The popular opinion is that the Introduction to a manuscript should be written after the Materials and Methods and Results and Discussion sections. So, why discuss the Introduction in the third installment of our special series on manuscript writing tips? The Introduction is where authors frequently run into trouble by writing either too much or too little. Therefore, the tips presented here for writing the Introduction section can be readily applied throughout the manuscript. In addition, understanding the purpose of the Introduction and its basic structure will prevent redundancies and allow you to frame the other sections of your manuscript more efficiently and effectively, even if you have yet to write the Introduction itself.
More Manuscript Tips:
For simplicity, let’s break the Introduction section down into three basic parts: (i) establishing the question to be studied, (ii) providing a rationale for studying this question, and (iii) briefly conveying how you will address the question.
Establishing the Question
The first few paragraphs of an Introduction should serve to establish for the reader what the study will explore, and provide context for your work. This means clearly defining how your results relate to previous studies. Let’s use a recent article as an example:
“Next generation sequencing is revolutionizing our understanding of the links between genotype and phenotype at scales that were unimaginable a few years ago. Genome-wide association studies are now routinely conducted to explore the genomic basis for phenotypic variation (1) or disease predisposition (2), as well as to identify the genomic elements that underlie adaptive evolutionary responses (3).
Although such genome level association studies are powerful, they are labor-intensive to execute, as they require not only sequencing of entire genomes, but also that the collected genomic data be carefully parsed, assembled, and accurately annotated. This is most easily done when closely related and well-annotated reference genomes are available for comparison. However, genome assembly and annotation become substantially more difficult with increasing evolutionary distance to the reference genome.”
The initial two paragraphs of the introduction clearly establish that the article will explore next-generation sequencing and, more specifically, the use of next-generation sequencing to compare genomes across evolutionarily divergent species.
The first paragraph is used by the authors to set the stage, so to speak, for their research by describing previous studies examining the link between genotype and phenotype. This is an important part of the manuscript as it enables the reader to place the work in a broader context. Today, many articles are published without sufficient background information, with the risk that readers without a deep knowledge of the field will not recognize the significance of the study.
The second paragraph introduces the reader to the specific question at the center of this particular study. By moving from the more general to more specific information related to this particular study, the authors are providing the readers a directed overview of the field (methodologies used in genome analysis, in this case).
Providing a Rationale
Now that the reader has a basic understanding of your research topic, the next step in writing the Introduction is to provide a clearly defined rationale for this particular study. You want the reader to understand why you undertook this project—and what your major goals were. This is especially important if the manuscript is intended for a “general interest” journal with a wide readership, rather than a more specialized field-specific journal. See here how the authors are able to clearly state the rationale for their research:
“Unfortunately, no technology yet exists that allows researchers to efficiently explore genetic variation across evolutionarily divergent organisms for large sets of pre-specified target genes, such as those that determine pelage color in vertebrates (5), or those involved in particular physiological adaptations (6,7). PCR amplification, the main and for a long time only technology for targeting specific DNA regions for sequencing, is generally too labor intensive, costly, and inconsistent to generate such multigene data sets.”
This paragraph firmly establishes the need for a new method to explore large sets of pre-defined genes across divergent species. At this stage in their Introduction, the authors have established (i) the current state of field and the techniques available in the first two paragraphs, and (ii) the rationale for this particular study. The wording is clear and direct—the fact that no technology is currently available to accomplish what the authors want to do provide a clear understanding of why they performed their study.
Explaining Your Approach
The final paragraphs of the Introduction should highlight how the study was accomplished and, briefly, the major findings. These paragraphs should prepare the reader for a deeper explanation of the experimental design, methodology, and the resulting data in the remainder of the article. The last paragraph of the Introduction should focus on how the study was done with a splash of major findings. (In a future installment of this series, I will describe how the Discussion section should do the opposite.)
Let’s look at a well-constructed final paragraph from the Introduction section of the gene capture article:
“Here we describe a gene capture method that is effective for capturing a pre-specified set of protein coding genes across species that have been evolving independently for hundreds of millions of years, using a single bait array. We have achieved this by tuning the stringency of the hybridization and washing steps of the procedure to optimize retention of target versus non-target DNA fragments, and by conducting two rounds of gene capture whereby the captured products from the first round are used as templates to augment a second round of gene capture.”
This paragraph works nicely because it clearly articulates how the study was done (second sentence), while at the same time explaining the major finding (in this case, a new method for capture of genes from divergent species) in the first sentence. You might wonder why the authors didn’t start with how the study was done and then move on to the major finding. By presenting the information in this way, we flow directly from the end of the Introduction into the Materials and Methods section, where the washing steps and hybridization conditions will be described in more detail.
Taking advantage of this basic structure for your Introduction will provide you with a strong starting point for composing this section.
In our next column, we will examine tips for creating a meaningful Materials and Methods section in the age of Supplementary Materials.