H2A.X and Oxidative DNA damage, in such that H2A.X increases in the presence of Oxidative DNA damage (due to the presence of brevotoxins). Based on these results, they have concluded that H2A.X is a good indicator of oxidative stress.

    11. oxidative stress

      Reactive oxygen species inhabit the cell and can result in harm and lead to irregular protein and RNA transcription. By being unable to remove and detoxify the reactive oxygen species, then an imbalance between the cell and body is created as a source of stress which can lead to further detrimental effects.

    12. loci

      The fixed position of a chromosomal unit which can carry a specific gene or origin of a phenotype trait.The position is usually used in order to determine what other factors attribute to a characteristic change.

    13. The regulatory role of DNA methylation during environmental responses was previously investigated in marine invertebrates, linking modifications in methylation of stress-responsive genes with phenotypic plasticity and adaptation (Gavery and Roberts, 2010)

      Previously, a link has been discovered between the methylation of genes undergoing stress, and the ability of one genotype to produce more than one phenotype in order to adapt to its environment.

    14. This finding has a dual relevance: first, it corroborates the specialization of histone variants and PTMs in the chromatin of molluscs (González- Romero et al., 2012; Rivera-Casas et al., 2016a,b), supporting a role for H2A.X during environmental responses in invertebrates (Suarez-Ulloa et al., 2015) and the evolutionary conservation of this mechanism (Kinner et al., 2008; Lee et al., 2014). Second, it validates the application of commercial antibodies to detect H2A.X in bivalves, opening new avenues for monitoring DNA damage and health in populations of marine invertebrates.

      The authors found that the histone varaints that were derived from the major histones such as H2A.X, were also passed down as an evolutionary trait. The authors also determined that the antibodies could detect the histones in the oysters, and is signified as a possible method to detect further damage done by the toxic.

    15. concomitantly


    16. The obtained results revealed an increase in H2A.X, concomitantly with the exposure of Eastern oysters to increasing concentrations of K. brevis (T1, T2), and followed by a slight decrease during the recovery phase (T3, Fig. 3C).

      The phosphorylation of H2A.X appeared to be positively correlated to the exposure of K. brevis to the Easter Oysters.

    17. assays

      An analytical technique to precisely measure and observe the certain behaviors of an factor or subject. The results is typically an intensive property of the target of the assay in numerical terms.

    18. C-terminal domain

      The end of an amino acid chain signified by a carboxylic group.They are usually the end of protein synthesis , and has signals in the shape of sequences to retain and sort certain protein.

    19. western blot

      A method to detect and analyze specific amino acids sequences in certain proteins. The proteins are extracted which is then used with this analytical tool to determine the antibodies they bind to.The sample is then put under electrophoresis and transferred onto a membrane.

    20. The role of histone variants was further investigated by studying H2A.X, H2A.Z and macroH2A protein expression levels (Fig. 3)

      The scientists further studied the relationship between histone proteins and stress levels after acknowledging that a possible cause and effect exists.

      By discovering that antibodies connected to the histones were valid, it also proved the oyster to be the best model to test on.

    21. These results suggest that oyster responses to K. brevis exposure do not involve specific modifications in H2A.X, H2A.Z and macroH2A transcription.

      Because of lack of change over the course in the experiment, it is concluded that there is no response from the oyster in K. brevis in terms of gene modification in H2A.X, H2A.Z, and macroH2A transcription.

    22. Different epigenetic mechanisms participate in environmental responses, including histone variants encompassing highly specialized functions (Talbert and Henikoff, 2014).

      As described by past research of Talbert and Heinkoff, they're are a variety of epigentic mechanisms that are influenced by different amounts of stress drawn by the environment. One of these are the now testing of the recently discovered histone variants and and how each histone respond to environmental stress such as toxins.

    23. These results, together with the absence of oyster mortality and the stability in water quality parameters throughout the experiment and across treatment groups, support the effectiveness of HAB simulation in ensuring exposure of Eastern oysters to brevetoxins through K. brevis ingestion.

      The results showed that the simulation was an accurate representation of what happens during HAB.

    24. Genomic DNA was purified from gill tissue as described elsewhere (Fernandez-Tajes et al., 2007)

      The authors recorded and purified DNA from the gill tissue of the oysters in order to measure DNA methylation.

      Later, the DNA sequences were amplified.

      By using PCR methods, the samples were digested in order to asses the patterns of methylation and used to identify loci using Gowers Coefficient of Similarity.

    25. Histone protein isolation was performed as described elsewhere (Ausio and Moore, 1998), adapting the protocol to oyster gill tissues in the present work

      The purpose in the experiment was conducted in the extraction of histone proteins. By using classic centrifuging and electrophoresis techniques, the histone proteins were separated in order to retrieve the different types of anti-proteins. The antibodies were then analyzed with the Western Blot using the antibodies.

    26. Dosage was adjusted to maintain homogeneous microalgae concentrations across replicates (Fig. 1B). Specimens (n = 2 oysters per biological replicate) were collected at 4 different time points: T0, before exposure begins; T1, after 3 h exposure; T2, after 5 h exposure; T3, after 24 h exposure.

      The collection of the the oysters were at different time intervals in order to monitor and view different relationships between the algae concentrations and oyster infection number.The gills were the main focus of the time intervals to indicate how much of the algae was found in the oysters system.

    27. hydrophobicity

      The state of being repelled from water due to the lack of attraction. This is normally caused by shifting polarities of cells and molecules.

    28. Experimental HAB simulation

      A 24h simulation using a culture of K. brevis and the eastern oyster specimens.

      They were fed less prior so that during the simulation they would actively feed.

      There were 4 time points where data was collected: 0hr, 3hr, 5hr, and 24hr.

      The oysters were opened and the gills were flash frozen for later examination. This is because the brevetoxins contact the gills first and thus would experience DNA damage first.

    29. Specimen collection and laboratory acclimatization

      Explains how oysters were collected and kept.

      Collected: Rookery Bay National Estuarine Research Reserve, Naples FL

      Kept: In lab tanks with controlled conditions. Fed twice a day.

    30. (Radwan and Ramsdell, 2008; Murrell and Gibson, 2009, 2011)

      Multiple research studies previously conducted show that brevetoxins are produced during FRT's.

    31. as illustrated by recent studies examining the role of DNA methylation in the Pacific oyster

      Gavery and Roberts view the oyster as one of the best ways to speculate and monitor the progress of DNA methylation. They used this oyster model to view how the toxins can influence the rate of methylation and how stress affects epigentics factors.

    32. The study of the epigenetic mechanisms mediating exposure-response relationships constitutes the basis for environmental epigenetic analyses (Baccarelli and Bollati, 2009; Bollati and Baccarelli, 2010), providing information about how different environmental factors influence phenotypic variation (Cortessis et al., 2012; Suarez-Ulloa et al., 2015; Etchegaray and Mostoslavsky, 2016)

      In one experiment, one of the authors (Suarez-Ulloa) had previously studied the cause-effect relationship between environmental factors and subsequent epigenetic modifications triggering adaptive responses in marine invertebrates.

    33. mortality

      Large scale death.

    34. sentinel organisms

      Sentinel organisms are defined as organisms used to detect risks for humans through advanced warnings. In this case, for the Eastern Oysters. Ex: Canaries in coal mines.

    35. Consequently, bivalve molluscs are generally used as sentinel organisms to study HAB pollution

      In previous experiments conducted on Eastern Oysters, the author has successfully used bivalve mollusks as sentinel organisms.

    36. brunt

      The worst of a specifed thing (HABs).

    37. Furthermore, brevetoxins convey critical disruptive effects at the most fundamental level, as they can induce DNA damage and apoptosis

      Toxins are known to disrupt cell actions. The scientists expand on this idea by using the experimental model of an oyster because oysters can be used to determine epigenetic modifications passed down through generations, ultimately showing red tide effects.

    38. aerosolized

      Suspended in air.

    39. Schematic

      Another way of saying a model or figure.

    40. biotoxins

      a substance produced by an organism. An example is when there is an accumulation in shellfish. If the shellfish is ingested by a human it can cause paralytic shellfish poisoning (PSP) which can cause damage to the nervous system and can paralyze muscles.

    41. aquaculture

      When aquatic animals and plants are raised and grown for food.

    42. Harmful Algal Blooms (HABs)

      As one of the consequences in the bloom of red algal in the Southern East coat waters, will lead to changes in the marine ecosystems that inhabit the waters by releasing toxicity as Harmful Algal Blooms.

      Read more at: https://oceanservice.noaa.gov/hazards/hab/

    43. Overall, the present work provides a basis to better understand how epi-genetic mechanisms participate in responses to environmental stress in marine invertebrates

      Another news story about possible epigenetic effects on marine life. This news story focuses on the current effects of the 1989 oil spill in Alaska on current herring populations.


    44. phosphorylation

      When a phosphate group is added to a compound. Many times the addition of a phosphate results in a conformational change which can activate or deactivate the compound.

    45. genotoxic effect of brevetoxins

      Yimizu, Chou, and Bando initially studied the structure of brevetoxin, and deemed it the most potent toxin found in Florida Red Tide.

    46. H2A.X, H2A.Z and macroH2A

      González-Romero has previously conducted research on the stability and function of the H2A protein, concluding that it participates in the unfolding of chromatin fibers and therefore modifying enzymes and polymerases that facilitate gene expression.

    47. histone

      Proteins found in chromatin.

    48. phenotypic

      The physical outward expression of a gene due to an organism's genotype.

      Genotype is based off of the coded alleles of an organism.

    49. epigenetic

      DNA is not changed. Instead its the genes that are expressed or inactivated change in an organism.

    50. causing high mortality rates and annual losses in excess
    51. brevetoxins

      Brevetoxins are neurotoxins produced by Karenia brevis.

      These neurotoxins accumulate in shellfish and is the cause of neurotoxic shellfish poisoning (NSP).

      NSP will cause disruption of neurological processes in humans.

    52. algal proliferations

      Proliferation is the rapid increase in cell growth or organism reproduction.

      Algal proliferation, in this paper, is the rapid growth of a the dinoflagellate Karenia brevis.

    53. DNAmethylation

      In DNA Methylation, a methyl group is added to the DNA in order to change the activity of the DNA segment. (For example: turning an "off" gene "on").

    1. strong differences in herbivore assemblages in three widespread species of Ficus: Each tree species had a different dominant lepidopteran herbivore species in the lowlands compared to montane habitats.

      In this study, it was found that a small amount (17%) of the caterpillar (aka Lepidoptera) were found to be feeding on the Ficus in both the highlands and lowlands.

      The study was done on the different species of caterpillar that fed in the highlands, in the lowlands and those that didn't feed on ficus as well. The results showed them which caterpillar species was dominant on the species on ficus in the lowlands and which were dominant on the species of ficus in the montane habitats/ highlands. The ones that were found to be dominant in the lowlands, typically did not feed on the highlands and vise versa.

      A Comparison of Caterpillar (Lepidoptera) Assemblages on Ficus Trees in Papua New Guinea

    2. covariate

      A variable similar to the independent variable, that is observed and can help increase the results of the experiment.

    3. Kursar, T. A., K. G. Dexter, J. Lokvam, R. T. Pennington, J. E. Richardson, M. G. Weber, E. T. Murakami, C. Drake, R. McGregor, and P. D. Coley. 2009. Proceedings of the National Academy of Sciences USA 106: 18073-18078.

      This paper is a different version of the same type of research. This study provided backup information to further prove what was being stated and identified in this research.

    4. four classes of constitutive leaf defenses were identified in the populations of P. subserratum: flavans, flavones, quinic acid derivatives, and oxidized terpenes.

      These express results for another question posed that clarifies variables that pertain to the specialization of the main topic. What is important is to grasp that this variable was accounted for in the process of understanding how specialization works in P. subserratum.

    5. We found that leaf thickness and leaf toughness did not show a significant effect of lineage, but instead exhibited significant variation related to soil type

      This information clarifies a question posed in the introduction. This knowledge fills the gaps of different variables that could affect the main goal of specialization.

    6. two-dimensional NMDS ordination

      It stands for Two-dimensional non-metric multidimensional scaling ordination and is used to visualize how similar individual cases of a dataset are on a small axes.


    7. chlorophyll

      Chlorophyll is a green pigment that is found in the chloroplasts of algae and plant cells. It works well to absorb sunlight which is then used to make carbohydrates, through a process called photosynthesis.

  2. Sep 2018
    1. mollusk

      Invertebrates that are grouped together because of their unsegmented bodies, preferences for aquatic or damp-marshy habitat and usually the presence of an outer shell. Some examples are snails, octopuses, and mussels. In this experiment, they used the marsh slug (Deroceras laeve).

    2. passerine

      A perching bird, as classified by certain criteria pertaining to body morphology and positioning of toes. Passerines makes up half of all bird species.

    3. Breeding seabird densities were almost two orders of magnitude higher on fox-free than on fox-infested islands (Fig. 2B) (Mann-Whitney rank sum, T = 36, P < 0.001) (12). We estimate that this reduction in seabird abundance translates to a decline in annual guano input from 361.9 to 5.7 g m–2 (median values; T = 42, P = 0.005) (12). The resulting difference in marine nutrient input is reflected in soil fertility. Total soil phosphorus on fox-free islands was more than three times that on fox-infested islands (Fig. 2C) (F1,16 = 8.01, P = 0.012) (12). Although seabird colonies are often concentrated on the perimeter of islands, guano-derived nutrients can be broadly redistributed across islands and not solely concentrated within the colonies (17).

      The results show that there are much higher numbers of breeding seabirds on fox-free islands than on infested ones. This makes sense because foxes are predators of many types of birds which would lower the abundance of mating birds. This decrease in birds also had effects on the amount of guano being distributed across the land. This number decreased and in turn affected different nutrients that are derived in the soil from the bird guano such as phosphorous. Fox-free islands saw three times more soil phosphorus than fox infested islands. In this experiment, there is a chain effect of sorts going on where the presence or absence of foxes affects sea bird populations, which then affects guano inputs to the island and the soil nutrients derived from this are dependent again on sea bird populations that distribute the guano.

    4. All islands were sampled at the completion of the growing season (August) between 2001 and 2003. We established a 30 m by 30 m plot at each of the grid crosspoints (12 to 32 per island, depending on island size) (12), within which we sampled plant species presence and cover; aboveground plant biomass; total soil N, P, and δ15N; and %N and δ15N from a common grass (in most cases Leymus mollis but in some instances Calamagrostis nutkanensis) and forb (Achillea borealis) (12).

      In this experiment, grids were designated over the island and 30 x 30 meter plots were established to sample within. In these plots the total soil nitrogen, phosphorous, amount of stable nitrogen isotope, and percentage nitrogen were sampled across grasses, forbs, dipterans, arachnids, passerines, and mollusks to determine how much of these nutrients were derived from the ocean. Organisms and soil that derive their nitrogen from a local source will have fewer amounts of nitrogen isotopes than those that get their nitrogen from higher trophic levels as is shown in Figure 3.

    5. forbs

      A general term to describe any herbaceous flowering plant that isn't a grass. In this experiment, they observed the species Achillea borealis, commonly known as boreal yarrow.

    6. 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.

    7. extirpation

      The phenomenon of a species or organism dying off or not being found in a specific area at all while it is still found elsewhere. If the foxes were allowed to persist uncontrolled, the sea birds may die off in the Aleutian Islands.

    8. Fox predation reduced seabird abundance and distribution, in turn reducing nutrient transport from sea to land. The more nutrient-impoverished ecosystem that resulted favored less productive forbs and shrubs over more productive grasses and sedges.

      Overall, the study found that the introduction of foxes turned the once-grassland into a tundra with less productive plants in its place because of the nutrient deprivation caused by fox predation on the birds, who are the main nutrient distributors on the archipelago.

      This shows the indirect effects that predation can have on ecosystems that rely so heavily on nutrient distribution from other living organisms, such as the seabirds. This also provides further evidence that trophic cascades do not only have to be top down; predators do effect herbivory, but there can be indirect effects from predators to plant communities through nutrient deprivation from predation on nutrient source organisms.

    9. maritime tundra

      Tundras are flat and treeless swaths of land that have soil that is permanently frozen; in this example, it is bordered by the sea.

    10. Experimental nutrient additions to a community representative of fox-infested islands over 3 years caused a 24-fold increase in grass biomass (24.33 ± 6.05 g m–2) compared with control plots (0.51 ± 0.38 g m–2 increase; two-factor analysis of variance, F1,20 = 23.96, P < 0.001) and a rapid shift in the plant community to a grass-dominated state. In fertilized plots, grass increased from 22 (±2.7%) to 96 (±17.3%) of total plant biomass, whereas grass biomass in control plots was relatively unchanged (11.4 ± 3.0% and 12.1 ± 1.2% of total biomass at the start and end of the experiment, respectively) (12). In a parallel experiment (18), we disturbed and fertilized plots to mimic the effects of both seabird burrowing and guano addition. Here we found that disturbance negatively rather than positively affected grass biomass; the effects of fertilization alone were far greater than the joint effects of disturbance and fertilization. These results confirm the importance of nutrient limitation in these ecosystems and establish that nutrient delivery in the form of seabird guano is sufficient to explain observed differences in terrestrial plant communities between islands with and without foxes.

      In this experiment, nutrients were added to a community that represented the fox-infested islands which increased the grass biomass and also created a more grass dominated environment overall.

      The nutrient additions were meant to represent the spread of guano by the seabirds. In the fox-infested islands the seabird populations were scarce, which decreased guano accumulation. Therefore, the added nutrients represented the guano production by seabirds in the absence of seabird on the island that is fox-infested.

      These nutrient additions are similar to the nutrient states of fox-free islands and show what the changes in ecosystem could have been like during the introduction of foxes.

      In another experiment, they tried to mimic the disturbance in soil of seabirds burrowing, this negatively impacted the grass biomass and it was shown that fertilization by itself had the greatest positive effect on grass biomass and distribution. This helps explain the higher incidence of grasses in the fox-free islands.

    11. geographical information system (GIS)

      A computer system that is designed to show geographical areas in different ways and can be manipulated for the collection of data. An example is the map of fox-free vs. fox-infested islands in Fig. 1 and the map of concentrated species in Fig. 3.

    12. Fig. 1. The Aleutian archipelago with sample islands indicated in red (fox-infested) and blue (fox-free). Adak Island, the location of fertilization experiments, is indicated with a yellow dot.

      This figure shows the islands that were studied and their relative position on Earth. There are 9 fox-infested areas shown in red and 9 fox-free areas shown in blue, the sample size of islands is the same so the results cannot be attributed to the sample size difference. The yellow dot is the location of fertilization experiments.

    13. We use this experiment to show how differing seabird densities on islands with and without foxes affect soil and plant nutrients; plant abundance, composition, and productivity; and nutrient flow to higher trophic levels

      This is very broadly what the experiment seeks to discover through looking at fox-infested and fox-free islands. This experiment is designed to assess effects of sea bird densities on soil nutrients and composition, plant abundance, primary productivity, and the flow of nutrients from lower organisms to higher ones (i.e. from plants to herbivores to carnivores.)

    14. insular ecosystems

      A geographic region of suitable habitat for a specific organism/organisms that is surrounded by unsuitable habitat. Therefore it is isolated via environmental conditions; in this case, the habitat of both the birds and foxes are the islands on which they reside that are surrounded by the ocean.

      Both the bird species and Alopex lagopus are bound to their corresponding landscape. The foxes are trapped on their respective island because they lack the ability to swim to a new location. The birds are unable to use the same islands as Alopex lagopus because of the predation of Alopex lagopus. Therefore, both species belong to an insular ecosystem because of the unsuitable landscape around them.

    15. Seabirds deliver nutrient-rich guano from productive ocean waters (9) to the nutrient-limited plant communities (10, 11).

      Plant species on the archipelago are dependent on the nutrients from guano. Guano, bird poop, is rich with minerals and nutrients, like Nitrogen and Phosphorus. The plant species richness has been found to increase as the nutrient availability increases.

  3. Aug 2018
    1. Despite great progress in food web ecology, the indirect effects of top predators on vegetation dynamics in terrestrial systems remain unresolved and actively debated

      In the paper by J. Halaj et al. food webs are studied using the ratio of an isotope of nitrogen and carbon to see how much of it exists in different trophic levels and how the food web interacts both above and below ground. This study shows more of the direct effects of top down tropic cascades which are shown by the predation of sea birds by foxes in the study by Croll which also elaborates on the indirect effects of predators on the environment through the predation of sea birds decreasing nutrients to the system and changing the plant community structure. There is also isotope testing being used in this study to see its distribution across different species and soils between the fox infested and fox free islands.

    2. Hairston et al. (1) proposed that plant productivity and composition were influenced by apex predators through cascading trophic interactions.

      According to Hairston et al. the populations of producers, consumers, and decomposers are limited by the resources they depend upon which are subject to limitation by the tropic levels both above through predation and below through low abundance. These limitations of herbivores by predation is helpful to the plant communities below as well. The Hairston et al. study provided the basis for the study of direct effects on top predators to terrestrial systems but this study further looks into the indirect effects of predation on plant communities. Providing evidence for indirect effects of nutrient deprivation due to predation using a large scale system that has room for replication.

    1. Fig. 1 High-resolution melting profiles showing the resolved Symbiodinium strain genotypes.

      Different genetic sequences melt at slightly different rates. Therefore, they can be analyzed using these melting point curves, where fluorescence is plotted on the y-axis and temperature on the x-axis.

      If the DNA strand is composed of many guanine and cytosine bases, it will take a higher temperature to break the hydrogen bonds apart as opposed to adenine and thymine bases. This is why the E2 clade fluoresced at a higher temperature than the other clades.

    2. electrophoresis

      A technique used in laboratories used to separate macromolecules based on size.The term refers to movement of charged particles in a fluid or gel under the influence of an electric field.

    3. temperature gradient capillary electrophoresis (TGCE)

      An instrument used to test for single nucleotide polymorphisms (SNP's) (common genetic variations among individuals) between DNA fragments.

    4. high-performance liquid chromatography (dHPLC)

      Denaturing High-Performance Liquid Chromatography (dHPLC) is a technique that is used to separate chemicals in a mixture. dHPLC has been used on 19 patients with auto-inflammatory syndrome suspicion to spot polymorphism in the gene MVK. This technique is a quick and low cost process in order to obtain accurate screening of the mutations.

    5. cloning

      The processes used to create copies of DNA fragments.

    6. real-time PCR

      PCR is a technique in the laboratory in which short sequences of DNA are amplified. Real-time PCR has been used to rapidly detect Salmonella from cloves. It has also been used to compare three different methods to extract DNA.