Thank you for your interest in Genetics: Genes, Genomes, and Evolution. Information gathered in this guide may be helpful as you consider how this text fits into your curriculum; we also invite you to read the Preface to the book that also describes our approach to teaching genetics.

This text developed from our own introductory genetics and molecular biology course and we anticipate it will be suitable for similar courses offered in the second year of an undergraduate curriculum, or possibly for an introductory biology course in the first year. The book does not assume any specific scientific background for students in either biology or chemistry, but is aimed towards students that have a background in these fields, either from a prior college biology or chemistry course or from advanced courses in high school.

Dobzhansky’s famous dictum that “Nothing in biology makes sense except in the light of evolution” is our organizing approach and provides the consistent narrative structure for the book.  While it has long been central to understanding biology, the statement was difficult to embrace fully in introductory genetics and molecular biology courses until genomic information became widely available.  Genomes record evolutionary history.  Using the analysis of genomes as the organizing basis for our book provides the opportunity to unite topics into one contemporary narrative.

Genomic analysis is inherently both molecular and evolutionary, and we have attempted to approach every chapter from this unified perspective.  Rather than relying on separate chapters on “genome analysis” or “evolutionary principles” and hoping that the student/reader can synthesize them, we include these ideas as part of every topic.  We do have chapters in which molecular genetics or evolutionary principles are more prominent, but all chapters attempt to integrate these concepts.

A Note on Chapter Order and Organization

Our integrative approach provides a central narrative theme to unify the topics covered in the book.  We have purposefully tried to avoid an encyclopedic approach to the text. While many of us teaching now learned how to use large reference books when we were students, our students by and large have learned from on-line tools.  These on-line resources provide a wealth of details but often leave students in need of guidelines to navigate the information and a unifying context in which to organize it. We therefore developed the textbook with these needs in mind, providing a strong narrative voice and guidance on the relationships between topics.

Traditional content areas are represented, but the emphasis has been to present material in a way that most clearly highlights the connections between genetics, evolution, and genomics. A common decision in planning an introductory genetics course is whether to teach the molecular basis of genes and DNA followed by the basic principles of transmission genetics or vice versa. Since these topics are closely related, this can lead to a ‘chicken and egg’ dilemma for students who need to understand one topic to fully appreciate the other. We have addressed this by introducing the basic principles of molecular genetics and the central dogma in broad strokes early in the textbook.  The first part of the book (the Prologue and Chapters 1 to 3) introduces gene function, genome structure, and natural genetic variation since these are the subjects that relate most directly to the contemporary genetics topics that students are most likely to encounter. The foundational principles and examples introduced in these first three chapters are developed in more detail in later sections of the book.

Because we emphasize evolutionary connections throughout, we don’t present bacterial genetics or population genetics in separate chapters, as many other books do. Instead we integrate information from bacteria, archaea and eukaryotes into each topic that emphasizes the central themes of evolution and genomics.  We have tried to avoid the approach that assigns different processes or organisms to separate chapters as much as possible.  Thus, when we present details about bacterial genetics in Chapter 11, we approach this topic from the evolutionary perspective of horizontal gene transfer.

Likewise, we have attempted to integrate ideas from population genetics in nearly every chapter, so that many of the concepts are familiar before we cover them in more detail in Chapter 16.

To provide an example that illustrates how we have integrated concepts from evolution, molecular genetics, and genomics, we can point to Chapter 4, entitled Descent with Modification.  The title, of course, is evolutionary and comes from Darwin himself.  The chapter describes DNA replication and repair, which provide the mechanisms by which descent with modification has occurred, and covers most of the information about DNA replication found in other genetics and molecular biology books.  The chapter then connects the outcome of DNA replication to the principles of phylogenetics, which rely on the accumulation of genetic changes.  This allows us to highlight how the mechanisms of genetic variation underlie fundamental evolutionary processes and relationships.

While we use this chapter as an example of our approach, content common to most genetics books can be found in every chapter but is viewed from a new perspective with a contemporary emphasis on genomics and evolution.

The final chapter on metagenomes provides students with an effective conclusion to the course. This is a relatively new topic not commonly found in other introductory genetics books.  This chapter draws from multiple previously introduced concepts; for example, it demonstrates that metagenomes provide a potential gene pool for horizontally- acquired DNA. Furthermore, by exploring how the content and structure of metagenomic communities are shaped by collective selection on and co-evolution of the composite genomes, it reinforces and helps students apply earlier concepts as well as introducing them to a highly relevant field of modern genetics. Although this is a rapidly changing topic, we chose it for the final chapter because it integrates so many of the principles covered in previous chapters.

During the years that we have taught our introductory course together, we have also found that changes in K-12 education have resulted in students entering university and college biology with greater prior exposure to the basic principles of molecular biology and Mendelian genetics. Our emphasis on genomics and evolution has led us to spend less time teaching classical Mendelian genetics during class. In fact, we no longer spend extensive time on this topic. (For further discussion of this change in emphasis see also Redfield RJ (2012) “Why Do We Have to Learn This Stuff?”—A New Genetics for 21st Century Students. PLoS Biol 10(7): e1001356. doi:10.1371/journal.pbio.1001356). This content is still provided in Chapter 5, but it is structured in a way that lends itself well to delivery through peer-guided learning groups or out-of-class reading assignments for students in cases where instructors might prefer to spend more time on other topics.

Some Pedagogical Options

Few instructors follow a textbook exactly in their lectures, so we have tried to offer some flexibility in coverage while maintaining a coherent organizing narrative.  In writing nearly every chapter, the most challenging questions we faced revolved around what topics to leave out or to move out of the main narrative of the chapter. The outcome of these discussions is an extensive set of text boxes.  We encourage you to use these boxes (as well as additional material that we are placing on the companion web site) to develop the course that best fits your needs.

We think that some of the boxes will be helpful or important for nearly every student in the course.  In particular, the Communicating Genetics boxes explain nomenclature and conventions used in illustrations and laboratory practices that can sometimes confuse students.  Almost every chapter has one or more Tool Boxes that connect a topic in the chapter to a laboratory or research method, so that experimental techniques are covered appropriately and in context. For example, the Tool Boxes in Chapter 2 discuss how the DNA structure so familiar to students provides the basis for gel electrophoresis and for nucleic acid hybridization.

We consider the Communicating Genetics boxes and the Tool Boxes to be an essential part of the text.  But we offer many other types of boxes for each chapter, which provide different ways for instructors to adapt the content to their needs. These other boxes provide additional details about a topic, more historical perspectives or connections to human biology, or a somewhat more quantitative approach than the description in the text. These boxes are extensions of the main text, providing helpful and informative paths through the topics, and may contain aspects of genetics that will intrigue students.

Other important features of the book provide well-established tools to support student learning.  The chapters are extensively illustrated, with drawings that attempt to capture the essential points in an accessible and attractive format; most of these professionally illustrated drawings began as diagrams that we use in class.

Each of the chapters also has an extensive set of study questions.  These range from relatively straightforward definitions to more difficult problems that challenge our best students.  While most of the study questions focus on topics that are covered in that chapter, a few connect back to concepts from previous chapters or look ahead to concepts in upcoming chapters to reinforce connections among the topics.  Many of the problems are based on data from the primary literature, illustrating questions that biologists have encountered in their research.

Solutions for all of the study questions are provided on the companion web site. Many of these solutions were written in collaboration with Haverford College students who emphasized issues that they encountered when they took the course, thus providing a more student-based set of answers.

Students who would like to explore more of the primary literature or dig deeper into material in the text and study questions should be pointed to the recommended Additional Readings list on the companion website.

The companion web site also offers a selection of short videos that we think of as online “office hours”.  In these videos, one of us explains a particular figure or concept, or solves one problem from among the study questions to provide a more personal and informal instructional aid.

The web site also offers a series of directed Journal Clubs that can help students become familiar with reading the scientific literature.  We use several of these each semester and in other courses as well.

Curricular revisions to meet the guidelines of ‘Vision and Change’

We have written this book, and developed the course from which this book is derived, very much in line with the core concepts and competencies identified by the AAAS/NSF Vision and Change in Undergraduate Biology Education Initiative (http://visionandchange.org/files/2013/11/aaas-VISchange-web1113.pdf ). Since the original Vision and Change study, many resources have been developed to promote and assist with the implementation of the suggested changes. Such resources include, but are by no means limited to:

PULSE (Partnership for Undergraduate Life Science Education): (http://www.pulsecommunity.org/page/recognition)

BioCORE Guide: (http://www.lifescied.org/content/13/2/200.full.pdf+html and http://www.lifescied.org/content/suppl/2014/05/16/13.2.200.DC1/Supplemental_Material_2.pdf)

C.R.E.A.T.E. (Consider, Read, Elucidate the hypotheses, Analyze and interpret the data, and Think of the next Experiment) method (http://teachcreate.org/).

The Vision and Change core concept of integrating evolution into the curriculum lies at the heart of this textbook. We open Chapter 1 with the recent example of genes affecting beak shape in Darwin’s finches to establish a solid foundational connection among genome analysis, evolutionary principles, and gene activity. This theme is then revisited and elaborated upon in subsequent chapters, often using beak shape in Darwin’s finches as an example in the text or in a study question. The relationships among evolution, genomics, and genetics are interwoven in our approach to teaching these topics. For students, developing the ability to understand these connections is a distinct strength to this approach, and we have found that our students remember and apply this foundational framework in subsequent biology courses.

The core concept of integration of information flow, exchange and storage into the curriculum is also stressed throughout but is particularly emphasized in the chapters that explore transcription, translation and DNA replication. Furthermore, in chapters 14 and 15, which cover gene regulatory networks and the genetic pathways that control cellular processes, students are encouraged to view these topics from the perspective of genetic information flow.

Integration of systems, another core concept, is achieved through two approaches in this textbook. First we introduce “The Five Great Ideas” of biology, which includes biology as an integrated system, in the Prologue and later revisit the connections between the “Great Ideas” and each genetics topic as the book progresses. We also cover scales of genetics from genes and molecules to genomes, cells and organisms through to populations of a species and populations of multiple species and metagenomes. We encourage our students to continually traverse these scales, emphasizing the system level relationships between these topics.  We have framed our approach to this book with this in mind.

The Vision and Change core concepts of structure and function and transformations of energy are perhaps less central to this textbook, and to most genetics books, but are nonetheless still included when relevant. The structure-function relationship of DNA, RNA and proteins is highlighted and structure-function relationships are also considered explicitly in the context of topics such as the cell cycle, for example.  Transformation of energy is introduced early on in the book through the discussion of anabolism and catabolism and is a theme in many of the examples of cellular and metagenomic processes explored in Chapters 14, 15 and 17.

In addition to these core concepts, the Vision and Change initiative identified important competencies. Many of these relate to the particular activities included in a course but they also align with many aspects of our approach in this textbook. For example, integration of the process of science and of the relationship between science and society into the curriculum are explored in more detail in many of the textboxes found in each chapter. Similarly the importance of integration of communication and collaboration into the curriculum lies behind our decision to include the series of Communicating Genetics boxes in the book to help students better understand the language and conventions of genetics. We have also incorporated data from scientific publications and databases into many figures to help students learn to interpret data as it is presented within the scientific community.  The directed Journal Clubs on the companion web site also guide the students through the analysis of data in research papers.

In terms of the integration of quantitative reasoning into the curriculum, the teaching of genetics lends itself well to applying basic numeracy and probability skills. We have highlighted specific examples in the “Quantitative” textboxes but elements of quantitative reasoning and graphical representation of data can be found throughout the main text and figures so that quantitative skills are not simply restricted to isolated examples. We also highlight an opportunity for integration of modeling and simulation into the curriculum in chapter 16 with a simulation of genetic drift.

Overall, the motivation and aspirations for redesigning our own curriculum are very much in line with the Vision and Change initiative. As a result, we hope that the textbook that we have developed will work well for other instructors interested in teaching genetics from this perspective.

A flipped classroom

Students find that the narrative style of the text engages them to do the background readings on their own before class, which is what we expect.  We use weekly online quizzes to encourage the students to keep up with the reading, a function that is offered with the multiple choice questions in the online homework resource accompanying the text.   Reading the chapters before class can create space for more discussion and active learning modules in the class meeting itself.

Despite the challenges of a large introductory class, there are a variety of options that have worked well for us in this format. The Journal Clubs provide a possible structure for a flipped classroom or dry lab group exercise that helps students learn to navigate and interpret relevant primary literature. The text boxes throughout the book also present material that instructors can use as topics for classroom discussions and activities. Similarly, study questions at the ends of chapters are divided into different categories, and the more challenging questions work well to inspire class activities as instructors guide students through the process of solving these problems.

Overall, we hope you will find this a useful textbook for providing a contemporary foundation for learning genetics while also offering flexible options for customizing course content.