Evolution, Function, and Deconstructing Histories: A New Generation of Anthropological Genetics

It has been an amazing decade for anthropological genetics. Our questions have remained the same—profound inquiries about human nature and diversity—but thanks to an array of new technologies, our answers become infinitely more insightful and accurate. A click away, we now have access to thousands of whole modern human genomes and hundreds of ancient individuals with genome-wide data. Our comparisons of these genomes become even more meaningful because we now know much more about what a variant at a given location of the genome may do to the expression of genes, functioning of proteins, cellular phenotypes, or processes in our organs. These new data sets build on existing concepts. A DNA sequence is still a DNA sequence, and a quantitative trait locus still marks a variable site associated with a given trait. What has changed is the massive amount of data generated, not for a single gene but for the entire genome, and not for a single individual but for thousands.

In this ocean of data, a new generation of genomic anthropologists has emerged, tackling fundamental questions of biological anthropology with novel computational know-how and a stronger appreciation of functional genetics. The future for genetic anthropology has never been brighter. This quantitative revolution in how we study human variation and evolution has allowed for qualitative leaps in our perception of humanness, and the American Association of Anthropological Genomics, as a young and dynamic organization, is at the forefront of these exciting new venues in applying genomics technologies to anthropological questions.

In 2016, Aaron Sams and I organized the annual AAAG symposium titled “Ancient Alleles in Modern Populations: Ancient Structure, Introgression, and Variation—Maintaining Adaptive Forces.” This special issue of Human Biology is mainly based on contributions by the speakers at this symposium, building on the rigorous discussions during the symposium. In the first article of this special issue, Alexandre M. Harris and Michael DeGiorgio provide a thorough conceptual summary of the state-of-the-art methods that are applied to genomic data to understand admixture between populations and species. Such methods have recently revealed that a tiny fraction of our variation is shared with now extinct species, such as Neanderthals. The data are so rich that even that tiny fraction amounts to tens of thousands of variants, which allow us to reveal signatures of recent admixture events from the archaic humans into modern human populations. The possibility of an admixture between Neanderthals and humans has been a major focal point in the field for decades. And ten years ago, genetic anthropology had little to say. Now, genomic approaches lead the way, describing not only the more precise timing and nature of such admixtures but also their impact on contemporary human populations. Touching on these issues, John Hawks’s article describes how admixture can leave signatures that influence how we understand population histories. Excavating these signatures allows us to paint a more accurate and bias-free picture of human diversity.

Similarly, when it comes to the evolution of our biological features that are key to our survival and underlie our variation, genomic approaches add new empirical zing to existing paradigms, such as the evolution of our immune system, our senses, and our cognitive abilities. Blending animal and cell-line models, it is now possible to measure the functional and evolutionary impact of genetic variation. In her article, Jessica F. Brinkworth touches on this exciting new front and makes a compelling case explaining the genetic diversity of the human immune system within the context of never-ending and ever-changing pathogenic pressures. Such approaches even allow direct estimation of the health of now extinct species, as is done here by Ali J. Berens, Taylor L. Cooper, and Joseph Lachance.

Maybe the most immediately visible impact of this quantitative revolution is the empirical definitiveness that it brought to studies of population history. As described in the article by Chenling Xu Antelope, Davide Marnetto, Fergal Casey, and Emilia Huerta-Sanchez, it is now possible to reconstruct the genetic histories of contemporary and ancient peoples with unprecedented power. Sometimes our...