Preface to the First Edition

When most people think about anthropology, the image that usually comes to mind is that of intrepid, Indiana Jones-like characters, traveling to remote and exotic locations; living and working under arduous conditions; digging up fossils, stone tools, or other evidence of our past; and making headlines by proclaiming that what they have found overturns everything we thought we knew about human evolution. However, there is another type of anthropology that is becoming an increasingly important source of information about our past, rivaling the study of fossils or artifacts, and that is molecular anthropology, which can be defined as the use of molecular genetic methods to address questions and issues of anthropological interest. More specifically, molecular anthropology uses genetic evidence to obtain insights into human origins, migrations, and population history, as well as the role of natural selection during human evolution, and the impact of particular cultural practices on patterns of human genetic variation. And while working in a molecular genetics laboratory or sitting in front of a computer (which is where most of the work is done nowadays) may lack the glamour and excitement of paleoanthropological fieldwork (although a lucky few of us do all too rarely get to go out and collect samples), molecular anthropology has already had, and is continuing to have, a major impact on our understanding of our evolutionary past - from the first demonstration of a surprisingly close relationship between humans and chimpanzees in the 1960s, to the mtDNA evidence for a recent African origin that developed in the 1980s, to the current fascination with whole-genome sequences from Neandertals and other archaic humans.

Molecular anthropology can thus be considered a full-fledged, mature subfield of biological anthropology (alongside paleoanthropology, primatology, and demography), and therefore deserving of equal coverage in the curricula of university anthropology departments. However, the treatment of molecular anthropology in most undergraduate textbooks in biological anthropology or human evolution is often quite superficial and generally leaves a lot to be desired - while there are some good advanced books, there is nothing really comparable for the beginning student, who may have little in the way of any previous background in science. The present book is an attempt to remedy this situation by assuming no prior knowledge of genetics and by trying to focus on understanding the logic and reasoning behind various methods and findings, while omitting (or at least, placing less emphasis on) the technical details.

In addition to beginning students, it is hoped that this book will be useful to professionals from other fields (such as linguists or archaeologists) who want to know more about molecular anthropology and how it might inform their own work, as well as the interested layperson. The power of the molecular approach to anthropology lies in the fact that each of us carries within us a record of our past in the DNA that we have inherited from our ancestors, and the challenge is to learn how to read that record from the patterns of DNA variation in people today (supplemented, increasingly, by DNA extracted from fossils). Most people are intensely interested in human origins in general and their own origins in particular, and a whole industry now exists that will allow you to investigate your own genetic ancestry (for a suitable fee, of course!). But if you like, you can go beyond "personal genomics" and carry out your own investigations - while most of us will never have the opportunity to go on expeditions to dig up fossils or artifacts, you don't need your own laboratory to study genetic history. Anyone with a computer and a reasonably fast Internet connection can download genetic data from public repositories and freely available software to carry out various analyses (or, for the truly ambitious, write your own software), and voilà, you too can do molecular anthropology research. This book is thus also intended for anyone interested in knowing more about what molecular anthropology is all about, as well as those who may be thinking about carrying out their own studies (but be forewarned that this is not a "how-to" book; you'll have to look elsewhere for step-by-step instructions - there are lots of resources on the Internet devoted to this sort of "armchair" molecular anthropology).

This book is loosely organized into three sections. The first six chapters are intended as introductory material for those who have never had any courses in genetics: Chapters 1 and 2 cover the basics of how genes are inherited, what they are, what they do, and how they do it; Chapter 3 introduces some basic properties about populations, including the important concept of effective population size; Chapter 4 sets up a simple (and highly unrealistic!) model of how genes behave in populations that nevertheless leads to some important insights; Chapter 5 makes the simple model of Chapter 4 more realistic by adding various evolutionary forces, with a focus on what happens to genetic variation within populations and genetic diversity between populations; and Chapter 6 covers some aspects of how genes themselves evolve.

The second section includes the next six chapters and provides an overview of the different types of genetic data and analyses that can be employed in molecular anthropology studies. Chapter 7 covers the various types of genetic markers that have been used and how they are analyzed in the laboratory, while Chapter 8 discusses issues that arise with sampling of populations (an important but often-overlooked aspect of molecular anthropology studies that can greatly impact the results) and Chapter 9 discusses the properties of different parts of the genome that are typically analyzed (which can also have a big impact on the results). The next three chapters focus on methods for analyzing genetic data, where the data come from populations (Chapter 10), which is the traditional approach, or from individuals (Chapter 11), which is a relatively new development made possible by new molecular methods; these two chapters focus largely on descriptive methods, while Chapter 12 is devoted to actually inferring demographic history from molecular data (i.e., estimating divergence times, changes in population size, etc.).

These first 12 chapters set the stage for the last eight chapters, which are devoted to what we have actually learned from molecular anthropology studies. We begin with what are (arguably) two of the most important contributions of the molecular approach to anthropology: namely, figuring out who is our closest living relative and just how close is the relationship (Chapter 13) and figuring out how our own species (modern humans) originated (Chapter 14). It turns out that the story of our origins in Chapter 14 is incomplete without the assistance of ancient DNA, and so, Chapter 15 then discusses the various issues that arise with the analysis of DNA from fossils, and what we have learned. Hopefully, it is not giving too much away at this point to say that the genetic evidence strongly supports an origin of our species in Africa; Chapter 16 then discusses what we have learned from genetic evidence about the migration of modern humans from Africa, as well as two of the major subsequent migrations of modern humans: the colonization of the New World and the colonization of the Pacific.

Up to this point, the focus of the book is on demographic aspects of human history, that is, when did events take place, where did they take place, who did they involve, were there changes in population size, and so forth. But another very important aspect of our evolution is adaptation: what were the genetic changes that were selected for during our evolutionary past that allowed us to evolve to become modern humans, and what sorts of adaptations occurred subsequently as our ancestors spread across and out of Africa? Chapter 17 discusses species-wide selection, that is, selection for adaptations that are shared by all modern humans and thus can be thought of as those changes that made us human. In Chapter 18, we discuss local selection, that is, selection that occurred only in some populations due to their particular environment, climate, diet, diseases/parasites, and so forth; these can be thought of as adaptations that allowed us to successfully colonize more of the globe than any other species (with the exception of our parasites, of course!).

Chapter 19 turns to some aspects of genes and culture, in particular, the impact of cultural practices on patterns of genetic variation, as well as how we can use genetic analyses to make inferences about some cultural practices - one of the examples discussed in this chapter is a genetic approach to dating the origin of clothing (I kid you not!). The book ends with a final chapter that describes some of the other ongoing and likely future developments in molecular anthropology - a risky business, given the rapid rate of technological and computational advancements in this field. For example, nobody writing a textbook a few years ago would have predicted that in 2013, we would have high-quality, whole-genome DNA sequences from Neandertals (and other archaic humans). It truly is an amazing time to be doing this sort of work, and I, for one, can't wait to see what we'll be able to do a few years from now.

In writing this book, I have in many places taken advantage of the fact that I have been actively involved in molecular...