Human Population Genetics

John H. Relethford

• Publisher: Wiley-Blackwell
• Year: 2012
• ISBN:
  9781118181621
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Evolution
• Index: Biological Sciences

Introductory guide to human population genetics and microevolutionary theory

Providing an introduction to mathematical population genetics, Human Population Genetics gives basic background on the mechanisms of human microevolution. This text combines mathematics, biology, and anthropology and is best suited for advanced undergraduate and graduate study.

Thorough and accessible, Human Population Genetics presents concepts and methods of population genetics specific to human population study, utilizing uncomplicated mathematics like high school algebra and basic concepts of probability to explain theories central to the field. By describing changes in the frequency of genetic variants from one generation to the next, this book hones in on the mathematical basis of evolutionary theory.

Human Population Genetics includes:

• Helpful formulae for learning ease
  
  

• Graphs and analogies that make basic points and relate the evolutionary process to mathematical ideas
  
  

• Glossary terms marked in boldface within the book the first time they appear
  
  

• In-text citations that act as reference points for further research
  
  

• Exemplary case studies
  
  

• Topics such as Hardy-Weinberg equilibrium, inbreeding, mutation, genetic drift, natural selection, and gene flow
  
  

Human Population Genetics solidifies knowledge learned in introductory biological anthropology or biology courses and makes it applicable to genetic study.

NOTE: errata for the first edition can be found at the author's website: http://employees.oneonta.edu/relethjh/HPG/errata.pdf

Chapter 1

Genetic, Mathematical, and Anthropological Background

My interest in human population genetics started with my difficulty in picking a major in college.

As is often the case, my interests as an undergraduate student were varied, including fields as different as sociology, biology, geography, history, and mathematics. Each of these fields appealed to me in some ways initially, but none sufficiently to take the 10 or more courses to complete an academic major. As I shifted almost daily in my search for a major, I stumbled across anthropology, a discipline that is characterized by academic breadth across the liberal arts. In the United States, anthropology departments are most often constructed around the four-field approach championed by the famous early twentieth-century anthropologist, Franz Boas. Here, anthropology is divided into four subfields: (1) cultural anthropology, which examines behaviors in current and recent human populations; (2) archaeology, which reconstructs cultural behavior in prehistoric and historic human societies; (3) linguistics, the study of language, a uniquely human form of communicating culture; and (4) biological anthropology (also known as physical anthropology), which focuses on the biological evolution and variation of the human species.

With its focus on both cultural and biological aspects of humanity, and its concern with natural science, social science, and the humanities, anthropology proved to be the perfect liberal arts major for someone like me, who had a difficult time picking any single major. Over time, however, I found myself gravitating more toward the subfield of biological anthropology as I became fascinated by the ways in which humanity had evolved. As I entered graduate school, I wound up concentrating more and more on the nature of human biological variation, and questions about our species' biological diversity. How are human populations similar to and different from each other biologically? How do these differences relate to the process of evolution, and how do these processes relate to human history, culture, and the environment? In one form or another, these questions have been at the root of many of the research topics I have focused on during my career, ranging from the effect of historical invasions on genetic diversity in Ireland, to changing patterns of marriage and migration in colonial Massachusetts, to the effect of history and geography on cranial shape across the world.

Underlying all of these questions is the subject of this book, human population genetics, which is a field that has the same breadth of topics that guided my search for a college major. Although this book focuses on human population genetics, it is important to realize that population genetics is a subject that concerns all organisms. Much of this book consists in explaining basic principles of population genetics, applicable to many species, with further illustration describing case studies from human populations. If you are reading this book in a course on general population genetics, as is often taught in biology departments, for example, you are likely to encounter further case studies on a variety of other species.

1.1 The Scope of Population Genetics

Before getting too far into the application of population genetics to the human species, it is useful to answer the basic question “What is population genetics?” This question can be answered by considering the nature of the broader field of genetics, the study of heredity in organisms. Genetics can be studied at various levels. The study of molecular genetics deals with the biochemical nature of heredity, specifically DNA and RNA. At this level, geneticists focus on the biochemical nature of heredity, including the structure and function of genes and other DNA sequences.

The study of Mendelian genetics, named after the Austrian monk, Gregor Mendel (1822–1884), is concerned with the process and pattern of genetic inheritance from parents to offspring. Mendel's work gave us a basic understanding of how inheritance works, and how discrete units of inheritance combine to produce genotypes and phenotypes. Whereas the focus of molecular genetics is on the transmission of information from cell to cell, Mendelian genetics focuses on the transmission of genetic information from one individual (a parent) to another (the offspring). Mendelian genetics is in essence a statistical subject, dealing with the probability of different genotypes and phenotypes in offspring. A classic example concerns two parents, each of which carries one copy of a recessive gene. The principles of probability show that the chance of any given offspring having two copies of that gene, one from each parent, is

. These principles will be reviewed later, but for now, you should just consider that the transmission of genetic information is subject to the laws of probability.

Population genetics takes this concern with the probability of transmitting genetic information from one generation to the next and extends it to the next level, an entire population (or set of populations, or even an entire species). In population genetics, we are concerned with the genetic composition of the entire population, and how this composition can change over time. For example, consider the classic example of the peppered moth in England. This species of moth comes in two forms, a dark-colored form and a light-colored form. Centuries ago, most moths were light-colored, and only about 1% were dark-colored. Dark-colored moths were rare because they would be more clearly visible against the light color of the tree trunks, making it easier for birds to see them and eat them. Over time, the environment changed, and the frequency of dark-colored moths increased as the frequency of the light-colored moths decreased. Because the color of the moths reflects genetic differences, this observed change is an example of the genetic composition of a species changing over time. Population genetics deals with explaining such changes. In this case, the initial origin of a different form is due to mutation, and the change in moth color over time reflects natural selection, because the environment had shifted following the Industrial Revolution, leading to darker tree trunks, thus creating a situation where dark-colored moths were less likely to be eaten by birds.

When the genetic makeup of a population changes over time, even in a single generation, we have a case of evolution. Population genetics is the branch of genetics that deals with evolutionary change in populations of organisms, and provides the mathematical basis of evolutionary theory. Note that I am using the word theory here in the context of the natural sciences, where a theory is a set of hypotheses that have been tested and have withstood the test of time, as compared with the popular use of the word theory as a simple hypothesis. When we speak of evolutionary theory, we are not stating that evolution may or may not exist, but instead are referring to a set of principles that explain the facts of evolution (in other words, beware of the statement that “evolution is a theory and not a fact,” because it is actually both a fact and a theory).

Evolution can be viewed over different scales of time and units of analysis. Population genetics deals with changes within a species over relatively short intervals of time, typically on the order of a small number of generations. This type of evolutionary change is also known as microevolution, and is contrasted with macroevolution, which focuses on the evolution of species and higher levels (genera, families, etc.), and typically deals with geological timescales, ranging from thousands to millions of years. Although macroevolution and microevolution are related in a theoretical sense, there is continued debate over the extent to which long-term macroevolutionary events are a straightforward extrapolation of microevolutionary trends (Simons 2002). The focus of this book is primarily on the theory of microevolution.

Population genetics is concerned with changes in genetic variation over time, that is, genetic differences and similarities. There are two ways of looking at genetic variation: variation within populations and variation between populations. The former refers to differences and similarities of individuals within a population; the latter refers to average differences between two or more populations. Later chapters will introduce quantitative measures of within-group and between-group variation based on genetic traits, but for the moment, I will use a simple analogy looking at adult human height. Picture yourself in a large classroom filled with students, and imagine that we measured everyone's height. We would use these measurements to compute how much variation existed within the classroom. If, for example, everyone in the class were of exactly the same height, there would be no variation. If, however, there were differences in height, with everyone being between 5 ft 8 in tall and 5 ft 10 in. tall, then variation would exist because not everyone would be the same. If everyone were between 5 and 6 ft tall, there would be even more variation.

On the other hand, suppose that we want to compare the height in your classroom with the height in the next classroom. An example would be if the average height in your classroom were 5 ft 9 in. and the average height in the other classroom were 5 ft 8 in. The difference in average height would be 1 in. This difference would be an example of variation between groups. If the average height of the two classes were the same, then there would be no variation between groups. In evolutionary terms, we are interested in changes in genetic variation that take place both within and between populations.

By studying genetic change over time and its effects on genetic variation within and between populations, we are able to apply the theory of population genetics to address a wide variety of questions about human variation and evolution. A small sample of such questions (which will be addressed in later chapters) includes

• How much inbreeding occurs in human populations, and what is the effect of this inbreeding?
• What does genetic variation tell us about our species' history?
• Can genetics to be used to trace ancient human migrations?
• Where did the first Americans come from?
• Why do some human populations have high frequencies of the harmful sickle cell allele?
• Are certain genes resistant to acquired immunodeficiency syndrome (AIDS)?
• Why do some small populations differ genetically from their neighbors to such an extent?
• What impact does geography have on our choice of mates?

Even this short list shows that population genetics has relevance to many questions about human biological variation and evolution. In addition, the general principles of population genetics are used to address the same concerns—variation and evolution—in all organisms. In short, population genetics is a key to understanding life. Although this book focuses on human populat...