A Chapter-by-Chapter Guide

We begin the Prologue of this book with the five great ideas of biology, as outlined by Sir Paul Nurse.  We use these ideas throughout the text to interconnect concepts about the chemistry of biological molecules, the idea of a gene, cells as basic building blocks of life, the organization of living systems, and natural selection and evolution.  As such, these ideas provide a framework for the information presented in the text.  We have found that many students are adept at acquiring biological information on specific topics but are challenged when asked to make connections between concepts and topics. However, once these integration skills have been emphasized and developed, the depth of understanding increases dramatically. We therefore model this approach explicitly throughout the text.

In Chapter 1, we introduce a recent study of the genomes of Darwin’s finches that identified genes that contribute to the differences in beak shape among these species.  In this way, we link one of the most important and familiar examples of natural selection among Darwin’s finches with the underlying genetic and genomic basis for the differences observed among these birds.  Using this example in our opening chapter prepares students to think across scales, from DNA to molecules to phenotypes to species and then to evolution in a community of organisms.  This perspective has only become possible because of our ability to sequence and compare genomes.
We then move on to describe in Chapter 2 the structure of DNA and the Central Dogma, highlighting features of the DNA molecule that have an impact on its function.  We point out modifications to the traditional view of the Central Dogma, and introduce students to the basic structure of a gene.  Chapter 3 covers the structure of the genome and the variation in genome organization found in different species, which are both the outcome of and the ingredients for natural selection.   This chapter discusses the structure of chromosomes, extra-chromosomal DNA and changes in the genome, and is one of the most important for integrating genomic findings with evolutionary and genetic principles.
In Chapter 4, we discuss DNA replication and repair, tying these concepts to Darwin’s concept of “descent with modification”, a fundamental principle of natural selection and evolution.  Several challenges to DNA replication that arise from its length and anti-parallel structure are presented, along with the processes that have evolved to address these challenges.  We introduce the many types of mutation that occur, and how the occurrence of such mutations and the effects of selection can be revealed by comparing the genomes of different organisms.  These comparisons provide us with the ability to reconstruct evolutionary history and develop phylogenetic trees based on DNA sequence changes.
The next section of the text, comprising Chapters 5-9, discusses Mendelian genetics, meiosis, the inheritance of two genes, sex-linked traits, and linkage and mapping.  These chapters present all the material found in a traditional genetics course, framed in the context of genomics and evolution.  For example, the relationship of the process of meiosis to Mendel’s laws of segregation and independent assortment are explored in a progressive approach that encourages students to think between topics and across scales.
We then bring these fundamental concepts of genetics and genomes together in Chapter 10 on complex traits and genome-wide association studies, which focuses primarily on human traits and diseases. We explore how these studies build upon the basic principles outlined in earlier chapters, to identify contributing genes and causative mutations.  While chapters on complex traits are found in many books, an approach that shows how genome-wide associations integrate genomic variation, complex phenotypes, and evolutionary history is novel.
Chapter 11 introduces the process of horizontal gene transfer, originally found among bacteria, but now known to occur in other types of organisms too.  Chapters 12 and 13 focus on the essential processes of transcription and translation that link genotype to phenotype.
In Chapter 14, operons in bacteria are introduced as an example of gene regulatory networks and are followed by a discussion of transcriptional regulatory networks in eukaryotic organisms, using recent information from many genome annotation projects such as ENCODE.   The tools of genetic analysis are covered in Chapter 15, beginning with Beadle and Tatum’s experiments in Neurospora and Jacob and Monod’s work with lac mutants, and moving into a discussion of more recent genetic screens for the identification of genes essential to embryonic development in Drosophila.
The final section of the text moves beyond individuals to populations and communities of organisms.  Population genetics with a human focus is the subject of Chapter 16, where we explore the assumptions of Hardy-Weinberg equilibrium model.  We review the many different types of evolutionary change that can operate, in addition to natural selection, to shape the genetic structure of a population and the imprints these leave at the level of the genome. Long-term studies of bacterial populations are featured as a method to explore evolution experimentally.  Chapter 17 concludes the text by introducing the relatively new field of metagenomics, in which genomic information is extracted directly from communities of organisms living in their natural environments, revealing evidence for their interdependence and co-evolution.