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Molecular Genetics in Ecology

What is Molecular Ecology?

Over the past few decades, molecular biology has revolutionized ecological research. During that time, methods for genetically characterizing individuals, populations, and species have developed at a truly impressive rate, and continue to provide us with a wealth of novel data and fascinating new insights into the ecology and evolution of plants, animals, fungi, algae, and bacteria. Molecular markers allow us, among other things, to quantify genetic diversity, track the movements of individuals, measure inbreeding, identify the remains of individuals, characterize new species, and retrace historical patterns of dispersal. More recently, increasingly sophisticated genomic techniques have provided remarkable insight into the functioning of different genes, and the ways in which evolutionary adaptations (or lack thereof) can influence the survival of organisms in changing environments. All of these applications are of great academic interest, and are also frequently used to address practical ecological questions such as which endangered populations are most at risk from inbreeding, or how much hybridization has occurred between genetically modified crops and their wild relatives. Every year it becomes easier and more cost-effective to acquire molecular genetic data, and laboratories around the world can now regularly accomplish previously unthinkable tasks such as describing entire communities based on nothing more than remnant DNA extracted from water samples, or comparing a suite of functional genes between individuals from different populations.

This third edition of Molecular Ecology has been substantially overhauled because of the tremendous leaps and bounds that have occurred in this field over the past few years. Arguably the most important development of the past decade has been the introduction and increasing cost-effectiveness of high throughput sequencing; this technology was initially limited to a few labs with hefty research budgets, but is now accessible to a large community of researchers who are able to obtain sequence data sets about which they could previously only dream (Figure 1.1). When this book was first published in 2005, a major reason for the excitement surrounding molecular ecology was the ease with which researchers could obtain genetic data from natural populations. While this is still true, the main difference between then and now is that studies conducted prior to 2005 were based on a handful of loci (gene regions), whereas molecular ecology studies are now often based on much larger numbers of loci, or in some cases entire genomes. As a result, we now have greater insight into virtually all of the topics covered in this book, including population genetics, evolutionary change, conservation genetics, and behavioral ecology. This first chapter introduces high throughput sequencing (HTS) as a topic that will be revisited in subsequent chapters. Other technologies that are becoming increasingly widespread in ecological studies, and which will be discussed in later chapters, include environmental DNA (eDNA) assays, metabarcoding, transcriptomics, and epigenetics. We will begin in this chapter by reviewing some principles of genetics and some widely used techniques that are essential to our understanding of molecular ecology.

Figure 1.1 Numbers of results, by year, of a search in Web of Science that queried "next-generation sequencing" or "high throughput sequencing" and restricted results to the categories of "ecology," "biodiversity conservation," or "marine freshwater biology."

DNA, RNA, and Protein

This section will provide a short review of the relationship between DNA, genes, and proteins, because this background is necessary in order to understand how molecular markers can be used to address ecological questions. Prokaryotes, which lack cell nuclei, have their DNA arranged in a closed double-stranded loop that lies free within the cell's cytoplasm. Most of the DNA within the cells of eukaryotes, on the other hand, is organized into chromosomes that can be found within the nucleus of each cell and which comprise the nuclear genome (also referred to as nuclear DNA, or nrDNA). Each chromosome includes a single DNA molecule that is divided into functional units called genes. The site that each gene occupies on a particular chromosome is referred to as its locus (plural loci). At each locus, different forms of the same gene may occur, and these are known as alleles.

Each allele is made up of a specific sequence of DNA. DNA sequences are determined by the arrangement of four nucleotides, each of which has a different chemical constituent known as a base. The four DNA bases are adenine (A), thymine (T), guanine (G), and cytosine (C), and these are linked together by a sugar-phosphate backbone to form a strand of DNA. In its native state, DNA is arranged as two strands of complementary sequences that are held together by hydrogen bonds in a double helix formation. No two alleles have exactly the same DNA sequence, although the similarity between two alleles from the same locus can be very high.

The function of some genes is to encode a particular protein, and the process in which genetic information is transferred from DNA to RNA to protein is known as gene expression. The DNA sequence of a protein-coding gene determines the structure of the protein that is synthesized. The first step of protein synthesis occurs when the coding region of DNA is transcribed into ribonucleic acid (RNA) through a process known as transcription. The result of transcription is a primary transcript, which is a single strand of RNA complementary to DNA sequences. RNA is made from the same bases as DNA with the exception of uracil (U), which replaces thymine (T). In prokaryotes, this transcript is also the messenger RNA (mRNA). In eukaryotes, the introns (non-coding segments of DNA) are excised following a process known as RNA splicing, producing a mature mRNA that is complementary to the exon (protein-coding) DNA template. mRNA sequences are then translated into protein sequences following a process known as translation (Figure 1.2). Translation is possible because each RNA molecule can be divided into triplets of bases (known as codons), most of which encode one of 20 different amino acids; these are the constituents of proteins (Table 1.1).

Specific combinations of amino acids give rise to polypeptides, which may form either part or all of a particular protein or, in combination with other molecules, a protein complex. If the DNA sequences from two or more alleles at the same locus are sufficiently different, the corresponding RNA triplets will encode different amino acids, and this will lead to alternative forms of the same protein. However, not all changes in DNA sequences will result in different proteins. Table 1.1 shows that there is some redundancy in the genetic code, for example leucine is specified by six different codons. This redundancy means that it is possible for two different DNA sequences to produce the same polypeptide product. The genetic code also signals "start" and "stop" functions: a stop codon (UAA, UAG, or UGA) signals the end of transcription, whereas a start codon (AUG, which encodes the amino acid methionine) marks the beginning of translation. These stop and start codons are therefore critical to gene functioning because they provide one of the mechanisms that controls gene expression. Gene expression can also be influenced by physical modifications to DNA molecules, which will be discussed below in the section on epigenetics.

Figure 1.2 DNA codes for RNA via transcription. The mature mRNA transcript is then used as a template that is translated into a protein. This is known as the central dogma of molecular biology.

Table 1.1 The eukaryotic nuclear genetic code (RNA sequences). A total of 61 codons specify 20 amino acids. An additional three stop codons (UAA, UAG, UGA) signal the end of translation. This genetic code is almost universal, although minor variations exist in some microbes and also in the mitochondrial DNA (mtDNA) of animals and fungi.

Allozymes

Ecology is a branch of biology that is primarily interested in how organisms in the wild interact with one another and with their physical environment. Historically, these interactions were studied through field observations and experimental manipulations. These observations and experiments typically included descriptions of phenotypes, which are based on one or more aspects of an organism's morphology, physiology, biochemistry, or behavior (Figure 1.3). What we may think of as traditional ecological studies have greatly enhanced our knowledge of many different species, and have made invaluable contributions to our understanding of the processes that maintain ecosystems. However, prior to the 1960s we knew very little about the genetics of natural populations; more specifically, we had little to no understanding of the genetic variation of populations, the genetic similarities among populations and species, the links between phenotype and genotype (an individual's complete set, or subset, of genes), and the roles of functional...